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Hampel KJ, Gerrard DL, Francis D, Armstrong J, Cameron M, Ostafin A, Mahoney B, Malik M, Sidiropoulos N. When False-Positives Arise: Troubleshooting a SARS-Coronavirus-2 (SARS-CoV-2) Detection Assay on a Semi-Automated Platform. J Appl Lab Med 2024; 9:716-727. [PMID: 38507614 DOI: 10.1093/jalm/jfae016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2023] [Accepted: 12/29/2023] [Indexed: 03/22/2024]
Abstract
BACKGROUND During the COVID-19 pandemic, many molecular diagnostic laboratories performed high-throughput SARS-CoV-2 testing often with implementation of automated workflows. In parallel, vaccination campaigns resulted increasingly in specimens from fully vaccinated patients, with resultant clinical inquiries regarding positive results in this patient population. This prompted a quality improvement initiative to investigate the semi-automated testing workflow for false-positive results. The troubleshooting workflow is described and procedural improvements are outlined that serve as a resource for other molecular diagnostic laboratories that need to overcome testing anomalies in a semi-automated environment. METHODS This workflow utilized the MagMax-96 Viral RNA kit and the CDC 2019-nCoV RT-qPCR Panel on the Agilent Bravo Liquid-Handler (Bravo). Screening of the environment, personnel, and the mechanical performance of instrumentation using low Ct checkerboard challenges was executed to identify sources of cross-contamination. Evaluation of the assay and reporting design was conducted. RESULTS Specimen contamination was observed during the viral extraction process on the Bravo. Changes to the program reduced plate contamination by 50% and importantly revealed consistent hallmarks of contaminated samples. We adjusted the reporting algorithm using these indicators of false positives. False positives that were identified made up 0.11% of the 45 000+ tests conducted over the following 8 months. CONCLUSIONS These adjustments provided confident and quality results while maintaining turnaround time for patients and pandemic-related public health initiatives. This corrected false-positive rate is concordant with previously published studies from diagnostic laboratories utilizing automated systems and may be considered a laboratory performance standard for this type of testing.
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Affiliation(s)
- Kenneth J Hampel
- Department of Pathology and Laboratory Medicine, University of Vermont Medical Center, Burlington, VT, United States
| | - Diana L Gerrard
- Department of Pathology and Laboratory Medicine, University of Vermont Medical Center, Burlington, VT, United States
| | - Denise Francis
- Department of Pathology and Laboratory Medicine, University of Vermont Medical Center, Burlington, VT, United States
| | - Jordan Armstrong
- Technical Assistance Center for Biotek Products, Agilent Technologies Inc., Winooski, VT, United States
| | - Margaret Cameron
- Department of Pathology and Laboratory Medicine, University of Vermont Medical Center, Burlington, VT, United States
| | - Alexa Ostafin
- Department of Pathology and Laboratory Medicine, University of Vermont Medical Center, Burlington, VT, United States
| | - Briege Mahoney
- Department of Pathology and Laboratory Medicine, University of Vermont Medical Center, Burlington, VT, United States
| | - Miles Malik
- Department of Pathology and Laboratory Medicine, University of Vermont Medical Center, Burlington, VT, United States
| | - Nikoletta Sidiropoulos
- Department of Pathology and Laboratory Medicine, University of Vermont Medical Center, Burlington, VT, United States
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2
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Kalairaj A, Rajendran S, Panda RC, Senthilvelan T. A study on waterlogging tolerance in sugarcane: a comprehensive review. Mol Biol Rep 2024; 51:747. [PMID: 38874798 DOI: 10.1007/s11033-024-09679-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2024] [Accepted: 05/27/2024] [Indexed: 06/15/2024]
Abstract
Sugarcane (Saccharum officinarum) is an important crop, native to tropical and subtropical regions and it is a major source of sugar and Bioenergy in the world. Abiotic stress is defined as environmental conditions that reduce growth and yield below the optimum level. To tolerate these abiotic stresses, plants initiate several molecular, cellular, and physiological changes. These responses to abiotic stresses are dynamic and complex; they may be reversible or irreversible. Waterlogging is an abiotic stress phenomenon that drastically reduces the growth and survival of sugarcane, which leads to a 15-45% reduction in cane's yield. The extent of damage due to waterlogging depends on genotypes, environmental conditions, stage of development and duration of stress. An improved understanding of the physiological, biochemical, and molecular responses of sugarcane to waterlogging stress could help to develop new breeding strategies to sustain high yields against this situation. The present review offers a summary of recent findings on the adaptation of sugarcane to waterlogging stress in terms of growth and development, yield and quality, as well as biochemical and adaptive-molecular processes that may contribute to flooding tolerance.
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Affiliation(s)
- Ashmitha Kalairaj
- Department of Bioinformatics, Saveetha School of Engineering, Saveetha Institute of Medical and Technical Sciences (SIMATS), Saveetha University, Thandalam, Chennai, Tamilnadu, 602 105, India
| | - Swethashree Rajendran
- Department of Bioinformatics, Saveetha School of Engineering, Saveetha Institute of Medical and Technical Sciences (SIMATS), Saveetha University, Thandalam, Chennai, Tamilnadu, 602 105, India
| | - Rames C Panda
- Chemical Engineering Division, RajaLakshmi Engineering College, Thandalam, Chennai, Tamilnadu, 602 105, India
| | - T Senthilvelan
- Department of Bioinformatics, Saveetha School of Engineering, Saveetha Institute of Medical and Technical Sciences (SIMATS), Saveetha University, Thandalam, Chennai, Tamilnadu, 602 105, India.
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3
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Lemmink IB, Straub LV, Bovee TFH, Mulder PPJ, Zuilhof H, Salentijn GI, Righetti L. Recent advances and challenges in the analysis of natural toxins. ADVANCES IN FOOD AND NUTRITION RESEARCH 2024; 110:67-144. [PMID: 38906592 DOI: 10.1016/bs.afnr.2024.05.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/23/2024]
Abstract
Natural toxins (NTs) are poisonous secondary metabolites produced by living organisms developed to ward off predators. Especially low molecular weight NTs (MW<∼1 kDa), such as mycotoxins, phycotoxins, and plant toxins, are considered an important and growing food safety concern. Therefore, accurate risk assessment of food and feed for the presence of NTs is crucial. Currently, the analysis of NTs is predominantly performed with targeted high pressure liquid chromatography tandem mass spectrometry (HPLC-MS/MS) methods. Although these methods are highly sensitive and accurate, they are relatively expensive and time-consuming, while unknown or unexpected NTs will be missed. To overcome this, novel on-site screening methods and non-targeted HPLC high resolution mass spectrometry (HRMS) methods have been developed. On-site screening methods can give non-specialists the possibility for broad "scanning" of potential geographical regions of interest, while also providing sensitive and specific analysis at the point-of-need. Non-targeted chromatography-HRMS methods can detect unexpected as well as unknown NTs and their metabolites in a lab-based approach. The aim of this chapter is to provide an insight in the recent advances, challenges, and perspectives in the field of NTs analysis both from the on-site and the laboratory perspective.
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Affiliation(s)
- Ids B Lemmink
- Laboratory of Organic Chemistry, Wageningen University & Research, Wageningen, The Netherlands; Wageningen Food Safety Research, Wageningen University & Research, Wageningen, The Netherlands
| | - Leonie V Straub
- Laboratory of Organic Chemistry, Wageningen University & Research, Wageningen, The Netherlands; Wageningen Food Safety Research, Wageningen University & Research, Wageningen, The Netherlands
| | - Toine F H Bovee
- Wageningen Food Safety Research, Wageningen University & Research, Wageningen, The Netherlands
| | - Patrick P J Mulder
- Wageningen Food Safety Research, Wageningen University & Research, Wageningen, The Netherlands
| | - Han Zuilhof
- Laboratory of Organic Chemistry, Wageningen University & Research, Wageningen, The Netherlands; School of Pharmaceutical Sciences and Technology, Tianjin University, Tianjin, P.R. China
| | - Gert Ij Salentijn
- Laboratory of Organic Chemistry, Wageningen University & Research, Wageningen, The Netherlands; Wageningen Food Safety Research, Wageningen University & Research, Wageningen, The Netherlands.
| | - Laura Righetti
- Laboratory of Organic Chemistry, Wageningen University & Research, Wageningen, The Netherlands; Wageningen Food Safety Research, Wageningen University & Research, Wageningen, The Netherlands.
