1
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Mori K, Watanabe M, Nanri K, Matsukura S, Ota Y, Homma N, Noda N. Clear zone formation in microdroplets for high-throughput screening for lactic acid bacteria. Front Microbiol 2024; 15:1452573. [PMID: 39364161 PMCID: PMC11447763 DOI: 10.3389/fmicb.2024.1452573] [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: 06/21/2024] [Accepted: 09/06/2024] [Indexed: 10/05/2024] Open
Abstract
Droplet microfluidic-based technology is a powerful tool for biotechnology, and it is also expected that it will be applied to culturing and screening methods. Using this technology, a new high-throughput screening method for lactic acid bacteria was developed. In this study, the conventional culture of lactic acid bacteria that form clear zones on an agar medium was reproduced in water-in-oil droplets, and only the droplets in which lactic acid bacteria grew were collected one by one. Using this method, the specific recovery of Lactiplantibacillus plantarum from a mixture of L. plantarum and Escherichia coli and the acquirement of lactic acid bacteria from an environmental sample were successful. This method could be applied to various conventional screening methods using the clear zone as a microbial growth indicator. This has expanded the possibilities of applying droplet microfluidic-based technology to microbial cultivations.
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Affiliation(s)
- Koji Mori
- NITE Biological Resource Center (NBRC), National Institute of Technology and Evaluation (NITE), Chiba, Japan
| | - Mizuki Watanabe
- NITE Biological Resource Center (NBRC), National Institute of Technology and Evaluation (NITE), Chiba, Japan
| | - Keiko Nanri
- NITE Biological Resource Center (NBRC), National Institute of Technology and Evaluation (NITE), Chiba, Japan
| | - Satoko Matsukura
- 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
| | | | - Naohiro Noda
- Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Ibaraki, Japan
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2
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Waeterschoot J, Kayahan E, Breukers J, Lammertyn J, Casadevall I Solvas X. The effects of droplet stabilization by surfactants and nanoparticles on leakage, cross-talk, droplet stability, and cell adhesion. RSC Adv 2024; 14:24115-24129. [PMID: 39091374 PMCID: PMC11292313 DOI: 10.1039/d4ra04298k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2024] [Accepted: 07/01/2024] [Indexed: 08/04/2024] Open
Abstract
Partially fluorinated nanoparticles (FNPs) have been proposed as a promising alternative for stabilising aqueous droplets in fluorinated oils. The exceptional energetic stability of FNPs at the droplet interface holds the potential for minimising leakage, enhancing stability, and promoting improved cell adhesion. However, their lower diffusion coefficient compared to surfactants presents challenges in achieving rapid droplet stabilisation, which is important in microfluidics applications. While several studies have focused on some of these aspects, a comprehensive study and direct comparison with conventional fluorosurfactants is still missing. In this manuscript, we undertake an examination and comparison of four crucial facets of both FNP- and surfactant-stabilised droplets: leakage of compounds, emulsion stability, droplet formation dynamics and cell adhesion. Contrary to what has previously been claimed, our findings demonstrate that FNPs only reduce leakage and cross-talk in very specific cases (e.g., resorufin), failing to provide enhanced compartmentalisation for highly hydrophobic dyes (e.g., rhodamine dyes). On the other hand, FNP-stabilised droplets indeed exhibit greater long-term stability compared to their surfactant-stabilised counterparts. Regarding the size of droplets generated via a diversity of microfluidic methods, no significant differences were observed between FNP-stabilised and surfactant-stabilised droplets. Finally, the previously reported improvements in cell adhesion and spreading on FNP-stabilised interfaces is limited to flat oil/water (o/w) interfaces and could not be observed within droplets. These comprehensive analyses shed light on the nuanced performance of FNPs and commercial fluorosurfactants as stabilising agents for aqueous droplets in fluorinated oils, contributing valuable insights for choosing the correct formulation for specific droplet-based microfluidics applications.
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Affiliation(s)
- Jorik Waeterschoot
- Biomimetics Group, Divison of Mechatronics, Biostatistics and Sensors (MeBios), Department of Biosystems KU Leuven, Willem de Croylaan 42 3001 Leuven Belgium
| | - Emine Kayahan
- Biomimetics Group, Divison of Mechatronics, Biostatistics and Sensors (MeBios), Department of Biosystems KU Leuven, Willem de Croylaan 42 3001 Leuven Belgium
| | - Jolien Breukers
- Biosensors Group, Divison of Mechatronics, Biostatistics and Sensors (MeBios), Department of Biosystems KU Leuven, Willem de Croylaan 42 3001 Heverlee Belgium
| | - Jeroen Lammertyn
- Biosensors Group, Divison of Mechatronics, Biostatistics and Sensors (MeBios), Department of Biosystems KU Leuven, Willem de Croylaan 42 3001 Heverlee Belgium
| | - Xavier Casadevall I Solvas
- Biomimetics Group, Divison of Mechatronics, Biostatistics and Sensors (MeBios), Department of Biosystems KU Leuven, Willem de Croylaan 42 3001 Leuven Belgium
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3
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Yang Y, Vagin SI, Rieger B, Destgeer G. Fabrication of Crescent Shaped Microparticles for Particle Templated Droplet Formation. Macromol Rapid Commun 2024; 45:e2300721. [PMID: 38615246 DOI: 10.1002/marc.202300721] [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: 12/12/2023] [Revised: 04/08/2024] [Indexed: 04/15/2024]
Abstract
Crescent-shaped hydrogel microparticles are shown to template uniform volume aqueous droplets upon simple mixing with aqueous and oil media for various bioassays. This emerging "lab on a particle" technique requires hydrogel particles with tunable material properties and dimensions. The crescent shape of the particles is attained by aqueous two-phase separation of polymers followed by photopolymerization of the curable precursor. In this work, the phase separation of poly(ethylene glycol) diacrylate (PEGDA, Mw 700) and dextran (Mw 40 000) for tunable manufacturing of crescent-shaped particles is investigated. The particles' morphology is precisely tuned by following a phase diagram, varying the UV intensity, and adjusting the flow rates of various streams. The fabricated particles with variable dimensions encapsulate uniform aqueous droplets upon mixing with an oil phase. The particles are fluorescently labeled with red and blue emitting dyes at variable concentrations to produce six color-coded particles. The blue fluorescent dye shows a moderate response to the pH change. The fluorescently labeled particles are able to tolerate an extremely acidic solution (pH 1) but disintegrate within an extremely basic solution (pH 14). The particle-templated droplets are able to effectively retain the disintegrating particle and the fluorescent signal at pH 14.
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Affiliation(s)
- Yimin Yang
- Control and Manipulation of Microscale Living Objects, Department of Electrical Engineering, TUM School of Computation, Information and Technology, TranslaTUM - Center for Translational Cancer Research, Technical University of Munich, Einsteinstraße 25, 81675, Munich, Germany
| | - Sergei I Vagin
- WACKER-Chair of Macromolecular Chemistry, Department of Chemistry, TUM School of Natural Sciences, Technical University of Munich, Lichtenbergstraße 4, 85748, Garching, Germany
| | - Bernhard Rieger
- WACKER-Chair of Macromolecular Chemistry, Department of Chemistry, TUM School of Natural Sciences, Technical University of Munich, Lichtenbergstraße 4, 85748, Garching, Germany
| | - Ghulam Destgeer
- Control and Manipulation of Microscale Living Objects, Department of Electrical Engineering, TUM School of Computation, Information and Technology, TranslaTUM - Center for Translational Cancer Research, Technical University of Munich, Einsteinstraße 25, 81675, Munich, Germany
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4
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Zhang Y, Agresti JJ, Zheng Y, Weitz DA. High-throughput direct screening of restriction endonuclease using a microfluidic fluorescence-activated drop sorter based on the SOS response in Escherichia coli. Analyst 2024; 149:3575-3584. [PMID: 38758107 DOI: 10.1039/d4an00106k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/18/2024]
Abstract
A restriction endonuclease (RE) is an enzyme that can recognize a specific DNA sequence and cleave that DNA into fragments with double-stranded breaks. This sequence-specific cleaving ability and its ease of use have made REs commonly used tools in molecular biology since their first isolation and characterization in 1970s. While artificial REs still face many challenges in large-scale synthesis and precise activity control for practical use, searching for new REs in natural samples remains a viable route to expanding the RE pool for fundamental research and industrial applications. In this paper, we propose a new strategy to search for REs in an efficient manner. We constructed a host bacterial cell to link the genotype of REs to the phenotype of β-galactosidase expression based on the bacterial SOS response, and used a high-throughput microfluidic platform to isolate, detect and sort the REs in microfluidic drops at a frequency of ∼800 drops per second. We employed this strategy to screen for the XbaI gene from the constructed libraries of varied sizes. In a single round of sorting, a 90-fold target enrichment was achieved within 1 h. Compared to conventional RE-screening methods, the direct screening approach that we propose excels at efficient search of desirable REs in natural samples - especially unculturable samples - and can be tailored to high-throughput screening of a wide range of genotoxic targets.
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Affiliation(s)
- Yizhe Zhang
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts, USA
- John A. Paulson School of Engineering and Applied Sciences, Harvard University, Cambridge, Massachusetts, USA.
| | - Jeremy J Agresti
- John A. Paulson School of Engineering and Applied Sciences, Harvard University, Cambridge, Massachusetts, USA.
| | - Yu Zheng
- New England BioLabs, Inc., Ipswich, MA 01938, USA
| | - David A Weitz
- John A. Paulson School of Engineering and Applied Sciences, Harvard University, Cambridge, Massachusetts, USA.
- Department of Physics, Harvard University, Cambridge, MA 02138, USA
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5
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Jain A, Stavrakis S, deMello A. Droplet-based microfluidics and enzyme evolution. Curr Opin Biotechnol 2024; 87:103097. [PMID: 38430713 DOI: 10.1016/j.copbio.2024.103097] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2024] [Accepted: 02/06/2024] [Indexed: 03/05/2024]
Abstract
Enzymes are widely used as catalysts in the chemical and pharmaceutical industries. While successful in many situations, they must usually be adapted to operate efficiently under nonnatural conditions. Enzyme engineering allows the creation of novel enzymes that are stable at elevated temperatures or have higher activities and selectivities. Current enzyme engineering techniques require the production and testing of enzyme variant libraries to identify members with desired attributes. Unfortunately, traditional screening methods cannot screen such large mutagenesis libraries in a robust and timely manner. Droplet-based microfluidic systems can produce, process, and sort picoliter droplets at kilohertz rates and have emerged as powerful tools for library screening and thus enzyme engineering. We describe how droplet-based microfluidics has been used to advance directed evolution.
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Affiliation(s)
- Ankit Jain
- Institute for Chemical and Bioengineering, Department of Chemistry and Applied Biosciences, ETH Zürich, Vladimir Prelog Weg 1, 8093 Zürich, Switzerland
| | - Stavros Stavrakis
- Institute for Chemical and Bioengineering, Department of Chemistry and Applied Biosciences, ETH Zürich, Vladimir Prelog Weg 1, 8093 Zürich, Switzerland
| | - Andrew deMello
- Institute for Chemical and Bioengineering, Department of Chemistry and Applied Biosciences, ETH Zürich, Vladimir Prelog Weg 1, 8093 Zürich, Switzerland.
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6
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Jeong H, Porello EAL, Rosario JG, Kuang D, Han SH, Sul JY, Lim B, Lee D, Kim J. SCO-pH: Microfluidic dynamic phenotyping platform for high-throughput screening of single cell acidification. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.08.593179. [PMID: 38766224 PMCID: PMC11100697 DOI: 10.1101/2024.05.08.593179] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2024]
Abstract
Studies on the dynamics of single cell phenotyping have been hampered by the lack of quantitative high-throughput metabolism assays. Extracellular acidification, a prominent phenotype, yields significant insights into cellular metabolism, including tumorigenicity. Here, we develop a versatile microfluidic system for single cell optical pH analysis (SCO-pH), which compartmentalizes single cells in 140-pL droplets and immobilizes approximately 40,000 droplets in a two-dimensional array for temporal extracellular pH analysis. SCO-pH distinguishes cells undergoing hyperglycolysis induced by oligomycin A from untreated cells by monitoring their extracellular acidification. To facilitate pH sensing in each droplet, we encapsulate a cell-impermeable pH probe whose fluorescence intensities are quantified. Using this approach, we can differentiate hyperglycolytic cells and concurrently observe single cell heterogeneity in extracellular acidification dynamics. This high-throughput system will be useful in applications that require dynamic phenotyping of single cells with significant heterogeneity.
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7
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Verma A, Mateo T, Quintero Botero J, Mohankumar N, Fraccia TP. Microfluidics-Based Drying-Wetting Cycles to Investigate Phase Transitions of Small Molecules Solutions. Life (Basel) 2024; 14:472. [PMID: 38672743 PMCID: PMC11050796 DOI: 10.3390/life14040472] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2024] [Revised: 03/24/2024] [Accepted: 03/28/2024] [Indexed: 04/28/2024] Open
Abstract
Drying-wetting cycles play a crucial role in the investigation of the origin of life as processes that both concentrate and induce the supramolecular assembly and polymerization of biomolecular building blocks, such as nucleotides and amino acids. Here, we test different microfluidic devices to study the dehydration-hydration cycles of the aqueous solutions of small molecules, and to observe, by optical microscopy, the insurgence of phase transitions driven by self-assembly, exploiting water pervaporation through polydimethylsiloxane (PDMS). As a testbed, we investigate solutions of the chromonic dye Sunset Yellow (SSY), which self-assembles into face-to-face columnar aggregates and produces nematic and columnar liquid crystal (LC) phases as a function of concentration. We show that the LC temperature-concentration phase diagram of SSY can be obtained with a fair agreement with previous reports, that droplet hydration-dehydration can be reversibly controlled and automated, and that the simultaneous incubation of samples with different final water contents, corresponding to different phases, can be implemented. These methods can be further extended to study the assembly of diverse prebiotically relevant small molecules and to characterize their phase transitions.
