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Vahabi H, Liu J, Dai Y, Joh DY, Britton R, Heggestad J, Kinnamon D, Rajput S, Chilkoti A. A gravity-driven droplet fluidic point-of-care test. DEVICE 2023; 1:100009. [PMID: 37872891 PMCID: PMC10588563 DOI: 10.1016/j.device.2023.100009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2023]
Abstract
We report a simple droplet fluidic point-of-care test (POCT) that uses gravity to manipulate the sequence, timing, and motion of droplets on a surface. To fabricate this POCT, we first developed a surface coating toolbox of nine different coatings with three levels of wettability and three levels of slipperiness that can be independently tailored. We then fabricated a device that has interconnected fluidic elements-pumps, flow resistors and flow guides-on a highly slippery solid surface to precisely control the timing and sequence of motion of multiple droplets and their interactions on the surface. We then used this device to carry out a multi-step enzymatic assay of a clinically relevant analyte-lactate dehydrogenase (LDH)-to demonstrate the application of this technology for point-of-care diagnosis.
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Affiliation(s)
- Hamed Vahabi
- Department of Biomedical Engineering, Duke University, Durham, NC, 27705
| | - Jason Liu
- Department of Biomedical Engineering, Duke University, Durham, NC, 27705
| | - Yifan Dai
- Department of Biomedical Engineering, Duke University, Durham, NC, 27705
| | - Daniel Y Joh
- Department of Biomedical Engineering, Duke University, Durham, NC, 27705
| | - Rhett Britton
- Department of Biomedical Engineering, Duke University, Durham, NC, 27705
| | - Jacob Heggestad
- Department of Biomedical Engineering, Duke University, Durham, NC, 27705
| | - David Kinnamon
- Department of Biomedical Engineering, Duke University, Durham, NC, 27705
| | - Satyam Rajput
- Department of Biomedical Engineering, Duke University, Durham, NC, 27705
| | - Ashutosh Chilkoti
- Department of Biomedical Engineering, Duke University, Durham, NC, 27705
- Lead contact:
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2
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Wang Y, Gao Y, Song Y. Microfluidics-Based Urine Biopsy for Cancer Diagnosis: Recent Advances and Future Trends. ChemMedChem 2022; 17:e202200422. [PMID: 36040297 DOI: 10.1002/cmdc.202200422] [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: 07/30/2022] [Revised: 08/23/2022] [Indexed: 11/08/2022]
Abstract
Urine biopsy, allowing for the detection, analysis and monitoring of numerous cancer-associated urinary biomarkers to provide insights into cancer occurrence, progression and metastasis, has emerged as an attractive liquid biopsy strategy with enormous advantages over traditional tissue biopsy, such as noninvasiveness, large sample volume, and simple sampling operation. Microfluidics enables precise manipulation of fluids in a tiny chip and exhibits outstanding performance in urine biopsy owing to its minimization, low cost, high integration, high throughput and low sample consumption. Herein, we review recent advances in microfluidic techniques employed in urine biopsy for cancer detection. After briefly summarizing the major urinary biomarkers used for cancer diagnosis, we provide an overview of the typical microfluidic techniques utilized to develop urine biopsy devices. Some prospects along with the major challenges to be addressed for the future of microfluidic-based urine biopsy are also discussed.
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Affiliation(s)
- Yanping Wang
- Nanjing University of Science and Technology, Sino-French Engineer School, CHINA
| | - Yanfeng Gao
- Nanjing University, College of Engineering and Applied Sciences, CHINA
| | - Yujun Song
- Nanjing University, Biomedical Engineering, 22 Hankou Road, 210093, Nanjing, CHINA
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3
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Liu X, Li X, Wu N, Luo Y, Zhang J, Yu Z, Shen F. Formation and Parallel Manipulation of Gradient Droplets on a Self-Partitioning SlipChip for Phenotypic Antimicrobial Susceptibility Testing. ACS Sens 2022; 7:1977-1984. [PMID: 35815869 DOI: 10.1021/acssensors.2c00734] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Flexible, robust, and user-friendly screening systems with a large dynamic range are highly desired in scientific research, industrial development, and clinical diagnostics. Droplet-based microfluidic systems with gradient concentrations of chemicals have been demonstrated as promising tools to provide confined microenvironments for screening tests with small reaction volumes. However, the generation and manipulation of gradient droplets, such as droplet merging, generally require sophisticated fluidic manipulation systems, potentially limiting their application in decentralized settings. We present a gradient-droplet SlipChip (gd-SlipChip) microfluidic device that enables instrument-free gradient droplet formation and parallel manipulation. The device can establish a gradient profile by free interfacial diffusion in a continuous fluidic channel. With a simple slipping step, gradient droplets can be generated by a surface tension-driven self-partitioning process. Additional reagents can be introduced in parallel to these gradient droplets with further slipping operations to initiate screening tests of the droplets over a large concentration range. To profile the concentration in the gradient droplets, we establish a numerical simulation model and verify it with hydrogen chloride (HCl) diffusion, as tested with a dual-color pH indicator (methyl orange and aniline blue). As a proof of concept, we tested this system with a gradient concentration of nitrofurantoin for the phenotypic antimicrobial susceptibility testing (AST) of Escherichia coli. The results of our gd-SlipChip-based AST on both reference and clinical strains of E. coli can be indicated by the bacterial growth profile within 3 h and are consistent with the clinical culture-based AST.
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Affiliation(s)
- Xu Liu
- School of Biomedical Engineering, Shanghai Jiao Tong University, 1954 Hua Shan Road, Shanghai 200030, China
| | - Xiang Li
- School of Biomedical Engineering, Shanghai Jiao Tong University, 1954 Hua Shan Road, Shanghai 200030, China
| | - Nannan Wu
- Shanghai Institute of Phage, Shanghai Public Health Clinical Center, Fudan University, Shanghai 200433, China
| | - Yang Luo
- School of Biomedical Engineering, Shanghai Jiao Tong University, 1954 Hua Shan Road, Shanghai 200030, China
| | - Jiajie Zhang
- School of Biomedical Engineering, Shanghai Jiao Tong University, 1954 Hua Shan Road, Shanghai 200030, China
| | - Ziqing Yu
- School of Biomedical Engineering, Shanghai Jiao Tong University, 1954 Hua Shan Road, Shanghai 200030, China
| | - Feng Shen
- School of Biomedical Engineering, Shanghai Jiao Tong University, 1954 Hua Shan Road, Shanghai 200030, China
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4
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Gervais T, Temiz Y, Aubé L, Delamarche E. Large-Scale Dried Reagent Reconstitution and Diffusion Control Using Microfluidic Self-Coalescence Modules. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2022; 18:e2105939. [PMID: 35307960 DOI: 10.1002/smll.202105939] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/18/2021] [Revised: 01/13/2022] [Indexed: 06/14/2023]
Abstract
The positioning and manipulation of large numbers of reagents in small aliquots are paramount to many fields in chemistry and the life sciences, such as combinatorial screening, enzyme activity assays, and point-of-care testing. Here, a capillary microfluidic architecture based on self-coalescence modules capable of storing thousands of dried reagent spots per square centimeter is reported, which can all be reconstituted independently without dispersion using a single pipetting step and ≤5 μL of a solution. A simple diffusion-based mathematical model is also provided to guide the spotting of reagents in this microfluidic architecture at the experimental design stage to enable either compartmentalization, mixing, or the generation of complex multi-reagent chemical patterns. Results demonstrate the formation of chemical patterns with high accuracy and versatility, and simple methods for integrating reagents and imaging the resulting chemical patterns.
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Affiliation(s)
- Thomas Gervais
- IBM Research Europe - Zurich, Rueschlikon, 8803, Switzerland
- Polytechnique Montréal, Montreal, H3C 3A7, Canada
- Centre de Recherche du Centre Hospitalier de l'Université de Montréal, Montreal, H2X0A9, Canada
| | - Yuksel Temiz
- IBM Research Europe - Zurich, Rueschlikon, 8803, Switzerland
| | - Lucas Aubé
- Polytechnique Montréal, Montreal, H3C 3A7, Canada
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5
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Wang Y, Gao Y, Yin Y, Pan Y, Wang Y, Song Y. Nanomaterial-assisted microfluidics for multiplex assays. Mikrochim Acta 2022; 189:139. [PMID: 35275267 DOI: 10.1007/s00604-022-05226-4] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Accepted: 02/10/2022] [Indexed: 02/07/2023]
Abstract
Simultaneous detection of different biomarkers from a single specimen in a single test, allowing more rapid, efficient, and low-cost analysis, is of great significance for accurate diagnosis of disease and efficient monitoring of therapy. Recently, developments in microfabrication and nanotechnology have advanced the integration of nanomaterials in microfluidic devices toward multiplex assays of biomarkers, combining both the advantages of microfluidics and the unique properties of nanomaterials. In this review, we focus on the state of the art in multiplexed detection of biomarkers based on nanomaterial-assisted microfluidics. Following an overview of the typical microfluidic analytical techniques and the most commonly used nanomaterials for biochemistry analysis, we highlight in detail the nanomaterial-assisted microfluidic strategies for different biomarkers. These highly integrated platforms with minimum sample consumption, high sensitivity and specificity, low detection limit, enhanced signals, and reduced detection time have been extensively applied in various domains and show great potential in future point-of-care testing and clinical diagnostics.