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4
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Onofri M, Severini S, Tommolini F, Lancia M, Gambelunghe C, Carlini L, Carnevali E. The Usefulness of qPCR Data for Sample Pre-Assessment and Interpretation of Genetic Typing Results. Genes (Basel) 2024; 15:744. [PMID: 38927680 PMCID: PMC11203103 DOI: 10.3390/genes15060744] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2024] [Revised: 05/31/2024] [Accepted: 06/04/2024] [Indexed: 06/28/2024] Open
Abstract
DNA quantification is a crucial step in the STR typing workflow for human identification purposes. Given the reaction's nature, qPCR assays may be subjected to the same stochastic effects of traditional PCR for low-input concentrations. The study aims to evaluate the precision of the PowerQuant® (Promega) kit assay measurements and the degree of variability for DNA templates falling below the optimal threshold of the PowerPlex® ESX-17 Fast STR typing kit (Promega). Five three-fold dilutions of the 2800 M control DNA (Promega) were set up. Each dilution (concentrations: 0.05, 0.0167, 0.0055, 0.00185, and 0.000617 ng/µL) was quantified and amplified in four replicates. Variability for qPCR results, STR profile completeness, and EPGs' peak height were evaluated. The qPCR-estimated concentration of casework samples was correlated with profile completeness and peak intensity, to assess the predictive value of qPCR results for the successful STR typing of scarce samples. qPCR was subjected to stochastic effects, of which the degree was inversely proportional to the initial input template. Quantitation results and the STR profile's characteristics were strongly correlated. Due to the intrinsic nature of real casework samples, a qPCR-derived DNA concentration threshold for correctly identifying probative STR profiles may be difficult to establish. Quantitation data may be useful in interpreting and corroborating STR typing results and for clearly illustrating them to the stakeholders.
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Affiliation(s)
- Martina Onofri
- Section of Legal Medicine, Department of Medicine and Surgery, Santa Maria Hospital, University of Perugia, 05100 Terni, Italy; (S.S.); (F.T.); (E.C.)
- Section of Legal Medicine, Department of Medicine and Surgery, University of Perugia, 06123 Perugia, Italy; (M.L.); (C.G.); (L.C.)
| | - Simona Severini
- Section of Legal Medicine, Department of Medicine and Surgery, Santa Maria Hospital, University of Perugia, 05100 Terni, Italy; (S.S.); (F.T.); (E.C.)
| | - Federica Tommolini
- Section of Legal Medicine, Department of Medicine and Surgery, Santa Maria Hospital, University of Perugia, 05100 Terni, Italy; (S.S.); (F.T.); (E.C.)
| | - Massimo Lancia
- Section of Legal Medicine, Department of Medicine and Surgery, University of Perugia, 06123 Perugia, Italy; (M.L.); (C.G.); (L.C.)
| | - Cristiana Gambelunghe
- Section of Legal Medicine, Department of Medicine and Surgery, University of Perugia, 06123 Perugia, Italy; (M.L.); (C.G.); (L.C.)
| | - Luigi Carlini
- Section of Legal Medicine, Department of Medicine and Surgery, Santa Maria Hospital, University of Perugia, 05100 Terni, Italy; (S.S.); (F.T.); (E.C.)
- Section of Legal Medicine, Department of Medicine and Surgery, University of Perugia, 06123 Perugia, Italy; (M.L.); (C.G.); (L.C.)
| | - Eugenia Carnevali
- Section of Legal Medicine, Department of Medicine and Surgery, Santa Maria Hospital, University of Perugia, 05100 Terni, Italy; (S.S.); (F.T.); (E.C.)
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5
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Mahdy OA, Salem MA, Abdelsalam M, Shaheed IB, Attia MM. Immunological and molecular evaluation of zoonotic metacercarial infection in freshwater fish: A cross-sectional analysis. Res Vet Sci 2024; 172:105239. [PMID: 38583195 DOI: 10.1016/j.rvsc.2024.105239] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2023] [Revised: 03/21/2024] [Accepted: 03/22/2024] [Indexed: 04/09/2024]
Abstract
Improperly cooked fish, carrying active metacercariae (MCs), can pose a significant risk for transmitting fish-borne zoonotic trematodes (FBZTs) to human consumers. This study aimed to enhance our understanding of FBZTs by conducting a comprehensive cross-sectional analysis involving various fish species, such as Nile tilapia (Oreochromis niloticus), African catfish (Clarias gariepinus), and red-belly tilapia (Tilapia zillii). These fish specimens were collected from distinct Egyptian governorates, specifically Giza, Kafr al-Shaykh, and Fayoum. The recovered flukes from experimentally infected domestic pigeons were identified as Prohemistomum vivax, Haplorchis pumilio, and Pygidiopsis genata based on morphological features. Furthermore, the identity of the retrieved adult flukes was confirmed using three species-specific primers for PCR amplification and sequencing analysis of the ITS rDNA region and have been deposited in GenBank with the following accession numbers: P. vivax (OR291421.1 and OR291422.1), P. genata (OP099561.1), and H. pumilio (OM439581.1-OP090510.1). Quantitative real-time PCR targeting the immunological genes Tumor Necrosis Factor-alpha (TNF-alpha) and Interleukin-1 (IL-1Β) was employed to compare the cellular immune response between infected with EMCs and uninfected O. niloticus. The results indicated a significant increase in TNF- and IL-1Β levels in FBZTs-infected vs un-infected fishes. Importantly, the presence of adult flukes and EMCs led to substantial histological alterations in both experimentally infected pigeons and naturally infected fish tissues. These changes included the necrosis of fish muscle bundles and a pronounced inflammatory reaction with muscular necrosis in the digestive tracts of experimentally infected pigeons.
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Affiliation(s)
- Olfat A Mahdy
- Parasitology Department, Faculty of Veterinary Medicine, Cairo University, Egypt.
| | - Mai A Salem
- Parasitology Department, Faculty of Veterinary Medicine, Cairo University, Egypt
| | - Mohamed Abdelsalam
- Department of Aquatic Animal Medicine and Management, Faculty of Veterinary Medicine, Cairo University, Egypt
| | - Iman B Shaheed
- Pathology Department, Faculty of Veterinary Medicine, Cairo University, Egypt
| | - Marwa M Attia
- Parasitology Department, Faculty of Veterinary Medicine, Cairo University, Egypt
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Chen Z, Luo G, Ren J, Wang Q, Zhao X, Wei L, Wang Y, Liu Y, Deng Y, Li S. Recent Advances in and Application of Fluorescent Microspheres for Multiple Nucleic Acid Detection. BIOSENSORS 2024; 14:265. [PMID: 38920569 PMCID: PMC11201543 DOI: 10.3390/bios14060265] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2024] [Revised: 05/17/2024] [Accepted: 05/21/2024] [Indexed: 06/27/2024]
Abstract
Traditional single nucleic acid assays can only detect one target while multiple nucleic acid assays can detect multiple targets simultaneously, providing comprehensive and accurate information. Fluorescent microspheres in multiplexed nucleic acid detection offer high sensitivity, specificity, multiplexing, flexibility, and scalability advantages, enabling precise, real-time results and supporting clinical diagnosis and research. However, multiplexed assays face challenges like complexity, costs, and sample handling issues. The review explores the recent advancements and applications of fluorescent microspheres in multiple nucleic acid detection. It discusses the versatility of fluorescent microspheres in various fields, such as disease diagnosis, drug screening, and personalized medicine. The review highlights the possibility of adjusting the performance of fluorescent microspheres by modifying concentrations and carrier forms, allowing for tailored applications. It emphasizes the potential of fluorescent microsphere technology in revolutionizing nucleic acid detection and advancing health, disease treatment, and medical research.
