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Adedokun G, Alipanah M, Fan ZH. Sample preparation and detection methods in point-of-care devices towards future at-home testing. LAB ON A CHIP 2024; 24:3626-3650. [PMID: 38952234 PMCID: PMC11270053 DOI: 10.1039/d3lc00943b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/03/2024]
Abstract
Timely and accurate diagnosis is critical for effective healthcare, yet nearly half the global population lacks access to basic diagnostics. Point-of-care (POC) testing offers partial solutions by enabling low-cost, rapid diagnosis at the patient's location. At-home POC devices have the potential to advance preventive care and early disease detection. Nevertheless, effective sample preparation and detection methods are essential for accurate results. This review surveys recent advances in sample preparation and detection methods at POC. The goal is to provide an in-depth understanding of how these technologies can enhance at-home POC devices. Lateral flow assays, nucleic acid tests, and virus detection methods are at the forefront of POC diagnostic technology, offering rapid and sensitive tools for identifying and measuring pathogens, biomarkers, and viral infections. By illuminating cutting-edge research on assay development for POC diagnostics, this review aims to accelerate progress towards widely available, user-friendly, at-home health monitoring tools that empower individuals in personalized healthcare in the future.
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Affiliation(s)
- George Adedokun
- Interdisciplinary Microsystems Group, Department of Mechanical and Aerospace Engineering, University of Florida, P.O. Box 116250, Gainesville, FL 32611, USA.
| | - Morteza Alipanah
- Interdisciplinary Microsystems Group, Department of Mechanical and Aerospace Engineering, University of Florida, P.O. Box 116250, Gainesville, FL 32611, USA.
| | - Z Hugh Fan
- Interdisciplinary Microsystems Group, Department of Mechanical and Aerospace Engineering, University of Florida, P.O. Box 116250, Gainesville, FL 32611, USA.
- J. Crayton Pruitt Family Department of Biomedical Engineering, University of Florida, P.O. Box 116131, Gainesville, FL 32611, USA
- Department of Chemistry, University of Florida, P.O. Box 117200, Gainesville, FL 32611, USA
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2
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Tao J, Liu D, Xiong J, Shan W, Dou L, Zhai W, Wang Y, Shen J, Wen K. MC-PRPA-HLFIA Cascade Detection System for Point-of-Care Testing Pan-Drug-Resistant Genes in Urinary Tract Infection Samples. Int J Mol Sci 2023; 24:ijms24076784. [PMID: 37047757 PMCID: PMC10095522 DOI: 10.3390/ijms24076784] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Revised: 03/21/2023] [Accepted: 04/02/2023] [Indexed: 04/14/2023] Open
Abstract
Recently, urinary tract infection (UTI) triggered by bacteria carrying pan-drug-resistant genes, including carbapenem resistance gene blaNDM and blaKPC, colistin resistance gene mcr-1, and tet(X) for tigecycline resistance, have been reported, posing a serious challenge to the treatment of clinical UTI. Therefore, point-of-care (POC) detection of these genes in UTI samples without the need for pre-culturing is urgently needed. Based on PEG 200-enhanced recombinase polymerase amplification (RPA) and a refined Chelex-100 lysis method with HRP-catalyzed lateral flow immunoassay (LFIA), we developed an MCL-PRPA-HLFIA cascade assay system for detecting these genes in UTI samples. The refined Chelex-100 lysis method extracts target DNA from UTI samples in 20 min without high-speed centrifugation or pre-incubation of urine samples. Following optimization, the cascade detection system achieved an LOD of 102 CFU/mL with satisfactory specificity and could detect these genes in both simulated and actual UTI samples. It takes less than an hour to complete the process without the use of high-speed centrifuges or other specialized equipment, such as PCR amplifiers. The MCL-PRPA-HLFIA cascade assay system provides new ideas for the construction of rapid detection methods for pan-drug-resistant genes in clinical UTI samples and provides the necessary medication guidance for UTI treatment.
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Affiliation(s)
- Jin Tao
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Veterinary Medicine, China Agricultural University, Beijing 100083, China
| | - Dejun Liu
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Veterinary Medicine, China Agricultural University, Beijing 100083, China
| | - Jincheng Xiong
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Veterinary Medicine, China Agricultural University, Beijing 100083, China
| | - Wenchong Shan
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Veterinary Medicine, China Agricultural University, Beijing 100083, China
| | - Leina Dou
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Veterinary Medicine, China Agricultural University, Beijing 100083, China
| | - Weishuai Zhai
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Veterinary Medicine, China Agricultural University, Beijing 100083, China
| | - Yang Wang
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Veterinary Medicine, China Agricultural University, Beijing 100083, China
| | - Jianzhong Shen
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Veterinary Medicine, China Agricultural University, Beijing 100083, China
| | - Kai Wen
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Veterinary Medicine, China Agricultural University, Beijing 100083, China
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3
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Nadar SS, Kelkar RK, Pise PV, Patil NP, Patil SP, Chaubal-Durve NS, Bhange VP, Tiwari MS, Patil PD. The untapped potential of magnetic nanoparticles for forensic investigations: A comprehensive review. Talanta 2021; 230:122297. [PMID: 33934767 DOI: 10.1016/j.talanta.2021.122297] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Revised: 03/01/2021] [Accepted: 03/03/2021] [Indexed: 02/07/2023]
Abstract
With a growing interest in precise and sensitive diagnosis for criminal investigations, nanoparticles (NPs) have intrigued scientific minds working in the field of forensic science due to their exceptional properties. Magnetic nanoparticles (MNPs) have emerged as a powerful tool for improving forensic analysis due to their super magnetic behavior combined with smaller dimensions. MNP-based applications can benefit criminologists to solve criminal mysteries with greater precision and pace. This review highlights the different types of MNP-based applications and their developmental and implicational aspects of forensic science. It also renders insight into the future prospects of a splendid blend of nanotechnology and forensic science, leading to a better scientific analysis.