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Affiliation(s)
- Ajay Verma
- IPGG, CBI UMR 8231—CNRS—ESPCI Paris, PSL Research University, 75005 Paris, France
| | - Tiphaine Mateo
- IPGG, CBI UMR 8231—CNRS—ESPCI Paris, PSL Research University, 75005 Paris, France
| | | | - Nishanth Mohankumar
- IPGG, CBI UMR 8231—CNRS—ESPCI Paris, PSL Research University, 75005 Paris, France
| | - Tommaso P. Fraccia
- IPGG, CBI UMR 8231—CNRS—ESPCI Paris, PSL Research University, 75005 Paris, France
- Department of Pharmacological and Biomolecular Sciences, University of Milan, 20133 Milan, Italy
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8
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Lu H, Blokhuis A, Turk-MacLeod R, Karuppusamy J, Franconi A, Woronoff G, Jeancolas C, Abrishamkar A, Loire E, Ferrage F, Pelupessy P, Jullien L, Szathmary E, Nghe P, Griffiths AD. Small-molecule autocatalysis drives compartment growth, competition and reproduction. Nat Chem 2024; 16:70-78. [PMID: 37550391 DOI: 10.1038/s41557-023-01276-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Accepted: 06/16/2023] [Indexed: 08/09/2023]
Abstract
Sustained autocatalysis coupled to compartment growth and division is a key step in the origin of life, but an experimental demonstration of this phenomenon in an artificial system has previously proven elusive. We show that autocatalytic reactions within compartments-when autocatalysis, and reactant and solvent exchange outpace product exchange-drive osmosis and diffusion, resulting in compartment growth. We demonstrate, using the formose reaction compartmentalized in aqueous droplets in an emulsion, that compartment volume can more than double. Competition for a common reactant (formaldehyde) causes variation in droplet growth rate based on the composition of the surrounding droplets. These growth rate variations are partially transmitted after selective division of the largest droplets by shearing, which converts growth-rate differences into differences in droplet frequency. This shows how a combination of properties of living systems (growth, division, variation, competition, rudimentary heredity and selection) can arise from simple physical-chemical processes and may have paved the way for the emergence of evolution by natural selection.
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Affiliation(s)
- Heng Lu
- Laboratoire de Biochimie, Chimie Biologie et Innovation, ESPCI Paris, Université PSL, Paris, France
| | - Alex Blokhuis
- Laboratoire de Biochimie, Chimie Biologie et Innovation, ESPCI Paris, Université PSL, Paris, France
| | - Rebecca Turk-MacLeod
- Laboratoire de Biochimie, Chimie Biologie et Innovation, ESPCI Paris, Université PSL, Paris, France
| | - Jayaprakash Karuppusamy
- Laboratoire de Biochimie, Chimie Biologie et Innovation, ESPCI Paris, Université PSL, Paris, France
| | - Andrea Franconi
- Laboratoire de Biochimie, Chimie Biologie et Innovation, ESPCI Paris, Université PSL, Paris, France
| | - Gabrielle Woronoff
- Laboratoire de Biochimie, Chimie Biologie et Innovation, ESPCI Paris, Université PSL, Paris, France
| | - Cyrille Jeancolas
- Laboratoire de Biochimie, Chimie Biologie et Innovation, ESPCI Paris, Université PSL, Paris, France
| | - Afshin Abrishamkar
- Laboratoire de Biochimie, Chimie Biologie et Innovation, ESPCI Paris, Université PSL, Paris, France
| | - Estelle Loire
- Institut de Chimie Physique, Université Paris-Saclay, Orsay, France
| | - Fabien Ferrage
- Laboratoire des Biomolécules, LBM, Département de chimie, École Normale Supérieure, Université PSL, Sorbonne Université, CNRS, Paris, France
| | - Philippe Pelupessy
- Laboratoire des Biomolécules, LBM, Département de chimie, École Normale Supérieure, Université PSL, Sorbonne Université, CNRS, Paris, France
| | - Ludovic Jullien
- PASTEUR, Département de Chimie, École Normale Supérieure, Université PSL, Sorbonne Université, Paris, France
| | - Eörs Szathmary
- Centre for Ecological Research, Institute of Evolution, Budapest, Hungary.
- Department of Plant Systematics, Ecology and Theoretical Biology, Eötvös University, Budapest, Hungary.
- Parmenides Foundation, Center for the Conceptual Foundations of Science, Pöcking, Germany.
- Konrad Lorenz Institute for Evolution and Cognition Research, Klosterneuburg, Austria.
| | - Philippe Nghe
- Laboratoire de Biochimie, Chimie Biologie et Innovation, ESPCI Paris, Université PSL, Paris, France.
- Laboratoire Biophysique et Evolution, Chimie Biologie et Innovation, ESPCI Paris, Université PSL, Paris, France.
| | - Andrew D Griffiths
- Laboratoire de Biochimie, Chimie Biologie et Innovation, ESPCI Paris, Université PSL, Paris, France.
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9
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Waeterschoot J, Gosselé W, Alizadeh Zeinabad H, Lammertyn J, Koos E, Casadevall i Solvas X. Formation of Giant Unilamellar Vesicles Assisted by Fluorinated Nanoparticles. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2023; 10:e2302461. [PMID: 37807811 PMCID: PMC10700689 DOI: 10.1002/advs.202302461] [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] [Received: 04/18/2023] [Revised: 07/31/2023] [Indexed: 10/10/2023]
Abstract
In the quest to produce artificial cells, one key challenge that remains to be solved is the recreation of a complex cellular membrane. Among the existing models, giant unilamellar vesicles (GUVs) are particularly interesting due to their intrinsic compartmentalisation ability and their resemblance in size and shape to eukaryotic cells. Many techniques have been developed to produce GUVs all having inherent advantages and disadvantages. Here, the authors show that fluorinated silica nanoparticles (FNPs) used to form Pickering emulsions in a fluorinated oil can destabilise lipid nanosystems to template the formation of GUVs. This technique enables GUV production across a broad spectrum of buffer conditions, while preventing the leakage of the encapsulated components into the oil phase. Furthermore, a simple centrifugation process is sufficient for the release of the emulsion-trapped GUVs, bypassing the need to use emulsion-destabilising chemicals. With fluorescent FNPs and transmission electron microscopy, the authors confirm that FNPs are efficiently removed, producing contaminant-free GUVs. Further experiments assessing the lateral diffusion of lipids and unilamellarity of the GUVs demonstrate that they are comparable to GUVs produced via electroformation. Finally, the ability of incorporating transmembrane proteins is demonstrated, highlighting the potential of this method for the production of GUVs for artificial cell applications.
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Affiliation(s)
- Jorik Waeterschoot
- Mechatronics, Biostatistics and Sensors (MeBioS) at KU LeuvenWillem de Croylaan 423001LeuvenBelgium
| | - Willemien Gosselé
- Mechatronics, Biostatistics and Sensors (MeBioS) at KU LeuvenWillem de Croylaan 423001LeuvenBelgium
| | - Hojjat Alizadeh Zeinabad
- Mechatronics, Biostatistics and Sensors (MeBioS) at KU LeuvenWillem de Croylaan 423001LeuvenBelgium
| | - Jeroen Lammertyn
- Mechatronics, Biostatistics and Sensors (MeBioS) at KU LeuvenWillem de Croylaan 423001LeuvenBelgium
| | - Erin Koos
- Soft MatterRheology and Technology (SMaRT) at KU LeuvenCelestijnenlaan 200J3000LeuvenBelgium
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10
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Vian A, Pochitaloff M, Yen ST, Kim S, Pollock J, Liu Y, Sletten EM, Campàs O. In situ quantification of osmotic pressure within living embryonic tissues. Nat Commun 2023; 14:7023. [PMID: 37919265 PMCID: PMC10622550 DOI: 10.1038/s41467-023-42024-9] [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: 02/08/2023] [Accepted: 09/27/2023] [Indexed: 11/04/2023] Open
Abstract
Mechanics is known to play a fundamental role in many cellular and developmental processes. Beyond active forces and material properties, osmotic pressure is believed to control essential cell and tissue characteristics. However, it remains very challenging to perform in situ and in vivo measurements of osmotic pressure. Here we introduce double emulsion droplet sensors that enable local measurements of osmotic pressure intra- and extra-cellularly within 3D multicellular systems, including living tissues. After generating and calibrating the sensors, we measure the osmotic pressure in blastomeres of early zebrafish embryos as well as in the interstitial fluid between the cells of the blastula by monitoring the size of droplets previously inserted in the embryo. Our results show a balance between intracellular and interstitial osmotic pressures, with values of approximately 0.7 MPa, but a large pressure imbalance between the inside and outside of the embryo. The ability to measure osmotic pressure in 3D multicellular systems, including developing embryos and organoids, will help improve our understanding of its role in fundamental biological processes.
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Affiliation(s)
- Antoine Vian
- Department of Mechanical Engineering, University of California, Santa Barbara, CA, USA
- Cluster of Excellence Physics of Life, TU Dresden, 01062, Dresden, Germany
| | - Marie Pochitaloff
- Department of Mechanical Engineering, University of California, Santa Barbara, CA, USA
- Cluster of Excellence Physics of Life, TU Dresden, 01062, Dresden, Germany
| | - Shuo-Ting Yen
- Department of Mechanical Engineering, University of California, Santa Barbara, CA, USA
- Cluster of Excellence Physics of Life, TU Dresden, 01062, Dresden, Germany
| | - Sangwoo Kim
- Department of Mechanical Engineering, University of California, Santa Barbara, CA, USA
| | - Jennifer Pollock
- Department of Mechanical Engineering, University of California, Santa Barbara, CA, USA
| | - Yucen Liu
- Department of Mechanical Engineering, University of California, Santa Barbara, CA, USA
| | - Ellen M Sletten
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA, USA
| | - Otger Campàs
- Department of Mechanical Engineering, University of California, Santa Barbara, CA, USA.
- Cluster of Excellence Physics of Life, TU Dresden, 01062, Dresden, Germany.
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany.
- Center for Systems Biology Dresden, 01307, Dresden, Germany.
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11
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Shah V, Yang X, Arnheim A, Udani S, Tseng D, Luo Y, Ouyang M, Destgeer G, Garner OB, Koydemir HC, Ozcan A, Di Carlo D. Amphiphilic Particle-Stabilized Nanoliter Droplet Reactors with a Multimodal Portable Reader for Distributive Biomarker Quantification. ACS NANO 2023; 17:19952-19960. [PMID: 37824510 PMCID: PMC10604076 DOI: 10.1021/acsnano.3c04994] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/03/2023] [Accepted: 10/06/2023] [Indexed: 10/14/2023]
Abstract
Compartmentalization, leveraging microfluidics, enables highly sensitive assays, but the requirement for significant infrastructure for their design, build, and operation limits access. Multimaterial particle-based technologies thermodynamically stabilize monodisperse droplets as individual reaction compartments with simple liquid handling steps, precluding the need for expensive microfluidic equipment. Here, we further improve the accessibility of this lab on a particle technology to resource-limited settings by combining this assay system with a portable multimodal reader, thus enabling nanoliter droplet assays in an accessible platform. We show the utility of this platform in measuring N-terminal propeptide B-type natriuretic peptide (NT-proBNP), a heart failure biomarker, in complex medium and patient samples. We report a limit of detection of ∼0.05 ng/mL and a linear response between 0.2 and 2 ng/mL in spiked plasma samples. We also show that, owing to the plurality of measurements per sample, "swarm" sensing acquires better statistical quantitation with a portable reader. Monte Carlo simulations show the increasing capability of this platform to differentiate between negative and positive samples, i.e., below or above the clinical cutoff for acute heart failure (∼0.1 ng/mL), as a function of the number of particles measured. Our platform measurements correlate with gold standard ELISA measurement in cardiac patient samples, and achieve lower variation in measurement across samples compared to the standard well plate-based ELISA. Thus, we show the capabilities of a cost-effective droplet-reader system in accurately measuring biomarkers in nanoliter droplets for diseases that disproportionately affect underserved communities in resource-limited settings.
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Affiliation(s)
- Vishwesh Shah
- Department
of Bioengineering, University of California
- Los Angeles, Los Angeles, California 90095, United States
| | - Xilin Yang
- Department
of Electrical and Computer Engineering, University of California - Los Angeles, Los Angeles, California 90095, United States
| | - Alyssa Arnheim
- Department
of Bioengineering, University of California
- Los Angeles, Los Angeles, California 90095, United States
| | - Shreya Udani
- Department
of Bioengineering, University of California
- Los Angeles, Los Angeles, California 90095, United States
| | - Derek Tseng
- Department
of Electrical and Computer Engineering, University of California - Los Angeles, Los Angeles, California 90095, United States
| | - Yi Luo
- Department
of Electrical and Computer Engineering, University of California - Los Angeles, Los Angeles, California 90095, United States
| | - Mengxing Ouyang
- Department
of Bioengineering, University of California
- Los Angeles, Los Angeles, California 90095, United States
| | - Ghulam Destgeer
- Department
of Electrical Engineering, Technical University
of Munich, Munich 80333, Germany
| | - Omai B. Garner
- Department
of Pathology and Laboratory Medicine, University
of California - Los Angeles, Los
Angeles, California 90095, United States
| | - Hatice C. Koydemir
- Center
for Remote Health Technologies and Systems, Texas A&M Engineering Experiment Station, College Station, Texas 77843, United States
- Department
of Biomedical Engineering, Texas A&M
University, College Station, Texas 77843, United States
| | - Aydogan Ozcan
- Department
of Electrical and Computer Engineering, University of California - Los Angeles, Los Angeles, California 90095, United States
- California
Nanosystems Institute (CNSI), University
of California - Los Angeles, Los
Angeles, California 90095, United States
| | - Dino Di Carlo
- Department
of Bioengineering, University of California
- Los Angeles, Los Angeles, California 90095, United States
- California
Nanosystems Institute (CNSI), University
of California - Los Angeles, Los
Angeles, California 90095, United States
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12
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Choi JH, Jang W, Lim YJ, Mun SJ, Bong KW. Highly Flexible Deep-Learning-Based Automatic Analysis for Graphically Encoded Hydrogel Microparticles. ACS Sens 2023; 8:3158-3166. [PMID: 37489756 DOI: 10.1021/acssensors.3c00857] [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] [Indexed: 07/26/2023]
Abstract
Graphically encoded hydrogel microparticle (HMP)-based bioassay is a diagnostic tool characterized by exceptional multiplex detectability and robust sensitivity and specificity. Specifically, deep learning enables highly fast and accurate analyses of HMPs with diverse graphical codes. However, previous related studies have found the use of plain particles as data to be disadvantageous for accurate analyses of HMPs loaded with functional nanomaterials. Furthermore, the manual data annotation method used in existing approaches is highly labor-intensive and time-consuming. In this study, we present an efficient deep-learning-based analysis of encoded HMPs with diverse graphical codes and functional nanomaterials, utilizing the auto-annotation and synthetic data mixing methods for model training. The auto-annotation enhanced the throughput of dataset preparation up to 0.11 s/image. Using synthetic data mixing, a mean average precision of 0.88 was achieved in the analysis of encoded HMPs with magnetic nanoparticles, representing an approximately twofold improvement over the standard method. To evaluate the practical applicability of the proposed automatic analysis strategy, a single-image analysis was performed after the triplex immunoassay for the preeclampsia-related protein biomarkers. Finally, we accomplished a processing throughput of 0.353 s per sample for analyzing the result image.
