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Wu Z, Zhao S. Three-Way Junction-Assisted Rolling Circle Amplification Integrated with trans-Cleavage of Cas12a for Sensitive and Reliable Detection of miRNA. Appl Biochem Biotechnol 2024; 196:3115-3125. [PMID: 37624508 DOI: 10.1007/s12010-023-04691-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/16/2023] [Indexed: 08/26/2023]
Abstract
MicroRNAs (miRNAs) serve a crucial role in numerous biological processes, such as acute pancreatitis development. Due to its low abundance and high similarity among homogeneous family members, sensitive and reliable detection of microRNA remains a formidable challenge. By combining the three-way junction-assisted rolling circle amplification (RCA) with the trans-cleavage of Cas12a, we propose a novel fluorescent technique for sensitive miRNA detection. In order to increase the amplification efficiency of RCA-based methods, catalytic hairpin amplification (CHA) is incorporated into the RCA process, playing the roles of specific target recognition and three-way junction formation. Consequently, the method demonstrated a six-orders-of-magnitude detection range and a LOD as low as 27 aM, making it a promising method for the early diagnosis of various diseases.
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Affiliation(s)
- Zhiquan Wu
- Emergency and Critical Care Center, The Third Affiliated Hospital of Chongqing Medical University, Chongqing City, 401120, China
| | - Shuqi Zhao
- Department of Hematology, The Third Affiliated Hospital of Chongqing Medical University, Shuanghu Branch Road, Yubei District, Chongqing City, 401120, China.
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2
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Popgeorgiev N, Krupovic M, Hiblot J, Fancello L, Monteil-Bouchard S, Desnues C. A New Inovirus from the Human Blood Encodes Proteins with Nuclear Subcellular Localization. Viruses 2024; 16:475. [PMID: 38543840 PMCID: PMC10975378 DOI: 10.3390/v16030475] [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: 12/29/2023] [Revised: 01/30/2024] [Accepted: 02/06/2024] [Indexed: 05/23/2024] Open
Abstract
Viruses infecting bacteria (bacteriophages) represent the most abundant viral particles in the human body. They participate in the control of the human-associated bacterial communities and play an important role in the dissemination of virulence genes. Here, we present the identification of a new filamentous single-stranded DNA phage of the family Inoviridae, named Ralstonia Inoviridae Phage 1 (RIP1), in the human blood. Metagenomics and PCR analyses detected the RIP1 genome in blood serum, in the absence of concomitant bacterial infection or contamination, suggesting inovirus persistence in the human blood. Finally, we have experimentally demonstrated that the RIP1-encoded rolling circle replication initiation protein and serine integrase have functional nuclear localization signals and upon expression in eukaryotic cells both proteins were translocated into the nucleus. This observation adds to the growing body of data suggesting that phages could have an overlooked impact on the evolution of eukaryotic cells.
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Affiliation(s)
- Nikolay Popgeorgiev
- Université de Lyon, Centre de Recherche en Cancérologie de Lyon, U1052 INSERM, UMR CNRS 5286, Université Lyon I, Centre Léon Bérard, 28 rue Laennec, 69008 Lyon, France
- Institut Universitaire de France (IUF), 75013 Paris, France
| | - Mart Krupovic
- Archaeal Virology Unit, Institut Pasteur, Université Paris Cité, 75015 Paris, France
| | - Julien Hiblot
- Department of Chemical Biology, Max Planck Institute for Medical Research, Jahnstrasse 29, 69120 Heidelberg, Germany;
| | - Laura Fancello
- Interdisciplinary Research Institute of Grenoble, IRIG-Biosanté, University Grenoble Alpes, CEA, INSERM, UMR 1292, 38000 Grenoble, France;
| | - Sonia Monteil-Bouchard
- Microbiologie Environnementale Biotechnologie, Institut Méditerranéen d’Océanologie, 163 Avenue de Luminy, 13009 Marseille, France; (S.M.-B.); (C.D.)
| | - Christelle Desnues
- Microbiologie Environnementale Biotechnologie, Institut Méditerranéen d’Océanologie, 163 Avenue de Luminy, 13009 Marseille, France; (S.M.-B.); (C.D.)
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3
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Zhou Q, Ding X, Du W, Wang H, Wu S, Li J, Yang S. Multi-enzymatic systems synergize new RCA technique amplified super-long dsDNA from DNA circle. Anal Chim Acta 2024; 1291:342220. [PMID: 38280785 DOI: 10.1016/j.aca.2024.342220] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2023] [Accepted: 01/05/2024] [Indexed: 01/29/2024]
Abstract
BACKGROUND In the field of DNA amplification, there are great challenges in the effectively amplify of long-chain amplification, especially amplification up to several hundred kb level. RESULTS A novel technique for the unbiased whole genome amplification from a thimbleful of DNA circles, such as low as 10 ng/ 10 μL of the circular cpDNA or low as 5 ng/ 10 μL of the plasmid, is developed, which can amplify an abundance of the whole genome sequences. Specifically, the new technique that combines rolling-amplification and triple-enzyme system presents a tightly controlled process of a series of buffers/reactions and optimized procedures, that applies from the primer-template duplexes to the Elution step. The result of this technique provides a new approach for extending RCA capacity, where it can reach 200 kb from the circular cpDNA amplification and 150 kb from the plasmid DNA amplification, that demonstrates superior breadth and evenness of genome coverage, high reproducibility, small amplification bias with the amplification efficiency. SIGNIFICANCE AND NOVELTY This new technique will develop into one of the powerful tools for isothermal DNA amplification in vitro, genome sequencing/analysis, phylogenetic analysis, physical mapping, and other molecular biology applications.
