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Chen W, Chen B, Li X, Xu G, Yang L, Wu J, Yu H. Non-canonical amino acids uncover the significant impact of Tyr671 on Taq DNA polymerase catalytic activity. FEBS J 2024; 291:2876-2896. [PMID: 38362811 DOI: 10.1111/febs.17091] [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: 06/12/2023] [Revised: 11/20/2023] [Accepted: 02/01/2024] [Indexed: 02/17/2024]
Abstract
Responsible for synthesizing the complementary strand of the DNA template, DNA polymerase is a crucial enzyme in DNA replication, recombination and repair. A highly conserved tyrosine (Tyr), located at the C-terminus of the O-helix in family A DNA polymerases, plays a critical role in enzyme activity and fidelity. Here, we combined the technology of genetic code extension to incorporate non-canonical amino acids and molecular dynamics (MD) simulations to uncover the mechanisms by which Tyr671 impacts substrate binding and conformation transitions in a DNA polymerase from Thermus aquaticus. Five non-canonical amino acids, namely l-3,4-dihydroxyphenylalanine (l-DOPA), p-aminophenylalanine (pAF), p-acetylphenylalanine (pAcF), p-cyanophenylalanine (pCNF) and p-nitrophenylalanine (pNTF), were individually incorporated at position 671. Strikingly, Y671pAF and Y671DOPA were active, but with lower activity compared to Y671F and wild-type. Y671pAF showed a higher fidelity than the Y671F, despite both possessing lower fidelity than the wild-type. Metadynamics and long-timescale MD simulations were carried out to probe the role of mutations in affecting protein structure, including open conformation, open-to-closed conformation transition, closed conformation, and closed-to-open conformation transition. The MD simulations clearly revealed that the size of the 671 amino acid residue and interactions with substrate or nearby residues were critical for Tyr671 to determine enzyme activity and fidelity.
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Affiliation(s)
- Wanyi Chen
- Institute of Bioengineering, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, China
- ZJU-Hangzhou Global Scientific and Technological Innovation Centre, Hangzhou, China
| | - Binbin Chen
- Institute of Bioengineering, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, China
- ZJU-Hangzhou Global Scientific and Technological Innovation Centre, Hangzhou, China
| | - Xinjia Li
- Institute of Bioengineering, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, China
- ZJU-Hangzhou Global Scientific and Technological Innovation Centre, Hangzhou, China
| | - Gang Xu
- Institute of Bioengineering, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, China
| | - Lirong Yang
- Institute of Bioengineering, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, China
- ZJU-Hangzhou Global Scientific and Technological Innovation Centre, Hangzhou, China
| | - Jianping Wu
- Institute of Bioengineering, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, China
- ZJU-Hangzhou Global Scientific and Technological Innovation Centre, Hangzhou, China
| | - Haoran Yu
- Institute of Bioengineering, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, China
- ZJU-Hangzhou Global Scientific and Technological Innovation Centre, Hangzhou, China
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2
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Roy SD, Ramasamy S, Obbineni JM. An evaluation of nucleic acid-based molecular methods for the detection of plant viruses: a systematic review. Virusdisease 2024; 35:357-376. [PMID: 39071869 PMCID: PMC11269559 DOI: 10.1007/s13337-024-00863-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2024] [Accepted: 04/15/2024] [Indexed: 07/30/2024] Open
Abstract
Precise and timely diagnosis of plant viruses is a prerequisite for the implementation of efficient management strategies, considering factors like globalization of trade and climate change facilitating the spread of viruses that lead to agriculture yield losses of billions yearly worldwide. Symptomatic diagnosis alone may not be reliable due to the diverse symptoms and confusion with plant abiotic stresses. It is crucial to detect plant viruses accurately and reliably and do so with little time. A complete understanding of the various detection methods is necessary to achieve this. Enzyme-linked immunosorbent assay (ELISA), has become more popular as a method for detecting viruses but faces limitations such as antibody availability, cost, sample volume, and time. Advanced techniques like polymerase chain reaction (PCR) have surpassed ELISA with its various sensitive variants. Over the last decade, nucleic acid-based molecular methods have gained popularity and have quickly replaced other techniques, such as serological techniques for detecting plant viruses due to their specificity and accuracy. Hence, this review enables the reader to understand the strengths and weaknesses of each molecular technique starting with PCR and its variations, along with various isothermal amplification followed by DNA microarrays, and next-generation sequencing (NGS). As a result of the development of new technologies, NGS is becoming more and more accessible and cheaper, and it looks possible that this approach will replace others as a favoured approach for carrying out regular diagnosis. NGS is also becoming the method of choice for identifying novel viruses. Supplementary Information The online version contains supplementary material available at 10.1007/s13337-024-00863-0.
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Affiliation(s)
- Subha Deep Roy
- School of Biosciences and Technology, Vellore Institute of Technology, Vellore, Tamil Nadu India
- School of Agricultural Innovations and Advanced Learning, Vellore Institute of Technology, Vellore, Tamil Nadu India
| | | | - Jagan M. Obbineni
- School of Agricultural Innovations and Advanced Learning, Vellore Institute of Technology, Vellore, Tamil Nadu India
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3
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Bonilla DA, Orozco CA, Forero DA, Odriozola A. Techniques, procedures, and applications in host genetic analysis. ADVANCES IN GENETICS 2024; 111:1-79. [PMID: 38908897 DOI: 10.1016/bs.adgen.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: 06/24/2024]
Abstract
This chapter overviews genetic techniques' fundamentals and methodological features, including different approaches, analyses, and applications that have contributed to advancing health and disease. The aim is to describe laboratory methodologies and analyses employed to understand the genetic landscape of different biological contexts, from conventional techniques to cutting-edge technologies. Besides describing detailed aspects of the polymerase chain reaction (PCR) and derived types as one of the principles for many novel techniques, we also discuss microarray analysis, next-generation sequencing, and genome editing technologies such as transcription activator-like effector nucleases (TALENs) and the clustered regularly interspaced short palindromic repeats (CRISPR) and CRISPR-associated (Cas) systems. These techniques study several phenotypes, ranging from autoimmune disorders to viral diseases. The significance of integrating diverse genetic methodologies and tools to understand host genetics comprehensively and addressing the ethical, legal, and social implications (ELSI) associated with using genetic information is highlighted. Overall, the methods, procedures, and applications in host genetic analysis provided in this chapter furnish researchers and practitioners with a roadmap for navigating the dynamic landscape of host-genome interactions.
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Affiliation(s)
- Diego A Bonilla
- Hologenomiks Research Group, Department of Genetics, Physical Anthropology and Animal Physiology, University of the Basque Country (UPV/EHU), Leioa, Spain; Research Division, Dynamical Business & Science Society-DBSS International SAS, Bogotá, Colombia.
| | - Carlos A Orozco
- Grupo de Investigación en Biología del Cáncer, Instituto Nacional de Cancerología de Colombia, Bogotá, Colombia
| | - Diego A Forero
- School of Health and Sport Sciences, Fundación Universitaria del Área Andina, Bogotá, Colombia
| | - Adrián Odriozola
- Hologenomiks Research Group, Department of Genetics, Physical Anthropology and Animal Physiology, University of the Basque Country (UPV/EHU), Leioa, Spain
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Karbalaei M, Mosavat A, Soleimanpour S, Farsiani H, Ghazvini K, Amini AA, Sankian M, Rezaee SA. Production and Evaluation of Ag85B:HspX:hFcγ1 Immunogenicity as an Fc Fusion Recombinant Multi-Stage Vaccine Candidate Against Mycobacterium tuberculosis. Curr Microbiol 2024; 81:127. [PMID: 38575759 DOI: 10.1007/s00284-024-03655-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2023] [Accepted: 02/29/2024] [Indexed: 04/06/2024]
Abstract
An urgent need is to introduce an effective vaccine against Mycobacterium tuberculosis (M.tb) infection. In the present study, a multi-stage M.tb immunodominant Fcγ1 fusion protein (Ag85B:HspX:hFcγ1) was designed and produced, and the immunogenicity of purified protein was evaluated. This recombinant fusion protein was produced in the Pichia pastoris expression system. The HiTrap-rPA column affinity chromatography purified and confirmed the fusion protein using ELISA and Western blotting methods. The co-localisation assay was used to confirm its proper folding and function. IFN-γ, IL-12, IL-4, and TGF-β expression in C57BL/6 mice then evaluated the immunogenicity of the construct in the presence and absence of BCG. After expression optimisation, medium-scale production and the Western blotting test confirmed suitable production of Ag85B:HspX:hFcγ1. The co-localisation results on antigen-presenting cells (APCs) showed that Ag85B:HspX:hFcγ1 properly folded and bound to hFcγRI. This strong co-localisation with its receptor can confirm inducing proper Th1 responses. The in vivo immunisation assay showed no difference in the expression of IL-4 but a substantial increase in the expression of IFN-γ and IL-12 (P ≤ 0.02) and a moderate increase in TGF-β (P = 0.05). In vivo immunisation assay revealed that Th1-inducing pathways have been stimulated, as IFN-γ and IL-12 strongly, and TGF-β expression moderately increased in Ag85B:HspX:hFcγ1 group and Ag85B:HspX:hFcγ1+BCG. Furthermore, the production of IFN-γ from splenocytes in the Ag85B:HspX:hFcγ1 group was enormously higher than in other treatments. Therefore, this Fc fusion protein can make a selective multi-stage delivery system for inducing appropriate Th1 responses and is used as a subunit vaccine alone or in combination with others.
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Affiliation(s)
- Mohsen Karbalaei
- Department of Microbiology and Virology, School of Medicine, Jiroft University of Medical Sciences, Jiroft, Iran
| | - Arman Mosavat
- Blood Borne Infections Research Center, Academic Center for Education, Culture, and Research (ACECR), Razavi Khorasan, Mashhad, Iran
| | - Saman Soleimanpour
- Antimicrobial Resistance Research Center, Mashhad University of Medical Sciences, Mashhad, Iran
- Department of Microbiology and Virology, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Hadi Farsiani
- Antimicrobial Resistance Research Center, Mashhad University of Medical Sciences, Mashhad, Iran
- Department of Microbiology and Virology, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Kiarash Ghazvini
- Antimicrobial Resistance Research Center, Mashhad University of Medical Sciences, Mashhad, Iran
- Department of Microbiology and Virology, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Abbas Ali Amini
- Cancer and Immunology Research Center, Research Institute for Health Development, Kurdistan University of Medical Sciences, Sanandaj, Iran
| | - Mojtaba Sankian
- Immunology Research Center, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Seyed Abdolrahim Rezaee
- Inflammation and Inflammatory Diseases Division, Faculty of Medicine, Immunology Research Center, Mashhad University of Medical Sciences, Azadi-Square, Medical Campus, Mashhad, 9177948564, Iran.
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Dung TTN, Phat VV, Vinh C, Lan NPH, Phuong NLN, Ngan LTQ, Thwaites G, Thwaites L, Rabaa M, Nguyen ATK, Duy PT. Development and validation of multiplex real-time PCR for simultaneous detection of six bacterial pathogens causing lower respiratory tract infections and antimicrobial resistance genes. BMC Infect Dis 2024; 24:164. [PMID: 38326753 PMCID: PMC10848345 DOI: 10.1186/s12879-024-09028-2] [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: 06/17/2023] [Accepted: 01/18/2024] [Indexed: 02/09/2024] Open
Abstract
BACKGROUND Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, Escherichia coli, Streptococcus pneumoniae and Staphylococcus aureus are major bacterial causes of lower respiratory tract infections (LRTIs) globally, leading to substantial morbidity and mortality. The rapid increase of antimicrobial resistance (AMR) in these pathogens poses significant challenges for their effective antibiotic therapy. In low-resourced settings, patients with LRTIs are prescribed antibiotics empirically while awaiting several days for culture results. Rapid pathogen and AMR gene detection could prompt optimal antibiotic use and improve outcomes. METHODS Here, we developed multiplex quantitative real-time PCR using EvaGreen dye and melting curve analysis to rapidly identify six major pathogens and fourteen AMR genes directly from respiratory samples. The reproducibility, linearity, limit of detection (LOD) of real-time PCR assays for pathogen detection were evaluated using DNA control mixes and spiked tracheal aspirate. The performance of RT-PCR assays was subsequently compared with the gold standard, conventional culture on 50 tracheal aspirate and sputum specimens of ICU patients. RESULTS The sensitivity of RT-PCR assays was 100% for K. pneumoniae, A. baumannii, P. aeruginosa, E. coli and 63.6% for S. aureus and the specificity ranged from 87.5% to 97.6%. The kappa correlation values of all pathogens between the two methods varied from 0.63 to 0.95. The limit of detection of target bacteria was 1600 CFU/ml. The quantitative results from the PCR assays demonstrated 100% concordance with quantitative culture of tracheal aspirates. Compared to culture, PCR assays exhibited higher sensitivity in detecting mixed infections and S. pneumoniae. There was a high level of concordance between the detection of AMR gene and AMR phenotype in single infections. CONCLUSIONS Our multiplex quantitative RT-PCR assays are fast and simple, but sensitive and specific in detecting six bacterial pathogens of LRTIs and their antimicrobial resistance genes and should be further evaluated for clinical utility.
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Affiliation(s)
- Tran Thi Ngoc Dung
- Molecular Epidemiology Group, Oxford University Clinical Research Unit, 764 Vo Van Kiet Street, Ward 1, District 5, Ho Chi Minh City, Vietnam
| | - Voong Vinh Phat
- Molecular Epidemiology Group, Oxford University Clinical Research Unit, 764 Vo Van Kiet Street, Ward 1, District 5, Ho Chi Minh City, Vietnam
| | - Chau Vinh
- Molecular Epidemiology Group, Oxford University Clinical Research Unit, 764 Vo Van Kiet Street, Ward 1, District 5, Ho Chi Minh City, Vietnam
| | | | | | | | - Guy Thwaites
- Molecular Epidemiology Group, Oxford University Clinical Research Unit, 764 Vo Van Kiet Street, Ward 1, District 5, Ho Chi Minh City, Vietnam
- Centre for Tropical Medicine and Global Health, Nuffield Department of Clinical Medicine, Oxford University, Oxford, UK
| | - Louise Thwaites
- Molecular Epidemiology Group, Oxford University Clinical Research Unit, 764 Vo Van Kiet Street, Ward 1, District 5, Ho Chi Minh City, Vietnam
- Centre for Tropical Medicine and Global Health, Nuffield Department of Clinical Medicine, Oxford University, Oxford, UK
| | - Maia Rabaa
- Molecular Epidemiology Group, Oxford University Clinical Research Unit, 764 Vo Van Kiet Street, Ward 1, District 5, Ho Chi Minh City, Vietnam
- Centre for Tropical Medicine and Global Health, Nuffield Department of Clinical Medicine, Oxford University, Oxford, UK
| | - Anh T K Nguyen
- Molecular Epidemiology Group, Oxford University Clinical Research Unit, 764 Vo Van Kiet Street, Ward 1, District 5, Ho Chi Minh City, Vietnam
- Hospital for Tropical Diseases, Ho Chi Minh City, Vietnam
| | - Pham Thanh Duy
- Molecular Epidemiology Group, Oxford University Clinical Research Unit, 764 Vo Van Kiet Street, Ward 1, District 5, Ho Chi Minh City, Vietnam.
- Centre for Tropical Medicine and Global Health, Nuffield Department of Clinical Medicine, Oxford University, Oxford, UK.
