1
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Cazorla A, Martín-Martín S, Delgado ÁV, Jiménez ML. Electro-optics of confined systems. J Colloid Interface Sci 2024; 658:52-60. [PMID: 38096679 DOI: 10.1016/j.jcis.2023.11.180] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Revised: 11/13/2023] [Accepted: 11/28/2023] [Indexed: 01/12/2024]
Abstract
Confinement in microenvironments occurs in many natural systems and technological applications. However, little is known about the behaviour of the immersed nanoparticles. In this work we show that their diffusion, electro-orientation and electric field induced polarization can be determined through electric birefringence experiments. We analyze aqueous dispersions of silver nanowires and clay particles confined inside microdroplets. We have observed that confinement reduces the amount of particles that can be oriented by the external electric field. However, the polarizability of the oriented particles is not affected by the presence of the oil/water boundary, and it is the same as in unbounded media, which agrees with the fact that the electric polarization and related phenomena are short-ranged.
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Affiliation(s)
- Ana Cazorla
- Department of Applied Physics, University of Granada, Avda. de Fuente Nueva sn, 18071, Granada, Spain.
| | - Sergio Martín-Martín
- Department of Applied Physics, University of Granada, Avda. de Fuente Nueva sn, 18071, Granada, Spain.
| | - Ángel V Delgado
- Department of Applied Physics, University of Granada, Avda. de Fuente Nueva sn, 18071, Granada, Spain.
| | - María L Jiménez
- Department of Applied Physics, University of Granada, Avda. de Fuente Nueva sn, 18071, Granada, Spain.
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2
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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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3
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McCully AL, Loop Yao M, Brower KK, Fordyce PM, Spormann AM. Double emulsions as a high-throughput enrichment and isolation platform for slower-growing microbes. ISME COMMUNICATIONS 2023; 3:47. [PMID: 37160952 PMCID: PMC10169782 DOI: 10.1038/s43705-023-00241-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Revised: 03/27/2023] [Accepted: 04/12/2023] [Indexed: 05/11/2023]
Abstract
Our understanding of in situ microbial physiology is primarily based on physiological characterization of fast-growing and readily-isolatable microbes. Microbial enrichments to obtain novel isolates with slower growth rates or physiologies adapted to low nutrient environments are plagued by intrinsic biases for fastest-growing species when using standard laboratory isolation protocols. New cultivation tools to minimize these biases and enrich for less well-studied taxa are needed. In this study, we developed a high-throughput bacterial enrichment platform based on single cell encapsulation and growth within double emulsions (GrowMiDE). We showed that GrowMiDE can cultivate many different microorganisms and enrich for underrepresented taxa that are never observed in traditional batch enrichments. For example, preventing dominance of the enrichment by fast-growing microbes due to nutrient privatization within the double emulsion droplets allowed cultivation of slower-growing Negativicutes and Methanobacteria from stool samples in rich media enrichment cultures. In competition experiments between growth rate and growth yield specialist strains, GrowMiDE enrichments prevented competition for shared nutrient pools and enriched for slower-growing but more efficient strains. Finally, we demonstrated the compatibility of GrowMiDE with commercial fluorescence-activated cell sorting (FACS) to obtain isolates from GrowMiDE enrichments. Together, GrowMiDE + DE-FACS is a promising new high-throughput enrichment platform that can be easily applied to diverse microbial enrichments or screens.
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Affiliation(s)
- Alexandra L McCully
- Department of Civil and Environmental Engineering, Stanford University, Stanford, CA, USA
| | - McKenna Loop Yao
- Department of Chemical Engineering, Stanford University, Stanford, CA, USA
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, CA, USA
| | - Kara K Brower
- Department of Bioengineering, Stanford University, Stanford, CA, USA
| | - Polly M Fordyce
- Department of Bioengineering, Stanford University, Stanford, CA, USA
- Department of Genetics, Stanford University, Stanford, CA, USA
- ChEM-H Institute, Stanford University, Stanford, CA, USA
- Chan Zuckerberg Biohub, San Francisco, CA, USA
| | - Alfred M Spormann
- Department of Civil and Environmental Engineering, Stanford University, Stanford, CA, USA.
- Department of Chemical Engineering, Stanford University, Stanford, CA, USA.
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4
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Gantz M, Neun S, Medcalf EJ, van Vliet LD, Hollfelder F. Ultrahigh-Throughput Enzyme Engineering and Discovery in In Vitro Compartments. Chem Rev 2023; 123:5571-5611. [PMID: 37126602 PMCID: PMC10176489 DOI: 10.1021/acs.chemrev.2c00910] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Novel and improved biocatalysts are increasingly sourced from libraries via experimental screening. The success of such campaigns is crucially dependent on the number of candidates tested. Water-in-oil emulsion droplets can replace the classical test tube, to provide in vitro compartments as an alternative screening format, containing genotype and phenotype and enabling a readout of function. The scale-down to micrometer droplet diameters and picoliter volumes brings about a >107-fold volume reduction compared to 96-well-plate screening. Droplets made in automated microfluidic devices can be integrated into modular workflows to set up multistep screening protocols involving various detection modes to sort >107 variants a day with kHz frequencies. The repertoire of assays available for droplet screening covers all seven enzyme commission (EC) number classes, setting the stage for widespread use of droplet microfluidics in everyday biochemical experiments. We review the practicalities of adapting droplet screening for enzyme discovery and for detailed kinetic characterization. These new ways of working will not just accelerate discovery experiments currently limited by screening capacity but profoundly change the paradigms we can probe. By interfacing the results of ultrahigh-throughput droplet screening with next-generation sequencing and deep learning, strategies for directed evolution can be implemented, examined, and evaluated.
