1
|
Wang Y, Zhu L, Guo P, Zhang Y, Lan X, Xu W. Research progress of All-in-One PCR tube biosensors based on functional modification and intelligent fabrication. Biosens Bioelectron 2024; 246:115824. [PMID: 38029707 DOI: 10.1016/j.bios.2023.115824] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Revised: 10/30/2023] [Accepted: 11/06/2023] [Indexed: 12/01/2023]
Abstract
PCR amplification technology is the cornerstone of molecular biology. All-in-One PCR tube, as an emerging integrated device, is booming in biosensors application. All-in-One PCR tube biosensors are integrated PCR tubes designed for signal recognition, signal amplification or signal output. They enable "one-pot" detection within functionally modified and intelligently fabricated PCR tubes, effectively overcoming the limitations of conventional PCR applications, like complex procedural steps, risk of contamination and so on. Based on this, the review article summarizes the recent advance of All-in-One PCR tube biosensors for the first time as well as systematically categorizes five approaches of functional modification, three types of intelligent fabrication and relevant property characterization techniques. More emphasis is placed on the review of five ways of functional modification, including physical modification, chemical modification, UV photografting surface treatment, plasma surface modification, and layer-by-layer assembly coating. Moreover, All-in-One PCR tube biosensors covering different recognition elements range from small molecules to protein are detailed discussed on principle of sensing, providing a deeper understanding of the design and application of All-in-One-tube biosensor. Last, the future opportunities and challenges in this fascinating field are also deliberated.
Collapse
Affiliation(s)
- Yanhui Wang
- Key Laboratory of Precision Nutrition and Food Quality, Beijing Laboratory for Food Quality and Safety, Department of Nutrition and Health, China Agricultural University, Beijing, 100191, China
| | - Longjiao Zhu
- Key Laboratory of Precision Nutrition and Food Quality, Beijing Laboratory for Food Quality and Safety, Department of Nutrition and Health, China Agricultural University, Beijing, 100191, China
| | - Peijin Guo
- Key Laboratory of Precision Nutrition and Food Quality, Beijing Laboratory for Food Quality and Safety, Department of Nutrition and Health, China Agricultural University, Beijing, 100191, China
| | - Yangzi Zhang
- Key Laboratory of Precision Nutrition and Food Quality, Beijing Laboratory for Food Quality and Safety, Department of Nutrition and Health, China Agricultural University, Beijing, 100191, China
| | - Xinyue Lan
- Key Laboratory of Precision Nutrition and Food Quality, Beijing Laboratory for Food Quality and Safety, Department of Nutrition and Health, China Agricultural University, Beijing, 100191, China
| | - Wentao Xu
- Key Laboratory of Precision Nutrition and Food Quality, Beijing Laboratory for Food Quality and Safety, Department of Nutrition and Health, China Agricultural University, Beijing, 100191, China.
| |
Collapse
|
2
|
Wen K, Chen Y, Meng X, Botros S, Dai W, Stojanovic MN, Tomer R, Lin Q. A Microfluidic Dual-Aptamer Sandwich Assay for Rapid and Cost-Effective Detection of Recombinant Proteins. Microchem J 2023; 188:108454. [PMID: 36992861 PMCID: PMC10041396 DOI: 10.1016/j.microc.2023.108454] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
While monitoring expression of recombinant proteins is essential for obtaining high-quality biopharmaceutical and biotechnological products, existing assays for recombinant protein detection are laborious, time-consuming and expensive. This paper presents a microfluidic approach to rapid and cost-effective detection of tag-fused recombinant proteins via a dual-aptamer sandwich assay. Our approach addresses limitations in current methods for both dual-aptamer assays and generation of aptamers for such assays by first using microfluidic technology to isolate the aptamers rapidly and then employing these aptamers to implement a microfluidic dual-aptamer assay for tag-fused recombinant protein detection. The use of microfluidic technology enables the fast generation of aptamers and rapid detection of recombinant proteins with minimized consumption of reagents. In addition, compared with antibodies, aptamers as low-cost affinity reagents with an ability of reversible denaturation further decreases the cost of recombinant protein detection. For demonstration, an aptamer pair is isolated rapidly toward His-tagged IgE within two days, and then used in the microfluidic dual-aptamer assay for detecting His-tagged IgE in cell culture media within 10 min and with a limit of detection of 7.1 nM.
