1
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Li Q, Lu J, Liu J, Li J, Zhang G, Du G, Chen J. High-throughput droplet microfluidics screening and genome sequencing analysis for improved amylase-producing Aspergillus oryzae. BIOTECHNOLOGY FOR BIOFUELS AND BIOPRODUCTS 2023; 16:185. [PMID: 38031105 PMCID: PMC10685594 DOI: 10.1186/s13068-023-02437-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2023] [Accepted: 11/21/2023] [Indexed: 12/01/2023]
Abstract
BACKGROUND The exceptional protein secretion capacity, intricate post-translational modification processes, and inherent safety features of A. oryzae make it a promising expression system. However, heterologous protein expression levels of existing A. oryzae species cannot meet the requirement for industrial-scale production. Therefore, establishing an efficient screening technology is significant for the development of the A. oryzae expression system. RESULTS In this work, a high-throughput screening method suitable for A. oryzae has been established by combining the microfluidic system and flow cytometry. Its screening efficiency can reach 350 droplets per minute. The diameter of the microdroplet was enlarged to 290 µm to adapt to the polar growth of A. oryzae hyphae. Through enrichment and screening from approximately 450,000 droplets within 2 weeks, a high-producing strain with α-amylase increased by 6.6 times was successfully obtained. Furthermore, 29 mutated genes were identified by genome resequencing of high-yield strains, with 15 genes subjected to editing and validation. Two genes may individually influence α-amylase expression in A. oryzae by affecting membrane-associated multicellular processes and regulating the transcription of related genes. CONCLUSIONS The developed high-throughput screening strategy provides a reference for other filamentous fungi and Streptomyces. Besides, the strains with different excellent characteristics obtained by efficient screening can also provide materials for the analysis of genetic and regulatory mechanisms in the A. oryzae expression system.
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Affiliation(s)
- Qinghua Li
- Science Center for Future Foods, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, Jiangsu, China
- National Engineering Research Center for Cereal Fermentation and Food Biomanufacturing, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, Jiangsu, China
| | - Jinchang Lu
- Science Center for Future Foods, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, Jiangsu, China
- National Engineering Research Center for Cereal Fermentation and Food Biomanufacturing, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, Jiangsu, China
| | - Jingya Liu
- Science Center for Future Foods, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, Jiangsu, China
- National Engineering Research Center for Cereal Fermentation and Food Biomanufacturing, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, Jiangsu, China
| | - Jianghua Li
- Science Center for Future Foods, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, Jiangsu, China
- School of Biotechnology and Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, Jiangsu, China
| | - Guoqiang Zhang
- Science Center for Future Foods, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, Jiangsu, China.
- National Engineering Research Center for Cereal Fermentation and Food Biomanufacturing, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, Jiangsu, China.
| | - Guocheng Du
- Science Center for Future Foods, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, Jiangsu, China
- School of Biotechnology and Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, Jiangsu, China
- The Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, Jiangsu, China
| | - Jian Chen
- Science Center for Future Foods, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, Jiangsu, China
- National Engineering Research Center for Cereal Fermentation and Food Biomanufacturing, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, Jiangsu, China
- School of Biotechnology and Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, Jiangsu, China
- The Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, Jiangsu, China
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2
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Ladeveze S, Zurek PJ, Kaminski TS, Emond S, Hollfelder F. Versatile Product Detection via Coupled Assays for Ultrahigh-Throughput Screening of Carbohydrate-Active Enzymes in Microfluidic Droplets. ACS Catal 2023; 13:10232-10243. [PMID: 37560191 PMCID: PMC10407846 DOI: 10.1021/acscatal.3c01609] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2023] [Revised: 06/06/2023] [Indexed: 08/11/2023]
Abstract
Enzyme discovery and directed evolution are the two major contemporary approaches for the improvement of industrial processes by biocatalysis in various fields. Customization of catalysts for improvement of single enzyme reactions or de novo reaction development is often complex and tedious. The success of screening campaigns relies on the fraction of sequence space that can be sampled, whether for evolving a particular enzyme or screening metagenomes. Ultrahigh-throughput screening (uHTS) based on in vitro compartmentalization in water-in-oil emulsion of picoliter droplets generated in microfluidic systems allows screening rates >1 kHz (or >107 per day). Screening for carbohydrate-active enzymes (CAZymes) catalyzing biotechnologically valuable reactions in this format presents an additional challenge because the released carbohydrates are difficult to monitor in high throughput. Activated substrates with large optically active hydrophobic leaving groups provide a generic optical readout, but the molecular recognition properties of sugars will be altered by the incorporation of such fluoro- or chromophores and their typically higher reactivity, as leaving groups with lowered pKa values compared to native substrates make the observation of promiscuous reactions more likely. To overcome these issues, we designed microdroplet assays in which optically inactive carbohydrate products are made visible by specific cascades: the primary reaction of an unlabeled substrate leads to an optical signal downstream. Successfully implementing such assays at the picoliter droplet scale allowed us to detect glucose, xylose, glucuronic acid, and arabinose as final products of complex oligosaccharide degradation by glycoside hydrolases by absorbance measurements. Enabling the use of uHTS for screening CAZyme reactions that have been thus far elusive will chart a route toward faster and easier development of specific and efficient biocatalysts for biovalorization, directing enzyme discovery by challenging catalysts for reaction with natural rather than model substrates.
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Affiliation(s)
| | - Paul J. Zurek
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge CB21GA, U.K.
| | | | | | - Florian Hollfelder
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge CB21GA, U.K.
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3
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Kim IJ, Jeong D, Kim SR. Upstream processes of citrus fruit waste biorefinery for complete valorization. BIORESOURCE TECHNOLOGY 2022; 362:127776. [PMID: 35970501 DOI: 10.1016/j.biortech.2022.127776] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Revised: 08/08/2022] [Accepted: 08/09/2022] [Indexed: 06/15/2023]
Abstract
Citrus fruit waste (CW) is a useful biomass and its valorization into fuels and biochemicals has received much attention. For economic feasibility, increased efficiency of the preceding extraction and enzyme saccharification processes is necessary. However, at present, there is a lack of systematic reviews addressing these two integral upstream processes in concert for CW biorefinery. Here, the state-of-the-art advancements in enzyme extraction and saccharification processes-using which relevant essential oils, flavonoids, and sugars can be obtained-are reviewed. Specifically, the extraction options for two commercially available CW-derived products, essential oils and pectin, are discussed. With respect to enzyme saccharification, the use of an undefined commercial mixture routinely results in suboptimal sugar production. In this respect, applicable strategies for enzyme mixture customization are suggested for maximizing the hydrolytic efficiency of CW. The enzyme degradation system for CW-derived carbohydrates and its extensive application for sugar production are also discussed.