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Affiliation(s)
- Yanping Wang
- Sino-French Engineer School, Nanjing University of Science and Technology, Nanjing, 210094, China
| | - Yanfeng Gao
- College of Engineering and Applied Sciences, Jiangsu Key Laboratory of Artificial Functional Materials, State Key Laboratory of Analytical Chemistry for Life Science, Nanjing University, Nanjing, 210023, China
| | - Yi Yin
- Department of General Surgery, Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, Nanjing, 210008, China
| | - Yongchun Pan
- College of Engineering and Applied Sciences, Jiangsu Key Laboratory of Artificial Functional Materials, State Key Laboratory of Analytical Chemistry for Life Science, Nanjing University, Nanjing, 210023, China
| | - Yuzhen Wang
- Key Laboratory of Flexible Electronics & Institute of Advanced Materials, Jiangsu National Synergistic Innovation Center for Advanced Materials, Nanjing Tech University, Nanjing, 211816, China
| | - Yujun Song
- College of Engineering and Applied Sciences, Jiangsu Key Laboratory of Artificial Functional Materials, State Key Laboratory of Analytical Chemistry for Life Science, Nanjing University, Nanjing, 210023, China.
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Catterton MA, Ball AG, Pompano RR. Rapid Fabrication by Digital Light Processing 3D Printing of a SlipChip with Movable Ports for Local Delivery to Ex Vivo Organ Cultures. MICROMACHINES 2021; 12:993. [PMID: 34442615 PMCID: PMC8399530 DOI: 10.3390/mi12080993] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Revised: 08/14/2021] [Accepted: 08/18/2021] [Indexed: 12/28/2022]
Abstract
SlipChips are two-part microfluidic devices that can be reconfigured to change fluidic pathways for a wide range of functions, including tissue stimulation. Currently, fabrication of these devices at the prototype stage requires a skilled microfluidic technician, e.g., for wet etching or alignment steps. In most cases, SlipChip functionality requires an optically clear, smooth, and flat surface that is fluorophilic and hydrophobic. Here, we tested digital light processing (DLP) 3D printing, which is rapid, reproducible, and easily shared, as a solution for fabrication of SlipChips at the prototype stage. As a case study, we sought to fabricate a SlipChip intended for local delivery to live tissue slices through a movable microfluidic port. The device was comprised of two multi-layer components: an enclosed channel with a delivery port and a culture chamber for tissue slices with a permeable support. Once the design was optimized, we demonstrated its function by locally delivering a chemical probe to slices of hydrogel and to living tissue with up to 120 µm spatial resolution. By establishing the design principles for 3D printing of SlipChip devices, this work will enhance the ability to rapidly prototype such devices at mid-scale levels of production.
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Affiliation(s)
- Megan A Catterton
- Department of Chemistry, University of Virginia College of Arts and Science, Charlottesville, VA 22904, USA;
| | - Alexander G Ball
- Department of Microbiology, Immunology and Cancer Biology, University of Virginia School of Medicine, Charlottesville, VA 22903, USA;
| | - Rebecca R Pompano
- Department of Chemistry, University of Virginia College of Arts and Science, Charlottesville, VA 22904, USA;
- Carter Immunology Center and UVA Cancer Center, University of Virginia, Charlottesville, VA 22903, USA
- Department of Biomedical Engineering, University of Virginia School of Engineering and Applied Sciences, Charlottesville, VA 22904-4259, USA
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7
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Yu Z, Lyu W, Yu M, Wang Q, Qu H, Ismagilov RF, Han X, Lai D, Shen F. Self-partitioning SlipChip for slip-induced droplet formation and human papillomavirus viral load quantification with digital LAMP. Biosens Bioelectron 2020; 155:112107. [DOI: 10.1016/j.bios.2020.112107] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2019] [Revised: 02/05/2020] [Accepted: 02/17/2020] [Indexed: 01/20/2023]
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8
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Savela ES, Schoepp NG, Cooper MM, Rolando JC, Klausner JD, Soge OO, Ismagilov RF. Surfactant-enhanced DNA accessibility to nuclease accelerates phenotypic β-lactam antibiotic susceptibility testing of Neisseria gonorrhoeae. PLoS Biol 2020; 18:e3000651. [PMID: 32191696 PMCID: PMC7081974 DOI: 10.1371/journal.pbio.3000651] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2019] [Accepted: 02/14/2020] [Indexed: 11/19/2022] Open
Abstract
Rapid antibiotic susceptibility testing (AST) for Neisseria gonorrhoeae (Ng) is critically needed to counter widespread antibiotic resistance. Detection of nucleic acids in genotypic AST can be rapid, but it has not been successful for β-lactams (the largest antibiotic class used to treat Ng). Rapid phenotypic AST for Ng is challenged by the pathogen's slow doubling time and the lack of methods to quickly quantify the pathogen's response to β-lactams. Here, we asked two questions: (1) Is it possible to use nucleic acid quantification to measure the β-lactam susceptibility phenotype of Ng very rapidly, using antibiotic-exposure times much shorter than the 1- to 2-h doubling time of Ng? (2) Would such short-term antibiotic exposures predict the antibiotic resistance profile of Ng measured by plate growth assays over multiple days? To answer these questions, we devised an innovative approach for performing a rapid phenotypic AST that measures DNA accessibility to exogenous nucleases after exposure to β-lactams (termed nuclease-accessibility AST [nuc-aAST]). We showed that DNA in antibiotic-susceptible cells has increased accessibility upon exposure to β-lactams and that a judiciously chosen surfactant permeabilized the outer membrane and enhanced this effect. We tested penicillin, cefixime, and ceftriaxone and found good agreement between the results of the nuc-aAST after 15-30 min of antibiotic exposure and the results of the gold-standard culture-based AST measured over days. These results provide a new pathway toward developing a critically needed phenotypic AST for Ng and additional global-health threats.
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Affiliation(s)
- Emily S. Savela
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California, United States of America
| | - Nathan G. Schoepp
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California, United States of America
| | - Matthew M. Cooper
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California, United States of America
| | - Justin C. Rolando
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California, United States of America
| | - Jeffrey D. Klausner
- David Geffen School of Medicine, Division of Infectious Disease, University of California Los Angeles, Los Angeles, California, United States of America
| | - Olusegun O. Soge
- Neisseria Reference Laboratory, Department of Global Health, University of Washington, Seattle, Washington, United States of America
| | - Rustem F. Ismagilov
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California, United States of America
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California, United States of America
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Zhukov DV, Khorosheva EM, Khazaei T, Du W, Selck DA, Shishkin AA, Ismagilov RF. Microfluidic SlipChip device for multistep multiplexed biochemistry on a nanoliter scale. LAB ON A CHIP 2019; 19:3200-3211. [PMID: 31441477 DOI: 10.1039/c9lc00541b] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
We have developed a multistep microfluidic device that expands the current SlipChip capabilities by enabling multiple steps of droplet merging and multiplexing. Harnessing the interfacial energy between carrier and sample phases, this manually operated device accurately meters nanoliter volumes of reagents and transfers them into on-device reaction wells. Judiciously shaped microfeatures and surface-energy traps merge droplets in a parallel fashion. Wells can be tuned for different volumetric capacities and reagent types, including for pre-spotted reagents that allow for unique identification of original well contents even after their contents are pooled. We demonstrate the functionality of the multistep SlipChip by performing RNA transcript barcoding on-device for synthetic spiked-in standards and for biologically derived samples. This technology is a good candidate for a wide range of biological applications that require multiplexing of multistep reactions in nanoliter volumes, including single-cell analyses.
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Affiliation(s)
- Dmitriy V Zhukov
- Division of Chemistry and Chemical Engineering, California Institute of Technology, 1200 E. California Blvd, Pasadena, CA 91125, USA.
| | - Eugenia M Khorosheva
- Division of Chemistry and Chemical Engineering, California Institute of Technology, 1200 E. California Blvd, Pasadena, CA 91125, USA.
| | - Tahmineh Khazaei
- Division of Biology and Biological Engineering, California Institute of Technology, 1200 E. California Blvd, Pasadena, CA 91125, USA
| | - Wenbin Du
- Department of Chemistry and Institute for Biophysical Dynamics, The University of Chicago, 929 East 57th Street, Chicago, Illinois 60637, USA
| | - David A Selck
- Division of Chemistry and Chemical Engineering, California Institute of Technology, 1200 E. California Blvd, Pasadena, CA 91125, USA.
| | - Alexander A Shishkin
- Division of Biology and Biological Engineering, California Institute of Technology, 1200 E. California Blvd, Pasadena, CA 91125, USA
| | - Rustem F Ismagilov
- Division of Chemistry and Chemical Engineering, California Institute of Technology, 1200 E. California Blvd, Pasadena, CA 91125, USA. and Division of Biology and Biological Engineering, California Institute of Technology, 1200 E. California Blvd, Pasadena, CA 91125, USA
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10
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Lyu W, Yu M, Qu H, Yu Z, Du W, Shen F. Slip-driven microfluidic devices for nucleic acid analysis. BIOMICROFLUIDICS 2019; 13:041502. [PMID: 31312285 PMCID: PMC6625959 DOI: 10.1063/1.5109270] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/07/2019] [Accepted: 07/01/2019] [Indexed: 05/17/2023]
Abstract
Slip-driven microfluidic devices can manipulate fluid by the relative movement of microfluidic plates that are in close contact. Since the demonstration of the first SlipChip device, many slip-driven microfluidic devices with different form factors have been developed, including SlipPAD, SlipDisc, sliding stripe, and volumetric bar chart chip. Slip-driven microfluidic devices can be fabricated from glass, quartz, polydimethylsiloxane, paper, and plastic with various fabrication methods: etching, casting, wax printing, laser cutting, micromilling, injection molding, etc. The slipping operation of the devices can be performed manually, by a micrometer with a base station, or autonomously, by a clockwork mechanism. A variety of readout methods other than fluorescence microscopy have been demonstrated, including both fluorescence detection and colorimetric detection by mobile phones, direct visual detection, and real-time fluorescence imaging. This review will focus on slip-driven microfluidic devices for nucleic acid analysis, including multiplex nucleic acid detection, digital nucleic acid quantification, real-time nucleic acid amplification, and sample-in-answer-out nucleic acid analysis. Slip-driven microfluidic devices present promising approaches for both life science research and clinical molecular diagnostics.
