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Song T, Gupta S, Sorokin Y, Frenkel O, Cytryn E, Friedman J. A Burkholderia cenocepacia-like environmental isolate strongly inhibits the plant fungal pathogen Zymoseptoria tritici. Appl Environ Microbiol 2024; 90:e0222223. [PMID: 38624199 PMCID: PMC11107150 DOI: 10.1128/aem.02222-23] [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: 12/21/2023] [Accepted: 03/20/2024] [Indexed: 04/17/2024] Open
Abstract
Fungal phytopathogens cause significant reductions in agricultural yields annually, and overusing chemical fungicides for their control leads to environmental pollution and the emergence of resistant pathogens. Exploring natural isolates with strong antagonistic effects against pathogens can improve our understanding of their ecology and develop new treatments for the future. We isolated and characterized a novel bacterial strain associated with the species Burkholderia cenocepacia, termed APO9, which strongly inhibits Zymoseptoria tritici, a commercially important pathogenic fungus causing Septoria tritici blotch in wheat. Additionally, this strain exhibits inhibitory activity against four other phytopathogens. We found that physical contact plays a crucial role for APO9's antagonistic capacity. Genome sequencing of APO9 and biosynthetic gene cluster (BGC) analysis identified nine classes of BGCs and three types of secretion systems (types II, III, and IV), which may be involved in the inhibition of Z. tritici and other pathogens. To identify genes driving APO9's inhibitory activity, we screened a library containing 1,602 transposon mutants and identified five genes whose inactivation reduced inhibition efficiency. One such gene encodes for a diaminopimelate decarboxylase located in a terpenoid biosynthesis gene cluster. Phylogenetic analysis revealed that while some of these genes are also found across the Burkholderia genus, as well as in other Betaproteobacteria, the combination of these genes is unique to the Burkholderia cepacia complex. These findings suggest that the inhibitory capacity of APO9 is complex and not limited to a single mechanism, and may play a role in the interaction between various Burkholderia species and various phytopathogens within diverse plant ecosystems. IMPORTANCE The detrimental effects of fungal pathogens on crop yields are substantial. The overuse of chemical fungicides contributes not only to environmental pollution but also to the emergence of resistant pathogens. Investigating natural isolates with strong antagonistic effects against pathogens can improve our understanding of their ecology and develop new treatments for the future. We discovered and examined a unique bacterial strain that demonstrates significant inhibitory activity against several phytopathogens. Our research demonstrates that this strain has a wide spectrum of inhibitory actions against plant pathogens, functioning through a complex mechanism. This plays a vital role in the interactions between plant microbiota and phytopathogens.
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Affiliation(s)
- Tingting Song
- The Institute of Environmental Sciences, The Hebrew University of Jerusalem, Rehovot, Israel
| | - Suyash Gupta
- The Institute of Environmental Sciences, The Hebrew University of Jerusalem, Rehovot, Israel
- Institute of Soil, Water and Environmental Sciences, Agricultural Research Organization, Rishon Lezion, Israel
- Institute of Plant Protection, Agricultural Research Organization, Rishon Lezion, Israel
| | - Yael Sorokin
- The Institute of Environmental Sciences, The Hebrew University of Jerusalem, Rehovot, Israel
| | - Omer Frenkel
- Institute of Plant Protection, Agricultural Research Organization, Rishon Lezion, Israel
| | - Eddie Cytryn
- Institute of Soil, Water and Environmental Sciences, Agricultural Research Organization, Rishon Lezion, Israel
| | - Jonathan Friedman
- The Institute of Environmental Sciences, The Hebrew University of Jerusalem, Rehovot, Israel
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2
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Zhao Z, Zhai H, Zuo P, Wang T, Xie R, Tian M, Song R, Xu X, Li Z. Image-activated pico-injection for single-cell analysis. Talanta 2024; 272:125765. [PMID: 38346358 DOI: 10.1016/j.talanta.2024.125765] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2023] [Revised: 01/29/2024] [Accepted: 02/06/2024] [Indexed: 03/17/2024]
Abstract
The addition of reagents into preformed droplets is a crucial yet intricate task in droplet-based applications where sequential reactions is required. Pico-injection offers high throughput and robustness in accomplishing this task, but the existing pico-injection techniques work in an indiscriminate manner, making it difficult to target particular groups of droplets. Here we report image-activated pico-injection (imgPico) for label-free, on-demand reagent supplementation into droplets. The imgPico detects the droplets of interest by real-time image analysis and makes decisions for the downstream pico-injection operation. We studied the performance of different algorithms for the image analysis and optimized the experimental settings of the imgPico. In the validation experiment, the imgPico successfully injected fluorescent dyes into droplets encapsulating one, two, and three cells, respectively, as expected. We further demonstrated the utility of imgPico by targeting droplets encapsulating single cells in droplet-based single-cell RNA sequencing (scRNA-seq) using exceedingly high cell density, and the results showed that the imgPico effectively reduced the presence of doublets in the scRNA-seq data. With the merits of being label-free and versatile, the imgPico represents a technical advance with potential applications in single-cell analysis.
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Affiliation(s)
- Zhantao Zhao
- Department of Biomedical Engineering, Medical School, Shenzhen University, Shenzhen, 518060, China; Guangdong Key Laboratory for Biomedical Measurements and Ultrasound Imaging, Department of Biomedical Engineering, Medical School, Shenzhen University, Shenzhen, 518060, China
| | - Heng Zhai
- Department of Biomedical Engineering, Medical School, Shenzhen University, Shenzhen, 518060, China; Guangdong Key Laboratory for Biomedical Measurements and Ultrasound Imaging, Department of Biomedical Engineering, Medical School, Shenzhen University, Shenzhen, 518060, China
| | - Peng Zuo
- ThunderBio Innovation, Shenzhen, 518108, China
| | - Tao Wang
- Department of Biomedical Engineering, Medical School, Shenzhen University, Shenzhen, 518060, China; Guangdong Key Laboratory for Biomedical Measurements and Ultrasound Imaging, Department of Biomedical Engineering, Medical School, Shenzhen University, Shenzhen, 518060, China
| | - Run Xie
- Department of Biomedical Engineering, Medical School, Shenzhen University, Shenzhen, 518060, China; Guangdong Key Laboratory for Biomedical Measurements and Ultrasound Imaging, Department of Biomedical Engineering, Medical School, Shenzhen University, Shenzhen, 518060, China
| | - Mu Tian
- Department of Biomedical Engineering, Medical School, Shenzhen University, Shenzhen, 518060, China; Guangdong Key Laboratory for Biomedical Measurements and Ultrasound Imaging, Department of Biomedical Engineering, Medical School, Shenzhen University, Shenzhen, 518060, China
| | - Ruyuan Song
- ThunderBio Innovation, Shenzhen, 518108, China
| | - Xiaonan Xu
- ThunderBio Innovation, Shenzhen, 518108, China
| | - Zida Li
- Department of Biomedical Engineering, Medical School, Shenzhen University, Shenzhen, 518060, China; Guangdong Key Laboratory for Biomedical Measurements and Ultrasound Imaging, Department of Biomedical Engineering, Medical School, Shenzhen University, Shenzhen, 518060, China.
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3
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Shao F, Li H, Hsieh K, Zhang P, Li S, Wang TH. Automated and miniaturized screening of antibiotic combinations via robotic-printed combinatorial droplet platform. Acta Pharm Sin B 2024; 14:1801-1813. [PMID: 38572105 PMCID: PMC10985126 DOI: 10.1016/j.apsb.2023.11.027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2023] [Revised: 11/22/2023] [Accepted: 11/24/2023] [Indexed: 04/05/2024] Open
Abstract
Antimicrobial resistance (AMR) has become a global health crisis in need of novel solutions. To this end, antibiotic combination therapies, which combine multiple antibiotics for treatment, have attracted significant attention as a potential approach for combating AMR. To facilitate advances in antibiotic combination therapies, most notably in investigating antibiotic interactions and identifying synergistic antibiotic combinations however, there remains a need for automated high-throughput platforms that can create and examine antibiotic combinations on-demand, at scale, and with minimal reagent consumption. To address these challenges, we have developed a Robotic-Printed Combinatorial Droplet (RoboDrop) platform by integrating a programmable droplet microfluidic device that generates antibiotic combinations in nanoliter droplets in automation, a robotic arm that arranges the droplets in an array, and a camera that images the array of thousands of droplets in parallel. We further implement a resazurin-based bacterial viability assay to accelerate our antibiotic combination testing. As a demonstration, we use RoboDrop to corroborate two pairs of antibiotics with known interactions and subsequently identify a new synergistic combination of cefsulodin, penicillin, and oxacillin against a model E. coli strain. We therefore envision RoboDrop becoming a useful tool to efficiently identify new synergistic antibiotic combinations toward combating AMR.
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Affiliation(s)
- Fangchi Shao
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Hui Li
- Department of Mechanical Engineering, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Kuangwen Hsieh
- Department of Mechanical Engineering, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Pengfei Zhang
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Sixuan Li
- Department of Mechanical Engineering, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Tza-Huei Wang
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD 21218, USA
- Department of Mechanical Engineering, Johns Hopkins University, Baltimore, MD 21218, USA
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4
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Nan L, Zhang H, Weitz DA, Shum HC. Development and future of droplet microfluidics. LAB ON A CHIP 2024; 24:1135-1153. [PMID: 38165829 DOI: 10.1039/d3lc00729d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/04/2024]
Abstract
Over the past two decades, advances in droplet-based microfluidics have facilitated new approaches to process and analyze samples with unprecedented levels of precision and throughput. A wide variety of applications has been inspired across multiple disciplines ranging from materials science to biology. Understanding the dynamics of droplets enables optimization of microfluidic operations and design of new techniques tailored to emerging demands. In this review, we discuss the underlying physics behind high-throughput generation and manipulation of droplets. We also summarize the applications in droplet-derived materials and droplet-based lab-on-a-chip biotechnology. In addition, we offer perspectives on future directions to realize wider use of droplet microfluidics in industrial production and biomedical analyses.
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Affiliation(s)
- Lang Nan
- Department of Mechanical Engineering, The University of Hong Kong, Pokfulam Road, Hong Kong, China.
- Advanced Biomedical Instrumentation Centre, Hong Kong Science Park, Shatin, New Territories, Hong Kong, China
| | - Huidan Zhang
- John A. Paulson School of Engineering and Applied Sciences, Harvard University, Cambridge, MA, 02138, USA
| | - David A Weitz
- John A. Paulson School of Engineering and Applied Sciences, Harvard University, Cambridge, MA, 02138, USA
- Advanced Biomedical Instrumentation Centre, Hong Kong Science Park, Shatin, New Territories, Hong Kong, China
| | - Ho Cheung Shum
- Department of Mechanical Engineering, The University of Hong Kong, Pokfulam Road, Hong Kong, China.
- Advanced Biomedical Instrumentation Centre, Hong Kong Science Park, Shatin, New Territories, Hong Kong, China
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5
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Yang D, Yu Z, Zheng M, Yang W, Liu Z, Zhou J, Huang L. Artificial intelligence-accelerated high-throughput screening of antibiotic combinations on a microfluidic combinatorial droplet system. LAB ON A CHIP 2023; 23:3961-3977. [PMID: 37605875 DOI: 10.1039/d3lc00647f] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/23/2023]
Abstract
Microfluidic platforms have been employed as an effective tool for drug screening and exhibit the advantages of lower reagent consumption, higher throughput and a higher degree of automation. Despite the great advancement, it remains challenging to screen complex antibiotic combinations in a simple, high-throughput and systematic manner. Meanwhile, the large amounts of datasets generated during the screening process generally outpace the abilities of the conventional manual or semi-automatic data analysis. To address these issues, we propose an artificial intelligence-accelerated high-throughput combinatorial drug evaluation system (AI-HTCDES), which not only allows high-throughput production of antibiotic combinations with varying concentrations, but can also automatically analyze the dynamic growth of bacteria under the action of different antibiotic combinations. Based on this system, several antibiotic combinations displaying an additive effect are discovered, and the dosage regimens of each component in the combinations are determined. This strategy not only provides useful guidance in the clinical use of antibiotic combination therapy and personalized medicine, but also offers a promising tool for the combinatorial screenings of other medicines.
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Affiliation(s)
- Deyu Yang
- School of Biomedical Engineering, Sun Yat-sen University, Shenzhen 518107, China.
| | - Ziming Yu
- School of Biomedical Engineering, Sun Yat-sen University, Shenzhen 518107, China.
| | - Mengxin Zheng
- School of Biomedical Engineering, Sun Yat-sen University, Shenzhen 518107, China.
| | - Wei Yang
- School of Biomedical Engineering, Sun Yat-sen University, Shenzhen 518107, China.
| | - Zhangcai Liu
- School of Biomedical Engineering, Sun Yat-sen University, Shenzhen 518107, China.
| | - Jianhua Zhou
- School of Biomedical Engineering, Sun Yat-sen University, Shenzhen 518107, China.
- Key Laboratory of Sensing Technology and Biomedical Instruments of Guangdong Province, School of Biomedical Engineering, Sun Yat-sen University, Guangzhou 510275, China
| | - Lu Huang
- School of Biomedical Engineering, Sun Yat-sen University, Shenzhen 518107, China.
