1
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Langmuir–Blodgett based ordered deposition of functionalized iron oxide nanoparticles for ultrasensitive detection of Escherichia coli O157: H7. Microchem J 2022. [DOI: 10.1016/j.microc.2022.107708] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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2
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Pandit S, Li M, Chen Y, Rahimi S, Mokkapati V, Merlo A, Yurgens A, Mijakovic I. Graphene-Based Sensor for Detection of Bacterial Pathogens. SENSORS 2021; 21:s21238085. [PMID: 34884089 PMCID: PMC8662450 DOI: 10.3390/s21238085] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Revised: 11/24/2021] [Accepted: 11/28/2021] [Indexed: 11/23/2022]
Abstract
Microbial colonization to biomedical surfaces and biofilm formation is one of the key challenges in the medical field. Recalcitrant biofilms on such surfaces cause serious infections which are difficult to treat using antimicrobial agents, due to their complex structure. Early detection of microbial colonization and monitoring of biofilm growth could turn the tide by providing timely guidance for treatment or replacement of biomedical devices. Hence, there is a need for sensors, which could generate rapid signals upon bacterial colonization. In this study, we developed a simple prototype sensor based on pristine, non-functionalized graphene. The detection principle is a change in electrical resistance of graphene upon exposure to bacterial cells. Without functionalization with specific receptors, such sensors cannot be expected to be selective to certain bacteria. However, we demonstrated that two different bacterial species can be detected and differentiated by our sensor due to their different growth dynamics, adherence pattern, density of adhered bacteria and microcolonies formation. These distinct behaviors of tested bacteria depicted distinguishable pattern of resistance change, resistance versus gate voltage plot and hysteresis effect. This sensor is simple to fabricate, can easily be miniaturized, and can be effective in cases when precise identification of species is not needed.
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Affiliation(s)
- Santosh Pandit
- Department of Biology and Biological Engineering, Chalmers University of Technology, 412 96 Göteborg, Sweden; (S.P.); (Y.C.); (S.R.); (V.M.); (A.M.)
| | - Mengyue Li
- Department of Microtechnology and Nanoscience, Chalmers University of Technology, 412 96 Göteborg, Sweden; (M.L.); (A.Y.)
| | - Yanyan Chen
- Department of Biology and Biological Engineering, Chalmers University of Technology, 412 96 Göteborg, Sweden; (S.P.); (Y.C.); (S.R.); (V.M.); (A.M.)
| | - Shadi Rahimi
- Department of Biology and Biological Engineering, Chalmers University of Technology, 412 96 Göteborg, Sweden; (S.P.); (Y.C.); (S.R.); (V.M.); (A.M.)
| | - Vrss Mokkapati
- Department of Biology and Biological Engineering, Chalmers University of Technology, 412 96 Göteborg, Sweden; (S.P.); (Y.C.); (S.R.); (V.M.); (A.M.)
| | - Alessandra Merlo
- Department of Biology and Biological Engineering, Chalmers University of Technology, 412 96 Göteborg, Sweden; (S.P.); (Y.C.); (S.R.); (V.M.); (A.M.)
| | - August Yurgens
- Department of Microtechnology and Nanoscience, Chalmers University of Technology, 412 96 Göteborg, Sweden; (M.L.); (A.Y.)
| | - Ivan Mijakovic
- Department of Biology and Biological Engineering, Chalmers University of Technology, 412 96 Göteborg, Sweden; (S.P.); (Y.C.); (S.R.); (V.M.); (A.M.)
- Novo Nordisk Foundation, Center for Biosustainability, Technical University of Denmark, 2800 Kongens Lyngby, Denmark
- Correspondence: ; Tel.: +46-(0)7-0982-8446
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3
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Moss AC, Herr AE. In-gel fluorescence detection by DNA polymerase elongation. APL Bioeng 2020; 4:046104. [PMID: 33263097 PMCID: PMC7680656 DOI: 10.1063/5.0021149] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Accepted: 10/07/2020] [Indexed: 11/14/2022] Open
Abstract
Fluorescence-based DNA readouts are increasingly important in biological research, owing to enhanced analytical sensitivity and multiplexing capability. In this study, we characterize an in-gel polymerase elongation process to understand the reaction kinetics and transport limitations, and we evaluate DNA sequence design to develop signal amplification strategies. Using fluorescently labeled nucleotides, we scrutinize polymerase elongation on single-stranded overhangs of DNA immobilized in polyacrylamide hydrogels. When polymerase elongation reactions were carried out with reactants diffused into the gels, we observed reaction completion after 2 h, indicating that the process was efficient but much slower than that predicted by models. Confocal microscopy revealed a nonuniform post-reaction fluorescence profile of the elongated DNA throughout the depth of the gel and that the time for complete fluorescence penetration was proportional to the immobilized DNA concentration. These observations suggest retarded diffusion of the polymerase, attributable to interactions between diffusing polymerase and immobilized DNA. This study will ultimately inform assay design by providing insight into the reaction completion time to ensure spatial uniformity of the fluorescence signal. In agreement with our hypothesis that incorporation of multiple labeled nucleotides per DNA strand results in an increased signal, incorporation of four labeled nucleotides resulted in a 2.3-fold increase in fluorescence intensity over one labeled nucleotide. Our results further suggest that the fluorescence signal increases with spacing between labeled nucleotides, validating the number of and spacing between labeled nucleotides as tunable parameters for signal amplification. In-gel polymerase-based fluorescence readout is promising for signal amplification when considering both transport limitations and DNA sequence design.
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Affiliation(s)
| | - Amy E. Herr
- Author to whom correspondence should be addressed:
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4
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Hydrogels for Efficient Multiplex PCR. BIOTECHNOL BIOPROC E 2020. [DOI: 10.1007/s12257-020-0134-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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5
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Sheng L, Lu Y, Deng S, Liao X, Zhang K, Ding T, Gao H, Liu D, Deng R, Li J. A transcription aptasensor: amplified, label-free and culture-independent detection of foodborne pathogens via light-up RNA aptamers. Chem Commun (Camb) 2019; 55:10096-10099. [PMID: 31380872 DOI: 10.1039/c9cc05036a] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
We report a transcription aptasensor by using a light-up RNA aptamer. It allows for sensitive, label-free and culture-free detection of intact foodborne pathogens, and no separation, purification or enrichment processes are involved.