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Affiliation(s)
- Weiyuan Lyu
- School of Biomedical Engineering, Shanghai Jiao Tong University, 1954 Huashan Road, Shanghai 200030, China
| | - Mengchao Yu
- School of Biomedical Engineering, Shanghai Jiao Tong University, 1954 Huashan Road, Shanghai 200030, China
| | - Haijun Qu
- School of Biomedical Engineering, Shanghai Jiao Tong University, 1954 Huashan Road, Shanghai 200030, China
| | | | - Wenbin Du
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100080, China
| | - Feng Shen
- School of Biomedical Engineering, Shanghai Jiao Tong University, 1954 Huashan Road, Shanghai 200030, China
- Author to whom correspondence should be addressed:
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11
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Li Y, Xuan J, Hu R, Zhang P, Lou X, Yang Y. Microfluidic triple-gradient generator for efficient screening of chemical space. Talanta 2019; 204:569-575. [PMID: 31357335 DOI: 10.1016/j.talanta.2019.06.018] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2019] [Revised: 05/27/2019] [Accepted: 06/06/2019] [Indexed: 12/22/2022]
Abstract
Generation of a combinatorial gradient for multiple chemicals is essential for studies of biochemical stimuli, chemoattraction, protein crystallization and others. While currently available platforms require complex design/settings to obtain a double-gradient chemical matrix, we herein report for the first time a simple triple-gradient matrix (TGM) device for efficient screening of chemical space. The TGM device is composed of two glass slides and works following the concept of SlipChip. The device utilizes XYZ space to distribute three chemicals and establishes a chemical gradient matrix within 5 min. The established matrix contains 24 or 104 screening conditions depending on the device used, which covers a concentration range of [0.117-1, 0.117-1 and 0.686-1] and [0.0830-1, 0.0830-1, 0.686-1] respectively for the three chemicals. With the triple gradients built simultaneously, this TGM device provides order-of-magnitude improvement in screening efficiency over existing single- or double-gradient generators. As a proof of concept, we applied the device to screen the crystallization conditions for two model proteins of lysozyme and trypsin and confirmed the crystal structures using X-ray diffraction. Furthermore, we successfully obtained the crystallization condition of adhesin competence repressor, a protein that senses the alterations in intracellular zinc concentrations. We expect the TGM system to be widely used as an analytical platform for material synthesis and chemical screening beyond for protein crystallization.
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Affiliation(s)
- Ying Li
- State Key Laboratory of Magnetic Resonance and Atomic Molecular Physics, Wuhan National Laboratory for Optoelectronics, National Center for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Chinese Academy of Sciences, Wuhan, Hubei, 430071, China.
| | - Jie Xuan
- Chemistry and Biochemistry Department, Brigham Young University, Provo, UT 84602, USA
| | - Rui Hu
- State Key Laboratory of Magnetic Resonance and Atomic Molecular Physics, Wuhan National Laboratory for Optoelectronics, National Center for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Chinese Academy of Sciences, Wuhan, Hubei, 430071, China
| | - Pengchao Zhang
- Houston Methodist Research Institute, Houston, TX, 77030, USA
| | - Xiaohua Lou
- Houston Methodist Research Institute, Houston, TX, 77030, USA
| | - Yunhuang Yang
- State Key Laboratory of Magnetic Resonance and Atomic Molecular Physics, Wuhan National Laboratory for Optoelectronics, National Center for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Chinese Academy of Sciences, Wuhan, Hubei, 430071, China.
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12
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Microfluidic Technologies and Platforms for Protein Crystallography. Bioanalysis 2019. [DOI: 10.1007/978-981-13-6229-3_2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
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13
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Catterton MA, Dunn AF, Pompano RR. User-defined local stimulation of live tissue through a movable microfluidic port. LAB ON A CHIP 2018; 18:2003-2012. [PMID: 29904762 PMCID: PMC6039252 DOI: 10.1039/c8lc00204e] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
Many in vivo tissue responses begin locally, yet most in vitro stimuli are delivered globally. Microfluidics has a unique ability to provide focal stimulation to tissue samples with precise control over fluid location, flow rate, and composition. However, previous devices utilizing fixed ports beneath the tissue required manual alignment of the tissue over the ports, increasing the risk of mechanical damage. Here we present a novel microfluidic device that allows the user to define the location of fluid delivery to a living tissue slice without manipulating the tissue itself. The device utilized a two-component SlipChip design to create a mobile port beneath the tissue slice. A culture chamber perforated by an array of ports housed a tissue slice and was separated by a layer of fluorocarbon oil from a single delivery port, fed by a microfluidic channel in the movable layer below. We derived and validated a physical model, based on interfacial tension and flow resistance, to predict the conditions under which fluid delivery occurred without leakage into the gap between layers. Aqueous solution was delivered reproducibly to samples of tissue and gel, and the width of the delivery region was controlled primarily by convection. Tissue slice viability was not affected by stimulation on the device. As a proof-of-principle, we showed that live slices of lymph node tissue could be sequentially targeted for precise stimulation. In the future this device may serve as a platform to study the effects of fluid flow in tissues and to perform local drug screening.
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Affiliation(s)
- Megan A Catterton
- Department of Chemistry, University of Virginia, Charlottesville, VA, USA.
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14
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Jalali M, White AR, Marti J, Sheng J. Fabrication and characterization of a scalable surface textured with pico-liter oil drops for mechanistic studies of bacteria-oil interactions. Sci Rep 2018; 8:7612. [PMID: 29765086 PMCID: PMC5954110 DOI: 10.1038/s41598-018-25812-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2017] [Accepted: 04/30/2018] [Indexed: 11/27/2022] Open
Abstract
Texturing a large surface with oily micro-drops with controlled size, shape and volume provides an unprecedented capability in investigating complex interactions of bacteria, cells and interfaces. It has particular implications in understanding key microbial processes involved in remediation of environmental disasters, such as Deepwater Horizon oil spill. This work presents a development of scalable micro-transfer molding to functionalize a substrate with oily drop array to generate a microcosm mimicking bacteria encountering a rising droplet cloud. The volume of each drop within a large “printed” surface can be tuned by varying base geometry and area with characteristic scales from 5 to 50 μm. Contrary to macroscopic counterparts, drops with non-Laplacian shapes, i.e. sharp corners, that appears to violate Young-Laplacian relationship locally, are produced. Although the drop relaxes into a spherical cap with constant mean curvature, the contact line with sharp corners remains pinned. Relaxation times from initial to asymptotic shape require extraordinarily long time (>7 days). We demonstrate that non-Laplacian drops are the direct results of self-pinning of contact line by nanoparticles in the oil. This technique has been applied to study biofilm formation at the oil-water interface and can be readily extended to other colloidal fluids.
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Affiliation(s)
- Maryam Jalali
- Department of Engineering, Texas A&M University, Corpus Christi, Texas, USA
| | - Andrew R White
- Department of Engineering, Texas A&M University, Corpus Christi, Texas, USA
| | - James Marti
- Nano Fabrication Center, University of Minnesota, Twin City, Minnesota, USA
| | - Jian Sheng
- Department of Engineering, Texas A&M University, Corpus Christi, Texas, USA.
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15
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Verma MS, Tsaloglou MN, Sisley T, Christodouleas D, Chen A, Milette J, Whitesides GM. Sliding-strip microfluidic device enables ELISA on paper. Biosens Bioelectron 2017; 99:77-84. [PMID: 28738231 PMCID: PMC5628584 DOI: 10.1016/j.bios.2017.07.034] [Citation(s) in RCA: 91] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2017] [Revised: 07/12/2017] [Accepted: 07/12/2017] [Indexed: 02/08/2023]
Abstract
This article describes a 3D microfluidic paper-based analytical device that can be used to conduct an enzyme-linked immunosorbent assay (ELISA). The device comprises two parts: a sliding strip (which contains the active sensing area) and a structure surrounding the sliding strip (which holds stored reagents—buffers, antibodies, and enzymatic substrate—and distributes fluid). Running an ELISA involves adding sample (e.g. blood) and water, moving the sliding strip at scheduled times, and analyzing the resulting color in the sensing area visually or using a flatbed scanner. We demonstrate that this device can be used to detect C-reactive protein (CRP)—a biomarker for neonatal sepsis, pelvic inflammatory disease, and inflammatory bowel diseases—at a concentration range of 1–100 ng/mL in 1000-fold diluted blood (1–100 µg/mL in undiluted blood). The accuracy of the device (as characterized by the area under the receiver operator characteristics curve) is 89% and 83% for cut-offs of 10 ng/mL (for neonatal sepsis and pelvic inflammatory disease) and 30 ng/mL (for inflammatory bowel diseases) CRP in 1000-fold diluted blood respectively. In resource-limited settings, the device can be used as a part of a kit (containing the device, a fixed-volume capillary, a pre-filled tube, a syringe, and a dropper); this kit would cost ~ $0.50 when produced in large scale (>100,000 devices/week). This kit has the technical characteristics to be employed as a pre-screening tool, when combined with other data such as patient history and clinical signs. 3D microfluidic paper-based analytical device performs ELISA with colorimetric results. Two components enable separation of reagents in the device: a sliding-strip and a functional dock. All required reagents (antibodies, enzyme, substrate, buffers) are stored in the device. User only needs to add sample and water using the provided kit. Device can detect C-reactive protein for possible pre-screening of neonatal sepsis, pelvic inflammatory disease, or inflammatory bowel diseases.
