1
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Naquin T, Jain S, Zhang J, Xu X, Yao G, Naquin CM, Yang S, Xia J, Wang J, Jimenez S, Huang TJ. An Acoustofluidic Picoinjector. SENSORS AND ACTUATORS. B, CHEMICAL 2024; 418:136294. [PMID: 39131888 PMCID: PMC11308560 DOI: 10.1016/j.snb.2024.136294] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/13/2024]
Abstract
Droplet microfluidics has emerged as a valuable technology for a multitude of chemical and biomedical applications, offering the capability to create independent microenvironments for high-throughput assays. Central to numerous droplet microfluidic applications is the picoinjection of materials into individual droplets, yet existing picoinjection methods often exhibit high power requirements, lack biocompatibility, and/or suffer from limited controllability. Here, we present an acoustofluidic picoinjector that generates acoustic pressure at the droplet interface to enable on-demand, energy-efficient, and biocompatible injection at high precision. We validate our platform by performing acid-base titrations by iteratively injecting picoliter volume reagents into droplets to induce pH transitions detectable by color change in solution. Additionally, we demonstrate the versatility of the acoustofluidic picoinjector in the synthesis of metallic nanoparticles, yielding highly monodisperse and reproducible particle morphologies compared to conventional bulk-phase techniques. By facilitating controlled delivery of reagents or biological samples with unparalleled accuracy, acoustofluidic picoinjection broadens the utility of droplet microfluidics for a myriad of applications in chemical and biological research.
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Affiliation(s)
| | | | - Jinxin Zhang
- Thomas Lord Department of Mechanical Engineering and Materials Science, Duke University, Durham, NC 27708, USA
| | - Xianchen Xu
- Thomas Lord Department of Mechanical Engineering and Materials Science, Duke University, Durham, NC 27708, USA
| | - Gary Yao
- Thomas Lord Department of Mechanical Engineering and Materials Science, Duke University, Durham, NC 27708, USA
| | - Chloe M. Naquin
- Thomas Lord Department of Mechanical Engineering and Materials Science, Duke University, Durham, NC 27708, USA
| | - Shujie Yang
- Thomas Lord Department of Mechanical Engineering and Materials Science, Duke University, Durham, NC 27708, USA
| | - Jianping Xia
- Thomas Lord Department of Mechanical Engineering and Materials Science, Duke University, Durham, NC 27708, USA
| | - Janna Wang
- Thomas Lord Department of Mechanical Engineering and Materials Science, Duke University, Durham, NC 27708, USA
| | - Sebastian Jimenez
- Thomas Lord Department of Mechanical Engineering and Materials Science, Duke University, Durham, NC 27708, USA
| | - Tony Jun Huang
- Thomas Lord Department of Mechanical Engineering and Materials Science, Duke University, Durham, NC 27708, USA
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2
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Autour A, Merten CA. Fluorescence-activated droplet sequencing (FAD-seq) directly provides sequences of screening hits in antibody discovery. Proc Natl Acad Sci U S A 2024; 121:e2405342121. [PMID: 39240970 PMCID: PMC11406258 DOI: 10.1073/pnas.2405342121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2024] [Accepted: 08/04/2024] [Indexed: 09/08/2024] Open
Abstract
Droplet microfluidics has become a very powerful tool in high-throughput screening, including antibody discovery. Screens are usually carried out by physically sorting droplets hosting cells of the desired phenotype, breaking them, recovering the encapsulated cells, and sequencing the paired antibody light and heavy chain genes at the single-cell level. This series of multiple consecutive manipulation steps of rare screening hits is complex and challenging, resulting in a significant loss of clones with the desired phenotype or large fractions of cells with incomplete antibody information. Here, we present fluorescence-activated droplet sequencing, in which droplets showing the desired phenotype are selectively picoinjected with reagents for RT-PCR. Subsequently, light and heavy chain genes are natively paired, fused into a single-chain fragment variant format, and amplified before off-chip transfer and downstream nanopore sequencing. This workflow is sufficiently sensitive for obtaining different paired full-length antibody sequences from as little as five droplets, fulfilling the desired phenotype. Replacing physical sorting by specific sequencing overcomes a general bottleneck in droplet microfluidic screening and should be compatible with many more applications.
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Affiliation(s)
- Alexis Autour
- Institute of Bioengineering, School of Engineering, École Polytechnique Fédérale de Lausanne, Lausanne 1015, Switzerland
- European Molecular Biology Laboratory, Heidelberg 69117, Germany
| | - Christoph A Merten
- Institute of Bioengineering, School of Engineering, École Polytechnique Fédérale de Lausanne, Lausanne 1015, Switzerland
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3
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Cowell TW, Jing W, Noh H, Han HS. Drop-by-Drop Addition of Reagents to a Double Emulsion. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2024:e2404121. [PMID: 39101620 DOI: 10.1002/smll.202404121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/21/2024] [Revised: 07/08/2024] [Indexed: 08/06/2024]
Abstract
Developments in droplet microfluidics have facilitated an era of high-throughput, sensitive single-cell, or single-molecule measurements capable of tackling the heterogeneity present in biological systems. Relying on single emulsion (SE) compartments, droplet assays achieve absolute quantification of nucleic acids, massively parallel single-cell profiling, and more. Double emulsions (DEs) have seen recent interest for their potential to build upon SE techniques. DEs are compatible with flow cytometry enabling high-throughput multi-parameter drop screening and eliminate content mixing due to coalescence during lengthy workflows. Despite these strengths, DEs lack important technical functions that exist in SEs such as methods for adding reagents to droplets on demand. Consequently, DEs cannot be used for multistep workflows which has limited their adoption in assay development. Here, strategies to enable reagent addition and other active manipulations on DEs are reported by converting DE inputs to SEs on chip. After conversion, drops are manipulated using existing SE techniques, including reagent addition, before reforming a DE at the outlet. Device designs and operation conditions achieving drop-by-drop reagent addition to DEs are identified and used as part of a multi-step aptamer screening assay performed entirely in DE drops. This work enables the further development of multistep DE droplet assays.
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Affiliation(s)
- Thomas W Cowell
- Department of Chemistry, University of Illinois at Urbana-Champaign, 505 South Matthews Ave, Urbana, IL, 61801, USA
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, 1206 W Gregory Dr., Urbana, IL, 61801, USA
| | - Wenyang Jing
- Department of Biophysics, University of Illinois at Urbana-Champaign, 600 South Matthews Ave, Urbana, IL, 61801, USA
| | - Heewon Noh
- Department of Chemistry, University of Illinois at Urbana-Champaign, 505 South Matthews Ave, Urbana, IL, 61801, USA
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, 600 South Matthews Ave, Urbana, IL, 61801, USA
| | - Hee-Sun Han
- Department of Chemistry, University of Illinois at Urbana-Champaign, 505 South Matthews Ave, Urbana, IL, 61801, USA
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, 1206 W Gregory Dr., Urbana, IL, 61801, USA
- Department of Biophysics, University of Illinois at Urbana-Champaign, 600 South Matthews Ave, Urbana, IL, 61801, USA
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, 600 South Matthews Ave, Urbana, IL, 61801, USA
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4
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Vladisaljević GT. Droplet Microfluidics for High-Throughput Screening and Directed Evolution of Biomolecules. MICROMACHINES 2024; 15:971. [PMID: 39203623 PMCID: PMC11356158 DOI: 10.3390/mi15080971] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/24/2024] [Revised: 07/23/2024] [Accepted: 07/26/2024] [Indexed: 09/03/2024]
Abstract
Directed evolution is a powerful technique for creating biomolecules such as proteins and nucleic acids with tailor-made properties for therapeutic and industrial applications by mimicking the natural evolution processes in the laboratory. Droplet microfluidics improved classical directed evolution by enabling time-consuming and laborious steps in this iterative process to be performed within monodispersed droplets in a highly controlled and automated manner. Droplet microfluidic chips can generate, manipulate, and sort individual droplets at kilohertz rates in a user-defined microchannel geometry, allowing new strategies for high-throughput screening and evolution of biomolecules. In this review, we discuss directed evolution studies in which droplet-based microfluidic systems were used to screen and improve the functional properties of biomolecules. We provide a systematic overview of basic on-chip fluidic operations, including reagent mixing by merging continuous fluid streams and droplet pairs, reagent addition by picoinjection, droplet generation, droplet incubation in delay lines, chambers and hydrodynamic traps, and droplet sorting techniques. Various microfluidic strategies for directed evolution using single and multiple emulsions and biomimetic materials (giant lipid vesicles, microgels, and microcapsules) are highlighted. Completely cell-free microfluidic-assisted in vitro compartmentalization methods that eliminate the need to clone DNA into cells after each round of mutagenesis are also presented.
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Affiliation(s)
- Goran T Vladisaljević
- Department of Chemical Engineering, Loughborough University, Loughborough LE11 3TU, UK
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5
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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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6
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Ma Z, Ma M, Cao X, Jiang Y, Gao D. Droplet digital molecular beacon-LAMP assay via pico-injection for ultrasensitive detection of pathogens. Mikrochim Acta 2024; 191:430. [PMID: 38949666 DOI: 10.1007/s00604-024-06509-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2024] [Accepted: 06/13/2024] [Indexed: 07/02/2024]
Abstract
A pico-injection-aided digital droplet detection platform is presented that integrates loop-mediated isothermal amplification (LAMP) with molecular beacons (MBs) for the ultrasensitive and quantitative identification of pathogens, leveraging the sequence-specific detection capabilities of MBs. The microfluidic device contained three distinct functional units including droplet generation, pico-injection, and droplet counting. Utilizing a pico-injector, MBs are introduced into each droplet to specifically identify LAMP amplification products, thereby overcoming issues related to temperature incompatibility. Our methodology has been validated through the quantitative detection of Escherichia coli, achieving a detection limit as low as 9 copies/μL in a model plasmid containing the malB gene and 3 CFU/μL in a spiked milk sample. The total analysis time was less than 1.5 h. The sensitivity and robustness of this platform further demonstrated the potential for rapid pathogen detection and diagnosis, particularly when integrated with cutting-edge microfluidic technologies.
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Affiliation(s)
- Zhiyuan Ma
- The State Key Laboratory of Chemical Oncogenomics, Shenzhen International Graduate School and Open FIESTA, Shenzhen International Graduate School, Tsinghua University, Shenzhen, 518055, People's Republic of China
- Key Laboratory of Metabolomics at Shenzhen, Graduate School at Shenzhen, Tsinghua University, Shenzhen, 518055, China
| | - Mengshao Ma
- The State Key Laboratory of Chemical Oncogenomics, Shenzhen International Graduate School and Open FIESTA, Shenzhen International Graduate School, Tsinghua University, Shenzhen, 518055, People's Republic of China
- Key Laboratory of Metabolomics at Shenzhen, Graduate School at Shenzhen, Tsinghua University, Shenzhen, 518055, China
| | - Xiaobao Cao
- Guangzhou Laboratory, Guangdong Province, 510320, China.
| | - Yuyang Jiang
- The State Key Laboratory of Chemical Oncogenomics, Shenzhen International Graduate School and Open FIESTA, Shenzhen International Graduate School, Tsinghua University, Shenzhen, 518055, People's Republic of China
- Department of HIV/AIDS Prevention and Control, Shenzhen Center for Disease Control and Prevention, Shenzhen, 518000, China
| | - Dan Gao
- The State Key Laboratory of Chemical Oncogenomics, Shenzhen International Graduate School and Open FIESTA, Shenzhen International Graduate School, Tsinghua University, Shenzhen, 518055, People's Republic of China.
- Key Laboratory of Metabolomics at Shenzhen, Graduate School at Shenzhen, Tsinghua University, Shenzhen, 518055, China.
- School of Pharmaceutical Sciences, Tsinghua University, Beijing, 100084, People's Republic of China.
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7
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Krishnamurthy A, Anand RK. Electrokinetic Desalting and Salting of Water-in-Oil Droplets. Anal Chem 2024; 96:9876-9884. [PMID: 38842795 DOI: 10.1021/acs.analchem.4c00534] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2024]
Abstract
Droplet-based microfluidic platforms demand modifications to the droplet composition to facilitate reactions and analyses. However, limited techniques exist to modify the droplet contents post their generation. Here, ion transport across two ion-exchange membranes possessing distinct selectivity is employed to introduce ions into (salt) or extract ions from (desalt) water-in-oil droplets. The ion concentration distribution and transport mechanisms are visualized using a precipitation reaction and a charged fluorescent tracer. Furthermore, current measurements reveal characteristic regimes in desalting and salting modes and demonstrate that the rates of ion transport linearly correlate with applied voltage and the ionic strength of the droplets. Importantly, up to 98% desalting efficiency is achieved. This technique advances droplet-based sample preparation through the straightforward manipulation of droplet contents.