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Affiliation(s)
- In Jung Kim
- Department of Applied Biosciences, Graduate School, Kyungpook National University, Daegu 41566, Korea
| | - Deokyeol Jeong
- School of Food Science and Biotechnology, Kyungpook National University, Daegu 41566, Korea
| | - Soo Rin Kim
- School of Food Science and Biotechnology, Kyungpook National University, Daegu 41566, Korea; Research Institute of Tailored Food Technology, Kyungpook National University, Daegu 41566, Korea.
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4
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Davis AN, Samlali K, Kapadia JB, Perreault J, Shih SCC, Kharma N. Digital Microfluidics Chips for the Execution and Real-Time Monitoring of Multiple Ribozymatic Cleavage Reactions. ACS OMEGA 2021; 6:22514-22524. [PMID: 34514224 PMCID: PMC8427639 DOI: 10.1021/acsomega.1c00239] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/18/2021] [Accepted: 07/22/2021] [Indexed: 06/08/2023]
Abstract
In this paper, we describe the design and performance of two digital microfluidics (DMF) chips capable of executing multiple ribozymatic reactions, with proper controls, in response to short single-stranded DNA inducers. Since the fluorescence output of a reaction is measurable directly from the chip, without the need for gel electrophoresis, a complete experiment involving up to eight reactions (per chip) can be carried out reliably, relatively quickly, and efficiently. The ribozymes can also be used as biosensors of the concentration of oligonucleotide inputs, with high sensitivity, low limits of quantification and of detection, and excellent signal-to-noise ratio. The presented chips are readily usable devices that can be used to automate, speed up, and reduce the costs of ribozymatic reaction experiments.
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Affiliation(s)
- Alen N. Davis
- Department
of Electrical and Computer Engineering, Concordia University, Montreal, Québec H3G 1M8, Canada
| | - Kenza Samlali
- Department
of Electrical and Computer Engineering, Concordia University, Montreal, Québec H3G 1M8, Canada
- Centre
for Applied Synthetic Biology, Concordia
University, Montréal, Québec H4B 1R6, Canada
| | - Jay B. Kapadia
- Department
of Electrical and Computer Engineering, Concordia University, Montreal, Québec H3G 1M8, Canada
| | - Jonathan Perreault
- Centre
for Applied Synthetic Biology, Concordia
University, Montréal, Québec H4B 1R6, Canada
- Armand-Frappier
Health Biotechnology Center, Institut national
de la recherche scientifique, Laval, Québec H7V 1B7, Canada
| | - Steve C. C. Shih
- Department
of Electrical and Computer Engineering, Concordia University, Montreal, Québec H3G 1M8, Canada
- Centre
for Applied Synthetic Biology, Concordia
University, Montréal, Québec H4B 1R6, Canada
- Department
of Biology, Concordia University, Montréal, Québec H4B 1R6, Canada
| | - Nawwaf Kharma
- Department
of Electrical and Computer Engineering, Concordia University, Montreal, Québec H3G 1M8, Canada
- Centre
for Applied Synthetic Biology, Concordia
University, Montréal, Québec H4B 1R6, Canada
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5
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Robotics for enzyme technology: innovations and technological perspectives. Appl Microbiol Biotechnol 2021; 105:4089-4097. [PMID: 33970318 DOI: 10.1007/s00253-021-11302-1] [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: 12/12/2020] [Revised: 04/09/2021] [Accepted: 04/17/2021] [Indexed: 10/21/2022]
Abstract
The use of robotics in the life science sector has created a considerable and significant impact on a wide range of research areas, including enzyme technology due to their immense applications in enzyme and microbial engineering as an indispensable tool in high-throughput screening applications. Scientists are experiencing the advanced applications of various biological robots (nanobots), fabricated based on bottom-up or top-down approaches for making nanotechnology scaffolds. Nanobots and enzyme-powered nanomotors are particularly attractive because they are self-propelled vehicles, which consume biocompatible fuels. These smart nanostructures are widely used as drug delivery systems for the efficient treatment of various diseases. This review gives insights into the escalating necessity of robotics and nanobots and their ever-widening applications in enzyme technology, including biofuel production and biomedical applications. It also offers brief insights into high-throughput robotic platforms that are currently being used in enzyme screening applications for monitoring and control of microbial growth conditions. KEY POINTS: • Robotics and their applications in biotechnology are highlighted. • Robotics for high-throughput enzyme screening and microbial engineering are described. • Nanobots and enzyme-powered nanomotors as controllable drug delivery systems are reviewed.
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6
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Samlali K, Ahmadi F, Quach ABV, Soffer G, Shih SCC. One Cell, One Drop, One Click: Hybrid Microfluidics for Mammalian Single Cell Isolation. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2020; 16:e2002400. [PMID: 32705796 DOI: 10.1002/smll.202002400] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Revised: 06/18/2020] [Indexed: 06/11/2023]
Abstract
Generating a stable knockout cell line is a complex process that can take several months to complete. In this work, a microfluidic method that is capable of isolating single cells in droplets, selecting successful edited clones, and expansion of these isoclones is introduced. Using a hybrid microfluidics method, droplets in channels can be individually addressed using a co-planar electrode system. In the hybrid microfluidics device, it is shown that single cells can be trapped and subsequently encapsulate them on demand into pL-sized droplets. Furthermore, droplets containing single cells are either released, kept in the traps, or merged with other droplets by the application of an electric potential to the electrodes that is actuated through an in-house user interface. This high precision control is used to successfully sort and recover single isoclones to establish monoclonal cell lines, which is demonstrated with a heterozygous NCI-H1299 lung squamous cell population resulting from loss-of-function eGFP and RAF1 gene knockout transfections.