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Affiliation(s)
- Qiang Zhou
- Key Laboratory of Biology and Genetics Improvement of Soybean, Ministry of Agriculture of the People's Republic of China, Nanjing Agricultural University, Nanjing, 210095, PR China; Zhongshan Biological Breeding Laboratory (ZSBBL), Nanjing Agricultural University, Nanjing, 210095, PR China; National Innovation Platform for Soybean Breeding and Industry-Education Integration, Nanjing Agricultural University, Nanjing, 210095, PR China; State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Nanjing Agricultural University, Nanjing, 210095, PR China; National Center for Soybean Improvement, Nanjing Agricultural University, Nanjing, 210095, PR China; Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, 210095, PR China; Soybean Research Institute, Nanjing Agricultural University, Nanjing, 210095, PR China; College of Agriculture, Nanjing Agricultural University, Nanjing, 210095, PR China.
| | - Xianlong Ding
- Key Laboratory of Biology and Genetics Improvement of Soybean, Ministry of Agriculture of the People's Republic of China, Nanjing Agricultural University, Nanjing, 210095, PR China; Zhongshan Biological Breeding Laboratory (ZSBBL), Nanjing Agricultural University, Nanjing, 210095, PR China; National Innovation Platform for Soybean Breeding and Industry-Education Integration, Nanjing Agricultural University, Nanjing, 210095, PR China; State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Nanjing Agricultural University, Nanjing, 210095, PR China; National Center for Soybean Improvement, Nanjing Agricultural University, Nanjing, 210095, PR China; Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, 210095, PR China; Soybean Research Institute, Nanjing Agricultural University, Nanjing, 210095, PR China; College of Agriculture, Nanjing Agricultural University, Nanjing, 210095, PR China.
| | - Wanqing Du
- Key Laboratory of Biology and Genetics Improvement of Soybean, Ministry of Agriculture of the People's Republic of China, Nanjing Agricultural University, Nanjing, 210095, PR China; Zhongshan Biological Breeding Laboratory (ZSBBL), Nanjing Agricultural University, Nanjing, 210095, PR China; National Innovation Platform for Soybean Breeding and Industry-Education Integration, Nanjing Agricultural University, Nanjing, 210095, PR China; State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Nanjing Agricultural University, Nanjing, 210095, PR China; National Center for Soybean Improvement, Nanjing Agricultural University, Nanjing, 210095, PR China; Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, 210095, PR China; Soybean Research Institute, Nanjing Agricultural University, Nanjing, 210095, PR China; College of Agriculture, Nanjing Agricultural University, Nanjing, 210095, PR China.
| | - Hongjie Wang
- Key Laboratory of Biology and Genetics Improvement of Soybean, Ministry of Agriculture of the People's Republic of China, Nanjing Agricultural University, Nanjing, 210095, PR China; Zhongshan Biological Breeding Laboratory (ZSBBL), Nanjing Agricultural University, Nanjing, 210095, PR China; National Innovation Platform for Soybean Breeding and Industry-Education Integration, Nanjing Agricultural University, Nanjing, 210095, PR China; State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Nanjing Agricultural University, Nanjing, 210095, PR China; National Center for Soybean Improvement, Nanjing Agricultural University, Nanjing, 210095, PR China; Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, 210095, PR China; Soybean Research Institute, Nanjing Agricultural University, Nanjing, 210095, PR China; College of Agriculture, Nanjing Agricultural University, Nanjing, 210095, PR China.
| | - Shuo Wu
- Key Laboratory of Biology and Genetics Improvement of Soybean, Ministry of Agriculture of the People's Republic of China, Nanjing Agricultural University, Nanjing, 210095, PR China; Zhongshan Biological Breeding Laboratory (ZSBBL), Nanjing Agricultural University, Nanjing, 210095, PR China; National Innovation Platform for Soybean Breeding and Industry-Education Integration, Nanjing Agricultural University, Nanjing, 210095, PR China; State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Nanjing Agricultural University, Nanjing, 210095, PR China; National Center for Soybean Improvement, Nanjing Agricultural University, Nanjing, 210095, PR China; Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, 210095, PR China; Soybean Research Institute, Nanjing Agricultural University, Nanjing, 210095, PR China; College of Agriculture, Nanjing Agricultural University, Nanjing, 210095, PR China.
| | - Jun Li
- Key Laboratory of Biology and Genetics Improvement of Soybean, Ministry of Agriculture of the People's Republic of China, Nanjing Agricultural University, Nanjing, 210095, PR China; Zhongshan Biological Breeding Laboratory (ZSBBL), Nanjing Agricultural University, Nanjing, 210095, PR China; National Innovation Platform for Soybean Breeding and Industry-Education Integration, Nanjing Agricultural University, Nanjing, 210095, PR China; State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Nanjing Agricultural University, Nanjing, 210095, PR China; National Center for Soybean Improvement, Nanjing Agricultural University, Nanjing, 210095, PR China; Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, 210095, PR China; Soybean Research Institute, Nanjing Agricultural University, Nanjing, 210095, PR China; College of Agriculture, Nanjing Agricultural University, Nanjing, 210095, PR China.