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Ruengdit C, Punyamung M, Intasai N, Pornprasert S. Single-tube multiplex real-time PCR with EvaGreen and high-resolution melting analysis for diagnosis of α0-thalassemia--SEA,--THAI, and--CR type deletions. PLoS One 2023; 18:e0293838. [PMID: 37930985 PMCID: PMC10627449 DOI: 10.1371/journal.pone.0293838] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2023] [Accepted: 10/20/2023] [Indexed: 11/08/2023] Open
Abstract
Regions with a high prevalence of α-thalassemia (α-thal) require simple, rapid, and accurate tests for carrier screening and prenatal diagnosis. Diagnosis of multiple deletions in a single tube is necessary to clearly identify individuals with α0-thalassemia in the routine setting, especially in at-risk couples. Therefore, we aimed to develop a single-tube multiplex real-time PCR with EvaGreen and high-resolution melting (HRM) analysis for the identification of α0-thalassemia Southeast Asian (SEA), Thai and Chiang Rai (CR) type deletions. The results of the HRM analysis indicated that the amplified fragments from α0-thal--CR,--THAI,--SEA, and the wild-type α-globin gene had specific peak heights at mean melting temperature (Tm) values of 85.40°C, 86.50°C, 87.65°C, and 91.04°C, respectively. The frequencies of α0-thal--SEA,--THAI,--CR obtained from routine testing in 2,135 samples were 17.89%, 0.19% and 0.19%, respectively. This method would be useful for preventing Hb Bart's hydrops fetalis. Detection of multiple deletions in a single run is cost-effective, highly accurate and timesaving. This technique could enable wider α-thalassemia diagnosis in high prevalence areas and served as an example for thalassemia routine setting.
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Affiliation(s)
- Chedtapak Ruengdit
- Department of Medical Technology, Faculty of Associated Medical Sciences, Chiang Mai University, Chiang Mai, Thailand
| | - Manoo Punyamung
- Associated Medical Sciences Clinical Service Center, Faculty of Associated Medical Sciences, Chiang Mai University, Chiang Mai, Thailand
| | - Nutjeera Intasai
- Department of Medical Technology, Faculty of Associated Medical Sciences, Chiang Mai University, Chiang Mai, Thailand
| | - Sakorn Pornprasert
- Department of Medical Technology, Faculty of Associated Medical Sciences, Chiang Mai University, Chiang Mai, Thailand
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7
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Li X, Chen B, Chen W, Pu Z, Qi X, Yang L, Wu J, Yu H. Customized multiple sequence alignment as an effective strategy to improve performance of Taq DNA polymerase. Appl Microbiol Biotechnol 2023; 107:6507-6525. [PMID: 37658164 DOI: 10.1007/s00253-023-12744-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Revised: 08/06/2023] [Accepted: 08/24/2023] [Indexed: 09/03/2023]
Abstract
Engineering Taq DNA polymerase (TaqPol) for improved activity, stability and sensitivity was critical for its wide applications. Multiple sequence alignment (MSA) has been widely used in engineering enzymes for improved properties. Here, we first designed TaqPol mutations based on MSA of 2756 sequences from both thermophilic and non-thermophilic organisms. Two double mutations were generated including a variant H676F/R677G showing a decrease in both activity and stability, and a variant Y686R/E687K showing an improved activity, but a decreased stability. Mutations targeted on coevolutionary residues of Arg677 and Tyr686 were then applied to rescue stability or activity loss of the double mutants, which achieved a partial success. Sequence analysis revealed that the two mutations are abundant in non-thermophilic sequences but not in thermophilic homologues. Then, a small-scale MSA containing sequences from only thermophilic organisms was applied to predict 13 single variants and two of them, E507Q and E734N showed a simultaneous increase in both stability and activity, even in sensitivity. A customized MSA was hence more effective in engineering a thermophilic enzyme and could be used in engineering other enzymes. Molecular dynamics simulations revealed the impact of mutations on the protein dynamics and interactions between TaqPol and substrates. KEY POINTS: • The pool of sequence for alignment is critical to engineering Taq DNA polymerase. • The variants with low properties can be rescued by mutations in coevolving network. • Improving binding with DNA can improve DNA polymerase stability and activity.
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Affiliation(s)
- Xinjia Li
- Institute of Bioengineering, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, 310027, Zhejiang, China
- ZJU-Hangzhou Global Scientific and Technological Innovation Centre, Hangzhou, 311200, Zhejiang, China
| | - Binbin Chen
- Institute of Bioengineering, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, 310027, Zhejiang, China
- ZJU-Hangzhou Global Scientific and Technological Innovation Centre, Hangzhou, 311200, Zhejiang, China
| | - Wanyi Chen
- Institute of Bioengineering, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, 310027, Zhejiang, China
- ZJU-Hangzhou Global Scientific and Technological Innovation Centre, Hangzhou, 311200, Zhejiang, China
| | - Zhongji Pu
- Institute of Bioengineering, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, 310027, Zhejiang, China
- ZJU-Hangzhou Global Scientific and Technological Innovation Centre, Hangzhou, 311200, Zhejiang, China
| | - Xin Qi
- Building No.4, Zhongguancun Dongsheng International Science Park, No. 1 North Yongtaizhuang Road, Haidian District, Beijing, 100192, China
| | - Lirong Yang
- Institute of Bioengineering, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, 310027, Zhejiang, China
- ZJU-Hangzhou Global Scientific and Technological Innovation Centre, Hangzhou, 311200, Zhejiang, China
| | - Jianping Wu
- Institute of Bioengineering, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, 310027, Zhejiang, China
- ZJU-Hangzhou Global Scientific and Technological Innovation Centre, Hangzhou, 311200, Zhejiang, China
| | - Haoran Yu
- Institute of Bioengineering, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, 310027, Zhejiang, China.
- ZJU-Hangzhou Global Scientific and Technological Innovation Centre, Hangzhou, 311200, Zhejiang, China.
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Barman SD, Frimand Z, De Morree A. Absolute Quantification of mRNA Isoforms in Adult Stem Cells Using Microfluidic Digital PCR. Bio Protoc 2023; 13:e4811. [PMID: 37719075 PMCID: PMC10501916 DOI: 10.21769/bioprotoc.4811] [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: 01/27/2023] [Revised: 06/20/2023] [Accepted: 06/28/2023] [Indexed: 09/19/2023] Open
Abstract
Adult stem cells play key roles in homeostasis and tissue repair. These cells are regulated by a tight control of transcriptional programs. For example, muscle stem cells (MuSCs), located beneath the basal lamina, exist in the quiescent state but can transition to an activated, proliferative state upon injury. The control of MuSC state depends on the expression levels of myogenic transcription factors. Recent studies revealed the presence of different mRNA isoforms, with distinct biological regulation. Quantifying the exact expression levels of the mRNA isoforms encoding these myogenic transcription factors is therefore key to understanding how MuSCs switch between cell states. Previously, quantitative real-time polymerase chain reaction (qRT-PCR) has been used to quantify RNA expression levels. However, qRT-PCR depends on large amounts of RNA input and only measures relative abundance. Here, we present a protocol for the absolute quantification of mRNA isoforms using microfluidic digital PCR (mdPCR). Primary MuSCs isolated from individual skeletal muscles (gastrocnemius and masseter) are lysed, and their RNA is reverse-transcribed into cDNA and copied into double-stranded DNA. Following exonuclease I digestion to remove remaining single-stranded DNA, the samples are loaded onto a mdPCR chip with TaqMan probes targeting the mRNA isoforms of interest, whereupon target molecules are amplified in nanoliter chambers. We demonstrate that mdPCR can give exact molecule counts per cell for mRNA isoforms encoding the myogenic transcription factor Pax3. This protocol enables the absolute quantification of low abundant mRNA isoforms in a fast, precise, and reliable way.
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Affiliation(s)
| | - Zofija Frimand
- Department of Biomedicine, Aarhus University, Central Jutland, Denmark
| | - Antoine De Morree
- Department of Biomedicine, Aarhus University, Central Jutland, Denmark
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Wang Y, Shi Y, Hellinga HW, Beese LS. Thermally controlled intein splicing of engineered DNA polymerases provides a robust and generalizable solution for accurate and sensitive molecular diagnostics. Nucleic Acids Res 2023; 51:5883-5894. [PMID: 37166959 PMCID: PMC10287962 DOI: 10.1093/nar/gkad368] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Revised: 04/18/2023] [Accepted: 05/09/2023] [Indexed: 05/12/2023] Open
Abstract
DNA polymerases are essential for nucleic acid synthesis, cloning, sequencing and molecular diagnostics technologies. Conditional intein splicing is a powerful tool for controlling enzyme reactions. We have engineered a thermal switch into thermostable DNA polymerases from two structurally distinct polymerase families by inserting a thermally activated intein domain into a surface loop that is integral to the polymerase active site, thereby blocking DNA or RNA template access. The fusion proteins are inactive, but retain their structures, such that the intein excises during a heat pulse delivered at 70-80°C to generate spliced, active polymerases. This straightforward thermal activation step provides a highly effective, one-component 'hot-start' control of PCR reactions that enables accurate target amplification by minimizing unwanted by-products generated by off-target reactions. In one engineered enzyme, derived from Thermus aquaticus DNA polymerase, both DNA polymerase and reverse transcriptase activities are controlled by the intein, enabling single-reagent amplification of DNA and RNA under hot-start conditions. This engineered polymerase provides high-sensitivity detection for molecular diagnostics applications, amplifying 5-6 copies of the tested DNA and RNA targets with >95% certainty. The design principles used to engineer the inteins can be readily applied to construct other conditionally activated nucleic acid processing enzymes.
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Affiliation(s)
- You Wang
- Department of Biochemistry, Duke University Medical Center, Durham, NC 27710, USA
| | - Yuqian Shi
- Department of Biochemistry, Duke University Medical Center, Durham, NC 27710, USA
| | - Homme W Hellinga
- Department of Biochemistry, Duke University Medical Center, Durham, NC 27710, USA
| | - Lorena S Beese
- Department of Biochemistry, Duke University Medical Center, Durham, NC 27710, USA
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Chauhan K, Kim DM, Cho E, Kim DE. Facilitation of Dye-Based Quantitative Real-Time Polymerase Chain Reaction with Poly(ethylene glycol)-Engrafted Graphene Oxide. NANOMATERIALS (BASEL, SWITZERLAND) 2023; 13:1348. [PMID: 37110934 PMCID: PMC10144433 DOI: 10.3390/nano13081348] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Revised: 04/08/2023] [Accepted: 04/10/2023] [Indexed: 06/19/2023]
Abstract
Quantitative real-time polymerase chain reaction (qPCR) is an important and extensively utilized technique in medical and biotechnological applications. qPCR enables the real-time detection of nucleic acid during amplification, thus surpassing the necessity of post-amplification gel electrophoresis for amplicon detection. Despite being widely employed in molecular diagnostics, qPCR exhibits limitations attributed to nonspecific DNA amplification that compromises the efficiency and fidelity of qPCR. Herein, we demonstrate that poly(ethylene glycol)-engrafted nanosized graphene oxide (PEG-nGO) can significantly improve the efficiency and specificity of qPCR by adsorbing single-stranded DNA (ssDNA) without affecting the fluorescence of double-stranded DNA binding dye during DNA amplification. PEG-nGO adsorbs surplus ssDNA primers in the initial phase of PCR, having lower concentrations of DNA amplicons and thus minimizing the nonspecific annealing of ssDNA and false amplification due to primer dimerization and erroneous priming. As compared to conventional qPCR, the addition of PEG-nGO and the DNA binding dye, EvaGreen, in the qPCR setup (dubbed as PENGO-qPCR) significantly enhances the specificity and sensitivity of DNA amplification by preferential adsorption of ssDNA without inhibiting DNA polymerase activity. The PENGO-qPCR system for detection of influenza viral RNA exhibited a 67-fold higher sensitivity than the conventional qPCR setup. Thus, the performance of a qPCR can be greatly enhanced by adding PEG-nGO as a PCR enhancer as well as EvaGreen as a DNA binding dye to the qPCR mixture, which exhibits a significantly improved sensitivity of the qPCR.
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11
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Alaeenovin E, Parvizi P, Ghafari SM. Two Leishmania species separation targeting the ITS-rDNA and Cyt b genes by developing and evaluating HRM- qPCR. Rev Soc Bras Med Trop 2022; 55:S0037-86822022000100342. [PMID: 36542013 PMCID: PMC9757716 DOI: 10.1590/0037-8682-0186-2022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Accepted: 08/24/2022] [Indexed: 12/23/2022] Open
Abstract
BACKGROUND Incidence of Cutaneous Leishmaniasis as an infectious and neglected disease is increasing, for the diagnosis of which several traditional methods and conventional PCR techniques have been developed, employing different genes for species identification. METHODS Leishmania parasites were sampled, DNA was extracted, and new specific and sensitive primers were designed. Two ITS-rDNA and Cyt b genes were targeted by qPCR using the High- Resolution Melting method to identify Leishmania parasites. The standard curves were drawn, compared, and identified by high-resolution melting curve analysis. RESULTS Melting temperature and Cycle of Threshold of ITS-rDNA was higher than Cyt b but Cyt b was more sensitive than ITS-rDNA when Leishmania major and Leishmania tropica were analyzed and evaluated. By aligning melt curves, normalizing fluorescence curves, and difference plotting melt curves, each Leishmania species was distinguished easily. L. major and L. tropica were separated at 83.6 °C and 84.7 °C, respectively, with less than 0.9 °C of temperature difference. Developing sensitivity and specificity of real-time PCR based on EvaGreen could detect DNA concentration to less than one pmol. CONCLUSIONS Precise identification of Leishmania parasites is crucial for strategies of disease control. Real-time PCR using EvaGreen provides rapid, highly sensitive, and specific detection of parasite's DNA. The modified High-Resolution Melting could determine unique curves and was able to detect single nucleotide polymorphisms according to small differences in the nucleotide content of Leishmania parasites.
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Affiliation(s)
- Elnaz Alaeenovin
- Pasteur Institute of Iran, Molecular Systematics Laboratory, Parasitology Department, Tehran, Iran
| | - Parviz Parvizi
- Pasteur Institute of Iran, Molecular Systematics Laboratory, Parasitology Department, Tehran, Iran
| | - Seyedeh Maryam Ghafari
- Pasteur Institute of Iran, Molecular Systematics Laboratory, Parasitology Department, Tehran, Iran
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12
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Machine learning to improve the interpretation of intercalating dye-based quantitative PCR results. Sci Rep 2022; 12:16445. [PMID: 36180590 PMCID: PMC9525288 DOI: 10.1038/s41598-022-21010-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Accepted: 09/21/2022] [Indexed: 11/16/2022] Open
Abstract
This study aimed to evaluate the contribution of Machine Learning (ML) approach in the interpretation of intercalating dye-based quantitative PCR (IDqPCR) signals applied to the diagnosis of mucormycosis. The ML-based classification approach was applied to 734 results of IDqPCR categorized as positive (n = 74) or negative (n = 660) for mucormycosis after combining “visual reading” of the amplification and denaturation curves with clinical, radiological and microbiological criteria. Fourteen features were calculated to characterize the curves and injected in several pipelines including four ML-algorithms. An initial subset (n = 345) was used for the conception of classifiers. The classifier predictions were combined with majority voting to estimate performances of 48 meta-classifiers on an external dataset (n = 389). The visual reading returned 57 (7.7%), 568 (77.4%) and 109 (14.8%) positive, negative and doubtful results respectively. The Kappa coefficients of all the meta-classifiers were greater than 0.83 for the classification of IDqPCR results on the external dataset. Among these meta-classifiers, 6 exhibited Kappa coefficients at 1. The proposed ML-based approach allows a rigorous interpretation of IDqPCR curves, making the diagnosis of mucormycosis available for non-specialists in molecular diagnosis. A free online application was developed to classify IDqPCR from the raw data of the thermal cycler output (http://gepamy-sat.asso.st/).