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Affiliation(s)
- Kenza Samlali
- Department of Electrical and Computer Engineering, Concordia University, Montréal, Québec, H3G 1M8, Canada
- Centre for Applied Synthetic Biology, Concordia University, Montréal, Québec, H4B 1R6, Canada
| | - Fatemeh Ahmadi
- Department of Electrical and Computer Engineering, Concordia University, Montréal, Québec, H3G 1M8, Canada
- Centre for Applied Synthetic Biology, Concordia University, Montréal, Québec, H4B 1R6, Canada
| | - Angela B V Quach
- Centre for Applied Synthetic Biology, Concordia University, Montréal, Québec, H4B 1R6, Canada
- Department of Biology, Concordia University, Montréal, Québec, H4B 1R6, Canada
| | - Guy Soffer
- Department of Electrical and Computer Engineering, Concordia University, Montréal, Québec, H3G 1M8, Canada
- Centre for Applied Synthetic Biology, Concordia University, Montréal, Québec, H4B 1R6, Canada
| | - Steve C C Shih
- Department of Electrical and Computer Engineering, Concordia University, Montréal, Québec, H3G 1M8, Canada
- Centre for Applied Synthetic Biology, Concordia University, Montréal, Québec, H4B 1R6, Canada
- Department of Biology, Concordia University, Montréal, Québec, H4B 1R6, Canada
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7
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Babahosseini H, Padmanabhan S, Misteli T, DeVoe DL. A programmable microfluidic platform for multisample injection, discretization, and droplet manipulation. BIOMICROFLUIDICS 2020; 14:014112. [PMID: 32038741 PMCID: PMC7002170 DOI: 10.1063/1.5143434] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/26/2019] [Accepted: 01/26/2020] [Indexed: 05/03/2023]
Abstract
A programmable microfluidic platform enabling on-demand sampling, compartmentalization, and manipulation of multiple aqueous volumes is presented. The system provides random-access actuation of a microtrap array supporting selective discretization of picoliter volumes from multiple sample inputs. The platform comprises two interconnected chips, with parallel T-junctions and multiplexed microvalves within one chip enabling programmable injection of aqueous sample plugs, and nanoliter volumes transferred to a second microtrap array chip in which the plugs are actively discretized into picoliter droplets within a static array of membrane displacement actuators. The system employs two different multiplexer designs that reduce the number of input signals required for both sample injection and discretization. This versatile droplet-based technology offers flexible sample workflows and functionalities for the formation and manipulation of heterogeneous picoliter droplets, with particular utility for applications in biochemical synthesis and cell-based assays requiring flexible and programmable operation of parallel and multistep droplet processes. The platform is used here for the selective encapsulation of differentially labeled cells within a discrete droplet array.
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Affiliation(s)
| | - Supriya Padmanabhan
- Department of Chemical and Biomolecular Engineering, University of Maryland, College Park, Maryland 20742, USA
| | - Tom Misteli
- National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Don L. DeVoe
- Author to whom correspondence should be addressed:. Tel.: +1-301-405-8125
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8
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Menezes R, Dramé-Maigné A, Taly V, Rondelez Y, Gines G. Streamlined digital bioassays with a 3D printed sample changer. Analyst 2020; 145:572-581. [DOI: 10.1039/c9an01744e] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Off-chip sample changer device increase the sample throughput of droplet digital bioassays.
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Affiliation(s)
- Roberta Menezes
- Centre de Recherche des Cordeliers
- INSERM
- Sorbonne Université
- USPC
- Université Paris Descartes
| | - Adèle Dramé-Maigné
- Laboratoire Gulliver
- UMR7083 CNRS
- ESPCI Paris
- PSL Research University
- 75005 Paris
| | - Valérie Taly
- Centre de Recherche des Cordeliers
- INSERM
- Sorbonne Université
- USPC
- Université Paris Descartes
| | - Yannick Rondelez
- Laboratoire Gulliver
- UMR7083 CNRS
- ESPCI Paris
- PSL Research University
- 75005 Paris
| | - Guillaume Gines
- Laboratoire Gulliver
- UMR7083 CNRS
- ESPCI Paris
- PSL Research University
- 75005 Paris
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9
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Bui HK, Seo TS. A micrometer head integrated microfluidic device for facile droplet size control and automatic measurement of a droplet size. Electrophoresis 2019; 41:306-310. [PMID: 31785603 DOI: 10.1002/elps.201900350] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2019] [Revised: 11/20/2019] [Accepted: 11/20/2019] [Indexed: 11/07/2022]
Abstract
A novel microfluidic droplet generator is proposed, which can control the droplet size through turning an integrated micrometer head with ease, and the size of the produced micro-droplet can be automatically and real-time monitored by an open-sourced software and off-the-shelf hardware.
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Affiliation(s)
- Hoang Khang Bui
- Department of Chemical Engineering, College of Engineering, Kyung Hee University, Gyeonggi-do, Republic of Korea
| | - Tae Seok Seo
- Department of Chemical Engineering, College of Engineering, Kyung Hee University, Gyeonggi-do, Republic of Korea
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10
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Grimmer A, Chen X, Hamidović M, Haselmayr W, Ren CL, Wille R. Simulation before fabrication: a case study on the utilization of simulators for the design of droplet microfluidic networks. RSC Adv 2018; 8:34733-34742. [PMID: 35548635 PMCID: PMC9086924 DOI: 10.1039/c8ra05531a] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2018] [Accepted: 09/30/2018] [Indexed: 11/21/2022] Open
Abstract
The functional performance of passively operated droplet microfluidics is sensitive with respect to the dimensions of the channel network, the fabrication precision as well as the applied pressure because the entire network is coupled together. Especially, the local and global hydrodynamic resistance changes caused by droplets make the task to develop a robust microfluidic design challenging as plenty of interdependencies which all affect the intended behavior have to be considered by the designer. After the design, its functionality is usually validated by fabricating a prototype and testing it with physical experiments. In case that the functionality is not implemented as desired, the designer has to go back, revise the design, and repeat the fabrication as well as experiments. This current design process based on multiple iterations of refining and testing the design produces high costs (financially as well as in terms of time). In this work, we show how a significant amount of those costs can be avoided when applying simulation before fabrication. To this end, we demonstrate how simulations on the 1D circuit analysis model can help in the design process by means of a case study. Therefore, we compare the design process with and without using simulation. As a case study, we use a microfluidic network which is capable of trapping and merging droplets with different content on demand. The case study demonstrates how simulation can help to validate the derived design by considering all local and global hydrodynamic resistance changes. Moreover, the simulations even allow further exploration of different designs which have not been considered before due to the high costs. Simulating microfluidic networks allows to check a design even before first prototypes are realized.![]()
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Affiliation(s)
- Andreas Grimmer
- Institute for Integrated Circuits
- Johannes Kepler University Linz
- 4040 Linz
- Austria
| | - Xiaoming Chen
- Department of Mechanical and Mechatronics Engineering
- University of Waterloo
- Waterloo
- Canada
| | - Medina Hamidović
- Institute for Communications Engineering and RF-Systems
- Johannes Kepler University Linz
- 4040 Linz
- Austria
| | - Werner Haselmayr
- Institute for Communications Engineering and RF-Systems
- Johannes Kepler University Linz
- 4040 Linz
- Austria
| | - Carolyn L. Ren
- Department of Mechanical and Mechatronics Engineering
- University of Waterloo
- Waterloo
- Canada
| | - Robert Wille
- Institute for Integrated Circuits
- Johannes Kepler University Linz
- 4040 Linz
- Austria
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11
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Wang Z, Oppegard SC, Eddington DT, Cheng J. Effect of localized hypoxia on Drosophila embryo development. PLoS One 2017; 12:e0185267. [PMID: 28934338 PMCID: PMC5608372 DOI: 10.1371/journal.pone.0185267] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2017] [Accepted: 09/08/2017] [Indexed: 01/09/2023] Open
Abstract
Environmental stress, such as oxygen deprivation, affects various cellular activities and developmental processes. In this study, we directly investigated Drosophila embryo development in vivo while cultured on a microfluidic device, which imposed an oxygen gradient on the developing embryos. The designed microfluidic device enabled both temporal and spatial control of the local oxygen gradient applied to the live embryos. Time-lapse live cell imaging was used to monitor the morphology and cellular migration patterns as embryos were placed in various geometries relative to the oxygen gradient. Results show that pole cell movement and tail retraction during Drosophila embryogenesis are highly sensitive to oxygen concentrations. Through modeling, we also estimated the oxygen permeability across the Drosophila embryonic layers for the first time using parameters measured on our oxygen control device.