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Affiliation(s)
- Maximilian Gantz
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Rd, Cambridge CB2 1GA, U.K
| | - Stefanie Neun
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Rd, Cambridge CB2 1GA, U.K
| | - Elliot J Medcalf
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Rd, Cambridge CB2 1GA, U.K
| | - Liisa D van Vliet
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Rd, Cambridge CB2 1GA, U.K
| | - Florian Hollfelder
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Rd, Cambridge CB2 1GA, U.K
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5
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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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6
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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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7
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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: 4] [Impact Index Per Article: 2.0] [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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8
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Qu F, Zhao L, Li L, Zhao S, Yang M, Yu J, Ho YP. Thermo-Induced Coalescence of Dual Cores in Double Emulsions for Single-Cell RT-PCR. Anal Chem 2022; 94:11670-11678. [PMID: 35968810 DOI: 10.1021/acs.analchem.2c02294] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Single-cell reverse-transcription polymerase chain reaction (RT-PCR) has shown significant promise for transcriptional profiling of heterogeneous cells. However, currently developed microfluidic droplet-based methodologies for single-cell RT-PCR often require complex chip design to accommodate the associated multistep processes as well as customized detection platforms for high-throughput analysis. Herein, we proposed a dual-core double emulsion (DE)-based method to streamline the single-cell RT-PCR through thermo-induced coalescence of the dual cores. The dual-core DEs were produced by pairing two water-in-oil single emulsions containing a single-cell/lysis buffer and RT-PCR mix, respectively. After complete lysis of single cells in one of the cores, the dual-core DEs were merged by gentle heating, made possible by the optimized glycerol concentration present in the cores. Upon the coalescence of dual cores, the alkaline lysis buffer present in the core of the cell lysate was neutralized by the reaction buffer presented in the RT-PCR core, allowing TaqMan assay-based RT-PCR to occur effectively within the DEs. To demonstrate the potential of this streamlined dual-core platform, AKR1B10-positive A549 cells and AKR1B10-negative HEK293 cells were investigated via the TaqMan assay. Subsequently, specific transcript of AKR1B10 was readily available for quantitative profiling at the single-cell level using a commercially available flow cytometer in a high-throughput manner.
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Affiliation(s)
- Fuyang Qu
- Department of Biomedical Engineering, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR 999077, China
| | - Liuyang Zhao
- Institute of Digestive Disease and Department of Medicine and Therapeutics, State Key Laboratory of Digestive Disease, Li Ka Shing Institute of Health Sciences, CUHK-Shenzhen Research Institute, The Chinese University of Hong Kong, Hong Kong SAR 999077, China
| | - Luoquan Li
- Department of Biomedical Engineering, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR 999077, China
| | - Shirui Zhao
- Department of Biomedical Engineering, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR 999077, China
| | - Mo Yang
- Department of Biomedical Engineering, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong SAR 999077, China
| | - Jun Yu
- Institute of Digestive Disease and Department of Medicine and Therapeutics, State Key Laboratory of Digestive Disease, Li Ka Shing Institute of Health Sciences, CUHK-Shenzhen Research Institute, The Chinese University of Hong Kong, Hong Kong SAR 999077, China
| | - Yi-Ping Ho
- Department of Biomedical Engineering, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR 999077, China.,Hong Kong Branch of CAS Center for Excellence in Animal Evolution and Genetics, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR 999077, China.,The Ministry of Education Key Laboratory of Regeneration Medicine, Shatin, New Territories, Hong Kong SAR 999077, China.,Centre for Novel Biomaterials, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR 999077, China
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9
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Wang J, Hahn S, Amstad E, Vogel N. Tailored Double Emulsions Made Simple. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2022; 34:e2107338. [PMID: 34706112 DOI: 10.1002/adma.202107338] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Revised: 10/22/2021] [Indexed: 06/13/2023]
Abstract
Double emulsions, such as water-in-oil-in-water droplets, are important material platforms for conducting fundamental research and for technological applications. To date, well-defined double-emulsion droplets consisting of a single water core and a thin oil shell can be exclusively formed with sophisticated microfluidic devices. The fabrication, preparation, and operation of such devices is challenging, which reduces the availability of tailored double emulsions to a limited community of experts. Here, a simple method is introduced to produce single-core double emulsions with high yield in large quantities, using a vortex mixer. Utilizing the density difference between the dispersed droplet and the continuous phase, this two-step emulsification method can achieve very small core droplet diameters below 10 μm and ultrathin shells with thicknesses below 1 μm. A detailed picture of the formation mechanism is provided and it is demonstrated that the process can be extended to produce multishell and multicore emulsions. Finally, its application is demonstrated to produce structurally colored colloidal supraparticles with unprecedented uniformity and yield. The method allows the creation of tailored double emulsions with minimal time, cost, effort, and expertise, and may widen its application to nonspecialized scientific communities.
