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Young TW, Kappler MP, Call ED, Brown QJ, Jacobson SC. Integrated In-Plane Nanofluidic Devices for Resistive-Pulse Sensing. ANNUAL REVIEW OF ANALYTICAL CHEMISTRY (PALO ALTO, CALIF.) 2024; 17:221-242. [PMID: 38608295 DOI: 10.1146/annurev-anchem-061622-030223] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/14/2024]
Abstract
Single-particle (or digital) measurements enhance sensitivity (10- to 100-fold improvement) and uncover heterogeneity within a population (one event in 100 to 10,000). Many biological systems are significantly influenced by rare or infrequent events, and determining what species is present, in what quantity, and the role of that species is critically important to unraveling many questions. To develop these measurement systems, resistive-pulse sensing is used as a label-free, single-particle detection technique and can be combined with a range of functional elements, e.g., mixers, reactors, filters, separators, and pores. Virtually, any two-dimensional layout of the micro- and nanofluidic conduits can be envisioned, designed, and fabricated in the plane of the device. Multiple nanopores in series lead to higher-precision measurements of particle size, shape, and charge, and reactions coupled directly with the particle-size measurements improve temporal response. Moreover, other detection techniques, e.g., fluorescence, are highly compatible with the in-plane format. These integrated in-plane nanofluidic devices expand the toolbox of what is possible with single-particle measurements.
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Affiliation(s)
- Tanner W Young
- Department of Chemistry, Indiana University, Bloomington, Indiana, USA;
| | - Michael P Kappler
- Department of Chemistry, Indiana University, Bloomington, Indiana, USA;
| | - Ethan D Call
- Department of Chemistry, Indiana University, Bloomington, Indiana, USA;
| | - Quintin J Brown
- Department of Chemistry, Indiana University, Bloomington, Indiana, USA;
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2
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Xu R, Ouyang L, Chen H, Zhang G, Zhe J. Recent Advances in Biomolecular Detection Based on Aptamers and Nanoparticles. BIOSENSORS 2023; 13:bios13040474. [PMID: 37185549 PMCID: PMC10136534 DOI: 10.3390/bios13040474] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Revised: 04/07/2023] [Accepted: 04/11/2023] [Indexed: 05/17/2023]
Abstract
The fast, accurate detection of biomolecules, ranging from nucleic acids and small molecules to proteins and cellular secretions, plays an essential role in various biomedical applications. These include disease diagnostics and prognostics, environmental monitoring, public health, and food safety. Aptamer recognition (DNA or RNA) has gained extensive attention for biomolecular detection due to its high selectivity, affinity, reproducibility, and robustness. Concurrently, biosensing with nanoparticles has been widely used for its high carrier capacity, stability and feasibility of incorporating optical and catalytic activity, and enhanced diffusivity. Biosensors based on aptamers and nanoparticles utilize the combination of their advantages and have become a promising technology for detecting of a wide variety of biomolecules with high sensitivity, reliability, specificity, and detection speed. Via various sensing mechanisms, target biomolecules have been quantified in terms of optical (e.g., colorimetric and fluorometric), magnetic, and electrical signals. In this review, we summarize the recent advances in and compare different aptamer-nanoparticle-based biosensors by nanoparticle types and detection mechanisms. We also share our views on the highlights and challenges of the different nanoparticle-aptamer-based biosensors.
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Affiliation(s)
- Ruiting Xu
- Department of Mechanical Engineering, University of Akron, Akron, OH 44325, USA
| | - Leixin Ouyang
- Department of Mechanical Engineering, University of Akron, Akron, OH 44325, USA
| | - Heyi Chen
- Department of Mechanical Engineering, University of Akron, Akron, OH 44325, USA
| | - Ge Zhang
- Department of Biomedical Engineering, University of Akron, Akron, OH 44325, USA
| | - Jiang Zhe
- Department of Mechanical Engineering, University of Akron, Akron, OH 44325, USA
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3
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Carey T, Li B, Sohn LL. Node-Pore Sensing for Characterizing Cells and Extracellular Vesicles. Methods Mol Biol 2022; 2394:171-183. [PMID: 35094328 PMCID: PMC10836821 DOI: 10.1007/978-1-0716-1811-0_11] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Node-Pore Sensing, NPS, is an extremely versatile and powerful technique for the analysis of cells and the detection of extracellular vesicles (EVs). NPS involves measuring the modulated current pulse caused by a cell transiting a microfluidic channel that has been segmented by a series of inserted nodes. As the current pulse reflects the number of nodes and segments of the channel, NPS can achieve exquisite sensitivity. Thus, when used as a Coulter counter, NPS can measure the sub-micron size increase of antibody-coated colloids to which EVs are specifically bound. By simply inserting between two nodes a "contraction" channel through which cells can squeeze, one can mechanically phenotype cells. We discuss the details of performing these two NPS applications.
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Affiliation(s)
- Thomas Carey
- The UC Berkeley-UC San Francisco Graduate Program in Bioengineering, University of California, Berkeley, Berkeley, CA, USA
| | - Brian Li
- The UC Berkeley-UC San Francisco Graduate Program in Bioengineering, University of California, Berkeley, Berkeley, CA, USA
| | - Lydia L Sohn
- The UC Berkeley-UC San Francisco Graduate Program in Bioengineering, University of California, Berkeley, Berkeley, CA, USA.
- Department of Mechanical Engineering, University of California, Berkeley, Berkeley, CA, USA.
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4
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Gil Rosa B, Akingbade OE, Guo X, Gonzalez-Macia L, Crone MA, Cameron LP, Freemont P, Choy KL, Güder F, Yeatman E, Sharp DJ, Li B. Multiplexed immunosensors for point-of-care diagnostic applications. Biosens Bioelectron 2022; 203:114050. [DOI: 10.1016/j.bios.2022.114050] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Revised: 12/22/2021] [Accepted: 01/25/2022] [Indexed: 12/14/2022]
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5
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Li B, Cotner KL, Liu NK, Hinz S, LaBarge MA, Sohn LL. Evaluating sources of technical variability in the mechano-node-pore sensing pipeline and their effect on the reproducibility of single-cell mechanical phenotyping. PLoS One 2021; 16:e0258982. [PMID: 34695165 PMCID: PMC8544830 DOI: 10.1371/journal.pone.0258982] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2021] [Accepted: 10/09/2021] [Indexed: 11/19/2022] Open
Abstract
Cellular mechanical properties can reveal physiologically relevant characteristics in many cell types, and several groups have developed microfluidics-based platforms to perform high-throughput single-cell mechanical testing. However, prior work has performed only limited characterization of these platforms' technical variability and reproducibility. Here, we evaluate the repeatability performance of mechano-node-pore sensing, a single-cell mechanical phenotyping platform developed by our research group. We measured the degree to which device-to-device variability and semi-manual data processing affected this platform's measurements of single-cell mechanical properties. We demonstrated high repeatability across the entire technology pipeline even for novice users. We then compared results from identical mechano-node-pore sensing experiments performed by researchers in two different laboratories with different analytical instruments, demonstrating that the mechanical testing results from these two locations are in agreement. Our findings quantify the expectation of technical variability in mechano-node-pore sensing even in minimally experienced hands. Most importantly, we find that the repeatability performance we measured is fully sufficient for interpreting biologically relevant single-cell mechanical measurements with high confidence.