Collapse
Affiliation(s)
- Kechun Wen
- Department of Mechanical Engineering, Columbia University, New York, NY, 10027, USA
| | - Yannan Chen
- Department of Biomedical Engineering, Columbia University, New York, NY, 10027, USA
| | - Xin Meng
- Department of Mechanical Engineering, Columbia University, New York, NY, 10027, USA
| | - Samantha Botros
- Department of Mechanical Engineering, Columbia University, New York, NY, 10027, USA
| | - Wenting Dai
- Department of Mechanical Engineering, Columbia University, New York, NY, 10027, USA
| | - Milan N. Stojanovic
- Division of Experimental Therapeutics, Department of Medicine and Department of Biomedical Engineering, Columbia University, New York, NY, 10032, USA
| | - Raju Tomer
- Department of Biological Sciences, Columbia University, New York, NY, 10027, USA
| | - Qiao Lin
- Department of Mechanical Engineering, Columbia University, New York, NY, 10027, USA
| |
Collapse
|
3
|
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.
Collapse
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.)
| |
Collapse
|
4
|
Farahani A, Sereshti H. An integrated microfluidic device for solid-phase extraction and spectrophotometric detection of opium alkaloids in urine samples. Anal Bioanal Chem 2019; 412:129-138. [PMID: 31773230 DOI: 10.1007/s00216-019-02214-1] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2019] [Revised: 09/20/2019] [Accepted: 10/14/2019] [Indexed: 02/08/2023]
Abstract
A novel lab-on-chip integrated microfluidic device for solid-phase extraction (SPE) and spectrophotometric detection of morphine (MOR), codeine (COD), and papaverine (PAP) was developed. The extracted analytes were analyzed with a miniature UV-Vis spectrophotometer. The SPE adsorptive phase composed of polyurethane/polyaniline (PU/PANI) nanofibers was fabricated by electrospinning and in situ oxidative polymerization techniques. The sorbent was characterized by Fourier transform infrared (FTIR) spectroscopy and scanning electron microscopy (SEM). The main factors of extraction such as desorption conditions, pH, salt effect, and extraction time were investigated. The partial least square (PLS) regression was applied to improve the quantification of analytes. The linear dynamic ranges (LDRs) for MOR, COD, and PAP were 4-240, 4-210, and 1-150 ng mL-1, respectively. Finally, the proposed method was successfully applied for the determination of MOR, COD, and PAP in human urine samples and the extraction recoveries were obtained in the range of 66.7-85.0% with RSDs < 8.3%.
Collapse
Affiliation(s)
- Ali Farahani
- School of Chemistry, College of Science, University of Tehran, Tehran, 141761-4411, Iran
| | - Hassan Sereshti
- School of Chemistry, College of Science, University of Tehran, Tehran, 141761-4411, Iran.
| |
Collapse
|
5
|
Nemr CR, Smith SJ, Liu W, Mepham AH, Mohamadi RM, Labib M, Kelley SO. Nanoparticle-Mediated Capture and Electrochemical Detection of Methicillin-Resistant Staphylococcus aureus. Anal Chem 2019; 91:2847-2853. [PMID: 30676721 DOI: 10.1021/acs.analchem.8b04792] [Citation(s) in RCA: 46] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
The spread of antibiotic-resistant bacteria poses a global threat to public health. Conventional bacterial detection and identification methods often require pre-enrichment and/or sample preprocessing and purification steps that can prolong diagnosis by days. Methicillin-resistant Staphylococcus aureus (MRSA) is one of the most widespread antibiotic-resistant bacteria and is the leading cause of hospital-acquired infections. Here, we have developed a method to specifically capture and detect MRSA directly from patient nasal swabs with no prior culture and minimal processing steps using a microfluidic device and antibody-functionalized magnetic nanoparticles. Bacteria are captured based on antibody recognition of a membrane-bound protein marker that confers β-lactam antibiotic resistance. MRSA identification is then achieved by the use of a strain-specific antibody functionalized with alkaline phosphatase for electrochemical detection. This approach ensures that only those bacteria of the target strain and resistance profile are measured. The method has a limit of detection of 845 CFU/mL and excellent discrimination against high concentrations of common nontarget nasal flora with a turnaround time of under 4.5 h. This detection method was successfully validated using clinical nasal swab specimens ( n = 30) and has the potential to be tailored to various bacterial targets.