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Affiliation(s)
- Aparna Krishnamurthy
- Department of Chemistry, Iowa State University, 1605 Gilman Hall, 2415 Osborn Drive, Ames, Iowa 50011, United States
| | - Robbyn K Anand
- Department of Chemistry, Iowa State University, 1605 Gilman Hall, 2415 Osborn Drive, Ames, Iowa 50011, United States
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8
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Gines G, Espada R, Dramé-Maigné A, Baccouche A, Larrouy N, Rondelez Y. Functional analysis of single enzymes combining programmable molecular circuits with droplet-based microfluidics. NATURE NANOTECHNOLOGY 2024; 19:800-809. [PMID: 38409552 DOI: 10.1038/s41565-024-01617-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Accepted: 01/22/2024] [Indexed: 02/28/2024]
Abstract
The analysis of proteins at the single-molecule level reveals heterogeneous behaviours that are masked in ensemble-averaged techniques. The digital quantification of enzymes traditionally involves the observation and counting of single molecules partitioned into microcompartments via the conversion of a profluorescent substrate. This strategy, based on linear signal amplification, is limited to a few enzymes with sufficiently high turnover rate. Here we show that combining the sensitivity of an exponential molecular amplifier with the modularity of DNA-enzyme circuits and droplet readout makes it possible to specifically detect, at the single-molecule level, virtually any D(R)NA-related enzymatic activity. This strategy, denoted digital PUMA (Programmable Ultrasensitive Molecular Amplifier), is validated for more than a dozen different enzymes, including many with slow catalytic rate, and down to the extreme limit of apparent single turnover for Streptococcus pyogenes Cas9. Digital counting uniquely yields absolute molar quantification and reveals a large fraction of inactive catalysts in all tested commercial preparations. By monitoring the amplification reaction from single enzyme molecules in real time, we also extract the distribution of activity among the catalyst population, revealing alternative inactivation pathways under various stresses. Our approach dramatically expands the number of enzymes that can benefit from quantification and functional analysis at single-molecule resolution. We anticipate digital PUMA will serve as a versatile framework for accurate enzyme quantification in diagnosis or biotechnological applications. These digital assays may also be utilized to study the origin of protein functional heterogeneity.
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Affiliation(s)
- Guillaume Gines
- Laboratoire Gulliver, UMR7083 CNRS/ESPCI Paris-PSL Research University, Paris, France.
| | - Rocίo Espada
- Laboratoire Gulliver, UMR7083 CNRS/ESPCI Paris-PSL Research University, Paris, France
| | - Adèle Dramé-Maigné
- Laboratoire Gulliver, UMR7083 CNRS/ESPCI Paris-PSL Research University, Paris, France
| | - Alexandre Baccouche
- LIMMS, IRL 2820 CNRS-Institute of Industrial Science, The University of Tokyo, Tokyo, Japan
| | - Nicolas Larrouy
- Laboratoire Gulliver, UMR7083 CNRS/ESPCI Paris-PSL Research University, Paris, France
| | - Yannick Rondelez
- Laboratoire Gulliver, UMR7083 CNRS/ESPCI Paris-PSL Research University, Paris, France
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9
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Zhao Z, Zhai H, Zuo P, Wang T, Xie R, Tian M, Song R, Xu X, Li Z. Image-activated pico-injection for single-cell analysis. Talanta 2024; 272:125765. [PMID: 38346358 DOI: 10.1016/j.talanta.2024.125765] [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: 09/30/2023] [Revised: 01/29/2024] [Accepted: 02/06/2024] [Indexed: 03/17/2024]
Abstract
The addition of reagents into preformed droplets is a crucial yet intricate task in droplet-based applications where sequential reactions is required. Pico-injection offers high throughput and robustness in accomplishing this task, but the existing pico-injection techniques work in an indiscriminate manner, making it difficult to target particular groups of droplets. Here we report image-activated pico-injection (imgPico) for label-free, on-demand reagent supplementation into droplets. The imgPico detects the droplets of interest by real-time image analysis and makes decisions for the downstream pico-injection operation. We studied the performance of different algorithms for the image analysis and optimized the experimental settings of the imgPico. In the validation experiment, the imgPico successfully injected fluorescent dyes into droplets encapsulating one, two, and three cells, respectively, as expected. We further demonstrated the utility of imgPico by targeting droplets encapsulating single cells in droplet-based single-cell RNA sequencing (scRNA-seq) using exceedingly high cell density, and the results showed that the imgPico effectively reduced the presence of doublets in the scRNA-seq data. With the merits of being label-free and versatile, the imgPico represents a technical advance with potential applications in single-cell analysis.
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Affiliation(s)
- Zhantao Zhao
- Department of Biomedical Engineering, Medical School, Shenzhen University, Shenzhen, 518060, China; Guangdong Key Laboratory for Biomedical Measurements and Ultrasound Imaging, Department of Biomedical Engineering, Medical School, Shenzhen University, Shenzhen, 518060, China
| | - Heng Zhai
- Department of Biomedical Engineering, Medical School, Shenzhen University, Shenzhen, 518060, China; Guangdong Key Laboratory for Biomedical Measurements and Ultrasound Imaging, Department of Biomedical Engineering, Medical School, Shenzhen University, Shenzhen, 518060, China
| | - Peng Zuo
- ThunderBio Innovation, Shenzhen, 518108, China
| | - Tao Wang
- Department of Biomedical Engineering, Medical School, Shenzhen University, Shenzhen, 518060, China; Guangdong Key Laboratory for Biomedical Measurements and Ultrasound Imaging, Department of Biomedical Engineering, Medical School, Shenzhen University, Shenzhen, 518060, China
| | - Run Xie
- Department of Biomedical Engineering, Medical School, Shenzhen University, Shenzhen, 518060, China; Guangdong Key Laboratory for Biomedical Measurements and Ultrasound Imaging, Department of Biomedical Engineering, Medical School, Shenzhen University, Shenzhen, 518060, China
| | - Mu Tian
- Department of Biomedical Engineering, Medical School, Shenzhen University, Shenzhen, 518060, China; Guangdong Key Laboratory for Biomedical Measurements and Ultrasound Imaging, Department of Biomedical Engineering, Medical School, Shenzhen University, Shenzhen, 518060, China
| | - Ruyuan Song
- ThunderBio Innovation, Shenzhen, 518108, China
| | - Xiaonan Xu
- ThunderBio Innovation, Shenzhen, 518108, China
| | - Zida Li
- Department of Biomedical Engineering, Medical School, Shenzhen University, Shenzhen, 518060, China; Guangdong Key Laboratory for Biomedical Measurements and Ultrasound Imaging, Department of Biomedical Engineering, Medical School, Shenzhen University, Shenzhen, 518060, China.
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10
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De Lora JA, Aubermann F, Frey C, Jahnke T, Wang Y, Weber S, Platzman I, Spatz JP. Evaluation of Acoustophoretic and Dielectrophoretic Forces for Droplet Injection in Droplet-Based Microfluidic Devices. ACS OMEGA 2024; 9:16097-16105. [PMID: 38617618 PMCID: PMC11007716 DOI: 10.1021/acsomega.3c09881] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/11/2023] [Revised: 03/05/2024] [Accepted: 03/18/2024] [Indexed: 04/16/2024]
Abstract
Acoustophoretic forces have been successfully implemented into droplet-based microfluidic devices to manipulate droplets. These acoustophoretic forces in droplet microfluidic devices are typically generated as in acoustofluidic devices through transducer actuation of a piezoelectric substrate such as lithium niobate (LiNbO3), which is inherently accompanied by the emergence of electrical fields. Understanding acoustophoretic versus dielectrophoretic forces produced by electrodes and transducers within active microfluidic devices is important for the optimization of device performance during design iterations. In this case study, we design microfluidic devices with a droplet injection module and report an experimental strategy to deduce the respective contribution of the acoustophoretic versus dielectrophoretic forces for the observed droplet injection. Our PDMS-based devices comprise a standard oil-in-water droplet-generating module connected to a T-junction injection module featuring actuating electrodes. We use two different electrode geometries produced within the same PDMS slab as the droplet production/injection channels by filling low-melting-point metal alloy into channels that template the electrode geometries. When these electrodes are constructed on LiNbO3 as the substrate, they have a dual function as a piezoelectric transducer, which we call embedded liquid metal interdigitated transducers (elmIDTs). To decipher the contribution of acoustophoretic versus dielectrophoretic forces, we build the same devices on either piezoelectric LiNbO3 or nonpiezo active glass substrates with different combinations of physical device characteristics (i.e., elmIDT geometry and alignment) and operate in a range of phase spaces (i.e., frequency, voltage, and transducer polarity). We characterize devices using techniques such as laser Doppler vibrometry (LDV) and infrared imaging, along with evaluating droplet injection for our series of device designs, constructions, and operating parameters. Although we find that LiNbO3 device designs generate acoustic fields, we demonstrate that droplet injection occurs only due to dielectrophoretic forces. We deduce that droplet injection is caused by the coupled dielectrophoretic forces arising from the operation of elmIDTs rather than by acoustophoretic forces for this specific device design. We arrive at this conclusion because equivalent droplet injection occurs without the presence of an acoustic field using the same electrode designs on nonpiezo active glass substrate devices. This work establishes a methodology to pinpoint the major contributing force of droplet manipulation in droplet-based acoustomicrofluidics.
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Affiliation(s)
- Jacqueline A. De Lora
- Department
of Cellular Biophysics, Max Planck Institute
for Medical Research, Jahnstraße 29, 69120 Heidelberg, Germany
- Institute
for Molecular Systems Engineering (IMSE), Heidelberg University, Im Neuenheimer Feld 225, 69120 Heidelberg, Germany
| | - Florian Aubermann
- Department
of Cellular Biophysics, Max Planck Institute
for Medical Research, Jahnstraße 29, 69120 Heidelberg, Germany
- Institute
for Molecular Systems Engineering (IMSE), Heidelberg University, Im Neuenheimer Feld 225, 69120 Heidelberg, Germany
- Max
Planck School Matter to Life, Jahnstraße 29, 69120 Heidelberg, Germany
| | - Christoph Frey
- Department
of Cellular Biophysics, Max Planck Institute
for Medical Research, Jahnstraße 29, 69120 Heidelberg, Germany
- Institute
for Molecular Systems Engineering (IMSE), Heidelberg University, Im Neuenheimer Feld 225, 69120 Heidelberg, Germany
| | - Timotheus Jahnke
- Department
of Cellular Biophysics, Max Planck Institute
for Medical Research, Jahnstraße 29, 69120 Heidelberg, Germany
- Institute
for Molecular Systems Engineering (IMSE), Heidelberg University, Im Neuenheimer Feld 225, 69120 Heidelberg, Germany
| | - Yuanzhen Wang
- Department
of Cellular Biophysics, Max Planck Institute
for Medical Research, Jahnstraße 29, 69120 Heidelberg, Germany
- Institute
for Molecular Systems Engineering (IMSE), Heidelberg University, Im Neuenheimer Feld 225, 69120 Heidelberg, Germany
| | - Sebastian Weber
- Department
of Cellular Biophysics, Max Planck Institute
for Medical Research, Jahnstraße 29, 69120 Heidelberg, Germany
- Institute
for Molecular Systems Engineering (IMSE), Heidelberg University, Im Neuenheimer Feld 225, 69120 Heidelberg, Germany
| | - Ilia Platzman
- Department
of Cellular Biophysics, Max Planck Institute
for Medical Research, Jahnstraße 29, 69120 Heidelberg, Germany
- Institute
for Molecular Systems Engineering (IMSE), Heidelberg University, Im Neuenheimer Feld 225, 69120 Heidelberg, Germany
| | - Joachim P. Spatz
- Department
of Cellular Biophysics, Max Planck Institute
for Medical Research, Jahnstraße 29, 69120 Heidelberg, Germany
- Institute
for Molecular Systems Engineering (IMSE), Heidelberg University, Im Neuenheimer Feld 225, 69120 Heidelberg, Germany
- Max
Planck School Matter to Life, Jahnstraße 29, 69120 Heidelberg, Germany
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11
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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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12
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López-Domene R, Manteca A, Rodriguez-Abetxuko A, Beloqui A, Cortajarena AL. In vitro Production of Hemin-Based Artificial Metalloenzymes. Chemistry 2024; 30:e202303254. [PMID: 38145337 DOI: 10.1002/chem.202303254] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2023] [Revised: 12/22/2023] [Accepted: 12/25/2023] [Indexed: 12/26/2023]
Abstract
Developing enzyme alternatives is pivotal to improving and enabling new processes in biotechnology and industry. Artificial metalloenzymes (ArMs) are combinations of protein scaffolds with metal elements, such as metal nanoclusters or metal-containing molecules with specific catalytic properties, which can be customized. Here, we engineered an ArM based on the consensus tetratricopeptide repeat (CTPR) scaffold by introducing a unique histidine residue to coordinate the hemin cofactor. Our results show that this engineered system exhibits robust peroxidase-like catalytic activity driven by the hemin. The expression of the scaffold and subsequent coordination of hemin was achieved by recombinant expression in bulk and through in vitro transcription and translation systems in water-in-oil drops. The ability to synthesize this system in emulsio paves the way to improve its properties by means of droplet microfluidic screenings, facilitating the exploration of the protein combinatorial space to discover improved or novel catalytic activities.