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Affiliation(s)
- Lele Sheng
- College of Biomass Science and Engineering, Healthy Food Evaluation Research Center, Sichuan University, Chengdu 610065, China.
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6
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Zhong M, Yang L, Yang H, Cheng C, Deng W, Tan Y, Xie Q, Yao S. An electrochemical immunobiosensor for ultrasensitive detection of Escherichia coli O157:H7 using CdS quantum dots-encapsulated metal-organic frameworks as signal-amplifying tags. Biosens Bioelectron 2018; 126:493-500. [PMID: 30476880 DOI: 10.1016/j.bios.2018.11.001] [Citation(s) in RCA: 93] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2018] [Revised: 10/31/2018] [Accepted: 11/01/2018] [Indexed: 12/17/2022]
Abstract
We report here cadmium sulfide quantum dots (CdS QDs)-encapsulated metal-organic frameworks as signal-amplifying tags for ultrasensitive electrochemical detection of Escherichia coli O157:H7 (E. coli O157:H7). CdS QDs were encapsulated in zeolitic imidazolate framework-8 (ZIF-8) to form CdS@ZIF-8 muti-core-shell particles by in situ growth of ZIF-8 in the presence of CdS QDs. To specifically recognize E. coli O157:H7 cells, CdS@ZIF-8 particles were coated with polyethyleneimine to introduce amino groups on their surfaces, followed by surface modification of anti-E. coli O157:H7 antibody. A sandwich-type electrochemical immunobiosensor for the detection of E. coli O157:H7 was fabricated using CdS@ZIF-8 particles as signal tags. Cd(II) ions were released from CdS@ZIF-8 tags by HCl leaching, enabling the detection of E. coli O157:H7 by differential pulse voltammetry. Under the optimized conditions, the linear range of the biosensor is from 10 to 108 colony forming units (CFU) per mL for E. coli O157:H7 detection, with the detection limit of 3 CFU mL-1 (S/N = 3). The sensitivity of the biosensor for E. coli O157:H7 detection using CdS@ZIF-8 particles as signal tags is 16 times that of a biosensor using CdS QDs as signal tags, because the number of CdS QDs labeled to each bacterial cell increases greatly resulting from a great number of CdS QDs encapsulated in each CdS@ZIF-8 label. This method was successfully used to detect E. coli O157:H7 in milk samples.
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Affiliation(s)
- Miao Zhong
- Key Laboratory of Chemical Biology and Traditional Chinese Medicine Research (Ministry of Education of China), College of Chemistry and Chemical Engineering, Hunan Normal University, Changsha 410081, China
| | - Lu Yang
- Key Laboratory of Chemical Biology and Traditional Chinese Medicine Research (Ministry of Education of China), College of Chemistry and Chemical Engineering, Hunan Normal University, Changsha 410081, China
| | - Hui Yang
- Key Laboratory of Chemical Biology and Traditional Chinese Medicine Research (Ministry of Education of China), College of Chemistry and Chemical Engineering, Hunan Normal University, Changsha 410081, China
| | - Chang Cheng
- Key Laboratory of Chemical Biology and Traditional Chinese Medicine Research (Ministry of Education of China), College of Chemistry and Chemical Engineering, Hunan Normal University, Changsha 410081, China
| | - Wenfang Deng
- Key Laboratory of Chemical Biology and Traditional Chinese Medicine Research (Ministry of Education of China), College of Chemistry and Chemical Engineering, Hunan Normal University, Changsha 410081, China
| | - Yueming Tan
- Key Laboratory of Chemical Biology and Traditional Chinese Medicine Research (Ministry of Education of China), College of Chemistry and Chemical Engineering, Hunan Normal University, Changsha 410081, China.
| | - Qingji Xie
- Key Laboratory of Chemical Biology and Traditional Chinese Medicine Research (Ministry of Education of China), College of Chemistry and Chemical Engineering, Hunan Normal University, Changsha 410081, China
| | - Shouzhuo Yao
- Key Laboratory of Chemical Biology and Traditional Chinese Medicine Research (Ministry of Education of China), College of Chemistry and Chemical Engineering, Hunan Normal University, Changsha 410081, China
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7
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Kang TW, Han J, Lee S, Hwang IJ, Jeon SJ, Ju JM, Kim MJ, Yang JK, Jun B, Lee CH, Lee SU, Kim JH. 2D transition metal dichalcogenides with glucan multivalency for antibody-free pathogen recognition. Nat Commun 2018; 9:2549. [PMID: 29959329 PMCID: PMC6026184 DOI: 10.1038/s41467-018-04997-w] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2017] [Accepted: 06/05/2018] [Indexed: 12/31/2022] Open
Abstract
The ability to control the dimensions and properties of nanomaterials is fundamental to the creation of new functions and improvement of their performances in the applications of interest. Herein, we report a strategy based on glucan multivalent interactions for the simultaneous exfoliation and functionalization of two-dimensional transition metal dichalcogenides (TMDs) in an aqueous solution. The multivalent hydrogen bonding of dextran with bulk TMDs (WS2, WSe2, and MoSe2) in liquid exfoliation effectively produces TMD monolayers with binding multivalency for pathogenic bacteria. Density functional theory simulation reveals that the multivalent hydrogen bonding between dextran and TMD monolayers is very strong and thermodynamically favored (ΔEb = −0.52 eV). The resulting dextran/TMD hybrids (dex-TMDs) exhibit a stronger affinity (Kd = 11 nM) to Escherichia coli O157:H7 (E. coli) than E. coli-specific antibodies and aptamers. The dex-TMDs can effectively detect a single copy of E. coli based on their Raman signal. The detection of pathogenic microorganisms is key consideration for safety across a wide range of fields. Here, the authors report on the simultaneous exfoliation and functionalisation of transition metal dichalcogenides with dextran for antibody-free detection of pathogenic Escherichia coli.
