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Ganguly R, Lee CS. A Poisson-Independent Approach to Precision Nucleic Acid Quantification in Microdroplets. ACS Appl Bio Mater 2024. [PMID: 38658190 DOI: 10.1021/acsabm.4c00350] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/26/2024]
Abstract
Digital PCR (dPCR) has become indispensable in nucleic acid (NA) detection across various fields, including viral diagnostics and mutant detection. However, misclassification of partitions in dPCR can significantly impact accuracy. Despite existing methods to minimize misclassification bias, accurate classification remains elusive, especially for nonamplified target partitions. To address these challenges, this study introduces an innovative microdroplet-based competitive PCR platform for nucleic acid quantification in microfluidic devices independent of Poisson statistics. In this approach, the target concentration (T) is determined from the concentration of competitor DNA (C) at the equivalence point (E.P.), where C/T is 1. Competitive PCR ensures that the ratio of target to competitor DNA remains constant during amplification, reflected in the resultant fluorescence intensity, allowing the quantification of target DNA concentration at the equivalence point. The unique amplification technique eliminates Poisson distribution, addressing misclassification challenges. Additionally, our approach reduces the need for post-PCR procedures and shortens analytical time. We envision this platform as versatile, reproducible, and easily adaptable for driving significant progress in molecular biology and diagnostics.
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Affiliation(s)
- Reya Ganguly
- Department of Chemical Engineering and Applied Chemistry, Chungnam National University, 99 Daehak-ro, Yuseong-gu, Daejeon 34134, Republic of Korea
| | - Chang-Soo Lee
- Department of Chemical Engineering and Applied Chemistry, Chungnam National University, 99 Daehak-ro, Yuseong-gu, Daejeon 34134, Republic of Korea
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Kulkarni MB, Ayachit NH, Aminabhavi TM. A Short Review on Miniaturized Biosensors for the Detection of Nucleic Acid Biomarkers. Biosensors (Basel) 2023; 13:412. [PMID: 36979624 PMCID: PMC10046286 DOI: 10.3390/bios13030412] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/20/2023] [Revised: 03/17/2023] [Accepted: 03/20/2023] [Indexed: 06/18/2023]
Abstract
Even today, most biomarker testing is executed in centralized, dedicated laboratories using bulky instruments, automated analyzers, and increased analysis time and expenses. The development of miniaturized, faster, low-cost microdevices is immensely anticipated for substituting for these conventional laboratory-oriented assays and transferring diagnostic results directly onto the patient's smartphone using a cloud server. Pioneering biosensor-based approaches might make it possible to test biomarkers with reliability in a decentralized setting, but there are still a number of issues and restrictions that must be resolved before the development and use of several biosensors for the proper understanding of the measured biomarkers of numerous bioanalytes such as DNA, RNA, urine, and blood. One of the most promising processes to address some of the issues relating to the growing demand for susceptible, quick, and affordable analysis techniques in medical diagnostics is the creation of biosensors. This article critically discusses a short review of biosensors used for detecting nucleic acid biomarkers, and their use in biomedical prognostics will be addressed while considering several essential characteristics.
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Affiliation(s)
- Madhusudan B. Kulkarni
- School of Electronics and Communication Engineering, KLE Technological University, Vidyanagar, Hubballi 580023, Karnataka, India
- Medical Physics Department, Wisconsin Institutes for Medical Research, University of Wisconsin, Madison, WI 53705, USA
| | - Narasimha H. Ayachit
- School of Advanced Sciences, KLE Technological University, Hubballi 580031, Karnataka, India
| | - Tejraj M. Aminabhavi
- School of Advanced Sciences, KLE Technological University, Hubballi 580031, Karnataka, India
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Yang L, Wang X, Niu Y. Research Progress of DNA-Based Technologies for Postmortem Interval Estimation. Fa Yi Xue Za Zhi 2022; 38:747-753. [PMID: 36914391 DOI: 10.12116/j.issn.1004-5619.2022.420601] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 03/16/2023]
Abstract
In criminal investigations, postmortem interval (PMI) is important information to be inferred in homicide investigations, as well as the focus and the difficulty in forensic pathology research. Because the DNA content in different tissues is relatively constant and shows changes regularly with the extension of PMI, it has become a research hotspot of PMI estimation. This paper reviews the recent progress of PMI estimation technologies including DNA-based single cell gel electrophoresis, image analysis, flow cytometry, real-time fluorescence quantitative PCR and high-throughput sequencing, hoping to provide references for forensic medicine practice and scientific research.