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Affiliation(s)
- Shamraja S Nadar
- Department of Chemical Engineering, Institute of Chemical Technology, Mumbai, Maharashtra, 400019, India
| | - Radhika K Kelkar
- Department of Biotechnology Engineering, Kolhapur Institute of Technology's College of Engineering, Kolhapur, Maharashtra, 416234, India
| | - Pradnya V Pise
- Department of Biotechnology Engineering, Kolhapur Institute of Technology's College of Engineering, Kolhapur, Maharashtra, 416234, India
| | - Neha P Patil
- Department of Biotechnology Engineering, Kolhapur Institute of Technology's College of Engineering, Kolhapur, Maharashtra, 416234, India
| | - Sadhana P Patil
- Department of Biotechnology Engineering, Kolhapur Institute of Technology's College of Engineering, Kolhapur, Maharashtra, 416234, India
| | - Nivedita S Chaubal-Durve
- Department of Basic Science and Humanities, Mukesh Patel School of Technology Management and Engineering, SVKM's NMIMS University, Mumbai, 400056, Maharashtra, India
| | - Vivek P Bhange
- Department of Biotechnology, Priyadarshini Institute of Engineering and Technology, Nagpur, Maharashtra, 440019, India
| | - Manishkumar S Tiwari
- Department of Chemical Engineering, Mukesh Patel School of Technology Management and Engineering, SVKM's NMIMS University, Mumbai, 400056, Maharashtra, India
| | - Pravin D Patil
- Department of Basic Science and Humanities, Mukesh Patel School of Technology Management and Engineering, SVKM's NMIMS University, Mumbai, 400056, Maharashtra, India.
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4
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Obino D, Vassalli M, Franceschi A, Alessandrini A, Facci P, Viti F. An Overview on Microfluidic Systems for Nucleic Acids Extraction from Human Raw Samples. SENSORS 2021; 21:s21093058. [PMID: 33925730 PMCID: PMC8125272 DOI: 10.3390/s21093058] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Revised: 04/13/2021] [Accepted: 04/19/2021] [Indexed: 02/08/2023]
Abstract
Nucleic acid (NA) extraction is a basic step for genetic analysis, from scientific research to diagnostic and forensic applications. It aims at preparing samples for its application with biomolecular technologies such as isothermal and non-isothermal amplification, hybridization, electrophoresis, Sanger sequencing and next-generation sequencing. Multiple steps are involved in NA collection from raw samples, including cell separation from the rest of the specimen, cell lysis, NA isolation and release. Typically, this process needs molecular biology facilities, specialized instrumentation and labor-intensive operations. Microfluidic devices have been developed to analyze NA samples with high efficacy and sensitivity. In this context, the integration within the chip of the sample preparation phase is crucial to leverage the promise of portable, fast, user-friendly and economic point-of-care solutions. This review presents an overview of existing lab-on-a-chip (LOC) solutions designed to provide automated NA extraction from human raw biological fluids, such as whole blood, excreta (urine and feces), saliva. It mainly focuses on LOC implementation aspects, aiming to describe a detailed panorama of strategies implemented for different human raw sample preparations.
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Affiliation(s)
- Daniele Obino
- Institute of Biophysics, National Research Council, 16149 Genova, Italy; (D.O.); (F.V.)
| | - Massimo Vassalli
- Centre for the Cellular Microenvironment, James Watt School of Engineering, University of Glasgow, James Watt South Building, Glasgow G128LT, UK;
| | | | - Andrea Alessandrini
- Nanoscience Institute, National Research Council, 41125 Modena, Italy;
- Department of Physics, Informatics and Mathematics, University of Modena and Reggio Emilia, 41125 Modena, Italy
| | - Paolo Facci
- Institute of Biophysics, National Research Council, 16149 Genova, Italy; (D.O.); (F.V.)
- Correspondence:
| | - Federica Viti
- Institute of Biophysics, National Research Council, 16149 Genova, Italy; (D.O.); (F.V.)
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5
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Dizaji AN, Ozturk Y, Ghorbanpoor H, Cetak A, Akcakoca I, Kocagoz T, Avci H, Corrigan D, Guzel FD. Investigation of the Effect of Channel Structure and Flow Rate on On-Chip Bacterial Lysis. IEEE Trans Nanobioscience 2020; 20:86-91. [PMID: 33055026 DOI: 10.1109/tnb.2020.3031346] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Successful lysis of cells/microorganisms is a key step in the sample preparation in fields like molecular biology, bioengineering, and biomedical engineering. This study therefore aims to investigate the lysis of bacteria on-chip and its dependence on both microfluidic channel structure and flow rate. Effects of temperature on lysis on-chip were also investigated. To perform these investigations, three different microfluidic chips were designed and produced (straight, zigzag and circular configurations), while the length of the channels were kept constant. As an exemplary case, Mycobacterium smegmatis was chosen to represent the acid-fast bacteria. Bacterial suspensions of 1.5 McFarland were injected into the chips at various flow rates (0.6- [Formula: see text]/min) either at room temperature or 50° C. In order to understand the on-chip lysis performance fully, off-chip experiments were carried out at durations which are equal to those bacteria spent in the channel from inlet to the outlet at different flow rates. We also performed COMSOL multiphysics program simulations to evaluate further the effect of the applied parameters. As a result, we found that the structure and the flow rate do not affect lysis over all in all investigated channel types, however on-chip experiments at room temperature produced more effective lysis compared to the on-chip and the off-chip samples performed at higher temperatures. Interestingly on-chip experiments at higher tempratures do not result in effective lysis.
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6
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Paul R, Ostermann E, Wei Q. Advances in point-of-care nucleic acid extraction technologies for rapid diagnosis of human and plant diseases. Biosens Bioelectron 2020; 169:112592. [PMID: 32942143 PMCID: PMC7476893 DOI: 10.1016/j.bios.2020.112592] [Citation(s) in RCA: 76] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2020] [Revised: 09/01/2020] [Accepted: 09/02/2020] [Indexed: 12/22/2022]
Abstract
Global health and food security constantly face the challenge of emerging human and plant diseases caused by bacteria, viruses, fungi, and other pathogens. Disease outbreaks such as SARS, MERS, Swine Flu, Ebola, and COVID-19 (on-going) have caused suffering, death, and economic losses worldwide. To prevent the spread of disease and protect human populations, rapid point-of-care (POC) molecular diagnosis of human and plant diseases play an increasingly crucial role. Nucleic acid-based molecular diagnosis reveals valuable information at the genomic level about the identity of the disease-causing pathogens and their pathogenesis, which help researchers, healthcare professionals, and patients to detect the presence of pathogens, track the spread of disease, and guide treatment more efficiently. A typical nucleic acid-based diagnostic test consists of three major steps: nucleic acid extraction, amplification, and amplicon detection. Among these steps, nucleic acid extraction is the first step of sample preparation, which remains one of the main challenges when converting laboratory molecular assays into POC tests. Sample preparation from human and plant specimens is a time-consuming and multi-step process, which requires well-equipped laboratories and skilled lab personnel. To perform rapid molecular diagnosis in resource-limited settings, simpler and instrument-free nucleic acid extraction techniques are required to improve the speed of field detection with minimal human intervention. This review summarizes the recent advances in POC nucleic acid extraction technologies. In particular, this review focuses on novel devices or methods that have demonstrated applicability and robustness for the isolation of high-quality nucleic acid from complex raw samples, such as human blood, saliva, sputum, nasal swabs, urine, and plant tissues. The integration of these rapid nucleic acid preparation methods with miniaturized assay and sensor technologies would pave the road for the "sample-in-result-out" diagnosis of human and plant diseases, especially in remote or resource-limited settings.