- Key Laboratory of Sensing Technology and Biomedical Instruments of Guangdong Province, School of Biomedical Engineering, Sun Yat-sen University, Guangzhou 510275, China
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6
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Wu B, Xu X, Li G, Yang X, Du F, Tan W, Wang J, Dong S, Luo J, Wang X, Cao Z. High-Throughput Microfluidic Production of Droplets and Hydrogel Microspheres through Monolithically Integrated Microchannel Plates. Anal Chem 2023; 95:13586-13595. [PMID: 37624148 DOI: 10.1021/acs.analchem.3c02250] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/26/2023]
Abstract
In this paper, we present a highly effective microfluidic emulsion system using an integrated microchannel plate (MCP), a porous glass membrane that is readily available and densely packs millions of through-microchannels, for high-throughput production of monodisperse droplets. The physical controls of droplet formation, including viscosity, flow rate, and pore size, have been extensively explored for optimum emulsification conditions. The performance of the device has been validated where monodisperse droplets with a narrow coefficient of variance (<5%) can be achieved at a dispersed phase flux of 3 mL h-1 from a piece of 4 × 4 mm2 MCP. The average droplet size is two times the nominal membrane pore diameter and thus can be easily controlled by choosing the appropriate membrane type. The preparation of hydrogel microspheres has also been demonstrated with a high throughput of 1.5 × 106 particles min-1. These microspheres with a uniform size range and rough surface morphology provide suitable bioenvironments and serve as ideal carriers for cell culture. Mouse fibroblasts are shown to be cultured on these 3D scaffolds with an average cell viability of over 96%. The cell attachment rate can reach up to 112 ± 7% in 24 h and the proliferation ability increases with the number of culture days. Furthermore, the device has been applied in the droplet digital polymerase chain reaction for absolute quantification of lung cancer-related PLAU genes. The detection limit achieved was noted to be 0.5 copies/μL with a dynamic range of 105 ranging from 1 × 102 to 1 × 106 copies/μL. Given the easy fabrication, robust performance, and simple operation, the emulsion system sets the stage for the laboratory's droplet-based assays and applications in tissue engineering.
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Affiliation(s)
- Boxuan Wu
- College of Information Science and Electronic Engineering, Zhejiang University, Hangzhou 310027, P. R. China
- International Joint Innovation Center, Zhejiang University, Haining 314400, P. R. China
| | - Xuefeng Xu
- College of Information Science and Electronic Engineering, Zhejiang University, Hangzhou 310027, P. R. China
| | - Guangyang Li
- College of Information Science and Electronic Engineering, Zhejiang University, Hangzhou 310027, P. R. China
| | - Xi Yang
- College of Information Science and Electronic Engineering, Zhejiang University, Hangzhou 310027, P. R. China
| | - Feiya Du
- Department of Plastic and Cosmetic Center, First Affiliated Hospital of Zhejiang University, Hangzhou 310006, P. R. China
| | - Weiqiang Tan
- Department of Plastic Surgery, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou 310016, P. R. China
| | - Jianmin Wang
- Department of Obstetrics and Gynecology, Sir Run Run Shaw Hospital, Key Laboratory of Reproductive Dysfunction Management of Zhejiang Province, Zhejiang University School of Medicine, Hangzhou 310016, P. R. China
| | - Shurong Dong
- College of Information Science and Electronic Engineering, Zhejiang University, Hangzhou 310027, P. R. China
- International Joint Innovation Center, Zhejiang University, Haining 314400, P. R. China
| | - Jikui Luo
- College of Information Science and Electronic Engineering, Zhejiang University, Hangzhou 310027, P. R. China
- International Joint Innovation Center, Zhejiang University, Haining 314400, P. R. China
| | - Xiaozhi Wang
- College of Information Science and Electronic Engineering, Zhejiang University, Hangzhou 310027, P. R. China
| | - Zhen Cao
- College of Information Science and Electronic Engineering, Zhejiang University, Hangzhou 310027, P. R. China
- International Joint Innovation Center, Zhejiang University, Haining 314400, P. R. China
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7
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Ha NS, Onley JR, Deng K, Andeer P, Bowen BP, Gupta K, Kim PW, Kuch N, Kutschke M, Parker A, Song F, Fox B, Adams PD, de Raad M, Northen TR. A combinatorial droplet microfluidic device integrated with mass spectrometry for enzyme screening. LAB ON A CHIP 2023; 23:3361-3369. [PMID: 37401915 PMCID: PMC10484474 DOI: 10.1039/d2lc00980c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/05/2023]
Abstract
Mass spectrometry (MS) enables detection of different chemical species with a very high specificity; however, it can be limited by its throughput. Integrating MS with microfluidics has a tremendous potential to improve throughput and accelerate biochemical research. In this work, we introduce Drop-NIMS, a combination of a passive droplet loading microfluidic device and a matrix-free MS laser desorption ionization technique called nanostructure-initiator mass spectrometry (NIMS). This platform combines different droplets at random to generate a combinatorial library of enzymatic reactions that are deposited directly on the NIMS surface without requiring additional sample handling. The enzyme reaction products are then detected with MS. Drop-NIMS was used to rapidly screen enzymatic reactions containing low (on the order of nL) volumes of glycoside reactants and glycoside hydrolase enzymes per reaction. MS "barcodes" (small compounds with unique masses) were added to the droplets to identify different combinations of substrates and enzymes created by the device. We assigned xylanase activities to several putative glycoside hydrolases, making them relevant to food and biofuel industrial applications. Overall, Drop-NIMS is simple to fabricate, assemble, and operate and it has potential to be used with many other small molecule metabolites.
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Affiliation(s)
- Noel S Ha
- Joint BioEnergy Institute, Emeryville, CA, USA.
- Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Jenny R Onley
- Joint BioEnergy Institute, Emeryville, CA, USA.
- Sandia National Laboratories, Livermore, California, USA
| | - Kai Deng
- Joint BioEnergy Institute, Emeryville, CA, USA.
- Sandia National Laboratories, Livermore, California, USA
| | - Peter Andeer
- Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | | | - Kshitiz Gupta
- Joint BioEnergy Institute, Emeryville, CA, USA.
- Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Peter W Kim
- Joint BioEnergy Institute, Emeryville, CA, USA.
- Sandia National Laboratories, Livermore, California, USA
| | - Nathaniel Kuch
- University of Wisconsin - Madison, Madison, WI, USA
- Great Lakes Bioenergy Research Center, Wisconsin Energy Institute, Madison, WI, USA
| | | | - Alex Parker
- University of Wisconsin - Madison, Madison, WI, USA
| | - Fangchao Song
- Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Brian Fox
- University of Wisconsin - Madison, Madison, WI, USA
- Great Lakes Bioenergy Research Center, Wisconsin Energy Institute, Madison, WI, USA
| | - Paul D Adams
- Joint BioEnergy Institute, Emeryville, CA, USA.
- Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- University of California, Berkeley, CA, USA
| | - Markus de Raad
- Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Trent R Northen
- Joint BioEnergy Institute, Emeryville, CA, USA.
- Lawrence Berkeley National Laboratory, Berkeley, CA, USA
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8
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Trinh TND, Do HDK, Nam NN, Dan TT, Trinh KTL, Lee NY. Droplet-Based Microfluidics: Applications in Pharmaceuticals. Pharmaceuticals (Basel) 2023; 16:937. [PMID: 37513850 PMCID: PMC10385691 DOI: 10.3390/ph16070937] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2023] [Revised: 06/19/2023] [Accepted: 06/25/2023] [Indexed: 07/30/2023] Open
Abstract
Droplet-based microfluidics offer great opportunities for applications in various fields, such as diagnostics, food sciences, and drug discovery. A droplet provides an isolated environment for performing a single reaction within a microscale-volume sample, allowing for a fast reaction with a high sensitivity, high throughput, and low risk of cross-contamination. Owing to several remarkable features, droplet-based microfluidic techniques have been intensively studied. In this review, we discuss the impact of droplet microfluidics, particularly focusing on drug screening and development. In addition, we surveyed various methods of device fabrication and droplet generation/manipulation. We further highlight some promising studies covering drug synthesis and delivery that were updated within the last 5 years. This review provides researchers with a quick guide that includes the most up-to-date and relevant information on the latest scientific findings on the development of droplet-based microfluidics in the pharmaceutical field.
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Affiliation(s)
- Thi Ngoc Diep Trinh
- Department of Materials Science, School of Applied Chemistry, Tra Vinh University, Tra Vinh City 87000, Vietnam
| | - Hoang Dang Khoa Do
- NTT Hi-Tech Institute, Nguyen Tat Thanh University, Ward 13, District 04, Ho Chi Minh City 70000, Vietnam
| | - Nguyen Nhat Nam
- Biotechnology Center, School of Agriculture and Aquaculture, Tra Vinh University, Tra Vinh City 87000, Vietnam
| | - Thach Thi Dan
- Department of Materials Science, School of Applied Chemistry, Tra Vinh University, Tra Vinh City 87000, Vietnam
| | - Kieu The Loan Trinh
- BioNano Applications Research Center, Gachon University, 1342 Seongnam-daero, Sujeong-gu, Seongnam-si 13120, Republic of Korea
| | - Nae Yoon Lee
- Department of BioNano Technology, Gachon University, 1342 Seongnam-daero, Sujeong-gu, Seongnam-si 13120, Republic of Korea
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Smith PT, Ye Z, Pietryga J, Huang J, Wahl CB, Hedlund Orbeck JK, Mirkin CA. Molecular Thin Films Enable the Synthesis and Screening of Nanoparticle Megalibraries Containing Millions of Catalysts. J Am Chem Soc 2023. [PMID: 37311072 DOI: 10.1021/jacs.3c03910] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Megalibraries are centimeter-scale chips containing millions of materials synthesized in parallel using scanning probe lithography. As such, they stand to accelerate how materials are discovered for applications spanning catalysis, optics, and more. However, a long-standing challenge is the availability of substrates compatible with megalibrary synthesis, which limits the structural and functional design space that can be explored. To address this challenge, thermally removable polystyrene films were developed as universal substrate coatings that decouple lithography-enabled nanoparticle synthesis from the underlying substrate chemistry, thus providing consistent lithography parameters on diverse substrates. Multi-spray inking of the scanning probe arrays with polymer solutions containing metal salts allows patterning of >56 million nanoreactors designed to vary in composition and size. These are subsequently converted to inorganic nanoparticles via reductive thermal annealing, which also removes the polystyrene to deposit the megalibrary. Megalibraries with mono-, bi-, and trimetallic materials were synthesized, and nanoparticle size was controlled between 5 and 35 nm by modulating the lithography speed. Importantly, the polystyrene coating can be used on conventional substrates like Si/SiOx, as well as substrates typically more difficult to pattern on, such as glassy carbon, diamond, TiO2, BN, W, or SiC. Finally, high-throughput materials discovery is performed in the context of photocatalytic degradation of organic pollutants using Au-Pd-Cu nanoparticle megalibraries on TiO2 substrates with 2,250,000 unique composition/size combinations. The megalibrary was screened within 1 h by developing fluorescent thin-film coatings on top of the megalibrary as proxies for catalytic turnover, revealing Au0.53Pd0.38Cu0.09-TiO2 as the most active photocatalyst composition.
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Affiliation(s)
- Peter T Smith
- Department of Chemistry, Northwestern University, Evanston, Illinois 60208, United States
- International Institute for Nanotechnology, Evanston, Illinois 60208, United States
| | - Zihao Ye
- Department of Chemistry, Northwestern University, Evanston, Illinois 60208, United States
- International Institute for Nanotechnology, Evanston, Illinois 60208, United States
| | - Jacob Pietryga
- International Institute for Nanotechnology, Evanston, Illinois 60208, United States
- Department of Materials Science and Engineering, Northwestern University, Evanston, Illinois 60208, United States
| | - Jin Huang
- Department of Chemistry, Northwestern University, Evanston, Illinois 60208, United States
- International Institute for Nanotechnology, Evanston, Illinois 60208, United States
| | - Carolin B Wahl
- International Institute for Nanotechnology, Evanston, Illinois 60208, United States
- Department of Materials Science and Engineering, Northwestern University, Evanston, Illinois 60208, United States
| | - Jenny K Hedlund Orbeck
- Department of Chemistry, Northwestern University, Evanston, Illinois 60208, United States
- International Institute for Nanotechnology, Evanston, Illinois 60208, United States
| | - Chad A Mirkin
- Department of Chemistry, Northwestern University, Evanston, Illinois 60208, United States
- International Institute for Nanotechnology, Evanston, Illinois 60208, United States
- Department of Materials Science and Engineering, Northwestern University, Evanston, Illinois 60208, United States
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10
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Zhang L, Parvin R, Chen M, Hu D, Fan Q, Ye F. High-throughput microfluidic droplets in biomolecular analytical system: A review. Biosens Bioelectron 2023; 228:115213. [PMID: 36906989 DOI: 10.1016/j.bios.2023.115213] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Revised: 02/13/2023] [Accepted: 03/06/2023] [Indexed: 03/11/2023]
Abstract
Droplet microfluidic technology has revolutionized biomolecular analytical research, as it has the capability to reserve the genotype-to-phenotype linkage and assist for revealing the heterogeneity. Massive and uniform picolitre droplets feature dividing solution to the level that single cell and single molecule in each droplet can be visualized, barcoded, and analyzed. Then, the droplet assays can unfold intensive genomic data, offer high sensitivity, and screen and sort from a large number of combinations or phenotypes. Based on these unique advantages, this review focuses on up-to-date research concerning diverse screening applications utilizing droplet microfluidic technology. The emerging progress of droplet microfluidic technology is first introduced, including efficient and scaling-up in droplets encapsulation, and prevalent batch operations. Then the new implementations of droplet-based digital detection assays and single-cell muti-omics sequencing are briefly examined, along with related applications such as drug susceptibility testing, multiplexing for cancer subtype identification, interactions of virus-to-host, and multimodal and spatiotemporal analysis. Meanwhile, we specialize in droplet-based large-scale combinational screening regarding desired phenotypes, with an emphasis on sorting for immune cells, antibodies, enzymatic properties, and proteins produced by directed evolution methods. Finally, some challenges, deployment and future perspective of droplet microfluidics technology in practice are also discussed.