| | - Shouping Yang
- Key Laboratory of Biology and Genetics Improvement of Soybean, Ministry of Agriculture of the People's Republic of China, Nanjing Agricultural University, Nanjing, 210095, PR China; Zhongshan Biological Breeding Laboratory (ZSBBL), Nanjing Agricultural University, Nanjing, 210095, PR China; National Innovation Platform for Soybean Breeding and Industry-Education Integration, Nanjing Agricultural University, Nanjing, 210095, PR China; State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Nanjing Agricultural University, Nanjing, 210095, PR China; National Center for Soybean Improvement, Nanjing Agricultural University, Nanjing, 210095, PR China; Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, 210095, PR China; Soybean Research Institute, Nanjing Agricultural University, Nanjing, 210095, PR China; College of Agriculture, Nanjing Agricultural University, Nanjing, 210095, PR China.
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Trippa D, Scalenghe R, Basso MF, Panno S, Davino S, Morone C, Giovino A, Oufensou S, Luchi N, Yousefi S, Martinelli F. Next-generation methods for early disease detection in crops. PEST MANAGEMENT SCIENCE 2024; 80:245-261. [PMID: 37599270 DOI: 10.1002/ps.7733] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/20/2023] [Accepted: 08/21/2023] [Indexed: 08/22/2023]
Abstract
Plant pathogens are commonly identified in the field by the typical disease symptoms that they can cause. The efficient early detection and identification of pathogens are essential procedures to adopt effective management practices that reduce or prevent their spread in order to mitigate the negative impacts of the disease. In this review, the traditional and innovative methods for early detection of the plant pathogens highlighting their major advantages and limitations are presented and discussed. Traditional techniques of diagnosis used for plant pathogen identification are focused typically on the DNA, RNA (when molecular methods), and proteins or peptides (when serological methods) of the pathogens. Serological methods based on mainly enzyme-linked immunosorbent assay (ELISA) are the most common method used for pathogen detection due to their high-throughput potential and low cost. This technique is not particularly reliable and sufficiently sensitive for many pathogens detection during the asymptomatic stage of infection. For non-cultivable pathogens in the laboratory, nucleic acid-based technology is the best choice for consistent pathogen detection or identification. Lateral flow systems are innovative tools that allow fast and accurate results even in field conditions, but they have sensitivity issues to be overcome. PCR assays performed on last-generation portable thermocyclers may provide rapid detection results in situ. The advent of portable instruments can speed pathogen detection, reduce commercial costs, and potentially revolutionize plant pathology. This review provides information on current methodologies and procedures for the effective detection of different plant pathogens. © 2023 The Authors. Pest Management Science published by John Wiley & Sons Ltd on behalf of Society of Chemical Industry.
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Affiliation(s)
- Daniela Trippa
- Dipartimento di Scienze Agrarie Alimentari e Forestali, Università degli Studi di Palermo, Palermo, Italy
| | - Riccardo Scalenghe
- Dipartimento di Scienze Agrarie Alimentari e Forestali, Università degli Studi di Palermo, Palermo, Italy
| | | | - Stefano Panno
- Dipartimento di Scienze Agrarie Alimentari e Forestali, Università degli Studi di Palermo, Palermo, Italy
| | - Salvatore Davino
- Dipartimento di Scienze Agrarie Alimentari e Forestali, Università degli Studi di Palermo, Palermo, Italy
| | - Chiara Morone
- Regione Piemonte - Phytosanitary Division, Torino, Italy
| | - Antonio Giovino
- Council for Agricultural Research and Economics (CREA)-Research Centre for Plant Protection and Certification (CREA-DC), Palermo, Italy
| | - Safa Oufensou
- Dipartimento di Agraria, Università degli Studi di Sassari, Sassari, Italy
| | - Nicola Luchi
- National Research Council, Institute for Sustainable Plant Protection, (CNR-IPSP), Florence, Italy
| | - Sanaz Yousefi
- Department of Horticultural Science, Bu-Ali Sina University, Hamedan, Iran
| | - Federico Martinelli
- Department of Biology, University of Florence, Florence, Italy
- National Research Council, Institute for Sustainable Plant Protection, (CNR-IPSP), Florence, Italy
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5
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Sun Y, Ko DH, Gao J, Fu K, Gao Y, Zhang Q, Baldi S, Hong T, Ivanov I, He Y, Tian H. Unraveling the salt tolerance of Phi29 DNA polymerase using compartmentalized self-replication and microfluidics platform. Front Microbiol 2023; 14:1267196. [PMID: 38029082 PMCID: PMC10661337 DOI: 10.3389/fmicb.2023.1267196] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2023] [Accepted: 10/24/2023] [Indexed: 12/01/2023] Open
Abstract
In Phi29-α-hemolysin (α-HL) nanopore sequencing systems, a strong electrochemical signal is dependent on a high concentration of salt. However, high salt concentrations adversely affect polymerase activity. Sequencing by synthesis (SBS) requires the use of phi29 polymerase without exonuclease activity to prevent the degradation of modified nucleotide tags; however, the lack of exonuclease activity also affects polymerase processivity. This study aimed to optimize phi29 polymerase for improved salt tolerance and processivity while maintaining its lack of exonuclease activity to meet the requirements of nanopore sequencing. Using salt tolerance compartmentalized self-replication (stCSR) and a microfluidic platform, we obtained 11 mutant sites with enhanced salt tolerance attributes. Sequencing and biochemical analyses revealed that the substitution of conserved amino acids such as G197D, Y369E, T372N, and I378R plays a critical role in maintaining the processivity of exonuclease-deficient phi29 polymerase under high salt conditions. Furthermore, Y369E and T372N have been identified as important determinants of DNA polymerase binding affinity. This study provides insights into optimizing polymerase processability under high-salt conditions for real-time polymerase nanopore sequencing, paving the way for improved performance and applications in nanopore sequencing technologies.