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Affiliation(s)
- Brian Li
- UC Berkeley–UCSF Graduate Program in Bioengineering, University of California, Berkeley and San Francisco, California, United States of America
| | - Kristen L. Cotner
- UC Berkeley–UCSF Graduate Program in Bioengineering, University of California, Berkeley and San Francisco, California, United States of America
| | - Nathaniel K. Liu
- Department of Mechanical Engineering, University of California, Berkeley, California, United States of America
| | - Stefan Hinz
- Department of Population Sciences, Beckman Research Institute, City of Hope, Duarte, California, United States of America
| | - Mark A. LaBarge
- Department of Population Sciences, Beckman Research Institute, City of Hope, Duarte, California, United States of America
| | - Lydia L. Sohn
- UC Berkeley–UCSF Graduate Program in Bioengineering, University of California, Berkeley and San Francisco, California, United States of America
- Department of Mechanical Engineering, University of California, Berkeley, California, United States of America
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6
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Kozminsky M, Scheideler OJ, Li B, Liu NK, Sohn LL. Multiplexed DNA-Directed Patterning of Antibodies for Applications in Cell Subpopulation Analysis. ACS APPLIED MATERIALS & INTERFACES 2021; 13:46421-46430. [PMID: 34546726 PMCID: PMC8817232 DOI: 10.1021/acsami.1c15047] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Antibodies provide the functional biospecificity that has enabled the development of sensors, diagnostic tools, and assays in both laboratory and clinical settings. However, as multimarker screening becomes increasingly necessary due to the heterogeneity and complexity of human pathology, new methods must be developed that are capable of coordinating the precise assembly of multiple, distinct antibodies. To address this technological challenge, we engineered a bottom-up, high-throughput method in which DNA patterns, comprising unique 20-base pair oligonucleotides, are patterned onto a substrate using photolithography. These microfabricated surface patterns are programmed to hybridize with, and instruct the multiplexed assembly of, antibodies conjugated with the complementary DNA strands. We demonstrate that this simple, yet robust, approach preserves the antibody-binding functionality in two common applications: antibody-based cell capture and label-free surface marker screening. Using a simple proof-of-concept capture device, we achieved high purity separation of a breast cancer cell line, MCF-7, from a blood cell line, Jurkat, with capture purities of 77.4% and 96.6% when using antibodies specific for the respective cell types. We also show that antigen-antibody interactions slow cell trajectories in flow in the next-generation microfluidic node-pore sensing (NPS) device, enabling the differentiation of MCF-7 and Jurkat cells based on EpCAM surface-marker expression. Finally, we use a next-generation NPS device patterned with antibodies against E-cadherin, N-cadherin, and β-integrin-three markers that are associated with epithelial-mesenchymal transitions-to perform label-free surface marker screening of MCF10A, MCF-7, and Hs 578T breast epithelial cells. Our high-throughput, highly versatile technique enables rapid development of customized, antibody-based assays across a host of diverse diseases and research thrusts.
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Affiliation(s)
- Molly Kozminsky
- California Institute of Quantitative Biosciences, University of California, Berkeley, 174 Stanley Hall, Berkeley, California 94720, United States
| | - Olivia J Scheideler
- The UC Berkeley-UC San Francisco Graduate Program in Bioengineering, University of California, Berkeley, 306 Stanley Hall, Berkeley, California 94720, United States
| | - Brian Li
- The UC Berkeley-UC San Francisco Graduate Program in Bioengineering, University of California, Berkeley, 306 Stanley Hall, Berkeley, California 94720, United States
| | - Nathaniel K Liu
- Department of Mechanical Engineering, University of California, Berkeley, 5118 Etcheverry Hall, Berkeley, California 94720, United States
| | - Lydia L Sohn
- California Institute of Quantitative Biosciences, University of California, Berkeley, 174 Stanley Hall, Berkeley, California 94720, United States
- The UC Berkeley-UC San Francisco Graduate Program in Bioengineering, University of California, Berkeley, 306 Stanley Hall, Berkeley, California 94720, United States
- Department of Mechanical Engineering, University of California, Berkeley, 5118 Etcheverry Hall, Berkeley, California 94720, United States
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7
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Choi J, Jia Z, Riahipour R, McKinney CJ, Amarasekara CA, Weerakoon-Ratnayake KM, Soper SA, Park S. Label-Free Identification of Single Mononucleotides by Nanoscale Electrophoresis. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2021; 17:e2102567. [PMID: 34558175 PMCID: PMC8542607 DOI: 10.1002/smll.202102567] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Revised: 07/15/2021] [Indexed: 06/13/2023]
Abstract
Nanoscale electrophoresis allows for unique separations of single molecules, such as DNA/RNA nucleobases, and thus has the potential to be used as single molecular sensors for exonuclease sequencing. For this to be envisioned, label-free detection of the nucleotides to determine their electrophoretic mobility (i.e., time-of-flight, TOF) for highly accurate identification must be realized. Here, for the first time a novel nanosensor is shown that allows discriminating four 2-deoxyribonucleoside 5'-monophosphates, dNMPs, molecules in a label-free manner by nanoscale electrophoresis. This is made possible by positioning two sub-10 nm in-plane pores at both ends of a nanochannel column used for nanoscale electrophoresis and measuring the longitudinal transient current during translocation of the molecules. The dual nanopore TOF sensor with 0.5, 1, and 5 µm long nanochannel column lengths discriminates different dNMPs with a mean accuracy of 55, 66, and 94%, respectively. This nanosensor format can broadly be applicable to label-free detection and discrimination of other single molecules, vesicles, and particles by changing the dimensions of the nanochannel column and in-plane nanopores and integrating different pre- and postprocessing units to the nanosensor. This is simple to accomplish because the nanosensor is contained within a fluidic network made in plastic via replication.