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Affiliation(s)
- Jun Hee Choi
- Department of Chemical and Biological Engineering, Korea University, Seoul 02841, South Korea
| | - Wookyoung Jang
- Department of Chemical and Biological Engineering, Korea University, Seoul 02841, South Korea
| | - Yong Jun Lim
- Department of Chemical and Biological Engineering, Korea University, Seoul 02841, South Korea
| | - Seok Joon Mun
- Department of Chemical and Biological Engineering, Korea University, Seoul 02841, South Korea
| | - Ki Wan Bong
- Department of Chemical and Biological Engineering, Korea University, Seoul 02841, South Korea
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13
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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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14
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Prabhakar RG, Fan G, Alnahhas RN, Hirning AJ, Bennett MR, Shamoo Y. Indirect Enrichment of Desirable, but Less Fit Phenotypes, from a Synthetic Microbial Community Using Microdroplet Confinement. ACS Synth Biol 2023; 12:1239-1251. [PMID: 36929925 PMCID: PMC11259032 DOI: 10.1021/acssynbio.3c00008] [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: 03/18/2023]
Abstract
Spatial structure within microbial communities can provide nearly limitless opportunities for social interactions and are an important driver for evolution. As metabolites are often molecular signals, metabolite diffusion within microbial communities can affect the composition and dynamics of the community in a manner that can be challenging to deconstruct. We used encapsulation of a synthetic microbial community within microdroplets to investigate the effects of spatial structure and metabolite diffusion on population dynamics and to examine the effects of cheating by one member of the community. The synthetic community was composed of three strains: a "Producer" that makes the diffusible quorum sensing molecule (N-(3-oxododecanoyl)-l-homoserine lactone, C12-oxo-HSL) or AHL; a "Receiver" that is killed by AHL; and a Non-Producer or "cheater" that benefits from the extinction of the Receivers, but without the costs associated with the AHL synthesis. We demonstrate that despite rapid diffusion of AHL between microdroplets, the spatial structure imposed by the microdroplets allows a more efficient but transient enrichment of more rare and slower-growing Producer subpopulations. Eventually, the Non-Producer population drove the Producers to extinction. By including fluorescence-activated microdroplet sorting and providing sustained competition by the Receiver strain, we demonstrate a strategy for indirect enrichment of a rare and unlabeled Producer. The ability to screen and enrich metabolite Producers from a much larger population under conditions of rapid diffusion provides an important framework for the development of applications in synthetic ecology and biotechnology.
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Affiliation(s)
| | - Gaoyang Fan
- Department of Mathematics, University of Houston, Houston, Texas, 77204, United States
| | - Razan N Alnahhas
- Department of Biosciences, Rice University, Houston, Texas, 77005, United States
| | - Andrew J Hirning
- Department of Biosciences, Rice University, Houston, Texas, 77005, United States
| | - Matthew R Bennett
- Department of Biosciences, Rice University, Houston, Texas, 77005, United States
- Department of Bioengineering, Rice University, Houston, Texas, 77005, United States
| | - Yousif Shamoo
- Department of Biosciences, Rice University, Houston, Texas, 77005, United States
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15
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Bittermann MR, Morozova TI, Velandia SF, Mirzahossein E, Deblais A, Woutersen S, Bonn D. Surface-Mediated Molecular Transport of a Lipophilic Fluorescent Probe in Polydisperse Oil-in-Water Emulsions. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2023; 39:4207-4215. [PMID: 36919825 PMCID: PMC10061922 DOI: 10.1021/acs.langmuir.2c02597] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Revised: 03/07/2023] [Indexed: 06/18/2023]
Abstract
Emulsions often act as carriers for water-insoluble solutes that are delivered to a specific target. The molecular transport of solutes in emulsions can be facilitated by surfactants and is often limited by diffusion through the continuous phase. We here investigate this transport on a molecular scale by using a lipophilic molecular rotor as a proxy for solutes. Using fluorescence lifetime microscopy we track the transport of these molecules from the continuous phase toward the dispersed phase in polydisperse oil-in-water emulsions. We show that this transport comprises two time scales, which vary significantly with droplet size and surfactant concentration, and, depending on the type of surfactant used, can be limited either by transport across the oil-water interface or by diffusion through the continuous phase. By studying the time-resolved fluorescence of the fluorophore, accompanied by molecular dynamics simulations, we demonstrate how the rate of transport observed on a macroscopic scale can be explained in terms of the local environment that the probe molecules are exposed to.
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Affiliation(s)
- Marius R. Bittermann
- Van
der Waals-Zeeman Institute, IoP, University
of Amsterdam, Science Park 904, 1098 XH Amsterdam, Netherlands
| | | | - Santiago F. Velandia
- Van
der Waals-Zeeman Institute, IoP, University
of Amsterdam, Science Park 904, 1098 XH Amsterdam, Netherlands
| | - Elham Mirzahossein
- Van
der Waals-Zeeman Institute, IoP, University
of Amsterdam, Science Park 904, 1098 XH Amsterdam, Netherlands
| | - Antoine Deblais
- Van
der Waals-Zeeman Institute, IoP, University
of Amsterdam, Science Park 904, 1098 XH Amsterdam, Netherlands
| | - Sander Woutersen
- Van
’t Hoff Institute for Molecular Sciences, University of Amsterdam, Science Park 904, 1098 XH Amsterdam, Netherlands
| | - Daniel Bonn
- Van
der Waals-Zeeman Institute, IoP, University
of Amsterdam, Science Park 904, 1098 XH Amsterdam, Netherlands
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16
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Payne EM, Taraji M, Murray BE, Holland-Moritz DA, Moore JC, Haddad PR, Kennedy RT. Evaluation of Analyte Transfer between Microfluidic Droplets by Mass Spectrometry. Anal Chem 2023; 95:4662-4670. [PMID: 36862378 DOI: 10.1021/acs.analchem.2c04985] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/03/2023]
Abstract
Droplet microfluidics enables high-throughput experimentation and screening by encapsulating chemical and biochemical samples in aqueous droplets segmented by an immiscible fluid. In such experiments, it is critical that each droplet remains chemically distinct. A common approach is to use fluorinated oils with surfactants to stabilize droplets. However, some small molecules have been observed to transport between droplets under these conditions. Attempts to study and mitigate this effect have relied on evaluating crosstalk using fluorescent molecules, which inherently limits the analyte scope and conclusions drawn about the mechanism of the effect. In this work, transport of low molecular weight compounds between droplets was investigated using electrospray ionization mass spectrometry (ESI-MS) for measurement. The use of ESI-MS significantly expands the scope of analytes that can be tested. We tested 36 structurally diverse analytes that were found to exhibit crosstalk ranging from negligible to complete transfer using HFE 7500 as the carrier fluid and 008-fluorosurfactant as a surfactant. Using this data set, we developed a predictive tool showing that high log P and log D values correlate with high crosstalk, and high polar surface area and log S correlate with low crosstalk. We then investigated several carrier fluids, surfactants, and flow conditions. It was discovered that transport is strongly dependent on all of these factors and that experimental design and surfactant tailoring can reduce carryover. We present evidence for mixed crosstalk mechanisms including both micellar and oil partitioning transfer. By understanding the driving mechanisms, surfactant and oil compositions can be designed to better reduce chemical transport for screening workflows.
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Affiliation(s)
- Emory M Payne
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48103, United States
| | - Maryam Taraji
- The Australian Wine Research Institute, Adelaide, South Australia 5064, Australia.,Metabolomics Australia, Adelaide, South Australia 5064, Australia.,School of Natural Sciences, University of Tasmania, Hobart, Tasmania 7005, Australia
| | - Bridget E Murray
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48103, United States
| | - Daniel A Holland-Moritz
- Process Research and Development, Merck & Co., Inc., Rahway, New Jersey 07065, United States
| | - Jeffrey C Moore
- Process Research and Development, Merck & Co., Inc., Rahway, New Jersey 07065, United States
| | - Paul R Haddad
- School of Natural Sciences, University of Tasmania, Hobart, Tasmania 7005, Australia
| | - Robert T Kennedy
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48103, United States
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17
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Dufossez R, Ursuegui S, Baudrey S, Pernod K, Mouftakhir S, Oulad-Abdelghani M, Mosser M, Chaubet G, Ryckelynck M, Wagner A. Droplet Surface Immunoassay by Relocation (D-SIRe) for High-Throughput Analysis of Cytosolic Proteins at the Single-Cell Level. Anal Chem 2023; 95:4470-4478. [PMID: 36821722 DOI: 10.1021/acs.analchem.2c05168] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/25/2023]
Abstract
Enzyme-linked immunosorbent assay (ELISA) is a central analytic method in biological science for the detection of proteins. Introduction of droplet-based microfluidics allowed the development of miniaturized, less-consuming, and more sensitive ELISA assays by coencapsulating the biological sample and antibody-functionalized particles. We report herein an alternative in-droplet immunoassay format, which avoids the use of particles. It exploits the oil/aqueous-phase interface as a protein capture and detection surface. This is achieved using tailored perfluorinated surfactants bearing azide-functionalized PEG-based polar headgroups, which spontaneously react when meeting at the droplet formation site, with strained alkyne-functionalized antibodies solubilized in the water phase. The resulting antibody-functionalized inner surface can then be used to capture a target protein. This surface capture process leads to concomitant relocation at the surface of a labeled detection antibody and in turn to a drastic change in the shape of the fluorescence signal from a convex shape (not captured) to a characteristic concave shape (captured). This novel droplet surface immunoassay by fluorescence relocation (D-SIRe) proved to be fast and sensitive at 2.3 attomoles of analyte per droplet. It was further demonstrated to allow detection of cytosolic proteins at the single bacteria level.
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Affiliation(s)
- Robin Dufossez
- Bio-Functional Chemistry (UMR 7199), Institut du Médicament de Strasbourg, University of Strasbourg, 74 Route du Rhin, 67400 Illkirch-Graffenstaden, France
| | - Sylvain Ursuegui
- Bio-Functional Chemistry (UMR 7199), Institut du Médicament de Strasbourg, University of Strasbourg, 74 Route du Rhin, 67400 Illkirch-Graffenstaden, France
| | - Stephanie Baudrey
- Université de Strasbourg, CNRS, Architecture et Réactivité de l'ARN, UPR 9002, 67000 Strasbourg, France
| | - Ketty Pernod
- Bio-Functional Chemistry (UMR 7199), Institut du Médicament de Strasbourg, University of Strasbourg, 74 Route du Rhin, 67400 Illkirch-Graffenstaden, France
| | - Safae Mouftakhir
- Bio-Functional Chemistry (UMR 7199), Institut du Médicament de Strasbourg, University of Strasbourg, 74 Route du Rhin, 67400 Illkirch-Graffenstaden, France
| | - Mustapha Oulad-Abdelghani
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), INSERM U 1258, CNRS UMR 7104, University of Strasbourg, 67404 Illkirch, France
| | - Michel Mosser
- Bio-Functional Chemistry (UMR 7199), Institut du Médicament de Strasbourg, University of Strasbourg, 74 Route du Rhin, 67400 Illkirch-Graffenstaden, France
| | - Guilhem Chaubet
- Bio-Functional Chemistry (UMR 7199), Institut du Médicament de Strasbourg, University of Strasbourg, 74 Route du Rhin, 67400 Illkirch-Graffenstaden, France
| | - Michael Ryckelynck
- Université de Strasbourg, CNRS, Architecture et Réactivité de l'ARN, UPR 9002, 67000 Strasbourg, France
| | - Alain Wagner
- Bio-Functional Chemistry (UMR 7199), Institut du Médicament de Strasbourg, University of Strasbourg, 74 Route du Rhin, 67400 Illkirch-Graffenstaden, France
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18
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Design and construction of a microfluidics workstation for high-throughput multi-wavelength fluorescence and transmittance activated droplet analysis and sorting. Nat Protoc 2023; 18:1090-1136. [PMID: 36707723 DOI: 10.1038/s41596-022-00796-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2021] [Accepted: 11/09/2022] [Indexed: 01/28/2023]
Abstract
Droplet microfluidics has revolutionized quantitative high-throughput bioassays and screening, especially in the field of single-cell analysis where applications include cell characterization, antibody discovery and directed evolution. However, droplet microfluidic platforms capable of phenotypic, fluorescence-based readouts and sorting are still mostly found in specialized labs, because their setup is complex. Complementary to conventional FACS, microfluidic droplet sorters allow the screening of cell libraries for secreted factors, or even for the effects of secreted or surface-displayed factors on a second cell type. Furthermore, they also enable PCR-activated droplet sorting for the isolation of genetic material harboring specific markers. In this protocol, we provide a detailed step-by-step guide for the construction of a high-throughput droplet analyzer and sorter, which can be accomplished in ~45 working hours by nonspecialists. The resulting instrument is equipped with three lasers to excite the fluorophores in droplets and photosensors that acquire fluorescence signals in the blue (425-465 nm), green (505-545 nm) and red (580-630 nm) spectrum. This instrument also allows transmittance-activated droplet sorting by analyzing the brightfield light intensity transmitting through the droplets. The setup is validated by sorting droplets containing fluorescent beads at 200 Hz with 99.4% accuracy. We show results from an experiment where droplets hosting single cells were sorted on the basis of increased matrix metalloprotease activity as an application of our workstation in single-cell molecular biology, e.g., to analyze molecular determinants of cancer metastasis.