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Affiliation(s)
- Junwei Wang
- Institute of Particle Technology, Friedrich-Alexander University Erlangen-Nürnberg, 91058, Erlangen, Germany
| | - Simon Hahn
- Institute of Particle Technology, Friedrich-Alexander University Erlangen-Nürnberg, 91058, Erlangen, Germany
| | - Esther Amstad
- Institute of Materials, École Polytechnique Fédérale de Lausanne, Lausanne, 1015, Switzerland
| | - Nicolas Vogel
- Institute of Particle Technology, Friedrich-Alexander University Erlangen-Nürnberg, 91058, Erlangen, Germany
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10
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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: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 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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11
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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: 11] [Impact Index Per Article: 3.7] [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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12
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Huang H, Belwal T, Li L, Xu Y, Zou L, Lin X, Luo Z. Amphiphilic and Biocompatible DNA Origami-Based Emulsion Formation and Nanopore Release for Anti-Melanogenesis Therapy. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2021; 17:e2104831. [PMID: 34608748 DOI: 10.1002/smll.202104831] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Revised: 09/13/2021] [Indexed: 06/13/2023]
Abstract
Programmable engineered DNA origami provides infinite possibilities for customizing nanostructures with controllable precision and configurable functionality. Here, a strategy for fabricating an amphiphilic triangular DNA origami with a central nanopore that integrates phase-stabilizing, porous-gated, and affinity-delivering effects is presented. By introducing the DNA origami as a single-component surfactant, the water-in-oil-in-water (W/O/W) emulsion is effectively stabilized with decreased interfacial tension. Microscopic observation validates the attachment of the DNA origami onto the water-in-oil and oil-in-water interfaces. Furthermore, fluorescence studies and molecular docking simulations indicate the binding interactions of DNA origami with arbutin and coumaric acid at docking sites within central nanopores. These central nanopores are functionalized as molecular gates and affinity-based scaffold for the zero-order release of arbutin and coumaric acid at a constant rate regardless of concentration gradient throughout the whole releasing period. In vivo zebrafish results illustrate the advantages of this zero-order release for anti-melanogenesis therapy over direct exposure or Fickian diffusion. The DNA origami-based W/O/W emulsion presents anti-melanogenic effects against UV-B exposure without cardiotoxicity or motor toxicity. These results demonstrate that this non-toxic amphiphilic triangular DNA origami is capable of solely stabilizing the W/O/W emulsion as well as serving as nanopore gates and affinity-based scaffold for constant release.
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Affiliation(s)
- Hao Huang
- Key Laboratory of Agro-Products Postharvest Handling of Ministry of Agriculture and Rural Affairs, National-Local Joint Engineering Laboratory of Intelligent Food Technology and Equipment, Zhejiang Key Laboratory for Agro-Food Processing, College of Biosystems Engineering and Food Science, Zhejiang University, Hangzhou, 310058, China
| | - Tarun Belwal
- Key Laboratory of Agro-Products Postharvest Handling of Ministry of Agriculture and Rural Affairs, National-Local Joint Engineering Laboratory of Intelligent Food Technology and Equipment, Zhejiang Key Laboratory for Agro-Food Processing, College of Biosystems Engineering and Food Science, Zhejiang University, Hangzhou, 310058, China
| | - Li Li
- Key Laboratory of Agro-Products Postharvest Handling of Ministry of Agriculture and Rural Affairs, National-Local Joint Engineering Laboratory of Intelligent Food Technology and Equipment, Zhejiang Key Laboratory for Agro-Food Processing, College of Biosystems Engineering and Food Science, Zhejiang University, Hangzhou, 310058, China
| | - Yanqun Xu
- Key Laboratory of Agro-Products Postharvest Handling of Ministry of Agriculture and Rural Affairs, National-Local Joint Engineering Laboratory of Intelligent Food Technology and Equipment, Zhejiang Key Laboratory for Agro-Food Processing, College of Biosystems Engineering and Food Science, Zhejiang University, Hangzhou, 310058, China
| | - Ligen Zou
- Hangzhou Academy of Agricultural Sciences, Hangzhou, 310024, China
| | - Xingyu Lin
- Key Laboratory of Agro-Products Postharvest Handling of Ministry of Agriculture and Rural Affairs, National-Local Joint Engineering Laboratory of Intelligent Food Technology and Equipment, Zhejiang Key Laboratory for Agro-Food Processing, College of Biosystems Engineering and Food Science, Zhejiang University, Hangzhou, 310058, China
- Ningbo Research Institute, Zhejiang University, Ningbo, 315100, China
| | - Zisheng Luo
- Key Laboratory of Agro-Products Postharvest Handling of Ministry of Agriculture and Rural Affairs, National-Local Joint Engineering Laboratory of Intelligent Food Technology and Equipment, Zhejiang Key Laboratory for Agro-Food Processing, College of Biosystems Engineering and Food Science, Zhejiang University, Hangzhou, 310058, China
- Ningbo Research Institute, Zhejiang University, Ningbo, 315100, China
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13
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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 DOI: 10.1039/d1lc00344e] [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
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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14
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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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15
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Stucki A, Jusková P, Nuti N, Schmitt S, Dittrich PS. Synchronized Reagent Delivery in Double Emulsions for Triggering Chemical Reactions and Gene Expression. SMALL METHODS 2021; 5:e2100331. [PMID: 34927870 DOI: 10.1002/smtd.202100331] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Revised: 05/21/2021] [Indexed: 06/14/2023]
Abstract
Microfluidic methods for the formation of single and double emulsion (DE) droplets allow for the encapsulation and isolation of reactants inside nanoliter compartments. Such methods have greatly enhanced the toolbox for high-throughput screening for cell or enzyme engineering and drug discovery. However, remaining challenges in the supply of reagents into these enclosed compartments limit the applicability of droplet microfluidics. Here, a strategy is introduced for on-demand delivery of reactants in DEs. Lipid vesicles are used as reactant carriers, which are co-encapsulated in double emulsions and release their cargo upon addition of an external trigger, here the anionic surfactant sodium dodecyl sulfate (SDS). The reagent present inside the lipid vesicles stays isolated from the remaining content of the DE vessel until SDS enters the DE lumen and solubilizes the vesicles' lipid bilayer. The versatility of the method is demonstrated with two critical applications chosen as representative assays for high-throughput screening: the induction of gene expression in bacteria and the initiation of an enzymatic reaction. This method not only allows for the release of the lipid vesicle content inside DEs to be synchronized for all DEs but also for the release to be triggered at any desired time.