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Affiliation(s)
- Junseo Choi
- Department of Mechanical Engineering, Louisiana State University, Baton Rouge, LA 70803, USA
- Center of Bio-Modular Multiscale Systems for Precision Medicine, USA
| | - Zheng Jia
- Department of Mechanical Engineering, Louisiana State University, Baton Rouge, LA 70803, USA
- Center of Bio-Modular Multiscale Systems for Precision Medicine, USA
| | - Ramin Riahipour
- Department of Mechanical Engineering, Louisiana State University, Baton Rouge, LA 70803, USA
- Center of Bio-Modular Multiscale Systems for Precision Medicine, USA
| | - Collin J. McKinney
- Department of Chemistry, University of North Carolina, Chapel Hill, NC 27599, USA
- Center of Bio-Modular Multiscale Systems for Precision Medicine, USA
| | - Charuni A. Amarasekara
- Department of Chemistry, University of Kansas, Lawrence, KS 66047, USA
- Center of Bio-Modular Multiscale Systems for Precision Medicine, USA
| | - Kumuditha M. Weerakoon-Ratnayake
- Department of Chemistry, University of Kansas, Lawrence, KS 66047, USA
- Center of Bio-Modular Multiscale Systems for Precision Medicine, USA
| | - Steven A. Soper
- Department of Chemistry, University of Kansas, Lawrence, KS 66047, USA
- Center of Bio-Modular Multiscale Systems for Precision Medicine, USA
- Bioengineering Program, University of Kansas, Lawrence, KS 66047, USA
- Department of Kansas Biology and KUCC, University of Kansas Medical Center, Kansas City, KS 66160, USA
| | - Sunggook Park
- Department of Mechanical Engineering, Louisiana State University, Baton Rouge, LA 70803, USA
- Center of Bio-Modular Multiscale Systems for Precision Medicine, USA
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8
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Timp W, Timp G. Beyond mass spectrometry, the next step in proteomics. SCIENCE ADVANCES 2020; 6:eaax8978. [PMID: 31950079 PMCID: PMC6954058 DOI: 10.1126/sciadv.aax8978] [Citation(s) in RCA: 167] [Impact Index Per Article: 41.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/03/2019] [Accepted: 11/19/2019] [Indexed: 05/08/2023]
Abstract
Proteins can be the root cause of a disease, and they can be used to cure it. The need to identify these critical actors was recognized early (1951) by Sanger; the first biopolymer sequenced was a peptide, insulin. With the advent of scalable, single-molecule DNA sequencing, genomics and transcriptomics have since propelled medicine through improved sensitivity and lower costs, but proteomics has lagged behind. Currently, proteomics relies mainly on mass spectrometry (MS), but instead of truly sequencing, it classifies a protein and typically requires about a billion copies of a protein to do it. Here, we offer a survey that illuminates a few alternatives with the brightest prospects for identifying whole proteins and displacing MS for sequencing them. These alternatives all boast sensitivity superior to MS and promise to be scalable and seem to be adaptable to bioinformatics tools for calling the sequence of amino acids that constitute a protein.
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Affiliation(s)
- Winston Timp
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, USA
| | - Gregory Timp
- Departments of Electrical Engineering and Biological Sciences, University of Notre Dame, Notre Dame, IN, USA
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9
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Sano M, Kaji N, Rowat AC, Yasaki H, Shao L, Odaka H, Yasui T, Higashiyama T, Baba Y. Microfluidic Mechanotyping of a Single Cell with Two Consecutive Constrictions of Different Sizes and an Electrical Detection System. Anal Chem 2019; 91:12890-12899. [PMID: 31442026 DOI: 10.1021/acs.analchem.9b02818] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The mechanical properties of a cell, which include parameters such as elasticity, inner pressure, and tensile strength, are extremely important because changes in these properties are indicative of diseases ranging from diabetes to malignant transformation. Considering the heterogeneity within a population of cancer cells, a robust measurement system at the single cell level is required for research and in clinical purposes. In this study, a potential microfluidic device for high-throughput and practical mechanotyping were developed to investigate the deformability and sizes of cells through a single run. This mechanotyping device consisted of two different sizes of consecutive constrictions in a microchannel and measured the size of cells and related deformability during transit. Cell deformability was evaluated based on the transit and on the effects of cytoskeleton-affecting drugs, which were detected within 50 ms. The mechanotyping device was able to also measure a cell cycle without the use of fluorescent or protein tags.
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Affiliation(s)
- Mamiko Sano
- Department of Biomolecular Engineering, Graduate School of Engineering , Nagoya University , Furo-cho , Chikusa-ku, Nagoya 464-8603 , Japan.,Institute of Nano-Life-Systems, Institutes of Innovation for Future Society , Nagoya University , Furo-cho , Chikusa-ku, Nagoya 464-8603 , Japan
| | - Noritada Kaji
- Institute of Nano-Life-Systems, Institutes of Innovation for Future Society , Nagoya University , Furo-cho , Chikusa-ku, Nagoya 464-8603 , Japan.,Department of Applied Chemistry, Graduate School of Engineering , Kyushu University , Moto-oka 744 , Nishi-ku, Fukuoka 819-0395 , Japan.,Japan Science and Technology Agency, PRESTO , 4-1-8 Honcho , Kawaguchi , Saitama 332-0012 , Japan
| | - Amy C Rowat
- Department of Integrative Biology & Physiology , University of California Los Angeles , 610 Charles E Young Dr. East , Los Angeles , California 90095 , United States
| | - Hirotoshi Yasaki
- Department of Biomolecular Engineering, Graduate School of Engineering , Nagoya University , Furo-cho , Chikusa-ku, Nagoya 464-8603 , Japan.,Institute of Nano-Life-Systems, Institutes of Innovation for Future Society , Nagoya University , Furo-cho , Chikusa-ku, Nagoya 464-8603 , Japan
| | - Long Shao
- AGC Inc. , Suehiro 1-1 , Tsurumi-ku, Yokohama City , Kanagawa 230-0045 , Japan
| | - Hidefumi Odaka
- AGC Inc. , Suehiro 1-1 , Tsurumi-ku, Yokohama City , Kanagawa 230-0045 , Japan
| | - Takao Yasui
- Department of Biomolecular Engineering, Graduate School of Engineering , Nagoya University , Furo-cho , Chikusa-ku, Nagoya 464-8603 , Japan.,Institute of Nano-Life-Systems, Institutes of Innovation for Future Society , Nagoya University , Furo-cho , Chikusa-ku, Nagoya 464-8603 , Japan.,Japan Science and Technology Agency, PRESTO , 4-1-8 Honcho , Kawaguchi , Saitama 332-0012 , Japan
| | - Tetsuya Higashiyama
- Institute of Transformative Bio-Molecules (ITbM) , Nagoya University , Furo-cho , Chikusa-ku, Nagoya 464-8602 , Japan.,Division of Biological Science, Graduate School of Science , Nagoya University , Furo-cho , Chikusa-ku, Nagoya 464-8602 , Japan
| | - Yoshinobu Baba
- Department of Biomolecular Engineering, Graduate School of Engineering , Nagoya University , Furo-cho , Chikusa-ku, Nagoya 464-8603 , Japan.,Institute of Nano-Life-Systems, Institutes of Innovation for Future Society , Nagoya University , Furo-cho , Chikusa-ku, Nagoya 464-8603 , Japan.,Health Research Institute, National Institute of Advanced Industrial Science and Technology (AIST) , Hayashi-cho 2217-14 , Takamatsu 761-0395 , Japan.,College of Pharmacy , Kaohsiung Medical University , 100, Shih-Chuan First Road , Kaohsiung , 807 , Taiwan, R.O.C
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10
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Kim J, Li B, Scheideler OJ, Kim Y, Sohn LL. Visco-Node-Pore Sensing: A Microfluidic Rheology Platform to Characterize Viscoelastic Properties of Epithelial Cells. iScience 2019; 13:214-228. [PMID: 30870780 PMCID: PMC6416673 DOI: 10.1016/j.isci.2019.02.021] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2018] [Revised: 01/26/2019] [Accepted: 02/21/2019] [Indexed: 12/14/2022] Open
Abstract
Viscoelastic properties of cells provide valuable information regarding biological or clinically relevant cellular characteristics. Here, we introduce a new, electronic-based, microfluidic platform-visco-node-pore sensing (visco-NPS)-which quantifies cellular viscoelastic properties under periodic deformation. We measure the storage (G') and loss (G″) moduli (i.e., elasticity and viscosity, respectively) of cells. By applying a wide range of deformation frequencies, our platform quantifies the frequency dependence of viscoelastic properties. G' and G″ measurements show that the viscoelastic properties of malignant breast epithelial cells (MCF-7) are distinctly different from those of non-malignant breast epithelial cells (MCF-10A). With its sensitivity, visco-NPS can dissect the individual contributions of different cytoskeletal components to whole-cell mechanical properties. Moreover, visco-NPS can quantify the mechanical transitions of cells as they traverse the cell cycle or are initiated into an epithelial-mesenchymal transition. Visco-NPS identifies viscoelastic characteristics of cell populations, providing a biophysical understanding of cellular behavior and a potential for clinical applications.