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Affiliation(s)
- Zhu Chen
- MOE Key Lab of Rare Pediatric Diseases & Hengyang Medical School, University of South China, Hengyang 421001, China; (G.L.); (J.R.); (Q.W.); (X.Z.); (L.W.); (Y.L.); (Y.D.)
- Institute for Future Sciences, University of South China, Changsha 410008, China
| | - Gaoming Luo
- MOE Key Lab of Rare Pediatric Diseases & Hengyang Medical School, University of South China, Hengyang 421001, China; (G.L.); (J.R.); (Q.W.); (X.Z.); (L.W.); (Y.L.); (Y.D.)
- Institute for Future Sciences, University of South China, Changsha 410008, China
- Hunan Province Key Laboratory of Tumor Cellular & Molecular Pathology, Hunan Engineering Research Center for Early Diagnosis and Treatment of Liver Cancer, Cancer Research Institute, Hengyang Medical School, University of South China, Hengyang 421001, China
| | - Jie Ren
- MOE Key Lab of Rare Pediatric Diseases & Hengyang Medical School, University of South China, Hengyang 421001, China; (G.L.); (J.R.); (Q.W.); (X.Z.); (L.W.); (Y.L.); (Y.D.)
- Institute for Future Sciences, University of South China, Changsha 410008, China
| | - Qixuan Wang
- MOE Key Lab of Rare Pediatric Diseases & Hengyang Medical School, University of South China, Hengyang 421001, China; (G.L.); (J.R.); (Q.W.); (X.Z.); (L.W.); (Y.L.); (Y.D.)
- Institute for Future Sciences, University of South China, Changsha 410008, China
- Hunan Province Key Laboratory of Tumor Cellular & Molecular Pathology, Hunan Engineering Research Center for Early Diagnosis and Treatment of Liver Cancer, Cancer Research Institute, Hengyang Medical School, University of South China, Hengyang 421001, China
| | - Xinping Zhao
- MOE Key Lab of Rare Pediatric Diseases & Hengyang Medical School, University of South China, Hengyang 421001, China; (G.L.); (J.R.); (Q.W.); (X.Z.); (L.W.); (Y.L.); (Y.D.)
- Institute for Future Sciences, University of South China, Changsha 410008, China
- Institute of Cytology and Genetics, School of Basic Medical Sciences, Hengyang Medical School, University of South China, Hengyang 421001, China
| | - Linyu Wei
- MOE Key Lab of Rare Pediatric Diseases & Hengyang Medical School, University of South China, Hengyang 421001, China; (G.L.); (J.R.); (Q.W.); (X.Z.); (L.W.); (Y.L.); (Y.D.)
- Institute for Future Sciences, University of South China, Changsha 410008, China
- Institute of Cytology and Genetics, School of Basic Medical Sciences, Hengyang Medical School, University of South China, Hengyang 421001, China
| | - Yue Wang
- Hunan Key Laboratory of Biomedical Nanomaterials and Devices, Hunan University of Technology, Zhuzhou 412007, China;
| | - Yuan Liu
- MOE Key Lab of Rare Pediatric Diseases & Hengyang Medical School, University of South China, Hengyang 421001, China; (G.L.); (J.R.); (Q.W.); (X.Z.); (L.W.); (Y.L.); (Y.D.)
- Institute for Future Sciences, University of South China, Changsha 410008, China
| | - Yan Deng
- MOE Key Lab of Rare Pediatric Diseases & Hengyang Medical School, University of South China, Hengyang 421001, China; (G.L.); (J.R.); (Q.W.); (X.Z.); (L.W.); (Y.L.); (Y.D.)
- Institute for Future Sciences, University of South China, Changsha 410008, China
| | - Song Li
- MOE Key Lab of Rare Pediatric Diseases & Hengyang Medical School, University of South China, Hengyang 421001, China; (G.L.); (J.R.); (Q.W.); (X.Z.); (L.W.); (Y.L.); (Y.D.)
- Institute for Future Sciences, University of South China, Changsha 410008, China
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Song CY, Hsieh SL, Yang SY, Lin CY, Wang SW, Tsai CH, Lo YS, Fong YC, Tang CH. Visfatin Facilitates VEGF-D-Induced Lymphangiogenesis through Activating HIF-1α and Suppressing miR-2277-3p in Human Chondrosarcoma. Int J Mol Sci 2024; 25:5142. [PMID: 38791180 PMCID: PMC11121249 DOI: 10.3390/ijms25105142] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2024] [Revised: 05/07/2024] [Accepted: 05/08/2024] [Indexed: 05/26/2024] Open
Abstract
Chondrosarcoma is a malignant bone tumor that arises from abnormalities in cartilaginous tissue and is associated with lung metastases. Lymphangiogenesis plays an essential role in cancer metastasis. Visfatin is an adipokine reported to enhance tumor metastasis, but its relationship with VEGF-D generation and lymphangiogenesis in chondrosarcoma remains undetermined. Our results from clinical samples reveal that VEGF-D levels are markedly higher in chondrosarcoma patients than in normal individuals. Visfatin stimulation promotes VEGF-D-dependent lymphatic endothelial cell lymphangiogenesis. We also found that visfatin induces VEGF-D production by activating HIF-1α and reducing miR-2277-3p generation through the Raf/MEK/ERK signaling cascade. Importantly, visfatin controls chondrosarcoma-related lymphangiogenesis in vivo. Therefore, visfatin is a promising target in the treatment of chondrosarcoma lymphangiogenesis.
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Affiliation(s)
- Chang-Yu Song
- Graduate Institute of Biomedical Science, China Medical University, Taichung 40402, Taiwan; (C.-Y.S.); (S.-L.H.)
| | - Shang-Lin Hsieh
- Graduate Institute of Biomedical Science, China Medical University, Taichung 40402, Taiwan; (C.-Y.S.); (S.-L.H.)
- Minimally Invasive Spine and Joint Center, Buddhist Tzu Chi General Hospital Taichung Branch, Taichung 42721, Taiwan
| | - Shang-Yu Yang
- Department of Medical Laboratory Science and Biotechnology, Asia University, Taichung 41354, Taiwan;
| | - Chih-Yang Lin
- Translational Medicine Center, Shin-Kong Wu Ho-Su Memorial Hospital, Taipei 11104, Taiwan;
| | - Shih-Wei Wang
- Institute of Biomedical Sciences, Mackay Medical College, New Taipei City 25245, Taiwan;
- Department of Medicine, Mackay Medical College, New Taipei City 25245, Taiwan
| | - Chun-Hao Tsai
- Department of Sports Medicine, College of Health Care, China Medical University, Taichung 40432, Taiwan; (C.-H.T.); (Y.-C.F.)
- Department of Orthopedic Surgery, China Medical University Hospital, Taichung 40432, Taiwan;
| | - Yuan-Shun Lo
- Department of Orthopedic Surgery, China Medical University Hospital, Taichung 40432, Taiwan;
- Department of Orthopedic Surgery, China Medical University Beigang Hospital, Yunlin 65101, Taiwan
- Graduate Institute of Precision Engineering, National Chung Hsing University, Taichung 40227, Taiwan
| | - Yi-Chin Fong
- Department of Sports Medicine, College of Health Care, China Medical University, Taichung 40432, Taiwan; (C.-H.T.); (Y.-C.F.)
