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Devika PP, Alex S, Soni KB, Sindura KP, Ayisha R, Manju RV. Nano-PCR for the early detection of tomato leaf curl virus. 3 Biotech 2024; 14:5. [PMID: 38074290 PMCID: PMC10700262 DOI: 10.1007/s13205-023-03842-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2023] [Accepted: 11/02/2023] [Indexed: 01/19/2024] Open
Abstract
Nano-PCR is a potential tool for the early detection of plant viruses. In the current study, different concentrations of silver nanoparticles (20 nm) and magnesium oxide nanoparticles (50 nm) were included in the PCR mixture to improve the sensitivity of PCR for the detection of tomato leaf curl virus. The inclusion of nanoparticles in single or combination in PCR mixture has resulted in improvement of PCR sensitivity. Four-fold improvement was exhibited by the inclusion of 3 ng/µL silver nanoparticles, whereas the combination of silver and magnesium oxide nanoparticles (3 ng/µL and 200 ng/µL, respectively), resulted in a 4.5-fold improvement. The inclusion of 200 ng/µL of magnesium oxide nanoparticles in the PCR mixture exhibited a 7.6-fold increase in PCR sensitivity. Replacement of magnesium chloride with a combination of silver and magnesium oxide nanoparticles (3 ng/µL and 275 ng/µL, respectively) resulted in a 12-fold increase. A 13-fold improvement in PCR sensitivity was observed by the replacement of magnesium chloride in PCR buffer with 275 ng/µL of magnesium oxide nanoparticles. This could also produce detectable amplicon in PCR with a minimum of 25 cycles, resulting in a 26.5% reduction in the duration of PCR. This is the first report on the use of magnesium oxide nanoparticles in PCR for the early detection and better management of tomato leaf curl virus. Supplementary Information The online version contains supplementary material available at 10.1007/s13205-023-03842-2.
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Affiliation(s)
- P. P. Devika
- Department of Molecular Biology and Biotechnology, College of Agriculture, Vellayani, Kerala Agricultural University, Thiruvananthapuram, Kerala 695522 India
| | - Swapna Alex
- Department of Molecular Biology and Biotechnology, College of Agriculture, Vellayani, Kerala Agricultural University, Thiruvananthapuram, Kerala 695522 India
| | - K. B. Soni
- Department of Molecular Biology and Biotechnology, College of Agriculture, Vellayani, Kerala Agricultural University, Thiruvananthapuram, Kerala 695522 India
| | - K. P. Sindura
- Department of Molecular Biology and Biotechnology, College of Agriculture, Vellayani, Kerala Agricultural University, Thiruvananthapuram, Kerala 695522 India
| | - R. Ayisha
- Department of Plant Pathology, College of Agriculture, Vellanikkara, Kerala Agricultural University, Thrissur, Kerala 680656 India
| | - R. V. Manju
- Department of Plant Physiology, College of Agriculture, Vellayani, Kerala Agricultural University, Thiruvananthapuram, Kerala 695522 India
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Azzopardi M, Chong YJ, Ng B, Recchioni A, Logeswaran A, Ting DSJ. Diagnosis of Acanthamoeba Keratitis: Past, Present and Future. Diagnostics (Basel) 2023; 13:2655. [PMID: 37627913 PMCID: PMC10453105 DOI: 10.3390/diagnostics13162655] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2023] [Revised: 08/04/2023] [Accepted: 08/09/2023] [Indexed: 08/27/2023] Open
Abstract
Acanthamoeba keratitis (AK) is a painful and sight-threatening parasitic corneal infection. In recent years, the incidence of AK has increased. Timely and accurate diagnosis is crucial during the management of AK, as delayed diagnosis often results in poor clinical outcomes. Currently, AK diagnosis is primarily achieved through a combination of clinical suspicion, microbiological investigations and corneal imaging. Historically, corneal scraping for microbiological culture has been considered to be the gold standard. Despite its technical ease, accessibility and cost-effectiveness, the long diagnostic turnaround time and variably low sensitivity of microbiological culture limit its use as a sole diagnostic test for AK in clinical practice. In this review, we aim to provide a comprehensive overview of the diagnostic modalities that are currently used to diagnose AK, including microscopy with staining, culture, corneal biopsy, in vivo confocal microscopy, polymerase chain reaction and anterior segment optical coherence tomography. We also highlight emerging techniques, such as next-generation sequencing and artificial intelligence-assisted models, which have the potential to transform the diagnostic landscape of AK.