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13
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Shaik GM, Draberova L, Cernohouzova S, Tumova M, Bugajev V, Draber P. Pentacyclic triterpenoid ursolic acid interferes with mast cell activation via a lipid-centric mechanism affecting FcεRI signalosome functions. J Biol Chem 2022; 298:102497. [PMID: 36115460 PMCID: PMC9587013 DOI: 10.1016/j.jbc.2022.102497] [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: 05/09/2022] [Revised: 09/07/2022] [Accepted: 09/08/2022] [Indexed: 11/20/2022] Open
Abstract
Pentacyclic triterpenoids, including ursolic acid (UA), are bioactive compounds with multiple biological activities involving anti-inflammatory effects. However, the mode of their action on mast cells, key players in the early stages of allergic inflammation, and underlying molecular mechanisms remain enigmatic. To better understand the effect of UA on mast cell signaling, here we examined the consequences of short-term treatment of mouse bone marrow-derived mast cells with UA. Using IgE-sensitized and antigen- or thapsigargin-activated cells, we found that 15 min exposure to UA inhibited high affinity IgE receptor (FcεRI)–mediated degranulation, calcium response, and extracellular calcium uptake. We also found that UA inhibited migration of mouse bone marrow-derived mast cells toward antigen but not toward prostaglandin E2 and stem cell factor. Compared to control antigen-activated cells, UA enhanced the production of tumor necrosis factor-α at the mRNA and protein levels. However, secretion of this cytokine was inhibited. Further analysis showed that UA enhanced tyrosine phosphorylation of the SYK kinase and several other proteins involved in the early stages of FcεRI signaling, even in the absence of antigen activation, but inhibited or reduced their further phosphorylation at later stages. In addition, we show that UA induced changes in the properties of detergent-resistant plasma membrane microdomains and reduced antibody-mediated clustering of the FcεRI and glycosylphosphatidylinositol-anchored protein Thy-1. Finally, UA inhibited mobility of the FcεRI and cholesterol. These combined data suggest that UA exerts its effects, at least in part, via lipid-centric plasma membrane perturbations, hence affecting the functions of the FcεRI signalosome.
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Affiliation(s)
- Gouse M Shaik
- Department of Signal Transduction, Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czech Republic; Department of Biochemistry, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Lubica Draberova
- Department of Signal Transduction, Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czech Republic
| | - Sara Cernohouzova
- Department of Signal Transduction, Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czech Republic
| | - Magda Tumova
- Department of Signal Transduction, Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czech Republic
| | - Viktor Bugajev
- Department of Signal Transduction, Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czech Republic
| | - Petr Draber
- Department of Signal Transduction, Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czech Republic.
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14
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Giglioti R, Polli H, Tainá Azevedo B, Morita Katiki L, Eugênio Vercesi Filho A. Detection and quantification of adulteration in milk and dairy products: A novel and sensitive qPCR-based method. FOOD CHEMISTRY. MOLECULAR SCIENCES 2022; 4:100074. [PMID: 35415677 PMCID: PMC8991746 DOI: 10.1016/j.fochms.2022.100074] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Revised: 01/04/2022] [Accepted: 01/07/2022] [Indexed: 11/29/2022]
Abstract
A novel qPCR method was able to detect and quantify cow, buffalo, goat and sheep DNA in milk and dairy products. Established detection limit was 0.016 ng for the four species. The limit of detection of cow DNA in buffalo, goat and sheep DNA samples was 0.1% (0.01 ng) This method is able to detect and quantify adulteration between cows, buffaloes, goats and sheep dairy samples.
Species identification in dairy products has a notable importance in food traceability and adulteration control and consequently has a significant effect on the final economic value of foods. In the present study, we developed a method based on real-time quantitative PCR (qPCR) for detection and quantification of cow DNA in DNA samples from milk and dairy products from buffaloes, goats, and sheep. The qPCR reactions showed high specificity, and the amplifications only occurred to species-specific primers. The calibration curves allowed for the quantification of the amount of DNA of each species-specific primer, and the established detection limit was 0.016 ng for the four species. The detection limit of cow DNA in buffalo, goat and sheep DNA samples was 0.1% (0.01 ng). Although the present study aimed to detect and quantify cow DNA in buffalo, goat, and sheep dairy products, we believe that the qPCR assays can also be directed to differentiate and quantify goat × sheep, and/or buffalo × goat/sheep.
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Affiliation(s)
- Rodrigo Giglioti
- Instituto de Zootecnia, Rua Heitor Penteado, n. 56, Nova Odessa, São Paulo 13380-011, Brazil
| | - Hiago Polli
- Instituto de Zootecnia, Rua Heitor Penteado, n. 56, Nova Odessa, São Paulo 13380-011, Brazil
| | - Bianca Tainá Azevedo
- Instituto de Zootecnia, Rua Heitor Penteado, n. 56, Nova Odessa, São Paulo 13380-011, Brazil
| | - Luciana Morita Katiki
- Instituto de Zootecnia, Rua Heitor Penteado, n. 56, Nova Odessa, São Paulo 13380-011, Brazil
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15
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Brunetti A, Heungens K, Hubert J, Ioos R, Bianchi GL, De Amicis F, Chandelier A, Van Der Linde S, Perez-Sierra A, Gualandri V, Silletti MR, Trisciuzzi VN, Rimondi S, Baschieri T, Romano E, Lumia V, Luigi M, Faggioli F, Pilotti M. Interlaboratory Performance of a Real-Time PCR Method for Detection of Ceratocystisplatani, the Agent of Canker Stain of Platanus spp. J Fungi (Basel) 2022; 8:jof8080778. [PMID: 35893146 PMCID: PMC9330143 DOI: 10.3390/jof8080778] [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: 06/21/2022] [Revised: 07/19/2022] [Accepted: 07/21/2022] [Indexed: 11/16/2022] Open
Abstract
Ceratocystis platani (CP), an ascomycetous fungus, is the agent of canker stain, a lethal vascular disease of Platanus species. Ceratocystis platani has been listed as a quarantine pest (EPPO A2 list) due to extensive damage caused in Southern Europe and the Mediterranean region. As traditional diagnostic assays are ineffective, a Real-Time PCR detection method based on EvaGreen, SYBR Green, and Taqman assays was previously developed, validated in-house, and included in the official EPPO standard PM7/14 (2). Here, we describe the results of a test performance study performed by nine European laboratories for the purpose of an interlaboratory validation. Verification of the DNA extracted from biological samples guaranteed the high quality of preparations, and the stability and the homogeneity of the aliquots intended for the laboratories. All of the laboratories reproduced nearly identical standard curves with efficiencies close to 100%. Testing of blind-coded DNA extracted from wood samples revealed that all performance parameters—diagnostic sensitivity, diagnostic specificity, accuracy and reproducibility—were best fit in most cases both at the laboratory and at the assay level. The previously established limit of detection, 3 fg per PCR reaction, was also validated with similar excellent results. The high interlaboratory performance of this Real-Time PCR method confirms its value as a primary tool to safeguard C. platani-free countries by way of an accurate monitoring, and to investigate the resistance level of potentially canker stain-resistant Platanus genotypes.
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Affiliation(s)
- Angela Brunetti
- Council for Agricultural Research and Economics, Research Centre for Plant Protection and Certification (CREA-DC), 00156 Rome, Italy; (A.B.); (V.L.); (M.L.); (F.F.)
| | - Kurt Heungens
- Flanders Research Institute for Agriculture, Fisheries and Food (ILVO), 9940 Merelbeke, Belgium;
| | - Jacqueline Hubert
- Plant Health Laboratory for the French Agency for Food, Environmental and Occupational Health & Safety (ANSES) Mycology Unit, 54220 Malzéville, France; (J.H.); (R.I.)
| | - Renaud Ioos
- Plant Health Laboratory for the French Agency for Food, Environmental and Occupational Health & Safety (ANSES) Mycology Unit, 54220 Malzéville, France; (J.H.); (R.I.)
| | - Gian Luca Bianchi
- Agenzia Regionale Per lo Sviluppo Rurale—ERSA Servizio Fitosanitario e Chimico, Ricerca, Sperimentazione ed Assistenza Tecnica, Struttura Stabile Laboratorio di Fitopatologia e Biotecnologie, Pozzuolo del Friuli, 33050 Udine, Italy; (G.L.B.); (F.D.A.)
| | - Francesca De Amicis
- Agenzia Regionale Per lo Sviluppo Rurale—ERSA Servizio Fitosanitario e Chimico, Ricerca, Sperimentazione ed Assistenza Tecnica, Struttura Stabile Laboratorio di Fitopatologia e Biotecnologie, Pozzuolo del Friuli, 33050 Udine, Italy; (G.L.B.); (F.D.A.)
| | - Anne Chandelier
- Walloon Agricultural Research Centre—CRA-W Life Sciences Department, 5030 Gembloux, Belgium;
| | - Sietse Van Der Linde
- Forest Research Tree Health Diagnostic & Advisory Service, Alice Holt Lodge, Farnham, Surrey GU10 4LH, UK; (S.V.D.L.); (A.P.-S.)
| | - Ana Perez-Sierra
- Forest Research Tree Health Diagnostic & Advisory Service, Alice Holt Lodge, Farnham, Surrey GU10 4LH, UK; (S.V.D.L.); (A.P.-S.)
| | - Valeria Gualandri
- FEM-IASMA, Centro Trasferimento Tecnologico Dipartimento Sperimentazione e Servizi Tecnologici, Unità Protezione Piante e Biodiversità Agroforestale, S. Michele all’Adige, 38098 Trento, Italy;
| | - Maria Rosaria Silletti
- Centro di Ricerca, Sperimentazione e Formazione in Agricoltura, Basile Caramia, Locorotondo, 70010 Bari, Italy; (M.R.S.); (V.N.T.)
| | - Vito Nicola Trisciuzzi
- Centro di Ricerca, Sperimentazione e Formazione in Agricoltura, Basile Caramia, Locorotondo, 70010 Bari, Italy; (M.R.S.); (V.N.T.)
| | - Silvia Rimondi
- Servizio Fitosanitario Regione Emilia-Romagna, 40129 Bologna, Italy; (S.R.); (T.B.)
| | - Tiziana Baschieri
- Servizio Fitosanitario Regione Emilia-Romagna, 40129 Bologna, Italy; (S.R.); (T.B.)
| | - Elio Romano
- Council for Agricultural Research and Economics, Research Centre for Engineering and Agro-Food Processing (CREA-IT) Treviglio, 24047 Bergamo, Italy;
| | - Valentina Lumia
- Council for Agricultural Research and Economics, Research Centre for Plant Protection and Certification (CREA-DC), 00156 Rome, Italy; (A.B.); (V.L.); (M.L.); (F.F.)
| | - Marta Luigi
- Council for Agricultural Research and Economics, Research Centre for Plant Protection and Certification (CREA-DC), 00156 Rome, Italy; (A.B.); (V.L.); (M.L.); (F.F.)
| | - Francesco Faggioli
- Council for Agricultural Research and Economics, Research Centre for Plant Protection and Certification (CREA-DC), 00156 Rome, Italy; (A.B.); (V.L.); (M.L.); (F.F.)
| | - Massimo Pilotti
- Council for Agricultural Research and Economics, Research Centre for Plant Protection and Certification (CREA-DC), 00156 Rome, Italy; (A.B.); (V.L.); (M.L.); (F.F.)
- Correspondence: ; Tel.: +39-06-82070357
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16
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Development of Droplet Digital PCR Assay for Detection of Seed-Borne Burkholderia glumae and B. gladioli Causing Bacterial Panicle Blight Disease of Rice. Microorganisms 2022; 10:microorganisms10061223. [PMID: 35744741 PMCID: PMC9227566 DOI: 10.3390/microorganisms10061223] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Revised: 06/13/2022] [Accepted: 06/13/2022] [Indexed: 11/17/2022] Open
Abstract
Bacterial panicle blight of rice or bacterial grain rot of rice is a worldwide rice disease. Burkholderia glumae and B. gladioli are the causal agents. The early and accurate detection of seed-borne B. glumae and B. gladioli is critical for domestic and international quarantine and effective control of the disease. Here, genomic analyses revealed that B. gladioli contains five phylogroups and the BG1 primer pair designed to target the 3’-end sequence of a gene encoding a Rhs family protein is specific to B. glumae and two phylogroups within B. gladioli. Using the BG1 primer pair, a 138-bp DNA fragment was amplified only from the tested panicle blight pathogens B. glumae and B. gladioli. An EvaGreen droplet digital PCR (dPCR) assay on detection and quantification of the two pathogens was developed from a SYBR Green real-time quantitative PCR (qPCR). The detection limits of the EvaGreen droplet dPCR on the two pathogens were identical at 2 × 103 colony forming units (CFU)∙mL−1 from bacterial suspensions and 2 × 102 CFU∙seed−1 from rice seeds. The EvaGreen droplet dPCR assay showed 10-fold detection sensitivity of the SYBR Green qPCR and could detect a single copy of the target gene in a 20-μL assay. Together, the SYBR Green qPCR assay allows for routine high-throughput detection of the panicle blight pathogens and the EvaGreen droplet dPCR assay provides a high-sensitive and high-accurate diagnostic method for quarantine of the pathogens.
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17
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Savonnet M, Aubret M, Laurent P, Roupioz Y, Cubizolles M, Buhot A. Kinetics of Isothermal Dumbbell Exponential Amplification: Effects of Mix Composition on LAMP and Its Derivatives. BIOSENSORS 2022; 12:bios12050346. [PMID: 35624647 PMCID: PMC9138685 DOI: 10.3390/bios12050346] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Revised: 05/11/2022] [Accepted: 05/13/2022] [Indexed: 11/16/2022]
Abstract
Loop-mediated isothermal amplification (LAMP) is an exponential amplification method of DNA strands that is more and more used for its high performances. Thanks to its high sensitivity and selectivity, LAMP found numerous applications from the detection of pathogens or viruses through their genome amplification to its incorporation as an amplification strategy in protein or miRNA biomarker quantification. The LAMP method is composed of two stages: the first one consists in the transformation of the DNA strands into dumbbell structures formed of two stems and loops thanks to four primers; then, in the second stage, only two primers are required to amplify the dumbbells exponentially in numerous hairpins of increasing lengths. In this paper, we propose a theoretical framework to analyze the kinetics of the second stage of LAMP, the isothermal dumbbell exponential amplification (IDEA) as function of the physico-chemical parameters of the amplification reaction. Dedicated experiments validate the models. We believe these results may help the optimization of LAMP performances by reducing the number of experiments necessary to find the best parameters.
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Affiliation(s)
- Maud Savonnet
- Univ. Grenoble Alpes, CEA, CNRS, IRIG-SyMMES, 38000 Grenoble, France; (M.S.); (M.A.); (Y.R.)
- Microfluidic Systems and Bioengineering Lab, Technologies for Healthcare and Biology Department, Univ. Grenoble Alpes, CEA, LETI, 38000 Grenoble, France;
| | - Mathilde Aubret
- Univ. Grenoble Alpes, CEA, CNRS, IRIG-SyMMES, 38000 Grenoble, France; (M.S.); (M.A.); (Y.R.)
- Microfluidic Systems and Bioengineering Lab, Technologies for Healthcare and Biology Department, Univ. Grenoble Alpes, CEA, LETI, 38000 Grenoble, France;
| | - Patricia Laurent
- Microfluidic Systems and Bioengineering Lab, Technologies for Healthcare and Biology Department, Univ. Grenoble Alpes, CEA, LETI, 38000 Grenoble, France;
| | - Yoann Roupioz
- Univ. Grenoble Alpes, CEA, CNRS, IRIG-SyMMES, 38000 Grenoble, France; (M.S.); (M.A.); (Y.R.)
| | - Myriam Cubizolles
- Microfluidic Systems and Bioengineering Lab, Technologies for Healthcare and Biology Department, Univ. Grenoble Alpes, CEA, LETI, 38000 Grenoble, France;
- Correspondence: (M.C.); (A.B.)
| | - Arnaud Buhot
- Univ. Grenoble Alpes, CEA, CNRS, IRIG-SyMMES, 38000 Grenoble, France; (M.S.); (M.A.); (Y.R.)