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Affiliation(s)
- Ariane Stucki
- Department of Biosystems Science and Engineering, Bioanalytics Group, ETH Zürich, Mattenstrasse 26, Basel, CH-4058, Switzerland
- NCCR Molecular Systems Engineering, BPR 1095, Mattenstrasse 24a, Basel, CH-4058, Switzerland
| | - Petra Jusková
- Department of Biosystems Science and Engineering, Bioanalytics Group, ETH Zürich, Mattenstrasse 26, Basel, CH-4058, Switzerland
| | - Nicola Nuti
- Department of Biosystems Science and Engineering, Bioanalytics Group, ETH Zürich, Mattenstrasse 26, Basel, CH-4058, Switzerland
| | - Steven Schmitt
- Department of Biosystems Science and Engineering, Bioprocess Laboratory, ETH Zürich, Mattenstrasse 26, Basel, CH-4058, Switzerland
| | - Petra S Dittrich
- Department of Biosystems Science and Engineering, Bioanalytics Group, ETH Zürich, Mattenstrasse 26, Basel, CH-4058, Switzerland
- NCCR Molecular Systems Engineering, BPR 1095, Mattenstrasse 24a, Basel, CH-4058, Switzerland
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16
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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. [DOI: 10.1002/ange.202016154] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Ariane Stucki
- Department of Biosystems Science and Engineering ETH Zurich Mattenstrasse 26 CH-4058 Basel Switzerland
- National Competence Center in Research (NCCR) Molecular Systems Engineering Basel Switzerland
| | - Jaicy Vallapurackal
- Department of Chemistry University of Basel Mattenstrasse 24a CH-4058 Basel Switzerland
- National Competence Center in Research (NCCR) Molecular Systems Engineering Basel Switzerland
| | - Thomas R. Ward
- Department of Chemistry University of Basel Mattenstrasse 24a CH-4058 Basel Switzerland
- National Competence Center in Research (NCCR) Molecular Systems Engineering Basel Switzerland
| | - Petra S. Dittrich
- Department of Biosystems Science and Engineering ETH Zurich Mattenstrasse 26 CH-4058 Basel Switzerland
- National Competence Center in Research (NCCR) Molecular Systems Engineering Basel Switzerland
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17
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Yang J, Tu R, Yuan H, Wang Q, Zhu L. Recent advances in droplet microfluidics for enzyme and cell factory engineering. Crit Rev Biotechnol 2021; 41:1023-1045. [PMID: 33730939 DOI: 10.1080/07388551.2021.1898326] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
Enzymes and cell factories play essential roles in industrial biotechnology for the production of chemicals and fuels. The properties of natural enzymes and cells often cannot meet the requirements of different industrial processes in terms of cost-effectiveness and high durability. To rapidly improve their properties and performances, laboratory evolution equipped with high-throughput screening methods and facilities is commonly used to tailor the desired properties of enzymes and cell factories, addressing the challenges of achieving high titer and the yield of the target products at high/low temperatures or extreme pH, in unnatural environments or in the presence of unconventional media. Droplet microfluidic screening (DMFS) systems have demonstrated great potential for exploring vast genetic diversity in a high-throughput manner (>106/h) for laboratory evolution and have been increasingly used in recent years, contributing to the identification of extraordinary mutants. This review highlights the recent advances in concepts and methods of DMFS for library screening, including the key factors in droplet generation and manipulation, signal sources for sensitive detection and sorting, and a comprehensive summary of success stories of DMFS implementation for engineering enzymes and cell factories during the past decade.
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Affiliation(s)
- Jianhua Yang
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China.,National Technology Innovation Center of Synthetic Biology, Tianjin, China
| | - Ran Tu
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China.,National Technology Innovation Center of Synthetic Biology, Tianjin, China
| | - Huiling Yuan
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China.,National Technology Innovation Center of Synthetic Biology, Tianjin, China
| | - Qinhong Wang
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China.,National Technology Innovation Center of Synthetic Biology, Tianjin, China
| | - Leilei Zhu
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China.,National Technology Innovation Center of Synthetic Biology, Tianjin, China
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18
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Werner JG, Lee H, Wiesner U, Weitz DA. Ordered Mesoporous Microcapsules from Double Emulsion Confined Block Copolymer Self-Assembly. ACS NANO 2021; 15:3490-3499. [PMID: 33556234 DOI: 10.1021/acsnano.1c00068] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Polymeric microcapsules with shells containing homogeneous pores with uniform diameter on the nanometer scale are reported. The mesoporous microcapsules are obtained from confined self-assembly of amphiphilic block copolymers with a selective porogen in the shell of water-in-oil-in-water double emulsion drops. The use of double emulsion drops as a liquid template enables the formation of homogeneous capsules of 100s of microns in diameter, with aqueous cores encapsulated in a shell membrane with a tunable thickness of 100s of nanometers to 10s of microns. Microcapsules with shells that exhibit an ordered gyroidal morphology and three-dimensionally connected mesopores are obtained from the triblock terpolymer poly(isoprene)-block-poly(styrene)-block-poly(4-vinylpyridine) coassembled with pentadecylphenol as a porogen. The bicontinuous shell morphology yields nanoporous paths connecting the inside to the outside of the microcapsule after porogen removal; by contrast, one-dimensional hexagonally packed cylindrical pores, obtained from a traditional diblock copolymer system with parallel alignment to the surface, would block transport through the shell. To enable the mesoporous microcapsules to withstand harsh conditions, such as exposure to organic solvents, without rupture of the shell, we develop a cross-linking method of the nanostructured triblock terpolymer shell after its self-assembly. The microcapsules exhibit pH-responsive permeability to polymeric solutes, demonstrating their potential as a filtration medium for actively tunable macromolecular separation and purification. Furthermore, we report a tunable dual-phase separation method to fabricate microcapsules with hierarchically porous shells that exhibit ordered mesoporous membrane walls within sponge-like micron-sized macropores to further control shell permeability.