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Affiliation(s)
- Rajesh Paul
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC, 27695, USA
| | - Emily Ostermann
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC, 27695, USA
| | - Qingshan Wei
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC, 27695, USA; Emerging Plant Disease and Global Food Security Cluster, North Carolina State University, Raleigh, NC, 27695, USA.
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7
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Poly-L-histidine coated microfluidic devices for bacterial DNA purification without chaotropic solutions. Biomed Microdevices 2020; 22:44. [PMID: 32572586 DOI: 10.1007/s10544-020-00497-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
We present a disposable polymeric microfluidic device capable of reversibly binding and purifying Salmonella DNA through solid phase extraction (SPE). The microfluidic channels are first oxygen plasma treated and simultaneously micro-nanotextured, and then functionalized with amine groups via modification with L-histidine or poly-L-histidine. L-Histidine and poly-L-histidine bind on the plasma treated chip surface, and are not detached when rinsing with DNA purification protocol buffers. A pH-dependent protocol is applied on-chip to purify Salmonella DNA, which is first bound on the protonated amines at a pH (5.0) lower than their pKa of surface amine-groups which is 6.0 and then released at a pH higher than the pKa value (10.5). It was found that modification with poly-L-histidine resulted in higher surface density of amine groups onto microfluidic channel. Using the chip modified with poly-L-histidine, high recovery efficiency of at least 550 ng of isolated Salmonella DNA as well as DNA purification from Salmonella cell lysates corresponding to less than 5000 cells or 0.026 ng of Salmonella DNA was achieved. The protocol developed does not require ethanol or chaotropic solutions typically used in DNA purification, which are known inhibitors for downstream operations such as polymerase chain reactions (PCR) and which can also attack some polymeric microfluidic materials. Therefore, the microfluidic device and the related protocol hold promise for facile incorporation in microfluidics and Lab-on-a-chip (LOC) platforms for pathogen detection or in general for DNA purification.
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8
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Rodriguez-Quijada C, Lyons C, Santamaria C, Quinn S, Tlusty MF, Shiaris M, Hamad-Schifferli K. Optimization of paper-based nanoparticle immunoassays for direct detection of the bacterial pathogen V. parahaemolyticus in oyster hemolymph. ANALYTICAL METHODS : ADVANCING METHODS AND APPLICATIONS 2020; 12:3056-3063. [PMID: 32930166 DOI: 10.1039/d0ay00725k] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
The detection of foodborne pathogens is critical for disease control and infection prevention, especially in seafood consumed raw or undercooked. Paper-based diagnostic tools are promising for rapid fieldable detection and provide a readout by eye due to the use of gold nanoparticle immunoprobes. Here we study different strategies to overcome these challenges in a real biological matrix, oyster hemolymph, for the detection of the pathogenic bacteria Vibrio parahaemolyticus (Vp). Nanoparticle surface chemistry, nitrocellulose speed and blocking, running steps, and antibody concentrations on the NP and nitrocellulose were all studied. Their effect on paper immunoassay signal intensity was quantified to determine optimal conditions, which enabled the detection of Vp directly from hemolymph below pathogenic concentrations.
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Affiliation(s)
| | - Casandra Lyons
- Dept. of Biology, University of Massachusetts Boston, 100 Morrissey Blvd., Boston, MA 02125, USA
| | - Charles Santamaria
- Dept. of Biology, University of Massachusetts Boston, 100 Morrissey Blvd., Boston, MA 02125, USA
| | - Sara Quinn
- Dept. of Biology, University of Massachusetts Boston, 100 Morrissey Blvd., Boston, MA 02125, USA
| | - Michael F Tlusty
- School for the Environment, University of Massachusetts Boston, 100 Morrissey Blvd., Boston, MA 02125, USA
| | - Michael Shiaris
- Dept. of Biology, University of Massachusetts Boston, 100 Morrissey Blvd., Boston, MA 02125, USA
| | - Kimberly Hamad-Schifferli
- Dept. of Engineering, University of Masschusetts Boston, 100 Morrissey Blvd., Boston, MA 02125, USA.
- School for the Environment, University of Massachusetts Boston, 100 Morrissey Blvd., Boston, MA 02125, USA
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9
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Kalsi S, Valiadi M, Turner C, Sutton M, Morgan H. Sample pre-concentration on a digital microfluidic platform for rapid AMR detection in urine. LAB ON A CHIP 2018; 19:168-177. [PMID: 30516215 DOI: 10.1039/c8lc01249k] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
There is a growing need for rapid diagnostic methods to support stewardship of antibiotics.
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Affiliation(s)
- Sumit Kalsi
- Electronics and Computer Science, University of Southampton, Southampton SO17 1BJ, UK.
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10
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Horst AL, Rosenbohm JM, Kolluri N, Hardick J, Gaydos CA, Cabodi M, Klapperich CM, Linnes JC. A paperfluidic platform to detect Neisseria gonorrhoeae in clinical samples. Biomed Microdevices 2018; 20:35. [PMID: 29644437 PMCID: PMC6154386 DOI: 10.1007/s10544-018-0280-x] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Globally, the microbe Neisseria gonorrhoeae (NG) causes 106 million newly documented sexually transmitted infections each year. Once appropriately diagnosed, NG infections can be readily treated with antibiotics, but high-risk patients often do not return to the clinic for treatment if results are not provided at the point of care. A rapid, sensitive molecular diagnostic would help increase NG treatment and reduce the prevalence of this sexually transmitted disease. Here, we report on the design and development of a rapid, highly sensitive, paperfluidic device for point-of-care diagnosis of NG. The device integrates patient swab sample lysis, nucleic acid extraction, thermophilic helicase-dependent amplification (tHDA), an internal amplification control (NGIC), and visual lateral flow detection within an 80 min run time. Limits of NG detection for the NG/NGIC multiplex tHDA assay were determined within the device, and clinical performance was validated retroactively against qPCR-quantified patient samples in a proof-of-concept study. This paperfluidic diagnostic has a clinically relevant limit of detection of 500 NG cells per device with analytical sensitivity down to 10 NG cells per device. In triplicate testing of 40 total urethral and vaginal swab samples, the device had 95% overall sensitivity and 100% specificity, approaching current laboratory-based molecular NG diagnostics. This diagnostic platform could increase access to accurate NG diagnoses to those most in need.