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Affiliation(s)
- Matthew Azzopardi
- Department of Ophthalmology, Royal London Hospital, London E1 1BB, UK;
| | - Yu Jeat Chong
- Birmingham and Midland Eye Centre, Birmingham B18 7QH, UK; (B.N.); (A.R.)
| | - Benjamin Ng
- Birmingham and Midland Eye Centre, Birmingham B18 7QH, UK; (B.N.); (A.R.)
| | - Alberto Recchioni
- Birmingham and Midland Eye Centre, Birmingham B18 7QH, UK; (B.N.); (A.R.)
- Academic Unit of Ophthalmology, Institute of Inflammation and Ageing, University of Birmingham, Birmingham B15 2TT, UK
| | | | - Darren S. J. Ting
- Birmingham and Midland Eye Centre, Birmingham B18 7QH, UK; (B.N.); (A.R.)
- Academic Unit of Ophthalmology, Institute of Inflammation and Ageing, University of Birmingham, Birmingham B15 2TT, UK
- Academic Ophthalmology, School of Medicine, University of Nottingham, Nottingham NG7 2RD, UK
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Khnouf R, Al Shami F, Albiss BA, Salem N, Ababneh H, Mahasneh A. Enhancement of Salmonella Enteritidis Detection Using Nanoparticle-Assisted Real-Time Polymerase Chain Reaction. J Biomed Nanotechnol 2022. [DOI: 10.1166/jbn.2022.3401] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Improved; fast; and specific detection of pathogens has always been of great importance; more so with the increase of human population and human interaction. In this work we investigate the application of metal oxide nanoparticles (ZnO; Fe2O3; and TiO2)
in the detection of the pathogen Salmonella enteritidis using real-time quantitative PCR (qPCR). The nanoparticles were synthesized and characterized; and then they were added at different concentrations to qPCR for Salmonella enteritidis detection. qPCR provides numerical data such
as threshold cycle (Ct); efficiency; and DNA yield which make comparing the different tested conditions easier and more accurate. It has been observed that adding all three types of NPs at an optimum concentration 4×10−11 M for ZnO NPs, and 4×10−9
for Fe2O3 and TiO2 nanoparticles has led to increasing the efficiency of the reaction to 100% and to lowering the threshold cycle value by up to 6.6 for ZnO nanoparticles; hence increasing the DNA yield of the reaction; and lowering the detection time of the
pathogen by up to 50%.