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Affiliation(s)
- Lexiang Zhang
- Oujiang Laboratory (Zhejiang Lab for Regenerative Medicine, Vision and Brain Health), Wenzhou, Zhejiang, 325000, China; Zhejiang Engineering Research Center for Tissue Repair Materials, Wenzhou Institute, University of Chinese Academy of Sciences, Wenzhou, Zhejiang, 325000, China
| | - Rokshana Parvin
- Oujiang Laboratory (Zhejiang Lab for Regenerative Medicine, Vision and Brain Health), Wenzhou, Zhejiang, 325000, China; Zhejiang Engineering Research Center for Tissue Repair Materials, Wenzhou Institute, University of Chinese Academy of Sciences, Wenzhou, Zhejiang, 325000, China
| | - Mingshuo Chen
- Oujiang Laboratory (Zhejiang Lab for Regenerative Medicine, Vision and Brain Health), Wenzhou, Zhejiang, 325000, China; Zhejiang Engineering Research Center for Tissue Repair Materials, Wenzhou Institute, University of Chinese Academy of Sciences, Wenzhou, Zhejiang, 325000, China
| | - Dingmeng Hu
- Oujiang Laboratory (Zhejiang Lab for Regenerative Medicine, Vision and Brain Health), Wenzhou, Zhejiang, 325000, China; Zhejiang Engineering Research Center for Tissue Repair Materials, Wenzhou Institute, University of Chinese Academy of Sciences, Wenzhou, Zhejiang, 325000, China
| | - Qihui Fan
- Oujiang Laboratory (Zhejiang Lab for Regenerative Medicine, Vision and Brain Health), Wenzhou, Zhejiang, 325000, China; Zhejiang Engineering Research Center for Tissue Repair Materials, Wenzhou Institute, University of Chinese Academy of Sciences, Wenzhou, Zhejiang, 325000, China; Beijing National Laboratory for Condensed Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing, 100190, China.
| | - Fangfu Ye
- Oujiang Laboratory (Zhejiang Lab for Regenerative Medicine, Vision and Brain Health), Wenzhou, Zhejiang, 325000, China; Zhejiang Engineering Research Center for Tissue Repair Materials, Wenzhou Institute, University of Chinese Academy of Sciences, Wenzhou, Zhejiang, 325000, China; Beijing National Laboratory for Condensed Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing, 100190, China.
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11
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Thakku SG, Lirette J, Murugesan K, Chen J, Theron G, Banaei N, Blainey PC, Gomez J, Wong SY, Hung DT. Genome-wide tiled detection of circulating Mycobacterium tuberculosis cell-free DNA using Cas13. Nat Commun 2023; 14:1803. [PMID: 37002219 PMCID: PMC10064635 DOI: 10.1038/s41467-023-37183-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Accepted: 03/06/2023] [Indexed: 04/03/2023] Open
Abstract
Detection of microbial cell-free DNA (cfDNA) circulating in the bloodstream has emerged as a promising new approach for diagnosing infection. Microbial diagnostics based on cfDNA require assays that can detect rare and highly fragmented pathogen nucleic acids. We now report WATSON (Whole-genome Assay using Tiled Surveillance Of Nucleic acids), a method to detect low amounts of pathogen cfDNA that couples pooled amplification of genomic targets tiled across the genome with pooled CRISPR/Cas13-based detection of these targets. We demonstrate that this strategy of tiling improves cfDNA detection compared to amplification and detection of a single targeted locus. WATSON can detect cfDNA from Mycobacterium tuberculosis in plasma of patients with active pulmonary tuberculosis, a disease that urgently needs accurate, minimally-invasive, field-deployable diagnostics. We thus demonstrate the potential for translating WATSON to a lateral flow platform. WATSON demonstrates the ability to capitalize on the strengths of targeting microbial cfDNA to address the need for point-of-care diagnostic tests for infectious diseases.
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Affiliation(s)
| | | | - Kanagavel Murugesan
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Julie Chen
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Grant Theron
- DSI-NRF Centre of Excellence for Biomedical Tuberculosis Research and SAMRC Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - Niaz Banaei
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
- Department of Medicine, Division of Infectious Diseases and Geographic Medicine, Stanford University School of Medicine, Stanford, CA, USA
- Clinical Microbiology Laboratory, Stanford Health Care, Palo Alto, CA, USA
| | - Paul C Blainey
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
- Koch Institute for Integrative Cancer Research at MIT, Cambridge, MA, USA
| | - James Gomez
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Sharon Y Wong
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Deborah T Hung
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Department of Genetics, Harvard Medical School, Boston, MA, USA.
- Department of Molecular Biology and Center for Computational and Integrative Biology, Massachusetts General Hospital, Boston, MA, USA.
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12
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Liu FX, Cui JQ, Wu Z, Yao S. Recent progress in nucleic acid detection with CRISPR. LAB ON A CHIP 2023; 23:1467-1492. [PMID: 36723235 DOI: 10.1039/d2lc00928e] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
Recent advances in CRISPR-based biotechnologies have greatly expanded our capabilities to repurpose CRISPR for the development of molecular diagnostic systems. The key attribute that allows CRISPR to be widely utilized is its programmable and highly specific nature. In this review, we first illustrate the principle of the class 2 CRISPR nucleases for molecular diagnostics which originates from their immunologic defence systems. Next, we present the CRISPR-based schemes in the application of diagnostics with amplification-assisted or amplification-free strategies. By highlighting some of the recent advances we interpret how general bioengineering methodologies can be integrated with CRISPR. Finally, we discuss the challenges and exciting prospects for future CRISPR-based biosensing development. We hope that this review will guide the reader to systematically learn the start-of-the-art development of CRISPR-mediated nucleic acid detection and understand how to apply the CRISPR nucleases with different design concepts to more general applications in diagnostics and beyond.
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Affiliation(s)
- Frank X Liu
- Department of Mechanical and Aerospace Engineering, Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong.
| | - Johnson Q Cui
- Department of Mechanical and Aerospace Engineering, Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong.
| | - Zhihao Wu
- IIP-Advanced Materials, Interdisciplinary Program Office (IPO), Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong
| | - Shuhuai Yao
- Department of Mechanical and Aerospace Engineering, Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong.
- Department of Chemical and Biological Engineering, Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong
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13
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Payne EM, Taraji M, Murray BE, Holland-Moritz DA, Moore JC, Haddad PR, Kennedy RT. Evaluation of Analyte Transfer between Microfluidic Droplets by Mass Spectrometry. Anal Chem 2023; 95:4662-4670. [PMID: 36862378 DOI: 10.1021/acs.analchem.2c04985] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/03/2023]
Abstract
Droplet microfluidics enables high-throughput experimentation and screening by encapsulating chemical and biochemical samples in aqueous droplets segmented by an immiscible fluid. In such experiments, it is critical that each droplet remains chemically distinct. A common approach is to use fluorinated oils with surfactants to stabilize droplets. However, some small molecules have been observed to transport between droplets under these conditions. Attempts to study and mitigate this effect have relied on evaluating crosstalk using fluorescent molecules, which inherently limits the analyte scope and conclusions drawn about the mechanism of the effect. In this work, transport of low molecular weight compounds between droplets was investigated using electrospray ionization mass spectrometry (ESI-MS) for measurement. The use of ESI-MS significantly expands the scope of analytes that can be tested. We tested 36 structurally diverse analytes that were found to exhibit crosstalk ranging from negligible to complete transfer using HFE 7500 as the carrier fluid and 008-fluorosurfactant as a surfactant. Using this data set, we developed a predictive tool showing that high log P and log D values correlate with high crosstalk, and high polar surface area and log S correlate with low crosstalk. We then investigated several carrier fluids, surfactants, and flow conditions. It was discovered that transport is strongly dependent on all of these factors and that experimental design and surfactant tailoring can reduce carryover. We present evidence for mixed crosstalk mechanisms including both micellar and oil partitioning transfer. By understanding the driving mechanisms, surfactant and oil compositions can be designed to better reduce chemical transport for screening workflows.
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Affiliation(s)
- Emory M Payne
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48103, United States
| | - Maryam Taraji
- The Australian Wine Research Institute, Adelaide, South Australia 5064, Australia.,Metabolomics Australia, Adelaide, South Australia 5064, Australia.,School of Natural Sciences, University of Tasmania, Hobart, Tasmania 7005, Australia
| | - Bridget E Murray
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48103, United States
| | - Daniel A Holland-Moritz
- Process Research and Development, Merck & Co., Inc., Rahway, New Jersey 07065, United States
| | - Jeffrey C Moore
- Process Research and Development, Merck & Co., Inc., Rahway, New Jersey 07065, United States
| | - Paul R Haddad
- School of Natural Sciences, University of Tasmania, Hobart, Tasmania 7005, Australia
| | - Robert T Kennedy
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48103, United States
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14
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Reyes M, Leff SM, Gentili M, Hacohen N, Blainey PC. Microscale combinatorial stimulation of human myeloid cells reveals inflammatory priming by viral ligands. SCIENCE ADVANCES 2023; 9:eade5090. [PMID: 36827376 PMCID: PMC9956118 DOI: 10.1126/sciadv.ade5090] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/20/2022] [Accepted: 01/24/2023] [Indexed: 06/18/2023]
Abstract
Cells sense a wide variety of signals and respond by adopting complex transcriptional states. Most single-cell profiling is carried out today at cellular baseline, blind to cells' potential spectrum of functional responses. Exploring the space of cellular responses experimentally requires access to a large combinatorial perturbation space. Single-cell genomics coupled with multiplexing techniques provide a useful tool for characterizing cell states across several experimental conditions. However, current multiplexing strategies require programmatic handling of many samples in macroscale arrayed formats, precluding their application in large-scale combinatorial analysis. Here, we introduce StimDrop, a method that combines antibody-based cell barcoding with parallel droplet processing to automatically formulate cell population × stimulus combinations in a microfluidic device. We applied StimDrop to profile the effects of 512 sequential stimulation conditions on human dendritic cells. Our results demonstrate that priming with viral ligands potentiates hyperinflammatory responses to a second stimulus, and show transcriptional signatures consistent with this phenomenon in myeloid cells of patients with severe COVID-19.
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Affiliation(s)
- Miguel Reyes
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Samantha M. Leff
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | | | - Nir Hacohen
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Center for Cancer Research, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Paul C. Blainey
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
- Koch Institute for Integrative Cancer Research at MIT, Cambridge, MA, USA
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15
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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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16
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Shi W, Bell S, Iyer H, Brenden CK, Zhang Y, Kim S, Park I, Bashir R, Sweedler J, Vlasov Y. Integrated silicon microfluidic chip for picoliter-scale analyte segmentation and microscale printing for mass spectrometry imaging. LAB ON A CHIP 2022; 23:72-80. [PMID: 36477760 PMCID: PMC9764807 DOI: 10.1039/d2lc00688j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/24/2022] [Accepted: 11/12/2022] [Indexed: 06/17/2023]
Abstract
A silicon single-chip microfluidics system that integrates microscale fluidic channels, an analyte segmentation device, and a nozzle for electrohydrodynamic-assisted printing is designed for hyphenation with MALDI mass spectrometry (MS) imaging. A miniaturized T-junction segments analytes into monodisperse picoliter oil-isolated compartments. The printing nozzle deposits generated droplets one-by-one into an array on a conductive substrate without splitting or coalescing. Virtually single-shot MS analysis is enabled due to the ultrasmall droplet volumes and highly localized printing. The signal-to-noise ratio indicates that detection limits at the attomole level are achieved for γ-aminobutyric acid.
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Affiliation(s)
- Weihua Shi
- Department of Electrical and Computer Engineering, University of Illinois Urbana Champaign, IL 61801, USA.
| | - Sara Bell
- Department of Chemistry and the Beckman Institute, University of Illinois Urbana Champaign, IL 61801, USA
| | - Hrishikesh Iyer
- Department of Electrical and Computer Engineering, University of Illinois Urbana Champaign, IL 61801, USA.
| | | | - Yan Zhang
- Department of Electrical and Computer Engineering, University of Illinois Urbana Champaign, IL 61801, USA.
| | - Sungho Kim
- Department of Electrical and Computer Engineering, University of Illinois Urbana Champaign, IL 61801, USA.
| | - Insu Park
- Department of Bioengineering, University of Illinois Urbana Champaign, IL 61801, USA
| | - Rashid Bashir
- Department of Bioengineering, University of Illinois Urbana Champaign, IL 61801, USA
| | - Jonathan Sweedler
- Department of Chemistry and the Beckman Institute, University of Illinois Urbana Champaign, IL 61801, USA
| | - Yurii Vlasov
- Department of Electrical and Computer Engineering, University of Illinois Urbana Champaign, IL 61801, USA.