- Department of Orthopedic Surgery, China Medical University Hospital, Taichung 40432, Taiwan;
- Department of Orthopedic Surgery, China Medical University Beigang Hospital, Yunlin 65101, Taiwan
| | - Chih-Hsin Tang
- Graduate Institute of Biomedical Science, China Medical University, Taichung 40402, Taiwan; (C.-Y.S.); (S.-L.H.)
- Department of Medical Laboratory Science and Biotechnology, Asia University, Taichung 41354, Taiwan;
- Department of Pharmacology, School of Medicine, China Medical University, Taichung 40402, Taiwan
- Chinese Medicine Research Center, China Medical University, Taichung 40402, Taiwan
- Department of Medical Research, China Medical University Hsinchu Hospital, Hsinchu 30205, Taiwan
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Torres-Salvador F, Ojeda J, Castro C, Gerasimova Y, Chumbimuni-Torres K. A Single Electrochemical Biosensor Designed to Detect Any Virus. Anal Chem 2024; 96:5752-5756. [PMID: 38560822 DOI: 10.1021/acs.analchem.3c05962] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
Viruses are the primary cause of many infectious diseases in both humans and animals. Various testing methods require an amplification step of the viral RNA sample before detection, with quantitative reverse transcription polymerase chain reaction (RT-qPCR) being one of the most widely used along with lesser-known methods like Nucleic Acid Sequence-Based Amplification (NASBA). NASBA offers several advantages, such as isothermal amplification and high selectivity for specific sequences, making it an attractive option for low-income facilities. In this research, we employed a single electrochemical biosensor (E-Biosensor) designed for potentially detecting any virus by modifying the NASBA protocol. In this modified protocol, a reverse primer is designed with an additional 22-nucleotide sequence (tag region) at the 5'-end, which is added to the NASBA process. This tag region becomes part of the final amplicon generated by NASBA. It can hybridize with a single specific E-Biosensor probe set, enabling subsequent virus detection. Using this approach, we successfully detected three different viruses with a single E-Biosensor design, demonstrating the platform's potential for virus detection.
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Affiliation(s)
| | - Julio Ojeda
- Department of Chemistry, University of Central Florida, Orlando, Florida 32816, United States
| | - Cynthia Castro
- Department of Chemistry, University of Central Florida, Orlando, Florida 32816, United States
| | - Yulia Gerasimova
- Department of Chemistry, University of Central Florida, Orlando, Florida 32816, United States
| | - Karin Chumbimuni-Torres
- Department of Chemistry, University of Central Florida, Orlando, Florida 32816, United States
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Kumagai H, Furusawa H. Real-Time Monitoring of a Nucleic Acid Amplification Reaction Using a Mass Sensor Based on a Quartz-Crystal Microbalance. BIOSENSORS 2024; 14:155. [PMID: 38667148 PMCID: PMC11048521 DOI: 10.3390/bios14040155] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2024] [Revised: 03/21/2024] [Accepted: 03/23/2024] [Indexed: 04/28/2024]
Abstract
Nucleic acid amplification reactions such as polymerase chain reaction (PCR), which uses a DNA polymerase to amplify individual double-stranded DNA fragments, are a useful technique for visualizing the presence of specific genomes. Although the fluorescent labeling method is mainly used with DNA amplification, other detection methods should be considered for further improvements, such as miniaturization and cost reduction, of reaction-monitoring devices. In this study, the quartz-crystal microbalance (QCM) method, which can measure nanogram-order masses, was applied for the real-time detection of DNA fragments in a solution with nucleic acids. This was combined with an isothermal nucleic acid amplification reaction based on the recombinase polymerase amplification (RPA) method, which allowed DNA amplification at a constant temperature. When the DNA amplification reaction was initiated on a QCM sensor plate with an immobilized primer DNA strand, a significant increase in mass was observed compared to when the primer DNA was not immobilized. QCM was shown to be sufficiently sensitive for the in situ detection of amplified DNA fragments. Combining a portable QCM device and RPA offers a sensitive point-of-care method for detecting nucleic acids.
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Affiliation(s)
- Hideto Kumagai
- Graduate School of Organic Materials Science, Yamagata University, Yonezawa 992-8510, Japan
| | - Hiroyuki Furusawa
- Graduate School of Organic Materials Science, Yamagata University, Yonezawa 992-8510, Japan
- Institute for the Promotion of General Graduate Education (IPGE), Yamagata University, Yonezawa 992-8510, Japan
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10
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Lehnert T, Gijs MAM. Microfluidic systems for infectious disease diagnostics. LAB ON A CHIP 2024; 24:1441-1493. [PMID: 38372324 DOI: 10.1039/d4lc00117f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/20/2024]
Abstract
Microorganisms, encompassing both uni- and multicellular entities, exhibit remarkable diversity as omnipresent life forms in nature. They play a pivotal role by supplying essential components for sustaining biological processes across diverse ecosystems, including higher host organisms. The complex interactions within the human gut microbiota are crucial for metabolic functions, immune responses, and biochemical signalling, particularly through the gut-brain axis. Viruses also play important roles in biological processes, for example by increasing genetic diversity through horizontal gene transfer when replicating inside living cells. On the other hand, infection of the human body by microbiological agents may lead to severe physiological disorders and diseases. Infectious diseases pose a significant burden on global healthcare systems, characterized by substantial variations in the epidemiological landscape. Fast spreading antibiotic resistance or uncontrolled outbreaks of communicable diseases are major challenges at present. Furthermore, delivering field-proven point-of-care diagnostic tools to the most severely affected populations in low-resource settings is particularly important and challenging. New paradigms and technological approaches enabling rapid and informed disease management need to be implemented. In this respect, infectious disease diagnostics taking advantage of microfluidic systems combined with integrated biosensor-based pathogen detection offers a host of innovative and promising solutions. In this review, we aim to outline recent activities and progress in the development of microfluidic diagnostic tools. Our literature research mainly covers the last 5 years. We will follow a classification scheme based on the human body systems primarily involved at the clinical level or on specific pathogen transmission modes. Important diseases, such as tuberculosis and malaria, will be addressed more extensively.
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Affiliation(s)
- Thomas Lehnert
- Laboratory of Microsystems, École Polytechnique Fédérale de Lausanne, Lausanne, CH-1015, Switzerland.
| | - Martin A M Gijs
- Laboratory of Microsystems, École Polytechnique Fédérale de Lausanne, Lausanne, CH-1015, Switzerland.
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11
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Rai A, Ammi Z, Anes-Boulahbal DL, Assadi AA, Amrane A, Baaloudj O, Mouni L. Molecular Amplification and Cell Culturing Efficiency for Enteroviruses' Detection in Cerebrospinal Fluids of Algerian Patients Suffering from Meningitis. Viruses 2024; 16:170. [PMID: 38399946 PMCID: PMC10891896 DOI: 10.3390/v16020170] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2024] [Revised: 01/19/2024] [Accepted: 01/21/2024] [Indexed: 02/25/2024] Open
Abstract
Enteroviruses (EVs) represent a major cause of viral meningitis, being responsible for nearly 1 billion infections each year worldwide. Several techniques were developed to obtain better diagnostic results of EV infections. Herein, we evaluated the efficiency of EV detection through isolation on both Rhabdomyosarcoma (RD) and Vero cell line cultures, conventional reverse transcription-polymerase chain reaction (RT-PCR) and real-time RT-PCR. Thus, 50 cerebrospinal fluid (CSF) samples belonging to patients suspected to have viral meningitis in northern Algeria were collected, anonymously numbered from 1 to 50 and subjected to the above-mentioned techniques for EV detection. Using real-time RT-PCR, 34 CSF samples were revealed to be positive for viral origin of meningitis (68%). Thirteen of them were positive when the conventional RT-PCR was used (26%), and only three samples gave positive results when the cell culture technique was used (6%). Surprisingly, two cell culture-positive CSF samples, namely, 31 and 39, were negative using RT-PCR directly on the original samples. However, they turned to be positive when amplification was carried out on their corresponding cell culture supernatant. The cell-cultured viral isolates were then identified by sequencing their viral genome's VP1 regions. All of them were revealed to belong to the echovirus 27 strain. This investigation demonstrates that RT-PCR techniques are often more sensitive, accurate and much faster, providing reliable results within a clinically acceptable timeframe. However, viral isolation on cell cultures remains crucial to obtain enough viral load for serological tests or even to avoid the rare, but existing, false negative PCR.