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Affiliation(s)
- Audrey L Horst
- Department of Biomedical Engineering, Boston University, Boston, MA, USA
| | - Justin M Rosenbohm
- Department of Biomedical Engineering, Boston University, Boston, MA, USA
| | - Nikunja Kolluri
- Department of Biomedical Engineering, Boston University, Boston, MA, USA
| | - Justin Hardick
- School of Medicine, Johns Hopkins University, Baltimore, MD, USA
| | | | - Mario Cabodi
- Department of Biomedical Engineering, Boston University, Boston, MA, USA
| | | | - Jacqueline C Linnes
- Weldon School of Biomedical Engineering, Purdue University, West Lafayette, IN, USA.
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11
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Review: Microfluidics technologies for blood-based cancer liquid biopsies. Anal Chim Acta 2018; 1012:10-29. [PMID: 29475470 DOI: 10.1016/j.aca.2017.12.050] [Citation(s) in RCA: 63] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2017] [Revised: 12/29/2017] [Accepted: 12/30/2017] [Indexed: 12/19/2022]
Abstract
Blood-based liquid biopsies provide a minimally invasive alternative to identify cellular and molecular signatures that can be used as biomarkers to detect early-stage cancer, predict disease progression, longitudinally monitor response to chemotherapeutic drugs, and provide personalized treatment options. Specific targets in blood that can be used for detailed molecular analysis to develop highly specific and sensitive biomarkers include circulating tumor cells (CTCs), exosomes shed from tumor cells, cell-free circulating tumor DNA (cfDNA), and circulating RNA. Given the low abundance of CTCs and other tumor-derived products in blood, clinical evaluation of liquid biopsies is extremely challenging. Microfluidics technologies for cellular and molecular separations have great potential to either outperform conventional methods or enable completely new approaches for efficient separation of targets from complex samples like blood. In this article, we provide a comprehensive overview of blood-based targets that can be used for analysis of cancer, review microfluidic technologies that are currently used for isolation of CTCs, tumor derived exosomes, cfDNA, and circulating RNA, and provide a detailed discussion regarding potential opportunities for microfluidics-based approaches in cancer diagnostics.
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12
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Haddad Y, Dostalova S, Kudr J, Zitka O, Heger Z, Adam V. DNA-magnetic Particle Binding Analysis by Dynamic and Electrophoretic Light Scattering. J Vis Exp 2017. [PMID: 29155773 DOI: 10.3791/56815] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022] Open
Abstract
Isolation of DNA using magnetic particles is a field of high importance in biotechnology and molecular biology research. This protocol describes the evaluation of DNA-magnetic particles binding via dynamic light scattering (DLS) and electrophoretic light scattering (ELS). Analysis by DLS provides valuable information on the physicochemical properties of particles including particle size, polydispersity, and zeta potential. The latter describes the surface charge of the particle which plays major role in electrostatic binding of materials such as DNA. Here, a comparative analysis exploits three chemical modifications of nanoparticles and microparticles and their effects on DNA binding and elution. Chemical modifications by branched polyethylenimine, tetraethyl orthosilicate and (3-aminopropyl)triethoxysilane are investigated. Since DNA exhibits a negative charge, it is expected that zeta potential of particle surface will decrease upon binding of DNA. Forming of clusters should also affect particle size. In order to investigate the efficiency of these particles in isolation and elution of DNA, the particles are mixed with DNA in low pH (~6), high ionic strength and dehydration environment. Particles are washed on magnet and then DNA is eluted by Tris-HCl buffer (pH = 8). DNA copy number is estimated using quantitative polymerase chain reaction (PCR). Zeta potential, particle size, polydispersity and quantitative PCR data are evaluated and compared. DLS is an insightful and supporting method of analysis that adds a new perspective to the process of screening of particles for DNA isolation.