- Department of Bioengineering, University of Illinois Urbana Champaign, IL 61801, USA
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17
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Xie Y, Li H, Chen F, Udayakumar S, Arora K, Chen H, Lan Y, Hu Q, Zhou X, Guo X, Xiu L, Yin K. Clustered Regularly Interspaced short palindromic repeats-Based Microfluidic System in Infectious Diseases Diagnosis: Current Status, Challenges, and Perspectives. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2022; 9:e2204172. [PMID: 36257813 PMCID: PMC9731715 DOI: 10.1002/advs.202204172] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/20/2022] [Revised: 09/16/2022] [Indexed: 06/02/2023]
Abstract
Mitigating the spread of global infectious diseases requires rapid and accurate diagnostic tools. Conventional diagnostic techniques for infectious diseases typically require sophisticated equipment and are time consuming. Emerging clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated proteins (Cas) detection systems have shown remarkable potential as next-generation diagnostic tools to achieve rapid, sensitive, specific, and field-deployable diagnoses of infectious diseases, based on state-of-the-art microfluidic platforms. Therefore, a review of recent advances in CRISPR-based microfluidic systems for infectious diseases diagnosis is urgently required. This review highlights the mechanisms of CRISPR/Cas biosensing and cutting-edge microfluidic devices including paper, digital, and integrated wearable platforms. Strategies to simplify sample pretreatment, improve diagnostic performance, and achieve integrated detection are discussed. Current challenges and future perspectives contributing to the development of more effective CRISPR-based microfluidic diagnostic systems are also proposed.
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Affiliation(s)
- Yi Xie
- School of Global HealthChinese Center for Tropical Diseases ResearchShanghai Jiao Tong University School of MedicineShanghai200025P. R. China
- One Health CenterShanghai Jiao Tong University‐The University of EdinburghShanghai200025P. R. China
| | - Huimin Li
- School of Global HealthChinese Center for Tropical Diseases ResearchShanghai Jiao Tong University School of MedicineShanghai200025P. R. China
- One Health CenterShanghai Jiao Tong University‐The University of EdinburghShanghai200025P. R. China
| | - Fumin Chen
- School of Global HealthChinese Center for Tropical Diseases ResearchShanghai Jiao Tong University School of MedicineShanghai200025P. R. China
- One Health CenterShanghai Jiao Tong University‐The University of EdinburghShanghai200025P. R. China
| | - Srisruthi Udayakumar
- Division of Engineering in MedicineDepartment of MedicineBrigham and Women's Hospital and Harvard Medical SchoolBostonMA02139USA
| | - Khyati Arora
- Division of Engineering in MedicineDepartment of MedicineBrigham and Women's Hospital and Harvard Medical SchoolBostonMA02139USA
| | - Hui Chen
- Division of Engineering in MedicineDepartment of MedicineBrigham and Women's Hospital and Harvard Medical SchoolBostonMA02139USA
| | - Yang Lan
- Centre for Nature‐Inspired EngineeringDepartment of Chemical EngineeringUniversity College LondonLondonWC1E 7JEUK
| | - Qinqin Hu
- School of Global HealthChinese Center for Tropical Diseases ResearchShanghai Jiao Tong University School of MedicineShanghai200025P. R. China
- One Health CenterShanghai Jiao Tong University‐The University of EdinburghShanghai200025P. R. China
| | - Xiaonong Zhou
- School of Global HealthChinese Center for Tropical Diseases ResearchShanghai Jiao Tong University School of MedicineShanghai200025P. R. China
- One Health CenterShanghai Jiao Tong University‐The University of EdinburghShanghai200025P. R. China
| | - Xiaokui Guo
- School of Global HealthChinese Center for Tropical Diseases ResearchShanghai Jiao Tong University School of MedicineShanghai200025P. R. China
- One Health CenterShanghai Jiao Tong University‐The University of EdinburghShanghai200025P. R. China
| | - Leshan Xiu
- School of Global HealthChinese Center for Tropical Diseases ResearchShanghai Jiao Tong University School of MedicineShanghai200025P. R. China
- One Health CenterShanghai Jiao Tong University‐The University of EdinburghShanghai200025P. R. China
| | - Kun Yin
- School of Global HealthChinese Center for Tropical Diseases ResearchShanghai Jiao Tong University School of MedicineShanghai200025P. R. China
- One Health CenterShanghai Jiao Tong University‐The University of EdinburghShanghai200025P. R. China
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18
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Zath GK, Sperling RA, Hoffman CW, Bikos DA, Abbasi R, Abate AR, Weitz DA, Chang CB. Rapid parallel generation of a fluorescently barcoded drop library from a microtiter plate using the plate-interfacing parallel encapsulation (PIPE) chip. LAB ON A CHIP 2022; 22:4735-4745. [PMID: 36367139 PMCID: PMC10016142 DOI: 10.1039/d2lc00909a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
In drop-based microfluidics, an aqueous sample is partitioned into drops using individual pump sources that drive water and oil into a drop-making device. Parallelization of drop-making devices is necessary to achieve high-throughput screening of multiple experimental conditions, especially in time-sensitive studies. Here, we present the plate-interfacing parallel encapsulation (PIPE) chip, a microfluidic chip designed to generate 50 to 90 μm diameter drops of up to 96 different conditions in parallel by interfacing individual drop makers with a standard 384-well microtiter plate. The PIPE chip is used to generate two types of optically barcoded drop libraries consisting of two-color fluorescent particle combinations: a library of 24 microbead barcodes and a library of 192 quantum dot barcodes. Barcoded combinations in the drop libraries are rapidly measured within a microfluidic device using fluorescence detection and distinct barcoded populations in the fluorescence drop data are identified using DBSCAN data clustering. Signal analysis reveals that particle size defines the source of dominant noise present in the fluorescence intensity distributions of the barcoded drop populations, arising from Poisson loading for microbeads and shot noise for quantum dots. A barcoded population from a drop library is isolated using fluorescence-activated drop sorting, enabling downstream analysis of drop contents. The PIPE chip can improve multiplexed high-throughput assays by enabling simultaneous encapsulation of barcoded samples stored in a microtiter plate and reducing sample preparation time.
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Affiliation(s)
- Geoffrey K Zath
- Center for Biofilm Engineering, Montana State University, Bozeman, MT, USA.
- Department of Chemical and Biological Engineering, Montana State University, Bozeman, MT, USA
| | - Ralph A Sperling
- Department of Physics, School of Engineering and Applied Sciences, Harvard University, Cambridge, MA, USA
- Fraunhofer Institute for Microengineering and Microsystems IMM, Mainz, Germany
| | - Carter W Hoffman
- Center for Biofilm Engineering, Montana State University, Bozeman, MT, USA.
- Department of Chemical and Biological Engineering, Montana State University, Bozeman, MT, USA
- Department of Physiology and Biomedical Engineering, Mayo Clinic, Rochester, MN, USA
| | - Dimitri A Bikos
- Center for Biofilm Engineering, Montana State University, Bozeman, MT, USA.
- Department of Chemical and Biological Engineering, Montana State University, Bozeman, MT, USA
| | - Reha Abbasi
- Center for Biofilm Engineering, Montana State University, Bozeman, MT, USA.
- Department of Chemical and Biological Engineering, Montana State University, Bozeman, MT, USA
| | - Adam R Abate
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, CA, USA
| | - David A Weitz
- Department of Physics, School of Engineering and Applied Sciences, Harvard University, Cambridge, MA, USA
- Wyss Institute for Biologically Inspired Engineering at Harvard University, Boston, MA, USA
| | - Connie B Chang
- Center for Biofilm Engineering, Montana State University, Bozeman, MT, USA.
- Department of Chemical and Biological Engineering, Montana State University, Bozeman, MT, USA
- Department of Physiology and Biomedical Engineering, Mayo Clinic, Rochester, MN, USA
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19
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Combinatorial perturbation sequencing on single cells using microwell-based droplet random pairing. Biosens Bioelectron 2022; 220:114913. [DOI: 10.1016/j.bios.2022.114913] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Revised: 11/09/2022] [Accepted: 11/11/2022] [Indexed: 11/13/2022]
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20
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Feng J, Neuzil J, Manz A, Iliescu C, Neuzil P. Microfluidic trends in drug screening and drug delivery. Trends Analyt Chem 2022. [DOI: 10.1016/j.trac.2022.116821] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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21
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Utharala R, Grab A, Vafaizadeh V, Peschke N, Ballinger M, Turei D, Tuechler N, Ma W, Ivanova O, Ortiz AG, Saez-Rodriguez J, Merten CA. A microfluidic Braille valve platform for on-demand production, combinatorial screening and sorting of chemically distinct droplets. Nat Protoc 2022; 17:2920-2965. [PMID: 36261631 DOI: 10.1038/s41596-022-00740-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Accepted: 06/16/2022] [Indexed: 11/09/2022]
Abstract
Droplet microfluidics is a powerful tool for a variety of biological applications including single-cell genetics, antibody discovery and directed evolution. All these applications make use of genetic libraries, illustrating the difficulty of generating chemically distinct droplets for screening applications. This protocol describes our Braille Display valving platform for on-demand generation of droplets with different chemical contents (16 different reagents and combinations thereof), as well as sorting droplets with different chemical properties, on the basis of fluorescence signals. The Braille Display platform is compact, versatile and cost efficient (only ~US$1,000 on top of a standard droplet microfluidics setup). The procedure includes manufacturing of microfluidic chips, assembly of custom hardware, co-encapsulation of cells and drugs into droplets, fluorescence detection of readout signals and data analysis using shared, freely available LabVIEW and Python packages. As a first application, we demonstrate the complete workflow for screening cancer cell drug sensitivities toward 74 conditions. Furthermore, we describe here an assay enabling the normalization of the observed drug sensitivity to the number of cancer cells per droplet, which additionally increases the robustness of the system. As a second application, we also demonstrate the sorting of droplets according to enzymatic activity. The drug screening application can be completed within 2 d; droplet sorting takes ~1 d; and all preparatory steps for manufacturing molds, chips and setting up the Braille controller can be accomplished within 1 week.
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Affiliation(s)
- Ramesh Utharala
- European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - Anna Grab
- European Molecular Biology Laboratory (EMBL), Heidelberg, Germany.,Clinical Cooperation Unit Molecular Hematology/Oncology, DKFZ Heidelberg and Translational Myeloma Research Group, Department of Internal Medicine V, University Hospital, Heidelberg, Germany
| | - Vida Vafaizadeh
- European Molecular Biology Laboratory (EMBL), Heidelberg, Germany.,Institute of Bioengineering, School of Engineering, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Nicolas Peschke
- European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - Martine Ballinger
- European Molecular Biology Laboratory (EMBL), Heidelberg, Germany.,Collaboration for joint PhD degree between EMBL and Heidelberg University, Faculty of Biosciences, Heidelberg, Germany
| | - Denes Turei
- European Molecular Biology Laboratory (EMBL), Heidelberg, Germany.,Faculty of Medicine and Heidelberg University Hospital, Institute of Computational Biomedicine, Heidelberg University, Heidelberg, Germany
| | - Nadine Tuechler
- European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - Wenwei Ma
- European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - Olga Ivanova
- Faculty of Medicine and Heidelberg University Hospital, Institute of Computational Biomedicine, Heidelberg University, Heidelberg, Germany
| | | | - Julio Saez-Rodriguez
- Faculty of Medicine and Heidelberg University Hospital, Institute of Computational Biomedicine, Heidelberg University, Heidelberg, Germany.,Faculty of Medicine, Joint Research Centre for Computational Biomedicine (JRC-COMBINE), RWTH Aachen University, Aachen, Germany
| | - Christoph A Merten
- Institute of Bioengineering, School of Engineering, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland.
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22
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Antibiotic combinations reduce Staphylococcus aureus clearance. Nature 2022; 610:540-546. [PMID: 36198788 PMCID: PMC9533972 DOI: 10.1038/s41586-022-05260-5] [Citation(s) in RCA: 34] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Accepted: 08/22/2022] [Indexed: 12/17/2022]
Abstract
The spread of antibiotic resistance is attracting increased attention to combination-based treatments. Although drug combinations have been studied extensively for their effects on bacterial growth1–11, much less is known about their effects on bacterial long-term clearance, especially at cidal, clinically relevant concentrations12–14. Here, using en masse microplating and automated image analysis, we systematically quantify Staphylococcus aureus survival during prolonged exposure to pairwise and higher-order cidal drug combinations. By quantifying growth inhibition, early killing and longer-term population clearance by all pairs of 14 antibiotics, we find that clearance interactions are qualitatively different, often showing reciprocal suppression whereby the efficacy of the drug mixture is weaker than any of the individual drugs alone. Furthermore, in contrast to growth inhibition6–10 and early killing, clearance efficacy decreases rather than increases as more drugs are added. However, specific drugs targeting non-growing persisters15–17 circumvent these suppressive effects. Competition experiments show that reciprocal suppressive drug combinations select against resistance to any of the individual drugs, even counteracting methicillin-resistant Staphylococcus aureus both in vitro and in a Galleria mellonella larva model. As a consequence, adding a β-lactamase inhibitor that is commonly used to potentiate treatment against β-lactam-resistant strains can reduce rather than increase treatment efficacy. Together, these results underscore the importance of systematic mapping the long-term clearance efficacy of drug combinations for designing more-effective, resistance-proof multidrug regimes. Different pairs of antibiotics show qualitatively different bacterial clearance interactions—some pairs show reciprocal suppression whereby the drug mixture efficacy is weaker than the individual drugs alone, and the clearance efficacy decreases as more drugs are added.