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Affiliation(s)
- Ruba Khnouf
- Department of Biomedical Engineering, Jordan University of Science and Technology, Irbid, 22110, Jordan
| | - Farah Al Shami
- Department of Applied Biological Sciences, Jordan University of Science and Technology, Irbid, 22110, Jordan
| | - Borhan A. Albiss
- Department of Applied Physics, Jordan University of Science and Technology, Irbid, 22110, Jordan
| | - Nida’ Salem
- Department of Plant Protection, The University of Jordan, Amman, 11942, Jordan
| | - Haneen Ababneh
- Department of Applied Biological Sciences, Jordan University of Science and Technology, Irbid, 22110, Jordan
| | - Amjad Mahasneh
- Department of Applied Biological Sciences, Jordan University of Science and Technology, Irbid, 22110, Jordan
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Wang L, He K, Sadak O, Wang X, Wang Q, Xu X. Visual detection of in vitro nucleic acid replication by submicro- and nano-sized materials. Biosens Bioelectron 2020; 169:112602. [PMID: 32947078 DOI: 10.1016/j.bios.2020.112602] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Revised: 08/29/2020] [Accepted: 09/06/2020] [Indexed: 12/15/2022]
Abstract
The rapid growth of in vitro nucleic acid replication has offered a powerful tool for clinical diagnosis, food safety detection and environmental monitorning. Successful implementation of various isothermal nucleic acid amplification methods enables rapid replication of target sequences without the participant of a thermal cycler. Point-of-need analysis possesses great superiorities in user-friendly, instant results analysis, low manufacturing, and consumable costs. To meet the great challenge of point-of-need analysis, developing simple and rapid visual methods becomes crucial. Submicro- and nanomaterials possess unique surface properties, which enables their rapid response to DNA amplicons. Their unique optical, magnetic, catalytic, and other physical/chemical properties have been frequently employed for the visual detection of in vitro nucleic acid replications. Herein, we aim to review the submicro- and nanomaterials-based visual methods for detection of nucleic acid amplification. The visual methods are classified according to the designing strategies (e.g. LSPR, bridging flocculation, luminescence, catalytic reaction, separation, etc.). The basic principles, merits and drawbacks of each strategy are described. The application in analysis of nucleic acid targets and non-nucleic acid targets are discussed. The main challenges and future research directions are also highlighted in this rapidly emerging field.
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Affiliation(s)
- Liu Wang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Quality and Standard for Agro-products, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, China
| | - Kaiyu He
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Quality and Standard for Agro-products, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, China
| | - Omer Sadak
- Department of Electrical and Electronics Engineering, Ardahan University, 75000, Turkey
| | - Xinquan Wang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Quality and Standard for Agro-products, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, China.
| | - Qiang Wang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Quality and Standard for Agro-products, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, China
| | - Xiahong Xu
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Quality and Standard for Agro-products, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, China.
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Rasheed AK, Siddiqui R, Ahmed SMK, Gabriel S, Jalal MZ, John A, Khan NA. hBN Nanoparticle-Assisted Rapid Thermal Cycling for the Detection of Acanthamoeba. Pathogens 2020; 9:pathogens9100824. [PMID: 33036480 PMCID: PMC7601326 DOI: 10.3390/pathogens9100824] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2020] [Revised: 10/02/2020] [Accepted: 10/03/2020] [Indexed: 11/16/2022] Open
Abstract
Acanthamoeba are widely distributed in the environment and are known to cause blinding keratitis and brain infections with greater than 90% mortality rate. Currently, polymerase chain reaction (PCR) is a highly sensitive and promising technique in Acanthamoeba detection. Remarkably, the rate of heating-cooling and convective heat transfer of the PCR tube is limited by low thermal conductivity of the reagents mixture. The addition of nanoparticles to the reaction has been an interesting approach that could augment the thermal conductivity of the mixture and subsequently enhance heat transfer through the PCR tube. Here, we have developed hexagonal boron nitride (hBN) nanoparticle-based PCR assay for the rapid detection of Acanthamoeba to amplify DNA from low amoeba cell density. As low as 1 × 10-4 wt % was determined as the optimum concentration of hBN nanoparticles, which increased Acanthamoeba DNA yield up to ~16%. Further, it was able to reduce PCR temperature that led to a ~2.0-fold increase in Acanthamoeba DNA yield at an improved PCR specificity at 46.2 °C low annealing temperature. hBN nanoparticles further reduced standard PCR step time by 10 min and cycles by eight; thus, enhancing Acanthamoeba detection rapidly. Enhancement of Acanthamoeba PCR DNA yield is possibly due to the high adsorption affinity of hBN nanoparticles to purine (Guanine-G) due to the higher thermal conductivity achieved in the PCR mixture due to the addition of hBN. Although further research is needed to demonstrate these findings in clinical application, we propose that the interfacial layers, Brownian motion, and percolation network contribute to the enhanced thermal conductivity effect.