- Correspondence: (M.C.); (A.B.)
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18
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Coelho BJ, Veigas B, Bettencourt L, Águas H, Fortunato E, Martins R, Baptista PV, Igreja R. Digital Microfluidics-Powered Real-Time Monitoring of Isothermal DNA Amplification of Cancer Biomarker. BIOSENSORS 2022; 12:bios12040201. [PMID: 35448261 PMCID: PMC9028060 DOI: 10.3390/bios12040201] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Revised: 03/20/2022] [Accepted: 03/25/2022] [Indexed: 06/01/2023]
Abstract
We introduce a digital microfluidics (DMF) platform specifically designed to perform a loop-mediated isothermal amplification (LAMP) of DNA and applied it to a real-time amplification to monitor a cancer biomarker, c-Myc (associated to 40% of all human tumors), using fluorescence microscopy. We demonstrate the full manipulation of the sample and reagents on the DMF platform, resulting in the successful amplification of 90 pg of the target DNA (0.5 ng/µL) in less than one hour. Furthermore, we test the efficiency of an innovative mixing strategy in DMF by employing two mixing methodologies onto the DMF droplets-low frequency AC (alternating current) actuation as well as back-and-forth droplet motion-which allows for improved fluorescence readouts. Fluorophore bleaching effects are minimized through on-chip sample partitioning by DMF processes and sequential droplet irradiation. Finally, LAMP reactions require only 2 µL volume droplets, which represents a 10-fold volume reduction in comparison to benchtop LAMP.
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Affiliation(s)
- Beatriz Jorge Coelho
- Department of Materials Science, School of Science and Technology, NOVA University of Lisbon and CEMOP/UNINOVA, Campus de Caparica, 2829-516 Caparica, Portugal; (B.J.C.); (L.B.); (H.Á.); (E.F.); (R.M.)
- UCIBIO, I4HB, Life Sciences Department, School of Science and Technology, NOVA University of Lisbon, Campus de Caparica, 2829-516 Caparica, Portugal
| | - Bruno Veigas
- AlmaScience, Campus da Caparica, 2829-519 Caparica, Portugal;
| | - Luís Bettencourt
- Department of Materials Science, School of Science and Technology, NOVA University of Lisbon and CEMOP/UNINOVA, Campus de Caparica, 2829-516 Caparica, Portugal; (B.J.C.); (L.B.); (H.Á.); (E.F.); (R.M.)
| | - Hugo Águas
- Department of Materials Science, School of Science and Technology, NOVA University of Lisbon and CEMOP/UNINOVA, Campus de Caparica, 2829-516 Caparica, Portugal; (B.J.C.); (L.B.); (H.Á.); (E.F.); (R.M.)
| | - Elvira Fortunato
- Department of Materials Science, School of Science and Technology, NOVA University of Lisbon and CEMOP/UNINOVA, Campus de Caparica, 2829-516 Caparica, Portugal; (B.J.C.); (L.B.); (H.Á.); (E.F.); (R.M.)
| | - Rodrigo Martins
- Department of Materials Science, School of Science and Technology, NOVA University of Lisbon and CEMOP/UNINOVA, Campus de Caparica, 2829-516 Caparica, Portugal; (B.J.C.); (L.B.); (H.Á.); (E.F.); (R.M.)
| | - Pedro V. Baptista
- UCIBIO, I4HB, Life Sciences Department, School of Science and Technology, NOVA University of Lisbon, Campus de Caparica, 2829-516 Caparica, Portugal
| | - Rui Igreja
- Department of Materials Science, School of Science and Technology, NOVA University of Lisbon and CEMOP/UNINOVA, Campus de Caparica, 2829-516 Caparica, Portugal; (B.J.C.); (L.B.); (H.Á.); (E.F.); (R.M.)
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19
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Bigot J, Godmer A, Prudenté L, Angebault C, Brissot E, Bige N, Voiriot G, Leger PL, Petit-Hoang C, Atallah S, Gouache E, Senghor Y, Valot S, Hennequin C, Guitard J. Diagnosis of mucormycosis using an intercalating dye-based quantitative PCR. Med Mycol 2022; 60:6533518. [DOI: 10.1093/mmy/myac015] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Revised: 02/14/2022] [Accepted: 02/17/2022] [Indexed: 11/13/2022] Open
Abstract
Abstract
PCR-based methods applied to various body fluids emerged in recent years as a promising approach for the diagnosis of mucormycosis. In this study, we set up and assess the value of a qPCR to detect a wide variety of Mucorales species in a single tube. A pair of degenerated primers targeting the rDNA operon was used in a qPCR utilizing an intercalating fluorescent dye. Analytical assessment, using a wide variety of both Mucorales strains (8 genera, 11 species) and non-Mucorales strains (9 genera, 14 species), showed 100% sensitivity and specificity rates with a limit of detection at 3 rDNA copy/ qPCR reaction. Subsequently, 364 clinical specimens from 166 at-risk patients were prospectively tested with the assay. All the seven patients classified as proven/probable mucormycosis using the EORTC-MSG criteria had a positive qPCR as well as a patient with a proven uncharacterized invasive mould infection. In addition, 3 out of 7 patients with possible mould invasive infections had at least one positive qPCR test. Sensitivity was calculated between 73.33% to 100% and specificity between 98.10% to 100%. The qPCR method proposed showed excellent performances and would be an important adjunctive tool for the difficult diagnosis of mucormycosis diagnosis.
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Affiliation(s)
- Jeanne Bigot
- Sorbonne Université, Inserm, Centre de Recherche Saint-Antoine, CRSA, AP-HP, Hôpital Saint-Antoine, Service de Parasitologie-Mycologie, F-75012 Paris, France
| | - Alexandre Godmer
- Sorbonne Université, INSERM, U1135, Centre d'Immunologie et des Maladies Infectieuses, CIMI-Paris, F-75013, Paris, France
- Sorbonne-Université, Hôpital Saint-Antoine, Département de Bactériologie, Paris, France
| | - Lysa Prudenté
- APHP, Hôpital St Antoine, Laboratoire de parasitologie mycologie, F-75012 Paris, France
| | - Cécile Angebault
- Univ-Paris-Est-Créteil (UPEC), Faculté de Santé, EA DYNAMiC 7380 ; AP-HP, CHU Henri Mondor, Unité de Parasitologie-Mycologie, Département de Prévention, Diagnostic et Traitement des Infections, F-94010, France
| | - Eolia Brissot
- Sorbonne Université, INSERM U938, APHP, Hôpital Saint Antoine, Service d'Hématologie et Thérapie Cellulaire, F-75012 Paris, France
| | - Naike Bige
- APHP, Hôpital Saint Antoine, Service de Réanimation Médicale, F-75012 Paris, France
| | - Guillaume Voiriot
- APHP, Hôpital Tenon, Service de Médecine Intensive et Réanimation, F-75020 Paris, France
| | - Pierre-Louis Leger
- APHP, Hôpital Saint Trousseau, Service de Réanimation Pédiatrique, F-75012 Paris, France
| | - Camille Petit-Hoang
- APHP, Hôpital Tenon, Service de Urgences Néphrologiques et Transplantation Rénale, F-75020 Paris
| | - Sarah Atallah
- APHP, Hôpital Tenon, Service de Oto-Rhino-Laryngologie, F-75012 Paris, France
| | - Elodie Gouache
- APHP, Hôpital Trousseau, Département d'Hématologie et d'Oncologie Pédiatrique, F-75012 Paris, France
| | - Yaye Senghor
- APHP, Hôpital St Antoine, Laboratoire de parasitologie mycologie, F-75012 Paris, France
| | - Stéphane Valot
- Laboratoire de Parasitologie-Mycologie, Plateforme de Biologie Hospitalo-Universitaire, F-21070 Dijon, France
| | - Christophe Hennequin
- Sorbonne Université, Inserm, Centre de Recherche Saint-Antoine, CRSA, AP-HP, Hôpital Saint-Antoine, Service de Parasitologie-Mycologie, F-75012 Paris, France
| | - Juliette Guitard
- Sorbonne Université, Inserm, Centre de Recherche Saint-Antoine, CRSA, AP-HP, Hôpital Saint-Antoine, Service de Parasitologie-Mycologie, F-75012 Paris, France
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Nair SG, El-Yazbi AF, El-Yazbi AF. Investigation of nucleic acid damage induced by a novel ruthenium anti-cancer drug using multiple analytical techniques: Sequence specificity and damage kinetics. Int J Biol Macromol 2022; 198:68-76. [PMID: 34963625 DOI: 10.1016/j.ijbiomac.2021.12.113] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Revised: 12/16/2021] [Accepted: 12/18/2021] [Indexed: 12/21/2022]
Abstract
Cis-diacetonitrilo-bis(bipyridine) ruthenium(II) chloride is a recently introduced cis-platin analogue that has anti-cancer properties with lower side effects. However, the sequence dependence of its DNA damaging mechanism is unclear. Here, we present a simple, sensitive, multiplexed mix-and-read assay for ascertaining the molecular mechanism of DNA damage induced by the studied ruthenium complex (Ru-complex). The damage kinetics and sequence specificity for the Ru-complex induced DNA damage are examined by studying the induced damage in various oligonucleotide sequences by EvaGreen-DNA intercalator probe. High-through-put measurements were established using a 96-well microplate platform that allows multiple sequences to be measured simultaneously. The results show that the extent of damage increases with an increasing number of guanines, with considerable amount of damage at GA, GT and GC sites, in particular. Furthermore, the interaction of Ru-complex with DNA was confirmed using thermal analysis and MALDI-TOF-MS. Results indicate that the activated Ru-complex preferentially binds via both mono- and di-adduct formation at G and GG sites, respectively. Moreover, the developed method was successfully applied for the determination of the potency of the studied Ru-complex to induce DNA damage in K-Ras and N-Ras family of genes, one of the most common oncogenic events in cancer.
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Affiliation(s)
- Sindhu G Nair
- Department of Chemistry, University of Alberta, Edmonton, Alberta T6G 2G2, Canada; Department of Biological Sciences, University of Alberta, Edmonton, Alberta T6G 2E9, Canada
| | - Ahmed F El-Yazbi
- Department of Pharmacology and Toxicology, Faculty of Pharmacy, Alexandria University, Alexandria 21561, Egypt; Faculty of Pharmacy, Alalamein International University, Alalamein, Egypt
| | - Amira F El-Yazbi
- Department of Chemistry, University of Alberta, Edmonton, Alberta T6G 2G2, Canada; Department of Pharmaceutical Analytical Chemistry, Faculty of Pharmacy, Alexandria University, Alexandria 21526, Egypt.
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21
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Mote RD, Laxmikant VS, Singh SB, Tiwari M, Singh H, Srivastava J, Tripathi V, Seshadri V, Majumdar A, Subramanyam D. A cost-effective and efficient approach for generating and assembling reagents for conducting real-time PCR. J Biosci 2021. [PMID: 34845993 PMCID: PMC8626763 DOI: 10.1007/s12038-021-00231-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Real-time PCR is a widely used technique for quantification of gene expression. However, commercially available kits for real-time PCR are very expensive. The ongoing coronavirus pandemic has severely hampered the economy in a number of developing countries, resulting in a reduction in available research funding. The fallout of this will result in limiting educational institutes and small enterprises from using cutting edge biological techniques such as real-time PCR. Here, we report a cost-effective approach for preparing and assembling cDNA synthesis and real-time PCR mastermixes with similar efficiencies as commercially available kits. Our results thus demonstrate an alternative to commercially available kits.
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22
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LoopTag FRET Probe System for Multiplex qPCR Detection of Borrelia Species. Life (Basel) 2021; 11:life11111163. [PMID: 34833039 PMCID: PMC8624210 DOI: 10.3390/life11111163] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2021] [Revised: 10/27/2021] [Accepted: 10/28/2021] [Indexed: 12/19/2022] Open
Abstract
Background: Laboratory diagnosis of Lyme borreliosis refers to some methods with known limitations. Molecular diagnostics using specific nucleic acid probes may overcome some of these limitations. Methods: We describe the novel reporter fluorescence real-time polymerase chain reaction (PCR) probe system LoopTag for detection of Borrelia species. Advantages of the LoopTag system include having cheap conventional fluorescence dyes, easy primer design, no restrictions for PCR product lengths, robustness, high sequence specificity, applicability for multiplex real-time PCRs, melting curve analysis (single nucleotide polymorphism analysis) over a large temperature range, high sensitivity, and easy adaptation of conventional PCRs. Results: Using the LoopTag probe system we were able to detect all nine tested European species belonging to the Borrelia burgdorferi (sensu lato) complex and differentiated them from relapsing fever Borrelia species. As few as 10 copies of Borrelia in one PCR reaction were detectable. Conclusion: We established a novel multiplex probe real-time PCR system, designated LoopTag, that is simple, robust, and incorporates melting curve analysis for the detection and in the differentiation of European species belonging to the Borrelia burgdorferi s.l. complex.
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Wan J, Zheng L, Kong L, Lu Z, Tao Y, Feng Z, Lv F, Meng F, Bie X. Development of a rapid detection method for real-time fluorescent quantitative PCR of Salmonella spp. and Salmonella Enteritidis in ready-to-eat fruits and vegetables. Lebensm Wiss Technol 2021. [DOI: 10.1016/j.lwt.2021.111837] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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24
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Mapping human calreticulin regions important for structural stability. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2021; 1869:140710. [PMID: 34358706 DOI: 10.1016/j.bbapap.2021.140710] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 05/04/2021] [Revised: 07/24/2021] [Accepted: 08/02/2021] [Indexed: 12/28/2022]
Abstract
Calreticulin (CALR) is a highly conserved multifunctional chaperone protein primarily present in the endoplasmic reticulum, where it regulates Ca2+ homeostasis. Recently, CALR has gained special interest for its diverse functions outside the endoplasmic reticulum, including the cell surface and extracellular space. Although high-resolution structures of CALR exist, it has not yet been established how different regions and individual amino acid residues contribute to structural stability of the protein. In the present study, we have identified key residues determining the structural stability of CALR. We used a Saccharomyces cerevisiae expression system to express and purify 50 human CALR mutants, which were analysed for several parameters including secretion titer, melting temperature (Tm), stability and oligomeric state. Our results revealed the importance of a previously identified small patch of conserved surface residues, amino acids 166-187 ("cluster 2") for structural stability of the human CALR protein. Two residues, Tyr172 and Asp187, were critical for maintaining the native structure of the protein. Mutant D187A revealed a severe drop in secretion titer, it was thermally unstable, prone to degradation, and oligomer formation. Tyr172 was critical for thermal stability of CALR and interacted with the third free Cys163 residue. This illustrates an unusual thermal stability of CALR dominated by Asp187, Tyr172 and Cys163, which may interact as part of a conserved structural unit. Besides structural clusters, we found a correlation of some measured parameter values in groups of CALR mutants that cause myeloproliferative neoplasms (MPN) and in mutants that may be associated with sudden unexpected death (SUD).
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25
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Mikulin I, Ljubić I, Piantanida I, Vasilev A, Mondeshki M, Kandinska M, Uzelac L, Martin-Kleiner I, Kralj M, Tumir LM. Polycationic Monomeric and Homodimeric Asymmetric Monomethine Cyanine Dyes with Hydroxypropyl Functionality-Strong Affinity Nucleic Acids Binders. Biomolecules 2021; 11:biom11081075. [PMID: 34439741 PMCID: PMC8391988 DOI: 10.3390/biom11081075] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Revised: 07/15/2021] [Accepted: 07/19/2021] [Indexed: 11/16/2022] Open
Abstract
New analogs of the commercial asymmetric monomethine cyanine dyes thiazole orange (TO) and thiazole orange homodimer (TOTO) with hydroxypropyl functionality were synthesized and their properties in the presence of different nucleic acids were studied. The novel compounds showed strong, micromolar and submicromolar affinities to all examined DNA ds-polynucleotides and poly rA-poly rU. The compounds studied showed selectivity towards GC-DNA base pairs over AT-DNA, which included both binding affinity and a strong fluorescence response. CD titrations showed aggregation along the polynucleotide with well-defined supramolecular chirality. The single dipyridinium-bridged dimer showed intercalation at low dye-DNA/RNA ratios. All new cyanine dyes showed potent micromolar antiproliferative activity against cancer cell lines, making them promising theranostic agents.