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Affiliation(s)
- Yaping Sun
- Research Center of Molecular Diagnostics and Sequencing, Research Institute of Tsinghua University in Shenzhen, Shenzhen, China
| | - Danny Hsu Ko
- Research Center of Molecular Diagnostics and Sequencing, Axbio Biotechnology (Shenzhen) Co., Ltd., Shenzhen, China
| | - Jie Gao
- Research Center of Molecular Diagnostics and Sequencing, Axbio Biotechnology (Shenzhen) Co., Ltd., Shenzhen, China
| | - Kang Fu
- Research Center of Molecular Diagnostics and Sequencing, Axbio Biotechnology (Shenzhen) Co., Ltd., Shenzhen, China
| | - Yaping Gao
- Research Center of Molecular Diagnostics and Sequencing, Research Institute of Tsinghua University in Shenzhen, Shenzhen, China
| | - Qiwen Zhang
- Research Center of Molecular Diagnostics and Sequencing, Axbio Biotechnology (Shenzhen) Co., Ltd., Shenzhen, China
| | - Salem Baldi
- Research Center of Molecular Diagnostics and Sequencing, Axbio Biotechnology (Shenzhen) Co., Ltd., Shenzhen, China
| | - Tao Hong
- Research Center of Molecular Diagnostics and Sequencing, Axbio Biotechnology (Shenzhen) Co., Ltd., Shenzhen, China
| | - Igor Ivanov
- Research Center of Molecular Diagnostics and Sequencing, Axbio Biotechnology (Shenzhen) Co., Ltd., Shenzhen, China
| | - Yun He
- Research Center of Molecular Diagnostics and Sequencing, Research Institute of Tsinghua University in Shenzhen, Shenzhen, China
| | - Hui Tian
- Research Center of Molecular Diagnostics and Sequencing, Axbio Biotechnology (Shenzhen) Co., Ltd., Shenzhen, China
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6
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Kim KW, Lee B, Eom S, Shin D, Park C, Kim S, Yi H. Universal primers for rift valley fever virus whole-genome sequencing. Sci Rep 2023; 13:18688. [PMID: 37907670 PMCID: PMC10618441 DOI: 10.1038/s41598-023-45848-z] [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: 02/08/2023] [Accepted: 10/24/2023] [Indexed: 11/02/2023] Open
Abstract
Rift Valley fever (RVF) is a mosquito-borne zoonotic disease causing acute hemorrhagic fever. Accurate identification of mutations and phylogenetic characterization of RVF virus (RVFV) require whole-genome analysis. Universal primers to amplify the entire RVFV genome from clinical samples with low copy numbers are currently unavailable. Thus, we aimed to develop universal primers applicable for all known RVFV strains. Based on the genome sequences available from public databases, we designed eight pairs of universal PCR primers covering the entire RVFV genome. To evaluate primer universality, four RVFV strains (ZH548, Kenya 56 (IB8), BIME-01, and Lunyo), encompassing viral phylogenetic diversity, were chosen. The nucleic acids of the test strains were chemically synthesized or extracted via cell culture. These RNAs were evaluated using the PCR primers, resulting in successful amplification with expected sizes (0.8-1.7 kb). Sequencing confirmed that the products covered the entire genome of the RVFV strains tested. Primer specificity was confirmed via in silico comparison against all non-redundant nucleotide sequences using the BLASTn alignment tool in the NCBI database. To assess the clinical applicability of the primers, mock clinical specimens containing human and RVFV RNAs were prepared. The entire RVFV genome was successfully amplified and sequenced at a viral concentration of 108 copies/mL. Given the universality, specificity, and clinical applicability of the primers, we anticipate that the RVFV universal primer pairs and the developed method will aid in RVFV phylogenomics and mutation detection.