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Affiliation(s)
- Zhinan Wang
- Department of Bioengineering, University of Illinois at Chicago, Chicago, Illinois, United States of America
| | - Shawn C. Oppegard
- Department of Bioengineering, University of Illinois at Chicago, Chicago, Illinois, United States of America
| | - David T. Eddington
- Department of Bioengineering, University of Illinois at Chicago, Chicago, Illinois, United States of America
| | - Jun Cheng
- Department of Bioengineering, University of Illinois at Chicago, Chicago, Illinois, United States of America
- * E-mail:
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12
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Shaikeea AJD, Basu S, Tyagi A, Sharma S, Hans R, Bansal L. Universal representations of evaporation modes in sessile droplets. PLoS One 2017; 12:e0184997. [PMID: 28915263 PMCID: PMC5600401 DOI: 10.1371/journal.pone.0184997] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2017] [Accepted: 09/04/2017] [Indexed: 11/18/2022] Open
Abstract
In this work, we provide a simple method to represent the contact line dynamics of an evaporating sessile droplet. As a droplet evaporates, two distinct contact line dynamics are observed. They are collectively known as modes of evaporation, namely Constant Contact Radius (CCR) and Constant Contact Angle (CCA). Another intermediate mode-Stick-Slide (SS) or mixed mode is also commonly observed. In this article, we are able to provide a graphical representation to these modes (named as MOE plot), which is visually more comprehensive especially for comparative studies. In addition, the method facilitates quantitative estimation for mode of evaporation (named as MOE fraction or MOEf), which doesn't exist in literature. Thus, various substrates can now be compared based on mode of evaporation (or contact line dynamics), which are governed by fluid property and surface characteristics.
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Affiliation(s)
| | - Saptarshi Basu
- Department of Mechanical Engineering, Indian Institute of Science, Bangalore, India
| | - Abhishek Tyagi
- Department of Mechanical Engineering, Indian Institute of Science, Bangalore, India
| | - Saksham Sharma
- Department of Mechanical Engineering, Indian Institute of Science, Bangalore, India
| | - Rishabh Hans
- Department of Mechanical Engineering, Indian Institute of Science, Bangalore, India
| | - Lalit Bansal
- Department of Mechanical Engineering, Indian Institute of Science, Bangalore, India
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13
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Qu X, Zhang H, Chen H, Aldalbahi A, Li L, Tian Y, Weitz DA, Pei H. Convection-Driven Pull-Down Assays in Nanoliter Droplets Using Scaffolded Aptamers. Anal Chem 2017; 89:3468-3473. [PMID: 28207249 DOI: 10.1021/acs.analchem.6b04475] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
One of the great challenges in cellular studies is to develop a rapid and biocompatible analytical tool for single-cell analysis. We report a rapid, DNA nanostructure-supported aptamer pull-down (DNaPull) assay under convective flux in a glass capillary for analyzing the contents of droplets with nano- or picoliter volumes. We have demonstrated that the scaffolded aptamer can greatly improve the efficiency of target molecules' pull down. The convective flux allows complete reaction in <5 min, which is an 18-fold improvement compared to purely diffusive flux (traditional model of the stationary case). This established DNaPull assay can serve as a rapid and sensitive analytical platform for analyzing a variety of bioactive molecules, including small molecules [ATP, limit of detecton (LOD) of 1 μM], a drug (cocaine, LOD of 1 μM), and a biomarker (thrombin, LOD of 0.1 nM). Significantly, the designed microfluidic device compartmentalizes live cells into nanoliter-sized droplets to present single-cell samples. As a proof of concept, we demonstrated that cellular molecules (ATP) from a discrete number of HNE1 cells (zero to five cells) lysed inside nanoliter-sized droplets can be analyzed using our DNaPull assay, in which the intracellular ATP level was estimated to be ∼3.4 mM. Given the rapid assay feature and single-cell sample analysis ability, we believe that our analytical platform of convection-driven DNaPull in a glass capillary can provide a new paradigm in biosensor design and will be valuable for single-cell analysis.
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Affiliation(s)
- Xiangmeng Qu
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes, School of Chemistry and Molecular Engineering, East China Normal University , 500 Dongchuan Road, Shanghai 200241, P. R. China.,Harvard John A. Paulson School of Engineering and Applied Sciences, Harvard University , Cambridge, Massachusetts 02138, United States
| | - Hongbo Zhang
- Harvard John A. Paulson School of Engineering and Applied Sciences, Harvard University , Cambridge, Massachusetts 02138, United States.,Division of Pharmaceutical Chemistry and Technology, Faculty of Pharmacy, University of Helsinki , FI-00014 Helsinki, Finland
| | - Hong Chen
- Pen-Tung Sah Institute of Micro-Nano Science and Technology, Xiamen University , Xiamen 361005, P. R. China
| | - Ali Aldalbahi
- Chemistry Department, King Saud University , Riyadh 11451, Saudi Arabia
| | - Li Li
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes, School of Chemistry and Molecular Engineering, East China Normal University , 500 Dongchuan Road, Shanghai 200241, P. R. China
| | - Yang Tian
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes, School of Chemistry and Molecular Engineering, East China Normal University , 500 Dongchuan Road, Shanghai 200241, P. R. China
| | - David A Weitz
- Harvard John A. Paulson School of Engineering and Applied Sciences, Harvard University , Cambridge, Massachusetts 02138, United States
| | - Hao Pei
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes, School of Chemistry and Molecular Engineering, East China Normal University , 500 Dongchuan Road, Shanghai 200241, P. R. China
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14
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Pinsolle A, Charmantray F, Hecquet L, Sarrazin F. Droplet millifluidics for kinetic study of transketolase. BIOMICROFLUIDICS 2016; 10:064103. [PMID: 27917251 PMCID: PMC5106428 DOI: 10.1063/1.4966619] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/15/2016] [Accepted: 10/18/2016] [Indexed: 06/06/2023]
Abstract
We present a continuous-flow reactor at the millifluidic scale coupled with an online, non-intrusive spectroscopic monitoring method for determining the kinetic parameters of an enzyme, transketolase (TK) used in biocatalysis for the synthesis of polyols by carboligation. The millifluidic system used is based on droplet flow, a well-established method for kinetic chemical data acquisition. The TK assay is based on the direct quantitative measurement of bicarbonate ions released during the transketolase-catalysed reaction in the presence of hydroxypyruvic acid as the donor, thanks to an irreversible reaction: bicarbonate ions react with phosphoenolpyruvate (PEP) in the presence of PEP carboxylase as the first auxiliary enzyme. The oxaloacetate formed is reduced to malate by NADH in the reaction catalysed by malate dehydrogenase as the second auxiliary enzyme. The extent of oxidation of NADH was measured by spectrophotometry at 340 nm. This system gives a direct, quantitative, generic method to evaluate the TK activity versus different substrates. We demonstrate the accuracy of this strategy to determine the enzymatic kinetic parameters and to study the substrate specificity of a thermostable TK from thermophilic microorganism Geobacillus stearothermophilus, offering promising prospects in biocatalysis. Millifluidic systems are useful in this regard as they can be used to rapidly evaluate the TK activity towards various substrates, and also different sets of conditions, identifying the optimal operating environment while minimizing resource consumption and ensuring high control over the operating conditions.