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19
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Prabhakar RG, Fan G, Alnahhas RN, Hirning AJ, Bennett MR, Shamoo Y. Indirect enrichment of desirable, but less fit phenotypes, from a synthetic microbial community using microdroplet confinement. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.11.523444. [PMID: 36711600 PMCID: PMC9882018 DOI: 10.1101/2023.01.11.523444] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Spatial structure within microbial communities can provide nearly limitless opportunities for social interactions and are an important driver for evolution. As metabolites are often molecular signals, metabolite diffusion within microbial communities can affect the composition and dynamics of the community in a manner that can be challenging to deconstruct. We used encapsulation of a synthetic microbial community within microdroplets to investigate the effects of spatial structure and metabolite diffusion on population dynamics and to examine the effects of cheating by one member of the community. The synthetic community was comprised of three strains: a 'Producer' that makes the diffusible quorum sensing molecule ( N -(3-Oxododecanoyl)-L-homoserine lactone, C12-oxo-HSL) or AHL; a 'Receiver' that is killed by AHL and a Non-Producer or 'cheater' that benefits from the extinction of the Receivers, but without the costs associated with the AHL synthesis. We demonstrate that despite rapid diffusion of AHL between microdroplets, the spatial structure imposed by the microdroplets allow a more efficient but transient enrichment of more rare and slower growing 'Producer' subpopulations. Eventually, the Non-Producer population drove the Producers to extinction. By including fluorescence-activated microdroplet sorting and providing sustained competition by the Receiver strain, we demonstrate a strategy for indirect enrichment of a rare and unlabeled Producer. The ability to screen and enrich metabolite Producers from a much larger population under conditions of rapid diffusion provides an important framework for the development of applications in synthetic ecology and biotechnology. Abstract Figure
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Affiliation(s)
| | - Gaoyang Fan
- Department of Mathematics, University of Houston, Houston, Texas, United States
| | - Razan N Alnahhas
- Department of Biomedical Engineering, Boston University, Boston, Massachusetts 02215, United States
| | - Andrew J Hirning
- Department of Biosciences, Rice University, Houston, United States
| | - Matthew R Bennett
- Department of Biosciences, Rice University, Houston, United States
- Department of Bioengineering, Rice University, Houston, United States
| | - Yousif Shamoo
- Department of Biosciences, Rice University, Houston, United States
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20
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Ruszczak A, Jankowski P, Vasantham SK, Scheler O, Garstecki P. Physicochemical Properties Predict Retention of Antibiotics in Water-in-Oil Droplets. Anal Chem 2023; 95:1574-1581. [PMID: 36598882 PMCID: PMC9850403 DOI: 10.1021/acs.analchem.2c04644] [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] [Indexed: 01/05/2023]
Abstract
Water-in-oil droplet microfluidics promises capacity for high-throughput single-cell antimicrobial susceptibility assays and investigation of drug resistance mechanisms. Every droplet must serve as an isolated environment with a controlled antibiotic concentration in such assays. While technologies for generation, incubation, screening, and sorting droplets mature, predictable retention of active molecules inside droplets remains a major outstanding challenge. Here, we analyzed 36 descriptors of the antibiotic molecules against experimental results on the cross-talk of antibiotics in droplets. We show that partition coefficient and fractional polar surface area are the key physicochemical properties that predict antibiotic retention. We verified the prediction by monitoring growth inhibition by antibiotic-loaded neighboring droplets. Our experiments also demonstrate that transfer of antibiotics between droplets is concentration- and distance-dependent. Our findings immediately apply to designing droplet antibiotic assays and give deeper insight into the retention of small molecules in water-in-oil emulsions.
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Affiliation(s)
- Artur Ruszczak
- Institute
of Physical Chemistry, Polish Academy of Sciences, Kasprzaka 44/52, 01-224 Warsaw, Poland
| | - Paweł Jankowski
- Institute
of Physical Chemistry, Polish Academy of Sciences, Kasprzaka 44/52, 01-224 Warsaw, Poland
| | - Shreyas K. Vasantham
- Institute
of Physical Chemistry, Polish Academy of Sciences, Kasprzaka 44/52, 01-224 Warsaw, Poland
| | - Ott Scheler
- Department
of Chemistry and Biotechnology, Tallinn
University of Technology (TalTech), Akadeemia tee 15, Tallinn 12618, Estonia,
| | - Piotr Garstecki
- Institute
of Physical Chemistry, Polish Academy of Sciences, Kasprzaka 44/52, 01-224 Warsaw, Poland,
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21
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Utharala R, Grab A, Vafaizadeh V, Peschke N, Ballinger M, Turei D, Tuechler N, Ma W, Ivanova O, Ortiz AG, Saez-Rodriguez J, Merten CA. A microfluidic Braille valve platform for on-demand production, combinatorial screening and sorting of chemically distinct droplets. Nat Protoc 2022; 17:2920-2965. [PMID: 36261631 DOI: 10.1038/s41596-022-00740-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Accepted: 06/16/2022] [Indexed: 11/09/2022]
Abstract
Droplet microfluidics is a powerful tool for a variety of biological applications including single-cell genetics, antibody discovery and directed evolution. All these applications make use of genetic libraries, illustrating the difficulty of generating chemically distinct droplets for screening applications. This protocol describes our Braille Display valving platform for on-demand generation of droplets with different chemical contents (16 different reagents and combinations thereof), as well as sorting droplets with different chemical properties, on the basis of fluorescence signals. The Braille Display platform is compact, versatile and cost efficient (only ~US$1,000 on top of a standard droplet microfluidics setup). The procedure includes manufacturing of microfluidic chips, assembly of custom hardware, co-encapsulation of cells and drugs into droplets, fluorescence detection of readout signals and data analysis using shared, freely available LabVIEW and Python packages. As a first application, we demonstrate the complete workflow for screening cancer cell drug sensitivities toward 74 conditions. Furthermore, we describe here an assay enabling the normalization of the observed drug sensitivity to the number of cancer cells per droplet, which additionally increases the robustness of the system. As a second application, we also demonstrate the sorting of droplets according to enzymatic activity. The drug screening application can be completed within 2 d; droplet sorting takes ~1 d; and all preparatory steps for manufacturing molds, chips and setting up the Braille controller can be accomplished within 1 week.
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Affiliation(s)
- Ramesh Utharala
- European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - Anna Grab
- European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
- Clinical Cooperation Unit Molecular Hematology/Oncology, DKFZ Heidelberg and Translational Myeloma Research Group, Department of Internal Medicine V, University Hospital, Heidelberg, Germany
| | - Vida Vafaizadeh
- European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
- Institute of Bioengineering, School of Engineering, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Nicolas Peschke
- European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - Martine Ballinger
- European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
- Collaboration for joint PhD degree between EMBL and Heidelberg University, Faculty of Biosciences, Heidelberg, Germany
| | - Denes Turei
- European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
- Faculty of Medicine and Heidelberg University Hospital, Institute of Computational Biomedicine, Heidelberg University, Heidelberg, Germany
| | - Nadine Tuechler
- European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - Wenwei Ma
- European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - Olga Ivanova
- Faculty of Medicine and Heidelberg University Hospital, Institute of Computational Biomedicine, Heidelberg University, Heidelberg, Germany
| | | | - Julio Saez-Rodriguez
- Faculty of Medicine and Heidelberg University Hospital, Institute of Computational Biomedicine, Heidelberg University, Heidelberg, Germany
- Faculty of Medicine, Joint Research Centre for Computational Biomedicine (JRC-COMBINE), RWTH Aachen University, Aachen, Germany
| | - Christoph A Merten
- Institute of Bioengineering, School of Engineering, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland.
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22
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Zath GK, Sperling RA, Hoffman CW, Bikos DA, Abbasi R, Abate AR, Weitz DA, Chang CB. Rapid parallel generation of a fluorescently barcoded drop library from a microtiter plate using the plate-interfacing parallel encapsulation (PIPE) chip. LAB ON A CHIP 2022; 22:4735-4745. [PMID: 36367139 PMCID: PMC10016142 DOI: 10.1039/d2lc00909a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
In drop-based microfluidics, an aqueous sample is partitioned into drops using individual pump sources that drive water and oil into a drop-making device. Parallelization of drop-making devices is necessary to achieve high-throughput screening of multiple experimental conditions, especially in time-sensitive studies. Here, we present the plate-interfacing parallel encapsulation (PIPE) chip, a microfluidic chip designed to generate 50 to 90 μm diameter drops of up to 96 different conditions in parallel by interfacing individual drop makers with a standard 384-well microtiter plate. The PIPE chip is used to generate two types of optically barcoded drop libraries consisting of two-color fluorescent particle combinations: a library of 24 microbead barcodes and a library of 192 quantum dot barcodes. Barcoded combinations in the drop libraries are rapidly measured within a microfluidic device using fluorescence detection and distinct barcoded populations in the fluorescence drop data are identified using DBSCAN data clustering. Signal analysis reveals that particle size defines the source of dominant noise present in the fluorescence intensity distributions of the barcoded drop populations, arising from Poisson loading for microbeads and shot noise for quantum dots. A barcoded population from a drop library is isolated using fluorescence-activated drop sorting, enabling downstream analysis of drop contents. The PIPE chip can improve multiplexed high-throughput assays by enabling simultaneous encapsulation of barcoded samples stored in a microtiter plate and reducing sample preparation time.
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Affiliation(s)
- Geoffrey K Zath
- Center for Biofilm Engineering, Montana State University, Bozeman, MT, USA.
- Department of Chemical and Biological Engineering, Montana State University, Bozeman, MT, USA
| | - Ralph A Sperling
- Department of Physics, School of Engineering and Applied Sciences, Harvard University, Cambridge, MA, USA
- Fraunhofer Institute for Microengineering and Microsystems IMM, Mainz, Germany
| | - Carter W Hoffman
- Center for Biofilm Engineering, Montana State University, Bozeman, MT, USA.
- Department of Chemical and Biological Engineering, Montana State University, Bozeman, MT, USA
- Department of Physiology and Biomedical Engineering, Mayo Clinic, Rochester, MN, USA
| | - Dimitri A Bikos
- Center for Biofilm Engineering, Montana State University, Bozeman, MT, USA.
- Department of Chemical and Biological Engineering, Montana State University, Bozeman, MT, USA
| | - Reha Abbasi
- Center for Biofilm Engineering, Montana State University, Bozeman, MT, USA.
- Department of Chemical and Biological Engineering, Montana State University, Bozeman, MT, USA
| | - Adam R Abate
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, CA, USA
| | - David A Weitz
- Department of Physics, School of Engineering and Applied Sciences, Harvard University, Cambridge, MA, USA
- Wyss Institute for Biologically Inspired Engineering at Harvard University, Boston, MA, USA
| | - Connie B Chang
- Center for Biofilm Engineering, Montana State University, Bozeman, MT, USA.
- Department of Chemical and Biological Engineering, Montana State University, Bozeman, MT, USA
- Department of Physiology and Biomedical Engineering, Mayo Clinic, Rochester, MN, USA
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23
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Loveday EK, Sanchez HS, Thomas MM, Chang CB. Single-Cell Infection of Influenza A Virus Using Drop-Based Microfluidics. Microbiol Spectr 2022; 10:e0099322. [PMID: 36125315 PMCID: PMC9603537 DOI: 10.1128/spectrum.00993-22] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Accepted: 08/22/2022] [Indexed: 12/30/2022] Open
Abstract
Drop-based microfluidics has revolutionized single-cell studies and can be applied toward analyzing tens of thousands to millions of single cells and their products contained within picoliter-sized drops. Drop-based microfluidics can shed insight into single-cell virology, enabling higher-resolution analysis of cellular and viral heterogeneity during viral infection. In this work, individual A549, MDCK, and siat7e cells were infected with influenza A virus (IAV) and encapsulated into 100-μm-size drops. Initial studies of uninfected cells encapsulated in drops demonstrated high cell viability and drop stability. Cell viability of uninfected cells in the drops remained above 75%, and the average drop radii changed by less than 3% following cell encapsulation and incubation over 24 h. Infection parameters were analyzed over 24 h from individually infected cells in drops. The number of IAV viral genomes and infectious viruses released from A549 and MDCK cells in drops was not significantly different from bulk infection as measured by reverse transcriptase quantitative PCR (RT-qPCR) and plaque assay. The application of drop-based microfluidics in this work expands the capacity to propagate IAV viruses and perform high-throughput analyses of individually infected cells. IMPORTANCE Drop-based microfluidics is a cutting-edge tool in single-cell research. Here, we used drop-based microfluidics to encapsulate thousands of individual cells infected with influenza A virus within picoliter-sized drops. Drop stability, cell loading, and cell viability were quantified from three different cell lines that support influenza A virus propagation. Similar levels of viral progeny as determined by RT-qPCR and plaque assay were observed from encapsulated cells in drops compared to bulk culture. This approach enables the ability to propagate influenza A virus from encapsulated cells, allowing for future high-throughput analysis of single host cell interactions in isolated microenvironments over the course of the viral life cycle.