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Affiliation(s)
- Kwan Woo Kim
- Department of Public Health Sciences, Graduate School, Korea University, Seoul, Republic of Korea
- Interdisciplinary Program in Precision Public Health, Korea University, Seoul, Republic of Korea
- Center for Study of Emerging and Re-emerging Viruses, Korea Virus Research Institute, Institute for Basic Science (IBS), Daejeon, Republic of Korea
| | - Banseok Lee
- Interdisciplinary Program in Precision Public Health, Korea University, Seoul, Republic of Korea
- Integrated Biomedical and Life Science, Graduate School, Korea University, Seoul, Republic of Korea
| | - Sujeong Eom
- Interdisciplinary Program in Precision Public Health, Korea University, Seoul, Republic of Korea
- Integrated Biomedical and Life Science, Graduate School, Korea University, Seoul, Republic of Korea
| | - Donghoon Shin
- Interdisciplinary Program in Precision Public Health, Korea University, Seoul, Republic of Korea
- Integrated Biomedical and Life Science, Graduate School, Korea University, Seoul, Republic of Korea
| | - Changwoo Park
- Microbiological Analysis Team, Group for Biometrology, Korea Research Institute of Standards and Science (KRISS), Daejeon, Republic of Korea
- Convergent Research Center for Emerging Virus Infection, Korea Research Institute of Chemical Technology (KRICT), Daejeon, Republic of Korea
- Department of Agricultural Biotechnology, Seoul National University, Seoul, Republic of Korea
| | - Seil Kim
- Microbiological Analysis Team, Group for Biometrology, Korea Research Institute of Standards and Science (KRISS), Daejeon, Republic of Korea.
- Convergent Research Center for Emerging Virus Infection, Korea Research Institute of Chemical Technology (KRICT), Daejeon, Republic of Korea.
- Department of Bio-Analysis Science, University of Science and Technology, Daejeon, Republic of Korea.
| | - Hana Yi
- Interdisciplinary Program in Precision Public Health, Korea University, Seoul, Republic of Korea.
- Integrated Biomedical and Life Science, Graduate School, Korea University, Seoul, Republic of Korea.
- School of Biosystems and Biomedical Sciences, Korea University, Seoul, Republic of Korea.
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7
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Han P, Fan H, Tong Y. Identification of a novel family B DNA polymerase from Enterococcus phage IME199 and its overproduction in Escherichia coli BL21(DE3). Microb Cell Fact 2023; 22:217. [PMID: 37865739 PMCID: PMC10590003 DOI: 10.1186/s12934-023-02228-6] [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: 07/31/2023] [Accepted: 10/11/2023] [Indexed: 10/23/2023] Open
Abstract
BACKGROUND Identification and characterization of novel, faithful and processive DNA polymerases is a driving force in the development of DNA amplification methods. Purification of proteins from natural phages is often time-consuming, cumbersome and low yielding. Escherichia coli is a host bacterium widely used for the production of recombinant proteins, is the cell factory of choice for in vitro studies of phage protein function. RESULTS We expressed the gene encoding Enterococcus faecium phage IME199 DNA polymerase (IME199 DNAP) in Escherichia coli BL21(DE3), and characterized protein function. IME199 DNAP has 3'-5' exonuclease activity, but does not have 5'-3' exonuclease activity. In addition, IME199 DNAP has dNTP-dependent 5'-3' polymerase activity and can amplify DNA at 15-35 °C and a pH range of 5.5-9.5. The amino acid residues Asp30, Glu32, Asp112 and Asp251 are the 3'-5' exonuclease active sites of IME199 DNAP, while residues Asp596 and Tyr639 are essential for DNA synthesis by IME199 DNAP. More importantly, the IME199 DNAP has strand displacement and processive synthesis capabilities, and can perform rolling circle amplification and multiple displacement amplification with very low error rates (approximately 3.67 × 10-6). CONCLUSIONS A novel family B DNA polymerase was successfully overproduced in Escherichia coli BL21(DE3). Based on the characterized properties, IME199 DNAP is expected to be developed as a high-fidelity polymerase for DNA amplification at room temperature.
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Affiliation(s)
- Pengjun Han
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, 100029, China
| | - Huahao Fan
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, 100029, China.
| | - Yigang Tong
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, 100029, China.
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering, Beijing University of Chemical Technology, Beijing, 100029, China.
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8
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Strawn IK, Steiner PJ, Newton MS, Baumer ZT, Whitehead TA. A method for generating user-defined circular single-stranded DNA from plasmid DNA using Golden Gate intramolecular ligation. Biotechnol Bioeng 2023; 120:3057-3066. [PMID: 37366288 PMCID: PMC10527171 DOI: 10.1002/bit.28471] [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: 12/02/2022] [Revised: 05/26/2023] [Accepted: 06/05/2023] [Indexed: 06/28/2023]
Abstract
Construction of user-defined long circular single stranded DNA (cssDNA) and linear single stranded DNA (lssDNA) is important for various biotechnological applications. Many current methods for synthesis of these ssDNA molecules do not scale to multikilobase constructs. Here we present a robust methodology for generating user-defined cssDNA employing Golden Gate assembly, a nickase, and exonuclease degradation. Our technique is demonstrated for three plasmids with insert sizes ranging from 2.1 to 3.4 kb, requires no specialized equipment, and can be accomplished in 5 h with a yield of 33%-43% of the theoretical. To produce lssDNA, we evaluated different CRISPR-Cas9 cleavage conditions and reported a 52 ± 8% cleavage efficiency of cssDNA. Thus, our current method does not compete with existing protocols for lssDNA generation. Nevertheless, our protocol can make long, user-defined cssDNA readily available to biotechnology researchers.