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23
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Zare Harofte S, Soltani M, Siavashy S, Raahemifar K. Recent Advances of Utilizing Artificial Intelligence in Lab on a Chip for Diagnosis and Treatment. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2022; 18:e2203169. [PMID: 36026569 DOI: 10.1002/smll.202203169] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/21/2022] [Revised: 07/16/2022] [Indexed: 05/14/2023]
Abstract
Nowadays, artificial intelligence (AI) creates numerous promising opportunities in the life sciences. AI methods can be significantly advantageous for analyzing the massive datasets provided by biotechnology systems for biological and biomedical applications. Microfluidics, with the developments in controlled reaction chambers, high-throughput arrays, and positioning systems, generate big data that is not necessarily analyzed successfully. Integrating AI and microfluidics can pave the way for both experimental and analytical throughputs in biotechnology research. Microfluidics enhances the experimental methods and reduces the cost and scale, while AI methods significantly improve the analysis of huge datasets obtained from high-throughput and multiplexed microfluidics. This review briefly presents a survey of the role of AI and microfluidics in biotechnology. Also, the incorporation of AI with microfluidics is comprehensively investigated. Specifically, recent studies that perform flow cytometry cell classification, cell isolation, and a combination of them by gaining from both AI methods and microfluidic techniques are covered. Despite all current challenges, various fields of biotechnology can be remarkably affected by the combination of AI and microfluidic technologies. Some of these fields include point-of-care systems, precision, personalized medicine, regenerative medicine, prognostics, diagnostics, and treatment of oncology and non-oncology-related diseases.
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Affiliation(s)
- Samaneh Zare Harofte
- Department of Mechanical Engineering, K. N. Toosi University of Technology, Tehran, 19967-15433, Iran
| | - Madjid Soltani
- Department of Mechanical Engineering, K. N. Toosi University of Technology, Tehran, 19967-15433, Iran
- Department of Electrical and Computer Engineering, Faculty of Engineering, University of Waterloo, Waterloo, ON, N2L 3G1, Canada
- Centre for Biotechnology and Bioengineering (CBB), University of Waterloo, Waterloo, ON, N2L 3G1, Canada
- Advanced Bioengineering Initiative Center, Multidisciplinary International Complex, K. N. Toosi University of Technology, Tehran, 14176-14411, Iran
- Cancer Biology Research Center, Cancer Institute of Iran, Tehran University of Medical Sciences, Tehran, 14197-33141, Iran
| | - Saeed Siavashy
- Department of Mechanical Engineering, K. N. Toosi University of Technology, Tehran, 19967-15433, Iran
| | - Kaamran Raahemifar
- Data Science and Artificial Intelligence Program, College of Information Sciences and Technology (IST), Penn State University, State College, PA, 16801, USA
- School of Optometry and Vision Science, Faculty of Science, University of Waterloo, 200 University Ave. W, Waterloo, ON, N2L 3G1, Canada
- Department of Chemical Engineering, Faculty of Engineering, University of Waterloo, 200 University Ave. W, Waterloo, ON, N2L 3G1, Canada
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24
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Postek W, Pacocha N, Garstecki P. Microfluidics for antibiotic susceptibility testing. LAB ON A CHIP 2022; 22:3637-3662. [PMID: 36069631 DOI: 10.1039/d2lc00394e] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
The rise of antibiotic resistance is a threat to global health. Rapid and comprehensive analysis of infectious strains is critical to reducing the global use of antibiotics, as informed antibiotic use could slow down the emergence of resistant strains worldwide. Multiple platforms for antibiotic susceptibility testing (AST) have been developed with the use of microfluidic solutions. Here we describe microfluidic systems that have been proposed to aid AST. We identify the key contributions in overcoming outstanding challenges associated with the required degree of multiplexing, reduction of detection time, scalability, ease of use, and capacity for commercialization. We introduce the reader to microfluidics in general, and we analyze the challenges and opportunities related to the field of microfluidic AST.
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Affiliation(s)
- Witold Postek
- Institute of Physical Chemistry of the Polish Academy of Sciences, ul. Kasprzaka 44/52, 01-224 Warszawa, Poland.
- Broad Institute of MIT and Harvard, Merkin Building, 415 Main St, Cambridge, MA 02142, USA.
| | - Natalia Pacocha
- Institute of Physical Chemistry of the Polish Academy of Sciences, ul. Kasprzaka 44/52, 01-224 Warszawa, Poland.
| | - Piotr Garstecki
- Institute of Physical Chemistry of the Polish Academy of Sciences, ul. Kasprzaka 44/52, 01-224 Warszawa, Poland.
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25
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Huang Z, Liu S, Pei X, Li S, He Y, Tong Y, Liu G. Fluorescence Signal-Readout of CRISPR/Cas Biosensors for Nucleic Acid Detection. BIOSENSORS 2022; 12:bios12100779. [PMID: 36290917 PMCID: PMC9599699 DOI: 10.3390/bios12100779] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Revised: 08/27/2022] [Accepted: 09/07/2022] [Indexed: 05/25/2023]
Abstract
The CRISPR/Cas system is now being used extensively in nucleic acid detection applications, particularly after the trans-cleavage activity of several Cas effectors was found. A CRISPR/Cas system combined with multiple signal-readout techniques has been developed for various molecular diagnostics applications. Fluorescence is now a widely utilized dominant read-out technique in CRISPR biosensors. An in-depth understanding of various fluorescence readout types and variables affecting the fluorescence signals can facilitate better experimental designs to effectively improve the analytical performance. There are the following two commonly used types of CRISPR/Cas detection modes: the first is based on binding activity, such as Cas9 and dCas9; the second is based on cleavage activity, such as Cas12a, Cas12b, Cas13, and Cas14. In this review, fluorescence signal-readout strategies from the last 5 years based on the binding activity and cleavage activity of the CRISPR/Cas system with fundamentals and examples are fully discussed. A detailed comparison of the available fluorescent reporter sequences and design principles is summarized. Current challenges and further applications of CRISPR-based detection methods will be discussed according to the most recent developments.
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Affiliation(s)
- Zhaohe Huang
- Institute of Cosmetic Regulatory Science and College of Chemistry and Materials Engineering, Beijing Technology and Business University, Beijing 100048, China
| | - Sitong Liu
- Institute of Cosmetic Regulatory Science and College of Chemistry and Materials Engineering, Beijing Technology and Business University, Beijing 100048, China
| | - Xiaojing Pei
- Institute of Cosmetic Regulatory Science and College of Chemistry and Materials Engineering, Beijing Technology and Business University, Beijing 100048, China
| | - Shujing Li
- Institute of Cosmetic Regulatory Science and College of Chemistry and Materials Engineering, Beijing Technology and Business University, Beijing 100048, China
| | - Yifan He
- Institute of Cosmetic Regulatory Science and College of Chemistry and Materials Engineering, Beijing Technology and Business University, Beijing 100048, China
| | - Yigang Tong
- College of Chemistry and Materials Engineering, Beijing Technology and Business University, Beijing 100029, China
| | - Guoqi Liu
- Biotecnovo (Beijing) Co., Ltd., Beijing Economic and Technological Development Zone, Beijing 100176, China
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26
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Recent advances in clustered regularly interspaced short palindromic repeats-based detection of severe acute respiratory syndrome coronavirus 2. Se Pu 2022; 40:773-781. [PMID: 36156623 PMCID: PMC9520371 DOI: 10.3724/sp.j.1123.2022.08001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
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27
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Macaraniag C, Luan Q, Zhou J, Papautsky I. Microfluidic techniques for isolation, formation, and characterization of circulating tumor cells and clusters. APL Bioeng 2022; 6:031501. [PMID: 35856010 PMCID: PMC9288269 DOI: 10.1063/5.0093806] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Accepted: 06/28/2022] [Indexed: 12/13/2022] Open
Abstract
Circulating tumor cell (CTC) clusters that are shed from the primary tumor into the bloodstream are associated with a poor prognosis, elevated metastatic potential, higher proliferation rate, and distinct molecular features compared to single CTCs. Studying CTC clusters may give us information on the differences in the genetic profiles, somatic mutations, and epigenetic changes in circulating cells compared to the primary tumor and metastatic sites. Microfluidic systems offer the means of studying CTC clusters through the ability to efficiently isolate these rare cells from the whole blood of patients in a liquid biopsy. Microfluidics can also be used to develop in vitro models of CTC clusters and make possible their characterization and analysis. Ultimately, microfluidic systems can offer the means to gather insight on the complexities of the metastatic process, the biology of cancer, and the potential for developing novel or personalized therapies. In this review, we aim to discuss the advantages and challenges of the existing microfluidic systems for working with CTC clusters. We hope that an improved understanding of the role microfluidics can play in isolation, formation, and characterization of CTC clusters, which can lead to increased sophistication of microfluidic platforms in cancer research.
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Affiliation(s)
- Celine Macaraniag
- Department of Biomedical Engineering, University of Illinois Chicago, Chicago, Illinois 60607, USA
| | - Qiyue Luan
- Department of Biomedical Engineering, University of Illinois Chicago, Chicago, Illinois 60607, USA
| | - Jian Zhou
- Department of Biomedical Engineering, University of Illinois Chicago, Chicago, Illinois 60607, USA
| | - Ian Papautsky
- Department of Biomedical Engineering, University of Illinois Chicago, Chicago, Illinois 60607, USA
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28
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Hemez C, Clarelli F, Palmer AC, Bleis C, Abel S, Chindelevitch L, Cohen T, Abel zur Wiesch P. Mechanisms of antibiotic action shape the fitness landscapes of resistance mutations. Comput Struct Biotechnol J 2022; 20:4688-4703. [PMID: 36147681 PMCID: PMC9463365 DOI: 10.1016/j.csbj.2022.08.030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2022] [Revised: 08/12/2022] [Accepted: 08/12/2022] [Indexed: 11/15/2022] Open
Abstract
Antibiotic-resistant pathogens are a major public health threat. A deeper understanding of how an antibiotic's mechanism of action influences the emergence of resistance would aid in the design of new drugs and help to preserve the effectiveness of existing ones. To this end, we developed a model that links bacterial population dynamics with antibiotic-target binding kinetics. Our approach allows us to derive mechanistic insights on drug activity from population-scale experimental data and to quantify the interplay between drug mechanism and resistance selection. We find that both bacteriostatic and bactericidal agents can be equally effective at suppressing the selection of resistant mutants, but that key determinants of resistance selection are the relationships between the number of drug-inactivated targets within a cell and the rates of cellular growth and death. We also show that heterogeneous drug-target binding within a population enables resistant bacteria to evolve fitness-improving secondary mutations even when drug doses remain above the resistant strain's minimum inhibitory concentration. Our work suggests that antibiotic doses beyond this "secondary mutation selection window" could safeguard against the emergence of high-fitness resistant strains during treatment.
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Affiliation(s)
- Colin Hemez
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Graduate Program in Biophysics, Harvard University, Boston, MA 02115, USA
- Corresponding authors at: Broad Institute, 75 Ames St, Room 3035, Cambridge, MA 02412, USA (C. Hemez). Department of Pharmacy, UiT – The Arctic University of Norway, 9019 Tromsø, Norway (P. Abel zur Wiesch).
| | - Fabrizio Clarelli
- Department of Pharmacy, UiT – The Arctic University of Norway, 9019 Tromsø, Norway
- Center for Infectious Disease Dynamics, Department of Biology, Pennsylvania State University, University Park, PA 16802, USA
| | - Adam C. Palmer
- Department of Pharmacology, Computational Medicine Program, Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Christina Bleis
- Department of Pharmacy, UiT – The Arctic University of Norway, 9019 Tromsø, Norway
- Center for Infectious Disease Dynamics, Department of Biology, Pennsylvania State University, University Park, PA 16802, USA
| | - Sören Abel
- Department of Pharmacy, UiT – The Arctic University of Norway, 9019 Tromsø, Norway
- Center for Infectious Disease Dynamics, Department of Biology, Pennsylvania State University, University Park, PA 16802, USA
- Division of Infection Control, Norwegian Institute of Public Health, Oslo 0318, Norway
| | - Leonid Chindelevitch
- Department of Infectious Disease Epidemiology, Imperial College, London SW7 2AZ, UK
| | - Theodore Cohen
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT 06520, USA
| | - Pia Abel zur Wiesch
- Department of Pharmacy, UiT – The Arctic University of Norway, 9019 Tromsø, Norway
- Center for Infectious Disease Dynamics, Department of Biology, Pennsylvania State University, University Park, PA 16802, USA
- Division of Infection Control, Norwegian Institute of Public Health, Oslo 0318, Norway
- Corresponding authors at: Broad Institute, 75 Ames St, Room 3035, Cambridge, MA 02412, USA (C. Hemez). Department of Pharmacy, UiT – The Arctic University of Norway, 9019 Tromsø, Norway (P. Abel zur Wiesch).
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29
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Droplet-based methods for tackling antimicrobial resistance. Curr Opin Biotechnol 2022; 76:102755. [PMID: 35841864 DOI: 10.1016/j.copbio.2022.102755] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Revised: 06/03/2022] [Accepted: 06/13/2022] [Indexed: 11/21/2022]
Abstract
Application of droplet-based methods enables (i) faster detection, (ii) increased sensitivity, (iii) characterization of the level of heterogeneity in response to antibiotics by bacterial populations, and (iv) expanded screening of the effectiveness of antibiotic combinations. Hereby, we discuss the key steps and parameters of droplet-based experiments to investigate antimicrobial resistance. We also review recent findings accomplished with these methods and highlight their advantages and capacity to yield new insights into the problem of antimicrobial resistance.