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Affiliation(s)
- Mohit S Verma
- Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, MA 02138, USA
| | - Maria-Nefeli Tsaloglou
- Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, MA 02138, USA; Diagnostics for All, 4 Technology Way, Salem, MA 02138, USA
| | - Tyler Sisley
- Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, MA 02138, USA
| | - Dionysios Christodouleas
- Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, MA 02138, USA
| | - Austin Chen
- Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, MA 02138, USA
| | - Jonathan Milette
- Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, MA 02138, USA
| | - George M Whitesides
- Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, MA 02138, USA; Wyss Institute for Biologically Inspired Engineering, Harvard University, 60 Oxford Street, Cambridge, MA 02138, USA; Kavli Institute for Bionano Science and Technology, Harvard University, 29 Oxford Street, Cambridge, MA 02138, USA.
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16
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Liang YR, Zhu LN, Gao J, Zhao HX, Zhu Y, Ye S, Fang Q. 3D-Printed High-Density Droplet Array Chip for Miniaturized Protein Crystallization Screening under Vapor Diffusion Mode. ACS APPLIED MATERIALS & INTERFACES 2017; 9:11837-11845. [PMID: 28306245 DOI: 10.1021/acsami.6b15933] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
Here we describe the combination of three-dimensional (3D) printed chip and automated microfluidic droplet-based screening techniques for achieving massively parallel, nanoliter-scale protein crystallization screening under vapor diffusion mode. We fabricated high-density microwell array chips for sitting-drop vapor diffusion crystallization utilizing the advantage of the 3D-printing technique in producing high-aspect-ratio chips. To overcome the obstacle of 3D-printed microchips in performing long-term reactions caused by their porousness and gas permeability properties in chip body, we developed a two-step postprocessing method, including paraffin filling and parylene coating, to achieve high sealability and stability. We also developed a simple method especially suitable for controlling the vapor diffusion speed of nanoliter-scale droplets by changing the layer thickness of covering oil. With the above methods, 84 tests of nanoliter-scale protein crystallization under vapor diffusion mode were successfully achieved in the 7 × 12 droplet array chip with a protein consumption of 10 nL for each test, which is 20-100 times lower than that in the conventional large-volume screening system. Such a nanoliter-scale vapor diffusion system was applied to two model proteins with commercial precipitants and displayed advantages over that under microbatch mode. It identified more crystallization conditions, especially for the protein samples with lower concentrations.
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Affiliation(s)
- Yi-Ran Liang
- Institute of Microanalytical Systems, Department of Chemistry and Innovation Center for Cell Signaling Network, and ‡Life Sciences Institute and Innovation Center for Cell Signaling Network, Zhejiang University , Hangzhou, 310058, China
| | - Li-Na Zhu
- Institute of Microanalytical Systems, Department of Chemistry and Innovation Center for Cell Signaling Network, and ‡Life Sciences Institute and Innovation Center for Cell Signaling Network, Zhejiang University , Hangzhou, 310058, China
| | - Jie Gao
- Institute of Microanalytical Systems, Department of Chemistry and Innovation Center for Cell Signaling Network, and ‡Life Sciences Institute and Innovation Center for Cell Signaling Network, Zhejiang University , Hangzhou, 310058, China
| | - Hong-Xia Zhao
- Institute of Microanalytical Systems, Department of Chemistry and Innovation Center for Cell Signaling Network, and ‡Life Sciences Institute and Innovation Center for Cell Signaling Network, Zhejiang University , Hangzhou, 310058, China
| | - Ying Zhu
- Institute of Microanalytical Systems, Department of Chemistry and Innovation Center for Cell Signaling Network, and ‡Life Sciences Institute and Innovation Center for Cell Signaling Network, Zhejiang University , Hangzhou, 310058, China
| | - Sheng Ye
- Institute of Microanalytical Systems, Department of Chemistry and Innovation Center for Cell Signaling Network, and ‡Life Sciences Institute and Innovation Center for Cell Signaling Network, Zhejiang University , Hangzhou, 310058, China
| | - Qun Fang
- Institute of Microanalytical Systems, Department of Chemistry and Innovation Center for Cell Signaling Network, and ‡Life Sciences Institute and Innovation Center for Cell Signaling Network, Zhejiang University , Hangzhou, 310058, China
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17
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Robertson K. Using flow technologies to direct the synthesis and assembly of materials in solution. Chem Cent J 2017; 11:4. [PMID: 28101131 PMCID: PMC5215996 DOI: 10.1186/s13065-016-0229-1] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2016] [Accepted: 12/02/2016] [Indexed: 02/08/2023] Open
Abstract
In the pursuit of materials with structure-related function, directing the assembly of materials is paramount. The resultant structure can be controlled by ordering of reactants, spatial confinement and control over the reaction/crystallisation times and stoichiometries. These conditions can be administered through the use of flow technologies as evidenced by the growing widespread application of microfluidics for the production of nanomaterials; the function of which is often dictated or circumscribed by size. In this review a range of flow technologies is explored for use in the control of self-assembled systems: including techniques for reagent ordering, mixing control and high-throughput optimisation. The examples given encompass organic, inorganic and biological systems and focus on control of shape, function, composition and size.Graphical abstract.
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Affiliation(s)
- K Robertson
- Department of Chemistry, University of Bath, Bath, BA2 7AY UK
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18
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Abstract
The volumetric bar-chart chip (V-Chip) is a microfluidics-based, point-of-care (POC) device for the multiplexed and quantitative measurement of biomarkers. Volumetric readouts, based on the measurement of oxygen generated by a reaction between catalase and hydrogen peroxide, allow instant visual quantitation of target biomarkers and provide visualized bar charts without any assistance from instruments and without the need for data processing or graphics plotting. V-Chip shows potential capabilities in POC and personalized diagnostics; for instance, it can be utilized for making high-throughput, multiplexed, and quantitative measurements. Further, this system is highly portable and can be performed at low cost. The development of the V-Chip thus marks a POC milestone and opens up the possibility of instrument-free personalized diagnostics. Here, we describe the protocols for the fabrication of V-Chip and the use of silica nanoparticles as the probe carrier for the V-Chip-based enzyme-linked immunosorbent assay (ELISA) for the detection of biomarkers.
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Affiliation(s)
- Yujun Song
- Department of Nanomedicine, Houston Methodist Research Institute, 6670 Bertner Avenue, Houston, TX, 77030, USA
- Department of Cell and Developmental Biology, Weill Medical College of Cornell University, New York, NY, 10065, USA
| | - Ying Li
- Department of Nanomedicine, Houston Methodist Research Institute, 6670 Bertner Avenue, Houston, TX, 77030, USA
- Department of Cell and Developmental Biology, Weill Medical College of Cornell University, New York, NY, 10065, USA
| | - Lidong Qin
- Department of Nanomedicine, Houston Methodist Research Institute, 6670 Bertner Avenue, Houston, TX, 77030, USA.
- Department of Cell and Developmental Biology, Weill Medical College of Cornell University, New York, NY, 10065, USA.
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19
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Hu J, Cui X, Gong Y, Xu X, Gao B, Wen T, Lu TJ, Xu F. Portable microfluidic and smartphone-based devices for monitoring of cardiovascular diseases at the point of care. Biotechnol Adv 2016; 34:305-20. [DOI: 10.1016/j.biotechadv.2016.02.008] [Citation(s) in RCA: 72] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2015] [Revised: 02/16/2016] [Accepted: 02/16/2016] [Indexed: 01/08/2023]
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20
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Xie Y, Wei X, Yang Q, Guan Z, Liu D, Liu X, Zhou L, Zhu Z, Lin Z, Yang C. A Shake&Read distance-based microfluidic chip as a portable quantitative readout device for highly sensitive point-of-care testing. Chem Commun (Camb) 2016; 52:13377-13380. [DOI: 10.1039/c6cc07928h] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
We developed a Shake&Read distance-based microfluidic chip for simple, disposable, equipment-free, visual and quantitative POCT.
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21
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Wang Y, Li Y, Thérien-Aubin H, Ma J, Zandstra PW, Kumacheva E. Two-dimensional arrays of cell-laden polymer hydrogel modules. BIOMICROFLUIDICS 2016; 10:014110. [PMID: 26858822 PMCID: PMC4723409 DOI: 10.1063/1.4940430] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2015] [Accepted: 01/07/2016] [Indexed: 05/05/2023]
Abstract
Microscale technologies offer the capability to generate in vitro artificial cellular microenvironments that recapitulate the spatial, biochemical, and biophysical characteristics of the native extracellular matrices and enable systematic, quantitative, and high-throughput studies of cell fate in their respective environments. We developed a microfluidic platform for the generation of two-dimensional arrays of micrometer-size cell-laden hydrogel modules (HMs) for cell encapsulation and culture. Fibroblast cells (NIH 3T3) and non-adherent T cells (EL4) encapsulated in HMs showed high viability and proliferation. The platform was used for real-time studies of the effect of spatial constraints and structural and mechanical properties of HMs on cell growth, both on the level of individual cells. Due to the large number of cell-laden HMs and stochastic cell distribution, cell studies were conducted in a time- and labor efficient manner. The platform has a broad range of applications in the exploration of the role of chemical and biophysical cues on individual cells, studies of in vitro cell migration, and the examination of cell-extracellular matrix and cell-cell interactions.