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Affiliation(s)
- Yazan Haddad
- Department of Chemistry and Biochemistry, Mendel University in Brno; Central European Institute of Technology, Brno University of Technology
| | - Simona Dostalova
- Department of Chemistry and Biochemistry, Mendel University in Brno; Central European Institute of Technology, Brno University of Technology
| | - Jiri Kudr
- Department of Chemistry and Biochemistry, Mendel University in Brno; Central European Institute of Technology, Brno University of Technology
| | - Ondrej Zitka
- Department of Chemistry and Biochemistry, Mendel University in Brno; Central European Institute of Technology, Brno University of Technology
| | - Zbynek Heger
- Department of Chemistry and Biochemistry, Mendel University in Brno; Central European Institute of Technology, Brno University of Technology
| | - Vojtech Adam
- Department of Chemistry and Biochemistry, Mendel University in Brno; Central European Institute of Technology, Brno University of Technology;
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13
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Mortazavi SM, Khatami M, Sharifi I, Heli H, Kaykavousi K, Sobhani Poor MH, Kharazi S, Nobre MAL. Bacterial Biosynthesis of Gold Nanoparticles Using Salmonella enterica subsp. enterica serovar Typhi Isolated from Blood and Stool Specimens of Patients. J CLUST SCI 2017. [DOI: 10.1007/s10876-017-1267-0] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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14
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Xu B, Du Y, Lin J, Qi M, Shu B, Wen X, Liang G, Chen B, Liu D. Simultaneous Identification and Antimicrobial Susceptibility Testing of Multiple Uropathogens on a Microfluidic Chip with Paper-Supported Cell Culture Arrays. Anal Chem 2016; 88:11593-11600. [PMID: 27934103 DOI: 10.1021/acs.analchem.6b03052] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Affiliation(s)
- Banglao Xu
- Department
of Laboratory Medicine, Guangzhou First People’s Hospital, Affiliated Hospital of Guangzhou Medical University, Guangzhou 510180, China
- Clinical Molecular Medicine and Molecular Diagnosis Key Laboratory of Guangdong Province, Guangzhou 510180, China
| | - Yan Du
- Department
of Laboratory Medicine, Guangzhou First People’s Hospital, Affiliated Hospital of Guangzhou Medical University, Guangzhou 510180, China
| | - Jinqiong Lin
- Department
of Laboratory Medicine, Guangzhou First People’s Hospital, Affiliated Hospital of Guangzhou Medical University, Guangzhou 510180, China
| | - Mingyue Qi
- Department
of Laboratory Medicine, Guangzhou First People’s Hospital, Affiliated Hospital of Guangzhou Medical University, Guangzhou 510180, China
| | - Bowen Shu
- Department
of Laboratory Medicine, Guangzhou First People’s Hospital, Affiliated Hospital of Guangzhou Medical University, Guangzhou 510180, China
- Clinical Molecular Medicine and Molecular Diagnosis Key Laboratory of Guangdong Province, Guangzhou 510180, China
| | - Xiaoxia Wen
- Department
of Laboratory Medicine, Guangzhou First People’s Hospital, Affiliated Hospital of Guangzhou Medical University, Guangzhou 510180, China
| | - Guangtie Liang
- Department
of Laboratory Medicine, Guangzhou First People’s Hospital, Affiliated Hospital of Guangzhou Medical University, Guangzhou 510180, China
- Clinical Molecular Medicine and Molecular Diagnosis Key Laboratory of Guangdong Province, Guangzhou 510180, China
| | - Bin Chen
- Department
of Laboratory Medicine, Guangzhou First People’s Hospital, Affiliated Hospital of Guangzhou Medical University, Guangzhou 510180, China
- Clinical Molecular Medicine and Molecular Diagnosis Key Laboratory of Guangdong Province, Guangzhou 510180, China
| | - Dayu Liu
- Department
of Laboratory Medicine, Guangzhou First People’s Hospital, Affiliated Hospital of Guangzhou Medical University, Guangzhou 510180, China
- Clinical Molecular Medicine and Molecular Diagnosis Key Laboratory of Guangdong Province, Guangzhou 510180, China
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15
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Plasma micro-nanotextured polymeric micromixer for DNA purification with high efficiency and dynamic range. Anal Chim Acta 2016; 942:58-67. [DOI: 10.1016/j.aca.2016.09.007] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2016] [Revised: 05/23/2016] [Accepted: 09/07/2016] [Indexed: 11/21/2022]
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16
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Valiadi M, Kalsi S, Jones IGF, Turner C, Sutton JM, Morgan H. Simple and rapid sample preparation system for the molecular detection of antibiotic resistant pathogens in human urine. Biomed Microdevices 2016; 18:18. [PMID: 26846875 PMCID: PMC4742488 DOI: 10.1007/s10544-016-0031-9] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Antibiotic resistance in urinary tract infections (UTIs) can cause significant complications without quick detection and appropriate treatment. We describe a new approach to capture, concentrate and prepare amplification-ready DNA from antibiotic resistant bacteria in human urine samples. Klebsiella pneumoniae NCTC13443 (bla CTX-M-15 positive) spiked into filtered human urine was used as a model system. Bacteria were captured using anion exchange diaethylaminoethyl (DEAE) magnetic microparticles and concentrated 200-fold within ~3.5 min using a custom, valve-less microfluidic chip. Eight samples were processed in parallel, and DNA was released using heat lysis from an integrated resistive heater. The crude cell lysate was used for real time Recombinase Polymerase Amplification (RPA) of the bla CTX-M-15 gene. The end to end processing time was approximately 15 min with a limit of detection of 1000 bacteria in 1 mL urine.
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Affiliation(s)
- Martha Valiadi
- Electronics and Computer Science, University of Southampton, Southampton, SO17 1BJ, UK
- Institute for Life Sciences, University of Southampton, Southampton, SO17 1BJ, UK
| | - Sumit Kalsi
- Electronics and Computer Science, University of Southampton, Southampton, SO17 1BJ, UK
- Institute for Life Sciences, University of Southampton, Southampton, SO17 1BJ, UK
| | - Isaac G F Jones
- Electronics and Computer Science, University of Southampton, Southampton, SO17 1BJ, UK
- Institute for Life Sciences, University of Southampton, Southampton, SO17 1BJ, UK
| | - Carrie Turner
- National Infections Service, Public Health England, Porton Down, Salisbury, SP4 0JG, UK
| | - J Mark Sutton
- National Infections Service, Public Health England, Porton Down, Salisbury, SP4 0JG, UK
| | - Hywel Morgan
- Electronics and Computer Science, University of Southampton, Southampton, SO17 1BJ, UK.
- Institute for Life Sciences, University of Southampton, Southampton, SO17 1BJ, UK.
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17
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18
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Reinholt SJ, Baeumner AJ. Microfluidic Isolation of Nucleic Acids. Angew Chem Int Ed Engl 2014; 53:13988-4001. [DOI: 10.1002/anie.201309580] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2013] [Indexed: 01/03/2023]
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19
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Van Heirstraeten L, Spang P, Schwind C, Drese KS, Ritzi-Lehnert M, Nieto B, Camps M, Landgraf B, Guasch F, Corbera AH, Samitier J, Goossens H, Malhotra-Kumar S, Roeser T. Integrated DNA and RNA extraction and purification on an automated microfluidic cassette from bacterial and viral pathogens causing community-acquired lower respiratory tract infections. LAB ON A CHIP 2014; 14:1519-26. [PMID: 24615272 DOI: 10.1039/c3lc51339d] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
In this paper, we describe the development of an automated sample preparation procedure for etiological agents of community-acquired lower respiratory tract infections (CA-LRTI). The consecutive assay steps, including sample re-suspension, pre-treatment, lysis, nucleic acid purification, and concentration, were integrated into a microfluidic lab-on-a-chip (LOC) cassette that is operated hands-free by a demonstrator setup, providing fluidic and valve actuation. The performance of the assay was evaluated on viral and Gram-positive and Gram-negative bacterial broth cultures previously sampled using a nasopharyngeal swab. Sample preparation on the microfluidic cassette resulted in higher or similar concentrations of pure bacterial DNA or viral RNA compared to manual benchtop experiments. The miniaturization and integration of the complete sample preparation procedure, to extract purified nucleic acids from real samples of CA-LRTI pathogens to, and above, lab quality and efficiency, represent important steps towards its application in a point-of-care test (POCT) for rapid diagnosis of CA-LRTI.