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Affiliation(s)
- Emma Kate Loveday
- Center for Biofilm Engineering, Montana State University, Bozeman, Montana, USA
- Department of Chemical and Biological Engineering, Montana State University, Bozeman, Montana, USA
| | - Humberto S. Sanchez
- Center for Biofilm Engineering, Montana State University, Bozeman, Montana, USA
- Department of Chemical and Biological Engineering, Montana State University, Bozeman, Montana, USA
| | - Mallory M. Thomas
- Center for Biofilm Engineering, Montana State University, Bozeman, Montana, USA
- Microbiology and Cell Biology, Montana State University, Bozeman, Montana, USA
| | - Connie B. Chang
- Center for Biofilm Engineering, Montana State University, Bozeman, Montana, USA
- Department of Chemical and Biological Engineering, Montana State University, Bozeman, Montana, USA
- Department of Physiology and Biomedical Engineering, Mayo Clinic, Rochester, Minnesota, USA
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24
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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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25
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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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26
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Yakimov AS, Denisov IA, Bukatin AS, Lukyanenko KA, Belousov KI, Kukhtevich IV, Esimbekova EN, Evstrapov AA, Belobrov PI. Droplet Microfluidic Device for Chemoenzymatic Sensing. MICROMACHINES 2022; 13:1146. [PMID: 35888963 PMCID: PMC9325247 DOI: 10.3390/mi13071146] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Revised: 07/15/2022] [Accepted: 07/18/2022] [Indexed: 12/14/2022]
Abstract
The rapid detection of pollutants in water can be performed with enzymatic probes, the catalytic light-emitting activity of which decreases in the presence of many types of pollutants. Herein, we present a microfluidic system for continuous chemoenzymatic biosensing that generates emulsion droplets containing two enzymes of the bacterial bioluminescent system (luciferase and NAD(P)H:FMN-oxidoreductase) with substrates required for the reaction. The developed chip generates "water-in-oil" emulsion droplets with a volume of 0.1 μL and a frequency of up to 12 drops per minute as well as provides the efficient mixing of reagents in droplets and their distancing. The bioluminescent signal from each individual droplet was measured by a photomultiplier tube with a signal-to-noise ratio of up to 3000/1. The intensity of the luminescence depended on the concentration of the copper sulfate with the limit of its detection of 5 μM. It was shown that bioluminescent enzymatic reactions could be carried out in droplet reactors in dispersed streams. The parameters and limitations required for the bioluminescent reaction to proceed were also studied. Hereby, chemoenzymatic sensing capabilities powered by a droplet microfluidics manipulation technique may serve as the basis for early-warning online water pollution systems.
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Affiliation(s)
- Anton S. Yakimov
- Laboratory of Physical and Chemical Technologies for the Development of Hard-to-Recover Hydrocarbon Reserves, Siberian Federal University, 660041 Krasnoyarsk, Russia;
| | - Ivan A. Denisov
- Laboratory of Physical and Chemical Technologies for the Development of Hard-to-Recover Hydrocarbon Reserves, Siberian Federal University, 660041 Krasnoyarsk, Russia;
- Laboratory of Bioluminescent Biotechnologies, Siberian Federal University, 660041 Krasnoyarsk, Russia;
| | - Anton S. Bukatin
- Laboratory of Renewable Energy Sources, Alferov University, 194021 Saint Petersburg, Russia; (A.S.B.); (K.I.B.)
- Institute for Analytical Instrumentation RAS, 194021 Saint Petersburg, Russia;
| | - Kirill A. Lukyanenko
- Laboratory of Bioluminescent Biotechnologies, Siberian Federal University, 660041 Krasnoyarsk, Russia;
- Laboratory for Biomolecular and Medical Technologies, Prof. V.F. Voino-Yasenetsky Krasnoyarsk State Medical University, 660022 Krasnoyarsk, Russia
- Laboratory for Digital Controlled Drugs and Theranostics, Federal Research Center “Krasnoyarsk Science Center SB RAS”, 660036 Krasnoyarsk, Russia
| | - Kirill I. Belousov
- Laboratory of Renewable Energy Sources, Alferov University, 194021 Saint Petersburg, Russia; (A.S.B.); (K.I.B.)
| | - Igor V. Kukhtevich
- Institute of Silicate Chemistry of RAS, 199034 Saint Petersburg, Russia;
- Institute of Functional Epigenetics, Helmholtz Zentrum München, 85764 Neuherberg, Germany
| | - Elena N. Esimbekova
- Institute of Biophysics SB RAS, 660036 Krasnoyarsk, Russia;
- Department of Biophysics, Siberian Federal University, 660041 Krasnoyarsk, Russia;
| | | | - Peter I. Belobrov
- Department of Biophysics, Siberian Federal University, 660041 Krasnoyarsk, Russia;
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27
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Hattori K, Goda Y, Yamashita M, Yoshioka Y, Kojima R, Ota S. Droplet Array-Based Platform for Parallel Optical Analysis of Dynamic Extracellular Vesicle Secretion from Single Cells. Anal Chem 2022; 94:11209-11215. [PMID: 35797226 DOI: 10.1021/acs.analchem.2c01609] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Extracellular vesicles (EVs) are essential intercellular communication tools, but the regulatory mechanisms governing heterogeneous EV secretion are still unclear due to the lack of methods for precise analysis. Monitoring the dynamics of secretion from individually isolated cells is crucial because in bulk analysis, secretion activity can be perturbed by cell-cell interactions, and a cell population rarely performs secretion in a magnitude- or duration-synchronized manner. Although various microfluidic techniques have been adopted to evaluate the abundance of single-cell-derived EVs, none can track their secretion dynamics continually for extended periods. Here, we have developed a droplet array-based method that allowed us to optically quantify the EV secretion dynamics of >300 single cells every 2 h for 36 h, which covers the cell doubling time of many cell types. The experimental results clearly show the highly heterogeneous nature of single-cell EV secretion and suggest that cell division facilitates EV secretion, showing the usefulness of this platform for discovering EV regulation machinery.
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Affiliation(s)
- Kazuki Hattori
- Research Center for Advanced Science and Technology, The University of Tokyo, Tokyo 153-8904, Japan
| | - Yuki Goda
- Research Center for Advanced Science and Technology, The University of Tokyo, Tokyo 153-8904, Japan
| | - Minato Yamashita
- Research Center for Advanced Science and Technology, The University of Tokyo, Tokyo 153-8904, Japan
| | - Yusuke Yoshioka
- Department of Molecular and Cellular Medicine, Institute of Medical Science, Tokyo Medical University, Tokyo 160-0023, Japan
| | - Ryosuke Kojima
- Graduate School of Medicine, The University of Tokyo, Tokyo 113-0033, Japan.,PRESTO, Japan Science and Technology Agency (JST), Saitama 332-0012, Japan
| | - Sadao Ota
- Research Center for Advanced Science and Technology, The University of Tokyo, Tokyo 153-8904, Japan
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28
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Seo S, Prabhakar RG, Disney-McKeethen S, Song X, Shamoo Y. Microfluidic platform for spatially segregated experimental evolution studies with E. coli. STAR Protoc 2022; 3:101332. [PMID: 35496805 PMCID: PMC9048157 DOI: 10.1016/j.xpro.2022.101332] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
Abstract
Microdroplet emulsions allow investigators to build controllable microenvironments for applications in experimental evolution and synthetic ecology. We designed a microfluidic platform that uses highly homogenous microdroplets to enable these experiments. We also present a step-by-step protocol for the rapid production of highly homogeneous microdroplets suitable for experimental evolution. We also describe protocols for the propagation and serial passage of microbial populations across a range of selection schemes and potential spatial structures. For complete details on the use and execution of this protocol, please refer to Seo et al. (2021). Microfluidics for the study of microbial evolution and biomarker discovery Highly homogenous microdroplets as spatially segregated microenvironments Platform to identify evolutionary trajectories leading to antimicrobial resistance
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29
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Weisgerber D, Hatori M, Li X, Abate AR. Polyhedral Particles with Controlled Concavity by Indentation Templating. Anal Chem 2022; 94:7475-7482. [PMID: 35578791 PMCID: PMC9161221 DOI: 10.1021/acs.analchem.1c04884] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Accepted: 03/31/2022] [Indexed: 11/30/2022]
Abstract
Current methods for fabricating microparticles offer limited control over size and shape. Here, we demonstrate a droplet microfluidic method to form polyhedral microparticles with controlled concavity. By manipulating Laplace pressure, buoyancy, and particle rheology, we generate microparticles with diverse shapes and curvatures. Additionally, we demonstrate the particles provide increased capture efficiency when used for particle-templated emulsification. Our approach enables microparticles with enhanced chemical and biological functionality.
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Affiliation(s)
- Daniel
W. Weisgerber
- Department
of Bioengineering and Therapeutic Sciences University of California, San Francisco 1700 Fourth Street, San Francisco, California 94158, United States
| | - Makiko Hatori
- Department
of Bioengineering and Therapeutic Sciences University of California, San Francisco 1700 Fourth Street, San Francisco, California 94158, United States
| | - Xiangpeng Li
- Department
of Bioengineering and Therapeutic Sciences University of California, San Francisco 1700 Fourth Street, San Francisco, California 94158, United States
| | - Adam R. Abate
- Department
of Bioengineering and Therapeutic Sciences University of California, San Francisco 1700 Fourth Street, San Francisco, California 94158, United States
- Chan
Zuckerberg Biohub 499
Illinois Street, San Francisco, California 94158, United States
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30
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Gimeno‐Pérez M, Finnigan JD, Echeverria C, Charnock SJ, Hidalgo A, Mate DM. A Coupled Ketoreductase-Diaphorase Assay for the Detection of Polyethylene Terephthalate-Hydrolyzing Activity. CHEMSUSCHEM 2022; 15:e202102750. [PMID: 35315974 PMCID: PMC9321771 DOI: 10.1002/cssc.202102750] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/30/2021] [Revised: 03/22/2022] [Indexed: 06/14/2023]
Abstract
In the last two decades, several PET-degrading enzymes from already known microorganisms or metagenomic sources have been discovered to face the growing environmental concern of polyethylene terephthalate (PET) accumulation. However, there is a limited number of high-throughput screening protocols for PET-hydrolyzing activity that avoid the use of surrogate substrates. Herein, a microplate fluorescence screening assay was described. It was based on the coupled activity of ketoreductases (KREDs) and diaphorase to release resorufin in the presence of the products of PET degradation. Six KREDs were identified in a commercial panel that were able to use the PET building block, ethylene glycol, as substrate. The most efficient KRED, KRED61, was combined with the diaphorase from Clostridium kluyveri to monitor the PET degradation reaction catalyzed by the thermostable variant of the cutinase-type polyesterase from Saccharomonospora viridis AHK190. The PET degradation products were measured both fluorimetrically and by HPLC, with excellent correlation between both methods.
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Affiliation(s)
- María Gimeno‐Pérez
- Department of Molecular BiologyUniversidad Autónoma de MadridCampus de CantoblancoMadrid28049Spain
- Center of Molecular Biology “Severo Ochoa” (UAM-CSIC)Nicolás Cabrera 1Madrid28049Spain
- Institute for Molecular Biology-IUBMUniversidad Autónoma de MadridCampus de CantoblancoMadrid28049Spain
| | | | - Coro Echeverria
- Institute of Polymer Science and TechnologySpanish Research CouncilJuan de la Cierva 328006MadridSpain
| | | | - Aurelio Hidalgo
- Department of Molecular BiologyUniversidad Autónoma de MadridCampus de CantoblancoMadrid28049Spain
- Center of Molecular Biology “Severo Ochoa” (UAM-CSIC)Nicolás Cabrera 1Madrid28049Spain
- Institute for Molecular Biology-IUBMUniversidad Autónoma de MadridCampus de CantoblancoMadrid28049Spain
| | - Diana M. Mate
- Department of Molecular BiologyUniversidad Autónoma de MadridCampus de CantoblancoMadrid28049Spain
- Center of Molecular Biology “Severo Ochoa” (UAM-CSIC)Nicolás Cabrera 1Madrid28049Spain
- Institute for Molecular Biology-IUBMUniversidad Autónoma de MadridCampus de CantoblancoMadrid28049Spain
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31
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Geersens É, Vuilleumier S, Ryckelynck M. Growth-Associated Droplet Shrinkage for Bacterial Quantification, Growth Monitoring, and Separation by Ultrahigh-Throughput Microfluidics. ACS OMEGA 2022; 7:12039-12047. [PMID: 35449964 PMCID: PMC9016821 DOI: 10.1021/acsomega.2c00248] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Accepted: 03/17/2022] [Indexed: 05/08/2023]
Abstract
Microbiology still relies on en masse cultivation for selection, isolation, and characterization of microorganisms of interest. This constrains the diversity of microbial types and metabolisms that can be investigated in the laboratory also because of intercellular competition during cultivation. Cell individualization by droplet-based microfluidics prior to experimental analysis provides an attractive alternative to access a larger fraction of the microbial biosphere, miniaturizing the required equipment and minimizing reagent use for increased and more efficient analytical throughput. Here, we show that cultivation of a model two-strain bacterial community in droplets significantly reduces representation bias in the grown culture compared to batch cultivation. Further, and based on the droplet shrinkage observed upon cell proliferation, we provide proof-of-concept for a simple strategy that allows absolute quantification of microbial cells in a sample as well as selective recovery of microorganisms of interest for subsequent experimental characterization.
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Affiliation(s)
- Émilie Geersens
- Université
de Strasbourg, CNRS, Architecture
et Réactivité de l’ARN, UPR 9002, 67000 Strasbourg, France
- Université
de Strasbourg, CNRS, Génétique
Moléculaire, Génomique, Microbiologie, UMR 7156, 67000 Strasbourg, France
| | - Stéphane Vuilleumier
- Université
de Strasbourg, CNRS, Génétique
Moléculaire, Génomique, Microbiologie, UMR 7156, 67000 Strasbourg, France
| | - Michael Ryckelynck
- Université
de Strasbourg, CNRS, Architecture
et Réactivité de l’ARN, UPR 9002, 67000 Strasbourg, France
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32
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33
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Imai R, Kano H. Label-free enzymatic reaction monitoring in water-in-oil microdroplets using ultra-broadband multiplex coherent anti-Stokes Raman scattering spectroscopy. BIOMEDICAL OPTICS EXPRESS 2022; 13:1506-1515. [PMID: 35414981 PMCID: PMC8973173 DOI: 10.1364/boe.449914] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Revised: 01/24/2022] [Accepted: 02/05/2022] [Indexed: 06/14/2023]
Abstract
We propose a system for monitoring an enzymatic reaction, i.e., dehydrogenation of ethanol catalyzed by alcohol dehydrogenase, in microdroplets using ultra-broadband multiplex coherent anti-Stokes Raman scattering (CARS) spectroscopy. The reaction solution was encapsulated in water-in-oil microdroplets with diameters of 50 µm. The reaction was monitored by measuring the concentration of coenzymes from the CARS spectrum obtained in one-second exposure time. The results obtained using our system was consistent with those of the conventional fluorescence measurement system and indicate the potential of CARS spectroscopy for droplet-based high-throughput screening of enzymes.