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Affiliation(s)
- Yihe Wang
- Department of Chemistry, University of Toronto , Toronto, Ontario M5S 3H6, Canada
| | - Yunfeng Li
- Department of Chemistry, University of Toronto , Toronto, Ontario M5S 3H6, Canada
| | | | - Jennifer Ma
- Institute of Biomaterials & Biomedical Engineering, University of Toronto , 164 College Street, Toronto, Ontario M5S 3G9, Canada
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22
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MAEKI M, YAMAGUCHI H, TOKESHI M, MIYAZAKI M. Microfluidic Approaches for Protein Crystal Structure Analysis. ANAL SCI 2016; 32:3-9. [DOI: 10.2116/analsci.32.3] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Affiliation(s)
- Masatoshi MAEKI
- Division of Applied Chemistry, Faculty of Engineering, Hokkaido University
- Advanced Manufacturing Research Institute, National Institute of Advanced Industrial Science and Technology
| | | | - Manabu TOKESHI
- Division of Applied Chemistry, Faculty of Engineering, Hokkaido University
| | - Masaya MIYAZAKI
- Advanced Manufacturing Research Institute, National Institute of Advanced Industrial Science and Technology
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23
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Chan HN, Shu Y, Xiong B, Chen Y, Chen Y, Tian Q, Michael SA, Shen B, Wu H. Simple, Cost-Effective 3D Printed Microfluidic Components for Disposable, Point-of-Care Colorimetric Analysis. ACS Sens 2015. [DOI: 10.1021/acssensors.5b00100] [Citation(s) in RCA: 86] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Ho Nam Chan
- Department of Chemistry and ‡Division of Biomedical Engineering, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong, China
| | - Yiwei Shu
- Department of Chemistry and ‡Division of Biomedical Engineering, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong, China
| | - Bin Xiong
- Department of Chemistry and ‡Division of Biomedical Engineering, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong, China
| | - Yangfan Chen
- Department of Chemistry and ‡Division of Biomedical Engineering, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong, China
| | - Yin Chen
- Department of Chemistry and ‡Division of Biomedical Engineering, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong, China
| | - Qian Tian
- Department of Chemistry and ‡Division of Biomedical Engineering, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong, China
| | - Sean A. Michael
- Department of Chemistry and ‡Division of Biomedical Engineering, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong, China
| | - Bo Shen
- Department of Chemistry and ‡Division of Biomedical Engineering, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong, China
| | - Hongkai Wu
- Department of Chemistry and ‡Division of Biomedical Engineering, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong, China
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24
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Microfluidic Slipchip-based Reaction Microarray with Dual Concentration Gradient. CHINESE JOURNAL OF ANALYTICAL CHEMISTRY 2015. [DOI: 10.1016/s1872-2040(15)60868-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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25
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Liu X, Yi Q, Han Y, Liang Z, Shen C, Zhou Z, Sun JL, Li Y, Du W, Cao R. A robust microfluidic device for the synthesis and crystal growth of organometallic polymers with highly organized structures. Angew Chem Int Ed Engl 2014; 54:1846-50. [PMID: 25504832 DOI: 10.1002/anie.201411008] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2014] [Indexed: 01/07/2023]
Abstract
A simple and robust microfluidic device was developed to synthesize organometallic polymers with highly organized structures. The device is compatible with organic solvents. Reactants are loaded into pairs of reservoirs connected by a 15 cm long microchannel prefilled with solvents, thus allowing long-term counter diffusion for self-assembly of organometallic polymers. The process can be monitored, and the resulting crystalline polymers are harvested without damage. The device was used to synthesize three insoluble silver acetylides as single crystals of X-ray diffraction quality. Importantly, for the first time, the single-crystal structure of silver phenylacetylide was determined. The reported approach may have wide applications, such as crystallization of membrane proteins, synthesis and crystal growth of organic, inorganic, and polymeric coordination compounds, whose single crystals cannot be obtained using traditional methods.
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Affiliation(s)
- Xiao Liu
- School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi'an 710062 (China); Department of Chemistry, Renmin University of China, Beijing 100872 (China)
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26
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Liu X, Yi Q, Han Y, Liang Z, Shen C, Zhou Z, Sun JL, Li Y, Du W, Cao R. A Robust Microfluidic Device for the Synthesis and Crystal Growth of Organometallic Polymers with Highly Organized Structures. Angew Chem Int Ed Engl 2014. [DOI: 10.1002/ange.201411008] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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27
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Zhu Z, Guan Z, Jia S, Lei Z, Lin S, Zhang H, Ma Y, Tian ZQ, Yang CJ. Au@Pt Nanoparticle Encapsulated Target-Responsive Hydrogel with Volumetric Bar-Chart Chip Readout for Quantitative Point-of-Care Testing. Angew Chem Int Ed Engl 2014. [DOI: 10.1002/ange.201405995] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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28
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Zhu Z, Guan Z, Jia S, Lei Z, Lin S, Zhang H, Ma Y, Tian ZQ, Yang CJ. Au@Pt nanoparticle encapsulated target-responsive hydrogel with volumetric bar-chart chip readout for quantitative point-of-care testing. Angew Chem Int Ed Engl 2014; 53:12503-7. [PMID: 25113247 DOI: 10.1002/anie.201405995] [Citation(s) in RCA: 104] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2014] [Indexed: 01/03/2023]
Abstract
Point-of-care testing (POCT) with the advantages of speed, simplicity, portability, and low cost is critical for the measurement of analytes in a variety of environments where access to laboratory infrastructure is lacking. While qualitative POCTs are widely available, quantitative POCTs present significant challenges. Here we describe a novel method that integrates an Au core/Pt shell nanoparticle (Au@PtNP) encapsulated target-responsive hydrogel with a volumetric bar-chart chip (V-Chip) for quantitative POCT. Upon target introduction, the hydrogel immediately dissolves and releases Au@PtNPs, which can efficiently catalyze the decomposition of H2 O2 to generate a large volume of O2 to move of an ink bar in the V-Chip. The concentration of the target introduced can be visually quantified by reading the traveling distance of the ink bar. This method has the potential to be used for portable and quantitative detection of a wide range of targets without any external instrument.
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Affiliation(s)
- Zhi Zhu
- State Key Laboratory of Physical Chemistry of Solid Surfaces the MOE Key Laboratory of Spectrochemical Analysis & Instrumentation, Key Laboratory for Chemical Biology of Fujian Province, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005 (China)
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29
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Ma L, Datta SS, Karymov MA, Pan Q, Begolo S, Ismagilov RF. Individually addressable arrays of replica microbial cultures enabled by splitting SlipChips. Integr Biol (Camb) 2014; 6:796-805. [PMID: 24953827 PMCID: PMC4131746 DOI: 10.1039/c4ib00109e] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Isolating microbes carrying genes of interest from environmental samples is important for applications in biology and medicine. However, this involves the use of genetic assays that often require lysis of microbial cells, which is not compatible with the goal of obtaining live cells for isolation and culture. This paper describes the design, fabrication, biological validation, and underlying physics of a microfluidic SlipChip device that addresses this challenge. The device is composed of two conjoined plates containing 1000 microcompartments, each comprising two juxtaposed wells, one on each opposing plate. Single microbial cells are stochastically confined and subsequently cultured within the microcompartments. Then, we split each microcompartment into two replica droplets, both containing microbial culture, and then controllably separate the two plates while retaining each droplet within each well. We experimentally describe the droplet retention as a function of capillary pressure, viscous pressure, and viscosity of the aqueous phase. Within each pair of replicas, one can be used for genetic analysis, and the other preserves live cells for growth. This microfluidic approach provides a facile way to cultivate anaerobes from complex communities. We validate this method by targeting, isolating, and culturing Bacteroides vulgatus, a core gut anaerobe, from a clinical sample. To date, this methodology has enabled isolation of a novel microbial taxon, representing a new genus. This approach could also be extended to the study of other microorganisms and even mammalian systems, and may enable targeted retrieval of solutions in applications including digital PCR, sequencing, single cell analysis, and protein crystallization.
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Affiliation(s)
- Liang Ma
- Division of Chemistry and Chemical Engineering, California Institute of Technology, 1200 E. California Blvd., Pasadena, California 91125, USA.
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30
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Cheow LF, Sarkar A, Kolitz S, Lauffenburger D, Han J. Detecting kinase activities from single cell lysate using concentration-enhanced mobility shift assay. Anal Chem 2014; 86:7455-62. [PMID: 25025773 PMCID: PMC4144746 DOI: 10.1021/ac502185v] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Electrokinetic preconcentration coupled with mobility shift assays can give rise to very high detection sensitivities. We describe a microfluidic device that utilizes this principle to detect cellular kinase activities by simultaneously concentrating and separating substrate peptides with different phosphorylation states. This platform is capable of reliably measuring kinase activities of single adherent cells cultured in nanoliter volume microwells. We also describe a novel method utilizing spacer peptides that significantly increase separation resolution while maintaining high concentration factors in this device. Thus, multiplexed kinase measurements can be implemented with single cell sensitivity. Multiple kinase activity profiling from single cell lysate could potentially allow us to study heterogeneous activation of signaling pathways that can lead to multiple cell fates.