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Affiliation(s)
- Rocío López-Domene
- Centre for Cooperative Research in Biomaterials (CIC biomaGUNE), Basque Research and Technology Alliance (BRTA), Paseo de Miramón 194, Donostia-San Sebastián, E-20014, Spain
- POLYMAT and Department of Applied Chemistry, Faculty of Chemistry, University of the Basque Country UPV/EHU, Donostia-San Sebastián, E-20018, Spain
| | - Aitor Manteca
- Centre for Cooperative Research in Biomaterials (CIC biomaGUNE), Basque Research and Technology Alliance (BRTA), Paseo de Miramón 194, Donostia-San Sebastián, E-20014, Spain
| | - Andoni Rodriguez-Abetxuko
- POLYMAT and Department of Applied Chemistry, Faculty of Chemistry, University of the Basque Country UPV/EHU, Donostia-San Sebastián, E-20018, Spain
| | - Ana Beloqui
- POLYMAT and Department of Applied Chemistry, Faculty of Chemistry, University of the Basque Country UPV/EHU, Donostia-San Sebastián, E-20018, Spain
- IKERBASQUE, Basque Foundation for Science, Plaza Euskadi 5, E-48009, Bilbao, Spain
| | - Aitziber L Cortajarena
- Centre for Cooperative Research in Biomaterials (CIC biomaGUNE), Basque Research and Technology Alliance (BRTA), Paseo de Miramón 194, Donostia-San Sebastián, E-20014, Spain
- IKERBASQUE, Basque Foundation for Science, Plaza Euskadi 5, E-48009, Bilbao, Spain
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13
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Zheng D, Zhang J, Jiang W, Xu Y, Meng H, Poh CL, Chen CH. Graphene oxide aptasensor droplet assay for detection of metabolites secreted by single cells applied to synthetic biology. LAB ON A CHIP 2023; 24:137-147. [PMID: 38054213 DOI: 10.1039/d3lc00959a] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/07/2023]
Abstract
Synthetic biology harnesses the power of natural microbes by re-engineering metabolic pathways to manufacture desired compounds. Droplet technology has emerged as a high-throughput tool to screen single cells for synthetic biology, while the challenges in sensitive flexible single-cell secretion assay for bioproduction of high-value chemicals remained. Here, a novel droplet modifiable graphene oxide (GO) aptasensor was developed, enabling sensitive flexible detection of different target compounds secreted from single cells. Fluorophore-labeled aptamers were stably anchored on GO through π-π stacking interactions to minimize the non-specific interactions for low-background detection of target compounds with high signal-to-noise ratios. The assay's versatility was exhibited by adapting aptamer sequences to measure metabolic secretions like ATP and naringenin. To show the case, engineered E. coli were constructed for the bioproduction of naringenin. The high signal-to-noise ratio assay (∼2.72) was approached to precisely measure the naringenins secreted from single E. coli in the droplets. Consequently, secretory cells (Gib) were clearly distinguished from wild-type (WT) cells, with a low overlap in cell populations (∼0%) for bioproduction.
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Affiliation(s)
- Dan Zheng
- Department of Biomedical Engineering, National University of Singapore, 4 Engineering Drive 3, 117583, Singapore.
| | - Jingyun Zhang
- Department of Biomedical Engineering, National University of Singapore, 4 Engineering Drive 3, 117583, Singapore.
| | - Wenxin Jiang
- Department of Biomedical Engineering, City University of Hong Kong, 83 Tat Chee Avenue, Kowloon Tong, Hong Kong, China.
| | - Ying Xu
- Department of Biomedical Engineering, City University of Hong Kong, 83 Tat Chee Avenue, Kowloon Tong, Hong Kong, China.
| | - Haixu Meng
- Department of Biomedical Engineering, City University of Hong Kong, 83 Tat Chee Avenue, Kowloon Tong, Hong Kong, China.
| | - Chueh Loo Poh
- Department of Biomedical Engineering, National University of Singapore, 4 Engineering Drive 3, 117583, Singapore.
| | - Chia-Hung Chen
- Department of Biomedical Engineering, City University of Hong Kong, 83 Tat Chee Avenue, Kowloon Tong, Hong Kong, China.
- City University of Hong Kong Shenzhen Research Institute, Shenzhen Virtual University Park, Shenzhen, China
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14
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Hoshino M, Ota Y, Suyama T, Morishita Y, Tsuneda S, Noda N. Water-in-oil droplet-mediated method for detecting and isolating infectious bacteriophage particles via fluorescent staining. Front Microbiol 2023; 14:1282372. [PMID: 38125569 PMCID: PMC10731258 DOI: 10.3389/fmicb.2023.1282372] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2023] [Accepted: 11/14/2023] [Indexed: 12/23/2023] Open
Abstract
Bacteriophages are the most abundant entities on Earth. In contrast with the number of phages considered to be in existence, current phage isolation and screening methods lack throughput. Droplet microfluidic technology has been established as a platform for high-throughput screening of biological and biochemical components. In this study, we developed a proof-of-concept method for isolating phages using water-in-oil droplets (droplets) as individual chambers for phage propagation and co-cultivating T2 phage and their host cell Escherichia coli within droplets. Liquid cultivation of microbes will facilitate the use of microbes that cannot grow on or degrade agar as host cells, ultimately resulting in the acquisition of phages that infect less known bacterial cells. The compartmentalizing characteristic of droplets and the use of a fluorescent dye to stain phages simultaneously enabled the enumeration and isolation of viable phage particles. We successfully recultivated the phages after simultaneously segregating single phage particles into droplets and inoculating them with their host cells within droplets. By recovering individual droplets into 96-well plates, we were able to isolate phage clones derived from single phage particles. The success rate for phage recovery was 35.7%. This study lays the building foundations for techniques yet to be developed that will involve the isolation and rupturing of droplets and provides a robust method for phage enumeration and isolation.
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Affiliation(s)
- Miu Hoshino
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba, Japan
- Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Ibaraki, Japan
| | - Yuri Ota
- Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Ibaraki, Japan
- On-chip Biotechnologies Co., Ltd., Tokyo, Japan
| | - Tetsushi Suyama
- Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Ibaraki, Japan
| | | | - Satoshi Tsuneda
- Department of Life Science and Medical Bioscience, School of Advanced Science and Engineering, Waseda University, Tokyo, Japan
| | - Naohiro Noda
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba, Japan
- Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Ibaraki, Japan
- Department of Life Science and Medical Bioscience, School of Advanced Science and Engineering, Waseda University, Tokyo, Japan
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15
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Liu W, Li H, Gao Q, Zhao D, Yu Y, Xiang Q, Cheng X, Wang ZL, Long W, Cheng T. Micro-Droplets Parameters Monitoring in a Microfluidic Chip via Liquid-Solid Triboelectric Nanogenerator. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2023; 35:e2307184. [PMID: 37717142 DOI: 10.1002/adma.202307184] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/20/2023] [Revised: 09/15/2023] [Indexed: 09/18/2023]
Abstract
The monitoring of micro-droplets parameters is significant to the development of droplet microfluidics. However, existing monitoring methods have drawbacks such as high cost, interference with droplet movement, and even the potential for cross-contamination. Herein, a micro-droplets monitoring method (MDMM) based on liquid-solid triboelectric nanogenerator (LS-TENG) is proposed, which can realize non-invasive and self-powered monitoring of micro-droplets in a microfluidic chip. The droplet frequency is monitored by voltage pulse frequency and a mathematical model is established to monitor the droplet length and velocity. Furthermore, this work constructs micro-droplets sensor (MDS) based on the MDMM to carry out the experiment. The coefficients of determination (R2 ) of the fitting curves of the micro-droplets frequency, length, and velocity monitoring are 0.998, 0.997, and 0.995, respectively. To prove the universal applicability of the MDMM, the micro-droplets generated by different liquid media and channel structures are monitored. Eventually, a micro-droplet monitoring system is built, which can realize the counting of micro-droplets and the monitoring of droplet frequency and length. This work provides a novel approach for monitoring micro-droplets parameters, which holds the potential to advance developments in the field of microfluidics.
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Affiliation(s)
- Wenkai Liu
- Faculty of Mechanical and Electrical Engineering, Kunming University of Science and Technology, Kunming, 650500, China
- Beijing Institute of Nanoenergy and Nanosystems, Chinese Academy of Sciences, Beijing, 101400, China
| | - Hengyu Li
- Beijing Institute of Nanoenergy and Nanosystems, Chinese Academy of Sciences, Beijing, 101400, China
- College of Materials Science and Opto-Electronic Technology, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Qi Gao
- Beijing Institute of Nanoenergy and Nanosystems, Chinese Academy of Sciences, Beijing, 101400, China
- School of Nanoscience and Engineering, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Da Zhao
- Beijing Institute of Nanoenergy and Nanosystems, Chinese Academy of Sciences, Beijing, 101400, China
| | - Yang Yu
- Beijing Institute of Nanoenergy and Nanosystems, Chinese Academy of Sciences, Beijing, 101400, China
- School of Nanoscience and Engineering, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Qin Xiang
- Faculty of Mechanical and Electrical Engineering, Kunming University of Science and Technology, Kunming, 650500, China
- Beijing Institute of Nanoenergy and Nanosystems, Chinese Academy of Sciences, Beijing, 101400, China
| | - Xiaojun Cheng
- Beijing Institute of Nanoenergy and Nanosystems, Chinese Academy of Sciences, Beijing, 101400, China
- School of Nanoscience and Engineering, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Zhong Lin Wang
- Beijing Institute of Nanoenergy and Nanosystems, Chinese Academy of Sciences, Beijing, 101400, China
- Georgia Institute of Technology, Atlanta, GA, 30332-0245, USA
| | - Wei Long
- Faculty of Mechanical and Electrical Engineering, Kunming University of Science and Technology, Kunming, 650500, China
| | - Tinghai Cheng
- Beijing Institute of Nanoenergy and Nanosystems, Chinese Academy of Sciences, Beijing, 101400, China
- School of Nanoscience and Engineering, University of Chinese Academy of Sciences, Beijing, 100049, China
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16
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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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17
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Yang T, Buholzer KJ, Sottini A, Cao X, deMello A, Nettels D, Schuler B. Rapid droplet-based mixing for single-molecule spectroscopy. Nat Methods 2023; 20:1479-1482. [PMID: 37749213 DOI: 10.1038/s41592-023-01995-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Accepted: 08/02/2023] [Indexed: 09/27/2023]
Abstract
Probing non-equilibrium dynamics with single-molecule spectroscopy is important for dissecting biomolecular mechanisms. However, existing microfluidic rapid-mixing systems for this purpose are incompatible with surface-adhesive biomolecules, exhibit undesirable flow dispersion and are often demanding to fabricate. Here we introduce droplet-based microfluidic mixing for single-molecule spectroscopy to overcome these limitations in a wide range of applications. We demonstrate its robust functionality with binding kinetics of even very surface-adhesive proteins on the millisecond timescale.
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Affiliation(s)
- Tianjin Yang
- Department of Biochemistry, University of Zurich, Zurich, Switzerland.
| | - Karin J Buholzer
- Department of Biochemistry, University of Zurich, Zurich, Switzerland
| | - Andrea Sottini
- Department of Biochemistry, University of Zurich, Zurich, Switzerland
| | - Xiaobao Cao
- Institute for Chemical and Bioengineering, ETH Zurich, Zurich, Switzerland
| | - Andrew deMello
- Institute for Chemical and Bioengineering, ETH Zurich, Zurich, Switzerland
| | - Daniel Nettels
- Department of Biochemistry, University of Zurich, Zurich, Switzerland
| | - Benjamin Schuler
- Department of Biochemistry, University of Zurich, Zurich, Switzerland.
- Department of Physics, University of Zurich, Zurich, Switzerland.
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18
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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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19
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Zhang Q, Ma S, Liu Z, Zhu B, Zhou Z, Li G, Meana JJ, González-Maeso J, Lu C. Droplet-based bisulfite sequencing for high-throughput profiling of single-cell DNA methylomes. Nat Commun 2023; 14:4672. [PMID: 37537185 PMCID: PMC10400590 DOI: 10.1038/s41467-023-40411-w] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Accepted: 07/26/2023] [Indexed: 08/05/2023] Open
Abstract
The genome-wide DNA methylation profile, or DNA methylome, is a critical component of the overall epigenomic landscape that modulates gene activities and cell fate. Single-cell DNA methylomic studies offer unprecedented resolution for detecting and profiling cell subsets based on methylomic features. However, existing single-cell methylomic technologies are based on use of tubes or well plates and these platforms are not easily scalable for handling a large number of single cells. Here we demonstrate a droplet-based microfluidic technology, Drop-BS, to construct single-cell bisulfite sequencing libraries for DNA methylome profiling. Drop-BS takes advantage of the ultrahigh throughput offered by droplet microfluidics to prepare bisulfite sequencing libraries of up to 10,000 single cells within 2 days. We apply the technology to profile mixed cell lines, mouse and human brain tissues to reveal cell type heterogeneity. Drop-BS offers a promising solution for single-cell methylomic studies requiring examination of a large cell population.
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Affiliation(s)
- Qiang Zhang
- Department of Chemical Engineering, Virginia Tech, Blacksburg, VA, 24061, USA
| | - Sai Ma
- Department of Biomedical Engineering and Mechanics, Virginia Tech, Blacksburg, VA, 24061, USA
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Zhengzhi Liu
- Department of Biomedical Engineering and Mechanics, Virginia Tech, Blacksburg, VA, 24061, USA
| | - Bohan Zhu
- Department of Chemical Engineering, Virginia Tech, Blacksburg, VA, 24061, USA
| | - Zirui Zhou
- Department of Chemical Engineering, Virginia Tech, Blacksburg, VA, 24061, USA
| | - Gaoshan Li
- Department of Chemical Engineering, Virginia Tech, Blacksburg, VA, 24061, USA
| | - J Javier Meana
- Department of Pharmacology, University of the Basque Country UPV/EHU, CIBERSAM, Biocruces Health Research Institute, E-48940, Leioa, Bizkaia, Spain
| | - Javier González-Maeso
- Department of Physiology and Biophysics, Virginia Commonwealth University School of Medicine, Richmond, VA, 23298, USA
| | - Chang Lu
- Department of Chemical Engineering, Virginia Tech, Blacksburg, VA, 24061, USA.