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Affiliation(s)
- Junghyun Kim
- Department of Mechanical Engineering, University of California at Berkeley, Berkeley, CA, USA
| | - Brian Li
- Graduate Program in Bioengineering, University of California, Berkeley, University of California, San Francisco, Berkeley, CA, USA
| | - Olivia J Scheideler
- Graduate Program in Bioengineering, University of California, Berkeley, University of California, San Francisco, Berkeley, CA, USA
| | - Youngbin Kim
- Department of Bioengineering, University of California at Berkeley, Berkeley, CA, USA
| | - Lydia L Sohn
- Department of Mechanical Engineering, University of California at Berkeley, Berkeley, CA, USA; Graduate Program in Bioengineering, University of California, Berkeley, University of California, San Francisco, Berkeley, CA, USA.
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11
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Carey TR, Cotner KL, Li B, Sohn LL. Developments in label-free microfluidic methods for single-cell analysis and sorting. WILEY INTERDISCIPLINARY REVIEWS. NANOMEDICINE AND NANOBIOTECHNOLOGY 2019; 11:e1529. [PMID: 29687965 PMCID: PMC6200655 DOI: 10.1002/wnan.1529] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/10/2017] [Revised: 03/06/2018] [Accepted: 03/23/2018] [Indexed: 11/08/2022]
Abstract
Advancements in microfluidic technologies have led to the development of many new tools for both the characterization and sorting of single cells without the need for exogenous labels. Label-free microfluidics reduce the preparation time, reagents needed, and cost of conventional methods based on fluorescent or magnetic labels. Furthermore, these devices enable analysis of cell properties such as mechanical phenotype and dielectric parameters that cannot be characterized with traditional labels. Some of the most promising technologies for current and future development toward label-free, single-cell analysis and sorting include electronic sensors such as Coulter counters and electrical impedance cytometry; deformation analysis using optical traps and deformation cytometry; hydrodynamic sorting such as deterministic lateral displacement, inertial focusing, and microvortex trapping; and acoustic sorting using traveling or standing surface acoustic waves. These label-free microfluidic methods have been used to screen, sort, and analyze cells for a wide range of biomedical and clinical applications, including cell cycle monitoring, rapid complete blood counts, cancer diagnosis, metastatic progression monitoring, HIV and parasite detection, circulating tumor cell isolation, and point-of-care diagnostics. Because of the versatility of label-free methods for characterization and sorting, the low-cost nature of microfluidics, and the rapid prototyping capabilities of modern microfabrication, we expect this class of technology to continue to be an area of high research interest going forward. New developments in this field will contribute to the ongoing paradigm shift in cell analysis and sorting technologies toward label-free microfluidic devices, enabling new capabilities in biomedical research tools as well as clinical diagnostics. This article is categorized under: Diagnostic Tools > Biosensing Diagnostic Tools > Diagnostic Nanodevices.
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Affiliation(s)
- Thomas R Carey
- UC Berkeley-UC San Francisco Graduate Program in Bioengineering, University of California, Berkeley Graduate Division, Berkeley, California
| | - Kristen L Cotner
- UC Berkeley-UC San Francisco Graduate Program in Bioengineering, University of California, Berkeley Graduate Division, Berkeley, California
| | - Brian Li
- UC Berkeley-UC San Francisco Graduate Program in Bioengineering, University of California, Berkeley Graduate Division, Berkeley, California
| | - Lydia L Sohn
- UC Berkeley-UC San Francisco Graduate Program in Bioengineering, University of California, Berkeley Graduate Division, Berkeley, California
- Department of Mechanical Engineering, University of California, Berkeley, Berkeley, California
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12
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Zhou J, Kondylis P, Haywood DG, Harms ZD, Lee LS, Zlotnick A, Jacobson SC. Characterization of Virus Capsids and Their Assembly Intermediates by Multicycle Resistive-Pulse Sensing with Four Pores in Series. Anal Chem 2018; 90:7267-7274. [PMID: 29708733 PMCID: PMC6039186 DOI: 10.1021/acs.analchem.8b00452] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Virus self-assembly is a critical step in the virus lifecycle. Understanding how viruses assemble and disassemble provides needed insight into developing antiviral pharmaceuticals. Few tools offer sufficient resolution to study assembly intermediates that differ in size by a few dimers. Our goal is to improve resistive-pulse sensing on nanofluidic devices to offer better particle-size and temporal resolution to study intermediates and capsids generated along the assembly pathway. To increase the particle-size resolution of the resistive-pulse technique, we measured the same, single virus particles up to a thousand times, cycling them back and forth across a series of nanopores by switching the polarity of the applied potential, i.e., virus ping-pong. Multiple pores in series provide a unique multipulse signature during each cycle that improves particle tracking and, therefore, identification of a single particle and reduces the number of cycles needed to make the requisite number of measurements. With T = 3 and T = 4 hepatitis B virus (HBV) capsids, we showed the standard deviation of the particle-size distribution decreased with the square root of the number of measurements and approached discriminating particles differing in size by single dimers. We then studied in vitro assembly of HBV capsids and observed that the ensemble of intermediates shift to larger sizes over 2 days of annealing. On the contrary, assembly reactions diluted to lower dimer concentrations an hour after initiation had fewer intermediates that persisted after the 2 day incubation and had a higher ratio of T = 4 to T = 3 capsids. These reactions indicate that labile T = 4 intermediates are formed rapidly, and dependent on conditions, intermediates may be trapped as metastable species or progress to yield complete capsids.
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Affiliation(s)
- Jinsheng Zhou
- Department of Chemistry, Indiana University, Bloomington, IN 47405
| | | | | | - Zachary D. Harms
- Department of Chemistry, Indiana University, Bloomington, IN 47405
| | - Lye Siang Lee
- Department of Molecular and Cellular Biochemistry, Indiana University, Bloomington, IN 47405
| | - Adam Zlotnick
- Department of Molecular and Cellular Biochemistry, Indiana University, Bloomington, IN 47405
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13
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Zhao X, Sadhu V, Le T, Pompili D, Javanmard M. Toward Wireless Health Monitoring via an Analog Signal Compression-Based Biosensing Platform. IEEE TRANSACTIONS ON BIOMEDICAL CIRCUITS AND SYSTEMS 2018; 12:461-470. [PMID: 29877811 DOI: 10.1109/tbcas.2018.2829512] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Wireless all-analog biosensor design for the concurrent microfluidic and physiological signal monitoring is presented in this paper. The key component is an all-analog circuit capable of compressing two analog sources into one analog signal by the analog joint source-channel coding (AJSCC). Two circuit designs are discussed, including the stacked-voltage-controlled voltage source (VCVS) design with the fixed number of levels, and an improved design, which supports a flexible number of AJSCC levels. Experimental results are presented on the wireless biosensor prototype, composed of printed circuit board realizations of the stacked-VCVS design. Furthermore, circuit simulation and wireless link simulation results are presented on the improved design. Results indicate that the proposed wireless biosensor is well suited for sensing two biological signals simultaneously with high accuracy, and can be applied to a wide variety of low-power and low-cost wireless continuous health monitoring applications.