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Affiliation(s)
- Lih Feng Cheow
- Department of Electrical Engineering and Computer Science and ‡Department of Biological Engineering, Massachusetts Institute of Technology , Cambridge, Massachusetts 02139, United States
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31
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Gene-targeted microfluidic cultivation validated by isolation of a gut bacterium listed in Human Microbiome Project's Most Wanted taxa. Proc Natl Acad Sci U S A 2014; 111:9768-73. [PMID: 24965364 DOI: 10.1073/pnas.1404753111] [Citation(s) in RCA: 110] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
This paper describes a microfluidics-based workflow for genetically targeted isolation and cultivation of microorganisms from complex clinical samples. Data sets from high-throughput sequencing suggest the existence of previously unidentified bacterial taxa and functional genes with high biomedical importance. Obtaining isolates of these targets, preferably in pure cultures, is crucial for advancing understanding of microbial genetics and physiology and enabling physical access to microbes for further applications. However, the majority of microbes have not been cultured, due in part to the difficulties of both identifying proper growth conditions and characterizing and isolating each species. We describe a method that enables genetically targeted cultivation of microorganisms through a combination of microfluidics and on- and off-chip assays. This method involves (i) identification of cultivation conditions for microbes using growth substrates available only in small quantities as well as the correction of sampling bias using a "chip wash" technique; and (ii) performing on-chip genetic assays while also preserving live bacterial cells for subsequent scale-up cultivation of desired microbes, by applying recently developed technology to create arrays of individually addressable replica microbial cultures. We validated this targeted approach by cultivating a bacterium, here referred to as isolate microfluidicus 1, from a human cecal biopsy. Isolate microfluidicus 1 is, to our knowledge, the first successful example of targeted cultivation of a microorganism from the high-priority group of the Human Microbiome Project's "Most Wanted" list, and, to our knowledge, the first cultured representative of a previously unidentified genus of the Ruminococcaceae family.
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32
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Wang S, Chen S, Wang J, Xu P, Luo Y, Nie Z, Du W. Interface solution isoelectric focusing with in situ MALDI-TOF mass spectrometry. Electrophoresis 2014; 35:2528-33. [DOI: 10.1002/elps.201400083] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2014] [Revised: 04/19/2014] [Accepted: 04/21/2014] [Indexed: 01/03/2023]
Affiliation(s)
- Shujun Wang
- Department of Chemistry; Renmin University of China; Beijing China
- State Key Laboratory of Microbial Resources; Institute of Microbiology; Chinese Academy of Sciences; Beijing China
| | - Suming Chen
- Beijing National Laboratory for Molecular Sciences; Key Laboratory of Analytical Chemistry for Living Biosystems; Institute of Chemistry; Chinese Academy of Sciences; Beijing China
| | - Jianing Wang
- Beijing National Laboratory for Molecular Sciences; Key Laboratory of Analytical Chemistry for Living Biosystems; Institute of Chemistry; Chinese Academy of Sciences; Beijing China
| | - Peng Xu
- State Key Laboratory of Microbial Resources; Institute of Microbiology; Chinese Academy of Sciences; Beijing China
| | - Yuanming Luo
- State Key Laboratory of Microbial Resources; Institute of Microbiology; Chinese Academy of Sciences; Beijing China
| | - Zongxiu Nie
- Beijing National Laboratory for Molecular Sciences; Key Laboratory of Analytical Chemistry for Living Biosystems; Institute of Chemistry; Chinese Academy of Sciences; Beijing China
| | - Wenbin Du
- State Key Laboratory of Microbial Resources; Institute of Microbiology; Chinese Academy of Sciences; Beijing China
- Department of Chemistry; Renmin University of China; Beijing China
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33
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Zhao Y, Pereira F, deMello AJ, Morgan H, Niu X. Droplet-based in situ compartmentalization of chemically separated components after isoelectric focusing in a Slipchip. LAB ON A CHIP 2014; 14:555-561. [PMID: 24292781 DOI: 10.1039/c3lc51067k] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
Isoelectric focusing (IEF) is a powerful and widely used technique for protein separation and purification. There are many embodiments of microscale IEF that use capillary or microfluidic chips for the analysis of small sample volumes. Nevertheless, collecting the separated sample volumes without causing remixing remains a challenge. Herein, we describe a microfluidic Slipchip device that is able to efficiently compartmentalize focused analyte bands in situ into microdroplets. The device contains a microfluidic "zig-zag" separation channel that is composed of a sequence of wells formed in the two halves of the Slipchip. The analytes are focused in the channel and then compartmentalised into droplets by slipping the chip. Importantly, sample droplets can be analysed on chip or collected for subsequent analysis using electrophoresis or mass spectrometry for example. To demonstrate this approach, we perform IEF separation using standard markers and protein samples, with on-chip post-processing. Compared to alternative approaches for sample collection, the method avoids remixing, is scalable and is easily hyphenated with the other analytical methods.
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Affiliation(s)
- Yan Zhao
- Faculty of Physical Sciences and Engineering, and Institute for Life Sciences, University of Southampton, Highfield, Southampton, SO17 1BJ, UK.
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34
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Puigmartí-Luis J. Microfluidic platforms: a mainstream technology for the preparation of crystals. Chem Soc Rev 2014; 43:2253-71. [DOI: 10.1039/c3cs60372e] [Citation(s) in RCA: 95] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
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35
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Abstract
With the experimental tools and knowledge that have accrued from a long history of reductionist biology, we can now start to put the pieces together and begin to understand how biological systems function as an integrated whole. Here, we describe how microfabricated tools have demonstrated promise in addressing experimental challenges in throughput, resolution, and sensitivity to support systems-based approaches to biological understanding.
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Affiliation(s)
- Mei Zhan
- Interdisciplinary Program in Bioengineering, Georgia Institute of Technology, Atlanta, Georgia, United States
| | - Loice Chingozha
- School of Chemical & Biomolecular Engineering, Georgia Institute of Technology, Atlanta, Georgia, United States
| | - Hang Lu
- School of Chemical & Biomolecular Engineering, Georgia Institute of Technology, Atlanta, Georgia, United States
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36
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Liu H, Li X, Crooks RM. Paper-Based SlipPAD for High-Throughput Chemical Sensing. Anal Chem 2013; 85:4263-7. [DOI: 10.1021/ac4008623] [Citation(s) in RCA: 88] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Hong Liu
- Department of Chemistry
and Biochemistry, The University of Texas at Austin, 105 East 24th Street,
Stop A5300, Austin, Texas 78712-1224, United States
| | - Xiang Li
- Department of Chemistry
and Biochemistry, The University of Texas at Austin, 105 East 24th Street,
Stop A5300, Austin, Texas 78712-1224, United States
| | - Richard M. Crooks
- Department of Chemistry
and Biochemistry, The University of Texas at Austin, 105 East 24th Street,
Stop A5300, Austin, Texas 78712-1224, United States
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37
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Schneider T, Kreutz J, Chiu DT. The potential impact of droplet microfluidics in biology. Anal Chem 2013; 85:3476-82. [PMID: 23495853 DOI: 10.1021/ac400257c] [Citation(s) in RCA: 133] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Droplet microfluidics, which involves micrometer-sized emulsion droplets on a microfabricated platform, is an active research endeavor that evolved out of the larger field of microfluidics. Recently, this subfield of microfluidics has started to attract greater interest because researchers have been able to demonstrate applications of droplets as miniaturized laboratories for biological measurements. This perspective explores the recent developments and the potential future biological applications of droplet microfluidics.
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Affiliation(s)
- Thomas Schneider
- Department of Chemistry, University of Washington, Seattle, Washington 98195, United States
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38
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Sun B, Shen F, McCalla SE, Kreutz JE, Karymov MA, Ismagilov RF. Mechanistic evaluation of the pros and cons of digital RT-LAMP for HIV-1 viral load quantification on a microfluidic device and improved efficiency via a two-step digital protocol. Anal Chem 2013; 85:1540-6. [PMID: 23324061 DOI: 10.1021/ac3037206] [Citation(s) in RCA: 73] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Here we used a SlipChip microfluidic device to evaluate the performance of digital reverse transcription-loop-mediated isothermal amplification (dRT-LAMP) for quantification of HIV viral RNA. Tests are needed for monitoring HIV viral load to control the emergence of drug resistance and to diagnose acute HIV infections. In resource-limited settings, in vitro measurement of HIV viral load in a simple format is especially needed, and single-molecule counting using a digital format could provide a potential solution. We showed here that when one-step dRT-LAMP is used for quantification of HIV RNA, the digital count is lower than expected and is limited by the yield of desired cDNA. We were able to overcome the limitations by developing a microfluidic protocol to manipulate many single molecules in parallel through a two-step digital process. In the first step we compartmentalize the individual RNA molecules (based on Poisson statistics) and perform reverse transcription on each RNA molecule independently to produce DNA. In the second step, we perform the LAMP amplification on all individual DNA molecules in parallel. Using this new protocol, we increased the absolute efficiency (the ratio between the concentration calculated from the actual count and the expected concentration) of dRT-LAMP 10-fold, from ∼2% to ∼23%, by (i) using a more efficient reverse transcriptase, (ii) introducing RNase H to break up the DNA:RNA hybrid, and (iii) adding only the BIP primer during the RT step. We also used this two-step method to quantify HIV RNA purified from four patient samples and found that in some cases, the quantification results were highly sensitive to the sequence of the patient's HIV RNA. We learned the following three lessons from this work: (i) digital amplification technologies, including dLAMP and dPCR, may give adequate dilution curves and yet have low efficiency, thereby providing quantification values that underestimate the true concentration. Careful validation is essential before a method is considered to provide absolute quantification; (ii) the sensitivity of dLAMP to the sequence of the target nucleic acid necessitates additional validation with patient samples carrying the full spectrum of mutations; (iii) for multistep digital amplification chemistries, such as a combination of reverse transcription with amplification, microfluidic devices may be used to decouple these steps from one another and to perform them under different, individually optimized conditions for improved efficiency.