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Affiliation(s)
- A Pinsolle
- Laboratory of the Future (LOF) , SOLVAY/CNRS UMR 5258, 178 avenue du Docteur Schweitzer, F-33608 Pessac Cedex, France
| | | | | | - F Sarrazin
- Laboratory of the Future (LOF) , SOLVAY/CNRS UMR 5258, 178 avenue du Docteur Schweitzer, F-33608 Pessac Cedex, France
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15
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Tang MYH, Shum HC. One-step immunoassay of C-reactive protein using droplet microfluidics. LAB ON A CHIP 2016; 16:4359-4365. [PMID: 27738692 DOI: 10.1039/c6lc01121g] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/14/2023]
Abstract
We present a wash-free high-sensitivity immunoassay of C-reactive proteins with droplet microfluidics. Microbeads are encapsulated within droplets for the immunoassay, and the droplets are scanned by a fluorescence detection platform to quantify the amount of proteins captured on the microbeads. The limit of detection determined by our platform is 0.01 μg mL-1, which is ten times more sensitive than conventional high-sensitivity C-reactive protein assays. With the decrease in diffusion distance within droplets, the immunoassay requires only half of the time required for similar conventional approaches. This approach for carrying out immunoassays can potentially be applied to other biomarkers beyond C-reactive proteins.
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Affiliation(s)
- Matthew Y H Tang
- Department of Mechanical Engineering, University of Hong Kong, Pokfulam Road, Hong Kong, China.
| | - Ho Cheung Shum
- Department of Mechanical Engineering, University of Hong Kong, Pokfulam Road, Hong Kong, China. and HKU-Shenzhen Institute of Research and Innovation (HKU-SIRI), Shenzhen, Guangdong 518000, China.
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16
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Ferrer M, Martínez-Martínez M, Bargiela R, Streit WR, Golyshina OV, Golyshin PN. Estimating the success of enzyme bioprospecting through metagenomics: current status and future trends. Microb Biotechnol 2016; 9:22-34. [PMID: 26275154 PMCID: PMC4720405 DOI: 10.1111/1751-7915.12309] [Citation(s) in RCA: 127] [Impact Index Per Article: 15.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2015] [Revised: 06/26/2015] [Accepted: 07/02/2015] [Indexed: 12/01/2022] Open
Abstract
Recent reports have suggested that the establishment of industrially relevant enzyme collections from environmental genomes has become a routine procedure. Across the studies assessed, a mean number of approximately 44 active clones were obtained in an average size of approximately 53,000 clones tested using naïve screening protocols. This number could be significantly increased in shorter times when novel metagenome enzyme sequences obtained by direct sequencing are selected and subjected to high-throughput expression for subsequent production and characterization. The pre-screening of clone libraries by naïve screens followed by the pyrosequencing of the inserts allowed for a 106-fold increase in the success rate of identifying genes encoding enzymes of interest. However, a much longer time, usually on the order of years, is needed from the time of enzyme identification to the establishment of an industrial process. If the hit frequency for the identification of enzymes performing at high turnover rates under real application conditions could be increased while still covering a high natural diversity, the very expensive and time-consuming enzyme optimization phase would likely be significantly shortened. At this point, it is important to review the current knowledge about the success of fine-tuned naïve- and sequence-based screening protocols for enzyme selection and to describe the environments worldwide that have already been subjected to enzyme screen programmes through metagenomic tools. Here, we provide such estimations and suggest the current challenges and future actions needed before environmental enzymes can be successfully introduced into the market.
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Affiliation(s)
- Manuel Ferrer
- Institute of Catalysis, Consejo Superior de Investigaciones Científicas (CSIC), Marie Curie 2, 28049, Madrid, Spain
| | - Mónica Martínez-Martínez
- Institute of Catalysis, Consejo Superior de Investigaciones Científicas (CSIC), Marie Curie 2, 28049, Madrid, Spain
| | - Rafael Bargiela
- Institute of Catalysis, Consejo Superior de Investigaciones Científicas (CSIC), Marie Curie 2, 28049, Madrid, Spain
| | - Wolfgang R Streit
- Biozentrum Klein Flottbek, Universität Hamburg, Ohnhorststraße 18, D-22609, Hamburg, Germany
| | - Olga V Golyshina
- School of Biological Sciences, Bangor University, LL57 2UW, Gwynedd, UK
| | - Peter N Golyshin
- School of Biological Sciences, Bangor University, LL57 2UW, Gwynedd, UK
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17
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Shih SCC, Goyal G, Kim PW, Koutsoubelis N, Keasling JD, Adams PD, Hillson NJ, Singh AK. A Versatile Microfluidic Device for Automating Synthetic Biology. ACS Synth Biol 2015; 4:1151-64. [PMID: 26075958 DOI: 10.1021/acssynbio.5b00062] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
New microbes are being engineered that contain the genetic circuitry, metabolic pathways, and other cellular functions required for a wide range of applications such as producing biofuels, biobased chemicals, and pharmaceuticals. Although currently available tools are useful in improving the synthetic biology process, further improvements in physical automation would help to lower the barrier of entry into this field. We present an innovative microfluidic platform for assembling DNA fragments with 10× lower volumes (compared to that of current microfluidic platforms) and with integrated region-specific temperature control and on-chip transformation. Integration of these steps minimizes the loss of reagents and products compared to that with conventional methods, which require multiple pipetting steps. For assembling DNA fragments, we implemented three commonly used DNA assembly protocols on our microfluidic device: Golden Gate assembly, Gibson assembly, and yeast assembly (i.e., TAR cloning, DNA Assembler). We demonstrate the utility of these methods by assembling two combinatorial libraries of 16 plasmids each. Each DNA plasmid is transformed into Escherichia coli or Saccharomyces cerevisiae using on-chip electroporation and further sequenced to verify the assembly. We anticipate that this platform will enable new research that can integrate this automated microfluidic platform to generate large combinatorial libraries of plasmids and will help to expedite the overall synthetic biology process.