Collapse
|
6
|
Hui J, Gu Y, Zhu Y, Chen Y, Guo SJ, Tao SC, Zhang Y, Liu P. Multiplex sample-to-answer detection of bacteria using a pipette-actuated capillary array comb with integrated DNA extraction, isothermal amplification, and smartphone detection. LAB ON A CHIP 2018; 18:2854-2864. [PMID: 30105321 DOI: 10.1039/c8lc00543e] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
A pipette-actuated capillary array comb (PAAC) system operated on a smartphone-based hand-held device has been successfully developed for the multiplex detection of bacteria in a "sample-to-answer" manner. The PAAC consists of eight open capillaries inserted into a cylindrical plastic base with a piece of chitosan-modified glass filter paper embedded in each capillary. During the sample preparation, a PAAC was mounted into a 1 mL pipette tip with an enlarged opening and was operated with a 1 mL pipette for liquid handling. The cell lysate was drawn and expelled through the capillaries three times to facilitate the DNA capture on the embedded filter discs. Following washes with water, the loop-mediated isothermal amplification (LAMP) reagents were aspirated into the capillaries, in which the primers were pre-fixed with chitosan. After that, the PAAC was loaded into the smartphone-based device for a one-hour amplification at 65 °C and end-point detection of calcein fluorescence in the capillaries. The DNA capture efficiency of a 1.1 mm-diameter filter disc was determined to be 97% of λ-DNA and the coefficient of variation among the eight capillaries in the PAAC was only 2.2%. The multiplex detection of genomic DNA extracted from Escherichia coli, Klebsiella pneumoniae, and Staphylococcus aureus provided limits of detection of 200, 500, and 500 copies, respectively, without any cross-contamination and cross reactions. "Sample-to-answer" detection of E. coli samples was successfully completed in 85 minutes, demonstrating a sensitivity of 200 cfu per capillary. The multiplex "sample-to-answer" detection, the streamlined operation, and the compact device should facilitate a broad range of applications of our PAAC system in point-of-care testing.
Collapse
Affiliation(s)
- Junhou Hui
- Department of Biomedical Engineering, School of Medicine, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Tsinghua University, Beijing, 100084, China.
| | | | | | | | | | | | | | | |
Collapse
|
7
|
Basha IHK, Ho ETW, Yousuff CM, Hamid NHB. Towards Multiplex Molecular Diagnosis-A Review of Microfluidic Genomics Technologies. MICROMACHINES 2017; 8:E266. [PMID: 30400456 PMCID: PMC6190060 DOI: 10.3390/mi8090266] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/15/2017] [Revised: 06/30/2017] [Accepted: 07/16/2017] [Indexed: 12/21/2022]
Abstract
Highly sensitive and specific pathogen diagnosis is essential for correct and timely treatment of infectious diseases, especially virulent strains, in people. Point-of-care pathogen diagnosis can be a tremendous help in managing disease outbreaks as well as in routine healthcare settings. Infectious pathogens can be identified with high specificity using molecular methods. A plethora of microfluidic innovations in recent years have now made it increasingly feasible to develop portable, robust, accurate, and sensitive genomic diagnostic devices for deployment at the point of care. However, improving processing time, multiplexed detection, sensitivity and limit of detection, specificity, and ease of deployment in resource-limited settings are ongoing challenges. This review outlines recent techniques in microfluidic genomic diagnosis and devices with a focus on integrating them into a lab on a chip that will lead towards the development of multiplexed point-of-care devices of high sensitivity and specificity.