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Affiliation(s)
- Liesbet Van Heirstraeten
- Department of Medical Microbiology, Vaccine & Infectious Disease Institute (VAXINFECTIO), Universiteit Antwerpen, Antwerp, Belgium
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20
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Nan L, Jiang Z, Wei X. Emerging microfluidic devices for cell lysis: a review. LAB ON A CHIP 2014; 14:1060-73. [PMID: 24480982 DOI: 10.1039/c3lc51133b] [Citation(s) in RCA: 89] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Intracellular components containing information about genetic and disease characteristics are key substances to clinical diagnostics. Cell lysis is therefore a crucial step for efficient extraction and the subsequent analysis of intracellular components. With the advent of advanced manufacturing techniques, a number of micro systems have been proposed and applied for manipulating cells on chips. In this paper, we review emerging microfluidic devices for cell lysis. Different lysis mechanisms and related techniques are compared. The technical details, advantages, and limitations of various microfluidic devices are discussed.
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Affiliation(s)
- Lang Nan
- State Key Laboratory for Manufacturing Systems Engineering, Xi'An Jiaotong University, 28 Xianning West Road, 710049, Xi'An, China.
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21
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Ritzi-Lehnert M. Development of chip-compatible sample preparation for diagnosis of infectious diseases. Expert Rev Mol Diagn 2014; 12:189-206. [DOI: 10.1586/erm.11.98] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
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22
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Linnes JC, Fan A, Rodriguez NM, Lemieux B, Kong H, Klapperich CM. Paper-based molecular diagnostic for Chlamydia trachomatis.. RSC Adv 2014; 4:42245-42251. [PMID: 25309740 DOI: 10.1039/c4ra07911f] [Citation(s) in RCA: 65] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Herein we show the development of a minimally instrumented paper-based molecular diagnostic for point of care detection of sexually transmitted infections caused by Chlamydia trachomatis. This new diagnostic platform incorporates cell lysis, isothermal nucleic acid amplification, and lateral flow visual detection using only a pressure source and heat block, eliminating the need for expensive laboratory equipment. This paper-based test can be performed in less than one hour and has a clinically relevant limit of detection that is 100x more sensitive than current rapid immunoassays used for chlamydia diagnosis.
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Affiliation(s)
| | - Andy Fan
- Biomedical Engineering, Boston University, Boston, MA, 02215
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23
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Novel Approaches of Genomic DNA Isolation for Identification of Cultivable Bacteria. Jundishapur J Microbiol 2013. [DOI: 10.5812/jjm.8339] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
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24
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Inci F, Tokel O, Wang S, Gurkan UA, Tasoglu S, Kuritzkes DR, Demirci U. Nanoplasmonic quantitative detection of intact viruses from unprocessed whole blood. ACS NANO 2013; 7:4733-45. [PMID: 23688050 PMCID: PMC3700402 DOI: 10.1021/nn3036232] [Citation(s) in RCA: 96] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Infectious diseases such as HIV and hepatitis B pose an omnipresent threat to global health. Reliable, fast, accurate, and sensitive platforms that can be deployed at the point-of-care (POC) in multiple settings, such as airports and offices, for detection of infectious pathogens are essential for the management of epidemics and possible biological attacks. To the best of our knowledge, no viral load technology adaptable to the POC settings exists today due to critical technical and biological challenges. Here, we present for the first time a broadly applicable technology for quantitative, nanoplasmonic-based intact virus detection at clinically relevant concentrations. The sensing platform is based on unique nanoplasmonic properties of nanoparticles utilizing immobilized antibodies to selectively capture rapidly evolving viral subtypes. We demonstrate the capture, detection, and quantification of multiple HIV subtypes (A, B, C, D, E, G, and subtype panel) with high repeatability, sensitivity, and specificity down to 98 ± 39 copies/mL (i.e., HIV subtype D) using spiked whole blood samples and clinical discarded HIV-infected patient whole blood samples validated by the gold standard, i.e., RT-qPCR. This platform technology offers an assay time of 1 h and 10 min (1 h for capture, 10 min for detection and data analysis). The presented platform is also able to capture intact viruses at high efficiency using immuno-surface chemistry approaches directly from whole blood samples without any sample preprocessing steps such as spin-down or sorting. Evidence is presented showing the system to be accurate, repeatable, and reliable. Additionally, the presented platform technology can be broadly adapted to detect other pathogens having reasonably well-described biomarkers by adapting the surface chemistry. Thus, this broadly applicable detection platform holds great promise to be implemented at POC settings, hospitals, and primary care settings.
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Affiliation(s)
- Fatih Inci
- Demirci Bio-Acoustic-MEMS in Medicine (BAMM) Laboratory, Division of Biomedical Engineering, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02139, USA
| | - Onur Tokel
- Demirci Bio-Acoustic-MEMS in Medicine (BAMM) Laboratory, Division of Biomedical Engineering, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02139, USA
| | - ShuQi Wang
- Demirci Bio-Acoustic-MEMS in Medicine (BAMM) Laboratory, Division of Biomedical Engineering, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02139, USA
| | - Umut Atakan Gurkan
- Demirci Bio-Acoustic-MEMS in Medicine (BAMM) Laboratory, Division of Biomedical Engineering, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02139, USA
| | - Savas Tasoglu
- Demirci Bio-Acoustic-MEMS in Medicine (BAMM) Laboratory, Division of Biomedical Engineering, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02139, USA
| | - Daniel R. Kuritzkes
- Division of Infectious Diseases, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Utkan Demirci
- Demirci Bio-Acoustic-MEMS in Medicine (BAMM) Laboratory, Division of Biomedical Engineering, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02139, USA
- Division of Infectious Diseases, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115, USA
- Harvard-MIT Health Sciences and Technology, Cambridge, MA 02139, USA
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25
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Kulinsky L, Noroozi Z, Madou M. Present technology and future trends in point-of-care microfluidic diagnostics. Methods Mol Biol 2013; 949:3-23. [PMID: 23329432 DOI: 10.1007/978-1-62703-134-9_1] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
This work reviews present technologies and developing trends in Point-of-Care (POC) microfluidic diagnostics platforms. First, various fluidics technologies such as pressure-driven flows, capillary flows, electromagnetically driven flows, centrifugal fluidics, acoustically driven flows, and droplet fluidics are categorized. Then three broad categories of POC microfluidic testing devices are considered: lateral flow devices, desktop and handheld POC diagnostic platforms, and emergent molecular diagnostic POC systems. Such evolving trends as miniaturization, multiplexing, networking, new more sensitive detection schemes, and the importance of sample processing are discussed. It is concluded that POC microfluidic diagnostics has a potential to improve patient treatment outcome and bring substantial savings in overall healthcare costs.