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Affiliation(s)
- Jörg G Werner
- John A. Paulson School of Engineering and Applied Sciences, Harvard University, Cambridge, Massachusetts 02138, United States
- Department of Mechanical Engineering and Division of Materials Science and Engineering, Boston University, Boston, Massachusetts 02215, United States
| | - Hyomin Lee
- John A. Paulson School of Engineering and Applied Sciences, Harvard University, Cambridge, Massachusetts 02138, United States
- Department of Chemical Engineering, Pohang University of Science and Technology, Pohang, Gyeongbuk 37673, Republic of Korea
| | - Ulrich Wiesner
- Department of Materials Science and Engineering, Cornell University, Ithaca, New York 14850, United States
| | - David A Weitz
- John A. Paulson School of Engineering and Applied Sciences, Harvard University, Cambridge, Massachusetts 02138, United States
- Department of Physics, Harvard University, Cambridge, Massachusetts 02138, United States
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19
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Kessler M, Elettro H, Heimgartner I, Madasu S, Brakke KA, Gallaire F, Amstad E. Everything in its right place: controlling the local composition of hydrogels using microfluidic traps. LAB ON A CHIP 2020; 20:4572-4581. [PMID: 33146208 DOI: 10.1039/d0lc00691b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Many natural materials display locally varying compositions that impart unique mechanical properties to them which are still unmatched by manmade counterparts. Synthetic materials often possess structures that are well-defined on the molecular level, but poorly defined on the microscale. A fundamental difference that leads to this dissimilarity between natural and synthetic materials is their processing. Many natural materials are assembled from compartmentalized reagents that are released in well-defined and spatially confined regions, resulting in locally varying compositions. By contrast, synthetic materials are typically processed in bulk. Inspired by nature, we introduce a drop-based technique that enables the design of microstructured hydrogel sheets possessing tuneable locally varying compositions. This control in the spatial composition and microstructure is achieved with a microfluidic Hele-Shaw cell that possesses traps with varying trapping strengths to selectively immobilize different types of drops. This modular platform is not limited to the fabrication of hydrogels but can be employed for any material that can be processed into drops and solidified within them. It likely opens up new possibilities for the design of structured, load-bearing hydrogels, as well as for the next generation of soft actuators and sensors.
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Affiliation(s)
- Michael Kessler
- Soft Materials Laboratory, Institute of Materials, École Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland.
| | - Hervé Elettro
- Laboratory of Fluid Mechanics and Instabilities, Institute of Mechanical Engineering, École Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
| | - Isabelle Heimgartner
- Soft Materials Laboratory, Institute of Materials, École Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland.
| | - Soujanya Madasu
- Soft Materials Laboratory, Institute of Materials, École Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland.
| | - Kenneth A Brakke
- Mathematics Department, Susquehanna University, Selinsgrove, PA 17870, USA
| | - François Gallaire
- Laboratory of Fluid Mechanics and Instabilities, Institute of Mechanical Engineering, École Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
| | - Esther Amstad
- Soft Materials Laboratory, Institute of Materials, École Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland.
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20
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Benítez-Mateos AI, Zeballos N, Comino N, Moreno de Redrojo L, Randelovic T, López-Gallego F. Microcompartmentalized Cell-Free Protein Synthesis in Hydrogel μ-Channels. ACS Synth Biol 2020; 9:2971-2978. [PMID: 33170665 DOI: 10.1021/acssynbio.0c00462] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The rapid demand for protein-based molecules has stimulated much research on cell-free protein synthesis (CFPS); however, there are still many challenges in terms of cost-efficiency, process intensification, and sustainability. Herein, we describe the microcompartmentalization of CFPS of superfolded green fluorescent protein (sGFP) in alginate hydrogels, which were casted into a μ-channel device. CFPS was optimized for the microcompartmentalized environment and characterized in terms of synthesis yield. To extend the scope of this technology, the use of other biocompatible materials (collagen, laponite, and agarose) was explored. In addition, the diffusion of sGFP from the hydrogel microenvironment to the bulk was demonstrated, opening a promising opportunity for concurrent synthesis and delivery of proteins. Finally, we provide an application for this system: the CFPS of enzymes. The present design of the hydrogel μ-channel device may enhance the potential application of microcompartmentalized CFPS in biosensing, bioprototyping, and therapeutic development.