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Affiliation(s)
- Steve C. C. Shih
- Sandia National Laboratories, 7011 East Avenue, Livermore, California 94550, United States
| | - Garima Goyal
- Physical
Bioscience Division, Lawrence Berkeley National Laboratory, 1 Cyclotron
Road, Berkeley, California 94720, United States
| | - Peter W. Kim
- Sandia National Laboratories, 7011 East Avenue, Livermore, California 94550, United States
| | - Nicolas Koutsoubelis
- Physical
Bioscience Division, Lawrence Berkeley National Laboratory, 1 Cyclotron
Road, Berkeley, California 94720, United States
| | - Jay D. Keasling
- Physical
Bioscience Division, Lawrence Berkeley National Laboratory, 1 Cyclotron
Road, Berkeley, California 94720, United States
- Department of Chemical & Biomolecular Engineering, Department of Bioengineering, University of California, Berkeley, California 94720, United States
| | - Paul D. Adams
- Physical
Bioscience Division, Lawrence Berkeley National Laboratory, 1 Cyclotron
Road, Berkeley, California 94720, United States
| | - Nathan J. Hillson
- Physical
Bioscience Division, Lawrence Berkeley National Laboratory, 1 Cyclotron
Road, Berkeley, California 94720, United States
| | - Anup K. Singh
- Sandia National Laboratories, 7011 East Avenue, Livermore, California 94550, United States
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18
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19
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Malinowska KH, Rind T, Verdorfer T, Gaub HE, Nash MA. Quantifying Synergy, Thermostability, and Targeting of Cellulolytic Enzymes and Cellulosomes with Polymerization-Based Amplification. Anal Chem 2015; 87:7133-40. [DOI: 10.1021/acs.analchem.5b00936] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Klara H. Malinowska
- Lehrstuhl für Angewandte
Physik and Center for Nanoscience, Ludwig-Maximilians-Universität, 80799 Munich, Germany
| | - Thomas Rind
- Lehrstuhl für Angewandte
Physik and Center for Nanoscience, Ludwig-Maximilians-Universität, 80799 Munich, Germany
| | - Tobias Verdorfer
- Lehrstuhl für Angewandte
Physik and Center for Nanoscience, Ludwig-Maximilians-Universität, 80799 Munich, Germany
| | - Hermann E. Gaub
- Lehrstuhl für Angewandte
Physik and Center for Nanoscience, Ludwig-Maximilians-Universität, 80799 Munich, Germany
| | - Michael A. Nash
- Lehrstuhl für Angewandte
Physik and Center for Nanoscience, Ludwig-Maximilians-Universität, 80799 Munich, Germany
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20
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Usta OB, McCarty WJ, Bale S, Hegde M, Jindal R, Bhushan A, Golberg I, Yarmush ML. Microengineered cell and tissue systems for drug screening and toxicology applications: Evolution of in-vitro liver technologies. TECHNOLOGY 2015; 3:1-26. [PMID: 26167518 PMCID: PMC4494128 DOI: 10.1142/s2339547815300012] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/17/2023]
Abstract
The liver performs many key functions, the most prominent of which is serving as the metabolic hub of the body. For this reason, the liver is the focal point of many investigations aimed at understanding an organism's toxicological response to endogenous and exogenous challenges. Because so many drug failures have involved direct liver toxicity or other organ toxicity from liver generated metabolites, the pharmaceutical industry has constantly sought superior, predictive in-vitro models that can more quickly and efficiently identify problematic drug candidates before they incur major development costs, and certainly before they are released to the public. In this broad review, we present a survey and critical comparison of in-vitro liver technologies along a broad spectrum, but focus on the current renewed push to develop "organs-on-a-chip". One prominent set of conclusions from this review is that while a large body of recent work has steered the field towards an ever more comprehensive understanding of what is needed, the field remains in great need of several key advances, including establishment of standard characterization methods, enhanced technologies that mimic the in-vivo cellular environment, and better computational approaches to bridge the gap between the in-vitro and in-vivo results.
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Affiliation(s)
- O B Usta
- Center for Engineering in Medicine at Massachusetts General Hospital, Harvard Medical School and Shriners Hospital for Children, 51 Blossom St., Boston, MA 02114, USA
| | - W J McCarty
- Center for Engineering in Medicine at Massachusetts General Hospital, Harvard Medical School and Shriners Hospital for Children, 51 Blossom St., Boston, MA 02114, USA
| | - S Bale
- Center for Engineering in Medicine at Massachusetts General Hospital, Harvard Medical School and Shriners Hospital for Children, 51 Blossom St., Boston, MA 02114, USA
| | - M Hegde
- Center for Engineering in Medicine at Massachusetts General Hospital, Harvard Medical School and Shriners Hospital for Children, 51 Blossom St., Boston, MA 02114, USA
| | - R Jindal
- Center for Engineering in Medicine at Massachusetts General Hospital, Harvard Medical School and Shriners Hospital for Children, 51 Blossom St., Boston, MA 02114, USA
| | - A Bhushan
- Center for Engineering in Medicine at Massachusetts General Hospital, Harvard Medical School and Shriners Hospital for Children, 51 Blossom St., Boston, MA 02114, USA
| | - I Golberg
- Center for Engineering in Medicine at Massachusetts General Hospital, Harvard Medical School and Shriners Hospital for Children, 51 Blossom St., Boston, MA 02114, USA
| | - M L Yarmush
- Center for Engineering in Medicine at Massachusetts General Hospital, Harvard Medical School and Shriners Hospital for Children, 51 Blossom St., Boston, MA 02114, USA ; Department of Biomedical Engineering, Rutgers University, 599 Taylor Rd., Piscataway, NJ 08854, USA
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21
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Ng EX, Miller MA, Jing T, Lauffenburger DA, Chen CH. Low-volume multiplexed proteolytic activity assay and inhibitor analysis through a pico-injector array. LAB ON A CHIP 2015; 15:1153-1159. [PMID: 25553996 DOI: 10.1039/c4lc01162g] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Secreted active proteases, from families of enzymes such as matrix metalloproteinases (MMPs) and ADAMs (a disintegrin and metalloproteinases), participate in diverse pathological processes. To simultaneously measure multiple specific protease activities, a series of parallel enzyme reactions combined with a series of inhibitor analyses for proteolytic activity matrix analysis (PrAMA) are essential but limited due to the sample quantity requirements and the complexity of performing multiple reactions. To address these issues, we developed a pico-injector array to generate 72 different reactions in picoliter-volume droplets by controlling the sequence of combinational injections, which allowed simultaneous recording of a wide range of multiple enzyme reactions and measurement of inhibitor effects using small sample volumes (~10 μL). Multiple MMP activities were simultaneously determined by 9 different substrates and 2 inhibitors using injections from a pico-injector array. Due to the advantages of inhibitor analysis, the MMP/ADAM activities of MDA-MB-231, a breast cancer cell line, were characterized with high MMP-2, MMP-3 and ADAM-10 activity. This platform could be customized for a wide range of applications that also require multiple reactions with inhibitor analysis to enhance the sensitivity by encapsulating different chemical sensors.