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Affiliation(s)
- Bing Sun
- Division of Chemistry and Chemical Engineering, California Institute of Technology, 1200 East California Boulevard, Pasadena, California 91125, United States
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39
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Abstract
The field of microfluidics has exploded in the past decade, particularly in the area of chemical and biochemical analysis systems. Borrowing technology from the solid-state electronics industry and the production of microprocessor chips, researchers working with glass, silicon, and polymer substrates have fabricated macroscale laboratory components in miniaturized formats. These devices pump nanoliter volumes of liquid through micrometer-scale channels and perform complex chemical reactions and separations. The detection of reaction products is typically done fluorescently with off-chip optical components, and the analysis time from start to finish can be significantly shorter than that of conventional techniques. In this review we describe these microfluidic analysis systems, from the original continuous flow systems relying on electroosmotic pumping for liquid motion to the large diversity of microarray chips currently in use to the newer droplet-based devices and segmented flow systems. Although not currently widespread, microfluidic systems have the potential to become ubiquitous.
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Affiliation(s)
- Eric Livak-Dahl
- Department of Chemical Engineering, University of Michigan, Ann Arbor, MI 48109, USA.
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40
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Yoshizawa S. Micro and nanotechnological tools for study of RNA. Biochimie 2012; 94:1588-94. [PMID: 22484393 DOI: 10.1016/j.biochi.2012.03.018] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2012] [Accepted: 03/22/2012] [Indexed: 11/16/2022]
Abstract
Micro and nanotechnologies have originally contributed to engineering, especially in electronics. These technologies enable fabrication and assembly of materials at micrometer and nanometer scales and the manipulation of nano-objects. The power of these technologies has now been exploited in analyzes of biologically relevant molecules. In this review, the use of micro and nanotechnological tools in RNA research is described.
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Affiliation(s)
- Satoko Yoshizawa
- Centre de Génétique Moléculaire UPR 3404, CNRS, Université Paris-Sud, FRC3115 1 Ave de la Terrasse, 91190 Gif-sur-Yvette, France.
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41
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Pompano RR, Platt CE, Karymov MA, Ismagilov RF. Control of initiation, rate, and routing of spontaneous capillary-driven flow of liquid droplets through microfluidic channels on SlipChip. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2012; 28:1931-41. [PMID: 22233156 PMCID: PMC3271727 DOI: 10.1021/la204399m] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
This Article describes the use of capillary pressure to initiate and control the rate of spontaneous liquid-liquid flow through microfluidic channels. In contrast to flow driven by external pressure, flow driven by capillary pressure is dominated by interfacial phenomena and is exquisitely sensitive to the chemical composition and geometry of the fluids and channels. A stepwise change in capillary force was initiated on a hydrophobic SlipChip by slipping a shallow channel containing an aqueous droplet into contact with a slightly deeper channel filled with immiscible oil. This action induced spontaneous flow of the droplet into the deeper channel. A model predicting the rate of spontaneous flow was developed on the basis of the balance of net capillary force with viscous flow resistance, using as inputs the liquid-liquid surface tension, the advancing and receding contact angles at the three-phase aqueous-oil-surface contact line, and the geometry of the devices. The impact of contact angle hysteresis, the presence or absence of a lubricating oil layer, and adsorption of surface-active compounds at liquid-liquid or liquid-solid interfaces were quantified. Two regimes of flow spanning a 10(4)-fold range of flow rates were obtained and modeled quantitatively, with faster (mm/s) flow obtained when oil could escape through connected channels as it was displaced by flowing aqueous solution, and slower (micrometer/s) flow obtained when oil escape was mostly restricted to a micrometer-scale gap between the plates of the SlipChip ("dead-end flow"). Rupture of the lubricating oil layer (reminiscent of a Cassie-Wenzel transition) was proposed as a cause of discrepancy between the model and the experiment. Both dilute salt solutions and complex biological solutions such as human blood plasma could be flowed using this approach. We anticipate that flow driven by capillary pressure will be useful for the design and operation of flow in microfluidic applications that do not require external power, valves, or pumps, including on SlipChip and other droplet- or plug-based microfluidic devices. In addition, this approach may be used as a sensitive method of evaluating interfacial tension, contact angles, and wetting phenomena on chip.
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Affiliation(s)
- Rebecca R Pompano
- Department of Chemistry and Institute for Biophysical Dynamics, The University of Chicago, 929 East 57th Street, Chicago, Illinois 60637, United States
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42
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Thorson MR, Goyal S, Schudel BR, Zukoski CF, Zhang GGZ, Gong Y, Kenis PJA. A microfluidic platform for pharmaceutical salt screening. LAB ON A CHIP 2011; 11:3829-37. [PMID: 21956673 DOI: 10.1039/c1lc20645a] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
We describe a microfluidic platform comprised of 48 wells to screen for pharmaceutical salts. Solutions of pharmaceutical parent compounds (PCs) and salt formers (SFs) are mixed on-chip in a combinatorial fashion in arrays of 87.5-nanolitre wells, which constitutes a drastic reduction of the volume of PC solution needed per condition screened compared to typical high throughput pharmaceutical screening approaches. Nucleation and growth of salt crystals is induced by diffusive and/or convective mixing of solutions containing, respectively, PCs and SFs in a variety of solvents. To enable long term experiments, solvent loss was minimized by reducing the thickness of the absorptive polymeric material, polydimethylsiloxane (PDMS), and by using solvent impermeable top and bottom layers. Additionally, well isolation was enhanced via the incorporation of pneumatic valves that are closed at rest. Brightfield and polarized light microscopy and Raman spectroscopy were used for on-chip analysis and crystal identification. Using a gold-coated glass substrate and minimizing the thickness of the PDMS control layer drastically improved the signal-to-noise ratio for Raman spectra. Two drugs, naproxen (acid) and ephedrine (base), were used for validation of the platform's ability to screen for salts. Each PC was mixed combinatorially with potential SFs in a variety of solvents. Crystals were visualized using brightfield polarized light microscopy. Subsequent on-chip analyses of the crystals with Raman spectroscopy identified four different naproxen salts and five different ephedrine salts.
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Affiliation(s)
- Michael R Thorson
- Department of Chemical & Biomolecular Engineering, University of Illinois at Urbana-Champaign, USA
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43
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Kreutz JE, Munson T, Huynh T, Shen F, Du W, Ismagilov RF. Theoretical design and analysis of multivolume digital assays with wide dynamic range validated experimentally with microfluidic digital PCR. Anal Chem 2011; 83:8158-68. [PMID: 21981344 PMCID: PMC3216679 DOI: 10.1021/ac201658s] [Citation(s) in RCA: 111] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
This paper presents a protocol using theoretical methods and free software to design and analyze multivolume digital PCR (MV digital PCR) devices; the theory and software are also applicable to design and analysis of dilution series in digital PCR. MV digital PCR minimizes the total number of wells required for "digital" (single molecule) measurements while maintaining high dynamic range and high resolution. In some examples, multivolume designs with fewer than 200 total wells are predicted to provide dynamic range with 5-fold resolution similar to that of single-volume designs requiring 12,000 wells. Mathematical techniques were utilized and expanded to maximize the information obtained from each experiment and to quantify performance of devices and were experimentally validated using the SlipChip platform. MV digital PCR was demonstrated to perform reliably, and results from wells of different volumes agreed with one another. No artifacts due to different surface-to-volume ratios were observed, and single molecule amplification in volumes ranging from 1 to 125 nL was self-consistent. The device presented here was designed to meet the testing requirements for measuring clinically relevant levels of HIV viral load at the point-of-care (in plasma, <500 molecules/mL to >1,000,000 molecules/mL), and the predicted resolution and dynamic range was experimentally validated using a control sequence of DNA. This approach simplifies digital PCR experiments, saves space, and thus enables multiplexing using separate areas for each sample on one chip, and facilitates the development of new high-performance diagnostic tools for resource-limited applications. The theory and software presented here are general and are applicable to designing and analyzing other digital analytical platforms including digital immunoassays and digital bacterial analysis. It is not limited to SlipChip and could also be useful for the design of systems on platforms including valve-based and droplet-based platforms. In a separate publication by Shen et al. (J. Am. Chem. Soc., 2011, DOI: 10.1021/ja2060116), this approach is used to design and test digital RT-PCR devices for quantifying RNA.