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Affiliation(s)
- Ana I. Benítez-Mateos
- Heterogeneous Biocatalysis Laboratory, CICbiomaGUNE, Paseo Miramón 182. Edificio empresarial “C”, 20014 San Sebastián, Spain
- Heterogeneous Biocatalysis Laboratory, Instituto de Síntesis Química y Catálisis Homogénea (iSQCH), CSIC-Universidad de Zaragoza, C/Pedro Cerbuna 12, 50009 Zaragoza, Spain
- Department of Chemistry and Biochemistry, University of Bern, Freiestrasse 3, 3012 Bern, Switzerland
| | - Nicoll Zeballos
- Heterogeneous Biocatalysis Laboratory, CICbiomaGUNE, Paseo Miramón 182. Edificio empresarial “C”, 20014 San Sebastián, Spain
| | - Natalia Comino
- Heterogeneous Biocatalysis Laboratory, CICbiomaGUNE, Paseo Miramón 182. Edificio empresarial “C”, 20014 San Sebastián, Spain
| | - Lucía Moreno de Redrojo
- Heterogeneous Biocatalysis Laboratory, Instituto de Síntesis Química y Catálisis Homogénea (iSQCH), CSIC-Universidad de Zaragoza, C/Pedro Cerbuna 12, 50009 Zaragoza, Spain
| | - Teodora Randelovic
- Tissue MicroEnvironment (TME) Lab, Institute for Health Research Aragón (IISA), Avda. San Juan Bosco 13, 50009 Zaragoza, Spain
- Aragon Institute of Engineering Research (I3A), University of Zaragoza, Mariano Escuillor s/n, 50018 Zaragoza, Spain
| | - Fernando López-Gallego
- Heterogeneous Biocatalysis Laboratory, CICbiomaGUNE, Paseo Miramón 182. Edificio empresarial “C”, 20014 San Sebastián, Spain
- Heterogeneous Biocatalysis Laboratory, Instituto de Síntesis Química y Catálisis Homogénea (iSQCH), CSIC-Universidad de Zaragoza, C/Pedro Cerbuna 12, 50009 Zaragoza, Spain
- IKERBASQUE, Basque Foundation for Science, 48009 Bilbao, Spain
- ARAID, Aragon Foundation for Science, 50009 Zaragoza, Spain
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21
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Abstract
The formation of spontaneous double emulsions is a peculiar phenomenon in emulsion systems. When compared to the traditional one-step and two-step methods for preparing double emulsions, spontaneous emulsification can not only steadily load uniform water droplets into an oil phase, but can also facilitate the preparation of emulsions with higher stability. However, the limited solubility of salts, which are typically used to modify osmotic pressure, in organic oils has inhibited the viability of this method for the preparation of W/O/W double emulsions. In this paper, a redox-driven spontaneous emulsification method is developed and investigated. Instead of employing oil-soluble salts, an oxidation reaction is implemented in the oil phase, which produces cation radicals and iodide counterions to generate osmotic pressure. Additionally, amphiphilic polymer chains are harnessed as stabilizers for the newly formed W/O interfaces. Various characterization methods have been used to elucidate the mechanism of both the oxidation reaction and the spontaneous formation of double emulsions.
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Affiliation(s)
- Ruiting Li
- Department of Chemistry, Renmin University of China, Beijing 100872, China
| | - Zhen Wang
- Department of Chemistry, Renmin University of China, Beijing 100872, China
| | - Xinglei Tao
- Department of Chemistry, Renmin University of China, Beijing 100872, China
| | - Jichen Jia
- Department of Chemistry, Renmin University of China, Beijing 100872, China
| | - Xiaodong Lian
- Department of Chemistry, Renmin University of China, Beijing 100872, China
| | - Yapei Wang
- Department of Chemistry, Renmin University of China, Beijing 100872, China
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22
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Payne EM, Holland-Moritz DA, Sun S, Kennedy RT. High-throughput screening by droplet microfluidics: perspective into key challenges and future prospects. LAB ON A CHIP 2020; 20:2247-2262. [PMID: 32500896 DOI: 10.1039/d0lc00347f] [Citation(s) in RCA: 73] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
In two decades of development, impressive strides have been made for automating basic laboratory operations in droplet-based microfluidics, allowing the emergence of a new form of high-throughput screening and experimentation in nanoliter to femtoliter volumes. Despite advancements in droplet storage, manipulation, and analysis, the field has not yet been widely adapted for many high-throughput screening (HTS) applications. Broad adoption and commercial development of these techniques require robust implementation of strategies for the stable storage, chemical containment, generation of libraries, sample tracking, and chemical analysis of these small samples. We discuss these challenges for implementing droplet HTS and highlight key strategies that have begun to address these concerns. Recent advances in the field leave us optimistic about the future prospects of this rapidly developing technology.
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Affiliation(s)
- Emory M Payne
- Department of Chemistry, University of Michigan, Ann Arbor, MI, USA.
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23
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Li J, Qiu Y, Zhang Z, Li C, Li S, Zhang W, Guo Z, Yao J, Zhou L. Heterogeneous modification of through-hole microwell chips for ultralow cross-contamination digital polymerase chain reaction. Analyst 2020; 145:3116-3124. [PMID: 32162628 DOI: 10.1039/d0an00220h] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Chip-based dPCR (cdPCR) with a physical boundary between micro-units allows for high parallelism, robustness and sensitivity. However, cross-contamination between micro-units is still a problem that affects the accuracy of results. To overcome this problem, we introduced a heterogeneous modification strategy by microcontact printing to prepare a through-hole microwell chip (TMC) with a hydrophobic exterior surface and hydrophilic interior surface. The modified TMC can reduce cross-contamination (sample residual rate (SRR) of (4.9 ± 1.5)%) by an efficient partitioning yield (unit filling rate (UFR) of (91.1 ± 2.2)%). The sample-residual properties of modified TMCs could be tuned by the reaction conditions. As the contact time increased, the surface CA of the TMC increased, which caused decreases of the SRR and UFR. However, prolonging the contact time to 25 s would cause a sharp reduction of the UFR. The modified TMCs with high UFRs were used for further dPCR studies. The fluorescence images of dPCR chips were collected by fluorescence microscopy and a self-developed optical system, followed by image processing and data statistics to obtain quantitative results. The copy number variation results of the surface hydrophobic TMC was closer to the true value compared to that of the hydrophilic TMC. The results indicated that the sample residue on the hydrophilic TMC would increase the number of positive points, which would cause false positives and clustering error. The absolute quantitative results of gradient dilution plasmid DNA of JAK2 gene using modified TMC also proved that heterogeneous modification made the quantitative results more accurate. The heterogeneous modified TMC is expected to be used for high-throughput, high-sensitivity and high-specificity biological analyses, such as circulating tumor DNA and cell analysis.