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Affiliation(s)
- Ryo Imai
- Center for Technology Innovation - Healthcare, Research & Development Group, Hitachi, Ltd., 1-280 Higashi-koigakubo, Kokubunji, Tokyo 185-8601, Japan
| | - Hideaki Kano
- Department of Chemistry, Faculty of Science, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka 819-0395, Japan
- Department of Applied Physics, Graduate School of Pure and Applied Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8573, Japan
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34
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Postek W, Garstecki P. Droplet Microfluidics for High-Throughput Analysis of Antibiotic Susceptibility in Bacterial Cells and Populations. Acc Chem Res 2022; 55:605-615. [PMID: 35119826 PMCID: PMC8892833 DOI: 10.1021/acs.accounts.1c00729] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Antibiotic-resistant bacteria are an increasing concern both in everyday life and specialized environments such as healthcare. As the rate of antibiotic-resistant infections rises, so do complications to health and the risk of disability and death. Urgent action is required regarding the discovery of new antibiotics and rapid diagnosis of the resistance profile of an infectious pathogen as well as a better understanding of population and single-cell distribution of the resistance level. High-throughput screening is the major affordance of droplet microfluidics. Droplet screens can be exploited both to look for combinations of drugs that could stop an infection of multidrug-resistant bacteria and to search for the source of resistance via directed-evolution experiments or the analysis of various responses to a drug by genetically identical bacteria. In droplet techniques that have been used in this way for over a decade, aqueous droplets containing antibiotics and bacteria are manipulated both within and outside of the microfluidic devices. The diagnostics problem was approached by producing a series of microfluidic systems with integrated dilution modules for automated preparation of antibiotic concentration gradients, achieving the speed that allowed for high-throughput combinatorial assays. We developed a method for automated emulsification of a series of samples that facilitated measuring the resistance levels of thousands of individual cells encapsulated in droplets and quantifying the inoculum effect, the dependence of resistance level on bacterial cell count. Screening of single cells encapsulated in droplets with varying antibiotic contents has revealed a distribution of resistance levels within populations of clonally identical cells. To be able to screen bacteria from clinical samples, a study of fluorescent dyes in droplets determined that a derivative of a popular viability marker is more suitable for droplet assays. We have developed a detection system that analyzes the growth or death state of bacteria with antibiotics for thousands of droplets per second by measuring the scattering of light hitting the droplets without labeling the cells or droplets. The droplet-based microchemostats enabled long-term evolution of resistance experiments, which will be integrated with high-throughput single-cell assays to better understand the mechanism of resistance acquisition and loss. These techniques underlie automated combinatorial screens of antibiotic resistance in single cells from clinical samples. We hope that this Account will inspire new droplet-based research on the antibiotic susceptibility of bacteria.
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Affiliation(s)
- Witold Postek
- Institute of Physical Chemistry, Polish Academy of Sciences, ul. Kasprzaka 44/52, 01-224 Warszawa, Poland
| | - Piotr Garstecki
- Institute of Physical Chemistry, Polish Academy of Sciences, ul. Kasprzaka 44/52, 01-224 Warszawa, Poland
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35
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Crowe CD, Keating CD. Microfluidic Control of Coexisting Chemical Microenvironments within Multiphase Water-in-Fluorocarbon Droplets. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2022; 38:1811-1820. [PMID: 35090115 DOI: 10.1021/acs.langmuir.1c02929] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
The use of aqueous polymer-based phase separation within water-in-oil emulsion droplets provides a powerful platform for exploring the impact of compartmentalization and preferential partitioning on biologically relevant solutes. By forming an emulsion, a bulk solution is converted into a large number of chemically isolated microscale droplets. Microfluidic techniques provide an additional level of control over the formation of such systems. This enables the selective production of multiphase droplets with desired solution compositions and specific characteristics, such as solute partitioning. Here, we demonstrate control over the chemical microenvironment by adjusting the composition to increase tie line length for poly(ethylene glycol) (PEG)-dextran aqueous two-phase systems (ATPS) encapsulated within multiphase water-in-fluorocarbon oil emulsion droplets. Through rational adjustment of microfluidic parameters alone, ATPS droplets containing differing compositions could be produced during the course of a single experiment, with the produced droplets demonstrating a controllable range of tie line lengths. This provided control over partitioning behavior for biologically relevant macromolecules such that the difference in local protein concentration between adjacent phases could be rationally tuned. This work illustrates a broadly applicable technique to rationally create emulsified multiphase aqueous systems of desired compositions through the adjustment of microfluidic parameters alone, allowing for easy and rapid screening of various chemical microenvironments.
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Affiliation(s)
- Charles D Crowe
- Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
| | - Christine D Keating
- Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
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36
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Lussier F, Schröter M, Diercks NJ, Jahnke K, Weber C, Frey C, Platzman I, Spatz JP. pH-Triggered Assembly of Endomembrane Multicompartments in Synthetic Cells. ACS Synth Biol 2022; 11:366-382. [PMID: 34889607 PMCID: PMC8787813 DOI: 10.1021/acssynbio.1c00472] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Indexed: 11/29/2022]
Abstract
By using electrostatic interactions as driving force to assemble vesicles, the droplet-stabilized method was recently applied to reconstitute and encapsulate proteins, or compartments, inside giant unilamellar vesicles (GUVs) to act as minimal synthetic cells. However, the droplet-stabilized approach exhibits low production efficiency associated with the troublesome release of the GUVs from the stabilized droplets, corresponding to a major hurdle for the droplet-stabilized approach. Herein, we report the use of pH as a potential trigger to self-assemble droplet-stabilized GUVs (dsGUVs) by either bulk or droplet-based microfluidics. Moreover, pH enables the generation of compartmentalized GUVs with flexibility and robustness. By co-encapsulating pH-sensitive small unilamellar vesicles (SUVs), negatively charged SUVs, and/or proteins, we show that acidification of the droplets efficiently produces dsGUVs while sequestrating the co-encapsulated material. Most importantly, the pH-mediated assembly of dsGUVs significantly improves the production efficiency of free-standing GUVs (i.e., released from the stabilizing-droplets) compared to its previous implementation.
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Affiliation(s)
- Félix Lussier
- Department
of Cellular Biophysics, Max Planck Institute
for Medical Research, Jahnstraße 29, D-69120 Heidelberg, Germany
- Institute
for Molecular Systems Engineering (IMSE), Heidelberg University, Im Neuenheimer Feld 225, D-69120 Heidelberg, Germany
| | - Martin Schröter
- Department
of Cellular Biophysics, Max Planck Institute
for Medical Research, Jahnstraße 29, D-69120 Heidelberg, Germany
- Institute
for Molecular Systems Engineering (IMSE), Heidelberg University, Im Neuenheimer Feld 225, D-69120 Heidelberg, Germany
| | - Nicolas J. Diercks
- Department
of Cellular Biophysics, Max Planck Institute
for Medical Research, Jahnstraße 29, D-69120 Heidelberg, Germany
- Institute
for Molecular Systems Engineering (IMSE), Heidelberg University, Im Neuenheimer Feld 225, D-69120 Heidelberg, Germany
| | - Kevin Jahnke
- Biophysical
Engineering Group, Max Planck Institute
for Medical Research, Jahnstraße 29, D-69120 Heidelberg, Germany
- Department
of Physics and Astronomy, Heidelberg University, D-69120 Heidelberg, Germany
| | - Cornelia Weber
- Department
of Cellular Biophysics, Max Planck Institute
for Medical Research, Jahnstraße 29, D-69120 Heidelberg, Germany
- Institute
for Molecular Systems Engineering (IMSE), Heidelberg University, Im Neuenheimer Feld 225, D-69120 Heidelberg, Germany
| | - Christoph Frey
- Department
of Cellular Biophysics, Max Planck Institute
for Medical Research, Jahnstraße 29, D-69120 Heidelberg, Germany
- Institute
for Molecular Systems Engineering (IMSE), Heidelberg University, Im Neuenheimer Feld 225, D-69120 Heidelberg, Germany
| | - Ilia Platzman
- Department
of Cellular Biophysics, Max Planck Institute
for Medical Research, Jahnstraße 29, D-69120 Heidelberg, Germany
- Institute
for Molecular Systems Engineering (IMSE), Heidelberg University, Im Neuenheimer Feld 225, D-69120 Heidelberg, Germany
| | - Joachim P. Spatz
- Department
of Cellular Biophysics, Max Planck Institute
for Medical Research, Jahnstraße 29, D-69120 Heidelberg, Germany
- Institute
for Molecular Systems Engineering (IMSE), Heidelberg University, Im Neuenheimer Feld 225, D-69120 Heidelberg, Germany
- Max
Planck School Matter to Life, Jahnstraße 29, D-69120 Heidelberg, Germany
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37
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Liu D, Sun M, Zhang J, Hu R, Fu W, Xuanyuan T, Liu W. Single-cell droplet microfluidics for biomedical applications. Analyst 2022; 147:2294-2316. [DOI: 10.1039/d1an02321g] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
This review focuses on the recent advances in the fundamentals of single-cell droplet microfluidics and its applications in biomedicine, providing insights into design and establishment of single-cell microsystems and their further performance.
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Affiliation(s)
- Dan Liu
- Departments of Biomedical Engineering and Pathology, School of Basic Medical Science, Central South University, Changsha, Hunan 410013, China
| | - Meilin Sun
- Departments of Biomedical Engineering and Pathology, School of Basic Medical Science, Central South University, Changsha, Hunan 410013, China
| | - Jinwei Zhang
- Departments of Biomedical Engineering and Pathology, School of Basic Medical Science, Central South University, Changsha, Hunan 410013, China
| | - Rui Hu
- Departments of Biomedical Engineering and Pathology, School of Basic Medical Science, Central South University, Changsha, Hunan 410013, China
| | - Wenzhu Fu
- Departments of Biomedical Engineering and Pathology, School of Basic Medical Science, Central South University, Changsha, Hunan 410013, China
| | - Tingting Xuanyuan
- Departments of Biomedical Engineering and Pathology, School of Basic Medical Science, Central South University, Changsha, Hunan 410013, China
| | - Wenming Liu
- Departments of Biomedical Engineering and Pathology, School of Basic Medical Science, Central South University, Changsha, Hunan 410013, China
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38
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Zhang X, Qu Q, Zhou A, Wang Y, Zhang J, Xiong R, Lenders V, Manshian BB, Hua D, Soenen SJ, Huang C. Core-shell microparticles: From rational engineering to diverse applications. Adv Colloid Interface Sci 2022; 299:102568. [PMID: 34896747 DOI: 10.1016/j.cis.2021.102568] [Citation(s) in RCA: 35] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Revised: 11/16/2021] [Accepted: 11/20/2021] [Indexed: 12/24/2022]
Abstract
Core-shell microparticles, composed of solid, liquid, or gas bubbles surrounded by a protective shell, are gaining considerable attention as intelligent and versatile carriers that show great potential in biomedical fields. In this review, an overview is given of recent developments in design and applications of biodegradable core-shell systems. Several emerging methodologies including self-assembly, gas-shearing, and coaxial electrospray are discussed and microfluidics technology is emphasized in detail. Furthermore, the characteristics of core-shell microparticles in artificial cells, drug release and cell culture applications are discussed and the superiority of these advanced multi-core microparticles for the generation of artificial cells is highlighted. Finally, the respective developing orientations and limitations inherent to these systems are addressed. It is hoped that this review can inspire researchers to propel the development of this field with new ideas.
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39
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Nakamura A, Honma N, Tanaka Y, Suzuki Y, Shida Y, Tsuda Y, Hidaka K, Ogasawara W. 7-Aminocoumarin-4-acetic Acid as a Fluorescent Probe for Detecting Bacterial Dipeptidyl Peptidase Activities in Water-in-Oil Droplets and in Bulk. Anal Chem 2021; 94:2416-2424. [PMID: 34963280 PMCID: PMC8886566 DOI: 10.1021/acs.analchem.1c04108] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
![]()
Droplet-based
microfluidic systems are a powerful tool for biological
assays with high throughput. Water-in-oil droplets (WODLs) are typically
used in droplet-based microfluidic systems to culture microorganisms
and perform enzyme assays. However, because of the oil surrounding
the nanoliter and picoliter volumes of WODLs, availability of suitable
substrates is limited. For instance, although 7-amino-4-methylcoumarin
(AMC) is commonly used as a fluorescent probe of the substrate to
detect peptidase activity, AMC leaks from WODLs to the oil phase due
to its high hydrophobicity. Thus, AMC substrates cannot be used in
droplet-based microfluidic systems with WODLs. In this study, we developed
a peptidase substrate consisting of a dipeptide and 7-aminocoumarin-4-acetic
acid (ACA), an AMC-derived fluorogenic compound. ACA was retained
in the WODL for more than 7 days, and the dipeptidyl ACA substrate
detected dipeptidyl peptidase (DPP) activity in the WODL. Compared
to AMC substrates, the substrate specificity constants of DPPs for
ACA substrates increased up to 4.7-fold. Fluorescence-activated droplet
sorting made high-throughput screening of microorganisms based on
DPP activity using the dipeptidyl ACA substrate possible. Since ACA
could be applied to various substrates as a fluorescent probe, detectable
microbial enzyme activities for droplet-based microfluidic systems
can be largely expanded.