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Affiliation(s)
- Lan Yang
- School of Forensic Medicine, Shanxi Medical University, Jinzhong 030600, Shanxi Province, China
| | - Xin Wang
- Criminal Investigation Detachment of Huaibei Public Security Bureau, Huaibei 235000, Anhui Province, China
| | - Yong Niu
- Criminal Investigation Bureau of the Ministry of Public Security, Beijing 100006, China
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Handy SM, Ott BM, Hunter ES, Zhang S, Erickson DL, Wolle MM, Conklin SD, Lane CE. Suitability of DNA Sequencing Tools for Identifying Edible Seaweeds Sold in the United States. J Agric Food Chem 2020; 68:15516-15525. [PMID: 33334103 DOI: 10.1021/acs.jafc.0c03734] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Seaweeds have been consumed by billions of people around the world and are increasingly popular in United States (US) diets. Some seaweed species have been associated with adverse health effects-such as heavy metal toxicity-and higher priced seaweeds may be more prone to adulteration. Knowing which species of seaweeds are being marketed in the US is important for protecting human health and preventing economic adulteration. Therefore, the United States Food and Drug Administration is developing new DNA-based species identification tools to complement established chemical methods for verifying the accurate labeling of products. Here, seaweed products available in the United States were surveyed using a tiered approach to evaluate a variety of DNA extraction techniques followed by traditional DNA barcoding via Sanger sequencing; if needed, genome skimming of total extracted nuclear DNA via next-generation sequencing was performed. This two-tiered approach of DNA barcoding and genome skimming could identify most seaweed samples (41/46), even those in blends (2/2, 1 out of 3 labeled species in each). Only two commercial samples appeared to be mislabeled or to contain unintended algal species. Five samples, labeled as "hijiki" or "arame", could not be confirmed by these DNA-based identification methods.
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Affiliation(s)
- Sara M Handy
- Center for Food Safety and Applied Nutrition, Office of Regulatory Science, U.S. Food and Drug Administration, College Park 20740, Maryland, United States
| | - Brittany M Ott
- Center for Food Safety and Applied Nutrition, Office of Regulatory Science, U.S. Food and Drug Administration, College Park 20740, Maryland, United States
- Joint Institute for Food Safety and Applied Nutrition, University of Maryland, College Park 20742, Maryland, United States
| | - Elizabeth Sage Hunter
- Department of Biological Sciences, University of Rhode Island, Kingston 02881, Rhode Island, United States
| | - Shu Zhang
- DNA4 Technologies LLC, Baltimore 21227, Maryland, United States
| | - David L Erickson
- Joint Institute for Food Safety and Applied Nutrition, University of Maryland, College Park 20742, Maryland, United States
- DNA4 Technologies LLC, Baltimore 21227, Maryland, United States
| | - Mesay Mulugeta Wolle
- Center for Food Safety and Applied Nutrition, Office of Regulatory Science, U.S. Food and Drug Administration, College Park 20740, Maryland, United States
| | - Sean D Conklin
- Center for Food Safety and Applied Nutrition, Office of Regulatory Science, U.S. Food and Drug Administration, College Park 20740, Maryland, United States
| | - Christopher E Lane
- Department of Biological Sciences, University of Rhode Island, Kingston 02881, Rhode Island, United States
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Sherri N, Salloum N, Mouawad C, Haidar-Ahmad N, Shirinian M, Rahal EA. Epstein-Barr Virus DNA Enhances Diptericin Expression and Increases Hemocyte Numbers in Drosophila melanogaster via the Immune Deficiency Pathway. Front Microbiol 2018; 9:1268. [PMID: 29942298 PMCID: PMC6004391 DOI: 10.3389/fmicb.2018.01268] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2017] [Accepted: 05/24/2018] [Indexed: 12/22/2022] Open
Abstract
Infection with the Epstein-Barr virus (EBV) is associated with several malignancies and autoimmune diseases in humans. The following EBV infection and establishment of latency, recurrences frequently occur resulting in potential viral DNA shedding, which may then trigger the activation of immune pathways. We have previously demonstrated that levels of the pro-inflammatory cytokine IL-17, which is associated with several autoimmune diseases, are increased in response to EBV DNA injection in mice. Whether other pro-inflammatory pathways are induced in EBV DNA pathobiology remains to be investigated. The complexity of mammalian immune systems presents a challenge to studying differential activities of their intricate immune pathways in response to a particular immune stimulus. In this study, we used Drosophila melanogaster to identify innate humoral and cellular immune pathways that are activated in response to EBV DNA. Injection of wild-type adult flies with EBV DNA induced the immune deficiency (IMD) pathway resulting in enhanced expression of the antimicrobial peptide diptericin. Furthermore, EBV DNA increased the number of hemocytes in flies. Conditional silencing of the IMD pathway decreased diptericin expression in addition to curbing of hemocyte proliferation in response to challenge with EBV DNA. Comparatively, upon injecting mice with EBV DNA, we detected enhanced expression of tumor necrosis factor-α (TNFα); this enhancement is rather comparable to IMD pathway activation in flies. This study hence indicates that D. melanogaster could possibly be utilized to identify immune mediators that may also play a role in the response to EBV DNA in higher systems.