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14
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Kellman M, Rivest F, Pechacek A, Sohn L, Lustig M. Node-Pore Coded Coincidence Correction: Coulter Counters, Code Design, and Sparse Deconvolution. IEEE SENSORS JOURNAL 2018; 18:3068-3079. [PMID: 29988953 PMCID: PMC6034687 DOI: 10.1109/jsen.2018.2805865] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
We present a novel method to perform individual particle (e.g. cells or viruses) coincidence correction through joint channel design and algorithmic methods. Inspired by multiple-user communication theory, we modulate the channel response, with Node-Pore Sensing, to give each particle a binary Barker code signature. When processed with our modified successive interference cancellation method, this signature enables both the separation of coincidence particles and a high sensitivity to small particles. We identify several sources of modeling error and mitigate most effects using a data-driven self-calibration step and robust regression. Additionally, we provide simulation analysis to highlight our robustness, as well as our limitations, to these sources of stochastic system model error. Finally, we conduct experimental validation of our techniques using several encoded devices to screen a heterogeneous sample of several size particles.
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Affiliation(s)
- Michael Kellman
- Dept. of Electrical Engineering and Computer Sciences, University of California, Berkeley
| | - Francois Rivest
- Dept. of Mechanical Engineering, University of California, Berkeley
- Institute of Bioengineering, Ecole Polytechnique Federale de Lausanne, Switzerland
| | - Alina Pechacek
- Dept. of Electrical Engineering and Computer Sciences, University of California, Berkeley
| | - Lydia Sohn
- Dept. of Mechanical Engineering, University of California, Berkeley
- Graduate Program in Bioengineering, University of California Berkeley, Berkeley, CA, USA
| | - Michael Lustig
- Dept. of Electrical Engineering and Computer Sciences, University of California, Berkeley
- Graduate Program in Bioengineering, University of California Berkeley, Berkeley, CA, USA
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15
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Liu F, Ni L, Zhe J. Lab-on-a-chip electrical multiplexing techniques for cellular and molecular biomarker detection. BIOMICROFLUIDICS 2018; 12:021501. [PMID: 29682143 PMCID: PMC5893332 DOI: 10.1063/1.5022168] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/11/2018] [Accepted: 03/28/2018] [Indexed: 06/08/2023]
Abstract
Signal multiplexing is vital to develop lab-on-a-chip devices that can detect and quantify multiple cellular and molecular biomarkers with high throughput, short analysis time, and low cost. Electrical detection of biomarkers has been widely used in lab-on-a-chip devices because it requires less external equipment and simple signal processing and provides higher scalability. Various electrical multiplexing for lab-on-a-chip devices have been developed for comprehensive, high throughput, and rapid analysis of biomarkers. In this paper, we first briefly introduce the widely used electrochemical and electrical impedance sensing methods. Next, we focus on reviewing various electrical multiplexing techniques that had achieved certain successes on rapid cellular and molecular biomarker detection, including direct methods (spatial and time multiplexing), and emerging technologies (frequency, codes, particle-based multiplexing). Lastly, the future opportunities and challenges on electrical multiplexing techniques are also discussed.
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Affiliation(s)
- Fan Liu
- Department of Mechanical Engineering, University of Akron, Akron, Ohio 44325, USA
| | - Liwei Ni
- Department of Mechanical Engineering, University of Akron, Akron, Ohio 44325, USA
| | - Jiang Zhe
- Department of Mechanical Engineering, University of Akron, Akron, Ohio 44325, USA
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16
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Kim J, Han S, Lei A, Miyano M, Bloom J, Srivastava V, Stampfer MR, Gartner ZJ, LaBarge MA, Sohn LL. Characterizing cellular mechanical phenotypes with mechano-node-pore sensing. MICROSYSTEMS & NANOENGINEERING 2018; 4:17091. [PMID: 29780657 PMCID: PMC5958920 DOI: 10.1038/micronano.2017.91] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
The mechanical properties of cells change with their differentiation, chronological age, and malignant progression. Consequently, these properties may be useful label-free biomarkers of various functional or clinically relevant cell states. Here, we demonstrate mechano-node-pore sensing (mechano-NPS), a multi-parametric single-cell-analysis method that utilizes a four-terminal measurement of the current across a microfluidic channel to quantify simultaneously cell diameter, resistance to compressive deformation, transverse deformation under constant strain, and recovery time after deformation. We define a new parameter, the whole-cell deformability index (wCDI), which provides a quantitative mechanical metric of the resistance to compressive deformation that can be used to discriminate among different cell types. The wCDI and the transverse deformation under constant strain show malignant MCF-7 and A549 cell lines are mechanically distinct from non-malignant, MCF-10A and BEAS-2B cell lines, and distinguishes between cells treated or untreated with cytoskeleton-perturbing small molecules. We categorize cell recovery time, ΔTr, as instantaneous (ΔTr ~ 0 ms), transient (ΔTr ≤ 40ms), or prolonged (ΔTr > 40ms), and show that the composition of recovery types, which is a consequence of changes in cytoskeletal organization, correlates with cellular transformation. Through the wCDI and cell-recovery time, mechano-NPS discriminates between sub-lineages of normal primary human mammary epithelial cells with accuracy comparable to flow cytometry, but without antibody labeling. Mechano-NPS identifies mechanical phenotypes that distinguishes lineage, chronological age, and stage of malignant progression in human epithelial cells.