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Affiliation(s)
- Abdelwahab Rai
- Laboratoire de Gestion et Valorisation des Ressources Naturelles et Assurance Qualité, Faculté SNVST, Université de Bouira, Bouira 10000, Algeria;
| | - Zohra Ammi
- Faculté SNVST, Université de Bouira, Bouira 10000, Algeria;
| | - Dahbia Leila Anes-Boulahbal
- Laboratoire des Entérovirus, Département de Virologie, Institut Pasteur d’Alger, Annexe de Sidi-Fredj, Alger 16000, Algeria;
| | - Aymen Amin Assadi
- College of Engineering, Imam Mohammad Ibn Saud Islamic University, IMSIU, Riyadh 11432, Saudi Arabia;
- Ecole Nationale Supérieure de Chimie de Rennes, University Rennes, CNRS, ISCR-UMR 6226, 35000 Rennes, France;
| | - Abdeltif Amrane
- Ecole Nationale Supérieure de Chimie de Rennes, University Rennes, CNRS, ISCR-UMR 6226, 35000 Rennes, France;
| | - Oussama Baaloudj
- Laboratory of Reaction Engineering, Faculty of Mechanical Engineering and Process Engineering, Université des Sciences et de la Technologie Houari Boumediene, BP 32, Algiers 16111, Algeria;
| | - Lotfi Mouni
- Laboratoire de Gestion et Valorisation des Ressources Naturelles et Assurance Qualité, Faculté SNVST, Université de Bouira, Bouira 10000, Algeria;
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12
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Ripa A, Díaz-Caballero JA, Palacios-González MJ, Espinosa A, García-Zapata JL, Fernández-Garcia JL. Application of real-time PCR for the identification of the endangered species Galemys pyrenaicus through faecal samples. Mol Biol Rep 2024; 51:76. [PMID: 38180618 PMCID: PMC10770224 DOI: 10.1007/s11033-023-09010-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2023] [Accepted: 11/14/2023] [Indexed: 01/06/2024]
Abstract
BACKGROUND Currently, many micromammals are important targets for study. The endangered Galemys pyrenaicus is an outstanding example. Globally, their populations have suffered a substantial decline in last 20 years. In the surveyed area, the capture of desman is legally forbidden due to the high conservation concerns. Reason by non-invasive sampling through faeces is proposed for its monitoring. Furthermore, the confusion between faeces from desman and Mediterranean water shrews must be considered. Thus, the aim of this study was focused on developing RT-PCR assays to determine the presence of Galemys pyrenaicus and N. a. anomalus from non-invasive samples. METHODS AND RESULTS The study was conducted in the mountains of the System Central of Extremadura (Spain). A total of 186 samples were collected from 2018 to 2021 by experts where historically reported and/or our previous studies confirmed their presence. RT-PCR assays using hydrolysis probes were designed to detect genetic material from both desman and Mediterranean water shrews and its specificity was confirmed. The reliability of the method was further assessed by PCR sequencing of mitochondrial Cyb and d-loop, resulting fully compatible with the RT-PCR approach. Intraspecific phylogenetic relationship was reported to improve knowledge about mtDNA variability in the desman from the Central System. CONCLUSIONS We demonstrated that RT-PCR gives a gold opportunity to further map the species using faeces which minimizes disturbance and reports both population status and individual presence. Cost-effective RT-PCR combined with field-collected faeces allows us to better investigate the full range of occurrence of the species.
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Affiliation(s)
- Adriana Ripa
- Genetic and Animal Breeding, Faculty of Veterinary, Universidad de Extremadura, 10071, Cáceres, Spain
| | - José A Díaz-Caballero
- Dirección General Sostenibilidad, Consejería Para La Transición Ecológica y Sostenibilidad, Junta de Extremadura, 06800, Merida, Spain
- Área del Medio Natural, Sociedad de Gestión Pública de Extremadura (GPEX), Junta de Extremadura, Mérida, España
| | - María Jesús Palacios-González
- Dirección General Sostenibilidad, Consejería Para La Transición Ecológica y Sostenibilidad, Junta de Extremadura, 06800, Merida, Spain
| | - Antonio Espinosa
- Genetic and Animal Breeding, Faculty of Veterinary, Universidad de Extremadura, 10071, Cáceres, Spain
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13
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Downard KM. 25 Years Responding to Respiratory and Other Viruses with Mass Spectrometry. Mass Spectrom (Tokyo) 2023; 12:A0136. [PMID: 38053835 PMCID: PMC10694638 DOI: 10.5702/massspectrometry.a0136] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2023] [Accepted: 10/24/2023] [Indexed: 12/07/2023] Open
Abstract
This review article presents the development and application of mass spectrometry (MS) approaches, developed in the author's laboratory over the past 25 years, to detect; characterise, type and subtype; and distinguish major variants and subvariants of respiratory viruses such as influenza and severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). All features make use of matrix-assisted laser desorption ionisation (MALDI) mass maps, recorded for individual viral proteins or whole virus digests. A MALDI-based immunoassay in which antibody-peptide complexes were preserved on conventional MALDI targets without their immobilisation led to an approach that enabled their indirect detection. The site of binding, and thus the molecular antigenicity of viruses, could be determined. The same approach was employed to study antivirals bound to their target viral protein, the nature of the binding residues, and relative binding affinities. The benefits of high-resolution MS were exploited to detect sequence-conserved signature peptides of unique mass within whole virus and single protein digests. These enabled viruses to be typed, subtyped, their lineage determined, and variants and subvariants to be distinguished. Their detection using selected ion monitoring improved analytical sensitivity limits to aid the identification of viruses in clinical specimens. The same high-resolution mass map data, for a wide range of viral strains, were input into a purpose-built algorithm (MassTree) in order to both chart and interrogate viral evolution. Without the need for gene or protein sequences, or any sequence alignment, this phylonumerics approach also determines and displays single-point mutations associated with viral protein evolution in a single-tree building step.
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Affiliation(s)
- Kevin M. Downard
- Infectious Disease Responses Laboratory, Prince of Wales Clinical Research Sciences, Sydney, NSW, Australia
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14
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Srivastava P, Prasad D. Human Norovirus Detection: How Much Are We Prepared? Foodborne Pathog Dis 2023; 20:531-544. [PMID: 37792418 DOI: 10.1089/fpd.2023.0024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/05/2023] Open
Abstract
Norovirus (NoV) is known to be the second nonbacterial enteric pathogen after rotavirus that causes acute gastroenteritis. They can be spread from person to person through fecal-oral routes. Infection can lead to severe diarrhea, causing stomach pain, vomiting, and nausea. Rapid detection of NoV can control huge economic and productive losses. Genotyping various emerging NoV strains is important to compare the severity among different strains. Conventional immunological and molecular methods have evolved and contributed to developing detection techniques. Immunological (enzyme-linked immunosorbent assay) and molecular detection (reverse transcriptase polymerase chain reaction [RT-PCR], RT-quantitative PCR, loop-mediated isothermal amplification, nucleic acid sequence-based alignment, recombinase polymerase amplification) methods have been mainly used. The development of biosensors using aptasensor, affinity peptides, nanoparticles, microfluidics, and so on, are currently the most researched topics. The availability of next-generation sequencing technologies has greatly influenced the diagnosis of NoV. The complementation of advanced technologies is helpful in identification of new variants. In this study, techniques that are useful in detecting NoV are discussed. This review has investigated the availability of recent methods used in the detection, present status, and futuristic plan of action in case of outbreak and pandemic.