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Affiliation(s)
- Jason E. Kreutz
- Department of Chemistry and Institute for Biophysical Dynamics, The University of Chicago, 929, East. 57th St., Chicago, Illinois 60637
| | - Todd Munson
- University of Chicago, Computation Institute, Chicago, IL 60637 USA and Argonne Natl Lab, Argonne, IL 60439 USA
| | - Toan Huynh
- Department of Chemistry and Institute for Biophysical Dynamics, The University of Chicago, 929, East. 57th St., Chicago, Illinois 60637
| | - Feng Shen
- Department of Chemistry and Institute for Biophysical Dynamics, The University of Chicago, 929, East. 57th St., Chicago, Illinois 60637
| | - Wenbin Du
- Department of Chemistry and Institute for Biophysical Dynamics, The University of Chicago, 929, East. 57th St., Chicago, Illinois 60637
| | - Rustem F. Ismagilov
- Department of Chemistry and Institute for Biophysical Dynamics, The University of Chicago, 929, East. 57th St., Chicago, Illinois 60637
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Stacy R, Begley DW, Phan I, Staker BL, Van Voorhis WC, Varani G, Buchko GW, Stewart LJ, Myler PJ. Structural genomics of infectious disease drug targets: the SSGCID. Acta Crystallogr Sect F Struct Biol Cryst Commun 2011; 67:979-84. [PMID: 21904037 PMCID: PMC3169389 DOI: 10.1107/s1744309111029204] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2011] [Accepted: 07/19/2011] [Indexed: 11/29/2022]
Abstract
The Seattle Structural Genomics Center for Infectious Disease (SSGCID) is a consortium of researchers at Seattle BioMed, Emerald BioStructures, the University of Washington and Pacific Northwest National Laboratory that was established to apply structural genomics approaches to drug targets from infectious disease organisms. The SSGCID is currently funded over a five-year period by the National Institute of Allergy and Infectious Diseases (NIAID) to determine the three-dimensional structures of 400 proteins from a variety of Category A, B and C pathogens. Target selection engages the infectious disease research and drug-therapy communities to identify drug targets, essential enzymes, virulence factors and vaccine candidates of biomedical relevance to combat infectious diseases. The protein-expression systems, purified proteins, ligand screens and three-dimensional structures produced by SSGCID constitute a valuable resource for drug-discovery research, all of which is made freely available to the greater scientific community. This issue of Acta Crystallographica Section F, entirely devoted to the work of the SSGCID, covers the details of the high-throughput pipeline and presents a series of structures from a broad array of pathogenic organisms. Here, a background is provided on the structural genomics of infectious disease, the essential components of the SSGCID pipeline are discussed and a survey of progress to date is presented.
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Affiliation(s)
- Robin Stacy
- Seattle Structural Genomics Center for Infectious Disease, USA
- Seattle Biomedical Research Institute, 307 Westlake Avenue North, Suite 500, Seattle, WA 98109-5219, USA
| | - Darren W. Begley
- Seattle Structural Genomics Center for Infectious Disease, USA
- Emerald BioStructures, 7869 NE Day Road West, Bainbridge Island, WA 98110, USA
| | - Isabelle Phan
- Seattle Structural Genomics Center for Infectious Disease, USA
- Seattle Biomedical Research Institute, 307 Westlake Avenue North, Suite 500, Seattle, WA 98109-5219, USA
| | - Bart L. Staker
- Seattle Structural Genomics Center for Infectious Disease, USA
- Emerald BioStructures, 7869 NE Day Road West, Bainbridge Island, WA 98110, USA
| | - Wesley C. Van Voorhis
- Seattle Structural Genomics Center for Infectious Disease, USA
- Department of Medicine, Division of Allergy and Infectious Diseases, University of Washington, Box 357185, Seattle, WA 98195, USA
| | - Gabriele Varani
- Seattle Structural Genomics Center for Infectious Disease, USA
- Departments of Chemistry and Biochemistry, University of Washington, Box 351700, Seattle, WA 98185, USA
| | - Garry W. Buchko
- Seattle Structural Genomics Center for Infectious Disease, USA
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354, USA
| | - Lance J. Stewart
- Seattle Structural Genomics Center for Infectious Disease, USA
- Emerald BioStructures, 7869 NE Day Road West, Bainbridge Island, WA 98110, USA
| | - Peter J. Myler
- Seattle Structural Genomics Center for Infectious Disease, USA
- Seattle Biomedical Research Institute, 307 Westlake Avenue North, Suite 500, Seattle, WA 98109-5219, USA
- Departments of Global Health and Medical Education and Biomedical Informatics, University of Washington, Box 357238, Seattle, WA 98195, USA
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Pompano RR, Liu W, Du W, Ismagilov RF. Microfluidics using spatially defined arrays of droplets in one, two, and three dimensions. ANNUAL REVIEW OF ANALYTICAL CHEMISTRY (PALO ALTO, CALIF.) 2011; 4:59-81. [PMID: 21370983 DOI: 10.1146/annurev.anchem.012809.102303] [Citation(s) in RCA: 70] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
Spatially defined arrays of droplets differ from bulk emulsions in that droplets in arrays can be indexed on the basis of one or more spatial variables to enable identification, monitoring, and addressability of individual droplets. Spatial indexing is critical in experiments with hundreds to millions of unique compartmentalized microscale processes--for example, in applications such as digital measurements of rare events in a large sample, high-throughput time-lapse studies of the contents of individual droplets, and controlled droplet-droplet interactions. This review describes approaches for spatially organizing and manipulating droplets in one-, two-, and three-dimensional structured arrays, including aspiration, laminar flow, droplet traps, the SlipChip, self-assembly, and optical or electrical fields. This review also presents techniques to analyze droplets in arrays and applications of spatially defined arrays, including time-lapse studies of chemical, enzymatic, and cellular processes, as well as further opportunities in chemical, biological, and engineering sciences, including perturbation/response experiments and personal and point-of-care diagnostics.
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Affiliation(s)
- Rebecca R Pompano
- Department of Chemistry and Institute for Biophysical Dynamics, The University of Chicago, Chicago, Illinois 60637, USA
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46
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Abstract
This paper describes a SlipChip to perform digital PCR in a very simple and inexpensive format. The fluidic path for introducing the sample combined with the PCR mixture was formed using elongated wells in the two plates of the SlipChip designed to overlap during sample loading. This fluidic path was broken up by simple slipping of the two plates that removed the overlap among wells and brought each well in contact with a reservoir preloaded with oil to generate 1280 reaction compartments (2.6 nL each) simultaneously. After thermal cycling, end-point fluorescence intensity was used to detect the presence of nucleic acid. Digital PCR on the SlipChip was tested quantitatively by using Staphylococcus aureus genomic DNA. As the concentration of the template DNA in the reaction mixture was diluted, the fraction of positive wells decreased as expected from the statistical analysis. No cross-contamination was observed during the experiments. At the extremes of the dynamic range of digital PCR the standard confidence interval determined using a normal approximation of the binomial distribution is not satisfactory. Therefore, statistical analysis based on the score method was used to establish these confidence intervals. The SlipChip provides a simple strategy to count nucleic acids by using PCR. It may find applications in research applications such as single cell analysis, prenatal diagnostics, and point-of-care diagnostics. SlipChip would become valuable for diagnostics, including applications in resource-limited areas after integration with isothermal nucleic acid amplification technologies and visual readout.
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Shen F, Du W, Davydova EK, Karymov MA, Pandey J, Ismagilov RF. Nanoliter multiplex PCR arrays on a SlipChip. Anal Chem 2010; 82:4606-12. [PMID: 20446698 DOI: 10.1021/ac1007249] [Citation(s) in RCA: 98] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
The SlipChip platform was tested to perform high-throughput nanoliter multiplex PCR. The advantages of using the SlipChip platform for multiplex PCR include the ability to preload arrays of dry primers, instrument-free sample manipulation, small sample volume, and high-throughput capacity. The SlipChip was designed to preload one primer pair per reaction compartment and to screen up to 384 different primer pairs with less than 30 nanoliters of sample per reaction compartment. Both a 40-well and a 384-well design of the SlipChip were tested for multiplex PCR. In the geometries used here, the sample fluid was spontaneously compartmentalized into discrete volumes even before slipping of the two plates of the SlipChip, but slipping introduced additional capabilities that made devices more robust and versatile. The wells of this SlipChip were designed to overcome potential problems associated with thermal expansion. By using circular wells filled with oil and overlapping them with square wells filled with the aqueous PCR mixture, a droplet of aqueous PCR mixture was always surrounded by the lubricating fluid. In this design, during heating and thermal expansion, only oil was expelled from the compartment and leaking of the aqueous solution was prevented. Both 40-well and 384-well devices were found to be free from cross-contamination, and end point fluorescence detection provided reliable readout. Multiple samples could also be screened on the same SlipChip simultaneously. Multiplex PCR was validated on the 384-well SlipChip with 20 different primer pairs to identify 16 bacterial and fungal species commonly presented in blood infections. The SlipChip correctly identified five different bacterial or fungal species in separate experiments. In addition, the presence of the resistance gene mecA in methicillin resistant Staphylococcus aureus (MRSA) was identified. The SlipChip will be useful for applications involving PCR arrays and lays the foundation for new strategies for diagnostics, point-of-care devices, and immobilization-based arrays.
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Affiliation(s)
- Feng Shen
- Department of Chemistry and Institute for Biophysical Dynamics, The University of Chicago, 929 E 57th Street, Chicago, Illinois 60637, USA
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49
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Jebrail MJ, Ng AHC, Rai V, Hili R, Yudin AK, Wheeler AR. Synchronized Synthesis of Peptide-Based Macrocycles by Digital Microfluidics. Angew Chem Int Ed Engl 2010. [DOI: 10.1002/ange.201001604] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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50
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Jebrail MJ, Ng AHC, Rai V, Hili R, Yudin AK, Wheeler AR. Synchronized Synthesis of Peptide-Based Macrocycles by Digital Microfluidics. Angew Chem Int Ed Engl 2010; 49:8625-9. [DOI: 10.1002/anie.201001604] [Citation(s) in RCA: 86] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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