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Affiliation(s)
- Tae Woog Kang
- Department of Chemical Engineering, Hanyang University, Ansan, 426-791, Republic of Korea
| | - Juhee Han
- Department of Chemical Engineering, Hanyang University, Ansan, 426-791, Republic of Korea
| | - Sin Lee
- Department of Chemical Engineering, Hanyang University, Ansan, 426-791, Republic of Korea
| | - In-Jun Hwang
- Department of Chemical Engineering, Hanyang University, Ansan, 426-791, Republic of Korea
| | - Su-Ji Jeon
- Department of Chemical Engineering, Hanyang University, Ansan, 426-791, Republic of Korea
| | - Jong-Min Ju
- Department of Chemical Engineering, Hanyang University, Ansan, 426-791, Republic of Korea
| | - Man-Jin Kim
- Department of Chemical Engineering, Hanyang University, Ansan, 426-791, Republic of Korea
| | - Jin-Kyoung Yang
- Department of Chemical Engineering, Hanyang University, Ansan, 426-791, Republic of Korea
| | - Byoengsun Jun
- Department of Chemical and Molecular Engineering, Hanyang University, Ansan, 426-791, Republic of Korea
| | - Chi Ho Lee
- Department of Chemical and Molecular Engineering, Hanyang University, Ansan, 426-791, Republic of Korea
| | - Sang Uck Lee
- Department of Chemical and Molecular Engineering, Hanyang University, Ansan, 426-791, Republic of Korea.
| | - Jong-Ho Kim
- Department of Chemical Engineering, Hanyang University, Ansan, 426-791, Republic of Korea.
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8
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Hunt D, Figley C, Manage DP, Lauzon J, Figley R, Pilarski LM, McMullen LM, Pilarski PM. Monitoring food pathogens: Novel instrumentation for cassette PCR testing. PLoS One 2018; 13:e0197100. [PMID: 29746561 PMCID: PMC5945031 DOI: 10.1371/journal.pone.0197100] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2017] [Accepted: 04/26/2018] [Indexed: 01/13/2023] Open
Abstract
In this manuscript, we report the design and development of a fast, reliable instrument to run gel-based cassette polymerase chain reactions (PCR). Here termed the GelCycler Mark II, our instrument is a miniaturized molecular testing system that is fast, low cost and sensitive. Cassette PCR utilizes capillary reaction units that carry all reagents needed for PCR, including primers and Taq polymerase, except the sample, which is loaded at the time of testing. Cassette PCR carries out real time quantitative PCR followed by melt curve analysis (MCA) to verify amplicon identity at the expected melt temperature (Tm). The cassette PCR technology is well developed, particularly for detecting pathogens, and has been rigorously validated for detecting pathogenic Escherichia coli in meat samples. However, the work has been hindered by the lack of a robust and stable instrument to carry out the PCR, which requires fast and accurate temperature regulation, improved light delivery and fluorescent recording, and faster PCR reactions that maintain a high sensitivity of detection. Here, we report design and testing of a new instrument to address these shortcomings and to enable standardized testing by cassette PCR and commercial manufacture of a robust and accurate instrument that can be mass produced to deliver consistent performance. As a corollary to our new instrument development, we also report the use of an improved design approach using a machined aluminum cassette to meet the new instrument standards, prevent any light bleed across different trenches in each cassette, and allow testing of a larger number of samples for more targets in a single run. The GelCycler Mark II can detect and report E. coli contamination in 41 minutes. Sample positives are defined in as having a melt curve comparable to the internal positive control, with peak height exceeding that of the internal negative control. In a fractional analysis, as little as 1 bacterium per capillary reaction unit is directly detectable, with no enrichment step, in 35 cycles of PCR/MCA, in a total time of 53 minutes, making this instrument and technology among the very best for speed and sensitivity in screening food for pathogenic contamination.
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Affiliation(s)
- Darin Hunt
- CBF Systems Inc., College Plaza, Edmonton, AB, Canada
| | - Curtis Figley
- CBF Systems Inc., College Plaza, Edmonton, AB, Canada
| | - Dammika P. Manage
- Department of Oncology, University of Alberta and Cross Cancer Institute, Edmonton, AB, Canada
| | - Jana Lauzon
- Department of Oncology, University of Alberta and Cross Cancer Institute, Edmonton, AB, Canada
| | - Rachel Figley
- CBF Systems Inc., College Plaza, Edmonton, AB, Canada
| | - Linda M. Pilarski
- Department of Oncology, University of Alberta and Cross Cancer Institute, Edmonton, AB, Canada
| | - Lynn M. McMullen
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB, Canada
| | - Patrick M. Pilarski
- Division of Physical Medicine & Rehabilitation, Department of Medicine, University of Alberta, 5–005 Katz Group Centre for Pharmacy and Health Research, Edmonton, AB, Canada
- * E-mail:
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9
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Choi W, Yeom SY, Kim J, Jung S, Jung S, Shim TS, Kim SK, Kang JY, Lee SH, Cho IJ, Choi J, Choi N. Hydrogel micropost-based qPCR for multiplex detection of miRNAs associated with Alzheimer's disease. Biosens Bioelectron 2018; 101:235-244. [DOI: 10.1016/j.bios.2017.10.039] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2017] [Revised: 10/14/2017] [Accepted: 10/16/2017] [Indexed: 12/19/2022]
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10
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Multiplex real-time PCR using temperature sensitive primer-supplying hydrogel particles and its application for malaria species identification. PLoS One 2018; 13:e0190451. [PMID: 29293604 PMCID: PMC5749795 DOI: 10.1371/journal.pone.0190451] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2017] [Accepted: 12/14/2017] [Indexed: 11/19/2022] Open
Abstract
Real-time PCR, also called quantitative PCR (qPCR), has been powerful analytical tool for detection of nucleic acids since it developed. Not only for biological research but also for diagnostic needs, qPCR technique requires capacity to detect multiple genes in recent years. Solid phase PCR (SP-PCR) where one or two directional primers are immobilized on solid substrates could analyze multiplex genetic targets. However, conventional SP-PCR was subjected to restriction of application for lack of PCR efficiency and quantitative resolution. Here we introduce an advanced qPCR with primer-incorporated network (PIN). One directional primers are immobilized in the porous hydrogel particle by covalent bond and the other direction of primers are temporarily immobilized at so-called 'Supplimers'. Supplimers released the primers to aqueous phase in the hydrogel at the thermal cycling of PCR. It induced the high PCR efficiency over 92% with high reliability. It reduced the formation of primer dimers and improved the selectivity of qPCR thanks to the strategy of 'right primers supplied to right place only'. By conducting a six-plex qPCR of 30 minutes, we analyzed DNA samples originated from malaria patients and successfully identified malaria species in a single reaction.