Collapse
Affiliation(s)
- Ismail Hussain Kamal Basha
- Department of Electrical and Electronic Engineering, Universiti Teknologi PETRONAS, 32610 Seri Iskandar, Perak Darul Ridzuan, Malaysia.
| | - Eric Tatt Wei Ho
- Department of Electrical and Electronic Engineering, Universiti Teknologi PETRONAS, 32610 Seri Iskandar, Perak Darul Ridzuan, Malaysia.
| | - Caffiyar Mohamed Yousuff
- Department of Electrical and Electronic Engineering, Universiti Teknologi PETRONAS, 32610 Seri Iskandar, Perak Darul Ridzuan, Malaysia.
| | - Nor Hisham Bin Hamid
- Department of Electrical and Electronic Engineering, Universiti Teknologi PETRONAS, 32610 Seri Iskandar, Perak Darul Ridzuan, Malaysia.
| |
Collapse
|
8
|
Hulme J. Recent advances in the detection of methicillin resistant Staphylococcus aureus (MRSA). BIOCHIP JOURNAL 2017. [DOI: 10.1007/s13206-016-1201-9] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
|
9
|
Pereiro I, Tabnaoui S, Fermigier M, du Roure O, Descroix S, Viovy JL, Malaquin L. Magnetic fluidized bed for solid phase extraction in microfluidic systems. LAB ON A CHIP 2017; 17:1603-1615. [PMID: 28382356 DOI: 10.1039/c7lc00063d] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Fluidization, a process in which a granular solid phase behaves like a fluid under the influence of an imposed upward fluid flow, is routinely used in many chemical and biological engineering applications. It brings, to applications involving fluid-solid exchanges, advantages such as high surface to volume ratio, constant mixing, low flow resistance, continuous operation and high heat transfer. We present here the physics of a new miniaturized, microfluidic fluidized bed, in which gravity is replaced by a magnetic field created by an external permanent magnet, and the solid phase is composed of magnetic microbeads with diameters ranging from 1 to 5 μm. These beads can be functionalized with different ligands, catalysts or enzymes, in order to use the fluidized bed as a continuous purification column or bioreactor. It allows flow-through operations at flow rates ranging from 100 nL min-1 up to 5 μL min-1 at low driving pressures (<100 mbar) with intimate liquid/solid contact and a continuous recirculation of beads for enhanced target capture efficiencies. The physics of the system presents significant differences as compared to conventional fluidized beds, which are studied here. The effects of magnetic field profile, flow chamber shape and magnetic bead dipolar interactions on flow regimes are investigated, and the different regimes of operation are described. Qualitative rules to obtain optimal operation are deduced. Finally, an exemplary use as a platform for immunocapture is provided, presenting a limit of detection of 0.2 ng mL-1 for 200 μL volume samples.
Collapse
Affiliation(s)
- Iago Pereiro
- Laboratoire Physico Chimie Curie, Institut Curie, PSL Research University, CNRS UMR168, 75005, Paris, France.
| | | | | | | | | | | | | |
Collapse
|
10
|
Gan W, Gu Y, Han J, Li CX, Sun J, Liu P. Chitosan-Modified Filter Paper for Nucleic Acid Extraction and "in Situ PCR" on a Thermoplastic Microchip. Anal Chem 2017; 89:3568-3575. [PMID: 28230980 DOI: 10.1021/acs.analchem.6b04882] [Citation(s) in RCA: 53] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
Plastic microfluidic devices with embedded chitosan-modified Fusion 5 filter paper (unmodified one purchased from GE Healthcare) have been successfully developed for DNA extraction and concentration, utilizing two different mechanisms for DNA capture: the physical entanglement of long-chain DNA molecules with the fiber matrix of the filter paper and the electrostatic adsorption of DNA to the chitosan-modified filter fibers. This new method not only provided a high DNA extraction efficiency at a pH of 5 by synergistically combining these two capture mechanisms together, but also resisted the elution of DNA from filters at a pH > 8 due to the entanglement of DNA with fibers. As a result, PCR buffers can be directly loaded into the extraction chamber for "in situ PCR", in which the captured DNA were used for downstream analysis without any loss. We demonstrated that the capture efficiencies of a 3-mm-diameter filter disc in a microchip were 98% and 95% for K562 human genomic DNA and bacteriophage λ-DNA, respectively. The washes with DI water, PCR mixture, and TE buffer cannot elute the captured DNA. In addition, the filter disc can enrich 62% of λ-DNA from a diluted sample (0.05 ng/μL), providing a concentration factor more than 30-fold. Finally, a microdevice with a simple two-chamber structure was developed for on-chip cell lysis, DNA extraction, and 15-plex short tandem repeat amplification from blood. This DNA extraction coupled with "in situ PCR" has great potential to be utilized in fully integrated microsystems for rapid, near-patient nucleic acid testing.