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30
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Benítez-Mateos AI, Roura Padrosa D, Paradisi F. Multistep enzyme cascades as a route towards green and sustainable pharmaceutical syntheses. Nat Chem 2022; 14:489-499. [PMID: 35513571 DOI: 10.1038/s41557-022-00931-2] [Citation(s) in RCA: 62] [Impact Index Per Article: 31.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2021] [Accepted: 03/17/2022] [Indexed: 12/25/2022]
Abstract
Enzyme cascades are a powerful technology to develop environmentally friendly and cost-effective synthetic processes to manufacture drugs, as they couple different biotransformations in sequential reactions to synthesize the product. These biocatalytic tools can address two key parameters for the pharmaceutical industry: an improved selectivity of synthetic reactions and a reduction of potential hazards by using biocompatible catalysts, which can be produced from sustainable sources, which are biodegradable and, generally, non-toxic. Here we outline a broad variety of enzyme cascades used either in vivo (whole cells) or in vitro (purified enzymes) to specifically target pharmaceutically relevant molecules, from simple building blocks to complex drugs. We also discuss the advantages and requirements of multistep enzyme cascades and their combination with chemical catalysts through a series of reported examples. Finally, we examine the efficiency of enzyme cascades and how they can be further improved by enzyme engineering, process intensification in flow reactors and/or enzyme immobilization to meet all the industrial requirements.
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Affiliation(s)
- Ana I Benítez-Mateos
- Department of Chemistry, Biochemistry and Pharmaceutical Sciences, University of Bern, Bern, Switzerland
| | - David Roura Padrosa
- Department of Chemistry, Biochemistry and Pharmaceutical Sciences, University of Bern, Bern, Switzerland
| | - Francesca Paradisi
- Department of Chemistry, Biochemistry and Pharmaceutical Sciences, University of Bern, Bern, Switzerland.
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31
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De Stefano P, Bianchi E, Dubini G. The impact of microfluidics in high-throughput drug-screening applications. BIOMICROFLUIDICS 2022; 16:031501. [PMID: 35646223 PMCID: PMC9142169 DOI: 10.1063/5.0087294] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/03/2022] [Accepted: 05/02/2022] [Indexed: 05/05/2023]
Abstract
Drug discovery is an expensive and lengthy process. Among the different phases, drug discovery and preclinical trials play an important role as only 5-10 of all drugs that begin preclinical tests proceed to clinical trials. Indeed, current high-throughput screening technologies are very expensive, as they are unable to dispense small liquid volumes in an accurate and quick way. Moreover, despite being simple and fast, drug screening assays are usually performed under static conditions, thus failing to recapitulate tissue-specific architecture and biomechanical cues present in vivo even in the case of 3D models. On the contrary, microfluidics might offer a more rapid and cost-effective alternative. Although considered incompatible with high-throughput systems for years, technological advancements have demonstrated how this gap is rapidly reducing. In this Review, we want to further outline the role of microfluidics in high-throughput drug screening applications by looking at the multiple strategies for cell seeding, compartmentalization, continuous flow, stimuli administration (e.g., drug gradients or shear stresses), and single-cell analyses.
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Affiliation(s)
- Paola De Stefano
- Laboratory of Biological Structure Mechanics, Department of Chemistry, Materials and Chemical Engineering “G. Natta,” Politecnico di Milano, Italy
| | - Elena Bianchi
- Laboratory of Biological Structure Mechanics, Department of Chemistry, Materials and Chemical Engineering “G. Natta,” Politecnico di Milano, Italy
| | - Gabriele Dubini
- Laboratory of Biological Structure Mechanics, Department of Chemistry, Materials and Chemical Engineering “G. Natta,” Politecnico di Milano, Italy
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32
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Chen CH, Bepler T, Pepper K, Fu D, Lu TK. Synthetic molecular evolution of antimicrobial peptides. Curr Opin Biotechnol 2022; 75:102718. [PMID: 35395425 DOI: 10.1016/j.copbio.2022.102718] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Revised: 02/14/2022] [Accepted: 03/01/2022] [Indexed: 01/18/2023]
Abstract
As we learn more about how peptide structure and activity are related, we anticipate that antimicrobial peptides will be engineered to have strong potency and distinct functions and that synthetic peptides will have new biomedical applications, such as treatments for emerging infectious diseases. As a result of the enormous number of possible amino acid sequences and the low-throughput nature of antimicrobial peptide assays, computational tools for peptide design and optimization are needed for direct experimentation toward obtaining functional sequences. Recent developments in computational tools have improved peptide design, saving labor, reagents, costs, and time. At the same time, improvements in peptide synthesis and experimental platforms continue to reduce the cost and increase the throughput of peptide-drug screening. In this review, we discuss the current methods of peptide design and engineering, including in silico methods and peptide synthesis and screening, and highlight areas of potential improvement.
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Affiliation(s)
- Charles H Chen
- Synthetic Biology Center, Massachusetts Institute of Technology (MIT), Cambridge, MA 02139, USA; Synthetic Biology Group, Research Laboratory of Electronics, Massachusetts Institute of Technology (MIT), Cambridge, MA 02139, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
| | - Tristan Bepler
- Synthetic Biology Center, Massachusetts Institute of Technology (MIT), Cambridge, MA 02139, USA; Synthetic Biology Group, Research Laboratory of Electronics, Massachusetts Institute of Technology (MIT), Cambridge, MA 02139, USA; Simons Machine Learning Center, New York Structural Biology Center, New York, NY 10027, USA
| | - Karen Pepper
- Synthetic Biology Group, Research Laboratory of Electronics, Massachusetts Institute of Technology (MIT), Cambridge, MA 02139, USA
| | - Debbie Fu
- Department of Biology, Tufts University, Medford, MA 02155, USA
| | - Timothy K Lu
- Synthetic Biology Center, Massachusetts Institute of Technology (MIT), Cambridge, MA 02139, USA; Synthetic Biology Group, Research Laboratory of Electronics, Massachusetts Institute of Technology (MIT), Cambridge, MA 02139, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology (MIT), Cambridge, MA 02142, USA; Harvard-MIT Division of Health Sciences and Technology, Cambridge, MA 02139, USA; Department of Biological Engineering, Massachusetts Institute of Technology (MIT), Cambridge, MA 02142, USA; Senti Biosciences, South San Francisco, CA 94080, USA.
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33
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34
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Aubry G, Milisavljevic M, Lu H. Automated and Dynamic Control of Chemical Content in Droplets for Scalable Screens of Small Animals. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2022; 18:e2200319. [PMID: 35229457 PMCID: PMC9050880 DOI: 10.1002/smll.202200319] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/16/2022] [Indexed: 06/14/2023]
Abstract
Screening functional phenotypes in small animals is important for genetics and drug discovery. Multiphase microfluidics has great potential for enhancing throughput but has been hampered by inefficient animal encapsulation and limited control over the animal's environment in droplets. Here, a highly efficient single-animal encapsulation unit, a liquid exchanger system for controlling the droplet chemical environment dynamically, and an automation scheme for the programming and robust execution of complex protocols are demonstrated. By careful use of interfacial forces, the liquid exchanger unit allows for adding and removing chemicals from a droplet and, therefore, generating chemical gradients inaccessible in previous multiphase systems. Using Caenorhabditis elegans as an example, it is demonstrated that these advances can serve to analyze dynamic phenotyping, such as behavior and neuronal activity, perform forward genetic screen, and are scalable to manipulate animals of different sizes. This platform paves the way for large-scale screens of complex dynamic phenotypes in small animals.
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Affiliation(s)
- Guillaume Aubry
- School of Chemical & Biomolecular Engineering, Georgia Institute of Technology, Atlanta, GA, 30332, USA
| | - Marija Milisavljevic
- School of Chemical & Biomolecular Engineering, Georgia Institute of Technology, Atlanta, GA, 30332, USA
| | - Hang Lu
- School of Chemical & Biomolecular Engineering, Georgia Institute of Technology, Atlanta, GA, 30332, USA
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35
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Xu L, Li X, Li W, Chang K, Yang H, Tao N, Zhang P, Payne EM, Modavi C, Humphries J, Lu C, Abate AR. Microbowls with Controlled Concavity for Accurate Microscale Mass Spectrometry. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2022; 34:e2108194. [PMID: 35045587 PMCID: PMC9028217 DOI: 10.1002/adma.202108194] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Revised: 12/15/2021] [Indexed: 06/14/2023]
Abstract
Patterned surfaces can enhance the sensitivity of laser desorption ionization mass spectrometry by segregating and concentrating analytes, but their fabrication can be challenging. Here, a simple method to fabricate substrates patterned with micrometer-scale wells that yield more accurate and sensitive mass spectrometry measurements compared to flat surfaces is described. The wells can also concentrate and localize cells and beads for cell-based assays.
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Affiliation(s)
- Linfeng Xu
- Department of Bioengineering and Therapeutic SciencesUniversity of California, San FranciscoSan FranciscoCA94158USA
| | - Xiangpeng Li
- Department of Bioengineering and Therapeutic SciencesUniversity of California, San FranciscoSan FranciscoCA94158USA
| | - Wenzong Li
- Amyris Inc.5885 Hollis St #100EmeryvilleCA94608USA
| | - Kai‐chun Chang
- Department of Bioengineering and Therapeutic SciencesUniversity of California, San FranciscoSan FranciscoCA94158USA
| | - Hyunjun Yang
- Institute for Neurodegenerative DiseasesWeill Institute for NeurosciencesUniversity of CaliforniaSan FranciscoCA94158USA
| | | | - Pengfei Zhang
- Department of Bioengineering and Therapeutic SciencesUniversity of California, San FranciscoSan FranciscoCA94158USA
| | - Emory M. Payne
- Department of ChemistryUniversity of MichiganAnn ArborMI48104USA
| | - Cyrus Modavi
- Department of Bioengineering and Therapeutic SciencesUniversity of California, San FranciscoSan FranciscoCA94158USA
| | | | - Chia‐Wei Lu
- Amyris Inc.5885 Hollis St #100EmeryvilleCA94608USA
| | - Adam R. Abate
- Department of Bioengineering and Therapeutic SciencesUniversity of California, San FranciscoSan FranciscoCA94158USA
- Chan Zuckerberg BiohubSan FranciscoCA94158USA
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36
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Postek W, Garstecki P. Droplet Microfluidics for High-Throughput Analysis of Antibiotic Susceptibility in Bacterial Cells and Populations. Acc Chem Res 2022; 55:605-615. [PMID: 35119826 PMCID: PMC8892833 DOI: 10.1021/acs.accounts.1c00729] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Antibiotic-resistant bacteria are an increasing concern both in everyday life and specialized environments such as healthcare. As the rate of antibiotic-resistant infections rises, so do complications to health and the risk of disability and death. Urgent action is required regarding the discovery of new antibiotics and rapid diagnosis of the resistance profile of an infectious pathogen as well as a better understanding of population and single-cell distribution of the resistance level. High-throughput screening is the major affordance of droplet microfluidics. Droplet screens can be exploited both to look for combinations of drugs that could stop an infection of multidrug-resistant bacteria and to search for the source of resistance via directed-evolution experiments or the analysis of various responses to a drug by genetically identical bacteria. In droplet techniques that have been used in this way for over a decade, aqueous droplets containing antibiotics and bacteria are manipulated both within and outside of the microfluidic devices. The diagnostics problem was approached by producing a series of microfluidic systems with integrated dilution modules for automated preparation of antibiotic concentration gradients, achieving the speed that allowed for high-throughput combinatorial assays. We developed a method for automated emulsification of a series of samples that facilitated measuring the resistance levels of thousands of individual cells encapsulated in droplets and quantifying the inoculum effect, the dependence of resistance level on bacterial cell count. Screening of single cells encapsulated in droplets with varying antibiotic contents has revealed a distribution of resistance levels within populations of clonally identical cells. To be able to screen bacteria from clinical samples, a study of fluorescent dyes in droplets determined that a derivative of a popular viability marker is more suitable for droplet assays. We have developed a detection system that analyzes the growth or death state of bacteria with antibiotics for thousands of droplets per second by measuring the scattering of light hitting the droplets without labeling the cells or droplets. The droplet-based microchemostats enabled long-term evolution of resistance experiments, which will be integrated with high-throughput single-cell assays to better understand the mechanism of resistance acquisition and loss. These techniques underlie automated combinatorial screens of antibiotic resistance in single cells from clinical samples. We hope that this Account will inspire new droplet-based research on the antibiotic susceptibility of bacteria.
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Affiliation(s)
- Witold Postek
- Institute of Physical Chemistry, Polish Academy of Sciences, ul. Kasprzaka 44/52, 01-224 Warszawa, Poland
| | - Piotr Garstecki
- Institute of Physical Chemistry, Polish Academy of Sciences, ul. Kasprzaka 44/52, 01-224 Warszawa, Poland
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37
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Thakku SG, Ackerman CM, Myhrvold C, Bhattacharyya RP, Livny J, Ma P, Gomez GI, Sabeti PC, Blainey PC, Hung DT. Multiplexed detection of bacterial nucleic acids using Cas13 in droplet microarrays. PNAS NEXUS 2022; 1:pgac021. [PMID: 35450424 PMCID: PMC9013781 DOI: 10.1093/pnasnexus/pgac021] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Revised: 01/22/2022] [Accepted: 03/28/2022] [Indexed: 12/26/2022]
Abstract
Rapid and accurate diagnosis of infections is fundamental to individual patient care and public health management. Nucleic acid detection methods are critical to this effort, but are limited either in the breadth of pathogens targeted or by the expertise and infrastructure required. We present here a high-throughput system that enables rapid identification of bacterial pathogens, bCARMEN, which utilizes: (1) modular CRISPR-Cas13-based nucleic acid detection with enhanced sensitivity and specificity; and (2) a droplet microfluidic system that enables thousands of simultaneous, spatially multiplexed detection reactions at nanoliter volumes; and (3) a novel preamplification strategy that further enhances sensitivity and specificity. We demonstrate bCARMEN is capable of detecting and discriminating 52 clinically relevant bacterial species and several key antibiotic resistance genes. We further develop a simple proof of principle workflow using stabilized reagents and cell phone camera optical readout, opening up the possibility of a rapid point-of-care multiplexed bacterial pathogen identification and antibiotic susceptibility testing.