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11
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Kumar Y, Bansal S, Jaiswal P. Loop-Mediated Isothermal Amplification (LAMP): A Rapid and Sensitive Tool for Quality Assessment of Meat Products. Compr Rev Food Sci Food Saf 2017; 16:1359-1378. [DOI: 10.1111/1541-4337.12309] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2017] [Revised: 08/16/2017] [Accepted: 08/16/2017] [Indexed: 12/15/2022]
Affiliation(s)
- Yogesh Kumar
- ICAR-Central Inst. of Post-Harvest Engineering and Technology (CIPHET); Ludhiana India
| | - Sangita Bansal
- ICAR-Central Inst. of Post-Harvest Engineering and Technology (CIPHET); Ludhiana India
| | - Pranita Jaiswal
- ICAR-Central Inst. of Post-Harvest Engineering and Technology (CIPHET); Ludhiana India
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12
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Pandey A, Gurbuz Y, Ozguz V, Niazi JH, Qureshi A. Graphene-interfaced electrical biosensor for label-free and sensitive detection of foodborne pathogenic E. coli O157:H7. Biosens Bioelectron 2016; 91:225-231. [PMID: 28012318 DOI: 10.1016/j.bios.2016.12.041] [Citation(s) in RCA: 71] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2016] [Revised: 12/01/2016] [Accepted: 12/15/2016] [Indexed: 01/07/2023]
Abstract
E. coli O157:H7 is an enterohemorrhagic bacteria responsible for serious foodborne outbreaks that causes diarrhoea, fever and vomiting in humans. Recent foodborne E. coli outbreaks has left a serious concern to public health. Therefore, there is an increasing demand for a simple, rapid and sensitive method for pathogen detection in contaminated foods. In this study, we developed a label-free electrical biosensor interfaced with graphene for sensitive detection of pathogenic bacteria. This biosensor was fabricated by interfacing graphene with interdigitated microelectrodes of capacitors that were biofunctionalized with E. coli O157:H7 specific antibodies for sensitive pathogenic bacteria detection. Here, graphene nanostructures on the sensor surface provided superior chemical properties such as high carrier mobility and biocompatibility with antibodies and bacteria. The sensors transduced the signal based on changes in dielectric properties (capacitance) through (i) polarization of captured cell-surface charges, (ii) cells' internal bioactivity, (iii) cell-wall's electronegativity or dipole moment and their relaxation and (iv) charge carrier mobility of graphene that modulated the electrical properties once the pathogenic E. coli O157:H7 captured on the sensor surface. Sensitive capacitance changes thus observed with graphene based capacitors were specific to E. coli O157:H7 strain with a sensitivity as low as 10-100 cells/ml. The proposed graphene based electrical biosensor provided advantages of speed, sensitivity, specificity and in-situ bacterial detection with no chemical mediators, represents a versatile approach for detection of a wide variety of other pathogens.
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Affiliation(s)
- Ashish Pandey
- Sabanci University Nanotechnology Research and Application Center, Orta Mah., 34956 Istanbul, Turkey
| | - Yasar Gurbuz
- Faculty of Engineering and Natural Science, Sabanci University, Orhanli, Tuzla, 34956 Istanbul, Turkey
| | - Volkan Ozguz
- Sabanci University Nanotechnology Research and Application Center, Orta Mah., 34956 Istanbul, Turkey
| | - Javed H Niazi
- Sabanci University Nanotechnology Research and Application Center, Orta Mah., 34956 Istanbul, Turkey.
| | - Anjum Qureshi
- Sabanci University Nanotechnology Research and Application Center, Orta Mah., 34956 Istanbul, Turkey.
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13
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Ahmad F, Stedtfeld RD, Waseem H, Williams MR, Cupples AM, Tiedje JM, Hashsham SA. Most probable number - loop mediated isothermal amplification (MPN-LAMP) for quantifying waterborne pathogens in <25min. J Microbiol Methods 2016; 132:27-33. [PMID: 27856278 DOI: 10.1016/j.mimet.2016.11.010] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2016] [Revised: 11/12/2016] [Accepted: 11/12/2016] [Indexed: 01/20/2023]
Abstract
We are reporting a most probable number approach integrated to loop mediated isothermal technique (MPN-LAMP) focusing on Gram-negative Escherichia coli and Gram-positive Enterococcus faecalis bacterial cells without nucleic acids extraction. LAMP assays for uidA from E. coli and gelE from E. faecalis were successfully performed directly on cells up to single digit concentration using a commercial real time PCR instrument. Threshold time values of LAMP assays of bacterial cells, heat treated bacterial cells (95°C for 5min), and their purified genomic DNA templates were similar, implying that amplification could be achieved directly from bacterial cells at 63°C. Viability of bacterial cells was confirmed by using propidium monoazide in a LAMP assay with E. faecalis. To check its functionality on a microfluidic platform, MPN-LAMP assays targeting <10CFU of bacteria were also translated onto polymeric microchips and monitored by a low-cost fluorescence imaging system. The overall system provided signal-to-noise (SNR) ratios up to 800, analytical sensitivity of <10CFU, and time to positivity of about 20min. MPN-LAMP assays were performed for cell concentrations in the range of 105CFU to <10CFU. MPN values from LAMP assays confirmed that the amplifications were from <10CFU. The method described here, applicable directly on cells at 63°C, eliminates the requirement of complex nucleic acids extraction steps, facilitating the development of sensitive, rapid, low-cost, and field-deployable systems. This rapid MPN-LAMP approach has the potential to replace conventional MPN method for waterborne pathogens.