Collapse
Affiliation(s)
- Wupeng Gan
- Department of Biomedical Engineering, School of Medicine, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Tsinghua University , Beijing 100084, China
| | - Yin Gu
- Department of Biomedical Engineering, School of Medicine, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Tsinghua University , Beijing 100084, China
| | - Junping Han
- Technology Department of Chaoyang Sub-bureau, Beijing Public Security Bureau , Beijing 100102, China
| | - Cai-Xia Li
- Key Laboratory of Forensic Genetics, Beijing Engineering Research Center of Crime Scene Evidence Examination, National Engineering Laboratory for Crime Scene Evidence Examination, Institute of Forensic Science , Beijing 100038, China
| | - Jing Sun
- Key Laboratory of Forensic Genetics, Beijing Engineering Research Center of Crime Scene Evidence Examination, National Engineering Laboratory for Crime Scene Evidence Examination, Institute of Forensic Science , Beijing 100038, China
| | - Peng Liu
- Department of Biomedical Engineering, School of Medicine, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Tsinghua University , Beijing 100084, China
| |
Collapse
|
11
|
Functionalized electrospun poly(vinyl alcohol) nanofibers for on-chip concentration of E. coli cells. Anal Bioanal Chem 2016; 408:1327-34. [PMID: 26493980 DOI: 10.1007/s00216-015-9112-5] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2015] [Revised: 09/24/2015] [Accepted: 10/09/2015] [Indexed: 10/22/2022]
Abstract
Positively and negatively charged electrospun poly(vinyl alcohol) (PVA) nanofibers were incorporated into poly(methyl methacrylate) (PMMA) microchannels in order to facilitate on-chip concentration of Escherichia coli K12 cells. The effects of fiber distribution and fiber mat height on analyte retention were investigated. The 3D morphology of the mats was optimized to prevent size-related retention of the E. coli cells while also providing a large enough surface area for analyte concentration. Positively charged nanofibers produced an 87% retention and over 80-fold concentration of the bacterial cells by mere electrostatic interaction, while negatively charged nanofibers reduced nonspecific analyte retention when compared to an empty microfluidic channel. In order to take advantage of this reduction in nonspecific retention, these negatively charged nanofibers were then modified with anti-E. coli antibodies. These proof-of-principle experiments showed that antibody-functionalized negatively charged nanofiber mats were capable of the specific capture of 72% of the E. coli cells while also significantly reducing nonspecific analyte retention within the channel as expected. The ease of fabrication and immense surface area of the functionalized electrospun nanofibers make them a promising alternative for on-chip concentration of analytes. The pore size and fiber mat morphology, as well as surface functionality of the fibers, can be tailored to allow for specific capture and concentration of a wide range of analytes.