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20
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Monserrat Lopez D, Rottmann P, Puebla-Hellmann G, Drechsler U, Mayor M, Panke S, Fussenegger M, Lörtscher E. Direct electrification of silicon microfluidics for electric field applications. MICROSYSTEMS & NANOENGINEERING 2023; 9:81. [PMID: 37342556 PMCID: PMC10277806 DOI: 10.1038/s41378-023-00552-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Revised: 04/25/2023] [Accepted: 05/10/2023] [Indexed: 06/23/2023]
Abstract
Microfluidic systems are widely used in fundamental research and industrial applications due to their unique behavior, enhanced control, and manipulation opportunities of liquids in constrained geometries. In micrometer-sized channels, electric fields are efficient mechanisms for manipulating liquids, leading to deflection, injection, poration or electrochemical modification of cells and droplets. While PDMS-based microfluidic devices are used due to their inexpensive fabrication, they are limited in terms of electrode integration. Using silicon as the channel material, microfabrication techniques can be used to create nearby electrodes. Despite the advantages that silicon provides, its opacity has prevented its usage in most important microfluidic applications that need optical access. To overcome this barrier, silicon-on-insulator technology in microfluidics is introduced to create optical viewports and channel-interfacing electrodes. More specifically, the microfluidic channel walls are directly electrified via selective, nanoscale etching to introduce insulation segments inside the silicon device layer, thereby achieving the most homogeneous electric field distributions and lowest operation voltages feasible across microfluidic channels. These ideal electrostatic conditions enable a drastic energy reduction, as effectively shown via picoinjection and fluorescence-activated droplet sorting applications at voltages below 6 and 15 V, respectively, facilitating low-voltage electric field applications in next-generation microfluidics.
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Affiliation(s)
- Diego Monserrat Lopez
- IBM Research Europe - Zurich, Säumerstrasse 4, CH-8803 Rüschlikon, Switzerland
- ETH Zürich, Department of Biosystems Science and Engineering, Mattenstrasse 26, 4058 Basel, Switzerland
| | - Philipp Rottmann
- ETH Zürich, Department of Biosystems Science and Engineering, Mattenstrasse 26, 4058 Basel, Switzerland
| | - Gabriel Puebla-Hellmann
- IBM Research Europe - Zurich, Säumerstrasse 4, CH-8803 Rüschlikon, Switzerland
- University of Basel, Department of Chemistry, St. Johanns-Ring 19, CH-4056 Basel, Switzerland
| | - Ute Drechsler
- IBM Research Europe - Zurich, Säumerstrasse 4, CH-8803 Rüschlikon, Switzerland
| | - Marcel Mayor
- University of Basel, Department of Chemistry, St. Johanns-Ring 19, CH-4056 Basel, Switzerland
- Institute for Nanotechnology (INT), Karlsruhe Institute of Technology (KIT), P. O. Box 3640, 76021 Karlsruhe, Germany
| | - Sven Panke
- ETH Zürich, Department of Biosystems Science and Engineering, Mattenstrasse 26, 4058 Basel, Switzerland
| | - Martin Fussenegger
- ETH Zürich, Department of Biosystems Science and Engineering, Mattenstrasse 26, 4058 Basel, Switzerland
- University of Basel, Faculty of Life Science, Basel, Switzerland
| | - Emanuel Lörtscher
- IBM Research Europe - Zurich, Säumerstrasse 4, CH-8803 Rüschlikon, Switzerland
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21
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Murray BE, Penabad LI, Kennedy RT. Advances in coupling droplet microfluidics to mass spectrometry. Curr Opin Biotechnol 2023; 82:102962. [PMID: 37336080 DOI: 10.1016/j.copbio.2023.102962] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2023] [Revised: 05/12/2023] [Accepted: 05/23/2023] [Indexed: 06/21/2023]
Abstract
Droplet microfluidics enables development of workflows with low sample consumption and high throughput. Fluorescence-based assays are most used with droplet microfluidics; however, the requirement of a fluorescent reporter restricts applicability of this approach. The coupling of droplets to mass spectrometry (MS) has enabled selective assays on complex mixtures to broaden the analyte scope. Droplet microfluidics has been interfaced to MS via electrospray ionization (ESI) and matrix-assisted laser desorption ionization (MALDI). The works reviewed herein outline the development of this nascent field as well as initial exploration of its application in biotechnology and bioanalysis, including synthetic biology, reaction development, and in vivo sensing.
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Affiliation(s)
- Bridget E Murray
- Department of Chemistry, University of Michigan, 930 N. University Ave, Ann Arbor, MI 48109-1055, USA
| | - Laura I Penabad
- Department of Chemistry, University of Michigan, 930 N. University Ave, Ann Arbor, MI 48109-1055, USA
| | - Robert T Kennedy
- Department of Chemistry, University of Michigan, 930 N. University Ave, Ann Arbor, MI 48109-1055, USA.
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22
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Yu Y, Gao Y, He L, Fang B, Ge W, Yang P, Ju Y, Xie X, Lei L. Biomaterial-based gene therapy. MedComm (Beijing) 2023; 4:e259. [PMID: 37284583 PMCID: PMC10239531 DOI: 10.1002/mco2.259] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Revised: 03/17/2023] [Accepted: 03/21/2023] [Indexed: 06/08/2023] Open
Abstract
Gene therapy, a medical approach that involves the correction or replacement of defective and abnormal genes, plays an essential role in the treatment of complex and refractory diseases, such as hereditary diseases, cancer, and rheumatic immune diseases. Nucleic acids alone do not easily enter the target cells due to their easy degradation in vivo and the structure of the target cell membranes. The introduction of genes into biological cells is often dependent on gene delivery vectors, such as adenoviral vectors, which are commonly used in gene therapy. However, traditional viral vectors have strong immunogenicity while also presenting a potential infection risk. Recently, biomaterials have attracted attention for use as efficient gene delivery vehicles, because they can avoid the drawbacks associated with viral vectors. Biomaterials can improve the biological stability of nucleic acids and the efficiency of intracellular gene delivery. This review is focused on biomaterial-based delivery systems in gene therapy and disease treatment. Herein, we review the recent developments and modalities of gene therapy. Additionally, we discuss nucleic acid delivery strategies, with a focus on biomaterial-based gene delivery systems. Furthermore, the current applications of biomaterial-based gene therapy are summarized.
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Affiliation(s)
- Yi Yu
- Department of StomatologyThe Second Xiangya HospitalCentral South UniversityChangshaChina
| | - Yijun Gao
- Department of StomatologyThe Second Xiangya HospitalCentral South UniversityChangshaChina
| | - Liming He
- Department of StomatologyChangsha Stomatological HospitalChangshaChina
| | - Bairong Fang
- Department of Plastic and Aesthetic (Burn) SurgeryThe Second Xiangya HospitalCentral South UniversityChangshaChina
| | - Wenhui Ge
- Department of StomatologyThe Second Xiangya HospitalCentral South UniversityChangshaChina
| | - Pu Yang
- Department of Plastic and Aesthetic (Burn) SurgeryThe Second Xiangya HospitalCentral South UniversityChangshaChina
| | - Yikun Ju
- Department of Plastic and Aesthetic (Burn) SurgeryThe Second Xiangya HospitalCentral South UniversityChangshaChina
| | - Xiaoyan Xie
- Department of StomatologyThe Second Xiangya HospitalCentral South UniversityChangshaChina
| | - Lanjie Lei
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical EngineeringSoutheast UniversityNanjingChina
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23
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Zhang Q, Ma S, Liu Z, Zhu B, Zhou Z, Li G, Meana JJ, González-Maeso J, Lu C. Droplet-based bisulfite sequencing for high-throughput profiling of single-cell DNA methylomes. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.26.542421. [PMID: 37293095 PMCID: PMC10245959 DOI: 10.1101/2023.05.26.542421] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Genome-wide DNA methylation profile, or DNA methylome, is a critical component of the overall epigenomic landscape that modulates gene activities and cell fate. Single-cell DNA methylomic studies offer unprecedented resolution for detecting and profiling cell subsets based on methylomic features. However, existing single-cell methylomic technologies are all based on use of tubes or well plates and these platforms are not easily scalable for handling a large number of single cells. Here we demonstrate a droplet-based microfluidic technology, Drop-BS, to construct single-cell bisulfite sequencing libraries for DNA methylome profiling. Drop-BS takes advantage of the ultrahigh throughput offered by droplet microfluidics to prepare bisulfite sequencing libraries of up to 10,000 single cells within 2 d. We applied the technology to profile mixed cell lines, mouse and human brain tissues to reveal cell type heterogeneity. Drop-BS will pave the way for single-cell methylomic studies requiring examination of a large cell population.
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Affiliation(s)
- Qiang Zhang
- Department of Chemical Engineering, Virginia Tech, Blacksburg, VA 24061, USA
| | - Sai Ma
- Department of Biomedical Engineering and Mechanics, Virginia Tech, Blacksburg, VA 24061, USA
- Present address: Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Zhengzhi Liu
- Department of Biomedical Engineering and Mechanics, Virginia Tech, Blacksburg, VA 24061, USA
| | - Bohan Zhu
- Department of Chemical Engineering, Virginia Tech, Blacksburg, VA 24061, USA
| | - Zirui Zhou
- Department of Chemical Engineering, Virginia Tech, Blacksburg, VA 24061, USA
| | - Gaoshan Li
- Department of Chemical Engineering, Virginia Tech, Blacksburg, VA 24061, USA
| | - J. Javier Meana
- Department of Pharmacology, University of the Basque Country UPV/EHU, CIBERSAM, Biocruces Health Research Institute, E-48940 Leioa, Bizkaia, Spain
| | - Javier González-Maeso
- Department of Physiology and Biophysics, Virginia Commonwealth University School of Medicine, Richmond, VA 23298, USA
| | - Chang Lu
- Department of Chemical Engineering, Virginia Tech, Blacksburg, VA 24061, USA
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24
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Mangiarotti A, Chen N, Zhao Z, Lipowsky R, Dimova R. Wetting and complex remodeling of membranes by biomolecular condensates. Nat Commun 2023; 14:2809. [PMID: 37217523 DOI: 10.1038/s41467-023-37955-2] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Accepted: 04/05/2023] [Indexed: 05/24/2023] Open
Abstract
Cells compartmentalize parts of their interiors into liquid-like condensates, which can be reconstituted in vitro. Although these condensates interact with membrane-bound organelles, their potential for membrane remodeling and the underlying mechanisms of such interactions are not well-understood. Here, we demonstrate that interactions between protein condensates - including hollow ones, and membranes can lead to remarkable morphological transformations and provide a theoretical framework to describe them. Modulation of solution salinity or membrane composition drives the condensate-membrane system through two wetting transitions, from dewetting, through a broad regime of partial wetting, to complete wetting. When sufficient membrane area is available, fingering or ruffling of the condensate-membrane interface is observed, an intriguing phenomenon producing intricately curved structures. The observed morphologies are governed by the interplay of adhesion, membrane elasticity, and interfacial tension. Our results highlight the relevance of wetting in cell biology, and pave the way for the design of synthetic membrane-droplet based biomaterials and compartments with tunable properties.
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Affiliation(s)
- Agustín Mangiarotti
- Max Planck Institute of Colloids and Interfaces, Science Park Golm, 14476, Potsdam, Germany
| | - Nannan Chen
- Max Planck Institute of Colloids and Interfaces, Science Park Golm, 14476, Potsdam, Germany
- Department of Nutrition and Food Hygiene, Guangzhou Medical University, Guangzhou, 511436, China
| | - Ziliang Zhao
- Max Planck Institute of Colloids and Interfaces, Science Park Golm, 14476, Potsdam, Germany
- Leibniz Institute of Photonic Technology e.V., Albert-Einstein-Straße 9, 07745, Jena, Germany
- Institute of Applied Optics and Biophysics, Friedrich-Schiller-University Jena, Max-Wien Platz 1, 07743, Jena, Germany
| | - Reinhard Lipowsky
- Max Planck Institute of Colloids and Interfaces, Science Park Golm, 14476, Potsdam, Germany
| | - Rumiana Dimova
- Max Planck Institute of Colloids and Interfaces, Science Park Golm, 14476, Potsdam, Germany.
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25
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Zhang L, Parvin R, Chen M, Hu D, Fan Q, Ye F. High-throughput microfluidic droplets in biomolecular analytical system: A review. Biosens Bioelectron 2023; 228:115213. [PMID: 36906989 DOI: 10.1016/j.bios.2023.115213] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Revised: 02/13/2023] [Accepted: 03/06/2023] [Indexed: 03/11/2023]
Abstract
Droplet microfluidic technology has revolutionized biomolecular analytical research, as it has the capability to reserve the genotype-to-phenotype linkage and assist for revealing the heterogeneity. Massive and uniform picolitre droplets feature dividing solution to the level that single cell and single molecule in each droplet can be visualized, barcoded, and analyzed. Then, the droplet assays can unfold intensive genomic data, offer high sensitivity, and screen and sort from a large number of combinations or phenotypes. Based on these unique advantages, this review focuses on up-to-date research concerning diverse screening applications utilizing droplet microfluidic technology. The emerging progress of droplet microfluidic technology is first introduced, including efficient and scaling-up in droplets encapsulation, and prevalent batch operations. Then the new implementations of droplet-based digital detection assays and single-cell muti-omics sequencing are briefly examined, along with related applications such as drug susceptibility testing, multiplexing for cancer subtype identification, interactions of virus-to-host, and multimodal and spatiotemporal analysis. Meanwhile, we specialize in droplet-based large-scale combinational screening regarding desired phenotypes, with an emphasis on sorting for immune cells, antibodies, enzymatic properties, and proteins produced by directed evolution methods. Finally, some challenges, deployment and future perspective of droplet microfluidics technology in practice are also discussed.