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Affiliation(s)
- Farhan Ahmad
- Department of Civil and Environmental Engineering, Michigan State University, East Lansing, MI 48824, USA
| | - Robert D Stedtfeld
- Department of Civil and Environmental Engineering, Michigan State University, East Lansing, MI 48824, USA
| | - Hassan Waseem
- Department of Civil and Environmental Engineering, Michigan State University, East Lansing, MI 48824, USA
| | - Maggie R Williams
- Department of Civil and Environmental Engineering, Michigan State University, East Lansing, MI 48824, USA
| | - Alison M Cupples
- Department of Civil and Environmental Engineering, Michigan State University, East Lansing, MI 48824, USA
| | - James M Tiedje
- The Center for Microbial Ecology, Michigan State University, East Lansing, MI 48824, USA; Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI 48824, USA
| | - Syed A Hashsham
- Department of Civil and Environmental Engineering, Michigan State University, East Lansing, MI 48824, USA; The Center for Microbial Ecology, Michigan State University, East Lansing, MI 48824, USA.
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14
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Beyer A, Pollok S, Rudloff A, Cialla-May D, Weber K, Popp J. Fast-Track, One-Step E. coli
Detection: A Miniaturized Hydrogel Array Permits Specific Direct PCR and DNA Hybridization while Amplification. Macromol Biosci 2016; 16:1325-33. [DOI: 10.1002/mabi.201600098] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2016] [Revised: 05/03/2016] [Indexed: 12/18/2022]
Affiliation(s)
- Antje Beyer
- Leibniz-Institute of Photonic Technology; Jenaer BioChip Initiative; Albert-Einstein-Strasse 9 07745 Jena Germany
- Friedrich Schiller University Jena; Institute of Physical Chemistry and Abbe Centre of Photonics; Helmholtzweg 4 07743 Jena Germany
- InfectoGnostics Forschungscampus Jena; Zentrum für Angewandte Forschung; Philosophenweg 7 07743 Jena Germany
| | - Sibyll Pollok
- Leibniz-Institute of Photonic Technology; Jenaer BioChip Initiative; Albert-Einstein-Strasse 9 07745 Jena Germany
- InfectoGnostics Forschungscampus Jena; Zentrum für Angewandte Forschung; Philosophenweg 7 07743 Jena Germany
- Ernst-Abbe-Hochschule Jena; University of Applied Sciences; Carl-Zeiss-Promenade 2 07745 Jena Germany
| | - Anne Rudloff
- Leibniz-Institute of Photonic Technology; Jenaer BioChip Initiative; Albert-Einstein-Strasse 9 07745 Jena Germany
- InfectoGnostics Forschungscampus Jena; Zentrum für Angewandte Forschung; Philosophenweg 7 07743 Jena Germany
| | - Dana Cialla-May
- Leibniz-Institute of Photonic Technology; Jenaer BioChip Initiative; Albert-Einstein-Strasse 9 07745 Jena Germany
- Friedrich Schiller University Jena; Institute of Physical Chemistry and Abbe Centre of Photonics; Helmholtzweg 4 07743 Jena Germany
- InfectoGnostics Forschungscampus Jena; Zentrum für Angewandte Forschung; Philosophenweg 7 07743 Jena Germany
| | - Karina Weber
- Leibniz-Institute of Photonic Technology; Jenaer BioChip Initiative; Albert-Einstein-Strasse 9 07745 Jena Germany
- Friedrich Schiller University Jena; Institute of Physical Chemistry and Abbe Centre of Photonics; Helmholtzweg 4 07743 Jena Germany
- InfectoGnostics Forschungscampus Jena; Zentrum für Angewandte Forschung; Philosophenweg 7 07743 Jena Germany
| | - Jürgen Popp
- Leibniz-Institute of Photonic Technology; Jenaer BioChip Initiative; Albert-Einstein-Strasse 9 07745 Jena Germany
- Friedrich Schiller University Jena; Institute of Physical Chemistry and Abbe Centre of Photonics; Helmholtzweg 4 07743 Jena Germany
- InfectoGnostics Forschungscampus Jena; Zentrum für Angewandte Forschung; Philosophenweg 7 07743 Jena Germany
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Extensible Multiplex Real-time PCR of MicroRNA Using Microparticles. Sci Rep 2016; 6:22975. [PMID: 26964639 PMCID: PMC4786821 DOI: 10.1038/srep22975] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2015] [Accepted: 02/23/2016] [Indexed: 01/08/2023] Open
Abstract
Multiplex quantitative real-time PCR (qPCR), which measures multiple DNAs in a given sample, has received significant attention as a mean of verifying the rapidly increasing genetic targets of interest in single phenotype. Here we suggest a readily extensible qPCR for the expression analysis of multiple microRNA (miRNA) targets using microparticles of primer-immobilized networks as discrete reactors. Individual particles, 200~500 μm in diameter, are identified by two-dimensional codes engraved into the particles and the non-fluorescent encoding allows high-fidelity acquisition of signal in real-time PCR. During the course of PCR, the amplicons accumulate in the volume of the particles with high reliability and amplification efficiency over 95%. In a quick assay comprising of tens of particles holding different primers, each particle brings the independent real-time amplification curve representing the quantitative information of each target. Limited amount of sample was analyzed simultaneously in single chamber through this highly multiplexed qPCR; 10 kinds of miRNAs from purified extracellular vesicles (EVs).