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Affiliation(s)
- Ivana Mikulin
- Laboratory for Biomolecular Interactions and Spectroscopy, Division of Organic Chemistry and Biochemistry, Ruđer Bošković Institute, P.O. Box 180, 10002 Zagreb, Croatia; (I.M.); (I.L.); (I.P.)
| | - Ivana Ljubić
- Laboratory for Biomolecular Interactions and Spectroscopy, Division of Organic Chemistry and Biochemistry, Ruđer Bošković Institute, P.O. Box 180, 10002 Zagreb, Croatia; (I.M.); (I.L.); (I.P.)
| | - Ivo Piantanida
- Laboratory for Biomolecular Interactions and Spectroscopy, Division of Organic Chemistry and Biochemistry, Ruđer Bošković Institute, P.O. Box 180, 10002 Zagreb, Croatia; (I.M.); (I.L.); (I.P.)
| | - Aleksey Vasilev
- Faculty of Chemistry and Pharmacy, Department of Pharmaceutical and Applied Organic Chemistry, Sofia University “St. Kliment Ohridski”, 1000 Sofia, Bulgaria;
- Correspondence: (A.V.); (L.-M.T.); Tel.: +359-98-836-6528 (A.V.); +385-1-457-1220 (L.-M.T.)
| | - Mihail Mondeshki
- Department of Chemistry, Johannes Gutenberg Universität Mainz, Duesbergweg 10–14, 55128 Mainz, Germany;
| | - Meglena Kandinska
- Faculty of Chemistry and Pharmacy, Department of Pharmaceutical and Applied Organic Chemistry, Sofia University “St. Kliment Ohridski”, 1000 Sofia, Bulgaria;
| | - Lidija Uzelac
- Laboratory of Experimental Therapy, Division of Molecular Medicine, Ruđer Bošković Institute, P.O. Box 180, 10002 Zagreb, Croatia; (L.U.); (I.M.-K.); (M.K.)
| | - Irena Martin-Kleiner
- Laboratory of Experimental Therapy, Division of Molecular Medicine, Ruđer Bošković Institute, P.O. Box 180, 10002 Zagreb, Croatia; (L.U.); (I.M.-K.); (M.K.)
| | - Marijeta Kralj
- Laboratory of Experimental Therapy, Division of Molecular Medicine, Ruđer Bošković Institute, P.O. Box 180, 10002 Zagreb, Croatia; (L.U.); (I.M.-K.); (M.K.)
| | - Lidija-Marija Tumir
- Laboratory for Biomolecular Interactions and Spectroscopy, Division of Organic Chemistry and Biochemistry, Ruđer Bošković Institute, P.O. Box 180, 10002 Zagreb, Croatia; (I.M.); (I.L.); (I.P.)
- Correspondence: (A.V.); (L.-M.T.); Tel.: +359-98-836-6528 (A.V.); +385-1-457-1220 (L.-M.T.)
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26
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Nayeri T, Sarvi S, Daryani A. Toxoplasma gondii in mollusks and cold-blooded animals: a systematic review. Parasitology 2021; 148:895-903. [PMID: 33691818 PMCID: PMC11010209 DOI: 10.1017/s0031182021000433] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2020] [Revised: 01/31/2021] [Accepted: 02/09/2021] [Indexed: 12/22/2022]
Abstract
Toxoplasma gondii (T. gondii) is known for its ability to infect warm-blooded vertebrates. Although T. gondii does not appear to parasitize cold-blooded animals, the occurrence of T. gondii infection in marine mammals raises concerns that cold-blooded animals (frogs, toad, turtles, crocodiles, snakes, and fish) and shellfish are potential sources of T. gondii. Therefore, this systematic review aimed to determine the prevalence of T. gondii in mollusks and cold-blooded animals worldwide. We searched PubMed, ScienceDirect, ProQuest, Scopus, and Web of Science from inception to 1 August 2020 for eligible papers in the English language and identified 26 articles that reported the prevalence of T. gondii in mollusks and cold-blooded animals. These articles were subsequently reviewed and data extracted using a standard form. In total, 26 studies [involving 9 cross-sectional studies including 2988 samples of cold-blooded animals (129 positive cases for T. gondii) and 18 cross-sectional studies entailing 13 447 samples of shellfish (692 positive cases for T. gondii)] were included in this study. Although this study showed that shellfish and cold-blooded animals could be potential sources of T. gondii for humans and other hosts that feed on them, further investigations are recommended to determine the prevalence of T. gondii in shellfish and cold-blooded animals.
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Affiliation(s)
- Tooran Nayeri
- Toxoplasmosis Research Center, Mazandaran University of Medical Sciences, Sari, Iran
- Department of Parasitology, School of Medicine, Mazandaran University of Medical Sciences, Sari, Iran
- Student Research Committee, Mazandaran University of Medical Sciences, Sari, Iran
| | - Shahabeddin Sarvi
- Toxoplasmosis Research Center, Mazandaran University of Medical Sciences, Sari, Iran
- Department of Parasitology, School of Medicine, Mazandaran University of Medical Sciences, Sari, Iran
| | - Ahmad Daryani
- Toxoplasmosis Research Center, Mazandaran University of Medical Sciences, Sari, Iran
- Department of Parasitology, School of Medicine, Mazandaran University of Medical Sciences, Sari, Iran
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27
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Kolbeck PJ, Vanderlinden W, Gemmecker G, Gebhardt C, Lehmann M, Lak A, Nicolaus T, Cordes T, Lipfert J. Molecular structure, DNA binding mode, photophysical properties and recommendations for use of SYBR Gold. Nucleic Acids Res 2021; 49:5143-5158. [PMID: 33905507 PMCID: PMC8136779 DOI: 10.1093/nar/gkab265] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Revised: 03/29/2021] [Accepted: 04/05/2021] [Indexed: 01/08/2023] Open
Abstract
SYBR Gold is a commonly used and particularly bright fluorescent DNA stain, however, its chemical structure is unknown and its binding mode to DNA remains controversial. Here, we solve the structure of SYBR Gold by NMR and mass spectrometry to be [2-[N-(3-dimethylaminopropyl)-N-propylamino]-4-[2,3-dihydro-3-methyl-(benzo-1,3-thiazol-2-yl)-methylidene]-1-phenyl-quinolinium] and determine its extinction coefficient. We quantitate SYBR Gold binding to DNA using two complementary approaches. First, we use single-molecule magnetic tweezers (MT) to determine the effects of SYBR Gold binding on DNA length and twist. The MT assay reveals systematic lengthening and unwinding of DNA by 19.1° ± 0.7° per molecule upon binding, consistent with intercalation, similar to the related dye SYBR Green I. We complement the MT data with spectroscopic characterization of SYBR Gold. The data are well described by a global binding model for dye concentrations ≤2.5 μM, with parameters that quantitatively agree with the MT results. The fluorescence increases linearly with the number of intercalated SYBR Gold molecules up to dye concentrations of ∼2.5 μM, where quenching and inner filter effects become relevant. In summary, we provide a mechanistic understanding of DNA-SYBR Gold interactions and present practical guidelines for optimal DNA detection and quantitative DNA sensing applications using SYBR Gold.
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Affiliation(s)
- Pauline J Kolbeck
- Department of Physics and Center for NanoScience, LMU Munich, Amalienstrasse 54, 80799 Munich, Germany
| | - Willem Vanderlinden
- Department of Physics and Center for NanoScience, LMU Munich, Amalienstrasse 54, 80799 Munich, Germany
| | - Gerd Gemmecker
- Bavarian NMR Center (BNMRZ), Department of Chemistry, Technical University of Munich, Garching, Germany
| | - Christian Gebhardt
- Physical and Synthetic Biology, Faculty of Biology, LMU Munich, Planegg-Martinsried, Germany
| | - Martin Lehmann
- Plant Molecular Biology, Faculty of Biology, LMU Munich, Planegg-Martinsried, Germany
| | - Aidin Lak
- Department of Physics and Center for NanoScience, LMU Munich, Amalienstrasse 54, 80799 Munich, Germany
| | - Thomas Nicolaus
- Department of Physics and Center for NanoScience, LMU Munich, Amalienstrasse 54, 80799 Munich, Germany
| | - Thorben Cordes
- Physical and Synthetic Biology, Faculty of Biology, LMU Munich, Planegg-Martinsried, Germany
| | - Jan Lipfert
- Department of Physics and Center for NanoScience, LMU Munich, Amalienstrasse 54, 80799 Munich, Germany
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Zhang X, Yu H, Wang Z, Yang Q, Xia R, Qu Y, Tao R, Shi Y, Xiang P, Zhang S, Li C. Multi-locus identification of Psilocybe cubensis by high-resolution melting (HRM). Forensic Sci Res 2021; 7:490-497. [PMID: 36353314 PMCID: PMC9639532 DOI: 10.1080/20961790.2021.1875580] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
Abstract
Hallucinogenic mushroom is a kind of toxic strain containing psychoactive tryptamine substances such as psilocybin, psilocin and ibotenic acid, etc. The mushrooms containing hallucinogenic components are various, widely distributed and lack of standard to define, which made a great challenge to identification. Traditional identification methods, such as morphology and toxicology analysis, showed shortcomings in old or processed samples, while the DNA-based identification of hallucinogenic mushrooms would allow to identify these samples due to the stability of DNA. In this paper, four primer sets are designed to target Psilocybe cubensis DNA for increasing resolution of present identification method, and the target markers include largest subunit of RNA polymerase II (marked as PC-R1), psilocybin-related phosphotransferase gene (marked as PC-PT), glyceraldehyde 3-phosphate dehydrogenase (marked as PC-3) and translation EF1α (marked as PC-EF). Real-time PCR with high-resolution melting (HRM) assay were used for the differentiation of the fragments amplified by these primer sets, which were tested for specificity, reproducibility, sensitivity, mixture analysis and multiplex PCR. It was shown that the melting temperatures of PC-R1, PC-PT, PC-3 and PC-EF of P. cubensis were (87.93 ± 0.12) °C, (82.21 ± 0.14) °C, (79.72 ± 0.12) °C and (80.11 ± 0.19) °C in our kinds of independent experiments. Significant HRM characteristic can be shown with a low concentration of 62.5 pg/µL DNA sample, and P. cubensis could be detected in mixtures with Homo sapiens or Cannabis sativa. In summary, the method of HRM analysis can quickly and specifically distinguish P. cubensis from other species, which could be utilized for forensic science, medical diagnosis and drug trafficking cases. Supplemental data for this article are available online at https://doi.org/10.1080/20961790.2021.1875580.
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Affiliation(s)
- Xiaochun Zhang
- Department of Forensic Science, Medical School of Soochow University, Suzhou, China
- Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Academy of Forensic Sciences, Ministry of Justice, Shanghai, China
| | - Huan Yu
- Department of Forensic Science, Medical School of Soochow University, Suzhou, China
- Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Academy of Forensic Sciences, Ministry of Justice, Shanghai, China
| | - Ziwei Wang
- Department of Forensic Science, Medical School of Soochow University, Suzhou, China
- Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Academy of Forensic Sciences, Ministry of Justice, Shanghai, China
| | - Qi Yang
- Department of Forensic Science, Medical School of Soochow University, Suzhou, China
- Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Academy of Forensic Sciences, Ministry of Justice, Shanghai, China
| | - Ruocheng Xia
- Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Academy of Forensic Sciences, Ministry of Justice, Shanghai, China
- Department of Forensic Medicine, School of Basic Medical Science, Wenzhou Medical University, Wenzhou, China
| | - Yiling Qu
- Department of Forensic Science, Medical School of Soochow University, Suzhou, China
- Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Academy of Forensic Sciences, Ministry of Justice, Shanghai, China
| | - Ruiyang Tao
- Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Academy of Forensic Sciences, Ministry of Justice, Shanghai, China
- Institute of Forensic Medicine, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, China
| | - Yan Shi
- Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Academy of Forensic Sciences, Ministry of Justice, Shanghai, China
| | - Ping Xiang
- Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Academy of Forensic Sciences, Ministry of Justice, Shanghai, China
| | - Suhua Zhang
- Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Academy of Forensic Sciences, Ministry of Justice, Shanghai, China
| | - Chengtao Li
- Department of Forensic Science, Medical School of Soochow University, Suzhou, China
- Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Academy of Forensic Sciences, Ministry of Justice, Shanghai, China
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29
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Vishnuraj M, Devatkal S, Vaithiyanathan S, Uday Kumar R, Srinivas C, Mendiratta S. Detection of giblets in chicken meat products using microRNA markers and droplet digital PCR assay. Lebensm Wiss Technol 2021. [DOI: 10.1016/j.lwt.2020.110798] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
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30
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A Forensic Detection Method for Hallucinogenic Mushrooms via High-Resolution Melting (HRM) Analysis. Genes (Basel) 2021; 12:genes12020199. [PMID: 33572950 PMCID: PMC7911181 DOI: 10.3390/genes12020199] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Revised: 01/18/2021] [Accepted: 01/26/2021] [Indexed: 11/25/2022] Open
Abstract
In recent years, trafficking and abuse of hallucinogenic mushrooms have become a serious social problem. It is therefore imperative to identify hallucinogenic mushrooms of the genus Psilocybe for national drug control legislation. An internal transcribed spacer (ITS) is a DNA barcoding tool utilized for species identification. Many methods have been used to discriminate the ITS region, but they are often limited by having a low resolution. In this study, we sought to analyze the ITS and its fragments, ITS1 and ITS2, by using high-resolution melting (HRM) analysis, which is a rapid and sensitive method for evaluating sequence variation within PCR amplicons. The ITS HRM assay was tested for specificity, reproducibility, sensitivity, and the capacity to analyze mixture samples. It was shown that the melting temperatures of the ITS, ITS1, and ITS2 of Psilocybe cubensis were 83.72 ± 0.01, 80.98 ± 0.06, and 83.46 ± 0.08 °C, and for other species, we also obtained species-specific results. Finally, we performed ITS sequencing to validate the presumptive taxonomic identity of our samples, and the sequencing output significantly supported our HRM data. Taken together, these results indicate that the HRM method can quickly distinguish the DNA barcoding of Psilocybe cubensis and other fungi, which can be utilized for drug trafficking cases and forensic science.
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31
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Hosseini-Safa A, Shojaee S, Salami SA, Mohebali M, Hantoushzadeh S, Mousavi P, Dehghan Manshadi SA, Keshavarz Valian H. Development of High Resolution Melting Analysis as a Diagnostic Tool for Molecular Detection of Toxoplasma Infection in Pregnant Women and HIV Positive Cases. IRANIAN JOURNAL OF PUBLIC HEALTH 2020; 49:1983-1991. [PMID: 33346240 PMCID: PMC7719646 DOI: 10.18502/ijph.v49i10.4704] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Background Toxoplasma gondii is an obligate intracellular protozoan with worldwide distribution. Diagnosis of toxoplasmosis is a very critical issue, especially in pregnant women and immunocompromised patients. The aim of this study was rapid detection of T. gondii DNA in peripheral blood samples (PBS) employing HRM technique and using RE gene. Methods Totally, 242 samples from pregnant women and human immunodeficiency virus (HIV) patients were collected from different hospitals and medical centers of Tehran during Oct 2017 to Dec 2018. High resolution melting analysis (HRM) using partial sequences of repetitive element (RE) gene was done and compared with ELISA test. Results Overall, 51 were positive for acute toxoplasmosis that among them, 12 and 20 reported as positive in pregnant women and HIV+ patients, respectively using HRM technique. Among 70 patients in chronic phase of disease, 10 and 3 samples were reported as positive for pregnant women and HIV+ patients respectively. From 121 negative control, 3 (4.62%) samples associated with HIV+ patients, showed positive real-time PCR and HRM analysis results. Conclusion For the first time, HRM technique via employing RE gene was used for detection of T. gondii infection in PBS. This method is suitable, helpful and in parallel with serological methods for early diagnosis of acute as well as active form of toxoplasmosis in pregnant women and HIV+ patients. The use of techniques based on melt curve and through employing next-generation dyes for diagnosis of T. gondii would be accessible for patients in developing countries.