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Affiliation(s)
- Junghyun Kim
- Department of Mechanical Engineering, University of California at Berkeley, Berkeley, 94720-1740 CA USA
| | - Sewoon Han
- Department of Mechanical Engineering, University of California at Berkeley, Berkeley, 94720-1740 CA USA
| | - Andy Lei
- Department of Bioengineering, University of California at Berkeley, Berkeley, 94720-1762 CA USA
| | - Masaru Miyano
- Department of Population Sciences, Beckman Research Institute, City of Hope, Duarte, 91010 CA USA
| | - Jessica Bloom
- Department of Population Sciences, Beckman Research Institute, City of Hope, Duarte, 91010 CA USA
| | - Vasudha Srivastava
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, 94143 CA USA
| | - Martha R. Stampfer
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, CA, 94720 USA
| | - Zev J. Gartner
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, 94143 CA USA
- Graduate Program in Bioengineering, University of California, Berkeley, and
University of California, San Francisco, Berkeley, 94720 CA USA
| | - Mark A. LaBarge
- Department of Population Sciences, Beckman Research Institute, City of Hope, Duarte, 91010 CA USA
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, CA, 94720 USA
| | - Lydia L. Sohn
- Department of Mechanical Engineering, University of California at Berkeley, Berkeley, 94720-1740 CA USA
- Graduate Program in Bioengineering, University of California, Berkeley, and
University of California, San Francisco, Berkeley, 94720 CA USA
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17
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Liu R, Waheed W, Wang N, Civelekoglu O, Boya M, Chu CH, Sarioglu AF. Design and modeling of electrode networks for code-division multiplexed resistive pulse sensing in microfluidic devices. LAB ON A CHIP 2017; 17:2650-2666. [PMID: 28695944 DOI: 10.1039/c7lc00545h] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
A typical microfluidic device sorts, captures or fractionates sample constituents by exposing them to discriminating microenvironments. Direct electronic acquisition of such manipulation by a network of integrated sensors can provide a fast, integrated readout, replacing otherwise required microscopy. We have recently introduced a sensor technology, Microfluidic CODES, which allows us to multiplex resistive pulse sensors on a microfluidic device. Microfluidic CODES employs a network of micromachined coplanar electrodes such that particles passing over these electrodes produce distinguishable code sequences. In this paper, we explain the design process to specifically generate an orthogonal digital code set for an efficient and accurate demultiplexing of the sensor signals. We also introduce an equivalent circuit model for a network of code-multiplexed resistive pulse sensors by utilizing the Foster-Schwan model and conformal mapping, to model dynamic cell-electrode interaction in a non-uniform electric field. Our results closely match with both experimental measurements using cell lines and finite element analysis. The coding and modeling framework presented here will enable the design of code-division multiplexed resistive pulse sensors optimized to produce desired waveform patterns to ensure reliable and efficient decoding.
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Affiliation(s)
- Ruxiu Liu
- School of Electrical and Computer Engineering, Georgia Institute of Technology, Atlanta, GA 30332, USA.
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18
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Kondylis P, Zhou J, Harms ZD, Kneller AR, Lee LS, Zlotnick A, Jacobson SC. Nanofluidic Devices with 8 Pores in Series for Real-Time, Resistive-Pulse Analysis of Hepatitis B Virus Capsid Assembly. Anal Chem 2017; 89:4855-4862. [PMID: 28322548 PMCID: PMC5549943 DOI: 10.1021/acs.analchem.6b04491] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
To improve the precision of resistive-pulse measurements, we have used a focused ion beam instrument to mill nanofluidic devices with 2, 4, and 8 pores in series and compared their performance. The in-plane design facilitates the fabrication of multiple pores in series which, in turn, permits averaging of the series of pulses generated from each translocation event. The standard deviations (σ) of the pulse amplitude distributions decrease by 2.7-fold when the average amplitudes of eight pulses are compared to the amplitudes of single pulses. Similarly, standard deviations of the pore-to-pore time distributions decrease by 3.2-fold when the averages of the seven measurements from 8-pore devices are contrasted to single measurements from 2-pore devices. With signal averaging, the inherent uncertainty in the measurements decreases; consequently, the resolution (mean/σ) improves by a factor equal to the square root of the number of measurements. We took advantage of the improved size resolution of the 8-pore devices to analyze in real time the assembly of Hepatitis B Virus (HBV) capsids below the pseudocritical concentration. We observe that abundances of assembly intermediates change over time. During the first hour of the reaction, the abundance of smaller intermediates decreased, whereas the abundance of larger intermediates with sizes closer to a T = 4 capsid remained constant.
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Affiliation(s)
| | - Jinsheng Zhou
- Department of Chemistry, Indiana University, Bloomington, IN 47405
| | - Zachary D. Harms
- Department of Chemistry, Indiana University, Bloomington, IN 47405
| | | | - Lye Siang Lee
- Department of Molecular and Cellular Biochemistry, Indiana University, Bloomington, IN 47405
| | - Adam Zlotnick
- Department of Molecular and Cellular Biochemistry, Indiana University, Bloomington, IN 47405
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19
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Wang N, Liu R, Sarioglu AF. Microfluidic Platform with Multiplexed Electronic Detection for Spatial Tracking of Particles. J Vis Exp 2017. [PMID: 28362379 DOI: 10.3791/55311] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022] Open
Abstract
Microfluidic processing of biological samples typically involves differential manipulations of suspended particles under various force fields in order to spatially fractionate the sample based on a biological property of interest. For the resultant spatial distribution to be used as the assay readout, microfluidic devices are often subjected to microscopic analysis requiring complex instrumentation with higher cost and reduced portability. To address this limitation, we have developed an integrated electronic sensing technology for multiplexed detection of particles at different locations on a microfluidic chip. Our technology, called Microfluidic CODES, combines Resistive Pulse Sensing with Code Division Multiple Access to compress 2D spatial information into a 1D electrical signal. In this paper, we present a practical demonstration of the Microfluidic CODES technology to detect and size cultured cancer cells distributed over multiple microfluidic channels. As validated by the high-speed microscopy, our technology can accurately analyze dense cell populations all electronically without the need for an external instrument. As such, the Microfluidic CODES can potentially enable low-cost integrated lab-on-a-chip devices that are well suited for the point-of-care testing of biological samples.
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Affiliation(s)
- Ningquan Wang
- School of Electrical and Computer Engineering, Georgia Institute of Technology
| | - Ruxiu Liu
- School of Electrical and Computer Engineering, Georgia Institute of Technology
| | - A Fatih Sarioglu
- School of Electrical and Computer Engineering, Georgia Institute of Technology; Institute of Electronics and Nanotechnology, Georgia Institute of Technology; Petit Institute for Bioengineering and Biosciences, Georgia Institute of Technology;
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20
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Kellman M, Rivest F, Pechacek A, Sohn L, Lustig M. BARKER-CODED NODE-PORE RESISTIVE PULSE SENSING WITH BUILT-IN COINCIDENCE CORRECTION. PROCEEDINGS OF THE ... IEEE INTERNATIONAL CONFERENCE ON ACOUSTICS, SPEECH, AND SIGNAL PROCESSING. ICASSP (CONFERENCE) 2017; 2017:1053-1057. [PMID: 29410605 PMCID: PMC5797712 DOI: 10.1109/icassp.2017.7952317] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
A resistive pulse sensing device is able to extract quantities such as concentration and size distribution of particles, e.g. cells or microspheres, as they flow through the device's sensor region, i.e. channel, in an electrolyte solution. The dynamic range of detectable particle sizes is limited by the channel dimensions. In addition, signal interference from multiple particles transiting the channel simultaneously, i.e. coincidence event, further hinder the dynamic range. Coincidence data is often considered unusable and is discarded, reducing the throughput and introducing possible biases and errors into the distributions. Here, we propose a two-step solution. We code the channel such that the system response results in a Manchester encoded Barker-Code sequence, allowing us to take advantage of the code's pulse compression properties. We pose the parameter estimation problem as a sparse inverse problem, which enables estimation of particle sizes and velocities while resolving coincidences, and solve it with a successive interference cancellation algorithm. We introduce modifications to the algorithm to account for device fabrication variations and natural stochastic variations in flow. We demonstrate the ability to resolve coincidences and possible increases in the device's dynamic range by screening particles of different size through a Barker encoded device.