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Affiliation(s)
- Abdul Khaliq Rasheed
- Department of New Energy Science and Engineering, School of Energy and Chemical Engineering, Xiamen University Malaysia Campus, Bandar Sunsuria, Sepang 43900, Malaysia;
| | - Ruqaiyyah Siddiqui
- Department of Biology, Chemistry and Environmental Sciences, College of Arts and Sciences, American University of Sharjah, Sharjah 26666, UAE;
| | - Salma Mohammed Kabir Ahmed
- Department of Biological Sciences, School of Science and Technology, Sunway University, Bandar Sunway 47500, Malaysia; (S.M.K.A.); (S.G.)
| | - Shobana Gabriel
- Department of Biological Sciences, School of Science and Technology, Sunway University, Bandar Sunway 47500, Malaysia; (S.M.K.A.); (S.G.)
| | - Mohammed Zayan Jalal
- Department of Mechanical Engineering, Faculty of Engineering, International Islamic University Malaysia, Jalan Gombak 53100, Malaysia;
| | - Akbar John
- Institute of Oceanography and Maritime Studies, Kulliyyah of Science, International Islamic University Malaysia, Kuantan 25200, Malaysia;
| | - Naveed Ahmed Khan
- Department of Biology, Chemistry and Environmental Sciences, College of Arts and Sciences, American University of Sharjah, Sharjah 26666, UAE;
- Correspondence: ; Tel.: +971-6515-4752
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Kim JW, Kim M, Lee KK, Chung KH, Lee CS. Effects of Graphene Oxide-Gold Nanoparticles Nanocomposite on Highly Sensitive Foot-and-Mouth Disease Virus Detection. NANOMATERIALS 2020; 10:nano10101921. [PMID: 32993046 PMCID: PMC7601864 DOI: 10.3390/nano10101921] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/02/2020] [Revised: 09/21/2020] [Accepted: 09/23/2020] [Indexed: 11/29/2022]
Abstract
The polymerase chain reaction (PCR) has become a powerful molecular diagnostic technique over the past few decades, but remains somewhat impaired due to low specificity, poor sensitivity, and false positive results. Metal and carbon nanomaterials, quantum dots, and metal oxides, can improve the quality and productivity of PCR assays. Here, we describe the ability of PCR assisted with nanomaterials (nano-PCR) comprising a nanocomposite of graphene oxide (GO) and gold nanoparticles (AuNPs) for sensitive detection of the foot-and-mouth disease virus (FMDV). Graphene oxide and AuNPs have been widely applied as biomedical materials for diagnosis, therapy, and drug delivery due to their unique chemical and physical properties. Foot-and-mouth disease (FMD) is highly contagious and fatal for cloven-hoofed animals including pigs, and it can thus seriously damage the swine industry. Therefore, a highly sensitive, specific, and practical method is needed to detect FMDV. The detection limit of real-time PCR improved by ~1000 fold when assisted by GO-AuNPs. We also designed a system of detecting serotypes in a single assay based on melting temperatures. Our sensitive and specific nano-PCR system can be applied to diagnose early FMDV infection, and thus may prove to be useful for clinical and biomedical applications.
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Affiliation(s)
- Jong-Won Kim
- Bionanotechnology Research Center, Korea Research Institute of Bioscience & Biotechnology (KRIBB) 125 Gwahak-ro, Yuseong-gu, Daejeon 34141, Korea; (J.-W.K.); (M.K.); (K.K.L.)
- Dignostics Platform Research Section, Electronics and Telecommunications Research Institute (ETRI) 218 Gajeong-ro, Yuseong-gu, Daejeon 34129, Korea;
| | - Myeongkun Kim
- Bionanotechnology Research Center, Korea Research Institute of Bioscience & Biotechnology (KRIBB) 125 Gwahak-ro, Yuseong-gu, Daejeon 34141, Korea; (J.-W.K.); (M.K.); (K.K.L.)