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Affiliation(s)
- Ahmad Hosseini-Safa
- Department of Medical Parasitology and Mycology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
| | - Saeedeh Shojaee
- Department of Medical Parasitology and Mycology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
| | - Seyed Alireza Salami
- Department Biotechnology, School of Agricultural Sciences and Engineering, University of Tehran, Tehran, Iran
| | - Mehdi Mohebali
- Department of Medical Parasitology and Mycology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran.,Center for Research of Endemic Parasites of Iran (CREPI), Tehran University of Medical Sciences, Tehran, Iran
| | - Sedigheh Hantoushzadeh
- Maternal, Fetal and Neonatal Research Center, Vali-Asr Hospital, Imam Khomeini Hospital Complex, Tehran University of Medical Sciences, Tehran, Iran
| | - Parisa Mousavi
- Skin Diseases and Leishmaniasis Research Center, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Seyed Ali Dehghan Manshadi
- Department of Infectious Diseases and Tropical Medicine and Iranian Research Center for HIV/AIDS, Tehran University of Medical Sciences, Tehran, Iran
| | - Hossein Keshavarz Valian
- Department of Medical Parasitology and Mycology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran.,Center for Research of Endemic Parasites of Iran (CREPI), Tehran University of Medical Sciences, Tehran, Iran
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Purhonen J, Banerjee R, McDonald AE, Fellman V, Kallijärvi J. A sensitive assay for dNTPs based on long synthetic oligonucleotides, EvaGreen dye and inhibitor-resistant high-fidelity DNA polymerase. Nucleic Acids Res 2020; 48:e87. [PMID: 32573728 PMCID: PMC7470940 DOI: 10.1093/nar/gkaa516] [Citation(s) in RCA: 303] [Impact Index Per Article: 75.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2020] [Revised: 06/03/2020] [Accepted: 06/05/2020] [Indexed: 12/15/2022] Open
Abstract
Deoxyribonucleoside triphosphates (dNTPs) are vital for the biosynthesis and repair of DNA. Their cellular concentration peaks during the S phase of the cell cycle. In non-proliferating cells, dNTP concentrations are low, making their reliable quantification from tissue samples of heterogeneous cellular composition challenging. Partly because of this, the current knowledge related to the regulation of and disturbances in cellular dNTP concentrations derive mostly from cell culture experiments with little corroboration at the tissue or organismal level. Here, we fill the methodological gap by presenting a simple non-radioactive microplate assay for the quantification of dNTPs with a minimum requirement of 4-12 mg of biopsy material. In contrast to published assays, this assay is based on long synthetic single-stranded DNA templates (50-200 nucleotides), an inhibitor-resistant high-fidelity DNA polymerase, and the double-stranded-DNA-binding EvaGreen dye. The assay quantified reliably less than 50 fmol of each of the four dNTPs and discriminated well against ribonucleotides. Additionally, thermostable RNAse HII-mediated nicking of the reaction products and a subsequent shift in their melting temperature allowed near-complete elimination of the interfering ribonucleotide signal, if present. Importantly, the assay allowed measurement of minute dNTP concentrations in mouse liver, heart and skeletal muscle.
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Affiliation(s)
- Janne Purhonen
- Folkhälsan Research Center, Helsinki, Finland.,Stem Cells and Metabolism Research Program, Faculty of Medicine, University of Helsinki, Finland
| | - Rishi Banerjee
- Folkhälsan Research Center, Helsinki, Finland.,Stem Cells and Metabolism Research Program, Faculty of Medicine, University of Helsinki, Finland
| | | | - Vineta Fellman
- Folkhälsan Research Center, Helsinki, Finland.,Stem Cells and Metabolism Research Program, Faculty of Medicine, University of Helsinki, Finland.,Department of Clinical Sciences, Lund, Pediatrics, Lund University, Sweden.,Children's Hospital, Helsinki University Hospital, Finland
| | - Jukka Kallijärvi
- Folkhälsan Research Center, Helsinki, Finland.,Stem Cells and Metabolism Research Program, Faculty of Medicine, University of Helsinki, Finland
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33
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Paul R, Ostermann E, Gu Z, Ristaino JB, Wei Q. DNA Extraction from Plant Leaves Using a Microneedle Patch. ACTA ACUST UNITED AC 2020; 5:e20104. [PMID: 32074406 DOI: 10.1002/cppb.20104] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Isolation of high-quality DNA from infected plant specimens is an essential step for the molecular detection of plant pathogens. However, DNA isolation from plant cells surrounded by rigid polysaccharide cell walls involves complicated steps and requires benchtop laboratory equipment. As a result, plant DNA extraction is currently confined to well-equipped laboratories and sample preparation has become one of the major hurdles for on-site molecular detection of plant pathogens. To overcome this hurdle, a simple DNA extraction method from plant leaf tissues has been developed. A microneedle (MN) patch made of polyvinyl alcohol (PVA) can isolate plant or pathogenic DNA from different plant species within a minute. During DNA extraction, the polymeric MN patch penetrates into plant leaf tissues and breaks rigid plant cell walls to isolate intracellular DNA. The extracted DNA is polymerase chain reaction (PCR) amplifiable without additional purification. This minimally invasive method has successfully extracted Phytophthora infestans DNA from infected tomato leaves. Moreover, the MN patch could be used to isolate DNA from other plant pathogens directly in the field. Thus, it has great potential to become a rapid, on-site sample preparation technique for plant pathogen detection. © 2020 by John Wiley & Sons, Inc. Basic Protocol: Microneedle patch-based DNA extraction Support Protocol 1: Microneedle patch fabrication Support Protocol 2: Real-time PCR amplification of microneedle patch extracted DNA.
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Affiliation(s)
- Rajesh Paul
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, North Carolina
| | - Emily Ostermann
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, North Carolina
| | - Zhen Gu
- Bioengineering Department, University of California, Los Angeles, Los Angeles, California.,Jonsson Comprehensive Cancer Center, California NanoSystems Institute, and Center for Minimally Invasive Therapeutics, University of California, Los Angeles, Los Angeles, California
| | - Jean B Ristaino
- Department of Entomology and Plant Pathology, North Carolina State University, Raleigh, North Carolina.,Emerging Plant Disease and Global Food Security Cluster, North Carolina State University, Raleigh, North Carolina
| | - Qingshan Wei
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, North Carolina.,Emerging Plant Disease and Global Food Security Cluster, North Carolina State University, Raleigh, North Carolina
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34
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Luo Y, Viswanathan R, Hande MP, Loh AHP, Cheow LF. Massively parallel single-molecule telomere length measurement with digital real-time PCR. SCIENCE ADVANCES 2020; 6:eabb7944. [PMID: 32937369 PMCID: PMC7442360 DOI: 10.1126/sciadv.abb7944] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/19/2020] [Accepted: 07/09/2020] [Indexed: 05/02/2023]
Abstract
Telomere length is a promising biomarker for age-associated diseases and cancer, but there are still substantial challenges to routine telomere analysis in clinics because of the lack of a simple and rapid yet scalable method for measurement. We developed the single telomere absolute-length rapid (STAR) assay, a novel high-throughput digital real-time PCR approach for rapidly measuring the absolute lengths and quantities of individual telomere molecules. We show that this technique provides the accuracy and sensitivity to uncover associations between telomere length distribution and telomere maintenance mechanisms in cancer cell lines and primary tumors. The results indicate that the STAR assay is a powerful tool to enable the use of telomere length distribution as a biomarker in disease and population-wide studies.
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Affiliation(s)
- Yongqiang Luo
- Department of Biomedical Engineering, Faculty of Engineering, National University of Singapore, Singapore 117583, Singapore
- Institute for Health Innovation and Technology, National University of Singapore, Singapore 117599, Singapore
| | - Ramya Viswanathan
- Department of Biomedical Engineering, Faculty of Engineering, National University of Singapore, Singapore 117583, Singapore
- Institute for Health Innovation and Technology, National University of Singapore, Singapore 117599, Singapore
| | - Manoor Prakash Hande
- Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117593, Singapore
| | - Amos Hong Pheng Loh
- Department of Paediatric Surgery, KK Women's and Children's Hospital, Singapore 229899, Singapore
| | - Lih Feng Cheow
- Department of Biomedical Engineering, Faculty of Engineering, National University of Singapore, Singapore 117583, Singapore.
- Institute for Health Innovation and Technology, National University of Singapore, Singapore 117599, Singapore
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35
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Shabrangharehdasht M, Mirvaghefi A, Farahmand H. Effects of nanosilver on hematologic, histologic and molecular parameters of rainbow trout (Oncorhynchus mykiss). AQUATIC TOXICOLOGY (AMSTERDAM, NETHERLANDS) 2020; 225:105549. [PMID: 32599437 DOI: 10.1016/j.aquatox.2020.105549] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2020] [Revised: 06/11/2020] [Accepted: 06/15/2020] [Indexed: 05/02/2023]
Abstract
Efficient antibacterial and antifungal properties of silver nanoparticles (AgNPs) sparked its commercial application in several industrial and household products. Drastic increase of AgNPs production raised concerns over aquatic organisms' exposure. The toxic dose, mechanism of toxicity, physiological damages, gene expression alteration, hematological and blood parameter distortion by AgNP needs to be investigated to explore inevitable risk in aquatic animals. In this study, rainbow trout (Oncorhynchus mykiss) (122.4 ± 1.4 g, 23.8 ± 0.7 cm) were exposed to colloidal AgNPs (28.3 ± 12.6 um) to determine the lethal concentration (LC50)(8.9 mg/l). Sub-lethal concentrations (10 %LC50, 25 %LC50, plus LC50 value) impact on hematologic, histological and molecular responses were evaluated. Results showed sever damage to blood cells morphology, and hematologic parameters change including RBC, WBC, Hct and Hb in all AgNP-treated groups. Histological damage in gill and liver of exposed fish were observed. Significant up-regulating of HSP70 and P53 genes were detected in response to AgNPs, whereas, it was found that in comparison to HSP70 gene, P53 induction occurred in lower AgNPs concentrations and lower exposure time. These results indicate adversely effects of AgNPs exposure to aquatic environments.
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Affiliation(s)
| | - Alireza Mirvaghefi
- Department of Fisheries and Environmental Science, University of Tehran, Karaj, Iran.
| | - Hamid Farahmand
- Department of Fisheries and Environmental Science, University of Tehran, Karaj, Iran
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36
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Shen R, Jia Y, Mak PI, Martins RP. Clip-to-release on amplification (CRoA): a novel DNA amplification enhancer on and off microfluidics. LAB ON A CHIP 2020; 20:1928-1938. [PMID: 32352133 DOI: 10.1039/d0lc00318b] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Despite its high sensitivity, low cost, and high efficiency as a DNA amplification indicator with a yes/no answer, dsDNA-binding dye encounters incompatibility when used in microfluidic systems, resulting in problems such as false negative amplification results. Besides, its inhibition of amplification at high concentrations hinders its application both on-chip and off-chip. In this study, we propose a novel DNA amplification enhancer to counteract the drawbacks of dsDNA-binding dyes. It acts as a temporary reservoir for the free-floating dyes in solution and releases them on demand during the amplification process. Through this clip-to-release on amplification mechanism, the enhancer lowered the background fluorescence of sample droplets before amplification, enhanced the signal-to-background ratio of positive samples, and eliminated the false negative signal of on-chip PCR. Moreover, the enhancer increased the off-chip polymerase chain reaction (PCR) efficiency, boosted the fluorescence signal up to 10-fold, and made less nonspecific amplification product. All the factors affecting the enhancer's performance are investigated in detail, including its structure and concentration, and the types of dsDNA-binding dye used in the reaction. Finally, we demonstrated the broad application of the proposed amplification enhancer in various DNA amplification systems, for various genes, and on various amplification platforms. It would reignite the utilization of dsDNA dyes for wider applications in DNA analysis both on-chip and off-chip.
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Affiliation(s)
- Ren Shen
- State-Key Laboratory of Analog and Mixed-Signal VLSI, Institute of Microelectronics, University of Macau, Macau, China. and Faculty of Science and Technology - ECE, University of Macau, Macau, China
| | - Yanwei Jia
- State-Key Laboratory of Analog and Mixed-Signal VLSI, Institute of Microelectronics, University of Macau, Macau, China. and Faculty of Science and Technology - ECE, University of Macau, Macau, China and Faculty of Health Sciences, University of Macau, Macau, China
| | - Pui-In Mak
- State-Key Laboratory of Analog and Mixed-Signal VLSI, Institute of Microelectronics, University of Macau, Macau, China. and Faculty of Science and Technology - ECE, University of Macau, Macau, China
| | - Rui P Martins
- State-Key Laboratory of Analog and Mixed-Signal VLSI, Institute of Microelectronics, University of Macau, Macau, China. and Faculty of Science and Technology - ECE, University of Macau, Macau, China and On Leave from Instituto Superior Técnico, Universidade de Lisboa, Portugal
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37
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Newkirk SJ, Kong L, Jones MM, Habben CE, Dilts VL, Ye P, An W. Subfamily-specific quantification of endogenous mouse L1 retrotransposons by droplet digital PCR. Anal Biochem 2020; 601:113779. [PMID: 32442414 DOI: 10.1016/j.ab.2020.113779] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2020] [Revised: 05/06/2020] [Accepted: 05/14/2020] [Indexed: 11/18/2022]
Abstract
Long interspersed element type 1 (LINE-1; L1) mobilizes during early embryogenesis, neurogenesis, and germ cell development, accounting for 25% of disease-causing heritable insertions and 98% of somatic insertions in cancer. To better understand the regulation and impact of L1 mobilization in the genome, reliable methods for measuring L1 copy number variation (CNV) are needed. Here we present a comprehensive analysis of a droplet digital PCR (ddPCR) based method for quantifying endogenous mouse L1. We provide experimental evidence that ddPCR assays can be designed to target specific L1 subfamilies using diagnostic single nucleotide polymorphisms (SNPs). The target and off-target L1 subfamilies form distinct droplet clusters, which were experimentally verified using both synthetic gene fragments and endogenous L1 derived plasmid clones. We further provide a roadmap for in silico assay design and evaluation of target specificity, ddPCR testing, and optimization for L1 CNV quantification. The assay can achieve a sensitivity of 5% CNV with 8 technical replicates. With 24 technical replicates, it can detect 2% CNV because of the increased precision. The same approach will serve as a guide for the development of ddPCR based assays for quantifying human L1 copy number and any other high copy genomic target sequences.
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Affiliation(s)
- Simon J Newkirk
- Department of Pharmaceutical Sciences, South Dakota State University, Brookings, SD, 57007, United States.
| | - Lingqi Kong
- Department of Pharmaceutical Sciences, South Dakota State University, Brookings, SD, 57007, United States.
| | - Mason M Jones
- Department of Pharmaceutical Sciences, South Dakota State University, Brookings, SD, 57007, United States.
| | - Chase E Habben
- Department of Pharmaceutical Sciences, South Dakota State University, Brookings, SD, 57007, United States.
| | - Victoria L Dilts
- Department of Pharmaceutical Sciences, South Dakota State University, Brookings, SD, 57007, United States.
| | - Ping Ye
- Department of Pharmacy Practice, South Dakota State University, Brookings, SD, 57007, United States; Avera Research Institute, Sioux Falls, SD, 57108, United States.
| | - Wenfeng An
- Department of Pharmaceutical Sciences, South Dakota State University, Brookings, SD, 57007, United States.