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Affiliation(s)
| | | | | | | | - Jonathan Livny
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Peijun Ma
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | | | - Pardis C Sabeti
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Paul C Blainey
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Deborah T Hung
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
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38
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Abstract
Cell manipulation in droplets has emerged as one of the great successes of microfluidic technologies, with the development of single-cell screening. However, the droplet format has also served to go beyond single-cell studies, namely by considering the interactions between different cells or between cells and their physical or chemical environment. These studies pose specific challenges linked to the need for long-term culture of adherent cells or the diverse types of measurements associated with complex biological phenomena. Here we review the emergence of droplet microfluidic methods for culturing cells and studying their interactions. We begin by characterizing the quantitative aspects that determine the ability to encapsulate cells, transport molecules, and provide sufficient nutrients within the droplets. This is followed by an evaluation of the biological constraints such as the control of the biochemical environment and promoting the anchorage of adherent cells. This first part ends with a description of measurement methods that have been developed. The second part of the manuscript focuses on applications of these technologies for cancer studies, immunology, and stem cells while paying special attention to the biological relevance of the cellular assays and providing guidelines on improving this relevance.
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Affiliation(s)
- Sébastien Sart
- LadHyX, CNRS, Ecole Polytechnique, Institut Polytechnique de Paris, 91120 Palaiseau, France.,Physical Microfluidics and Bioengineering, Institut Pasteur, 25-28 Rue du Dr. Roux, 75015 Paris, France
| | - Gustave Ronteix
- LadHyX, CNRS, Ecole Polytechnique, Institut Polytechnique de Paris, 91120 Palaiseau, France.,Physical Microfluidics and Bioengineering, Institut Pasteur, 25-28 Rue du Dr. Roux, 75015 Paris, France
| | - Shreyansh Jain
- LadHyX, CNRS, Ecole Polytechnique, Institut Polytechnique de Paris, 91120 Palaiseau, France.,Physical Microfluidics and Bioengineering, Institut Pasteur, 25-28 Rue du Dr. Roux, 75015 Paris, France
| | - Gabriel Amselem
- LadHyX, CNRS, Ecole Polytechnique, Institut Polytechnique de Paris, 91120 Palaiseau, France.,Physical Microfluidics and Bioengineering, Institut Pasteur, 25-28 Rue du Dr. Roux, 75015 Paris, France
| | - Charles N Baroud
- LadHyX, CNRS, Ecole Polytechnique, Institut Polytechnique de Paris, 91120 Palaiseau, France.,Physical Microfluidics and Bioengineering, Institut Pasteur, 25-28 Rue du Dr. Roux, 75015 Paris, France
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39
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Li H, Zhang P, Hsieh K, Wang TH. Combinatorial nanodroplet platform for screening antibiotic combinations. LAB ON A CHIP 2022; 22:621-631. [PMID: 35015012 PMCID: PMC9035339 DOI: 10.1039/d1lc00865j] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
The emergence and spread of multidrug resistant bacterial strains and concomitant dwindling of effective antibiotics pose worldwide healthcare challenges. To address these challenges, advanced engineering tools are developed to personalize antibiotic treatments by speeding up the diagnostics that is critical to prevent antibiotic misuse and overuse and make full use of existing antibiotics. Meanwhile, it is necessary to investigate novel antibiotic strategies. Recently, repurposing mono antibiotics into combinatorial antibiotic therapies has shown great potential for treatment of bacterial infections. However, widespread adoption of drug combinations has been hindered by the complexity of screening techniques and the cost of reagent consumptions in practice. In this study, we developed a combinatorial nanodroplet platform for automated and high-throughput screening of antibiotic combinations while consuming orders of magnitude lower reagents than the standard microtiter-based screening method. In particular, the proposed platform is capable of creating nanoliter droplets with multiple reagents in an automatic manner, tuning concentrations of each component, performing biochemical assays with high flexibility (e.g., temperature and duration), and achieving detection with high sensitivity. A biochemical assay, based on the reduction of resazurin by the metabolism of bacteria, has been characterized and employed to evaluate the combinatorial effects of the antibiotics of interest. In a pilot study, we successfully screened pairwise combinations between 4 antibiotics for a model Escherichia coli strain.
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Affiliation(s)
- Hui Li
- Department of Mechanical Engineering, Johns Hopkins University, Baltimore, MD, USA.
| | - Pengfei Zhang
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, USA
| | - Kuangwen Hsieh
- Department of Mechanical Engineering, Johns Hopkins University, Baltimore, MD, USA.
| | - Tza-Huei Wang
- Department of Mechanical Engineering, Johns Hopkins University, Baltimore, MD, USA.
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, USA
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40
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A Monolithic 3D Printed Axisymmetric Co-Flow Single and Compound Emulsion Generator. MICROMACHINES 2022; 13:mi13020188. [PMID: 35208313 PMCID: PMC8877394 DOI: 10.3390/mi13020188] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/31/2021] [Revised: 01/12/2022] [Accepted: 01/12/2022] [Indexed: 11/24/2022]
Abstract
We report a microfluidic droplet generator which can produce single and compound droplets using a 3D axisymmetric co-flow structure. The design considered for the fabrication of the device integrated a user-friendly and cost-effective 3D printing process. To verify the performance of the device, single and compound emulsions of deionized water and mineral oil were generated and their features such as size, generation frequency, and emulsion structures were successfully characterized. In addition, the generation of bio emulsions such as alginate and collagen aqueous droplets in mineral oil was demonstrated in this study. Overall, the monolithic 3D printed axisymmetric droplet generator could offer any user an accessible and easy-to-utilize device for the generation of single and compound emulsions.
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41
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Uzoukwu EU, Phandanouvong-Lozano V, Usman H, Sfeir C, Niepa THR. Droplet-based microsystems as novel assessment tools for oral microbial dynamics. Biotechnol Adv 2022; 55:107903. [PMID: 34990774 DOI: 10.1016/j.biotechadv.2021.107903] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Revised: 12/03/2021] [Accepted: 12/30/2021] [Indexed: 12/11/2022]
Abstract
The human microbiome comprises thousands of microbial species that live in and on the body and play critical roles in human health and disease. Recent findings on the interplay among members of the oral microbiome, defined by a personalized set of microorganisms, have elucidated the role of bacteria and yeasts in oral health and diseases including dental caries, halitosis, and periodontal infections. However, the majority of these studies rely on traditional culturing methods which are limited in their ability of replicating the oral microenvironment, and therefore fail to evaluate key microbial interactions in microbiome dynamics. Novel culturing methods have emerged to address this shortcoming. Here, we reviewed the potential of droplet-based microfluidics as an alternative approach for culturing microorganisms and assessing the oral microbiome dynamics. We discussed the state of the art and recent progress in the field of oral microbiology. Although at its infancy, droplet-based microtechnology presents an interesting potential for elucidating oral microbial dynamics and pathophysiology. We highlight how new findings provided by current microfluidic-based methodologies could advance the investigation of the oral microbiome. We anticipate that our work involving the droplet-based microfluidic technique with a semipermeable membrane will lay the foundations for future microbial dynamics studies and further expand the knowledge of the oral microbiome and its implication in oral health.
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Affiliation(s)
| | | | - Huda Usman
- Department of Chemical and Petroleum Engineering, University of Pittsburgh, PA, USA
| | - Charles Sfeir
- Department of Bioengineering, University of Pittsburgh, PA, USA; Department of Periodontics and Preventive Dentistry, University of Pittsburgh, PA, USA; Department of Oral Biology, University of Pittsburgh, PA, USA; The Center for Craniofacial Regeneration, University of Pittsburgh, PA, USA; The McGowan Institute for Regenerative Medicine, University of Pittsburgh, PA, USA
| | - Tagbo H R Niepa
- Department of Chemical and Petroleum Engineering, University of Pittsburgh, PA, USA; Department of Bioengineering, University of Pittsburgh, PA, USA; Department of Civil and Environmental Engineering, University of Pittsburgh, PA, USA; Department of Mechanical Engineering and Materials Science, University of Pittsburgh, PA, USA; Center for Medicine and the Microbiome, University of Pittsburgh, PA, USA; The McGowan Institute for Regenerative Medicine, University of Pittsburgh, PA, USA.
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42
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Davis K, Greenstein T, Viau Colindres R, Aldridge BB. Leveraging laboratory and clinical studies to design effective antibiotic combination therapy. Curr Opin Microbiol 2021; 64:68-75. [PMID: 34628295 PMCID: PMC8671129 DOI: 10.1016/j.mib.2021.09.006] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2021] [Revised: 07/28/2021] [Accepted: 09/16/2021] [Indexed: 01/21/2023]
Abstract
Interest in antibiotic combination therapy is increasing due to antimicrobial resistance and a slowing antibiotic pipeline. However, aside from specific indications, combination therapy in the clinic is often not administered systematically; instead, it is used at the physician's discretion as a bet-hedging mechanism to increase the chances of appropriately targeting a pathogen(s) with an unknown antibiotic resistance profile. Some recent clinical trials have been unable to demonstrate superior efficacy of combination therapy over monotherapy. Other trials have shown a benefit of combination therapy in defined circumstances consistent with recent studies indicating that factors including species, strain, resistance profile, and microenvironment affect drug combination efficacy and drug interactions. In this review, we discuss how a careful study design that takes these factors into account, along with the different drug interaction and potency metrics for assessing combination performance, may provide the necessary insight to understand the best clinical use-cases for combination therapy.
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Affiliation(s)
- Kathleen Davis
- Department of Molecular Biology & Microbiology, Tufts University School of Medicine, United States; Stuart B. Levy Center for Integrated Management of Antimicrobial Resistance, United States
| | - Talia Greenstein
- Stuart B. Levy Center for Integrated Management of Antimicrobial Resistance, United States; Graduate School of Biomedical Sciences, Tufts University School of Medicine, United States
| | - Roberto Viau Colindres
- Stuart B. Levy Center for Integrated Management of Antimicrobial Resistance, United States; Department of Geographic Medicine and Infectious Diseases, Tufts Medical Center, United States
| | - Bree B Aldridge
- Department of Molecular Biology & Microbiology, Tufts University School of Medicine, United States; Stuart B. Levy Center for Integrated Management of Antimicrobial Resistance, United States; Graduate School of Biomedical Sciences, Tufts University School of Medicine, United States
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43
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Kehe J, Ortiz A, Kulesa A, Gore J, Blainey PC, Friedman J. Positive interactions are common among culturable bacteria. SCIENCE ADVANCES 2021; 7:eabi7159. [PMID: 34739314 PMCID: PMC8570599 DOI: 10.1126/sciadv.abi7159] [Citation(s) in RCA: 76] [Impact Index Per Article: 25.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Accepted: 09/16/2021] [Indexed: 05/19/2023]
Abstract
Interspecies interactions shape the structure and function of microbial communities. In particular, positive, growth-promoting interactions can substantially affect the diversity and productivity of natural and engineered communities. However, the prevalence of positive interactions and the conditions in which they occur are not well understood. To address this knowledge gap, we used kChip, an ultrahigh-throughput coculture platform, to measure 180,408 interactions among 20 soil bacteria across 40 carbon environments. We find that positive interactions, often described to be rare, occur commonly and primarily as parasitisms between strains that differ in their carbon consumption profiles. Notably, nongrowing strains are almost always promoted by strongly growing strains (85%), suggesting a simple positive interaction–mediated approach for cultivation, microbiome engineering, and microbial consortium design.
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Affiliation(s)
- Jared Kehe
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Anthony Ortiz
- Physics of Living Systems, Department of Physics, Massachusetts Institute of Technology, Cambridge, MA, USA
- Microbiology Graduate Program, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Anthony Kulesa
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Jeff Gore
- Physics of Living Systems, Department of Physics, Massachusetts Institute of Technology, Cambridge, MA, USA
- Microbiology Graduate Program, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Paul C. Blainey
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Koch Institute for Integrative Cancer Research at the Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Jonathan Friedman
- Department of Plant Pathology and Microbiology, The Hebrew University of Jerusalem, Rehovot, Israel
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44
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Ou Y, Cao S, Zhang J, Dong W, Yang Z, Yu Z. Droplet microfluidics on analysis of pathogenic microbes for wastewater-based epidemiology. Trends Analyt Chem 2021; 143:116333. [PMID: 34720276 PMCID: PMC8547957 DOI: 10.1016/j.trac.2021.116333] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Infectious diseases caused by pathogenic microbes have posed a major health issue for the public, such as the ongoing COVID-19 global pandemic. In recent years, wastewater-based epidemiology (WBE) is emerging as an effective and unbiased method for monitoring public health. Despite its increasing importance, the advancement of WBE requires more competent and streamlined analytical platforms. Herein we discuss the interactions between WBE and droplet microfluidics, focusing on the analysis of pathogens in droplets, which is hard to be tackled by traditional analytical tools. We highlight research works from three aspects, namely, quantitation of pathogen biomarkers in droplets, single-cell analysis in droplets, and living cell biosensors in droplets, as well as providing future perspectives on the synergy between WBE and droplet microfluidics.