- Dignostics Platform Research Section, Electronics and Telecommunications Research Institute (ETRI) 218 Gajeong-ro, Yuseong-gu, Daejeon 34129, Korea;
| | - Kyung Kwan Lee
- Bionanotechnology Research Center, Korea Research Institute of Bioscience & Biotechnology (KRIBB) 125 Gwahak-ro, Yuseong-gu, Daejeon 34141, Korea; (J.-W.K.); (M.K.); (K.K.L.)
- Dignostics Platform Research Section, Electronics and Telecommunications Research Institute (ETRI) 218 Gajeong-ro, Yuseong-gu, Daejeon 34129, Korea;
- Department of Life and Nanopharmaceutical Science, College of Pharmacy, Kyung Hee University, Seoul 02447, Korea
| | - Kwang Hyo Chung
- Dignostics Platform Research Section, Electronics and Telecommunications Research Institute (ETRI) 218 Gajeong-ro, Yuseong-gu, Daejeon 34129, Korea;
| | - Chang-Soo Lee
- Bionanotechnology Research Center, Korea Research Institute of Bioscience & Biotechnology (KRIBB) 125 Gwahak-ro, Yuseong-gu, Daejeon 34141, Korea; (J.-W.K.); (M.K.); (K.K.L.)
- Dignostics Platform Research Section, Electronics and Telecommunications Research Institute (ETRI) 218 Gajeong-ro, Yuseong-gu, Daejeon 34129, Korea;
- Department of Biotechnology, University of Science & Technology (UST), Daejeon 34113, Korea
- Correspondence:
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Uskoković V. Why have nanotechnologies been underutilized in the global uprising against the coronavirus pandemic? Nanomedicine (Lond) 2020; 15:1719-1734. [PMID: 32462968 PMCID: PMC7265684 DOI: 10.2217/nnm-2020-0163] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2020] [Accepted: 05/07/2020] [Indexed: 12/11/2022] Open
Abstract
Prior research on nanotechnologies in diagnostics, prevention and treatment of coronavirus infections is reviewed. Gold nanoparticles and semiconductor quantum dots in colorimetric and immunochromatographic assays, silica nanoparticles in the polymerase chain reaction and spike protein nanospheres as antigen carriers and adjuvants in vaccine formulations present notable examples in diagnostics and prevention, while uses of nanoparticles in coronavirus infection treatments have been merely sporadic. The current absence of antiviral therapeutics that specifically target human coronaviruses, including SARS-CoV-2, might be largely due to the underuse of nanotechnologies. Elucidating the interface between nanoparticles and coronaviruses is timely, but presents the only route to the rational design of precisely targeted therapeutics for coronavirus infections. Such a fundamental approach is also a viable prophylaxis against future pandemics of this type.
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Affiliation(s)
- Vuk Uskoković
- Department of Mechanical & Aerospace Engineering, University of California Irvine, Engineering Gateway 4200, Irvine, CA 92697, USA
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Madadelahi M, Ghazimirsaeed E, Shamloo A. Design and fabrication of a two-phase diamond nanoparticle aided fast PCR device. Anal Chim Acta 2019; 1068:28-40. [DOI: 10.1016/j.aca.2019.02.050] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2019] [Accepted: 02/27/2019] [Indexed: 01/13/2023]
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Shahi S, Zununi Vahed S, Fathi N, Sharifi S. Polymerase chain reaction (PCR)-based methods: Promising molecular tools in dentistry. Int J Biol Macromol 2018; 117:983-992. [DOI: 10.1016/j.ijbiomac.2018.05.085] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2018] [Revised: 05/13/2018] [Accepted: 05/14/2018] [Indexed: 02/06/2023]
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