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Affiliation(s)
- Akihiro Nakamura
- Department of Science of Technology Innovation, Nagaoka University of Technology, 1603-1 Kamitomioka, Nagaoka, Niigata 940-2188, Japan
| | - Nobuyuki Honma
- Department of Bioengineering, Nagaoka University of Technology, 1603-1 Kamitomioka, Nagaoka, Niigata 940-2188, Japan
| | - Yuma Tanaka
- Department of Bioengineering, Nagaoka University of Technology, 1603-1 Kamitomioka, Nagaoka, Niigata 940-2188, Japan
| | - Yoshiyuki Suzuki
- Department of Science of Technology Innovation, Nagaoka University of Technology, 1603-1 Kamitomioka, Nagaoka, Niigata 940-2188, Japan
| | - Yosuke Shida
- Department of Bioengineering, Nagaoka University of Technology, 1603-1 Kamitomioka, Nagaoka, Niigata 940-2188, Japan
| | - Yuko Tsuda
- Faculty of Pharmaceutical Sciences, Cooperative Research Center of Life Sciences, Kobe Gakuin University, 1-1-3 Minatojima, Chuo-ku, Kobe, Hyogo 650-8586, Japan
| | - Koushi Hidaka
- Graduate School of Health Sciences, Kobe University, 7-10-2 Tomogaoka, Suma-ku, Kobe, Hyogo 654-0142, Japan
| | - Wataru Ogasawara
- Department of Science of Technology Innovation, Nagaoka University of Technology, 1603-1 Kamitomioka, Nagaoka, Niigata 940-2188, Japan.,Department of Bioengineering, Nagaoka University of Technology, 1603-1 Kamitomioka, Nagaoka, Niigata 940-2188, Japan
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40
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Bell SE, Park I, Rubakhin SS, Bashir R, Vlasov Y, Sweedler JV. Droplet Microfluidics with MALDI-MS Detection: The Effects of Oil Phases in GABA Analysis. ACS MEASUREMENT SCIENCE AU 2021; 1:147-156. [PMID: 34939077 PMCID: PMC8679089 DOI: 10.1021/acsmeasuresciau.1c00017] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Indexed: 06/01/2023]
Abstract
Microfluidic and mass spectrometry (MS) methods are widely used to sample and probe the chemical composition of biological systems to elucidate chemical correlates of their healthy and disease states. Though matrix-assisted laser desorption/ionization-mass spectrometry (MALDI)-MS has been hyphenated to droplet microfluidics for offline analyses, the effects of parameters related to droplet generation, such as the type of oil phase used, have been understudied. To characterize these effects, five different oil phases were tested in droplet microfluidics for producing samples for MALDI-MS analysis. Picoliter to nanoliter aqueous droplets containing 0.1 to 100 mM γ-aminobutyric acid (GABA) and inorganic salts were generated inside a polydimethylsiloxane microfluidic chip and deposited onto a conductive glass slide. Optical microscopy, Raman spectroscopy, and MALDI-mass spectrometry imaging (MSI) of the droplet samples and surrounding areas revealed patterns of solvent and oil evaporation and analyte deposition. Optical microscopy detected the presence of salt crystals in 50-100 μm diameter dried droplets, and Raman and MSI were used to correlate GABA signals to the visible droplet footprints. MALDI-MS analyses revealed that droplets prepared in the presence of octanol oil led to the poorest detectability of GABA, whereas the oil phases containing FC-40 provided the best detectability; GABA signal was localized to the footprint of 65 pL droplets with a limit of detection of 23 amol. The effect of the surfactant perfluorooctanol on analyte detection was also investigated.
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Affiliation(s)
- Sara E. Bell
- Department
of Chemistry, University of Illinois Urbana−Champaign, Urbana, Illinois 61801, United States
- Beckman
Institute for Advanced Science and Technology, University of Illinois Urbana−Champaign, Urbana, Illinois 61801, United States
| | - Insu Park
- Holonyak
Micro & Nanotechnology Laboratory, University
of Illinois Urbana−Champaign, Urbana, Illinois 61801, United States
| | - Stanislav S. Rubakhin
- Department
of Chemistry, University of Illinois Urbana−Champaign, Urbana, Illinois 61801, United States
- Beckman
Institute for Advanced Science and Technology, University of Illinois Urbana−Champaign, Urbana, Illinois 61801, United States
| | - Rashid Bashir
- Beckman
Institute for Advanced Science and Technology, University of Illinois Urbana−Champaign, Urbana, Illinois 61801, United States
- Holonyak
Micro & Nanotechnology Laboratory, University
of Illinois Urbana−Champaign, Urbana, Illinois 61801, United States
- Department
of Electrical and Computer Engineering, University of Illinois Urbana−Champaign, Urbana, Illinois 61801, United States
- Department
of Bioengineering, University of Illinois
at Urbana−Champaign, Urbana, Illinois 61801, United States
| | - Yurii Vlasov
- Beckman
Institute for Advanced Science and Technology, University of Illinois Urbana−Champaign, Urbana, Illinois 61801, United States
- Holonyak
Micro & Nanotechnology Laboratory, University
of Illinois Urbana−Champaign, Urbana, Illinois 61801, United States
- Department
of Electrical and Computer Engineering, University of Illinois Urbana−Champaign, Urbana, Illinois 61801, United States
- Department
of Bioengineering, University of Illinois
at Urbana−Champaign, Urbana, Illinois 61801, United States
| | - Jonathan V. Sweedler
- Department
of Chemistry, University of Illinois Urbana−Champaign, Urbana, Illinois 61801, United States
- Beckman
Institute for Advanced Science and Technology, University of Illinois Urbana−Champaign, Urbana, Illinois 61801, United States
- Department
of Bioengineering, University of Illinois
at Urbana−Champaign, Urbana, Illinois 61801, United States
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41
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Manteca A, Gadea A, Van Assche D, Cossard P, Gillard-Bocquet M, Beneyton T, Innis CA, Baret JC. Directed Evolution in Drops: Molecular Aspects and Applications. ACS Synth Biol 2021; 10:2772-2783. [PMID: 34677942 PMCID: PMC8609573 DOI: 10.1021/acssynbio.1c00313] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Indexed: 11/29/2022]
Abstract
The process of optimizing the properties of biological molecules is paramount for many industrial and medical applications. Directed evolution is a powerful technique for modifying and improving biomolecules such as proteins or nucleic acids (DNA or RNA). Mimicking the mechanism of natural evolution, one can enhance a desired property by applying a suitable selection pressure and sorting improved variants. Droplet-based microfluidic systems offer a high-throughput solution to this approach by helping to overcome the limiting screening steps and allowing the analysis of variants within increasingly complex libraries. Here, we review cases where successful evolution of biomolecules was achieved using droplet-based microfluidics, focusing on the molecular processes involved and the incorporation of microfluidics to the workflow. We highlight the advantages and limitations of these microfluidic systems compared to low-throughput methods and show how the integration of these systems into directed evolution workflows can open new avenues to discover or improve biomolecules according to user-defined conditions.
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Affiliation(s)
- Aitor Manteca
- Univ.
Bordeaux, Institut National de la Santé et de la Recherche
Médicale, Centre National de la Recherche Scientifique, ARNA,
U1212, UMR 5320, Institut Européen de Chimie et Biologie, F-33600 Pessac, France
| | - Alejandra Gadea
- Univ.
Bordeaux, CNRS, CRPP, UMR 5031, F-33610, Pessac, France
| | | | - Pauline Cossard
- Univ.
Bordeaux, Institut National de la Santé et de la Recherche
Médicale, Centre National de la Recherche Scientifique, ARNA,
U1212, UMR 5320, Institut Européen de Chimie et Biologie, F-33600 Pessac, France
| | - Mélanie Gillard-Bocquet
- Univ.
Bordeaux, Institut National de la Santé et de la Recherche
Médicale, Centre National de la Recherche Scientifique, ARNA,
U1212, UMR 5320, Institut Européen de Chimie et Biologie, F-33600 Pessac, France
| | - Thomas Beneyton
- Univ.
Bordeaux, CNRS, CRPP, UMR 5031, F-33610, Pessac, France
| | - C. Axel Innis
- Univ.
Bordeaux, Institut National de la Santé et de la Recherche
Médicale, Centre National de la Recherche Scientifique, ARNA,
U1212, UMR 5320, Institut Européen de Chimie et Biologie, F-33600 Pessac, France
| | - Jean-Christophe Baret
- Univ.
Bordeaux, CNRS, CRPP, UMR 5031, F-33610, Pessac, France
- Institut
Universitaire de France, F-75231 Paris, France
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42
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Stucki A, Vallapurackal J, Ward TR, Dittrich PS. Droplet Microfluidics and Directed Evolution of Enzymes: An Intertwined Journey. Angew Chem Int Ed Engl 2021; 60:24368-24387. [PMID: 33539653 PMCID: PMC8596820 DOI: 10.1002/anie.202016154] [Citation(s) in RCA: 38] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2020] [Indexed: 12/12/2022]
Abstract
Evolution is essential to the generation of complexity and ultimately life. It relies on the propagation of the properties, traits, and characteristics that allow an organism to survive in a challenging environment. It is evolution that shaped our world over about four billion years by slow and iterative adaptation. While natural evolution based on selection is slow and gradual, directed evolution allows the fast and streamlined optimization of a phenotype under selective conditions. The potential of directed evolution for the discovery and optimization of enzymes is mostly limited by the throughput of the tools and methods available for screening. Over the past twenty years, versatile tools based on droplet microfluidics have been developed to address the need for higher throughput. In this Review, we provide a chronological overview of the intertwined development of microfluidics droplet-based compartmentalization methods and in vivo directed evolution of enzymes.
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Affiliation(s)
- Ariane Stucki
- Department of Biosystems Science and EngineeringETH ZurichMattenstrasse 26CH-4058BaselSwitzerland
- National Competence Center in Research (NCCR)Molecular Systems EngineeringBaselSwitzerland
| | - Jaicy Vallapurackal
- Department of ChemistryUniversity of BaselMattenstrasse 24aCH-4058BaselSwitzerland
- National Competence Center in Research (NCCR)Molecular Systems EngineeringBaselSwitzerland
| | - Thomas R. Ward
- Department of ChemistryUniversity of BaselMattenstrasse 24aCH-4058BaselSwitzerland
- National Competence Center in Research (NCCR)Molecular Systems EngineeringBaselSwitzerland
| | - Petra S. Dittrich
- Department of Biosystems Science and EngineeringETH ZurichMattenstrasse 26CH-4058BaselSwitzerland
- National Competence Center in Research (NCCR)Molecular Systems EngineeringBaselSwitzerland
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43
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Booth R, Insua I, Ahmed S, Rioboo A, Montenegro J. Supramolecular fibrillation of peptide amphiphiles induces environmental responses in aqueous droplets. Nat Commun 2021; 12:6421. [PMID: 34741043 PMCID: PMC8571317 DOI: 10.1038/s41467-021-26681-2] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Accepted: 10/17/2021] [Indexed: 02/02/2023] Open
Abstract
One-dimensional (1D) supramolecular polymers are commonly found in natural and synthetic systems to prompt functional responses that capitalise on hierarchical molecular ordering. Despite amphiphilic self-assembly being significantly studied in the context of aqueous encapsulation and autopoiesis, very little is currently known about the physico-chemical consequences and functional role of 1D supramolecular polymerisation confined in aqueous compartments. Here, we describe the different phenomena that resulted from the chemically triggered supramolecular fibrillation of synthetic peptide amphiphiles inside water microdroplets. The confined connection of suitable dormant precursors triggered a physically autocatalysed chemical reaction that resulted in functional environmental responses such as molecular uptake, fusion and chemical exchange. These results demonstrate the potential of minimalistic 1D supramolecular polymerisation to modulate the behaviour of individual aqueous entities with their environment and within communities.
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Affiliation(s)
- Richard Booth
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CiQUS), Departamento de Química Orgánica, Universidade de Santiago de Compostela, 15705, Santiago de Compostela, Spain
| | - Ignacio Insua
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CiQUS), Departamento de Química Orgánica, Universidade de Santiago de Compostela, 15705, Santiago de Compostela, Spain
| | - Sahnawaz Ahmed
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CiQUS), Departamento de Química Orgánica, Universidade de Santiago de Compostela, 15705, Santiago de Compostela, Spain
| | - Alicia Rioboo
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CiQUS), Departamento de Química Orgánica, Universidade de Santiago de Compostela, 15705, Santiago de Compostela, Spain
| | - Javier Montenegro
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CiQUS), Departamento de Química Orgánica, Universidade de Santiago de Compostela, 15705, Santiago de Compostela, Spain.
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44
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Klaus M, Zurek PJ, Kaminski TS, Pushpanath A, Neufeld K, Hollfelder F. Ultrahigh-Throughput Detection of Enzymatic Alcohol Dehydrogenase Activity in Microfluidic Droplets with a Direct Fluorogenic Assay. Chembiochem 2021; 22:3292-3299. [PMID: 34643305 PMCID: PMC9291573 DOI: 10.1002/cbic.202100322] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Revised: 09/13/2021] [Indexed: 12/02/2022]
Abstract
The exploration of large DNA libraries of metagenomic or synthetic origin is greatly facilitated by ultrahigh‐throughput assays that use monodisperse water‐in‐oil emulsion droplets as sequestered reaction compartments. Millions of samples can be generated and analysed in microfluidic devices at kHz speeds, requiring only micrograms of reagents. The scope of this powerful platform for the discovery of new sequence space is, however, hampered by the limited availability of assay substrates, restricting the functions and reaction types that can be investigated. Here, we broaden the scope of detectable biochemical transformations in droplet microfluidics by introducing the first fluorogenic assay for alcohol dehydrogenases (ADHs) in this format. We have synthesized substrates that release a pyranine fluorophore (8‐hydroxy‐1,3,6‐pyrenetrisulfonic acid, HPTS) when enzymatic turnover occurs. Pyranine is well retained in droplets for >6 weeks (i. e. 14‐times longer than fluorescein), avoiding product leakage and ensuring excellent assay sensitivity. Product concentrations as low as 100 nM were successfully detected, corresponding to less than one turnover per enzyme molecule on average. The potential of our substrate design was demonstrated by efficient recovery of a bona fide ADH with an >800‐fold enrichment. The repertoire of droplet screening is enlarged by this sensitive and direct fluorogenic assay to identify dehydrogenases for biocatalytic applications.