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Affiliation(s)
- Lexiang Zhang
- Oujiang Laboratory (Zhejiang Lab for Regenerative Medicine, Vision and Brain Health), Wenzhou, Zhejiang, 325000, China; Zhejiang Engineering Research Center for Tissue Repair Materials, Wenzhou Institute, University of Chinese Academy of Sciences, Wenzhou, Zhejiang, 325000, China
| | - Rokshana Parvin
- Oujiang Laboratory (Zhejiang Lab for Regenerative Medicine, Vision and Brain Health), Wenzhou, Zhejiang, 325000, China; Zhejiang Engineering Research Center for Tissue Repair Materials, Wenzhou Institute, University of Chinese Academy of Sciences, Wenzhou, Zhejiang, 325000, China
| | - Mingshuo Chen
- Oujiang Laboratory (Zhejiang Lab for Regenerative Medicine, Vision and Brain Health), Wenzhou, Zhejiang, 325000, China; Zhejiang Engineering Research Center for Tissue Repair Materials, Wenzhou Institute, University of Chinese Academy of Sciences, Wenzhou, Zhejiang, 325000, China
| | - Dingmeng Hu
- Oujiang Laboratory (Zhejiang Lab for Regenerative Medicine, Vision and Brain Health), Wenzhou, Zhejiang, 325000, China; Zhejiang Engineering Research Center for Tissue Repair Materials, Wenzhou Institute, University of Chinese Academy of Sciences, Wenzhou, Zhejiang, 325000, China
| | - Qihui Fan
- Oujiang Laboratory (Zhejiang Lab for Regenerative Medicine, Vision and Brain Health), Wenzhou, Zhejiang, 325000, China; Zhejiang Engineering Research Center for Tissue Repair Materials, Wenzhou Institute, University of Chinese Academy of Sciences, Wenzhou, Zhejiang, 325000, China; Beijing National Laboratory for Condensed Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing, 100190, China.
| | - Fangfu Ye
- Oujiang Laboratory (Zhejiang Lab for Regenerative Medicine, Vision and Brain Health), Wenzhou, Zhejiang, 325000, China; Zhejiang Engineering Research Center for Tissue Repair Materials, Wenzhou Institute, University of Chinese Academy of Sciences, Wenzhou, Zhejiang, 325000, China; Beijing National Laboratory for Condensed Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing, 100190, China.
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26
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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] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2022] [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)
| | | | | | | | - Florian Hollfelder
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Rd, Cambridge CB2 1GA, U.K.
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27
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Jian X, Guo X, Cai Z, Wei L, Wang L, Xing XH, Zhang C. Single-cell microliter-droplet screening system (MISS Cell): An integrated platform for automated high-throughput microbial monoclonal cultivation and picking. Biotechnol Bioeng 2023; 120:778-792. [PMID: 36477904 DOI: 10.1002/bit.28300] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Revised: 11/18/2022] [Accepted: 12/04/2022] [Indexed: 12/12/2022]
Abstract
Solid plates have been used for microbial monoclonal isolation, cultivation, and colony picking since 1881. However, the process is labor- and resource-intensive for high-throughput requirements. Currently, several instruments have been integrated for automated and high-throughput picking, but complicated and expensive. To address these issues, we report a novel integrated platform, the single-cell microliter-droplet screening system (MISS Cell), for automated, high-throughput microbial monoclonal colony cultivation and picking. We verified the monoclonality of droplet cultures in the MISS Cell and characterized culture performance. Compared with solid plates, the MISS Cell generated a larger number of monoclonal colonies with higher initial growth rates using fewer resources. Finally, we established a workflow for automated high-throughput screening of Corynebacterium glutamicum using the MISS Cell and identified high glutamate-producing strains. The MISS Cell can serve as a universal platform to efficiently produce monoclonal colonies in high-throughput applications, overcoming the limitations of solid plates to promote rapid development in biotechnology.
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Affiliation(s)
- Xingjin Jian
- Department of Chemical Engineering, Institute of Biochemical Engineering, Tsinghua University, Beijing, China.,Key Laboratory of Industrial Biocatalysis, Ministry of Education, Tsinghua University, Beijing, China
| | - Xiaojie Guo
- Department of Chemical Engineering, Institute of Biochemical Engineering, Tsinghua University, Beijing, China.,Key Laboratory of Industrial Biocatalysis, Ministry of Education, Tsinghua University, Beijing, China
| | - Zhengshuo Cai
- Department of Chemical Engineering, Institute of Biochemical Engineering, Tsinghua University, Beijing, China.,Key Laboratory of Industrial Biocatalysis, Ministry of Education, Tsinghua University, Beijing, China
| | - Longfeng Wei
- College of Life Sciences/Institute of Agro-bioengineering, Guizhou University, Guiyang, China
| | - Liyan Wang
- Luoyang TMAXTREE Biotechnology Co., Ltd., Luoyang, China
| | - Xin-Hui Xing
- Department of Chemical Engineering, Institute of Biochemical Engineering, Tsinghua University, Beijing, China.,Key Laboratory of Industrial Biocatalysis, Ministry of Education, Tsinghua University, Beijing, China.,Center for Synthetic & Systems Biology, Tsinghua University, Beijing, China
| | - Chong Zhang
- Department of Chemical Engineering, Institute of Biochemical Engineering, Tsinghua University, Beijing, China.,Key Laboratory of Industrial Biocatalysis, Ministry of Education, Tsinghua University, Beijing, China.,Center for Synthetic & Systems Biology, Tsinghua University, Beijing, China
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28
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Udono H, Gong J, Sato Y, Takinoue M. DNA Droplets: Intelligent, Dynamic Fluid. Adv Biol (Weinh) 2023; 7:e2200180. [PMID: 36470673 DOI: 10.1002/adbi.202200180] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Revised: 11/14/2022] [Indexed: 12/12/2022]
Abstract
Breathtaking advances in DNA nanotechnology have established DNA as a promising biomaterial for the fabrication of programmable higher-order nano/microstructures. In the context of developing artificial cells and tissues, DNA droplets have emerged as a powerful platform for creating intelligent, dynamic cell-like machinery. DNA droplets are a microscale membrane-free coacervate of DNA formed through phase separation. This new type of DNA system couples dynamic fluid-like property with long-established DNA programmability. This hybrid nature offers an advantageous route to facile and robust control over the structures, functions, and behaviors of DNA droplets. This review begins by describing programmable DNA condensation, commenting on the physical properties and fabrication strategies of DNA hydrogels and droplets. By presenting an overview of the development pathways leading to DNA droplets, it is shown that DNA technology has evolved from static, rigid systems to soft, dynamic systems. Next, the basic characteristics of DNA droplets are described as intelligent, dynamic fluid by showcasing the latest examples highlighting their distinctive features related to sequence-specific interactions and programmable mechanical properties. Finally, this review discusses the potential and challenges of numerical modeling able to connect a robust link between individual sequences and macroscopic mechanical properties of DNA droplets.
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Affiliation(s)
- Hirotake Udono
- Department of Computer Science, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku, Yokohama, Kanagawa, 226-8502, Japan
| | - Jing Gong
- Department of Life Science and Technology, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku, Yokohama, Kanagawa, 226-8502, Japan
| | - Yusuke Sato
- Department of Intelligent and Control Systems, Kyushu Institute of Technology, 680-4 Kawazu, Iizuka, Fukuoka, 820-8502, Japan
| | - Masahiro Takinoue
- Department of Computer Science, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku, Yokohama, Kanagawa, 226-8502, Japan
- Department of Life Science and Technology, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku, Yokohama, Kanagawa, 226-8502, Japan
- Living Systems Materialogy (LiSM) Research Group, International Research Frontiers Initiative (IRFI), Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku, Yokohama, Kanagawa, 226-8502, Japan
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29
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Baldauf L, Frey F, Arribas Perez M, Idema T, Koenderink GH. Branched actin cortices reconstituted in vesicles sense membrane curvature. Biophys J 2023:S0006-3495(23)00124-8. [PMID: 36806830 DOI: 10.1016/j.bpj.2023.02.018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Revised: 11/16/2022] [Accepted: 02/14/2023] [Indexed: 02/19/2023] Open
Abstract
The actin cortex is a complex cytoskeletal machinery that drives and responds to changes in cell shape. It must generate or adapt to plasma membrane curvature to facilitate diverse functions such as cell division, migration, and phagocytosis. Due to the complex molecular makeup of the actin cortex, it remains unclear whether actin networks are inherently able to sense and generate membrane curvature, or whether they rely on their diverse binding partners to accomplish this. Here, we show that curvature sensing is an inherent capability of branched actin networks nucleated by Arp2/3 and VCA. We develop a robust method to encapsulate actin inside giant unilamellar vesicles (GUVs) and assemble an actin cortex at the inner surface of the GUV membrane. We show that actin forms a uniform and thin cortical layer when present at high concentration and distinct patches associated with negative membrane curvature at low concentration. Serendipitously, we find that the GUV production method also produces dumbbell-shaped GUVs, which we explain using mathematical modeling in terms of membrane hemifusion of nested GUVs. We find that branched actin networks preferentially assemble at the neck of the dumbbells, which possess a micrometer-range convex curvature comparable with the curvature of the actin patches found in spherical GUVs. Minimal branched actin networks can thus sense membrane curvature, which may help mammalian cells to robustly recruit actin to curved membranes to facilitate diverse cellular functions such as cytokinesis and migration.
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Affiliation(s)
- Lucia Baldauf
- Department of Bionanoscience, Kavli Institute of Nanoscience Delft, Delft University of Technology, Delft, the Netherlands
| | - Felix Frey
- Department of Bionanoscience, Kavli Institute of Nanoscience Delft, Delft University of Technology, Delft, the Netherlands
| | - Marcos Arribas Perez
- Department of Bionanoscience, Kavli Institute of Nanoscience Delft, Delft University of Technology, Delft, the Netherlands
| | - Timon Idema
- Department of Bionanoscience, Kavli Institute of Nanoscience Delft, Delft University of Technology, Delft, the Netherlands.
| | - Gijsje H Koenderink
- Department of Bionanoscience, Kavli Institute of Nanoscience Delft, Delft University of Technology, Delft, the Netherlands.
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30
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Huang C, Han SI, Zhang H, Han A. Tutorial on Lateral Dielectrophoretic Manipulations in Microfluidic Systems. IEEE TRANSACTIONS ON BIOMEDICAL CIRCUITS AND SYSTEMS 2023; 17:21-32. [PMID: 37015136 PMCID: PMC10091972 DOI: 10.1109/tbcas.2022.3226675] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
Microfluidic lab-on-a-chip systems can offer cost- and time-efficient biological assays by providing high-throughput analysis at very small volume scale. Among these extremely broad ranges of assays, accurate and specific cell and reagent control is considered one of the most important functions. Dielectrophoretic (DEP)-based manipulation technologies have been extensively developed for these purposes due to their label-free and high selectivity natures as well as due to their simple microstructures. Here, we provide a tutorial on how to develop DEP-based microfluidic systems, including a detailed walkthrough of dielectrophoresis theory, instruction on how to conduct simulation and calculation of electric field and generated DEP force, followed with guidance on microfabricating two forms of DEP microfluidic systems, namely lateral DEP and droplet DEP, and how best to conduct experiments in such systems. Finally, we summarize most recent DEP-based microfluidic technologies and applications, including systems for blood diagnoses, pathogenicity studies, in-droplet content manipulations, droplet manipulations and merging, to name a few. We conclude by suggesting possible future directions on how DEP-based technologies can be utilized to overcome current challenges and improve the current status in microfluidic lab-on-a-chip systems.
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31
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Qiu L, Kong B, Kong T, Wang H. Recent advances in liver-on-chips: Design, fabrication, and applications. SMART MEDICINE 2023; 2:e20220010. [PMID: 39188562 PMCID: PMC11235950 DOI: 10.1002/smmd.20220010] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/21/2022] [Accepted: 10/20/2022] [Indexed: 08/28/2024]
Abstract
The liver is a multifunctional organ and the metabolic center of the human body. Most drugs and toxins are metabolized in the liver, resulting in varying degrees of hepatotoxicity. The damage of liver will seriously affect human health, so it is very important to study the prevention and treatment of liver diseases. At present, there are many research studies in this field. However, most of them are based on animal models, which are limited by the time-consuming processes and species difference between human and animals. In recent years, liver-on-chips have emerged and developed rapidly and are expected to replace animal models. Liver-on-chips refer to the use of a small number of liver cells on the chips to simulate the liver microenvironment and ultrastructure in vivo. They hold extensive applications in multiple fields by reproducing the unique physiological functions of the liver in vitro. In this review, we first introduced the physiology and pathology of liver and then described the cell system of liver-on-chips, the chip-based liver models, and the applications of liver-on-chips in liver transplantation, drug screening, and metabolic evaluation. Finally, we discussed the currently encountered challenges and future trends in liver-on-chips.