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38
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High-Resolution Melting (HRM) Curve Assay for the Identification of Eight Fusarium Species Causing Ear Rot in Maize. Pathogens 2020; 9:pathogens9040270. [PMID: 32272731 PMCID: PMC7238191 DOI: 10.3390/pathogens9040270] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2020] [Revised: 04/03/2020] [Accepted: 04/05/2020] [Indexed: 11/16/2022] Open
Abstract
Maize plants are often infected with fungal pathogens of the genus Fusarium. Taxonomic characterization of these species by microscopic examination of pure cultures or assignment to mating populations is time-consuming and requires specific expertise. Reliable taxonomic assignment may be strengthened by the analysis of DNA sequences. Species-specific PCR assays are available for most Fusarium pathogens, but the number of species that infect maize increases the labor and costs required for analysis. In this work, a diagnostic assay for major Fusarium pathogens of maize based on the analysis of melting curves of PCR amplicons was established. Short segments of genes RPB2 and TEF-1α, which have been widely used in molecular taxonomy of Fusarium, were amplified with universal primers in a real-time thermocycler and high-resolution melting (HRM) curves of the products were recorded. Among major Fusarium pathogens of maize ears, F. cerealis, F. culmorum, F. graminearum, F. equiseti, F. poae, F. temperatum, F. tricinctum, and F. verticillioides, all species except for the pair F. culmorum/F. graminearum could be distinguished by HRM analysis of a 304 bp segment of the RPB2 gene. The latter two species could be differentiated by HRM analysis of a 247 bp segment of the TEF-1α gene. The assay was validated with DNA extracted from pure cultures of fungal strains, successfully applied to total DNA extracted from infected maize ears and also to fungal mycelium that was added directly to the PCR master mix ("colony PCR"). HRM analysis thus offers a cost-efficient method suitable for the diagnosis of multiple fungal pathogens.
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39
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Sidstedt M, Rådström P, Hedman J. PCR inhibition in qPCR, dPCR and MPS-mechanisms and solutions. Anal Bioanal Chem 2020; 412:2009-2023. [PMID: 32052066 PMCID: PMC7072044 DOI: 10.1007/s00216-020-02490-2] [Citation(s) in RCA: 117] [Impact Index Per Article: 29.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2019] [Revised: 01/29/2020] [Accepted: 02/04/2020] [Indexed: 12/24/2022]
Abstract
DNA analysis has seen an incredible development in terms of instrumentation, assays and applications over the last years. Massively parallel sequencing (MPS) and digital PCR are now broadly applied in research and diagnostics, and quantitative PCR is used for more and more practises. All these techniques are based on in vitro DNA polymerization and fluorescence measurements. A major limitation for successful analysis is the various sample-related substances that interfere with the analysis, i.e. PCR inhibitors. PCR inhibition affects library preparation in MPS analysis and skews quantification in qPCR, and some inhibitors have been found to quench the fluorescence of the applied fluorophores. Here, we provide a deeper understanding of mechanisms of specific PCR inhibitors and how these impact specific analytical techniques. This background knowledge is necessary in order to take full advantage of modern DNA analysis techniques, specifically for analysis of samples with low amounts of template and high amounts of background material. The classical solution to handle PCR inhibition is to purify or dilute DNA extracts, which leads to DNA loss. Applying inhibitor-tolerant DNA polymerases, either single enzymes or blends, provides a more straightforward and powerful solution. This review includes mechanisms of specific PCR inhibitors as well as solutions to the inhibition problem in relation to cutting-edge DNA analysis.
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Affiliation(s)
- Maja Sidstedt
- Swedish National Forensic Centre, Swedish Police Authority, 581 94, Linköping, Sweden
| | - Peter Rådström
- Applied Microbiology, Department of Chemistry, Lund University, P.O. Box 124, 221 00, Lund, Sweden
| | - Johannes Hedman
- Swedish National Forensic Centre, Swedish Police Authority, 581 94, Linköping, Sweden.
- Applied Microbiology, Department of Chemistry, Lund University, P.O. Box 124, 221 00, Lund, Sweden.
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40
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Ouso DO, Otiende MY, Jeneby MM, Oundo JW, Bargul JL, Miller SE, Wambua L, Villinger J. Three-gene PCR and high-resolution melting analysis for differentiating vertebrate species mitochondrial DNA for biodiversity research and complementing forensic surveillance. Sci Rep 2020; 10:4741. [PMID: 32179808 PMCID: PMC7075967 DOI: 10.1038/s41598-020-61600-3] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2019] [Accepted: 02/27/2020] [Indexed: 11/09/2022] Open
Abstract
Reliable molecular identification of vertebrate species from morphologically unidentifiable tissue is critical for the prosecution of illegally-traded wildlife products, conservation-based biodiversity research, and identification of blood-meal hosts of hematophagous invertebrates. However, forensic identification of vertebrate tissue relies on sequencing of the mitochondrial cytochrome oxidase I (COI) 'barcode' gene, which remains costly for purposes of screening large numbers of unknown samples during routine surveillance. Here, we adapted a rapid, low-cost approach to differentiate 10 domestic and 24 wildlife species that are common in the East African illegal wildlife products trade based on their unique high-resolution melting profiles from COI, cytochrome b, and 16S ribosomal RNA gene PCR products. Using the approach, we identified (i) giraffe among covertly sampled meat from Kenyan butcheries, and (ii) forest elephant mitochondrial sequences among savannah elephant reference samples. This approach is being adopted for high-throughput pre-screening of potential bushmeat samples in East African forensic science pipelines.
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Affiliation(s)
- Daniel O Ouso
- International Centre of Insect Physiology and Ecology (icipe), P.O. Box 30772-00100, Nairobi, Kenya
- Biochemistry Department, Jomo Kenyatta University of Agriculture and Technology (JKUAT), P.O. Box 62000-00200, Nairobi, Kenya
| | - Moses Y Otiende
- Kenya Wildlife Service, Veterinary Department, P.O. Box 40241-00100, Nairobi, Kenya
| | - Maamun M Jeneby
- Institute of Primate Research, National Museums of Kenya, Department of Tropical and Infectious Diseases, P. O. Box 24481-00502, Karen, Nairobi, Kenya
| | - Joseph W Oundo
- International Centre of Insect Physiology and Ecology (icipe), P.O. Box 30772-00100, Nairobi, Kenya
| | - Joel L Bargul
- International Centre of Insect Physiology and Ecology (icipe), P.O. Box 30772-00100, Nairobi, Kenya
- Biochemistry Department, Jomo Kenyatta University of Agriculture and Technology (JKUAT), P.O. Box 62000-00200, Nairobi, Kenya
| | - Scott E Miller
- National Museum of Natural History, Smithsonian Institution, Washington, DC, USA
| | - Lillian Wambua
- International Centre of Insect Physiology and Ecology (icipe), P.O. Box 30772-00100, Nairobi, Kenya
- International Livestock Research Institute, Department of Animal Biosciences, P.O. Box 30709-00100, Nairobi, Kenya
| | - Jandouwe Villinger
- International Centre of Insect Physiology and Ecology (icipe), P.O. Box 30772-00100, Nairobi, Kenya.
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41
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Muñoz HE, Riche CT, Kong JE, van Zee M, Garner OB, Ozcan A, Di Carlo D. Fractal LAMP: Label-Free Analysis of Fractal Precipitate for Digital Loop-Mediated Isothermal Nucleic Acid Amplification. ACS Sens 2020; 5:385-394. [PMID: 31902202 DOI: 10.1021/acssensors.9b01974] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Nucleic acid amplification assays including loop-mediated isothermal amplification (LAMP) are routinely used in diagnosing diseases and monitoring water and food quality. The results of amplification in these assays are commonly measured with an analog fluorescence readout, which requires specialized optical equipment and can lack quantitative precision. Digital analysis of amplification in small fluid compartments based on exceeding a threshold fluorescence level can enhance the quantitative precision of nucleic acid assays (i.e., digital nucleic acid amplification assays), but still requires specialized optical systems for fluorescence readout and the inclusion of a fluorescent dye. Here, we report Fractal LAMP, an automated method to detect amplified DNA in subnanoliter scale droplets following LAMP in a label-free manner. Our computer vision algorithm achieves high accuracy detecting DNA amplification in droplets by identifying LAMP byproducts that form fractal structures observable in brightfield microscopy. The capabilities of Fractal LAMP are further realized by developing a Bayesian model to estimate DNA concentrations for unknown samples and a bootstrapping method to estimate the number of droplets required to achieve target limits of detection. This digital, label-free assay has the potential to lower reagent and reader cost for nucleic acid measurement while maintaining high quantitative accuracy over 3 orders of magnitude of concentration.
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Affiliation(s)
- Hector E. Muñoz
- Department of Bioengineering, University of California, Los Angeles, California 90095, United States
| | - Carson T. Riche
- Department of Bioengineering, University of California, Los Angeles, California 90095, United States
| | - Janay E. Kong
- Department of Bioengineering, University of California, Los Angeles, California 90095, United States
| | - Mark van Zee
- Department of Bioengineering, University of California, Los Angeles, California 90095, United States
| | - Omai B. Garner
- Department of Pathology & Laboratory Medicine, University of California, Los Angeles, California 90095, United States
| | - Aydogan Ozcan
- Department of Bioengineering, University of California, Los Angeles, California 90095, United States
- Department of Electrical and Computer Engineering, University of California, Los Angeles, California 90095, United States
- California NanoSystems Institute, University of California, Los Angeles, California 90095, United States
| | - Dino Di Carlo
- Department of Bioengineering, University of California, Los Angeles, California 90095, United States
- California NanoSystems Institute, University of California, Los Angeles, California 90095, United States
- Jonsson Comprehensive Cancer Center, University of California, Los Angeles, California 90095, United States
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42
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Veltkamp HW, Akegawa Monteiro F, Sanders R, Wiegerink R, Lötters J. Disposable DNA Amplification Chips with Integrated Low-Cost Heaters. MICROMACHINES 2020; 11:E238. [PMID: 32106462 PMCID: PMC7143804 DOI: 10.3390/mi11030238] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/24/2020] [Revised: 02/20/2020] [Accepted: 02/22/2020] [Indexed: 01/03/2023]
Abstract
Fast point-of-use detection of, for example, early-stage zoonoses, e.g., Q-fever, bovine tuberculosis, or the Covid-19 coronavirus, is beneficial for both humans and animal husbandry as it can save lives and livestock. The latter prevents farmers from going bankrupt after a zoonoses outbreak. This paper describes the development of a fabrication process and the proof-of-principle of a disposable DNA amplification chip with an integrated heater. Based on the analysis of the milling process, metal adhesion studies, and COMSOL MultiPhysics heat transfer simulations, the first batch of chips has been fabricated and successful multiple displacement amplification reactions are performed inside these chips. This research is the first step towards the development of an early-stage zoonoses detection device. Tests with real zoonoses and DNA specific amplification reactions still need to be done.
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Affiliation(s)
- Henk-Willem Veltkamp
- Department of Integrated Devices and Systems, University of Twente, P.O. Box 217, 7500 AE Enschede, The Netherlands; (F.A.M.); (R.S.); (R.W.); (J.L.)
| | - Fernanda Akegawa Monteiro
- Department of Integrated Devices and Systems, University of Twente, P.O. Box 217, 7500 AE Enschede, The Netherlands; (F.A.M.); (R.S.); (R.W.); (J.L.)
| | - Remco Sanders
- Department of Integrated Devices and Systems, University of Twente, P.O. Box 217, 7500 AE Enschede, The Netherlands; (F.A.M.); (R.S.); (R.W.); (J.L.)
| | - Remco Wiegerink
- Department of Integrated Devices and Systems, University of Twente, P.O. Box 217, 7500 AE Enschede, The Netherlands; (F.A.M.); (R.S.); (R.W.); (J.L.)
| | - Joost Lötters
- Department of Integrated Devices and Systems, University of Twente, P.O. Box 217, 7500 AE Enschede, The Netherlands; (F.A.M.); (R.S.); (R.W.); (J.L.)
- Bronkhorst High-Tech BV, Nijverheidsstraat 1A, 7261 AK Ruurlo, The Netherlands
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43
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Zeng Y, Liu M, Xia Y, Jiang X. Uracil-DNA-glycosylase-assisted loop-mediated isothermal amplification for detection of bacteria from urine samples with reduced contamination. Analyst 2020; 145:7048-7055. [PMID: 32894274 DOI: 10.1039/d0an01001d] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Urine specimens are detected by conventional culture method and colonies with more than 104 are identified by MALDI-TOF MS. Meanwhile, we analyze urine samples using FTA cards for simple DNA extraction and UDG-assisted LAMP.
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Affiliation(s)
- Yingmin Zeng
- Department of Clinical Laboratory
- Third Affiliated Hospital of Guangzhou Medical University
- Guangzhou
- People's Republic of China
| | - Meiling Liu
- Department of Clinical Laboratory
- Third Affiliated Hospital of Guangzhou Medical University
- Guangzhou
- People's Republic of China
| | - Yong Xia
- Department of Clinical Laboratory
- Third Affiliated Hospital of Guangzhou Medical University
- Guangzhou
- People's Republic of China
| | - Xingyu Jiang
- Department of Biomedical Engineering
- Southern University of Science and Technology
- Shenzhen
- People's Republic of China
- Beijing Engineering Research Center for BioNanotechnology and CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety
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44
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Alia JD, Flack JA. Unspecified verticality of Franck–Condon transitions, absorption and emission spectra of cyanine dyes, and a classically inspired approximation. RSC Adv 2020; 10:43153-43167. [PMID: 35514896 PMCID: PMC9058138 DOI: 10.1039/d0ra06774a] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2020] [Accepted: 11/18/2020] [Indexed: 12/19/2022] Open
Abstract
The computed vertical energy, Ev,a/f, from the equilibrium geometry of the initial electronic state is frequently considered as representative of the experimental excitation/emission energy, Eabs/fl = hc/λmax. Application of the quantum mechanical version of the Franck–Condon principle does not involve precise specification of nuclear positions before, after, or during an electronic transition. Moreover, the duration of an electronic transition is not experimentally accessible in spectra with resolved vibrational structure. It is shown that computed vibronic spectra based on TDDFT methods and application of quantum mechanical FC analysis predict Eabs = hc/λmax with a 10-fold improvement in accuracy compared to Ev,a for nine cyanine dyes. It is argued that part of the reason for accuracy when this FC analysis is compared to experiment as opposed to Ev,a/f is the unspecified verticality of transitions in the context of the quantum version of the FC principle. Classical FC transitions that preserve nuclear kinetic energy before and after an electronic transition were previously found to occur at a weighted average of final and initial electronic state molecular geometries known as the r-centroid. Inspired by this approach a qualitative method using computed vertical and adiabatic energies and the harmonic approximation is developed and applied yielding a 5-fold improvement in accuracy compared to Ev,a. This improvement results from the dominance of low frequency vibronic transitions in the cyanine dye major band. The model gives insight into the nature of the redshift when qPCR dye EvaGreen is complexed to λDNA and is applicable to the low frequency band of similar non cyanine dyes such as curcumin. It is found that the computed vibronic cyanine dye spectra from time-dependent FC analysis at 0 K and 298 K show decreased intensity at higher temperature suggestive of increased intensity with restricted motion shown when cyanine dyes are used in biomedical imaging. A 2-layer ONIOM model of the DNA minor groove indicates restricted motion of the TC-1 dye excited state in this setting indicative of enhanced fluorescence. Insight into cyanine dye λmax from quantum and classical FC principle; high accuracy with classically inspired approach.![]()
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Affiliation(s)
- Joseph D. Alia
- Division of Science and Mathematics
- University of Minnesota Morris
- USA
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Zhu J, Wang J, Cheng K, Chen H, An R, Zhang Y, Komiyama M, Liang X. Effective Characterization of DNA Ligation Kinetics by High-Resolution Melting Analysis. Chembiochem 2019; 21:785-788. [PMID: 31592561 DOI: 10.1002/cbic.201900489] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2019] [Revised: 10/07/2019] [Indexed: 12/31/2022]
Abstract
High-resolution melting (HRM) analysis has been improved and applied for the first time to quantitative analysis of enzymatic reactions. By using the relative ratios of peak intensities of substrates and products, the quantitativity of conventional HRM analysis has been improved to allow detailed kinetic analysis. As an example, the ligation of sticky ends through the action of T4 DNA ligase has been kinetically analyzed, with comprehensive data on substrate specificity and other properties having been obtained. For the first time, the kinetic parameters (kobs and apparent Km ) of sticky-end ligation were obtained for both fully matched and mismatched sticky ends. The effect of ATP concentration on sticky-end ligation was also investigated. The improved HRM method should also be applicable to versatile DNA-transforming enzymes, because the only requirement is that the products have Tm values different enough from the substrates.