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Affiliation(s)
- Lawrence Kulinsky
- Department of Mechanical and Aerospace Engineering, University of California, Irvine, CA, USA.
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26
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Burke JM, Smela E. A novel surface modification technique for forming porous polymer monoliths in poly(dimethylsiloxane). BIOMICROFLUIDICS 2012; 6:16506-1650610. [PMID: 22685511 PMCID: PMC3370402 DOI: 10.1063/1.3693589] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/23/2011] [Accepted: 02/17/2012] [Indexed: 05/09/2023]
Abstract
A new method of surface modification is described for enabling the in situ formation of homogenous porous polymer monoliths (PPMs) within poly(dimethylsiloxane) (PDMS) microfluidic channels that uses 365 nm UV illumination for polymerization. Porous polymer monolith formation in PDMS can be challenging because PDMS readily absorbs the monomers and solvents, changing the final monolith morphology, and because PDMS absorbs oxygen, which inhibits free-radical polymerization. The new approach is based on sequentially absorbing a non-hydrogen-abstracting photoinitiator and the monomers methyl methacrylate and ethylene diacrylate within the walls of the microchannel, and then polymerizing the surface treatment polymer within the PDMS, entangled with it but not covalently bound. Four different monolith compositions were tested, all of which yielded monoliths that were securely anchored and could withstand pressures exceeding the bonding strength of PDMS (40 psi) without dislodging. One was a recipe that was optimized to give a larger average pore size, required for low back pressure. This monolith was used to concentrate and subsequently mechanical lyse B lymphocytes.
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Affiliation(s)
- Jeffrey M Burke
- Mechanical Engineering Department, University of Maryland, College Park, Maryland 20742, USA
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27
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Mirsky P, Chatterjee A, Sauer-Budge AF, Sharon A. An automated, parallel processing approach to biomolecular sample preparation. ACTA ACUST UNITED AC 2012; 17:116-24. [PMID: 22357555 DOI: 10.1177/2211068211424102] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Sample preparation for DNA and RNA assays is a prime candidate for laboratory automation. A novel, parallel processing device that performs the three separate liquid-handling functions necessary for such sample preparation-dispensing, pipetting, and pressurizing-is presented. The device comprises an array of fine nozzles connected by fluidic channels to automatically and precisely distribute flow between one source and an array of points. The design principles, as well as the experimental and computational methods used to develop the device, are described. Test results, including accuracy, uniformity, volume range, and timing, are presented. The functionality of the device is demonstrated by performing a solid-phase extraction of DNA with two types of microcolumns.
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Affiliation(s)
- Paul Mirsky
- Fraunhofer Center for Manufacturing Innovation, Brookline, MA 02130, USA
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28
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Huang X, Yuan D. Recent Developments of Extraction and Micro-extraction Technologies with Porous Monoliths. Crit Rev Anal Chem 2012. [DOI: 10.1080/10408347.2012.629950] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2022]
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29
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Lin CC, Tseng CC, Chuang TK, Lee DS, Lee GB. Urine analysis in microfluidic devices. Analyst 2011; 136:2669-88. [PMID: 21617803 DOI: 10.1039/c1an15029d] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Microfluidics has attracted considerable attention since its early development in the 1980s and has experienced rapid growth in the past three decades due to advantages associated with miniaturization, integration and automation. Urine analysis is a common, fast and inexpensive clinical diagnostic tool in health care. In this article, we will be reviewing recent works starting from 2005 to the present for urine analysis using microfluidic devices or systems and to provide in-depth commentary about these techniques. Moreover, commercial strips that are often treated as chips and their readers for urine analysis will also be briefly discussed. We start with an introduction to the physiological significance of various components or measurement standards in urine analysis, followed by a brief introduction to enabling microfluidic technologies. Then, microfluidic devices or systems for sample pretreatments and for sensing urinary macromolecules, micromolecules, as well as multiplexed analysis are reviewed, in this sequence. Moreover, a microfluidic chip for urinary proteome profiling is also discussed, followed by a section discussing commercial products. Finally, the authors' perspectives on microfluidic-based urine analysis are provided. These advancements in microfluidic techniques for urine analysis may improve current routine clinical practices, particularly for point-of-care (POC) applications.