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Affiliation(s)
- Linjie Qiu
- The Eighth Affiliated HospitalSun Yat‐Sen UniversityShenzhenChina
- School of MedicineSun Yat‐Sen UniversityShenzhenChina
| | - Bin Kong
- Guangdong Key Laboratory for Biomedical Measurements and Ultrasound ImagingDepartment of Biomedical EngineeringSchool of MedicineShenzhen UniversityShenzhenChina
| | - Tiantian Kong
- Guangdong Key Laboratory for Biomedical Measurements and Ultrasound ImagingDepartment of Biomedical EngineeringSchool of MedicineShenzhen UniversityShenzhenChina
| | - Huan Wang
- The Eighth Affiliated HospitalSun Yat‐Sen UniversityShenzhenChina
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32
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Yu L, Wang X, Mu Q, Tam SST, Loi DSC, Chan AKY, Poon WS, Ng HK, Chan DTM, Wang J, Wu AR. scONE-seq: A single-cell multi-omics method enables simultaneous dissection of phenotype and genotype heterogeneity from frozen tumors. SCIENCE ADVANCES 2023; 9:eabp8901. [PMID: 36598983 PMCID: PMC9812385 DOI: 10.1126/sciadv.abp8901] [Citation(s) in RCA: 20] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
Single-cell multi-omics can provide a unique perspective on tumor cellular heterogeneity. Most previous single-cell whole-genome RNA sequencing (scWGS-RNA-seq) methods demonstrate utility with intact cells from fresh samples. Among them, many are not applicable to frozen samples that cannot produce intact single-cell suspensions. We have developed scONE-seq, a versatile scWGS-RNA-seq method that amplifies single-cell DNA and RNA without separating them from each other and hence is compatible with frozen biobanked samples. We benchmarked scONE-seq against existing methods using fresh and frozen samples to demonstrate its performance in various aspects. We identified a unique transcriptionally normal-like tumor clone by analyzing a 2-year frozen astrocytoma sample, demonstrating that performing single-cell multi-omics interrogation on biobanked tissue by scONE-seq could enable previously unidentified discoveries in tumor biology.
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Affiliation(s)
- Lei Yu
- Division of Life Science, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong S.A.R., China
| | - Xinlei Wang
- Division of Life Science, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong S.A.R., China
| | - Quanhua Mu
- Department of Chemical and Biological Engineering, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong S.A.R., China
| | - Sindy Sing Ting Tam
- Division of Life Science, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong S.A.R., China
| | - Danson Shek Chun Loi
- Division of Life Science, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong S.A.R., China
| | - Aden K. Y. Chan
- Department of Anatomical and Cellular Pathology, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong S.A.R., China
| | - Wai Sang Poon
- Department of Surgery, The Chinese University of Hong Kong, Hong Kong S.A.R., China
| | - Ho-Keung Ng
- Department of Anatomical and Cellular Pathology, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong S.A.R., China
| | - Danny T. M. Chan
- Department of Surgery, The Chinese University of Hong Kong, Hong Kong S.A.R., China
| | - Jiguang Wang
- Division of Life Science, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong S.A.R., China
- Department of Chemical and Biological Engineering, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong S.A.R., China
- State Key Laboratory of Molecular Neuroscience, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong S.A.R., China
- Hong Kong Center for Neurodegenerative Diseases, Hong Kong Science Park, Hong Kong S.A.R., China
| | - Angela Ruohao Wu
- Division of Life Science, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong S.A.R., China
- Department of Chemical and Biological Engineering, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong S.A.R., China
- Hong Kong Branch of the Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong S.A.R., China
- Center for Aging Science, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong S.A.R., China
- Corresponding author.
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Cowell T, Han HS. Double Emulsion Flow Cytometry for Rapid Single Genome Detection. Methods Mol Biol 2023; 2689:155-167. [PMID: 37430053 DOI: 10.1007/978-1-0716-3323-6_12] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/12/2023]
Abstract
Established techniques in droplet microfluidics have utilized single emulsion (SE) drops to compartmentalize and analyze single cells achieving high-throughput, low input analysis. Building upon this foundation, double emulsion (DE) droplet microfluidics has emerged with distinct advantages in terms of stable compartmentalization, resistance to merging, and most importantly direct compatibility with flow cytometry. In this chapter, we describe a simple-to-fabricate, single-layer DE drop generation device that achieves spatial control over surface wetting with a plasma treatment step. This easy-to-operate device allows for the robust production of single-core DEs with excellent control over the monodispersity. We further explain the use of these DE drops for single-molecule and single-cell assays. Detailed protocols are described to perform single molecule detection using droplet digital PCR in DE drops and automated detection of DE drops on a fluorescence-activated cell sorter (FACS). Due to the wide availability of FACS instruments, DE methods can facilitate the broader adoption of drop-based screening. As the applications of FACS-compatible DE droplets are immensely varied and extend well beyond what can be explored here, this chapter should be seen as an introduction to DE microfluidics.
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Affiliation(s)
- Thomas Cowell
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Hee-Sun Han
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL, USA.
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA.
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34
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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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35
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Profiling the total single-cell transciptome using droplet microfluidics. Nat Biotechnol 2022; 40:1766-1767. [PMID: 35764889 DOI: 10.1038/s41587-022-01370-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
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36
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Salmen F, De Jonghe J, Kaminski TS, Alemany A, Parada GE, Verity-Legg J, Yanagida A, Kohler TN, Battich N, van den Brekel F, Ellermann AL, Arias AM, Nichols J, Hemberg M, Hollfelder F, van Oudenaarden A. High-throughput total RNA sequencing in single cells using VASA-seq. Nat Biotechnol 2022; 40:1780-1793. [PMID: 35760914 PMCID: PMC9750877 DOI: 10.1038/s41587-022-01361-8] [Citation(s) in RCA: 75] [Impact Index Per Article: 37.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2021] [Accepted: 05/13/2022] [Indexed: 01/14/2023]
Abstract
Most methods for single-cell transcriptome sequencing amplify the termini of polyadenylated transcripts, capturing only a small fraction of the total cellular transcriptome. This precludes the detection of many long non-coding, short non-coding and non-polyadenylated protein-coding transcripts and hinders alternative splicing analysis. We, therefore, developed VASA-seq to detect the total transcriptome in single cells, which is enabled by fragmenting and tailing all RNA molecules subsequent to cell lysis. The method is compatible with both plate-based formats and droplet microfluidics. We applied VASA-seq to more than 30,000 single cells in the developing mouse embryo during gastrulation and early organogenesis. Analyzing the dynamics of the total single-cell transcriptome, we discovered cell type markers, many based on non-coding RNA, and performed in vivo cell cycle analysis via detection of non-polyadenylated histone genes. RNA velocity characterization was improved, accurately retracing blood maturation trajectories. Moreover, our VASA-seq data provide a comprehensive analysis of alternative splicing during mammalian development, which highlighted substantial rearrangements during blood development and heart morphogenesis.
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Affiliation(s)
- Fredrik Salmen
- Hubrecht Institute-KNAW (Royal Netherlands Academy of Arts and Sciences) and University Medical Center, Utrecht, Netherlands
- Oncode Institute, Utrecht, Netherlands
| | - Joachim De Jonghe
- Department of Biochemistry, University of Cambridge, Cambridge, UK
- Francis Crick Institute, London, UK
| | - Tomasz S Kaminski
- Department of Biochemistry, University of Cambridge, Cambridge, UK
- Department of Environmental Microbiology and Biotechnology, Institute of Microbiology, Faculty of Biology, University of Warsaw, Warsaw, Poland
| | - Anna Alemany
- Hubrecht Institute-KNAW (Royal Netherlands Academy of Arts and Sciences) and University Medical Center, Utrecht, Netherlands
- Oncode Institute, Utrecht, Netherlands
| | | | - Joe Verity-Legg
- Hubrecht Institute-KNAW (Royal Netherlands Academy of Arts and Sciences) and University Medical Center, Utrecht, Netherlands
- Oncode Institute, Utrecht, Netherlands
| | - Ayaka Yanagida
- Division of Stem Cell Therapy, Center for Stem Cell Biology and Regenerative Medicine, Institute of Medical Science, University of Tokyo, Tokyo, Japan
| | - Timo N Kohler
- Department of Biochemistry, University of Cambridge, Cambridge, UK
- Wellcome Trust - Medical Research Council Stem Cell Institute, University of Cambridge, Jeffrey Cheah Biomedical Centre, Cambridge, UK
| | - Nicholas Battich
- Hubrecht Institute-KNAW (Royal Netherlands Academy of Arts and Sciences) and University Medical Center, Utrecht, Netherlands
- Oncode Institute, Utrecht, Netherlands
| | - Floris van den Brekel
- Hubrecht Institute-KNAW (Royal Netherlands Academy of Arts and Sciences) and University Medical Center, Utrecht, Netherlands
- Oncode Institute, Utrecht, Netherlands
| | - Anna L Ellermann
- Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - Alfonso Martinez Arias
- Systems Bioengineering, DCEXS, Universidad Pompeu Fabra, Doctor Aiguader 88 ICREA (Institució Catalana de Recerca i Estudis Avançats), Barcelona, Spain
| | - Jennifer Nichols
- Wellcome Trust - Medical Research Council Stem Cell Institute, University of Cambridge, Jeffrey Cheah Biomedical Centre, Cambridge, UK
- Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, UK
| | - Martin Hemberg
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
- Evergrande Center for Immunologic Diseases, Harvard Medical School and Brigham and Women's Hospital, Boston, MA, USA
| | | | - Alexander van Oudenaarden
- Hubrecht Institute-KNAW (Royal Netherlands Academy of Arts and Sciences) and University Medical Center, Utrecht, Netherlands.
- Oncode Institute, Utrecht, Netherlands.
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37
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Jeyhani M, Navi M, Chan KWY, Kieda J, Tsai SSH. Water-in-water droplet microfluidics: A design manual. BIOMICROFLUIDICS 2022; 16:061503. [PMID: 36406338 PMCID: PMC9674389 DOI: 10.1063/5.0119316] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Accepted: 11/03/2022] [Indexed: 06/16/2023]
Abstract
Droplet microfluidics is utilized in a wide range of applications in biomedicine and biology. Applications include rapid biochemical analysis, materials generation, biochemical assays, and point-of-care medicine. The integration of aqueous two-phase systems (ATPSs) into droplet microfluidic platforms has potential utility in oil-free biological and biomedical applications, namely, reducing cytotoxicity and preserving the native form and function of costly biomolecular reagents. In this review, we present a design manual for the chemist, biologist, and engineer to design experiments in the context of their biological applications using all-in-water droplet microfluidic systems. We describe the studies achievable using these systems and the corresponding fabrication and stabilization methods. With this information, readers may apply the fundamental principles and recent advancements in ATPS droplet microfluidics to their research. Finally, we propose a development roadmap of opportunities to utilize ATPS droplet microfluidics in applications that remain underexplored.
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38
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Liu Y, Wang S, Lyu M, Xie R, Guo W, He Y, Shi X, Wang Y, Qi J, Zhu Q, Zhang H, Luo T, Chen H, Zhu Y, Dong X, Li Z, Gu Y, Liu L, Xu X, Liu Y. Droplet Microfluidics Enables Tracing of Target Cells at the Single-Cell Transcriptome Resolution. Bioengineering (Basel) 2022; 9:674. [PMID: 36354585 PMCID: PMC9687293 DOI: 10.3390/bioengineering9110674] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Revised: 11/05/2022] [Accepted: 11/07/2022] [Indexed: 11/10/2023] Open
Abstract
The rapid promotion of single-cell omics in various fields has begun to help solve many problems encountered in research, including precision medicine, prenatal diagnosis, and embryo development. Meanwhile, single-cell techniques are also constantly updated with increasing demand. For some specific target cells, the workflow from droplet screening to single-cell sequencing is a preferred option and should reduce the impact of operation steps, such as demulsification and cell recovery. We developed an all-in-droplet method integrating cell encapsulation, target sorting, droplet picoinjection, and single-cell transcriptome profiling on chips to achieve labor-saving monitoring of TCR-T cells. As a proof of concept, in this research, TCR-T cells were encapsulated, sorted, and performed single-cell transcriptome sequencing (scRNA-seq) by injecting reagents into droplets. It avoided the tedious operation of droplet breakage and re-encapsulation between droplet sorting and scRNA-seq. Moreover, convenient device operation will accelerate the progress of chip marketization. The strategy achieved an excellent recovery performance of single-cell transcriptome with a median gene number over 4000 and a cross-contamination rate of 8.2 ± 2%. Furthermore, this strategy allows us to develop a device with high integrability to monitor infused TCR-T cells, which will promote the development of adoptive T cell immunotherapy and their clinical application.