Collapse
|
12
|
Julich S, Hotzel H, Gärtner C, Trouchet D, Fawzy El Metwaly Ahmed M, Kemper N, Tomaso H. Evaluation of a microfluidic chip system for preparation of bacterial DNA from swabs, air, and surface water samples. Biologicals 2016; 44:574-580. [PMID: 27520284 PMCID: PMC5119575 DOI: 10.1016/j.biologicals.2016.06.013] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2015] [Revised: 12/17/2015] [Accepted: 06/29/2016] [Indexed: 11/18/2022] Open
Abstract
The detection of bacterial pathogens from complex sample matrices by PCR requires efficient DNA extraction. In this study, a protocol for extraction and purification of DNA from swabs, air, and water samples using a microfluidic chip system was established. The optimized protocol includes a combination of thermal, chemical and enzymatic lysis followed by chip-based DNA purification using magnetic particles. The procedure was tested using Gram-positive Bacillus thuringiensis Berliner var. kurstaki as a model organism for Bacillus anthracis and the attenuated live vaccine strain of Francisella tularensis subsp. holarctica as Gram-negative bacterium. The detection limits corresponded to 103 genome equivalents per milliliter (GE/ml) for surface water samples spiked with F. tularensis and 102 GE/ml for B. thuringiensis. In air, 10 GE of F. tularensis per 10 L and 1 GE of B. thuringiensis per 10 L were detectable. For swab samples obtained from artificially contaminated surfaces the detection limits were 4 × 103 GE/cm2 for F. tularensis and 4 × 102 GE/cm2 for B. thuringiensis. Suitability of the chip-assisted procedure for DNA preparation of real samples was demonstrated using livestock samples. The presence of thermophilic Campylobacter spp. DNA could be confirmed in air samples collected on pig and broiler farms. A microfluidic chip system for magnetic bead-based DNA preparation was evaluated. Bacterial DNA was recovered from swabs, air, and surface water. A universal protocol was used for Gram-positive and Gram-negative bacteria. 10 GE of F. tularensis and 1 GE of B. thuringiensis per 10 l air were detectable. Thermophilic Campylobacter DNA was detected in air samples of pig and broiler farms.
Collapse
Affiliation(s)
- Sandra Julich
- Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Institute of Bacterial Infections and Zoonoses, Naumburger Straße 96a, 07743 Jena, Germany
| | - Helmut Hotzel
- Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Institute of Bacterial Infections and Zoonoses, Naumburger Straße 96a, 07743 Jena, Germany
| | - Claudia Gärtner
- microfluidic ChipShop, Stockholmer Straße 20, 07747 Jena, Germany
| | - Daniel Trouchet
- Bertin Technologies, 10 Avenue André Marie Ampére, 78180 Montigny-le-Bretonneux, France
| | - Marwa Fawzy El Metwaly Ahmed
- Mansoura University, Faculty of Veterinary Medicine, Department of Animal Hygiene and Zoonoses, 60 El Gomhoria Street, 35516 Mansoura, Egypt
| | - Nicole Kemper
- University of Veterinary Medicine Hannover, Foundation, Institute of Animal Hygiene, Animal Welfare and Farm Animal Behaviour, Bischofsholer Damm 15, 30173 Hannover, Germany
| | - Herbert Tomaso
- Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Institute of Bacterial Infections and Zoonoses, Naumburger Straße 96a, 07743 Jena, Germany.
| |
Collapse
|
13
|
Rho HS, Yang Y, Hanke AT, Ottens M, Terstappen LWMM, Gardeniers H. Programmable v-type valve for cell and particle manipulation in microfluidic devices. LAB ON A CHIP 2016; 16:305-311. [PMID: 26648416 DOI: 10.1039/c5lc01206f] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
A new microfluidic valve or a "v-type valve" which can be flexibly actuated to focus a fluid flow and block a specific area of a microchannel is demonstrated. Valves with different design parameters were fabricated by multilayer soft lithography and characterized at various operating pressures. To evaluate the functionality of the valve, single microparticles (∅ 7 μm and ∅ 15 μm) and single cells were trapped from flowing suspensions. Continuous processes of particle capture and release were achieved by controlling the actuation and deactuation of the valve. Integration of the v-type valve with poly(dimethyl siloxane) (PDMS) monolithic valves in microfluidic devices was demonstrated to illustrate the potential of the system in various applications such as the creation of a solid phase column, the isolation of a specific number of particles in reactors, and the capture and release of particles or cells in the flow of two immiscible liquids. We believe that this new valve system will be suitable for manipulating particles and cells in a broad range of applications.