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Affiliation(s)
- Michael Kellman
- Dept. of Electrical Engineering and Computer Sciences, University of California, Berkeley
| | - Francois Rivest
- Dept. of Mechanical Engineering, University of California, Berkeley
- Institute of Bioengineering, Ecole Polytechnique Federale de Lausanne, Switzerland
| | - Alina Pechacek
- Dept. of Electrical Engineering and Computer Sciences, University of California, Berkeley
| | - Lydia Sohn
- Dept. of Mechanical Engineering, University of California, Berkeley
| | - Michael Lustig
- Dept. of Electrical Engineering and Computer Sciences, University of California, Berkeley
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21
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Liu R, Wang N, Kamili F, Sarioglu AF. Microfluidic CODES: a scalable multiplexed electronic sensor for orthogonal detection of particles in microfluidic channels. LAB ON A CHIP 2016; 16:1350-1357. [PMID: 27021807 DOI: 10.1039/c6lc00209a] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Numerous biophysical and biochemical assays rely on spatial manipulation of particles/cells as they are processed on lab-on-a-chip devices. Analysis of spatially distributed particles on these devices typically requires microscopy negating the cost and size advantages of microfluidic assays. In this paper, we introduce a scalable electronic sensor technology, called microfluidic CODES, that utilizes resistive pulse sensing to orthogonally detect particles in multiple microfluidic channels from a single electrical output. Combining the techniques from telecommunications and microfluidics, we route three coplanar electrodes on a glass substrate to create multiple Coulter counters producing distinct orthogonal digital codes when they detect particles. We specifically design a digital code set using the mathematical principles of Code Division Multiple Access (CDMA) telecommunication networks and can decode signals from different microfluidic channels with >90% accuracy through computation even if these signals overlap. As a proof of principle, we use this technology to detect human ovarian cancer cells in four different microfluidic channels fabricated using soft lithography. Microfluidic CODES offers a simple, all-electronic interface that is well suited to create integrated, low-cost lab-on-a-chip devices for cell- or particle-based assays in resource-limited settings.
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Affiliation(s)
- Ruxiu Liu
- School of Electrical and Computer Engineering, Georgia Institute of Technology, Atlanta, GA 30332, USA.
| | - Ningquan Wang
- School of Electrical and Computer Engineering, Georgia Institute of Technology, Atlanta, GA 30332, USA.
| | - Farhan Kamili
- School of Electrical and Computer Engineering, Georgia Institute of Technology, Atlanta, GA 30332, USA.
| | - A Fatih Sarioglu
- School of Electrical and Computer Engineering, Georgia Institute of Technology, Atlanta, GA 30332, USA. and Institute of Electronics and Nanotechnology, Georgia Institute of Technology, Atlanta, GA 30332, USA and Petit Institute for Bioengineering and Biosciences, Georgia Institute of Technology, Atlanta, GA 30332, USA
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22
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Harms ZD, Selzer L, Zlotnick A, Jacobson SC. Monitoring Assembly of Virus Capsids with Nanofluidic Devices. ACS NANO 2015; 9:9087-96. [PMID: 26266555 PMCID: PMC4753561 DOI: 10.1021/acsnano.5b03231] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
Virus assembly is a coordinated process in which typically hundreds of subunits react to form complex, symmetric particles. We use resistive-pulse sensing to characterize the assembly of hepatitis B virus core protein dimers into T = 3 and T = 4 icosahedral capsids. This technique counts and sizes intermediates and capsids in real time, with single-particle sensitivity, and at biologically relevant concentrations. Other methods are not able to produce comparable real-time, single-particle observations of assembly reactions below, near, and above the pseudocritical dimer concentration, at which the dimer and capsid concentrations are approximately equal. Assembly reactions across a range of dimer concentrations reveal three distinct patterns. At dimer concentrations as low as 50 nM, well below the pseudocritical dimer concentration of 0.5 μM, we observe a switch in the ratio of T = 3 to T = 4 capsids, which increases with decreasing dimer concentration. Far above the pseudocritical dimer concentration, kinetically trapped, incomplete T = 4 particles assemble rapidly, then slowly anneal into T = 4 capsids. At all dimer concentrations tested, T = 3 capsids form more rapidly than T = 4 capsids, suggesting distinct pathways for the two forms.
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Affiliation(s)
- Zachary D. Harms
- Department of Chemistry, Indiana University, Bloomington, IN 47405
| | - Lisa Selzer
- Department of Molecular and Cellular Biochemistry, Indiana University, Bloomington, IN 47405
| | - Adam Zlotnick
- Department of Molecular and Cellular Biochemistry, Indiana University, Bloomington, IN 47405
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23
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Harms ZD, Haywood DG, Kneller AR, Jacobson SC. Conductivity-based detection techniques in nanofluidic devices. Analyst 2015; 140:4779-91. [PMID: 25988434 PMCID: PMC4756766 DOI: 10.1039/c5an00075k] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
This review covers conductivity detection in fabricated nanochannels and nanopores. Improvements in nanoscale sensing are a direct result of advances in fabrication techniques, which produce devices with channels and pores with reproducible dimensions and in a variety of materials. Analytes of interest are detected by measuring changes in conductance as the analyte accumulates in the channel or passes transiently through the pore. These detection methods take advantage of phenomena enhanced at the nanoscale, such as ion current rectification, surface conductance, and dimensions comparable to the analytes of interest. The end result is the development of sensing technologies for a broad range of analytes, e.g., ions, small molecules, proteins, nucleic acids, and particles.
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Affiliation(s)
- Zachary D Harms
- Department of Chemistry, Indiana University, Bloomington, IN 47405, USA.
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24
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Jabart E, Rangarajan S, Lieu C, Hack J, Conboy I, Sohn LL. A Microfluidic Method for the Selection of Undifferentiated Human Embryonic Stem Cells and in Situ Analysis. MICROFLUIDICS AND NANOFLUIDICS 2015; 18:955-966. [PMID: 33688311 PMCID: PMC7939131 DOI: 10.1007/s10404-014-1485-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/15/2023]
Abstract
Conventional cell-sorting methods such as fluorescence-activated cell sorting (FACS) or magnetic-activated cell sorting (MACS) can suffer from certain shortcomings such as lengthy sample preparation time, cell modification through antibody labeling, and cell damage due to exposure to high shear forces or to attachment of superparamagnetic Microbeads. In light of these drawbacks, we have recently developed a label-free, microfluidic platform that can not only select cells with minimal sample preparation but also enable analysis of cells in situ. We demonstrate the utility of our platform by successfully isolating undifferentiated human embryonic stem cells (hESCs) from a heterogeneous population based on the undifferentiated stem-cell marker SSEA-4. Importantly, we show that, in contrast to MACS or FACS, cells isolated by our method have very high viability (~90%). Overall, our platform technology could likely be applied to other cell types beyond hESCs and to a variety of heterogeneous cell populations in order to select and analyze cells of interest.