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16
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Taylor BJ, Howell A, Martin KA, Manage DP, Gordy W, Campbell SD, Lam S, Jin A, Polley SD, Samuel RA, Atrazhev A, Stickel AJ, Birungi J, Mbonye AK, Pilarski LM, Acker JP, Yanow SK. A lab-on-chip for malaria diagnosis and surveillance. Malar J 2014; 13:179. [PMID: 24885206 PMCID: PMC4029813 DOI: 10.1186/1475-2875-13-179] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2014] [Accepted: 05/01/2014] [Indexed: 12/03/2022] Open
Abstract
Background Access to timely and accurate diagnostic tests has a significant impact in the management of diseases of global concern such as malaria. While molecular diagnostics satisfy this need effectively in developed countries, barriers in technology, reagent storage, cost and expertise have hampered the introduction of these methods in developing countries. In this study a simple, lab-on-chip PCR diagnostic was created for malaria that overcomes these challenges. Methods The platform consists of a disposable plastic chip and a low-cost, portable, real-time PCR machine. The chip contains a desiccated hydrogel with reagents needed for Plasmodium specific PCR. Chips can be stored at room temperature and used on demand by rehydrating the gel with unprocessed blood, avoiding the need for sample preparation. These chips were run on a custom-built instrument containing a Peltier element for thermal cycling and a laser/camera setup for amplicon detection. Results This diagnostic was capable of detecting all Plasmodium species with a limit of detection for Plasmodium falciparum of 2 parasites/μL of blood. This exceeds the sensitivity of microscopy, the current standard for diagnosis in the field, by ten to fifty-fold. In a blind panel of 188 patient samples from a hyper-endemic region of malaria transmission in Uganda, the diagnostic had high sensitivity (97.4%) and specificity (93.8%) versus conventional real-time PCR. The test also distinguished the two most prevalent malaria species in mixed infections, P. falciparum and Plasmodium vivax. A second blind panel of 38 patient samples was tested on a streamlined instrument with LED-based excitation, achieving a sensitivity of 96.7% and a specificity of 100%. Conclusions These results describe the development of a lab-on-chip PCR diagnostic from initial concept to ready-for-manufacture design. This platform will be useful in front-line malaria diagnosis, elimination programmes, and clinical trials. Furthermore, test chips can be adapted to detect other pathogens for a differential diagnosis in the field. The flexibility, reliability, and robustness of this technology hold much promise for its use as a novel molecular diagnostic platform in developing countries.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - Stephanie K Yanow
- School of Public Health, University of Alberta, WMC 2B4,59, 8440 - 112th Street, Edmonton, AB, Canada.
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17
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Srinivas RL, Johnson SD, Doyle PS. Oil-isolated hydrogel microstructures for sensitive bioassays on-chip. Anal Chem 2013; 85:12099-107. [PMID: 24237051 DOI: 10.1021/ac403201p] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
Multiplexed, sensitive, and on-chip molecular diagnostic assays are essential in both clinical and research settings. In past work, running reactions in nanoliter- to femtoliter-sized volumes such as microwells or droplets has led to significant increases in detection sensitivities. At the same time, hydrogels have emerged as attractive scaffolds for bioassays due to their nonfouling, flexible, and aqueous properties. In this paper, we combine these concepts and develop a novel platform in which hydrogel compartments are used as individually confined reaction volumes within a fluorinated oil phase. We fabricate functional and versatile hydrogel microstructures in microfluidic channels that are physically isolated from each other using a surfactant-free fluorinated oil phase, generating picoliter- to nanoliter-sized immobilized aqueous reaction compartments that are readily functionalized with biomolecules. In doing so, we achieve monodisperse reaction volumes with an aqueous interior while exploiting the unique chemistry of a hydrogel, which provides a solid and porous binding scaffold for biomolecules and is impenetrable to oil. Furthermore, our lithographically defined reaction volumes are readily customized with respect to geometry and chemistry within the same channel, allowing rational tuning of the confined reaction volume on a post-to-post basis without needing to use surfactants to maintain stability. We design and implement a multiplexed signal amplification assay in which gel-bound enzymes turn over small molecule substrate into fluorescent product in the oil-confined gel compartment, providing significant signal enhancement. Using short (20 min) amplification times, the encapsulation scheme provides up to 2 orders of magnitude boost of signal in nucleic acid detection assays relative to direct labeling and does not suffer from any cross-talk between the posts. We ultimately demonstrate up to 57-fold increase in nucleic acid detection sensitivity compared to a direct labeling scheme.
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Affiliation(s)
- Rathi L Srinivas
- Department of Chemical Engineering, Massachusetts Institute of Technology , Cambridge, Massachusetts 02139, United States
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18
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Manage DP, Lauzon J, Atrazhev A, Pang X, Pilarski LM. A novel method for sample delivery and testing of whole blood: gel strip PCR for point of care (POC) molecular diagnostics. LAB ON A CHIP 2013; 13:4011-4014. [PMID: 23966268 DOI: 10.1039/c3lc50755f] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
Testing of whole blood in miniaturized PCR is compromised by the opaque nature of whole blood that leads to physical masking of a fluorescent signal. We demonstrate a method to perform real-time PCR with whole blood that avoids interference from the opacity of whole blood.
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Affiliation(s)
- Dammika P Manage
- Department of Oncology, University of Alberta and Cross Cancer Institute, 11560 University Avenue, Edmonton, AB T6G 1Z2, Canada.
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19
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Zuo P, Li X, Dominguez DC, Ye BC. A PDMS/paper/glass hybrid microfluidic biochip integrated with aptamer-functionalized graphene oxide nano-biosensors for one-step multiplexed pathogen detection. LAB ON A CHIP 2013; 13:3921-8. [PMID: 23929394 PMCID: PMC3913183 DOI: 10.1039/c3lc50654a] [Citation(s) in RCA: 139] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
Infectious pathogens often cause serious public health concerns throughout the world. There is an increasing demand for simple, rapid and sensitive approaches for multiplexed pathogen detection. In this paper we have developed a polydimethylsiloxane (PDMS)/paper/glass hybrid microfluidic system integrated with aptamer-functionalized graphene oxide (GO) nano-biosensors for simple, one-step, multiplexed pathogen detection. The paper substrate used in this hybrid microfluidic system facilitated the integration of aptamer biosensors on the microfluidic biochip, and avoided complicated surface treatment and aptamer probe immobilization in a PDMS or glass-only microfluidic system. Lactobacillus acidophilus was used as a bacterium model to develop the microfluidic platform with a detection limit of 11.0 cfu mL(-1). We have also successfully extended this method to the simultaneous detection of two infectious pathogens - Staphylococcus aureus and Salmonella enterica. This method is simple and fast. The one-step 'turn on' pathogen assay in a ready-to-use microfluidic device only takes ~10 min to complete on the biochip. Furthermore, this microfluidic device has great potential in rapid detection of a wide variety of different other bacterial and viral pathogens.
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Affiliation(s)
- Peng Zuo
- Department of Chemistry, University of Texas at El Paso, 500 West University Ave, El Paso, Texas, 79968, USA.