Collapse
Affiliation(s)
- Hoon Suk Rho
- Mesoscale Chemical Systems Group, MESA+ Institute for Nanotechnology, University of Twente, The Netherlands.
| | - Yoonsun Yang
- Medical Cell BioPhysics Group, MIRA Institute for Biomedical Technology and Technical Medicine, University of Twente, The Netherlands
| | - Alexander T Hanke
- BioProcess Engineering group, Department of Biotechnology, Faculty of Applied Sciences, Delft University of Technology, The Netherlands
| | - Marcel Ottens
- BioProcess Engineering group, Department of Biotechnology, Faculty of Applied Sciences, Delft University of Technology, The Netherlands
| | - Leon W M M Terstappen
- Medical Cell BioPhysics Group, MIRA Institute for Biomedical Technology and Technical Medicine, University of Twente, The Netherlands
| | - Han Gardeniers
- Mesoscale Chemical Systems Group, MESA+ Institute for Nanotechnology, University of Twente, The Netherlands.
| |
Collapse
|
14
|
Comparison between a chimeric lysin ClyH and other enzymes for extracting DNA to detect methicillin resistant Staphylococcus aureus by quantitative PCR. World J Microbiol Biotechnol 2015; 32:1. [PMID: 26596268 DOI: 10.1007/s11274-015-1971-6] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2015] [Accepted: 10/14/2015] [Indexed: 02/01/2023]
Abstract
Extracting DNA from Staphylococcus aureus cells is important for detecting MRSA by PCR. However, S. aureus cells are known to be difficult to disrupt due to their compact cell walls. Here, we systematically studied the efficiency of a highly active lysin ClyH for extracting DNA of S. aureus in comparison with commonly used enzymes, such as lysostaphin and achromopeptidase (ACP), and its compatibility in quantitative PCR (qPCR) detection of MRSA. qPCR analysis of S. aureus specific gene femB showed that ClyH was much faster than lysostaphin, ACP and lysozyme for releasing DNA. Five minutes disruption with ClyH at room temperature was enough to release all the DNA from S. aureus. Analysis of the spiked nasal swabs by a dual qPCR assay of the β-lactam resistance mecA gene and the staphylococcal cassette chromosome (SCCmec)-open reading frame X (orfX) junction (SCCmec-orfX) after ClyH lysis showed 100% sensitivity and specificity to the commercial BD GeneOhm™ MRSA test with ACP lysis, but the lysis time was reduced from 20 min by ACP to 5 min by ClyH. Our research shows that ClyH could be a better option than the currently used enzymes for DNA extraction from S. aureus, which can provide simpler and faster PCR detection of MRSA.
Collapse
|
15
|
Adams NM, Bordelon H, Wang KKA, Albert LE, Wright DW, Haselton FR. Comparison of three magnetic bead surface functionalities for RNA extraction and detection. ACS APPLIED MATERIALS & INTERFACES 2015; 7:6062-9. [PMID: 25710198 DOI: 10.1021/am506374t] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
Magnetic beads are convenient for extracting nucleic acid biomarkers from biological samples prior to molecular detection. These beads are available with a variety of surface functionalities designed to capture particular subsets of RNA. We hypothesized that bead surface functionality affects binding kinetics, processing simplicity, and compatibility with molecular detection strategies. In this report, three magnetic bead surface chemistries designed to bind nucleic acids, silica, oligo (dT), and a specific oligonucleotide sequence were evaluated. Commercially available silica-coated and oligo (dT) beads, as well as beads functionalized with oligonucleotides complementary to respiratory syncytial virus (RSV) nucleocapsid gene, respectively recovered ∼75, ∼71, and ∼7% target RSV mRNA after a 1 min of incubation time in a surrogate patient sample spiked with the target. RSV-specific beads required much longer incubation times to recover amounts of the target comparable to the other beads (∼77% at 180 min). As expected, silica-coated beads extracted total RNA, oligo (dT) beads selectively extracted total mRNA, and RSV-specific beads selectively extracted RSV N gene mRNA. The choice of bead functionality is generally dependent on the target detection strategy. The silica-coated beads are most suitable for applications that require nucleic acids other than mRNA, especially with detection strategies that are tolerant of a high concentration of nontarget background nucleic acids, such as RT-PCR. On the other hand, oligo (dT) beads are best-suited for mRNA targets, as they bind biomarkers rapidly, have relatively high recovery, and enable detection strategies to be performed directly on the bead surface. Sequence-specific beads may be best for applications that are not tolerant of a high concentration of nontarget nucleic acids that require short RNA sequences without poly(A) tails, such as microRNAs, or that perform RNA detection directly on the bead surface.