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Affiliation(s)
- Jianming Zhu
- College of Food Science and Engineering, Ocean University of China, Qingdao, 266003, P. R. China
| | - Jing Wang
- College of Food Science and Engineering, Ocean University of China, Qingdao, 266003, P. R. China.,CAS Key laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, P. R. China
| | - Kai Cheng
- College of Food Science and Engineering, Ocean University of China, Qingdao, 266003, P. R. China
| | - Hui Chen
- College of Food Science and Engineering, Ocean University of China, Qingdao, 266003, P. R. China
| | - Ran An
- College of Food Science and Engineering, Ocean University of China, Qingdao, 266003, P. R. China
| | - Yaping Zhang
- College of Food Science and Engineering, Ocean University of China, Qingdao, 266003, P. R. China
| | - Makoto Komiyama
- College of Food Science and Engineering, Ocean University of China, Qingdao, 266003, P. R. China
| | - Xingguo Liang
- College of Food Science and Engineering, Ocean University of China, Qingdao, 266003, P. R. China.,Laboratory for Marine Drugs and Bioproducts, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266003, P. R. China
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Lin S, Zhang S, Wang S, Xie K, Jiang D, Xiao S, Chen X, Chen S. Development of an EvaGreen based real-time RT-PCR assay for rapid detection, quantitation and diagnosis of goose calicivirus. Mol Cell Probes 2019; 49:101489. [PMID: 31747564 DOI: 10.1016/j.mcp.2019.101489] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2019] [Revised: 11/01/2019] [Accepted: 11/16/2019] [Indexed: 02/06/2023]
Abstract
An unclassified calicivirus (CV) detected in geese was recently reported and proposed as a new member of the family Caliciviridae. There is limited information about the epidemiology, etiology and detection method of goose-origin CV (GCV) to date. In this study, an EvaGreen based fluorescence quantitative real-time RT-PCR assay was developed and optimized for the detection of GCVs. The assay sensitively detected GCV RNA template with a good linear standard curve. We also demonstrated the specificity and reproducibility of the detection method for GCVs. Thus, the method developed in this study will benefit the investigation of possible sporadic outbreaks of CV infections in geese, as well as epidemiological and etiological studies of GCVs.
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Affiliation(s)
- Su Lin
- Institute of Animal Husbandry and Veterinary Medicine, Fujian Academy of Agriculture Sciences, Fuzhou, 350003, China.
| | - Shizhong Zhang
- Institute of Animal Husbandry and Veterinary Medicine, Fujian Academy of Agriculture Sciences, Fuzhou, 350003, China.
| | - Shao Wang
- Institute of Animal Husbandry and Veterinary Medicine, Fujian Academy of Agriculture Sciences, Fuzhou, 350003, China.
| | - Kaichun Xie
- Animal Veterinary and Aquatic Product Bureau, Nanping, 353000, China.
| | - Dandan Jiang
- Institute of Animal Husbandry and Veterinary Medicine, Fujian Academy of Agriculture Sciences, Fuzhou, 350003, China.
| | - Shifeng Xiao
- Institute of Animal Husbandry and Veterinary Medicine, Fujian Academy of Agriculture Sciences, Fuzhou, 350003, China.
| | - Xiuqin Chen
- Institute of Animal Husbandry and Veterinary Medicine, Fujian Academy of Agriculture Sciences, Fuzhou, 350003, China; Fujian Animal Diseases Control Technology Development Center, Fuzhou, 350013, China.
| | - Shaoying Chen
- Institute of Animal Husbandry and Veterinary Medicine, Fujian Academy of Agriculture Sciences, Fuzhou, 350003, China; Fujian Animal Diseases Control Technology Development Center, Fuzhou, 350013, China.
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Redcenko O, Draberova L, Draber P. Carboxymethylcellulose enhances the production of single-stranded DNA aptamers generated by asymmetric PCR. Anal Biochem 2019; 589:113502. [PMID: 31704088 DOI: 10.1016/j.ab.2019.113502] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2019] [Revised: 11/04/2019] [Accepted: 11/04/2019] [Indexed: 10/25/2022]
Abstract
Nucleic acid aptamers are single-stranded (ss)DNA or RNA oligonucleotides that can take various conformations and bind specifically and with high affinity to selected targets. While the introduction of SELEX (systematic evolution of ligands by exponential enrichment) revolutionized the production of the aptamers, this procedure is impeded by the formation of undesirable by-products reflecting hybridization among complementary oligonucleotides in the ssDNA libraries during asymmetric PCR. To reduce nonspecific amplification we tested cellulose-derived compounds and found that sodium carboxymethylcellulose (CMC) at a concentration 0.05%-0.2% efficiently suppressed production of undesirable large DNA amplicons during asymmetric PCR in the course of SELEX. Formation of the PCR by-products was reduced by CMCs of low and medium viscosity more than by CMCs of high viscosity, and all of them bound to DNA oligonucleotides as determined by electrophoresis in agarose gels. In contrast to CMC, methylcellulose did not reduce the formation of the PCR by-products and did not bind to DNA. DNA aptamers selected in the presence of CMC could be used directly in enzyme-linked immunosorbent-like assay. The combined data suggest that CMC binds weekly to DNA oligonucleotides through hydroxyl groups and in this way inhibits low-affinity DNA-DNA hybridization and enhances the production of specific amplicons in asymmetric PCR.
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Affiliation(s)
- Oleksij Redcenko
- Department of Signal Transduction, Institute of Molecular Genetics of the Czech Academy of Sciences, CZ 14220, Prague, Czech Republic
| | - Lubica Draberova
- Department of Signal Transduction, Institute of Molecular Genetics of the Czech Academy of Sciences, CZ 14220, Prague, Czech Republic
| | - Petr Draber
- Department of Signal Transduction, Institute of Molecular Genetics of the Czech Academy of Sciences, CZ 14220, Prague, Czech Republic.
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Li L, Hu Z, Sun J, Guo K, Chu X, Wang X, Lu Y. Development of an EvaGreen-based real-time PCR assay for detection of Aleutian mink disease virus. J Virol Methods 2019; 275:113751. [PMID: 31639372 DOI: 10.1016/j.jviromet.2019.113751] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2017] [Revised: 10/03/2019] [Accepted: 10/11/2019] [Indexed: 11/18/2022]
Abstract
The objective of this study was to develop a rapid, sensitive and specific EvaGreen (EG)-based real-time PCR assay capable of detecting Aleutian mink disease virus (AMDV) and to evaluate the reliability of the assay for analysis of blood or tissue samples. For this assay, a pair of primers was designed based on a nonstructural protein (NS)-encoding gene of AMDV, and the identity of PCR products was identified based on a melting temperature of 82.8°C. The EG-based real-time PCR assay did not detect canine distemper virus or mink enteritis virus, and the assay could be used to detect Chinese and American AMDV strains, in contrast to a commercial TaqMan kit that could only detect American AMDV strains. The amplification efficiencies of the EG assay were 104.8% for the Chinese strain and 94.4% for the American strain, and the detection limit was 1 copy/μL of AMDV plasmid or 3 pg/μL of viral DNA (Chinese strain). The intra- and inter-assay variation coefficients of melting temperature were all lower than 0.15%, confirming the high reproducibility of the assay. Forty-five clinical blood samples were simultaneously analyzed using the EG real-time PCR, TaqMan kit and conventional PCR, and the detection rates were 91.1%, 0.0% and 86.7%, respectively. Serum samples were also collected from the corresponding blood samples and tested using the counterimmunoelectrophoresis (CIEP) assay, where positive samples accounted for 24.4% of the 45 samples. In conclusion, EG-based real-time PCR is a rapid, sensitive, universal assay that can be effectively utilized as a reliable and specific tool for detection and quantitation of AMDV.
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Affiliation(s)
- Li Li
- Heilongjiang Key Laboratory for Animal Disease Control and Pharmaceutical Development, College of Veterinary Medicine, Northeast Agricultural University, 600 Changjiang Road, Harbin 150030, PR China; Harbin Customs District P.R. China, 88 Songshan Road, Harbin 150008, PR China
| | - Zhe Hu
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, the Chinese Academy of Agriculture Sciences, 678 Haping Road, Harbin 150001, PR China
| | - Jinhui Sun
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, the Chinese Academy of Agriculture Sciences, 678 Haping Road, Harbin 150001, PR China; College of Animal Science and Technology, Northeast Agricultural University, 600 Changjiang Road, Harbin 150030, PR China
| | - Kui Guo
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, the Chinese Academy of Agriculture Sciences, 678 Haping Road, Harbin 150001, PR China
| | - Xiaoyu Chu
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, the Chinese Academy of Agriculture Sciences, 678 Haping Road, Harbin 150001, PR China
| | - Xiaojun Wang
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, the Chinese Academy of Agriculture Sciences, 678 Haping Road, Harbin 150001, PR China
| | - Yixin Lu
- Heilongjiang Key Laboratory for Animal Disease Control and Pharmaceutical Development, College of Veterinary Medicine, Northeast Agricultural University, 600 Changjiang Road, Harbin 150030, PR China.
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Quyen TL, Ngo TA, Bang DD, Madsen M, Wolff A. Classification of Multiple DNA Dyes Based on Inhibition Effects on Real-Time Loop-Mediated Isothermal Amplification (LAMP): Prospect for Point of Care Setting. Front Microbiol 2019; 10:2234. [PMID: 31681184 PMCID: PMC6803449 DOI: 10.3389/fmicb.2019.02234] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2019] [Accepted: 09/11/2019] [Indexed: 12/16/2022] Open
Abstract
LAMP has received great interest and is widely utilized in life sciences for nucleic acid analysis. To monitor a real-time LAMP assay, a fluorescence DNA dye is an indispensable component and therefore the selection of a suitable dye for real-time LAMP is a need. To aid this selection, we investigated the inhibition effects of twenty-three DNA dyes on real-time LAMP. Threshold time (Tt) values of each real-time LAMP were determined and used as an indicator of the inhibition effect. Based on the inhibition effects, the dyes were classified into four groups: (1) non-inhibition effect, (2) medium inhibition effect, (3) high inhibition effect, and (4) very high inhibition effect. The signal to noise ratio (SNR) and the limit of detection (LOD) of the dyes in groups 1, 2, and 3 were further investigated, and possible inhibition mechanisms of the DNA dyes on the real-time LAMP are suggested and discussed. Furthermore, a comparison of SYTO 9 in different LAMP reactions and different systems is presented. Of the 23 dyes tested, SYTO 9, SYTO 82, SYTO 16, SYTO 13, and Miami Yellow were the best dyes with no inhibitory effect, low LOD and high SNR in the real-time LAMP reactions. The present classification of the dyes will simplify the selection of fluorescence dye for real-time LAMP assays in point of care setting.
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Affiliation(s)
- Than Linh Quyen
- Department of Biotechnology and Biomedicine, Technical University of Denmark (DTU-Bioengineering), Lyngby, Denmark
| | - Tien Anh Ngo
- Laboratory of Applied Micro and Nanotechnology (LAMINATE), National Food Institute, Technical University of Denmark (DTU-Food), Lyngby, Denmark
| | - Dang Duong Bang
- Laboratory of Applied Micro and Nanotechnology (LAMINATE), National Food Institute, Technical University of Denmark (DTU-Food), Lyngby, Denmark
| | - Mogens Madsen
- Department of Biotechnology and Biomedicine, Technical University of Denmark (DTU-Bioengineering), Lyngby, Denmark
| | - Anders Wolff
- Department of Biotechnology and Biomedicine, Technical University of Denmark (DTU-Bioengineering), Lyngby, Denmark
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Arastehfar A, Wickes BL, Ilkit M, Pincus DH, Daneshnia F, Pan W, Fang W, Boekhout T. Identification of Mycoses in Developing Countries. J Fungi (Basel) 2019; 5:E90. [PMID: 31569472 PMCID: PMC6958481 DOI: 10.3390/jof5040090] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2019] [Revised: 09/22/2019] [Accepted: 09/26/2019] [Indexed: 12/12/2022] Open
Abstract
Extensive advances in technology offer a vast variety of diagnostic methods that save time and costs, but identification of fungal species causing human infections remains challenging in developing countries. Since the echinocandins, antifungals widely used to treat invasive mycoses, are still unavailable in developing countries where a considerable number of problematic fungal species are present, rapid and reliable identification is of paramount importance. Unaffordability, large footprints, lack of skilled personnel, and high costs associated with maintenance and infrastructure are the main factors precluding the establishment of high-precision technologies that can replace inexpensive yet time-consuming and inaccurate phenotypic methods. In addition, point-of-care lateral flow assay tests are available for the diagnosis of Aspergillus and Cryptococcus and are highly relevant for developing countries. An Aspergillus galactomannan lateral flow assay is also now available. Real-time PCR remains difficult to standardize and is not widespread in countries with limited resources. Isothermal and conventional PCR-based amplification assays may be alternative solutions. The combination of real-time PCR and serological assays can significantly increase diagnostic efficiency. However, this approach is too expensive for medical institutions in developing countries. Further advances in next-generation sequencing and other innovative technologies such as clustered regularly interspaced short palindromic repeats (CRISPR)-based diagnostic tools may lead to efficient, alternate methods that can be used in point-of-care assays, which may supplement or replace some of the current technologies and improve the diagnostics of fungal infections in developing countries.
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Affiliation(s)
- Amir Arastehfar
- Westerdijk Fungal Biodiversity Institute, 3584 CT Utrecht, The Netherlands.
| | - Brian L Wickes
- The Department of Microbiology, Immunology, and Molecular Genetics, The University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, USA.
| | - Macit Ilkit
- Division of Mycology, Department of Microbiology, Faculty of Medicine, University of Çukurova, Adana 01330, Turkey.
| | | | - Farnaz Daneshnia
- Westerdijk Fungal Biodiversity Institute, 3584 CT Utrecht, The Netherlands.
| | - Weihua Pan
- Department of Dermatology, Shanghai Key Laboratory of Molecular Medical Mycology, Shanghai Institute of Medical Mycology, Second Military Medical University, Shanghai 200003, China.
| | - Wenjie Fang
- Department of Dermatology, Shanghai Key Laboratory of Molecular Medical Mycology, Shanghai Institute of Medical Mycology, Second Military Medical University, Shanghai 200003, China.
| | - Teun Boekhout
- Westerdijk Fungal Biodiversity Institute, 3584 CT Utrecht, The Netherlands.
- Department of Dermatology, Shanghai Key Laboratory of Molecular Medical Mycology, Shanghai Institute of Medical Mycology, Second Military Medical University, Shanghai 200003, China.
- Institute of Biodiversity and Ecosystem Dynamics, University of Amsterdam, 1012 WX Amsterdam, The Netherlands.
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