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20
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Manage DP, Lauzon J, Atrazev A, Chavali R, Samuel RA, Chan B, Morrissey YC, Gordy W, Edwards AL, Larison K, Yanow SK, Acker JP, Zahariadis G, Pilarski LM. An enclosed in-gel PCR amplification cassette with multi-target, multi-sample detection for platform molecular diagnostics. LAB ON A CHIP 2013; 13:2576-84. [PMID: 23471315 DOI: 10.1039/c3lc41419a] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
This work describes a self-contained, simple, disposable, and inexpensive gel capillary cassette for DNA amplification in near point of care settings. The cassette avoids the need for pumps or valves during raw sample delivery or polymerase chain reaction (PCR) amplification steps. The cassette contains capillary reaction units that can be stored at room temperature for up to 3 months. The current cassette configuration format simultaneously tests up to 16 patients for two or more targets, accommodates different sample types on the same cassette, has integrated positive and negative controls and allows flexibility for multiple geometries. PCR reagents in the cassette are desiccated to allow storage at room temperature with rehydration by raw sample at the time of testing. The sample is introduced to the cassette via a transfer pipette simply by capillary force. DNA amplification was carried out in a portable prototype instrument for PCR thermal cycling with fluorescence detection of amplified products by melt curve analysis (MCA). To demonstrate performance, raw genital swabs and urine were introduced to the same cassette to simultaneously detect four sexually transmitted infections. Herpes Simplex Viruses (HSV-1 and HSV-2) were detected from raw genital swabs. Ureaplasma urealyticum (UU) and Mycoplasma homonis (MH) were detected from raw urine. Results for multiple patients were obtained in as little as 50 min. This platform allows multiparameter clinical testing with a pre-assembled cassette that requires only the introduction of raw sample. Modification of the prototype device to accommodate larger cassettes will ultimately provide high throughput simultaneous testing of even larger numbers of samples for many different targets, as is required for some clinical applications. Combinations of wax and/or polymer cassettes holding capillary reaction units are feasible. The components of the cassette are suited to mass production and robotic assembly to produce a readily manufactured disposable reaction cassette that can be configured for disease-specific testing panels. Rapid testing with a disposable reaction cassette on an inexpensive instrument will enable on the spot evaluation of patients in the clinic for faster medical decision-making and more informed therapeutic choices.
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Affiliation(s)
- Dammika P Manage
- Department of Oncology, University of Alberta, 11560 University Avenue, Edmonton, AB T6G 1Z2, Canada
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21
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Manage DP, Lauzon J, Atrazhev A, Morrissey YC, Edwards AL, Stickel AJ, Crabtree HJ, Pabbaraju K, Zahariadis G, Yanow SK, Pilarski LM. A miniaturized and integrated gel post platform for multiparameter PCR detection of herpes simplex viruses from raw genital swabs. LAB ON A CHIP 2012; 12:1664-1671. [PMID: 22426784 DOI: 10.1039/c2lc40061h] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
Herpes simplex virus (HSV) is one of the most prevalent viruses, with acute and recurrent infections in humans. The current gold standard for the diagnosis of HSV is viral culture which takes 2-14 days and has low sensitivity. In contrast, DNA amplification by polymerase chain reaction (PCR) can be performed within 1-2 h. We here describe a multiparameter PCR assay to simultaneously detect HSV-1 and HSV-2 DNA templates, together with integrated positive and negative controls, with product detection by melting curve analysis (MCA), in an array of semi-solid polyacrylamide gel posts. Each gel post is 0.67 μL in volume, and polymerized with all the components required for PCR. Both PCR and MCA can currently be performed in one hour and 20 min. Unprocessed genital swabs collected in universal transport medium were directly added to the reagents before or after polymerization, diffusing from atop the gel posts. The gel post platform detects HSV templates in as little as 2.5 nL of raw sample. In this study, 45 genital swab specimens were tested blindly as a preliminary validation of this platform. The concordance of PCR on gel posts with conventional PCR was 91%. The primer sequestration method introduced here (wherein different primers are placed in different sets of posts) enables the simultaneous detection of multiple pathogens for the same sample, together with positive and negative controls, on a single chip. This platform accepts unprocessed samples and is readily adaptable to detection of multiple different pathogens or biomarkers for point-of-care diagnostics.
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Affiliation(s)
- Dammika P Manage
- Department of Oncology, University of Alberta and Cross Cancer Institute, Edmonton, AB, Canada
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22
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Asanov A, Zepeda A, Vaca L. A platform for combined DNA and protein microarrays based on total internal reflection fluorescence. SENSORS 2012; 12:1800-15. [PMID: 22438738 PMCID: PMC3304140 DOI: 10.3390/s120201800] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/09/2011] [Revised: 01/13/2012] [Accepted: 02/02/2012] [Indexed: 11/20/2022]
Abstract
We have developed a novel microarray technology based on total internal reflection fluorescence (TIRF) in combination with DNA and protein bioassays immobilized at the TIRF surface. Unlike conventional microarrays that exhibit reduced signal-to-background ratio, require several stages of incubation, rinsing and stringency control, and measure only end-point results, our TIRF microarray technology provides several orders of magnitude better signal-to-background ratio, performs analysis rapidly in one step, and measures the entire course of association and dissociation kinetics between target DNA and protein molecules and the bioassays. In many practical cases detection of only DNA or protein markers alone does not provide the necessary accuracy for diagnosing a disease or detecting a pathogen. Here we describe TIRF microarrays that detect DNA and protein markers simultaneously, which reduces the probabilities of false responses. Supersensitive and multiplexed TIRF DNA and protein microarray technology may provide a platform for accurate diagnosis or enhanced research studies. Our TIRF microarray system can be mounted on upright or inverted microscopes or interfaced directly with CCD cameras equipped with a single objective, facilitating the development of portable devices. As proof-of-concept we applied TIRF microarrays for detecting molecular markers from Bacillus anthracis, the pathogen responsible for anthrax.