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Affiliation(s)
- Nour Sherri
- Department of Experimental Pathology, Microbiology, and Immunology, American University of Beirut, Beirut, Lebanon
| | - Noor Salloum
- Department of Experimental Pathology, Microbiology, and Immunology, American University of Beirut, Beirut, Lebanon
| | - Carine Mouawad
- Department of Experimental Pathology, Microbiology, and Immunology, American University of Beirut, Beirut, Lebanon
| | - Nathaline Haidar-Ahmad
- Department of Experimental Pathology, Microbiology, and Immunology, American University of Beirut, Beirut, Lebanon
| | - Margret Shirinian
- Department of Experimental Pathology, Microbiology, and Immunology, American University of Beirut, Beirut, Lebanon
| | - Elias A Rahal
- Department of Experimental Pathology, Microbiology, and Immunology, American University of Beirut, Beirut, Lebanon
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Brun C, Elchinger PH, Nonglaton G, Tidiane-Diagne C, Tiron R, Thuaire A, Gasparutto D, Baillin X. Metallic Conductive Nanowires Elaborated by PVD Metal Deposition on Suspended DNA Bundles. Small 2017; 13:1700956. [PMID: 28677894 DOI: 10.1002/smll.201700956] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/23/2017] [Revised: 05/03/2017] [Indexed: 06/07/2023]
Abstract
Metallic conductive nanowires (NWs) with DNA bundle core are achieved, thanks to an original process relying on double-stranded DNA alignment and physical vapor deposition (PVD) metallization steps involving a silicon substrate. First, bundles of DNA are suspended with a repeatable process between 2 µm high parallel electrodes with separating gaps ranging from 800 nm to 2 µm. The process consists in the drop deposition of a DNA lambda-phage solution on the electrodes followed by a naturally evaporation step. The deposition process is controlled by the DNA concentration within the buffer solution, the drop volume, and the electrode hydrophobicity. The suspended bundles are finally metallized with various thicknesses of titanium and gold by a PVD e-beam evaporation process. The achieved NWs have a width ranging from a few nanometers up to 100 nm. The electrical behavior of the achieved 60 and 80 nm width metallic NWs is shown to be Ohmic and their intrinsic resistance is estimated according to different geometrical models of the NW section area. For the 80 nm width NWs, a resistance of about few ohms is established, opening exploration fields for applications in microelectronics.
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Affiliation(s)
- Christophe Brun
- Université Grenoble Alpes, F-38000, Grenoble, France
- CEA, LETI, MINATEC Campus, F-38054, Grenoble, France
| | - Pierre-Henri Elchinger
- Université Grenoble Alpes, F-38000, Grenoble, France
- Laboratory of Plant & Cell Physiology, CEA/DRF/BIG, CNRS UMR5168, INRA UMR 1417, F-38054, Grenoble, France
| | - Guillaume Nonglaton
- Université Grenoble Alpes, F-38000, Grenoble, France
- CEA, LETI, MINATEC Campus, F-38054, Grenoble, France
| | - Cheikh Tidiane-Diagne
- Université Grenoble Alpes, F-38000, Grenoble, France
- CEA, LETI, MINATEC Campus, F-38054, Grenoble, France
| | - Raluca Tiron
- Université Grenoble Alpes, F-38000, Grenoble, France
- CEA, LETI, MINATEC Campus, F-38054, Grenoble, France
| | - Aurélie Thuaire
- Université Grenoble Alpes, F-38000, Grenoble, France
- CEA, LETI, MINATEC Campus, F-38054, Grenoble, France
| | - Didier Gasparutto
- Université Grenoble Alpes, F-38000, Grenoble, France
- INAC/SyMMES, UMR 5819 CEA CNRS UGA, MINATEC Campus, F-38054, Grenoble, France
| | - Xavier Baillin
- Université Grenoble Alpes, F-38000, Grenoble, France
- CEA, LETI, MINATEC Campus, F-38054, Grenoble, France
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