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Affiliation(s)
- Yang Liu
- BGI-Shenzhen, Shenzhen 518083, China
| | - Shiyu Wang
- BGI-Shenzhen, Shenzhen 518083, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Menghua Lyu
- BGI-Shenzhen, Shenzhen 518083, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Run Xie
- Department of Biomedical Engineering, School of Medicine, Shenzhen University, Shenzhen 518060, China
| | - Weijin Guo
- Department of Biomedical Engineering, Shantou University, Shantou 515063, China
| | - Ying He
- Department of Gynaecological Oncology, Cancer Hospital Chinese Academy of Medical Sciences, Shenzhen Center, Shenzhen 518116, China
| | - Xuyang Shi
- BGI-Shenzhen, Shenzhen 518083, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yang Wang
- BGI-Shenzhen, Shenzhen 518083, China
| | - Jingyu Qi
- BGI-Shenzhen, Shenzhen 518083, China
| | | | - Hui Zhang
- BGI-Shenzhen, Shenzhen 518083, China
| | - Tao Luo
- Department of Mechanical & Electrical Engineering, Xiamen University, Xiamen 361101, China
| | - Huaying Chen
- School of Mechanical Engineering and Automation, Harbin Institute of Technology, Shenzhen, Shenzhen 518055, China
| | - Yonggang Zhu
- School of Mechanical Engineering and Automation, Harbin Institute of Technology, Shenzhen, Shenzhen 518055, China
| | - Xuan Dong
- BGI-Shenzhen, Shenzhen 518083, China
| | - Zida Li
- Department of Biomedical Engineering, School of Medicine, Shenzhen University, Shenzhen 518060, China
| | - Ying Gu
- BGI-Shenzhen, Shenzhen 518083, China
| | - Longqi Liu
- BGI-Shenzhen, Shenzhen 518083, China
- Shenzhen Bay Laboratory, Shenzhen 518000, China
| | - Xun Xu
- BGI-Shenzhen, Shenzhen 518083, China
- Guangdong Provincial Key Laboratory of Genome Read and Write, BGI-Shenzhen, Shenzhen 518120, China
| | - Ya Liu
- BGI-Shenzhen, Shenzhen 518083, China
- Shenzhen Key Laboratory of Single-Cell Omics, BGI-Shenzhen, Shenzhen 518100, China
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39
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Hirschi S, Ward TR, Meier WP, Müller DJ, Fotiadis D. Synthetic Biology: Bottom-Up Assembly of Molecular Systems. Chem Rev 2022; 122:16294-16328. [PMID: 36179355 DOI: 10.1021/acs.chemrev.2c00339] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The bottom-up assembly of biological and chemical components opens exciting opportunities to engineer artificial vesicular systems for applications with previously unmet requirements. The modular combination of scaffolds and functional building blocks enables the engineering of complex systems with biomimetic or new-to-nature functionalities. Inspired by the compartmentalized organization of cells and organelles, lipid or polymer vesicles are widely used as model membrane systems to investigate the translocation of solutes and the transduction of signals by membrane proteins. The bottom-up assembly and functionalization of such artificial compartments enables full control over their composition and can thus provide specifically optimized environments for synthetic biological processes. This review aims to inspire future endeavors by providing a diverse toolbox of molecular modules, engineering methodologies, and different approaches to assemble artificial vesicular systems. Important technical and practical aspects are addressed and selected applications are presented, highlighting particular achievements and limitations of the bottom-up approach. Complementing the cutting-edge technological achievements, fundamental aspects are also discussed to cater to the inherently diverse background of the target audience, which results from the interdisciplinary nature of synthetic biology. The engineering of proteins as functional modules and the use of lipids and block copolymers as scaffold modules for the assembly of functionalized vesicular systems are explored in detail. Particular emphasis is placed on ensuring the controlled assembly of these components into increasingly complex vesicular systems. Finally, all descriptions are presented in the greater context of engineering valuable synthetic biological systems for applications in biocatalysis, biosensing, bioremediation, or targeted drug delivery.
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Affiliation(s)
- Stephan Hirschi
- Institute of Biochemistry and Molecular Medicine, University of Bern, Bühlstrasse 28, 3012 Bern, Switzerland.,Molecular Systems Engineering, National Centre of Competence in Research (NCCR), 4002 Basel, Switzerland
| | - Thomas R Ward
- Department of Chemistry, University of Basel, St. Johanns-Ring 19, 4056 Basel, Switzerland.,Molecular Systems Engineering, National Centre of Competence in Research (NCCR), 4002 Basel, Switzerland
| | - Wolfgang P Meier
- Department of Chemistry, University of Basel, St. Johanns-Ring 19, 4056 Basel, Switzerland.,Molecular Systems Engineering, National Centre of Competence in Research (NCCR), 4002 Basel, Switzerland
| | - Daniel J Müller
- Department of Biosystems Science and Engineering, ETH Zürich, Mattenstrasse 26, 4058 Basel, Switzerland.,Molecular Systems Engineering, National Centre of Competence in Research (NCCR), 4002 Basel, Switzerland
| | - Dimitrios Fotiadis
- Institute of Biochemistry and Molecular Medicine, University of Bern, Bühlstrasse 28, 3012 Bern, Switzerland.,Molecular Systems Engineering, National Centre of Competence in Research (NCCR), 4002 Basel, Switzerland
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40
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Postek W, Pacocha N, Garstecki P. Microfluidics for antibiotic susceptibility testing. LAB ON A CHIP 2022; 22:3637-3662. [PMID: 36069631 DOI: 10.1039/d2lc00394e] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
The rise of antibiotic resistance is a threat to global health. Rapid and comprehensive analysis of infectious strains is critical to reducing the global use of antibiotics, as informed antibiotic use could slow down the emergence of resistant strains worldwide. Multiple platforms for antibiotic susceptibility testing (AST) have been developed with the use of microfluidic solutions. Here we describe microfluidic systems that have been proposed to aid AST. We identify the key contributions in overcoming outstanding challenges associated with the required degree of multiplexing, reduction of detection time, scalability, ease of use, and capacity for commercialization. We introduce the reader to microfluidics in general, and we analyze the challenges and opportunities related to the field of microfluidic AST.
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Affiliation(s)
- Witold Postek
- Institute of Physical Chemistry of the Polish Academy of Sciences, ul. Kasprzaka 44/52, 01-224 Warszawa, Poland.
- Broad Institute of MIT and Harvard, Merkin Building, 415 Main St, Cambridge, MA 02142, USA.
| | - Natalia Pacocha
- Institute of Physical Chemistry of the Polish Academy of Sciences, ul. Kasprzaka 44/52, 01-224 Warszawa, Poland.
| | - Piotr Garstecki
- Institute of Physical Chemistry of the Polish Academy of Sciences, ul. Kasprzaka 44/52, 01-224 Warszawa, Poland.
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41
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Eenink BDG, Kaminski TS, Bornberg-Bauer E, Jose J, Hollfelder F, van Loo B. Vector redesign and in-droplet cell-growth improves enrichment and recovery in live Escherichia coli. Microb Biotechnol 2022; 15:2845-2853. [PMID: 36099491 PMCID: PMC9618318 DOI: 10.1111/1751-7915.14144] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2021] [Revised: 08/23/2022] [Accepted: 09/01/2022] [Indexed: 11/21/2022] Open
Abstract
Directed evolution (DE) is a widely used method for improving the function of biomolecules via multiple rounds of mutation and selection. Microfluidic droplets have emerged as an important means to screen the large libraries needed for DE, but this approach was so far partially limited by the need to lyse cells, recover DNA, and retransform into cells for the next round, necessitating the use of a high‐copy number plasmid or oversampling. The recently developed live cell recovery avoids some of these limitations by directly regrowing selected cells after sorting. However, repeated sorting cycles used to further enrich the most active variants ultimately resulted in unfavourable recovery of empty plasmid vector‐containing cells over those expressing the protein of interest. In this study, we found that engineering of the original expression vector solved the problem of false positives (i.e. plasmids lacking an insert) cells containing empty vectors. Five approaches to measure activity of cell‐displayed enzymes in microdroplets were compared. By comparing various cell treatment methods prior to droplet sorting two things were found. Substrate encapsulation from the start, that is prior to expression of enzyme, showed no disadvantage to post‐induction substrate addition by pico‐injection with respect to recovery of true positive variants. Furthermore in‐droplet cell growth prior to induction of enzyme production improves the total amount of cells retrieved (recovery) and proportion of true positive variants (enrichment) after droplet sorting.
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Affiliation(s)
- Bernard D G Eenink
- Institute for Evolution and Biodiversity, University of Münster, Münster, Germany
| | - Tomasz S Kaminski
- Department of Biochemistry, University of Cambridge, Cambridge, UK.,Department of Environmental Microbiology and Biotechnology, Faculty of Biology, Institute of Microbiology, University of Warsaw, Warsaw, Poland
| | - Erich Bornberg-Bauer
- Institute for Evolution and Biodiversity, University of Münster, Münster, Germany.,Department of Protein Evolution, Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Joachim Jose
- Institute of Pharmaceutical and Medicinal Chemistry, University of Münster, Münster, Germany
| | | | - Bert van Loo
- Institute for Evolution and Biodiversity, University of Münster, Münster, Germany.,Department of Applied Sciences, Northumbria University, Newcastle-upon-Tyne, UK
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42
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Breukers J, Op de Beeck H, Rutten I, López Fernández M, Eyckerman S, Lammertyn J. Highly flexible and accurate serial picoinjection in droplets by combined pressure and flow rate control. LAB ON A CHIP 2022; 22:3475-3488. [PMID: 35943442 DOI: 10.1039/d2lc00368f] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Picoinjection is a robust method for reagent addition into microfluidic droplets and has enabled the implementation of numerous multistep droplet assays. Although serial picoinjectors allow to screen many conditions in one run by injecting different combinations of reagents, their use is limited because it is complex to accurately control each injector independently. Here, we present a novel method for flexible, individual picoinjector control that allows to inject a predefined range of volumes by controlling the flow rate of the injector as well as turning off injection by setting the equilibrium pressure, which resulted in a stable interface of the injector liquid with the main microfluidic channel. Robust setting of the equilibrium pressure of an injector was achieved by applying accurate (R2 > 0.94) linear models between the injector and oil pressure in real-time. To illustrate the flexibility of this method, we performed several proof-of-concepts using 1, 2 or 3 picoinjectors loaded with fluorescent dyes. We successfully demonstrated picoinjection approaches using time-invariant settings, in which an injector setting was applied for prolonged times, and time-variant picoinjection, in which the injector settings were continuously varied in order to sweep the injected volumes, both resulting in monodisperse (CV < 3.4%) droplet libraries with different but reproducible fluorescent intensities. To illustrate the potential of the technology for fast compound concentration screenings, we studied the effect of a concentration range of a detergent on single-cell lysis. We anticipate that this robust and versatile methodology will make the serial picoinjection technology more accessible to researchers, allowing its wide implementation in numerous life science applications.
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Affiliation(s)
- Jolien Breukers
- Department of Biosystems, Biosensors Group, KU Leuven, Leuven 3001, Belgium.
| | - Hannah Op de Beeck
- Department of Biosystems, Biosensors Group, KU Leuven, Leuven 3001, Belgium.
| | - Iene Rutten
- Department of Biosystems, Biosensors Group, KU Leuven, Leuven 3001, Belgium.
| | - Montserrat López Fernández
- Confo Therapeutics, Technologiepark-Zwijnaarde 30, Ghent 9052, Belgium
- Center for Medical Biotechnology, VIB-Ghent University, Technologiepark-Zwijnaarde 75, Ghent 9052, Belgium
- Department of Biomolecular Medicine, Ghent University, Technologiepark-Zwijnaarde 75, Ghent 9052, Belgium
| | - Sven Eyckerman
- Center for Medical Biotechnology, VIB-Ghent University, Technologiepark-Zwijnaarde 75, Ghent 9052, Belgium
- Department of Biomolecular Medicine, Ghent University, Technologiepark-Zwijnaarde 75, Ghent 9052, Belgium
| | - Jeroen Lammertyn
- Department of Biosystems, Biosensors Group, KU Leuven, Leuven 3001, Belgium.
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43
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Wu H, Cao X, Meng Y, Richards D, Wu J, Ye Z, deMello AJ. DropCRISPR: A LAMP-Cas12a based digital method for ultrasensitive detection of nucleic acid. Biosens Bioelectron 2022; 211:114377. [DOI: 10.1016/j.bios.2022.114377] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Revised: 05/12/2022] [Accepted: 05/13/2022] [Indexed: 12/26/2022]
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44
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Oliveira SMD, Densmore D. Hardware, Software, and Wetware Codesign Environment for Synthetic Biology. BIODESIGN RESEARCH 2022; 2022:9794510. [PMID: 37850136 PMCID: PMC10521664 DOI: 10.34133/2022/9794510] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Accepted: 08/10/2022] [Indexed: 10/19/2023] Open
Abstract
Synthetic biology is the process of forward engineering living systems. These systems can be used to produce biobased materials, agriculture, medicine, and energy. One approach to designing these systems is to employ techniques from the design of embedded electronics. These techniques include abstraction, standards, modularity, automated design, and formal semantic models of computation. Together, these elements form the foundation of "biodesign automation," where software, robotics, and microfluidic devices combine to create exciting biological systems of the future. This paper describes a "hardware, software, wetware" codesign vision where software tools can be made to act as "genetic compilers" that transform high-level specifications into engineered "genetic circuits" (wetware). This is followed by a process where automation equipment, well-defined experimental workflows, and microfluidic devices are explicitly designed to house, execute, and test these circuits (hardware). These systems can be used as either massively parallel experimental platforms or distributed bioremediation and biosensing devices. Next, scheduling and control algorithms (software) manage these systems' actual execution and data analysis tasks. A distinguishing feature of this approach is how all three of these aspects (hardware, software, and wetware) may be derived from the same basic specification in parallel and generated to fulfill specific cost, performance, and structural requirements.