Collapse
Affiliation(s)
- Nicholas M Adams
- †Department of Biomedical Engineering, Vanderbilt University, Nashville, Tennessee 37235, United States
- ‡Department of Chemistry, Vanderbilt University, Nashville, Tennessee 37235, United States
| | - Hali Bordelon
- †Department of Biomedical Engineering, Vanderbilt University, Nashville, Tennessee 37235, United States
| | - Kwo-Kwang A Wang
- ‡Department of Chemistry, Vanderbilt University, Nashville, Tennessee 37235, United States
| | - Laura E Albert
- †Department of Biomedical Engineering, Vanderbilt University, Nashville, Tennessee 37235, United States
| | - David W Wright
- ‡Department of Chemistry, Vanderbilt University, Nashville, Tennessee 37235, United States
| | - Frederick R Haselton
- †Department of Biomedical Engineering, Vanderbilt University, Nashville, Tennessee 37235, United States
| |
Collapse
|
16
|
Rödiger S, Liebsch C, Schmidt C, Lehmann W, Resch-Genger U, Schedler U, Schierack P. Nucleic acid detection based on the use of microbeads: a review. Mikrochim Acta 2014. [DOI: 10.1007/s00604-014-1243-4] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
|
17
|
Lu X, Samuelson DR, Xu Y, Zhang H, Wang S, Rasco BA, Xu J, Konkel ME. Detecting and tracking nosocomial methicillin-resistant Staphylococcus aureus using a microfluidic SERS biosensor. Anal Chem 2013; 85:2320-7. [PMID: 23327644 DOI: 10.1021/ac303279u] [Citation(s) in RCA: 81] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
Rapid detection and differentiation of methicillin-resistant Staphylococcus aureus (MRSA) are critical for the early diagnosis of difficult-to-treat nosocomial and community acquired clinical infections and improved epidemiological surveillance. We developed a microfluidics chip coupled with surface enhanced Raman scattering (SERS) spectroscopy (532 nm) "lab-on-a-chip" system to rapidly detect and differentiate methicillin-sensitive S. aureus (MSSA) and MRSA using clinical isolates from China and the United States. A total of 21 MSSA isolates and 37 MRSA isolates recovered from infected humans were first analyzed by using polymerase chain reaction (PCR) and multilocus sequence typing (MLST). The mecA gene, which refers resistant to methicillin, was detected in all the MRSA isolates, and different allelic profiles were identified assigning isolates as either previously identified or novel clones. A total of 17 400 SERS spectra of the 58 S. aureus isolates were collected within 3.5 h using this optofluidic platform. Intra- and interlaboratory spectral reproducibility yielded a differentiation index value of 3.43-4.06 and demonstrated the feasibility of using this optofluidic system at different laboratories for bacterial identification. A global SERS-based dendrogram model for MRSA and MSSA identification and differentiation to the strain level was established and cross-validated (Simpson index of diversity of 0.989) and had an average recognition rate of 95% for S. aureus isolates associated with a recent outbreak in China. SERS typing correlated well with MLST indicating that it has high sensitivity and selectivity and would be suitable for determining the origin and possible spread of MRSA. A SERS-based partial least-squares regression model could quantify the actual concentration of a specific MRSA isolate in a bacterial mixture at levels from 5% to 100% (regression coefficient, >0.98; residual prediction deviation, >10.05). This optofluidic platform has advantages over traditional genotyping for ultrafast, automated, and reliable detection and epidemiological surveillance of bacterial infections.
Collapse
Affiliation(s)
- Xiaonan Lu
- School of Molecular Biosciences, College of Veterinary Medicine, Washington State University, Pullman, Washington 99164-7520, United States
| | | | | | | | | | | | | | | |
Collapse
|