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Affiliation(s)
- Pulkit Srivastava
- Department of Bioengineering and Biotechnology, Birla Institute of Technology, Mesra, Ranchi, India
| | - Dinesh Prasad
- Department of Bioengineering and Biotechnology, Birla Institute of Technology, Mesra, Ranchi, India
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15
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Papagiannis D, Perlepe G, Tendolouri T, Karakitsiou P, Damagka G, Kalaitzi A, Alevra S, Malli F, Gourgoulianis KI. Proportion of Respiratory Syncytial Virus, SARS-CoV-2, Influenza A/B, and Adenovirus Cases via Rapid Tests in the Community during Winter 2023-A Cross Sectional Study. Diseases 2023; 11:122. [PMID: 37754318 PMCID: PMC10529898 DOI: 10.3390/diseases11030122] [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: 07/26/2023] [Revised: 09/13/2023] [Accepted: 09/14/2023] [Indexed: 09/28/2023] Open
Abstract
Respiratory infections constitute a major reason for infants and children seeking medical advice and visiting health facilities, thus remaining a significant public threat with high morbidity and mortality. The predominant viruses causing viral respiratory infections are influenza A and B viruses (Flu-A, Flu-B), respiratory syncytial virus (RSV), adenovirus and coronaviruses. We aimed to record the proportion of RSV, SARS-CoV-2, influenza A/B and adenovirus cases with rapid antigen tests and validate the results with RT-PCR assays of upper respiratory specimens with a wide range of viral loads and (co)-infection patterns in children. Clinical samples were collected from early symptomatic children (presenting with fever and/or cough and/or headache within 5-7 days). The surveillance program was conducted in five private pediatric dispensaries and one pediatric care unit, from 10 January 2023 to 30 March 2023 in central Greece. The total sample of specimens collected was 784 young children and infants, of which 383 (48.8%) were female and 401 were male (51.2%). The mean age of participants was 7.3 + 5.5 years. The sensitivity of the FLU A & B test was 91.15% (95% CI: 84.33-95.67%), and the specificity was 98.96% (95% CI: 97.86-99.58%). The sensitivity and specificity of the adenovirus and RSV test was {92.45% (95% CI: 81.79-97.91%), 99.32% (95% CI: 98.41-99.78%)} and {92.59% (95% CI: 75.71-99.09%), 99.47% (95% CI: 98.65-99.86%)} respectively. Lastly, the sensitivity of the SARS-CoV-2 test was 100.00% (95% CI: 79.41-100.00%) and the specificity was 99.74% (95% CI: 99.06-99.97%). We recorded a proportion of 14.3% and 3.44% for influenza A and B, respectively, followed by a proportion of 6.9% for adenovirus, a proportion of 3.7% for RSV, and finally, a proportion of 2.3% for SARS-CoV-2. The combination of a new multiple rapid test with multiple antigens will probably be a useful tool with a financial impact for health systems targeting the early detection and appropriate treatment of respiratory infections in emergency departments in primary health care facilities.
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Affiliation(s)
- Dimitrios Papagiannis
- Public Health & Vaccines Laboratory, Department of Nursing, School of Health Sciences, University of Thessaly, 41110 Larissa, Greece
| | - Garifallia Perlepe
- Respiratory Medicine Department, Faculty of Medicine, University of Thessaly, 41500 Larissa, Greece; (G.P.); (K.I.G.)
| | - Theodora Tendolouri
- MD Private Sector of Greek Health System, Kanouta 1 Str. Trikala Thessaly, 42100 Trikala, Greece;
| | - Polyxeni Karakitsiou
- MD Private Sector of Greek Health System, Annas Komninis 1-3 Str. Trikala Thessaly, 42100 Trikala, Greece;
| | - Georgia Damagka
- MD Private Sector of Greek Health System, Lefkosias Str. 3 Larissa Thessaly, 41335 Larissa, Greece;
| | - Anna Kalaitzi
- Pediatric Department, General Hospital of Larissa, Tsakalof 1 Str. Larissa Thessaly, 41221 Larissa, Greece; (A.K.); (S.A.)
| | - Sofia Alevra
- Pediatric Department, General Hospital of Larissa, Tsakalof 1 Str. Larissa Thessaly, 41221 Larissa, Greece; (A.K.); (S.A.)
| | - Foteini Malli
- Respiratory Disorders Laboratory, Department of Nursing, University of Thessaly, 41110 Larissa, Greece;
| | - Konstantinos I. Gourgoulianis
- Respiratory Medicine Department, Faculty of Medicine, University of Thessaly, 41500 Larissa, Greece; (G.P.); (K.I.G.)
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16
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Bruno SM, Blaconà G, Lo Cicero S, Castelli G, Virgulti M, Testino G, Pierandrei S, Fuso A, Cimino G, Ferraguti G, Eramo A, Lucarelli M. Quantitative Evaluation of CFTR Gene Expression: A Comparison between Relative Quantification by Real-Time PCR and Absolute Quantification by Droplet Digital PCR. Genes (Basel) 2023; 14:1781. [PMID: 37761921 PMCID: PMC10531455 DOI: 10.3390/genes14091781] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Revised: 09/01/2023] [Accepted: 09/07/2023] [Indexed: 09/29/2023] Open
Abstract
In the precision medicine era of cystic fibrosis (CF), therapeutic interventions, by the so-called modulators, target the cystic fibrosis transmembrane conductance regulator (CFTR) protein. The levels of targetable CFTR proteins are a main variable in the success of patient-specific therapy. In turn, the CFTR protein level depends, at least in part, on the level of CFTR mRNA. Many mechanisms can modulate the CFTR mRNA level, for example, transcriptional rate, stability of the mRNA, epigenetics, and pathogenic variants that can affect mRNA production and degradation. Independently from the causes of variable CFTR mRNA levels, their exact quantitative assessment is of great importance in CF. Methods with high analytical sensitivity, precision, and accuracy are mandatory for the quantitative evaluation aimed at the amelioration of the diagnostic, prognostic, and therapeutic aspects. This paper compares, for the first time, two CFTR gene expression quantification methods: a well-established method for the relative quantification of CFTR mRNA using a real-time PCR and an innovative method for its absolute quantification using a droplet digital PCR. No comprehensive methods for absolute CFTR quantification via droplet digital PCR have been published so far. The accurate quantification of CFTR expression at the mRNA level is a critical step for the personalized therapeutic approaches of CF.