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Affiliation(s)
- Samuel M. D. Oliveira
- Department of Electrical and Computer Engineering, Boston University, MA 02215, USA
- Biological Design Center, Boston University, MA 02215, USA
| | - Douglas Densmore
- Department of Electrical and Computer Engineering, Boston University, MA 02215, USA
- Biological Design Center, Boston University, MA 02215, USA
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45
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Yu Y, Wen H, Li S, Cao H, Li X, Ma Z, She X, Zhou L, Huang S. Emerging microfluidic technologies for microbiome research. Front Microbiol 2022; 13:906979. [PMID: 36051769 PMCID: PMC9424851 DOI: 10.3389/fmicb.2022.906979] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Accepted: 07/26/2022] [Indexed: 11/13/2022] Open
Abstract
The importance of the microbiome is increasingly prominent. For example, the human microbiome has been proven to be strongly associated with health conditions, while the environmental microbiome is recognized to have a profound influence on agriculture and even the global climate. Furthermore, the microbiome can serve as a fascinating reservoir of genes that encode tremendously valuable compounds for industrial and medical applications. In the past decades, various technologies have been developed to better understand and exploit the microbiome. In particular, microfluidics has demonstrated its strength and prominence in the microbiome research. By taking advantage of microfluidic technologies, inherited shortcomings of traditional methods such as low throughput, labor-consuming, and high-cost are being compensated or bypassed. In this review, we will summarize a broad spectrum of microfluidic technologies that have addressed various needs in the field of microbiome research, as well as the achievements that were enabled by the microfluidics (or technological advances). Finally, how microfluidics overcomes the limitations of conventional methods by technology integration will also be discussed.
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Affiliation(s)
- Yue Yu
- CAS Key Laboratory of Quantitative Engineering Biology, Guangdong Provincial Key Laboratory of Synthetic Genomics, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
- Faculty of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Hui Wen
- CAS Key Laboratory of Quantitative Engineering Biology, Guangdong Provincial Key Laboratory of Synthetic Genomics, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
- Faculty of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Sihong Li
- CAS Key Laboratory of Quantitative Engineering Biology, Guangdong Provincial Key Laboratory of Synthetic Genomics, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
- Faculty of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Haojie Cao
- CAS Key Laboratory of Quantitative Engineering Biology, Guangdong Provincial Key Laboratory of Synthetic Genomics, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
- Faculty of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Xuefei Li
- CAS Key Laboratory of Quantitative Engineering Biology, Guangdong Provincial Key Laboratory of Synthetic Genomics, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
- Faculty of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Zhixin Ma
- CAS Key Laboratory of Quantitative Engineering Biology, Guangdong Provincial Key Laboratory of Synthetic Genomics, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
- Faculty of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Xiaoyi She
- CAS Key Laboratory of Quantitative Engineering Biology, Guangdong Provincial Key Laboratory of Synthetic Genomics, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
- Faculty of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Lei Zhou
- CAS Key Laboratory of Quantitative Engineering Biology, Guangdong Provincial Key Laboratory of Synthetic Genomics, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
- Faculty of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Shuqiang Huang
- CAS Key Laboratory of Quantitative Engineering Biology, Guangdong Provincial Key Laboratory of Synthetic Genomics, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
- Faculty of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
- University of Chinese Academy of Sciences, Beijing, China
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46
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Zhou C, Shim J, Fang Z, Meyer C, Gong T, Wong M, Tan C, Pan T. Microfluidic Printing-Based Method for the Multifactorial Study of Cell-Free Protein Networks. Anal Chem 2022; 94:11038-11046. [PMID: 35901235 PMCID: PMC9558566 DOI: 10.1021/acs.analchem.2c01851] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Protein networks can be assembled in vitro for basic biochemistry research, drug screening, and the creation of artificial cells. Two standard methodologies are used: manual pipetting and pipetting robots. Manual pipetting has limited throughput in the number of input reagents and the combination of reagents in a single sample. While pipetting robots are evident in improving pipetting efficiency and saving hands-on time, their liquid handling volume usually ranges from a few to hundreds of microliters. Microfluidic methods have been developed to minimize the reagent consumption and speed up screening but are challenging in multifactorial protein studies due to their reliance on complex structures and labeling dyes. Here, we engineered a new impact-printing-based methodology to generate printed microdroplet arrays containing water-in-oil droplets. The printed droplet volume was linearly proportional (R2 = 0.9999) to the single droplet number, and each single droplet volume was around 59.2 nL (coefficient of variation = 93.8%). Our new methodology enables the study of protein networks in both membrane-unbound and -bound states, without and with anchor lipids DGS-NTA(Ni), respectively. The methodology is demonstrated using a subnetwork of mitogen-activated protein kinase (MAPK). It takes less than 10 min to prepare 100 different droplet-based reactions, using <1 μL reaction volume at each reaction site. We validate the kinase (ATPase) activity of MEK1 (R4F)* and ERK2 WT individually and together under different concentrations, without and with the selective membrane attachment. Our new methodology provides a reagent-saving, efficient, and flexible way for protein network research and related applications.
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Affiliation(s)
- Chuqing Zhou
- Department of Biomedical Engineering, University of California, Davis, California, 95616, USA
| | - Jiyoung Shim
- Department of Biomedical Engineering, University of California, Davis, California, 95616, USA
| | - Zecong Fang
- Institute of Biomedical and Health Engineering, Shenzhen Institute of Advanced Technology, Chinese Academy of Science, Shenzhen, 518055, China
- Shenzhen Engineering Laboratory of Single-Molecule Detection and Instrument Development, Shenzhen, Guangdong, 518055, China
| | - Conary Meyer
- Department of Biomedical Engineering, University of California, Davis, California, 95616, USA
| | - Ting Gong
- Department of Biomedical Engineering, University of California, Davis, California, 95616, USA
| | - Matthew Wong
- Department of Biomedical Engineering, University of California, Davis, California, 95616, USA
| | - Cheemeng Tan
- Department of Biomedical Engineering, University of California, Davis, California, 95616, USA
| | - Tingrui Pan
- Institute of Biomedical and Health Engineering, Shenzhen Institute of Advanced Technology, Chinese Academy of Science, Shenzhen, 518055, China
- Shenzhen Engineering Laboratory of Single-Molecule Detection and Instrument Development, Shenzhen, Guangdong, 518055, China
- Suzhou Institute for Advanced Research, University of Science and Technology of China, Suzhou, 215123, China
- Department of Precision Machinery and Precision Instrumentation, University of Science and Technology of China, Hefei, 230026, China
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Mathur L, Szalai B, Du NH, Utharala R, Ballinger M, Landry JJM, Ryckelynck M, Benes V, Saez-Rodriguez J, Merten CA. Combi-seq for multiplexed transcriptome-based profiling of drug combinations using deterministic barcoding in single-cell droplets. Nat Commun 2022; 13:4450. [PMID: 35915108 PMCID: PMC9343464 DOI: 10.1038/s41467-022-32197-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Accepted: 07/21/2022] [Indexed: 02/07/2023] Open
Abstract
Anti-cancer therapies often exhibit only short-term effects. Tumors typically develop drug resistance causing relapses that might be tackled with drug combinations. Identification of the right combination is challenging and would benefit from high-content, high-throughput combinatorial screens directly on patient biopsies. However, such screens require a large amount of material, normally not available from patients. To address these challenges, we present a scalable microfluidic workflow, called Combi-Seq, to screen hundreds of drug combinations in picoliter-size droplets using transcriptome changes as a readout for drug effects. We devise a deterministic combinatorial DNA barcoding approach to encode treatment conditions, enabling the gene expression-based readout of drug effects in a highly multiplexed fashion. We apply Combi-Seq to screen the effect of 420 drug combinations on the transcriptome of K562 cells using only ~250 single cell droplets per condition, to successfully predict synergistic and antagonistic drug pairs, as well as their pathway activities.
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Affiliation(s)
- L Mathur
- Genome Biology Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
- Collaboration for joint PhD degree between EMBL and Heidelberg University, Faculty of Biosciences, Heidelberg, Germany
| | - B Szalai
- Department of Physiology, Faculty of Medicine, Semmelweis University, Budapest, Hungary
- Institute of Enzymology, Research Centre for Natural Sciences, Budapest, Hungary
- Turbine Simulated Cell Technologies Ltd, Budapest, Hungary
| | - N H Du
- Institute of Bioengineering, School of Engineering, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - R Utharala
- Genome Biology Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - M Ballinger
- Genome Biology Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - J J M Landry
- Genome Biology Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - M Ryckelynck
- Université de Strasbourg, CNRS, Architecture et Réactivité de l'ARN, UPR, 9002, Strasbourg, France
| | - V Benes
- Genome Biology Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - J 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.
| | - C A Merten
- Genome Biology Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany.
- Institute of Bioengineering, School of Engineering, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland.
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48
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Mukherjee S, Shit GC, Vajravelu K. Entropy Generation of Electrothermal Nanofluid Flow Between Two Permeable Walls Under Injection Process. JOURNAL OF NANOFLUIDS 2022. [DOI: 10.1166/jon.2022.1880] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
This paper aims to study the electroosmotic nanofluid flow and heat transfer phenomena in a microchannel with porous walls by paying due attention to the interaction of the injected fluid velocity and the net charge density in the base fluid on the development of zeta potential and
electroosmotic slip velocity. The novelty of this study is to obtain the integral expression for electroosmotic slip velocity which is found to converge to Smoluchowski velocity when the injected fluid velocity is low and porous permeability of channel wall becomes negligible. Under a weak
electric field condition, the enhancement of pressure gradient is found to increase the normalized temperature and decrease the normalized nanoparticle concentration. The bulk nanofluid temperature is found to follow an almost quadratic relationship with applied pressure gradient. Additionally,
in the absence of injection velocity, we observed a new expression for Soret number as a ratio of the cross sectional nanoparticle concentration to Joule heating parameter. Finally, a comparative study on the total entropy generation is carried out to minimize the loss of thermal energy due
to irreversible physical mechanisms such as heat transfer, viscous dissipation and Joule heating effects that take place during the fluid flow process in a microchannel. It is thereby observed that the total entropy generation follows a quadratic relation with the Joule heating parameter in
the absence of both injection and viscous dissipation. The increment in diffusive Reynolds number reduces EDL thickness near the upper channel bed. With an increment in the applied pressure gradient, the normalized temperature increases whereas the normalized nanoparticle concentration reduces.
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Affiliation(s)
- S. Mukherjee
- Department of Mathematics, Jadavpur University, Kolkata 700032, West Bengal, India
| | - G. C. Shit
- Department of Mathematics, Jadavpur University, Kolkata 700032, West Bengal, India
| | - K. Vajravelu
- Department of Mathematics, University of Central Florida, Orlando, 32816, Florida, USA
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Combining genetically encoded biosensors with droplet microfluidic system for enhanced glutaminase production by Bacillus amyloliquefaciens. Biochem Eng J 2022. [DOI: 10.1016/j.bej.2022.108586] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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50
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Xie X, Wang Y, Siu SY, Chan CW, Zhu Y, Zhang X, Ge J, Ren K. Microfluidic synthesis as a new route to produce novel functional materials. BIOMICROFLUIDICS 2022; 16:041301. [PMID: 36035887 PMCID: PMC9410731 DOI: 10.1063/5.0100206] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/22/2022] [Accepted: 07/28/2022] [Indexed: 06/15/2023]
Abstract
By geometrically constraining fluids into the sub-millimeter scale, microfluidics offers a physical environment largely different from the macroscopic world, as a result of the significantly enhanced surface effects. This environment is characterized by laminar flow and inertial particle behavior, short diffusion distance, and largely enhanced heat exchange. The recent two decades have witnessed the rapid advances of microfluidic technologies in various fields such as biotechnology; analytical science; and diagnostics; as well as physical, chemical, and biological research. On the other hand, one additional field is still emerging. With the advances in nanomaterial and soft matter research, there have been some reports of the advantages discovered during attempts to synthesize these materials on microfluidic chips. As the formation of nanomaterials and soft matters is sensitive to the environment where the building blocks are fed, the unique physical environment of microfluidics and the effectiveness in coupling with other force fields open up a lot of possibilities to form new products as compared to conventional bulk synthesis. This Perspective summarizes the recent progress in producing novel functional materials using microfluidics, such as generating particles with narrow and controlled size distribution, structured hybrid materials, and particles with new structures, completing reactions with a quicker rate and new reaction routes and enabling more effective and efficient control on reactions. Finally, the trend of future development in this field is also discussed.
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Affiliation(s)
- Xinying Xie
- Department of Chemistry, Hong Kong Baptist University, Hong Kong 999077, China
| | - Yisu Wang
- Department of Chemistry, Hong Kong Baptist University, Hong Kong 999077, China
| | - Sin-Yung Siu
- Department of Chemistry, Hong Kong Baptist University, Hong Kong 999077, China
| | - Chiu-Wing Chan
- Department of Chemistry, Hong Kong Baptist University, Hong Kong 999077, China
| | | | - Xuming Zhang
- Department of Applied Physics, Hong Kong Polytechnic University, Hong Kong 999077, China
| | | | - Kangning Ren
- Author to whom correspondence should be addressed: and
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