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Affiliation(s)
- Isabell K. Strawn
- Department of Chemical and Biological Engineering, University of Colorado, Boulder, CO 80305, USA
| | - Paul J. Steiner
- Department of Chemical and Biological Engineering, University of Colorado, Boulder, CO 80305, USA
| | - Matilda S. Newton
- Department of Chemical and Biological Engineering, University of Colorado, Boulder, CO 80305, USA
- Current address: Department of Molecular, Cellular and Developmental Biology and the Cooperative Institute for Research in Environmental Sciences, University of Colorado Boulder, Boulder, Colorado 80309, United States
| | - Zachary T. Baumer
- Department of Chemical and Biological Engineering, University of Colorado, Boulder, CO 80305, USA
| | - Timothy A. Whitehead
- Department of Chemical and Biological Engineering, University of Colorado, Boulder, CO 80305, USA
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9
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Vasinioti VI, Pellegrini F, Buonavoglia A, Capozza P, Cardone R, Diakoudi G, Desario C, Catella C, Vicenza T, Lucente MS, Di Martino B, Camero M, Elia G, Decaro N, Martella V, Lanave G. Investigating the genetic diversity of CRESS DNA viruses in cats identifies a novel feline circovirus and unveils exposure of cats to canine circovirus. Res Vet Sci 2023; 161:86-95. [PMID: 37327693 DOI: 10.1016/j.rvsc.2023.06.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2023] [Revised: 06/08/2023] [Accepted: 06/09/2023] [Indexed: 06/18/2023]
Abstract
Circular replication-associated protein (Rep)-encoding single stranded (CRESS) DNA viruses include Circoviruses which have been found in several animal species and in human specimens. Circoviruses are associated with severe disease in pigs and birds and with respiratory and gastrointestinal disorders and systemic disease in dogs. In cats there are only a few anecdotical studies reporting CRESS DNA viruses. In this study, a total of 530 samples (361 sera, 131 stools, and 38 respiratory swabs) from cats, were screened for the presence of CRESS DNA viruses. Overall, 48 (9.0%) of 530 samples tested positive using a pan-Rep PCR. A total of 30 Rep sequences were obtained. Ten sequences of fecal origin were tightly related to each other (82.4-100% nt identity) and more distantly related to mongoose circoviruses (68.3 to 77.2% nt identity). At genome level these circoviruses displayed the highest nt identity (74.3-78.7%) to mongoose circoviruses thus representing a novel circovirus species. Circoviruses from different animal hosts (n = 12) and from humans (n = 8) were also identified. However, six Rep sequences were obtained from serum samples, including canine circoviruses, a human cyclovirus and human and fish-associated CRESS DNA viruses. The presence of these viruses in the sera would imply, to various extent, virus replication in the animal host, able to sustain viremia. Overall, these findings indicate a wide genetic diversity of CRESS DNA viruses in cats and warrant further investigations.
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Affiliation(s)
- Violetta Iris Vasinioti
- Department of Veterinary Medicine, University of Bari Aldo Moro, S.p. per Casamassima Km 3, Valenzano, 70010 Bari, Italy
| | - Francesco Pellegrini
- Department of Veterinary Medicine, University of Bari Aldo Moro, S.p. per Casamassima Km 3, Valenzano, 70010 Bari, Italy
| | - Alessio Buonavoglia
- Department of Veterinary Medicine, University of Bari Aldo Moro, S.p. per Casamassima Km 3, Valenzano, 70010 Bari, Italy
| | - Paolo Capozza
- Department of Veterinary Medicine, University of Bari Aldo Moro, S.p. per Casamassima Km 3, Valenzano, 70010 Bari, Italy
| | - Roberta Cardone
- Department of Veterinary Medicine, University of Bari Aldo Moro, S.p. per Casamassima Km 3, Valenzano, 70010 Bari, Italy
| | - Georgia Diakoudi
- Department of Veterinary Medicine, University of Bari Aldo Moro, S.p. per Casamassima Km 3, Valenzano, 70010 Bari, Italy
| | - Costantina Desario
- Department of Veterinary Medicine, University of Bari Aldo Moro, S.p. per Casamassima Km 3, Valenzano, 70010 Bari, Italy
| | - Cristiana Catella
- Department of Veterinary Medicine, University of Bari Aldo Moro, S.p. per Casamassima Km 3, Valenzano, 70010 Bari, Italy
| | - Teresa Vicenza
- Department of Veterinary Medicine, University of Bari Aldo Moro, S.p. per Casamassima Km 3, Valenzano, 70010 Bari, Italy
| | - Maria Stella Lucente
- Department of Veterinary Medicine, University of Bari Aldo Moro, S.p. per Casamassima Km 3, Valenzano, 70010 Bari, Italy
| | - Barbara Di Martino
- Department of Veterinary Medicine, Università degli Studi di Teramo, SP18, 64100 Teramo, Italy
| | - Michele Camero
- Department of Veterinary Medicine, University of Bari Aldo Moro, S.p. per Casamassima Km 3, Valenzano, 70010 Bari, Italy
| | - Gabriella Elia
- Department of Veterinary Medicine, University of Bari Aldo Moro, S.p. per Casamassima Km 3, Valenzano, 70010 Bari, Italy
| | - Nicola Decaro
- Department of Veterinary Medicine, University of Bari Aldo Moro, S.p. per Casamassima Km 3, Valenzano, 70010 Bari, Italy
| | - Vito Martella
- Department of Veterinary Medicine, University of Bari Aldo Moro, S.p. per Casamassima Km 3, Valenzano, 70010 Bari, Italy
| | - Gianvito Lanave
- Department of Veterinary Medicine, University of Bari Aldo Moro, S.p. per Casamassima Km 3, Valenzano, 70010 Bari, Italy.