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Affiliation(s)
- Jinze Li
- CAS key Laboratory of Bio-medical Diagnostics, Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou 215163, China.
| | - Yajun Qiu
- CAS key Laboratory of Bio-medical Diagnostics, Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou 215163, China.
| | - Zhiqi Zhang
- CAS key Laboratory of Bio-medical Diagnostics, Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou 215163, China. and University of Science and Technology of China, Hefei 230026, China
| | - Chuanyu Li
- CAS key Laboratory of Bio-medical Diagnostics, Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou 215163, China. and University of Science and Technology of China, Hefei 230026, China
| | - Shuli Li
- CAS key Laboratory of Bio-medical Diagnostics, Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou 215163, China. and Shanghai University, Shanghai 200444, China
| | - Wei Zhang
- CAS key Laboratory of Bio-medical Diagnostics, Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou 215163, China.
| | - Zhen Guo
- CAS key Laboratory of Bio-medical Diagnostics, Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou 215163, China.
| | - Jia Yao
- CAS key Laboratory of Bio-medical Diagnostics, Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou 215163, China. and Soochow University, Suzhou 215163, China
| | - Lianqun Zhou
- CAS key Laboratory of Bio-medical Diagnostics, Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou 215163, China.
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24
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Laohakunakorn N, Grasemann L, Lavickova B, Michielin G, Shahein A, Swank Z, Maerkl SJ. Bottom-Up Construction of Complex Biomolecular Systems With Cell-Free Synthetic Biology. Front Bioeng Biotechnol 2020; 8:213. [PMID: 32266240 PMCID: PMC7105575 DOI: 10.3389/fbioe.2020.00213] [Citation(s) in RCA: 60] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2020] [Accepted: 03/03/2020] [Indexed: 12/16/2022] Open
Abstract
Cell-free systems offer a promising approach to engineer biology since their open nature allows for well-controlled and characterized reaction conditions. In this review, we discuss the history and recent developments in engineering recombinant and crude extract systems, as well as breakthroughs in enabling technologies, that have facilitated increased throughput, compartmentalization, and spatial control of cell-free protein synthesis reactions. Combined with a deeper understanding of the cell-free systems themselves, these advances improve our ability to address a range of scientific questions. By mastering control of the cell-free platform, we will be in a position to construct increasingly complex biomolecular systems, and approach natural biological complexity in a bottom-up manner.
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Affiliation(s)
- Nadanai Laohakunakorn
- School of Biological Sciences, Institute of Quantitative Biology, Biochemistry, and Biotechnology, University of Edinburgh, Edinburgh, United Kingdom
| | - Laura Grasemann
- School of Engineering, Institute of Bioengineering, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Barbora Lavickova
- School of Engineering, Institute of Bioengineering, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Grégoire Michielin
- School of Engineering, Institute of Bioengineering, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Amir Shahein
- School of Engineering, Institute of Bioengineering, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Zoe Swank
- School of Engineering, Institute of Bioengineering, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Sebastian J. Maerkl
- School of Engineering, Institute of Bioengineering, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
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Holland-Moritz DA, Wismer MK, Mann BF, Farasat I, Devine P, Guetschow ED, Mangion I, Welch CJ, Moore JC, Sun S, Kennedy RT. Mass Activated Droplet Sorting (MADS) Enables High-Throughput Screening of Enzymatic Reactions at Nanoliter Scale. Angew Chem Int Ed Engl 2020; 59:4470-4477. [PMID: 31868984 DOI: 10.1002/anie.201913203] [Citation(s) in RCA: 87] [Impact Index Per Article: 21.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2019] [Revised: 11/21/2019] [Indexed: 01/02/2023]
Abstract
Microfluidic droplet sorting enables the high-throughput screening and selection of water-in-oil microreactors at speeds and volumes unparalleled by traditional well-plate approaches. Most such systems sort using fluorescent reporters on modified substrates or reactions that are rarely industrially relevant. We describe a microfluidic system for high-throughput sorting of nanoliter droplets based on direct detection using electrospray ionization mass spectrometry (ESI-MS). Droplets are split, one portion is analyzed by ESI-MS, and the second portion is sorted based on the MS result. Throughput of 0.7 samples s-1 is achieved with 98 % accuracy using a self-correcting and adaptive sorting algorithm. We use the system to screen ≈15 000 samples in 6 h and demonstrate its utility by sorting 25 nL droplets containing transaminase expressed in vitro. Label-free ESI-MS droplet screening expands the toolbox for droplet detection and recovery, improving the applicability of droplet sorting to protein engineering, drug discovery, and diagnostic workflows.