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Affiliation(s)
- Alexander Asanov
- TIRF Technologies, 951 Aviation Parkway, Suite 700, Morrisville, NC 27560, USA
- Authors to whom correspondence should be addressed; E-Mails: (A.A.); (A.Z.); Tel.: +525-5622-9215 (A.Z.); Fax: +525-5622-9182 (A.Z.)
| | - Angélica Zepeda
- Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Ciudad Universitaria, DF 04510, México
- Authors to whom correspondence should be addressed; E-Mails: (A.A.); (A.Z.); Tel.: +525-5622-9215 (A.Z.); Fax: +525-5622-9182 (A.Z.)
| | - Luis Vaca
- Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Ciudad Universitaria, DF 04510, México; E-Mail:
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Desmarais SM, Leitner T, Barron AE. Quantitative experimental determination of primer-dimer formation risk by free-solution conjugate electrophoresis. Electrophoresis 2012; 33:483-91. [PMID: 22331820 DOI: 10.1002/elps.201100452] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2011] [Revised: 10/12/2011] [Accepted: 10/13/2011] [Indexed: 11/09/2022]
Abstract
DNA barcodes are short, unique ssDNA primers that "mark" individual biomolecules. To gain better understanding of biophysical parameters constraining primer-dimer formation between primers that incorporate barcode sequences, we have developed a capillary electrophoresis method that utilizes drag-tag-DNA conjugates to quantify dimerization risk between primer-barcode pairs. Results obtained with this unique free-solution conjugate electrophoresis approach are useful as quantitatively precise input data to parameterize computation models of dimerization risk. A set of fluorescently labeled, model primer-barcode conjugates were designed with complementary regions of differing lengths to quantify heterodimerization as a function of temperature. Primer-dimer cases comprised two 30-mer primers, one of which was covalently conjugated to a lab-made, chemically synthesized poly-N-methoxyethylglycine drag-tag, which reduced electrophoretic mobility of ssDNA to distinguish it from ds primer-dimers. The drag-tags also provided a shift in mobility for the dsDNA species, which allowed us to quantitate primer-dimer formation. In the experimental studies, pairs of oligonucleotide primer barcodes with fully or partially complementary sequences were annealed, and then separated by free-solution conjugate CE at different temperatures, to assess effects on primer-dimer formation. When less than 30 out of 30 base-pairs were bonded, dimerization was inversely correlated to temperature. Dimerization occurred when more than 15 consecutive base-pairs formed, yet non-consecutive base-pairs did not create stable dimers even when 20 out of 30 possible base-pairs bonded. The use of free-solution electrophoresis in combination with a peptoid drag-tag and different fluorophores enabled precise separation of short DNA fragments to establish a new mobility shift assay for detection of primer-dimer formation.
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Affiliation(s)
- Samantha M Desmarais
- Department of Bioengineering, Stanford University, Stanford, CA 94305-5444, USA.
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24
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Natali I, Carretti E, Angelova L, Baglioni P, Weiss RG, Dei L. Structural and mechanical properties of "peelable" organoaqueous dispersions with partially hydrolyzed poly(vinyl acetate)-borate networks: applications to cleaning painted surfaces. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2011; 27:13226-13235. [PMID: 21749078 DOI: 10.1021/la2015786] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
The preparation and structural characterization of a family of viscoelastic dispersions of borate cross-linked, 80% hydrolyzed poly(vinyl acetate) (80PVAc) in aqueous-organic liquids are presented. Correlations between mechanical properties (from rheological measurements) and the degree and nature of cross-linking (from (11)B NMR spectroscopy) are reported, and the results are used to assess their potential as low-impact cleaning agents for the surfaces of paintings. Because the dispersions can be prepared at room temperature by simple procedures from readily available materials and can contain up to 50% (w/w) of an organic liquid, they offer important advantages over previously described cleaning agents that are based on fully hydrolyzed PVAc (i.e., poly(vinyl alcohol). The mechanical properties of the various aqueous-organic dispersions, as determined quantitatively by rheological investigations and qualitatively by their ease of removal from a solid surface (i.e., the so-called "peel-off" ability) have been tuned systematically by varying the amount of organic liquid, its structure, and the concentrations of borax and 80PVAc. The (11)B NMR studies demonstrate that the concentration of borate ions actively participating in cross-linking increases significantly with the amount of organic liquid in the mixture. The degree of cross-linking remains constant when the 80PVAc and borax concentrations are varied, as long as their ratios are kept constant. Some of the 80PVAc-borax dispersions have been tested successfully as cleaning agents on the surface of a 16th-17th century oil-on-wood painting by Lodovico Cardi, "Il Cigoli", that was covered by a brown patina and on the surface of a Renaissance wall painting by Vecchietta in Santa Maria della Scala, Siena, Italy, that had a degraded polyacrylate coating from a previous conservation treatment.
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Affiliation(s)
- Irene Natali
- Department of Chemistry Ugo Schiff & CSGI Consortium, University of Florence, via della Lastruccia, 3-50019 Sesto Fiorentino, Italy
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Taylor BJ, Martin KA, Arango E, Agudelo OM, Maestre A, Yanow SK. Real-time PCR detection of Plasmodium directly from whole blood and filter paper samples. Malar J 2011; 10:244. [PMID: 21851640 PMCID: PMC3171379 DOI: 10.1186/1475-2875-10-244] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2011] [Accepted: 08/19/2011] [Indexed: 11/18/2022] Open
Abstract
Background Real-time PCR is a sensitive and specific method for the analysis of Plasmodium DNA. However, prior purification of genomic DNA from blood is necessary since PCR inhibitors and quenching of fluorophores from blood prevent efficient amplification and detection of PCR products. Methods Reagents designed to specifically overcome PCR inhibition and quenching of fluorescence were evaluated for real-time PCR amplification of Plasmodium DNA directly from blood. Whole blood from clinical samples and dried blood spots collected in the field in Colombia were tested. Results Amplification and fluorescence detection by real-time PCR were optimal with 40× SYBR® Green dye and 5% blood volume in the PCR reaction. Plasmodium DNA was detected directly from both whole blood and dried blood spots from clinical samples. The sensitivity and specificity ranged from 93-100% compared with PCR performed on purified Plasmodium DNA. Conclusions The methodology described facilitates high-throughput testing of blood samples collected in the field by fluorescence-based real-time PCR. This method can be applied to a broad range of clinical studies with the advantages of immediate sample testing, lower experimental costs and time-savings.
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Affiliation(s)
- Brian J Taylor
- Department of Oncology, University of Alberta, Edmonton, Canada
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