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Affiliation(s)
- Sabina Maria Bruno
- Department of Experimental Medicine, Sapienza University of Rome, 00161 Rome, Italy; (S.M.B.); (G.B.); (M.V.); (G.T.); (S.P.); (A.F.); (G.F.)
| | - Giovanna Blaconà
- Department of Experimental Medicine, Sapienza University of Rome, 00161 Rome, Italy; (S.M.B.); (G.B.); (M.V.); (G.T.); (S.P.); (A.F.); (G.F.)
| | - Stefania Lo Cicero
- Department of Oncology and Molecular Medicine, National Institute of Health, Istituto Superiore di Sanità, ISS, 00161 Rome, Italy; (S.L.C.); (G.C.); (A.E.)
| | - Germana Castelli
- Department of Oncology and Molecular Medicine, National Institute of Health, Istituto Superiore di Sanità, ISS, 00161 Rome, Italy; (S.L.C.); (G.C.); (A.E.)
| | - Mariarita Virgulti
- Department of Experimental Medicine, Sapienza University of Rome, 00161 Rome, Italy; (S.M.B.); (G.B.); (M.V.); (G.T.); (S.P.); (A.F.); (G.F.)
| | - Giancarlo Testino
- Department of Experimental Medicine, Sapienza University of Rome, 00161 Rome, Italy; (S.M.B.); (G.B.); (M.V.); (G.T.); (S.P.); (A.F.); (G.F.)
| | - Silvia Pierandrei
- Department of Experimental Medicine, Sapienza University of Rome, 00161 Rome, Italy; (S.M.B.); (G.B.); (M.V.); (G.T.); (S.P.); (A.F.); (G.F.)
| | - Andrea Fuso
- Department of Experimental Medicine, Sapienza University of Rome, 00161 Rome, Italy; (S.M.B.); (G.B.); (M.V.); (G.T.); (S.P.); (A.F.); (G.F.)
| | - Giuseppe Cimino
- Cystic Fibrosis Reference Center of Lazio Region, Policlinico Umberto I University Hospital, 00161 Rome, Italy;
| | - Giampiero Ferraguti
- Department of Experimental Medicine, Sapienza University of Rome, 00161 Rome, Italy; (S.M.B.); (G.B.); (M.V.); (G.T.); (S.P.); (A.F.); (G.F.)
| | - Adriana Eramo
- Department of Oncology and Molecular Medicine, National Institute of Health, Istituto Superiore di Sanità, ISS, 00161 Rome, Italy; (S.L.C.); (G.C.); (A.E.)
| | - Marco Lucarelli
- Department of Experimental Medicine, Sapienza University of Rome, 00161 Rome, Italy; (S.M.B.); (G.B.); (M.V.); (G.T.); (S.P.); (A.F.); (G.F.)
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Kieu Doan TN, Croyle MA. Physical characteristics and stability profile of recombinant plasmid DNA within a film matrix. Eur J Pharm Biopharm 2023; 190:270-283. [PMID: 37567395 DOI: 10.1016/j.ejpb.2023.08.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Revised: 07/14/2023] [Accepted: 08/08/2023] [Indexed: 08/13/2023]
Abstract
Plasmids are essential source material for production of biological drugs, vaccines and vectors for gene therapy. They are commonly formulated as frozen solutions. Considering the cost associated with maintenance of cold chain conditions during storage and transport, there is a significant need for alternative methods for stabilization of plasmids at ambient temperature. The objective of these studies was to identify a film-based formulation that preserved transfection efficiency of plasmids at 25 °C. A model plasmid, pAAVlacZ, was used for these studies. Transfection efficiency and agarose gel electrophoresis were utilized to assess bioactivity and changes in physical conformation of plasmid during storage. An amino acid, capable of sustaining a positive charge while supporting an alkaline environment within the film matrix, preserved transfection efficiency for 9 months at 25 °C. Addition of sugar and a plasticizer to the formulation preserved the plasmid in an amorphous state and improved handling properties of the film. The manner in which excipients were incorporated into bulk formulations and environmental humidity in which films were stored significantly impacted transfection efficiency of plasmid in the rehydrated solution. Taken together, these results suggest that plasmids can be stored for extended periods of time without refrigeration within a film matrix.
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Affiliation(s)
- Trang Nguyen Kieu Doan
- The University of Texas at Austin College of Pharmacy, Division of Molecular Pharmaceutics and Drug Delivery, Austin, TX 78712, United States
| | - Maria A Croyle
- The University of Texas at Austin College of Pharmacy, Division of Molecular Pharmaceutics and Drug Delivery, Austin, TX 78712, United States; John R. LaMontagne Center for Infectious Disease, The University of Texas at Austin, Austin, TX 78712, United States.
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18
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Saraç İ, Aydın SŞ, Özmen M, Doru Hİ, Tonkaz G, Çırçır MN, Akpınar F, Zengin O, Delice O, Aydınyılmaz F. Prevalence, Risk Factors, Prognosis, and Management of Pericardial Effusion in COVID-19. J Cardiovasc Dev Dis 2023; 10:368. [PMID: 37754797 PMCID: PMC10531872 DOI: 10.3390/jcdd10090368] [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: 06/03/2023] [Revised: 08/20/2023] [Accepted: 08/21/2023] [Indexed: 09/28/2023] Open
Abstract
Background: There is limited data in the literature about the clinical importance and prognosis of pericardial effusion (PE) in patients discharged after recovering from COVID-19, but large-scale studies have yet to be available. This study investigated the prevalence, risk factors, prognosis, late clinical outcomes, and management of PE in COVID-19. Materials and Methods: Between August 2020 and March 2021, 15,689 patients were followed up in our pandemic hospital due to COVID-19. Patients with positive polymerase chain reaction (PCR) test results and PE associated with COVID-19 in computed tomography (CT) were included in the study. The patients were divided into three groups according to PE size (mild, moderate, and large). Transthoracic echocardiography (TTE) records, laboratory data, clinical outcomes, and medical treatments of patients discharged from the hospital were retrospectively reviewed. Results: According to the PE size (mild, moderate, large) of 256 patients with PE at admission or discharge, the mean age was 62.17 ± 16.34, 69.12 ± 12.52, and 72.44 ± 15.26, respectively. The mean follow-up period of the patients was 25.2 ± 5.12 months. Of the patients in the study population, 53.5% were in the mild group, 30.4% in the moderate group, and 16.1% in the large group. PE became chronic in a total of 178 (69.6%) patients at the end of the mean three months, and chronicity increased as PE size increased. Despite the different anti-inflammatory treatments for PE in the acute phase, similar chronicity was observed. In addition, as the PE size increased, the patients' frequency of hospitalization, complications, and mortality rates showed statistical significance between the groups. Conclusions: The clinical prognosis of patients presenting with PE was quite poor; as PE in size increased, cardiac and noncardiac events and mortality rates were significantly higher. Patients with large PE associated with COVID-19 at discharge should be monitored at close intervals due to the chronicity of PE and the increased risk of tamponade.
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Affiliation(s)
- İbrahim Saraç
- Department of Cardiology, Erzurum City Hospital, Erzurum 25010, Turkey; (S.Ş.A.); (M.Ö.); (F.A.)
| | - Sidar Şiyar Aydın
- Department of Cardiology, Erzurum City Hospital, Erzurum 25010, Turkey; (S.Ş.A.); (M.Ö.); (F.A.)
| | - Murat Özmen
- Department of Cardiology, Erzurum City Hospital, Erzurum 25010, Turkey; (S.Ş.A.); (M.Ö.); (F.A.)
| | - Halil İbrahim Doru
- Department of Emergency Medicine, Erzurum City Hospital, Erzurum 25010, Turkey; (H.İ.D.); (M.N.Ç.); (O.Z.); (O.D.)
| | - Gökhan Tonkaz
- Department of Radiology, Giresun University Research Hospital, Giresun 28200, Turkey;
| | - Melike Nur Çırçır
- Department of Emergency Medicine, Erzurum City Hospital, Erzurum 25010, Turkey; (H.İ.D.); (M.N.Ç.); (O.Z.); (O.D.)
| | - Furkan Akpınar
- Department of Emergency Medicine, Erzurum City Hospital, Erzurum 25010, Turkey; (H.İ.D.); (M.N.Ç.); (O.Z.); (O.D.)
| | - Onur Zengin
- Department of Emergency Medicine, Erzurum City Hospital, Erzurum 25010, Turkey; (H.İ.D.); (M.N.Ç.); (O.Z.); (O.D.)
| | - Orhan Delice
- Department of Emergency Medicine, Erzurum City Hospital, Erzurum 25010, Turkey; (H.İ.D.); (M.N.Ç.); (O.Z.); (O.D.)
| | - Faruk Aydınyılmaz
- Department of Cardiology, Erzurum City Hospital, Erzurum 25010, Turkey; (S.Ş.A.); (M.Ö.); (F.A.)