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10
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Lichter EZ, Trease AJ, Cooper K, Stauch KL, Fox HS. Effects of Parkin on the Mitochondrial Genome in the Heart and Brain of Mitochondrial Mutator Mice. Adv Biol (Weinh) 2023; 7:e2300154. [PMID: 37376822 DOI: 10.1002/adbi.202300154] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Indexed: 06/29/2023]
Abstract
Mitochondrial dysfunction has been implicated in neurodegenerative diseases like Parkinson's disease (PD). This study investigates the role of Parkin, a protein involved in mitochondrial quality control, and strongly linked to PD, in the context of mitochondrial DNA (mtDNA) mutations. Mitochondrial mutator mice (PolgD257A/D257A ) (Polg) are used and bred with Parkin knockout (PKO) mice or mice with disinhibited Parkin (W402A). In the brain, mtDNA mutations are analyzed in synaptosomes, presynaptic neuronal terminals, which are far from neuronal soma, which likely renders mitochondria there more vulnerable compared with brain homogenate. Surprisingly, PKO results in reduced mtDNA mutations in the brain but increased control region multimer (CRM) in synaptosomes. In the heart, both PKO and W402A lead to increased mutations, with W402A showing more mutations in the heart than PKO. Computational analysis reveals many of these mutations are deleterious. These findings suggest that Parkin plays a tissue-dependent role in regulating mtDNA damage response, with differential effects in the brain and heart. Understanding the specific role of Parkin in different tissues may provide insights into the underlying mechanisms of PD and potential therapeutic strategies. Further investigation into these pathways can enhance the understanding of neurodegenerative diseases associated with mitochondrial dysfunction.
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Affiliation(s)
- Eliezer Z Lichter
- Department of Neurological Sciences, University of Nebraska Medical Center, Omaha, NE, 68198, USA
| | - Andrew J Trease
- Department of Neurological Sciences, University of Nebraska Medical Center, Omaha, NE, 68198, USA
| | - Kathryn Cooper
- School of Interdisciplinary Informatics, University of Nebraska Omaha, Omaha, NE, 68182, USA
| | - Kelly L Stauch
- Department of Neurological Sciences, University of Nebraska Medical Center, Omaha, NE, 68198, USA
| | - Howard S Fox
- Department of Neurological Sciences, University of Nebraska Medical Center, Omaha, NE, 68198, USA
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11
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Dhobale KV, Murugan B, Deb R, Kumar S, Sahoo L. Molecular Epidemiology of Begomoviruses Infecting Mungbean from Yellow Mosaic Disease Hotspot Regions of India. Appl Biochem Biotechnol 2023; 195:5158-5179. [PMID: 36853442 DOI: 10.1007/s12010-023-04402-3] [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] [Accepted: 02/17/2023] [Indexed: 03/01/2023]
Abstract
The major threat to mungbean (Vigna radiata L.) cultivation in the Indian subcontinent is yellow mosaic diseases (YMD), caused by Begomovirus containing bipartite genomes (DNA-A and DNA-B). In the current study, we address the epidemiology of begomoviruses infecting mungbean plants in three YMD hotspot regions of India. Full-length genomic components of the viruses from the symptomatic leaves were cloned by rolling circle amplification (RCA) and sequenced. Mungbean yellow mosaic virus (MYMV) was detected in Bihar and mungbean yellow mosaic India virus (MYMIV) in Assam and Orissa. Furthermore, we studied the population structure and genetic diversity of MYMV and MYMIV isolates of Vigna species reported to date from India. Interestingly, based on phylogenetics, we observed independent evolution of DNA-A and coevolution of DNA-B of MYMV and MYMIV. This finding is supported by the high mutation rate and recombination events in DNA-B, particularly in BV1 and BC1 genes over DNA-A, with high transition/transversion bias (R) for DNA-A over DNA-B. To investigate the effect of Begomovirus infection in plants, we constructed infectious clones (i.e. MYMV and MYMIV) and inoculated them to eight mungbean genotypes, cowpea (Vigna unguiculata L.) and tobacco (Nicotiana benthamiana) through agroinfiltration. The infected plants developed varying degrees of typical YMD symptoms. Based on the disease severity score and viral titre, mungbean genotypes were categorized as highly susceptible to MYMV (ML267) and MYMIV (K851) and immune to MYMV (PDM139, SML668) and MYMIV (Pusa Vishal). Conclusively, our findings may help prevent an epidemic of YMD in Vigna species and develop mungbean genotypes resistant to YMD via breeding programs.