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Affiliation(s)
- Ee Xien Ng
- Department of Biomedical Engineering, National University of Singapore, 9 Engineering Drive 1, Singapore 117575, Singapore.
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22
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Shih SCC, Gach PC, Sustarich J, Simmons BA, Adams PD, Singh S, Singh AK. A droplet-to-digital (D2D) microfluidic device for single cell assays. LAB ON A CHIP 2015; 15:225-36. [PMID: 25354549 DOI: 10.1039/c4lc00794h] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
We have developed a new hybrid droplet-to-digital microfluidic platform (D2D) that integrates droplet-in-channel microfluidics with digital microfluidics (DMF) for performing multi-step assays. This D2D platform combines the strengths of the two formats-droplets-in-channel for facile generation of droplets containing single cells, and DMF for on-demand manipulation of droplets including control of different droplet volumes (pL-μL), creation of a dilution series of ionic liquid (IL), and parallel single cell culturing and analysis for IL toxicity screening. This D2D device also allows for automated analysis that includes a feedback-controlled system for merging and splitting of droplets to add reagents, an integrated Peltier element for parallel cell culture at optimum temperature, and an impedance sensing mechanism to control the flow rate for droplet generation and preventing droplet evaporation. Droplet-in-channel is well-suited for encapsulation of single cells as it allows the careful manipulation of flow rates of aqueous phase containing cells and oil to optimize encapsulation. Once single cell containing droplets are generated, they are transferred to a DMF chip via a capillary where they are merged with droplets containing IL and cultured at 30 °C. The DMF chip, in addition to permitting cell culture and reagent (ionic liquid/salt) addition, also allows recovery of individual droplets for off-chip analysis such as further culturing and measurement of ethanol production. The D2D chip was used to evaluate the effect of IL/salt type (four types: NaOAc, NaCl, [C2mim] [OAc], [C2mim] [Cl]) and concentration (four concentrations: 0, 37.5, 75, 150 mM) on the growth kinetics and ethanol production of yeast and as expected, increasing IL concentration led to lower biomass and ethanol production. Specifically, [C2mim] [OAc] had inhibitory effects on yeast growth at concentrations 75 and 150 mM and significantly reduced their ethanol production compared to cells grown in other ILs/salts. The growth curve trends obtained by D2D matched conventional yeast culturing in microtiter wells, validating the D2D platform. We believe that our approach represents a generic platform for multi-step biochemical assays such as drug screening, digital PCR, enzyme assays, immunoassays and cell-based assays.
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Affiliation(s)
- Steve C C Shih
- Sandia National Laboratories, 7011 East Ave, Livermore, CA, USA.
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23
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Rhee M, Light YK, Yilmaz S, Adams PD, Saxena D, Meagher RJ, Singh AK. Pressure stabilizer for reproducible picoinjection in droplet microfluidic systems. LAB ON A CHIP 2014; 14:4533-9. [PMID: 25270338 PMCID: PMC4213212 DOI: 10.1039/c4lc00823e] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2023]
Abstract
Picoinjection is a promising technique to add reagents into pre-formed emulsion droplets on chip however, it is sensitive to pressure fluctuation, making stable operation of the picoinjector challenging. We present a chip architecture using a simple pressure stabilizer for consistent and highly reproducible picoinjection in multi-step biochemical assays with droplets. Incorporation of the stabilizer immediately upstream of a picoinjector or a combination of injectors greatly reduces pressure fluctuations enabling reproducible and effective picoinjection in systems where the pressure varies actively during operation. We demonstrate the effectiveness of the pressure stabilizer for an integrated platform for on-demand encapsulation of bacterial cells followed by picoinjection of reagents for lysing the encapsulated cells. The pressure stabilizer was also used for picoinjection of multiple displacement amplification (MDA) reagents to achieve genomic DNA amplification of lysed bacterial cells.
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Affiliation(s)
- Minsoung Rhee
- Sandia National Laboratories, Biotechnology and Bioengineering Department, Livermore, CA, USA.
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24
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Rendl M, Brandstetter T, Rühe J. Solid-phase extraction in segmented flow. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2014; 30:12804-12811. [PMID: 25300748 DOI: 10.1021/la502645z] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Two-phase flow systems are increasingly popular for miniaturized, high-throughput performance of analytical or chemical reactions. In this contribution, we extend a previously described method that allows to increase the range of applications of heterogeneous reactions in two-phase flow, i.e., reactions that rely on isolation and purification of the compound of interest for downstream analysis. Our concept is based on liquid plugs, which serve as miniaturized compartments for the analytical reactions. Purification of the target compound is achieved by extracting the analyte from the aqueous compartments using magnetic beads as solid carriers. In the present paper, we elucidate the influence of parameters such as the polarity of the liquid/liquid and solid/liquid interfaces, the magnetic forces and the fluidic conditions onto the extraction performance. The conditions for reliable extraction and purification of the target compounds are determined. Furthermore, we investigate how to facilitate breaking of the plugs through reduction of the surface tension of the solid/liquid interface. When a lower surface tension is employed, a smaller number of beads is required for the extraction process, which implies a higher sensitivity of the device. In addition, we generate channels with different surface chemistries, which are able to manipulate the flow of the two immiscible liquids. We describe a very simple way to generate such devices and show that we can achieve a transition from segmented flow of plugs to a side-by side flow of the two immiscible liquids, a key requirement for the purification of the compounds.
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Affiliation(s)
- Martin Rendl
- Laboratory for Chemistry and Physics of Interfaces, Department of Microsystems Engineering (IMTEK), University of Freiburg , Georges-Köhler-Allee 103, D-79110 Freiburg, Germany
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25
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Rhee M, Liu P, Meagher RJ, Light YK, Singh AK. Versatile on-demand droplet generation for controlled encapsulation. BIOMICROFLUIDICS 2014; 8:034112. [PMID: 25379072 PMCID: PMC4162415 DOI: 10.1063/1.4874715] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/18/2014] [Accepted: 04/23/2014] [Indexed: 05/11/2023]
Abstract
We present a droplet-based microfluidic system for performing bioassays requiring controlled analyte encapsulation by employing highly flexible on-demand droplet generation. On-demand droplet generation and encapsulation are achieved pneumatically using a microdispensing pump connected to a constant pressure source. The system generates single droplets to the collection route only when the pump is actuated with a designated pressure level and produces two-phase parallel flow to the waste route during the stand-by state. We analyzed the effect of actuation pressure on the stability and size of droplets and optimized conditions for generation of stable droplets over a wide pressure range. By increasing the duration of pump actuation, we could either trigger a short train of identical size droplets or generate a single larger droplet. We also investigated the methodology to control droplet contents by fine-tuning flow rates or implementing a resistance bridge between the pump and main channels. We demonstrated the integrated chip for on-demand mixing between two aqueous phases in droplets and on-demand encapsulation of Escherichia coli cells. Our unique on-demand feature for selective encapsulation is particularly appropriate for bioassays with extremely dilute samples, such as pathogens in a clinical sample, since it can significantly reduce the number of empty droplets that impede droplet collection and subsequent data analysis.