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Affiliation(s)
- Yangteng Ou
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Chemical Engineering, Nanjing Tech University, 30 Puzhu South Road, Nanjing, 211816, PR China.,Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK
| | - Shixiang Cao
- State Key Laboratory of Materials-Oriented Chemical Engineering, Nanjing Tech University, 30 Puzhu South Road, Nanjing, 211816, PR China
| | - Jing Zhang
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Chemical Engineering, Nanjing Tech University, 30 Puzhu South Road, Nanjing, 211816, PR China
| | - Weiliang Dong
- State Key Laboratory of Materials-Oriented Chemical Engineering, Nanjing Tech University, 30 Puzhu South Road, Nanjing, 211816, PR China
| | - Zhugen Yang
- School of Water, Energy and Environment, Cranfield University, Cranfield, MK43 0AL, UK
| | - Ziyi Yu
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Chemical Engineering, Nanjing Tech University, 30 Puzhu South Road, Nanjing, 211816, PR China
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45
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Jusková P, Schmitt S, Armbrecht L, Dittrich PS. Microbial factories: monitoring vitamin B 2 production by Escherichia coli in microfluidic cultivation chambers. LAB ON A CHIP 2021; 21:4071-4080. [PMID: 34618882 PMCID: PMC8547325 DOI: 10.1039/d1lc00621e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Accepted: 09/24/2021] [Indexed: 06/13/2023]
Abstract
Microbial cells represent a standard production host for various important biotechnological products. Production yields can be increased by optimising strains and growth conditions and understanding deviations in production rates over time or within the microbial population. We introduce here microfluidic cultivation chambers for highly parallel studies on microbial cultures, enabling continuous biosynthesis monitoring of the industrially relevant product by Escherichia coli cells. The growth chambers are defined by ring-valves that encapsulate a volume of 200 pL when activated. Bacterial cells, labelled with magnetic beads, are inoculated in a small magnetic trap, positioned in the centre of each chamber. Afterwards, the ring-valves are partially activated, allowing for exchange reagents, such as the addition of fresh media or specific inducers of biosynthesis, while the bacterial cells and their progeny are maintained inside. On this platform, we monitor the production of riboflavin (vitamin B2). We used different variants of a riboflavin-overproducing bacterial strain with different riboflavin production levels and could distinguish them on the level of individual micro-colonies. In addition, we could also observe differences in the bacterial morphology with respect to the production. The presented platform represents a flexible microfluidic tool for further studies of microbial cell factories.
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Affiliation(s)
- Petra Jusková
- Department of Biosystems Science and Engineering, Bioanalytics Group, ETH Zürich, Mattenstrasse 26, CH-4058 Basel, Switzerland.
| | - Steven Schmitt
- Department of Biosystems Science and Engineering, Bioprocess Laboratory, ETH Zürich, Mattenstrasse 26, CH-4058 Basel, Switzerland
| | - Lucas Armbrecht
- Department of Biosystems Science and Engineering, Bioanalytics Group, ETH Zürich, Mattenstrasse 26, CH-4058 Basel, Switzerland.
| | - Petra S Dittrich
- Department of Biosystems Science and Engineering, Bioanalytics Group, ETH Zürich, Mattenstrasse 26, CH-4058 Basel, Switzerland.
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46
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Ha NS, de Raad M, Han LZ, Golini A, Petzold CJ, Northen TR. Faster, better, and cheaper: harnessing microfluidics and mass spectrometry for biotechnology. RSC Chem Biol 2021; 2:1331-1351. [PMID: 34704041 PMCID: PMC8496484 DOI: 10.1039/d1cb00112d] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2021] [Accepted: 07/01/2021] [Indexed: 12/14/2022] Open
Abstract
High-throughput screening technologies are widely used for elucidating biological activities. These typically require trade-offs in assay specificity and sensitivity to achieve higher throughput. Microfluidic approaches enable rapid manipulation of small volumes and have found a wide range of applications in biotechnology providing improved control of reaction conditions, faster assays, and reduced reagent consumption. The integration of mass spectrometry with microfluidics has the potential to create high-throughput, sensitivity, and specificity assays. This review introduces the widely-used mass spectrometry ionization techniques that have been successfully integrated with microfluidics approaches such as continuous-flow system, microchip electrophoresis, droplet microfluidics, digital microfluidics, centrifugal microfluidics, and paper microfluidics. In addition, we discuss recent applications of microfluidics integrated with mass spectrometry in single-cell analysis, compound screening, and the study of microorganisms. Lastly, we provide future outlooks towards online coupling, improving the sensitivity and integration of multi-omics into a single platform.
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Affiliation(s)
- Noel S Ha
- Biological Systems and Engineering, Lawrence Berkeley National Laboratory Berkeley CA USA
- US Department of Energy Joint BioEnergy Institute Emeryville CA USA
| | - Markus de Raad
- Environmental Genomics and Systems Biology, Biosciences, Lawrence Berkeley National Laboratory Berkeley CA USA
| | - La Zhen Han
- Environmental Genomics and Systems Biology, Biosciences, Lawrence Berkeley National Laboratory Berkeley CA USA
- US Department of Energy Joint Genome Institute Berkeley CA USA
| | - Amber Golini
- Environmental Genomics and Systems Biology, Biosciences, Lawrence Berkeley National Laboratory Berkeley CA USA
- US Department of Energy Joint Genome Institute Berkeley CA USA
| | - Christopher J Petzold
- Biological Systems and Engineering, Lawrence Berkeley National Laboratory Berkeley CA USA
- US Department of Energy Joint BioEnergy Institute Emeryville CA USA
| | - Trent R Northen
- Biological Systems and Engineering, Lawrence Berkeley National Laboratory Berkeley CA USA
- US Department of Energy Joint BioEnergy Institute Emeryville CA USA
- Environmental Genomics and Systems Biology, Biosciences, Lawrence Berkeley National Laboratory Berkeley CA USA
- US Department of Energy Joint Genome Institute Berkeley CA USA
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47
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Nakagawa Y, Ohnuki S, Kondo N, Itto-Nakama K, Ghanegolmohammadi F, Isozaki A, Ohya Y, Goda K. Are droplets really suitable for single-cell analysis? A case study on yeast in droplets. LAB ON A CHIP 2021; 21:3793-3803. [PMID: 34581379 DOI: 10.1039/d1lc00469g] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Single-cell analysis has become one of the main cornerstones of biotechnology, inspiring the advent of various microfluidic compartments for cell cultivation such as microwells, microtrappers, microcapillaries, and droplets. A fundamental assumption for using such microfluidic compartments is that unintended stress or harm to cells derived from the microenvironments is insignificant, which is a crucial condition for carrying out unbiased single-cell studies. Despite the significance of this assumption, simple viability or growth tests have overwhelmingly been the assay of choice for evaluating culture conditions while empirical studies on the sub-lethal effect on cellular functions have been insufficient in many cases. In this work, we assessed the effect of culturing cells in droplets on the cellular function using yeast morphology as an indicator. Quantitative morphological analysis using CalMorph, an image-analysis program, demonstrated that cells cultured in flasks, large droplets, and small droplets significantly differed morphologically. From these differences, we identified that the cell cycle was delayed in droplets during the G1 phase and during the process of bud growth likely due to the checkpoint mechanism and impaired mitochondrial function, respectively. Furthermore, comparing small and large droplets, cells cultured in large droplets were morphologically more similar to those cultured in a flask, highlighting the advantage of increasing the droplet size. These results highlight a potential source of bias in cell analysis using droplets and reinforce the significance of assessing culture conditions of microfluidic cultivation methods for specific study cases.
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Affiliation(s)
- Yuta Nakagawa
- Department of Chemistry, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan.
| | - Shinsuke Ohnuki
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba 277-8562, Japan
| | - Naoko Kondo
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba 277-8562, Japan
| | - Kaori Itto-Nakama
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba 277-8562, Japan
| | - Farzan Ghanegolmohammadi
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba 277-8562, Japan
| | - Akihiro Isozaki
- Department of Chemistry, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan.
| | - Yoshikazu Ohya
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba 277-8562, Japan
- Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8654, Japan.
| | - Keisuke Goda
- Department of Chemistry, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan.
- Department of Bioengineering, Samueli School of Engineering, University of California, Los Angeles, 420 Westwood Plaza, California 90095, USA
- Institute of Technological Sciences, Wuhan University, Wuhan, Hubei 430072, China
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48
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Confining Trypanosoma brucei in emulsion droplets reveals population variabilities in division rates and improves in vitro cultivation. Sci Rep 2021; 11:18192. [PMID: 34521865 PMCID: PMC8440574 DOI: 10.1038/s41598-021-97356-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Accepted: 07/30/2021] [Indexed: 11/08/2022] Open
Abstract
Trypanosome parasites are infecting mammals in Sub-Saharan Africa and are transmitted between hosts through bites of the tsetse fly. The transmission from the insect vector to the mammal host causes a number of metabolic and physiological changes. A fraction of the population continuously adapt to the immune system of the host, indicating heterogeneity at the population level. Yet, the cell to cell variability in populations is mostly unknown. We develop here an analytical method for quantitative measurements at the single cell level based on encapsulation and cultivation of single-cell Trypanosoma brucei in emulsion droplets. We first show that mammalian stage trypanosomes survive for several hours to days in droplets, with an influence of droplet size on both survival and growth. We unravel various growth patterns within a population and find that droplet cultivation of trypanosomes results in 10-fold higher cell densities of the highest dividing cell variants compared to standard cultivation techniques. Some variants reach final cell titers in droplets closer to what is observed in nature than standard culture, of practical interest for cell production. Droplet microfluidics is therefore a promising tool for trypanosome cultivation and analysis with further potential for high-throughput single cell trypanosome analysis.
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49
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Chen DP, Chen C, Wu PY, Lin YH, Lin WT, Yan YL. Micro-Droplet Platform for Exploring the Mechanism of Mixed Field Agglutination in B 3 Subtype. BIOSENSORS 2021; 11:276. [PMID: 34436078 PMCID: PMC8393913 DOI: 10.3390/bios11080276] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Revised: 08/04/2021] [Accepted: 08/13/2021] [Indexed: 12/22/2022]
Abstract
B3 is the most common subtype of blood group B in the Taiwanese population, and most of the B3 individuals in the Taiwanese population have the IVS3 + 5 G > A (rs55852701) gene variation. Additionally, a typical mixed field agglutination is observed when the B3 subtype is tested with anti-B antibody or anti-AB antibody. The molecular biology of the gene variation in the B3 subtype has been identified, however, the mechanism of the mixed field agglutination caused by the type B3 blood samples is still unclear. Therefore, the purpose of this study was to understand the reason for the mixed field agglutination caused by B3. A micro-droplet platform was used to observe the agglutination of type B and type B3 blood samples in different blood sample concentrations, antibody concentrations, and at reaction times. We found that the agglutination reaction in every droplet slowed down with an increase in the dilution ratio of blood sample and antibody, whether type B blood or type B3 blood was used. However, as the reaction time increased, the complete agglutination in the droplet was seen in type B blood, while the mixed field agglutination still occurred in B3 within 1 min. In addition, the degree of agglutination was similar in each droplet, which showed high reproducibility. As a result, we inferred that there are two types of cells in the B3 subtype that simultaneously create a mixed field agglutination, rather than each red blood cell carrying a small amount of antigen, resulting in less agglutination.
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Affiliation(s)
- Ding-Ping Chen
- Department of Laboratory Medicine, Chang Gung Memorial Hospital, Taoyuan City 333, Taiwan; (D.-P.C.); (W.-T.L.); (Y.-L.Y.)
- Department of Medical Biotechnology and Laboratory Science, College of Medicine, Chang Gung University, Taoyuan City 333, Taiwan
- Graduate Institute of Biomedical Sciences, College of Medicine, Chang Gung University, Taoyuan City 333, Taiwan
| | - Chen Chen
- Department of Electronic Engineering, Chang Gung University, Taoyuan City 333, Taiwan; (C.C.); (P.-Y.W.)
| | - Pei-Yu Wu
- Department of Electronic Engineering, Chang Gung University, Taoyuan City 333, Taiwan; (C.C.); (P.-Y.W.)
| | - Yen-Heng Lin
- Department of Electronic Engineering, Chang Gung University, Taoyuan City 333, Taiwan; (C.C.); (P.-Y.W.)
- Graduate Institute of Biomedical Engineering, Chang Gung University, Taoyuan City 333, Taiwan
- Department of Otolaryngology-Head and Neck Surgery, Chang Gung Memorial Hospital, Taoyuan City 333, Taiwan
| | - Wei-Tzu Lin
- Department of Laboratory Medicine, Chang Gung Memorial Hospital, Taoyuan City 333, Taiwan; (D.-P.C.); (W.-T.L.); (Y.-L.Y.)
| | - Yi-Liang Yan
- Department of Laboratory Medicine, Chang Gung Memorial Hospital, Taoyuan City 333, Taiwan; (D.-P.C.); (W.-T.L.); (Y.-L.Y.)
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50
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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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