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Affiliation(s)
- Miriam Klaus
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, CB2 1GA, Cambridge, UK.,Current address: ICB Nuvisan GmbH, Müllerstraße 178, 13353, Berlin, Germany
| | - Paul Jannis Zurek
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, CB2 1GA, Cambridge, UK.,Johnson Matthey Plc, 260 Cambridge Science Park, CB4 0WE, Cambridge, UK.,Current address: BioNTech Cell & Gene Therapies GmbH, An der Goldgrube 12, 55131, Mainz, Germany
| | - Tomasz S Kaminski
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, CB2 1GA, Cambridge, UK.,Current address: Department of Environmental Microbiology and Biotechnology, Institute of Microbiology, Faculty of Biology, University of Warsaw, Miecznikowa 1, 02-096, Warsaw, Poland
| | - Ahir Pushpanath
- Johnson Matthey Plc, 260 Cambridge Science Park, CB4 0WE, Cambridge, UK
| | - Katharina Neufeld
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, CB2 1GA, Cambridge, UK.,Johnson Matthey Plc, 260 Cambridge Science Park, CB4 0WE, Cambridge, UK.,Current address: Janssen Pharmaceutica, Turnhoutseweg 30, 2340, Beerse, Belgium
| | - Florian Hollfelder
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, CB2 1GA, Cambridge, UK
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45
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Hartner NT, Wink K, Raddatz CR, Thoben C, Schirmer M, Zimmermann S, Belder D. Coupling Droplet Microfluidics with Ion Mobility Spectrometry for Monitoring Chemical Conversions at Nanoliter Scale. Anal Chem 2021; 93:13615-13623. [PMID: 34592821 DOI: 10.1021/acs.analchem.1c02883] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We introduce the coupling of droplet microfluidics and ion mobility spectrometry (IMS) to address the challenges of label-free and chemical-specific detection of compounds in individual droplets. In analogy to the established use of mass spectrometry, droplet-IMS coupling can be also achieved via electrospray ionization but with significantly less instrumental effort. Because IMS instruments do not require high-vacuum systems, they are very compact, cost-effective, and robust, making them an ideal candidate as a chemical-specific end-of-line detector for segmented flow experiments. Herein, we demonstrate the successful coupling of droplet microfluidics with a custom-built high-resolution drift tube IMS system for monitoring chemical reactions in nL-sized droplets in an oil phase. The analytes contained in each droplet were assigned according to their characteristic ion mobility with limit of detections down to 200 nM to 1 μM and droplet frequencies ranging from 0.1 to 0.5 Hz. Using a custom sheath flow electrospray interface, we have further achieved the chemical-specific monitoring of a biochemical transformation catalyzed by a few hundred yeast cells, at single droplet level.
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Affiliation(s)
- Nora T Hartner
- Institute of Analytical Chemistry, Leipzig University, Linnéstraße 3, 04103 Leipzig, Germany
| | - Konstantin Wink
- Institute of Analytical Chemistry, Leipzig University, Linnéstraße 3, 04103 Leipzig, Germany
| | - Christian-Robert Raddatz
- Department of Sensors and Measurement Technology, Institute of Electrical Engineering and Measurement Technology, Leibniz University Hannover, Appelstraße 9A, 30167 Hannover, Germany
| | - Christian Thoben
- Department of Sensors and Measurement Technology, Institute of Electrical Engineering and Measurement Technology, Leibniz University Hannover, Appelstraße 9A, 30167 Hannover, Germany
| | - Martin Schirmer
- Helmholtz Centre for Environmental Research - UFZ Leipzig, Leipzig 04318, Germany
| | - Stefan Zimmermann
- Department of Sensors and Measurement Technology, Institute of Electrical Engineering and Measurement Technology, Leibniz University Hannover, Appelstraße 9A, 30167 Hannover, Germany
| | - Detlev Belder
- Institute of Analytical Chemistry, Leipzig University, Linnéstraße 3, 04103 Leipzig, Germany
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46
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Van Lent J, Breukers J, Ven K, Ampofo L, Horta S, Pollet F, Imbrechts M, Geukens N, Vanhoorelbeke K, Declerck P, Lammertyn J. Miniaturized single-cell technologies for monoclonal antibody discovery. LAB ON A CHIP 2021; 21:3627-3654. [PMID: 34505611 DOI: 10.1039/d1lc00243k] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Antibodies (Abs) are among the most important class of biologicals, showcasing a high therapeutic and diagnostic value. In the global therapeutic Ab market, fully-human monoclonal Abs (FH-mAbs) are flourishing thanks to their low immunogenicity and high specificity. The rapidly emerging field of single-cell technologies has paved the way to efficiently discover mAbs by facilitating a fast screening of the antigen (Ag)-specificity and functionality of Abs expressed by B cells. This review summarizes the principles and challenges of the four key concepts to discover mAbs using these technologies, being confinement of single cells using either droplet microfluidics or microstructure arrays, identification of the cells of interest, retrieval of those cells and single-cell sequence determination required for mAb production. This review reveals the enormous potential for mix-and-matching of the above-mentioned strategies, which is illustrated by the plethora of established, highly integrated devices. Lastly, an outlook is given on the many opportunities and challenges that still lie ahead to fully exploit miniaturized single-cell technologies for mAb discovery.
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Affiliation(s)
- Julie Van Lent
- Department of Biosystems, Biosensors Group, KU Leuven, Leuven 3001, Belgium.
| | - Jolien Breukers
- Department of Biosystems, Biosensors Group, KU Leuven, Leuven 3001, Belgium.
| | - Karen Ven
- Department of Biosystems, Biosensors Group, KU Leuven, Leuven 3001, Belgium.
| | - Louanne Ampofo
- Department of Biosystems, Biosensors Group, KU Leuven, Leuven 3001, Belgium.
- Laboratory for Therapeutic and Diagnostic Antibodies, KU Leuven, Leuven 3000, Belgium
| | - Sara Horta
- Laboratory for Thrombosis Research, IRF Life Sciences, KU Leuven Campus Kulak Kortrijk, Kortrijk 8500, Belgium
| | - Francesca Pollet
- Department of Biosystems, Biosensors Group, KU Leuven, Leuven 3001, Belgium.
| | - Maya Imbrechts
- Laboratory for Therapeutic and Diagnostic Antibodies, KU Leuven, Leuven 3000, Belgium
- PharmAbs, The KU Leuven Antibody Center, KU Leuven, Leuven 3000, Belgium
| | - Nick Geukens
- PharmAbs, The KU Leuven Antibody Center, KU Leuven, Leuven 3000, Belgium
| | - Karen Vanhoorelbeke
- Laboratory for Thrombosis Research, IRF Life Sciences, KU Leuven Campus Kulak Kortrijk, Kortrijk 8500, Belgium
- PharmAbs, The KU Leuven Antibody Center, KU Leuven, Leuven 3000, Belgium
| | - Paul Declerck
- Laboratory for Therapeutic and Diagnostic Antibodies, KU Leuven, Leuven 3000, Belgium
- PharmAbs, The KU Leuven Antibody Center, KU Leuven, Leuven 3000, Belgium
| | - Jeroen Lammertyn
- Department of Biosystems, Biosensors Group, KU Leuven, Leuven 3001, Belgium.
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47
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Wang Y, Shah V, Lu A, Pachler E, Cheng B, Di Carlo D. Counting of enzymatically amplified affinity reactions in hydrogel particle-templated drops. LAB ON A CHIP 2021; 21:3438-3448. [PMID: 34378611 PMCID: PMC11288628 DOI: 10.1039/d1lc00344e] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Counting of numerous compartmentalized enzymatic reactions underlies quantitative and high sensitivity immunodiagnostic assays. However, digital enzyme-linked immunosorbent assays (ELISA) require specialized instruments which have slowed adoption in research and clinical labs. We present a lab-on-a-particle solution to digital counting of thousands of single enzymatic reactions. Hydrogel particles are used to bind enzymes and template the formation of droplets that compartmentalize reactions with simple pipetting steps. These hydrogel particles can be made at a high throughput, stored, and used during the assay to create ∼500 000 compartments within 2 minutes. These particles can also be dried and rehydrated with sample, amplifying the sensitivity of the assay by driving affinity interactions on the hydrogel surface. We demonstrate digital counting of β-galactosidase enzyme at a femtomolar detection limit with a dynamic range of 3 orders of magnitude using standard benchtop equipment and experiment techniques. This approach can faciliate the development of digital ELISAs with reduced need for specialized microfluidic devices, instruments, or imaging systems.
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Affiliation(s)
- Yilian Wang
- Department of Bioengineering, University of California, Los Angeles, CA, USA.
| | - Vishwesh Shah
- Department of Bioengineering, University of California, Los Angeles, CA, USA.
| | - Angela Lu
- Department of Bioengineering, University of California, Los Angeles, CA, USA.
| | - Ella Pachler
- Department of Bioengineering, University of California, Los Angeles, CA, USA.
| | - Brian Cheng
- Department of Bioengineering, University of California, Los Angeles, CA, USA.
| | - Dino Di Carlo
- Department of Bioengineering, University of California, Los Angeles, CA, USA.
- Department of Mechanical and Aerospace Engineering, California NanoSystems Institute, Jonsson Comprehensive Cancer Center, University of California, Los Angeles, CA, USA
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Chowdhury MS, Zheng W, Singh AK, Ong ILH, Hou Y, Heyman JA, Faghani A, Amstad E, Weitz DA, Haag R. Linear triglycerol-based fluorosurfactants show high potential for droplet-microfluidics-based biochemical assays. SOFT MATTER 2021; 17:7260-7267. [PMID: 34337643 DOI: 10.1039/d1sm00890k] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Fluorosurfactants have expanded the landscape of high-value biochemical assays in microfluidic droplets, but little is known about how the spatial geometries and polarity of the head group contribute to the performance of fluorosurfactants. To decouple this, we design, synthesize, and characterize two linear and two dendritic glycerol- or tris-based surfactants with a common perfluoropolyether tail. To reveal the influence of spatial geometry, we choose inter-droplet cargo transport as a stringent test case. Using surfactants with linear di- and triglycerol, we show that the inter-droplet cargo transport is minimal compared with their dendritic counterparts. When we encapsulated a less-leaky sodium fluorescent dye into the droplets, quantitatively, we find that the mean fluorescence intensity of the PFPE-dTG stabilized PBS-only droplets after 72 h was ∼3 times that of the signal detected in PBS-only droplets stabilized by PFPE-lTG. We also demonstrate that the post-functionalization of PFPE-lTG having a linear geometry and four hydroxy groups enables the 'from-Droplet' fishing of the biotin-streptavidin protein complex without the trade-off between fishing efficiency and droplet stability. Thus, our approach to design user-friendly surfactants reveals the aspects of spatial geometry and facile tunability of the polar head groups that have not been captured or exploited before.
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Affiliation(s)
- Mohammad Suman Chowdhury
- Institut für Chemie und Biochemie, Freie Universität Berlin, Takustrasse 3, 14195 Berlin, Germany.
| | - Wenshan Zheng
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, USA
| | - Abhishek Kumar Singh
- Institut für Chemie und Biochemie, Freie Universität Berlin, Takustrasse 3, 14195 Berlin, Germany.
| | - Irvine Lian Hao Ong
- Soft Materials Laboratory, Institute of Materials, École Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland
| | - Yong Hou
- Institut für Chemie und Biochemie, Freie Universität Berlin, Takustrasse 3, 14195 Berlin, Germany.
| | - John A Heyman
- School of Engineering and Applied Sciences, Department of Physics, Harvard University, 29 Oxford Street, Cambridge, MA 02138, USA
| | - Abbas Faghani
- Institut für Chemie und Biochemie, Freie Universität Berlin, Takustrasse 3, 14195 Berlin, Germany.
| | - Esther Amstad
- Soft Materials Laboratory, Institute of Materials, École Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland
| | - David A Weitz
- School of Engineering and Applied Sciences, Department of Physics, Harvard University, 29 Oxford Street, Cambridge, MA 02138, USA
| | - Rainer Haag
- Institut für Chemie und Biochemie, Freie Universität Berlin, Takustrasse 3, 14195 Berlin, Germany.
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49
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Małecki J, Muszyński S, Sołowiej BG. Proteins in Food Systems-Bionanomaterials, Conventional and Unconventional Sources, Functional Properties, and Development Opportunities. Polymers (Basel) 2021; 13:2506. [PMID: 34372109 PMCID: PMC8347159 DOI: 10.3390/polym13152506] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Revised: 07/25/2021] [Accepted: 07/27/2021] [Indexed: 02/03/2023] Open
Abstract
Recently, food companies from various European countries have observed increased interest in high-protein food and other products with specific functional properties. This review article intends to present proteins as an increasingly popular ingredient in various food products that frequently draw contemporary consumers' attention. The study describes the role of conventional, unconventional, and alternative sources of protein in the human body. Furthermore, the study explores proteins' nutritional value and functional properties, their use in the food industry, and the application of proteins in bionanomaterials. Due to the expected increase in demand for high-protein products, the paper also examines the health benefits and risks of consuming these products, current market trends, and consumer preferences.
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Affiliation(s)
- Jan Małecki
- Department of Dairy Technology and Functional Foods, Faculty of Food Sciences and Biotechnology, University of Life Sciences in Lublin, Skromna 8, 20-704 Lublin, Poland;
- EUROHANSA Sp. z o.o., Letnia 10-14, 87-100 Toruń, Plant in Puławy, Wiślana 8, 24-100 Puławy, Poland
| | - Siemowit Muszyński
- Department of Biophysics, Faculty of Environmental Biology, University of Life Sciences in Lublin, Akademicka 13, 20-950 Lublin, Poland;
| | - Bartosz G. Sołowiej
- Department of Dairy Technology and Functional Foods, Faculty of Food Sciences and Biotechnology, University of Life Sciences in Lublin, Skromna 8, 20-704 Lublin, Poland;
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50
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Shi N, Mohibullah M, Easley CJ. Active Flow Control and Dynamic Analysis in Droplet Microfluidics. ANNUAL REVIEW OF ANALYTICAL CHEMISTRY (PALO ALTO, CALIF.) 2021; 14:133-153. [PMID: 33979546 PMCID: PMC8956363 DOI: 10.1146/annurev-anchem-122120-042627] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Droplet-based microfluidics has emerged as an important subfield within the microfluidic and general analytical communities. Indeed, several unique applications such as digital assay readout and single-cell sequencing now have commercial systems based on droplet microfluidics. Yet there remains room for this research area to grow. To date, most analytical readouts are optical in nature, relatively few studies have integrated sample preparation, and passive means for droplet formation and manipulation have dominated the field. Analytical scientists continue to expand capabilities by developing droplet-compatible method adaptations, for example, by interfacing to mass spectrometers or automating droplet sampling for temporally resolved analysis. In this review, we highlight recently developed fluidic control techniques and unique integrations of analytical methodology with droplet microfluidics-focusing on automation and the connections to analog/digital domains-and we conclude by offering a perspective on current challenges and future applications.
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Affiliation(s)
- Nan Shi
- Department of Chemistry and Biochemistry, Auburn University, Auburn, Alabama 36849, USA;
| | - Md Mohibullah
- Department of Chemistry and Biochemistry, Auburn University, Auburn, Alabama 36849, USA;
| | - Christopher J Easley
- Department of Chemistry and Biochemistry, Auburn University, Auburn, Alabama 36849, USA;
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