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Affiliation(s)
- E. Jabart
- Dept. of Bioengineering, University of California, Berkeley 94720, USA
| | - S. Rangarajan
- Dept. of Bioengineering, University of California, Berkeley 94720, USA
| | - C. Lieu
- School of Medicine, Creighton University, Omaha, NE 68178, USA
| | - J. Hack
- Dept. of Mechanical Engineering, University of California, Berkeley 94720, USA
| | - I. Conboy
- Dept. of Bioengineering, University of California, Berkeley 94720, USA
| | - L. L. Sohn
- Dept. of Mechanical Engineering, University of California, Berkeley 94720, USA
- Author to whom correspondence should be addressed: , 510-642-5434
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25
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Balakrishnan KR, Whang JC, Hwang R, Hack JH, Godley LA, Sohn LL. Node-pore sensing enables label-free surface-marker profiling of single cells. Anal Chem 2015; 87:2988-95. [PMID: 25625182 PMCID: PMC4350414 DOI: 10.1021/ac504613b] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
![]()
Flow cytometry is a ubiquitous, multiparametric
method for characterizing
cellular populations. However, this method can grow increasingly complex
with the number of proteins that need to be screened simultaneously:
spectral emission overlap of fluorophores and the subsequent need
for compensation, lengthy sample preparation, and multiple control
tests that need to be performed separately must all be considered.
These factors lead to increased costs, and consequently, flow cytometry
is performed in core facilities with a dedicated technician operating
the instrument. Here, we describe a low-cost, label-free microfluidic
method that can determine the phenotypic profiles of single cells.
Our method employs Node-Pore Sensing to measure the transit times
of cells as they interact with a series of different antibodies, each
corresponding to a specific cell-surface antigen, that have been functionalized
in a single microfluidic channel. We demonstrate the capabilities
of our method not only by screening two acute promyelocytic leukemia
human cells lines (NB4 and AP-1060) for myeloid antigens, CD13, CD14,
CD15, and CD33, simultaneously, but also by distinguishing a mixture
of cells of similar size—AP-1060 and NALM-1—based on
surface markers CD13 and HLA-DR. Furthermore, we show that our method
can screen complex subpopulations in clinical samples: we successfully
identified the blast population in primary human bone marrow samples
from patients with acute myeloid leukemia and screened these cells
for CD13, CD34, and HLA-DR. We show that our label-free method is
an affordable, highly sensitive, and user-friendly technology that
has the potential to transform cellular screening at the benchside.
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Affiliation(s)
- Karthik R Balakrishnan
- Department of Mechanical Engineering, University of California , Berkeley, California 94720, United States
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26
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Harms Z, Haywood DG, Kneller AR, Selzer L, Zlotnick A, Jacobson SC. Single-particle electrophoresis in nanochannels. Anal Chem 2015; 87:699-705. [PMID: 25489919 PMCID: PMC4287839 DOI: 10.1021/ac503527d] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2014] [Accepted: 11/28/2014] [Indexed: 02/05/2023]
Abstract
Electrophoretic mobilities and particle sizes of individual Hepatitis B Virus (HBV) capsids were measured in nanofluidic channels with two nanopores in series. The channels and pores had three-dimensional topography and were milled directly in glass substrates with a focused ion beam instrument assisted by an electron flood gun. The nanochannel between the two pores was 300 nm wide, 100 nm deep, and 2.5 μm long, and the nanopores at each end had dimensions 45 nm wide, 45 nm deep, and 400 nm long. With resistive-pulse sensing, the nanopores fully resolved pulse amplitude distributions of T = 3 HBV capsids (32 nm outer diameter) and T = 4 HBV capsids (35 nm outer diameter) and had sufficient peak capacity to discriminate intermediate species from the T = 3 and T = 4 capsid distributions in an assembly reaction. Because the T = 3 and T = 4 capsids have a wiffle-ball geometry with a hollow core, the observed change in current due to the capsid transiting the nanopore is proportional to the volume of electrolyte displaced by the volume of capsid protein, not the volume of the entire capsid. Both the signal-to-noise ratio of the pulse amplitude and resolution between the T = 3 and T = 4 distributions of the pulse amplitudes increase as the electric field strength is increased. At low field strengths, transport of the larger T = 4 capsid through the nanopores is hindered relative to the smaller T = 3 capsid due to interaction with the pores, but at sufficiently high field strengths, the T = 3 and T = 4 capsids had the same electrophoretic mobilities (7.4 × 10(-5) cm(2) V(-1) s(-1)) in the nanopores and in the nanochannel with the larger cross-sectional area.
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Affiliation(s)
- Zachary
D. Harms
- Department of Chemistry and Department of Molecular and Cellular Biochemistry, Indiana University, Bloomington, Indiana 47405, United States
| | - Daniel G. Haywood
- Department of Chemistry and Department of Molecular and Cellular Biochemistry, Indiana University, Bloomington, Indiana 47405, United States
| | - Andrew R. Kneller
- Department of Chemistry and Department of Molecular and Cellular Biochemistry, Indiana University, Bloomington, Indiana 47405, United States
| | - Lisa Selzer
- Department of Chemistry and Department of Molecular and Cellular Biochemistry, Indiana University, Bloomington, Indiana 47405, United States
| | - Adam Zlotnick
- Department of Chemistry and Department of Molecular and Cellular Biochemistry, Indiana University, Bloomington, Indiana 47405, United States
| | - Stephen C. Jacobson
- Department of Chemistry and Department of Molecular and Cellular Biochemistry, Indiana University, Bloomington, Indiana 47405, United States
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27
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Haywood DG, Saha-Shah A, Baker LA, Jacobson SC. Fundamental studies of nanofluidics: nanopores, nanochannels, and nanopipets. Anal Chem 2014; 87:172-87. [PMID: 25405581 PMCID: PMC4287834 DOI: 10.1021/ac504180h] [Citation(s) in RCA: 157] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Affiliation(s)
- Daniel G Haywood
- Department of Chemistry, Indiana University , Bloomington, Indiana 47405-7102, United States
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Terejánszky P, Makra I, Fürjes P, Gyurcsányi RE. Calibration-Less Sizing and Quantitation of Polymeric Nanoparticles and Viruses with Quartz Nanopipets. Anal Chem 2014; 86:4688-97. [DOI: 10.1021/ac500184z] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Affiliation(s)
- Péter Terejánszky
- MTA-BME
“Lendület” Chemical Nanosensors Research Group,
Department of Inorganic and Analytical Chemistry, Budapest University of Technology and Economics, Szt. Gellért tér 4, Budapest, 1111 Hungary
| | - István Makra
- MTA-BME
“Lendület” Chemical Nanosensors Research Group,
Department of Inorganic and Analytical Chemistry, Budapest University of Technology and Economics, Szt. Gellért tér 4, Budapest, 1111 Hungary
| | - Péter Fürjes
- MEMS
Laboratory, HAS Research Centre for Natural Sciences, Konkoly-Thege
út 29-33, Budapest, 1121 Hungary
| | - Róbert E. Gyurcsányi
- MTA-BME
“Lendület” Chemical Nanosensors Research Group,
Department of Inorganic and Analytical Chemistry, Budapest University of Technology and Economics, Szt. Gellért tér 4, Budapest, 1111 Hungary
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