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Affiliation(s)
- Minsoung Rhee
- Sandia National Laboratories , Livermore, California 94550, USA
| | - Peng Liu
- Sandia National Laboratories , Livermore, California 94550, USA
| | | | - Yooli K Light
- Sandia National Laboratories , Livermore, California 94550, USA
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26
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Culbertson CT, Mickleburgh TG, Stewart-James SA, Sellens KA, Pressnall M. Micro total analysis systems: fundamental advances and biological applications. Anal Chem 2014; 86:95-118. [PMID: 24274655 PMCID: PMC3951881 DOI: 10.1021/ac403688g] [Citation(s) in RCA: 106] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
| | - Tom G. Mickleburgh
- Department of Chemistry, Kansas State University, Manhattan, Kansas 66506, USA
| | | | - Kathleen A. Sellens
- Department of Chemistry, Kansas State University, Manhattan, Kansas 66506, USA
| | - Melissa Pressnall
- Department of Chemistry, Kansas State University, Manhattan, Kansas 66506, USA
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27
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Najah M, Mayot E, Mahendra-Wijaya IP, Griffiths AD, Ladame S, Drevelle A. New Glycosidase Substrates for Droplet-Based Microfluidic Screening. Anal Chem 2013; 85:9807-14. [DOI: 10.1021/ac4022709] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Majdi Najah
- Institut
de Science et d’Ingénierie Supramoléculaires
(ISIS), Université de Strasbourg, CNRS UMR 7006, 8 allée
Gaspard Monge, 67083 Strasbourg Cedex, France
- Ets J.
Soufflet,
division Biotechnologies-OSIRIS, quai
Sarrail, 10400 Nogent-sur-Seine, France
| | - Estelle Mayot
- Institut
de Science et d’Ingénierie Supramoléculaires
(ISIS), Université de Strasbourg, CNRS UMR 7006, 8 allée
Gaspard Monge, 67083 Strasbourg Cedex, France
- Ets J.
Soufflet,
division Biotechnologies-OSIRIS, quai
Sarrail, 10400 Nogent-sur-Seine, France
| | - I Putu Mahendra-Wijaya
- Institut
de Science et d’Ingénierie Supramoléculaires
(ISIS), Université de Strasbourg, CNRS UMR 7006, 8 allée
Gaspard Monge, 67083 Strasbourg Cedex, France
- Ets J.
Soufflet,
division Biotechnologies-OSIRIS, quai
Sarrail, 10400 Nogent-sur-Seine, France
| | - Andrew D. Griffiths
- Institut
de Science et d’Ingénierie Supramoléculaires
(ISIS), Université de Strasbourg, CNRS UMR 7006, 8 allée
Gaspard Monge, 67083 Strasbourg Cedex, France
- École Supérieure de Physique et de Chimie Industrielles de la Ville de Paris (ESPCI ParisTech), 10 rue Vauquelin, 75231 Paris Cedex, France
| | - Sylvain Ladame
- Institut
de Science et d’Ingénierie Supramoléculaires
(ISIS), Université de Strasbourg, CNRS UMR 7006, 8 allée
Gaspard Monge, 67083 Strasbourg Cedex, France
- Department
of Bioengineering, Imperial College London, South Kensington Campus, London SW72AZ, United Kingdom
| | - Antoine Drevelle
- Institut
de Science et d’Ingénierie Supramoléculaires
(ISIS), Université de Strasbourg, CNRS UMR 7006, 8 allée
Gaspard Monge, 67083 Strasbourg Cedex, France
- Ets J.
Soufflet,
division Biotechnologies-OSIRIS, quai
Sarrail, 10400 Nogent-sur-Seine, France
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28
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Prakash D, Nawani N, Prakash M, Bodas M, Mandal A, Khetmalas M, Kapadnis B. Actinomycetes: a repertory of green catalysts with a potential revenue resource. BIOMED RESEARCH INTERNATIONAL 2013; 2013:264020. [PMID: 23691495 PMCID: PMC3652136 DOI: 10.1155/2013/264020] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/25/2012] [Revised: 03/27/2013] [Accepted: 03/28/2013] [Indexed: 11/18/2022]
Abstract
Biocatalysis, one of the oldest technologies, is becoming a favorable alternative to chemical processes and a vital part of green technology. It is an important revenue generating industry due to a global market projected at $7 billion in 2013 with a growth of 6.7% for enzymes alone. Some microbes are important sources of enzymes and are preferred over sources of plant and animal origin. As a result, more than 50% of the industrial enzymes are obtained from bacteria. The constant search for novel enzymes with robust characteristics has led to improvisations in the industrial processes, which is the key for profit growth. Actinomycetes constitute a significant component of the microbial population in most soils and can produce extracellular enzymes which can decompose various materials. Their enzymes are more attractive than enzymes from other sources because of their high stability and unusual substrate specificity. Actinomycetes found in extreme habitats produce novel enzymes with huge commercial potential. This review attempts to highlight the global importance of enzymes and extends to signify actinomycetes as promising harbingers of green technology.
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Affiliation(s)
- Divya Prakash
- Dr. D. Y Patil Biotechnology & Bioinformatics Institute, Dr. D. Y. Patil Vidyapeeth, Pune 411 033, India
| | - Neelu Nawani
- Dr. D. Y Patil Biotechnology & Bioinformatics Institute, Dr. D. Y. Patil Vidyapeeth, Pune 411 033, India
| | - Mansi Prakash
- Dr. D. Y Patil Biotechnology & Bioinformatics Institute, Dr. D. Y. Patil Vidyapeeth, Pune 411 033, India
| | - Manish Bodas
- Dr. D. Y Patil Biotechnology & Bioinformatics Institute, Dr. D. Y. Patil Vidyapeeth, Pune 411 033, India
| | - Abul Mandal
- System Biology Research Center, School of Life Sciences, University of Skövde, P.O. Box 408, 541 28 Skövde, Sweden
| | - Madhukar Khetmalas
- Dr. D. Y Patil Biotechnology & Bioinformatics Institute, Dr. D. Y. Patil Vidyapeeth, Pune 411 033, India
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