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Affiliation(s)
- Chun-Che Lin
- Department of Engineering Science, National Cheng Kung University, Tainan, Taiwan
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30
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Namera A, Nakamoto A, Saito T, Miyazaki S. Monolith as a new sample preparation material: Recent devices and applications. J Sep Sci 2011; 34:901-24. [DOI: 10.1002/jssc.201000795] [Citation(s) in RCA: 90] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2010] [Revised: 01/12/2011] [Accepted: 01/15/2011] [Indexed: 11/07/2022]
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31
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32
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Porous monoliths: sorbents for miniaturized extraction in biological analysis. Anal Bioanal Chem 2010; 399:3345-57. [DOI: 10.1007/s00216-010-4190-x] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2010] [Revised: 09/01/2010] [Accepted: 09/01/2010] [Indexed: 10/19/2022]
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33
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Vázquez M, Paull B. Review on recent and advanced applications of monoliths and related porous polymer gels in micro-fluidic devices. Anal Chim Acta 2010; 668:100-13. [DOI: 10.1016/j.aca.2010.04.033] [Citation(s) in RCA: 61] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2010] [Revised: 04/15/2010] [Accepted: 04/16/2010] [Indexed: 10/19/2022]
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34
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Chatterjee A, Mirer PL, Zaldivar Santamaria E, Klapperich C, Sharon A, Sauer-Budge AF. RNA Isolation from Mammalian Cells Using Porous Polymer Monoliths: An Approach for High-Throughput Automation. Anal Chem 2010; 82:4344-56. [DOI: 10.1021/ac100063f] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Affiliation(s)
- Anirban Chatterjee
- Departments of Mechanical Engineering and Biomedical Engineering, Boston University, Boston, Massachusetts 02215, and Center for Manufacturing Innovation, Fraunhofer USA, Brookline, Massachusetts 02446
| | - Paul L. Mirer
- Departments of Mechanical Engineering and Biomedical Engineering, Boston University, Boston, Massachusetts 02215, and Center for Manufacturing Innovation, Fraunhofer USA, Brookline, Massachusetts 02446
| | - Elvira Zaldivar Santamaria
- Departments of Mechanical Engineering and Biomedical Engineering, Boston University, Boston, Massachusetts 02215, and Center for Manufacturing Innovation, Fraunhofer USA, Brookline, Massachusetts 02446
| | - Catherine Klapperich
- Departments of Mechanical Engineering and Biomedical Engineering, Boston University, Boston, Massachusetts 02215, and Center for Manufacturing Innovation, Fraunhofer USA, Brookline, Massachusetts 02446
| | - Andre Sharon
- Departments of Mechanical Engineering and Biomedical Engineering, Boston University, Boston, Massachusetts 02215, and Center for Manufacturing Innovation, Fraunhofer USA, Brookline, Massachusetts 02446
| | - Alexis F. Sauer-Budge
- Departments of Mechanical Engineering and Biomedical Engineering, Boston University, Boston, Massachusetts 02215, and Center for Manufacturing Innovation, Fraunhofer USA, Brookline, Massachusetts 02446
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35
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Mahalanabis M, Do J, ALMuayad H, Zhang JY, Klapperich CM. An integrated disposable device for DNA extraction and helicase dependent amplification. Biomed Microdevices 2010; 12:353-9. [PMID: 20066496 PMCID: PMC2998058 DOI: 10.1007/s10544-009-9391-8] [Citation(s) in RCA: 76] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
Here we report the demonstration of an integrated microfluidic chip that performs helicase dependent amplification (HDA) on samples containing live bacteria. Combined chip-based sample preparation and isothermal amplification are attractive for world health applications, since the need for instrumentation to control flow rate and temperature changes are reduced or eliminated. Bacteria lysis, nucleic acid extraction, and DNA amplification with a fluorescent reporter are incorporated into a disposable polymer cartridge format. Smart passive fluidic control using a flap valve and a hydrophobic vent (with a nanoporous PTFE membrane) with a simple on-chip mixer eliminates multiple user operations. The device is able to detect as few as ten colony forming units (CFU) of E. coli in growth medium.
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Affiliation(s)
| | - Jaephil Do
- Department of Biomedical Engineering, Boston University, Boston, MA 02215, USA
| | - Hussam ALMuayad
- Department of Biomedical Engineering, Boston University, Boston, MA 02215, USA
| | - Jane Y. Zhang
- Department of Biomedical Engineering, Boston University, Boston, MA 02215, USA
| | - Catherine M. Klapperich
- Department of Biomedical Engineering, Boston University, Boston, MA 02215, USA, Department of Mechanical Engineering, Boston University, Boston, MA 02215, USA
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36
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Sauer-Budge AF, Mirer P, Chatterjee A, Klapperich CM, Chargin D, Sharon A. Low cost and manufacturable complete microTAS for detecting bacteria. LAB ON A CHIP 2009; 9:2803-10. [PMID: 19967117 DOI: 10.1039/b904854e] [Citation(s) in RCA: 60] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
In this paper, we present a fully integrated lab-on-a-chip and associated instrument for the detection of bacteria from liquid samples. The system conducts bacterial lysis, nucleic acid isolation and concentration, polymerase chain reaction (PCR), and end-point fluorescent detection. To enable truly low-cost manufacture of the single-use disposable chip, we designed the plastic chip in a planar format without any active components to be amenable to injection molding and utilized a novel porous polymer monolith (PPM) embedded with silica that has been shown to lyse bacteria and isolate the nucleic acids from clinical samples (M. D. Kulinski, M. Mahalanabis, S. Gillers, J. Y. Zhang, S. Singh and C. M. Klapperich, Biomed. Microdevices, 2009, 11, 671-678).(1) The chip is made of Zeonex(R), a thermoplastic with a high melting temperature to allow PCR, good UV transmissibility for UV-curing of the PPM, and low auto-fluorescence for fluorescence detection of the amplicon. We have built a prototype instrument to automate control of the fluids, temperature cycling, and optical detection with the capability of accommodating various chip designs. To enable fluid control without including valves or pumps on the chip, we utilized a remote valve switching technique. To allow fluid flow rate changes on the valveless chip, we incorporated speed changing fluid reservoirs. The PCR thermal cycling was achieved with a ceramic heater and air cooling, while end-point fluorescence detection was accomplished with an optical spectrometer; all integrated in the instrument. The chip seamlessly and automatically is mated to the instrument through an interface block that presses against the chip. The interface block aligns and ensures good contact of the chip to the temperature controlled region and the optics. The integrated functionality of the chip was demonstrated using Bacillus subtilis as a model bacterial target. A Taqman assay was employed on-chip to detect the isolated bacterial DNA.
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37
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Mahalanabis M, Al-Muayad H, Kulinski MD, Altman D, Klapperich CM. Cell lysis and DNA extraction of gram-positive and gram-negative bacteria from whole blood in a disposable microfluidic chip. LAB ON A CHIP 2009; 9:2811-7. [PMID: 19967118 DOI: 10.1039/b905065p] [Citation(s) in RCA: 127] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Sepsis caused by gram positive and gram negative bacteria is the leading cause of death in noncoronary ICUs and the tenth leading cause of death in the United States. We have developed a microfluidic sample preparation platform for rapid on-chip detection of infectious organisms for point-of-care diagnostics. The microfluidic chips are made of a robust thermoplastic and can be easily multiplexed for high throughput applications. Bacteria are lysed on-chip via hybrid chemical/mechanical method. Once lysed, the bacterial DNA is isolated using a microscale silica bead/polymer composite solid-phase-extraction (SPE) column. Lysis was confirmed using off-chip real time PCR. We isolated and detected both gram-negative (Escherichia coli) and gram-positive (Bacillussubtilis and Enterococcus faecalis) bacterial genomic DNA from microliter scale spiked whole human blood samples. The system performs better for gram-negative bacteria than it does for gram-positive bacteria, with limits of detection at 10(2) CFU/ml and 10(3)-10(4) CFU/ml, respectively. Total extraction times are less than one hour and can be further decreased by altering the channel geometry and pumping configuration.
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