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Affiliation(s)
| | - Michael K Wismer
- Scientific Engineering and Design, Merck & Co., Inc., 2000 Galloping Hill Road, Kenilworth, NJ, 07033, USA
| | - Benjamin F Mann
- Process Research and Development, Merck & Co., Inc., 126 E. Lincoln Ave, Rahway, NJ, 07065, USA
| | - Iman Farasat
- Janssen R&D, 1400 McKean Rd., Spring House, PA, 19477, USA
| | - Paul Devine
- Process Research and Development, Merck & Co., Inc., 126 E. Lincoln Ave, Rahway, NJ, 07065, USA
| | - Erik D Guetschow
- Process Research and Development, Merck & Co., Inc., 126 E. Lincoln Ave, Rahway, NJ, 07065, USA
| | - Ian Mangion
- Process Research and Development, Merck & Co., Inc., 126 E. Lincoln Ave, Rahway, NJ, 07065, USA
| | | | - Jeffrey C Moore
- Process Research and Development, Merck & Co., Inc., 126 E. Lincoln Ave, Rahway, NJ, 07065, USA
| | - Shuwen Sun
- Process Research and Development, Merck & Co., Inc., 126 E. Lincoln Ave, Rahway, NJ, 07065, USA
| | - Robert T Kennedy
- Dept. of Chemistry, University of Michigan, 930 N University, Ann Abor, MI, 48109, USA
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Holland‐Moritz DA, Wismer MK, Mann BF, Farasat I, Devine P, Guetschow ED, Mangion I, Welch CJ, Moore JC, Sun S, Kennedy RT. Mass Activated Droplet Sorting (MADS) Enables High‐Throughput Screening of Enzymatic Reactions at Nanoliter Scale. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.201913203] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
| | - Michael K. Wismer
- Scientific Engineering and Design Merck & Co., Inc. 2000 Galloping Hill Road Kenilworth NJ 07033 USA
| | - Benjamin F. Mann
- Process Research and Development Merck & Co., Inc. 126 E. Lincoln Ave Rahway NJ 07065 USA
| | - Iman Farasat
- Janssen R&D 1400 McKean Rd. Spring House PA 19477 USA
| | - Paul Devine
- Process Research and Development Merck & Co., Inc. 126 E. Lincoln Ave Rahway NJ 07065 USA
| | - Erik D. Guetschow
- Process Research and Development Merck & Co., Inc. 126 E. Lincoln Ave Rahway NJ 07065 USA
| | - Ian Mangion
- Process Research and Development Merck & Co., Inc. 126 E. Lincoln Ave Rahway NJ 07065 USA
| | | | - Jeffrey C. Moore
- Process Research and Development Merck & Co., Inc. 126 E. Lincoln Ave Rahway NJ 07065 USA
| | - Shuwen Sun
- Process Research and Development Merck & Co., Inc. 126 E. Lincoln Ave Rahway NJ 07065 USA
| | - Robert T. Kennedy
- Dept. of Chemistry University of Michigan 930 N University Ann Abor MI 48109 USA
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Ong ILH, Amstad E. Selectively Permeable Double Emulsions. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2019; 15:e1903054. [PMID: 31517446 DOI: 10.1002/smll.201903054] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/12/2019] [Revised: 08/12/2019] [Indexed: 06/10/2023]
Abstract
Natural organisms are made of different types of microcompartments, many of which are enclosed by cell membranes. For these organisms to display a proper function, the microcompartments must be selectively permeable. For example, cell membranes are typically permeable toward small, uncharged molecules such as water, selected nutrients, and cell signaling molecules, but impermeable toward many larger biomolecules. Here, it is reported for the first time dynamic compartments, namely surfactant-stabilized double emulsions, that display selective and tunable permeability. Selective permeability is imparted to double emulsions by stabilizing them with catechol-functionalized surfactants that transport molecules across the oil shell of double emulsions only if they electrostatically or hydrophobically attract encapsulants. These double emulsions are employed as semipermeable picoliter-sized vessels to controllably perform complexation reactions inside picoliter-sized aqueous cores. This thus far unmet level of control over the transport of reagents across oil phases opens up new possibilities to use double emulsion drops as dynamic and selectively permeable microcompartments to initiate and maintain chemical and biochemical reactions in picoliter-sized cell-mimetic compartments.
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Affiliation(s)
- Irvine Lian Hao Ong
- Soft Materials Laboratory, Institute of Materials, École Polytechnique Fédérale de Lausanne, 1015, Lausanne, Switzerland
| | - Esther Amstad
- Soft Materials Laboratory, Institute of Materials, École Polytechnique Fédérale de Lausanne, 1015, Lausanne, Switzerland
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Etienne G, Ong ILH, Amstad E. Bioinspired Viscoelastic Capsules: Delivery Vehicles and Beyond. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2019; 31:e1808233. [PMID: 31081156 DOI: 10.1002/adma.201808233] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2018] [Revised: 04/01/2019] [Indexed: 06/09/2023]
Abstract
Microcapsules are often used as individually dispersed carriers of active ingredients to prolong their shelf life or to protect premature reactions with substances contained in the surrounding. This study goes beyond this application and employs microcapsules as principal building blocks of macroscopic 3D materials with well-defined granular structures. To achieve this goal and inspired by nature, capsules are fabricated from block-copolymer surfactants that are functionalized with catechols, a metal-coordinating motive. These surfactants self-assemble at the surface of emulsion drops where they are ionically cross-linked to form viscoelastic capsules that display a low permeability even toward small encapsulants. It is demonstrated that the combination of the mechanical strength, flexibility, and stickiness of the capsules enables their additive manufacturing into macroscopic granular structures. Thereby, they open up new opportunities for 3D printing of soft, self-healing materials composed of individual compartments that can be functionalized with different types of spatially separated reagents.
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Affiliation(s)
- Gianluca Etienne
- Soft Materials Laboratory, Institute of Materials, École Polytechnique Fédérale de Lausanne (EPFL), CH-1015, Lausanne, Switzerland
| | - Irvine Lian Hao Ong
- Soft Materials Laboratory, Institute of Materials, École Polytechnique Fédérale de Lausanne (EPFL), CH-1015, Lausanne, Switzerland
| | - Esther Amstad
- Soft Materials Laboratory, Institute of Materials, École Polytechnique Fédérale de Lausanne (EPFL), CH-1015, Lausanne, Switzerland
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