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19
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Ryu IS, Kim DH, Ro JY, Park BG, Kim SH, Im JY, Lee JY, Yoon SJ, Kang H, Iwatsubo T, Teunissen CE, Cho HJ, Ryu JH. The microRNA-485-3p concentration in salivary exosome-enriched extracellular vesicles is related to amyloid β deposition in the brain of patients with Alzheimer's disease. Clin Biochem 2023:110603. [PMID: 37355215 DOI: 10.1016/j.clinbiochem.2023.110603] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Revised: 06/15/2023] [Accepted: 06/17/2023] [Indexed: 06/26/2023]
Abstract
OBJECTIVES Alzheimer's disease (AD) is an irreversible neurodegenerative disease characterized by progressive long-term memory loss and cognitive dysfunction. Neuroimaging tests for abnormal amyloid-β (Aβ) deposition are considered the most reliable methods for the diagnosis of AD; however, the cost for such testing is very high and generally not covered by national insurance systems. Accordingly, it is only recommended for individuals exhibiting clinical symptoms of AD supported by clinical cognitive assessments. Recently, it was suggested that dysregulated microRNA-485-3p (miRNA-485-3p) in the brain and cerebrospinal fluid is closely related to pathogenesis of AD. However, a relationship between circulating miRNA-485-3p in salivary exosome-enriched extracellular vesicles (EE-EV) and Aβ deposition in the brain has not been observed. DESIGN & METHODS Using quantitative real-time polymerase chain reaction, we analyzed miRNA-485-3p concentration in salivary EE-EV. We used receiver operating characteristic (ROC) curve analysis to evaluate its predictive value for Aβ positron emission tomography (Aβ-PET) positivity in patients with AD. RESULTS Our results showed that the miRNA-485-3p concentration in salivary EE-EV isolated from patients with AD was significantly increased compared with that in the healthy controls (p<0.0001). In the analysis of all participants, the miRNA-485-3p concentration was significantly increased in Aβ-PET-positive participants compared to Aβ-PET-negative participants (p<0.0001). Further analysis using only AD patients also showed that the miRNA-485-3p concentration was significantly increased in Aβ-PET-positive AD patients vs. Aβ-PET-negative AD patients (p=0.0063). The ROC curve analysis for differentiating Aβ-PET-positive and negative participants showed that the area under the curve for miRNA-485-3p was 0.9217. CONCLUSION These findings suggested that the miRNA-485-3p concentration in salivary EE-EV was closely related to Aβ deposition in the brain and had high diagnostic accuracy for predicting Aβ-PET positivity.
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Affiliation(s)
- In Soo Ryu
- BIORCHESTRA Co. Ltd., 17, Techno 4-ro, Yuseong-gu, Daejeon 34013, South Korea
| | - Dae Hoon Kim
- BIORCHESTRA Co. Ltd., 17, Techno 4-ro, Yuseong-gu, Daejeon 34013, South Korea
| | - Ju-Ye Ro
- BIORCHESTRA Co. Ltd., 17, Techno 4-ro, Yuseong-gu, Daejeon 34013, South Korea
| | - Byeong-Gyu Park
- BIORCHESTRA Co. Ltd., 17, Techno 4-ro, Yuseong-gu, Daejeon 34013, South Korea
| | - Seo Hyun Kim
- BIORCHESTRA Co. Ltd., 17, Techno 4-ro, Yuseong-gu, Daejeon 34013, South Korea
| | - Jong-Yeop Im
- BIORCHESTRA Co. Ltd., 17, Techno 4-ro, Yuseong-gu, Daejeon 34013, South Korea
| | - Jun-Young Lee
- Borame Medical Center 20, Boramae-ro 5-gil, Dongjak-gu, Seoul 07061, South Korea
| | - Soo Jin Yoon
- Daejeon Eulji Medical Center, 95, Dunsanseo-ro, Seo-gu, Daejeon 35233, South Korea
| | - Heeyoung Kang
- Gyeongsang National University Hospital, 501, Jinju-daero, Jinju 52828, South Korea
| | - Takeshi Iwatsubo
- Department of Neuropathology, Graduate School of Medicine, The University of Tokyo, Tokyo 113-0033, Japan
| | - Charlotte E Teunissen
- Neurochemistry Laboratory, Department of Clinical Chemistry, Amsterdam Neuroscience, Amsterdam University Medical Centers, Vrije Universiteit, Amsterdam 1081, Netherlands
| | - Hyun-Jeong Cho
- Department of Biomedical Laboratory Science, College of Medical Science, Konyang University, 158, Gwanjeodong-ro, Seo-gu, Daejeon 35365, South Korea.
| | - Jin-Hyeob Ryu
- BIORCHESTRA Co. Ltd., 17, Techno 4-ro, Yuseong-gu, Daejeon 34013, South Korea; BIORCHESTRA US., Inc., 1 Kendall square, Building 200, Suite 2-103, Cambridge, MA, 02139, United States.
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20
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Cheng L, Lan L, Ramalingam M, He J, Yang Y, Gao M, Shi Z. A review of current effective COVID-19 testing methods and quality control. Arch Microbiol 2023; 205:239. [PMID: 37195393 DOI: 10.1007/s00203-023-03579-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2022] [Revised: 05/04/2023] [Accepted: 05/04/2023] [Indexed: 05/18/2023]
Abstract
COVID-19 is a highly infectious disease caused by the SARS-CoV-2 virus, which primarily affects the respiratory system and can lead to severe illness. The virus is extremely contagious, early and accurate diagnosis of SARS-CoV-2 is crucial to contain its spread, to provide prompt treatment, and to prevent complications. Currently, the reverse transcriptase polymerase chain reaction (RT-PCR) is considered to be the gold standard for detecting COVID-19 in its early stages. In addition, loop-mediated isothermal amplification (LMAP), clustering rule interval short palindromic repeats (CRISPR), colloidal gold immunochromatographic assay (GICA), computed tomography (CT), and electrochemical sensors are also common tests. However, these different methods vary greatly in terms of their detection efficiency, specificity, accuracy, sensitivity, cost, and throughput. Besides, most of the current detection methods are conducted in central hospitals and laboratories, which is a great challenge for remote and underdeveloped areas. Therefore, it is essential to review the advantages and disadvantages of different COVID-19 detection methods, as well as the technology that can enhance detection efficiency and improve detection quality in greater details.
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Affiliation(s)
- Lijia Cheng
- Clinical Medical College & Affiliated Hospital, School of Basic Medical Sciences, Chengdu University, Chengdu, 610106, China.
| | - Liang Lan
- Clinical Medical College & Affiliated Hospital, School of Basic Medical Sciences, Chengdu University, Chengdu, 610106, China
| | - Murugan Ramalingam
- Clinical Medical College & Affiliated Hospital, School of Basic Medical Sciences, Chengdu University, Chengdu, 610106, China
| | - Jianrong He
- Clinical Medical College & Affiliated Hospital, School of Basic Medical Sciences, Chengdu University, Chengdu, 610106, China
| | - Yimin Yang
- Clinical Medical College & Affiliated Hospital, School of Basic Medical Sciences, Chengdu University, Chengdu, 610106, China
| | - Min Gao
- Clinical Medical College & Affiliated Hospital, School of Basic Medical Sciences, Chengdu University, Chengdu, 610106, China
| | - Zheng Shi
- Clinical Medical College & Affiliated Hospital, School of Basic Medical Sciences, Chengdu University, Chengdu, 610106, China.
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