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Affiliation(s)
- Kiran Vilas Dhobale
- Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati, India
| | - Bharatheeswaran Murugan
- Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati, India
| | - Rishav Deb
- Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati, India
| | - Sanjeev Kumar
- Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati, India
| | - Lingaraj Sahoo
- Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati, India.
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12
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Dye AE, Muga B, Mwangi J, Hoyer JS, Ly V, Rosado Y, Sharpee W, Mware B, Wambugu M, Labadie P, Deppong D, Jackai L, Jacobson A, Kennedy G, Ateka E, Duffy S, Hanley-Bowdoin L, Carbone I, Ascencio-Ibáñez JT. Cassava begomovirus species diversity changes during plant vegetative cycles. Front Microbiol 2023; 14:1163566. [PMID: 37303798 PMCID: PMC10248227 DOI: 10.3389/fmicb.2023.1163566] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Accepted: 04/17/2023] [Indexed: 06/13/2023] Open
Abstract
Cassava is a root crop important for global food security and the third biggest source of calories on the African continent. Cassava production is threatened by Cassava mosaic disease (CMD), which is caused by a complex of single-stranded DNA viruses (family: Geminiviridae, genus: Begomovirus) that are transmitted by the sweet potato whitefly (Bemisia tabaci). Understanding the dynamics of different cassava mosaic begomovirus (CMB) species through time is important for contextualizing disease trends. Cassava plants with CMD symptoms were sampled in Lake Victoria and coastal regions of Kenya before transfer to a greenhouse setting and regular propagation. The field-collected and greenhouse samples were sequenced using Illumina short-read sequencing and analyzed on the Galaxy platform. In the field-collected samples, African cassava mosaic virus (ACMV), East African cassava mosaic virus (EACMV), East African cassava mosaic Kenya virus (EACMKV), and East African cassava mosaic virus-Uganda variant (EACMV-Ug) were detected in samples from the Lake Victoria region, while EACMV and East African mosaic Zanzibar virus (EACMZV) were found in the coastal region. Many of the field-collected samples had mixed infections of EACMV and another begomovirus. After 3 years of regrowth in the greenhouse, only EACMV-like viruses were detected in all samples. The results suggest that in these samples, EACMV becomes the dominant virus through vegetative propagation in a greenhouse. This differed from whitefly transmission results. Cassava plants were inoculated with ACMV and another EACMV-like virus, East African cassava mosaic Cameroon virus (EACMCV). Only ACMV was transmitted by whiteflies from these plants to recipient plants, as indicated by sequencing reads and copy number data. These results suggest that whitefly transmission and vegetative transmission lead to different outcomes for ACMV and EACMV-like viruses.
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Affiliation(s)
- Anna E. Dye
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC, United States
| | - Brenda Muga
- Department of Horticulture, Jomo Kenyatta University of Agriculture and Technology, Nairobi, Kenya
| | - Jenniffer Mwangi
- Department of Horticulture, Jomo Kenyatta University of Agriculture and Technology, Nairobi, Kenya
| | - J. Steen Hoyer
- Department of Ecology, Evolution and Natural Resources, Rutgers University, New Brunswick, NJ, United States
| | - Vanessa Ly
- Department of Molecular and Structural Biochemistry, North Carolina State University, Raleigh, NC, United States
| | - Yamilex Rosado
- Department of Molecular and Structural Biochemistry, North Carolina State University, Raleigh, NC, United States
| | - William Sharpee
- International Livestock Research Institute (ILRI), Nairobi, Kenya
- Department of Entomology and Plant Pathology, North Carolina State University, Raleigh, NC, United States
| | - Benard Mware
- International Livestock Research Institute (ILRI), Nairobi, Kenya
| | - Mary Wambugu
- International Livestock Research Institute (ILRI), Nairobi, Kenya
| | - Paul Labadie
- Department of Entomology and Plant Pathology, North Carolina State University, Raleigh, NC, United States
| | - David Deppong
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC, United States
| | - Louis Jackai
- Department of Natural Resources and Environmental Design, North Carolina Agricultural and Technical State University, Greensboro, NC, United States
| | - Alana Jacobson
- Department of Entomology and Plant Pathology, Auburn University, Auburn, AL, United States
| | - George Kennedy
- Department of Entomology and Plant Pathology, North Carolina State University, Raleigh, NC, United States
| | - Elijah Ateka
- Department of Horticulture, Jomo Kenyatta University of Agriculture and Technology, Nairobi, Kenya
| | - Siobain Duffy
- Department of Ecology, Evolution and Natural Resources, Rutgers University, New Brunswick, NJ, United States
| | - Linda Hanley-Bowdoin
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC, United States
| | - Ignazio Carbone
- Center for Integrated Fungal Research, Department of Entomology and Plant Pathology, North Carolina State University, Raleigh, NC, United States
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Assessing the genomic composition, putative ecological relevance and biotechnological potential of plasmids from sponge bacterial symbionts. Microbiol Res 2022; 265:127183. [PMID: 36108440 DOI: 10.1016/j.micres.2022.127183] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Revised: 02/24/2022] [Accepted: 09/01/2022] [Indexed: 11/24/2022]
Abstract
Plasmid-mediated transfer of genes can have direct consequences in several biological processes within sponge microbial communities. However, very few studies have attempted genomic and functional characterization of plasmids from marine host-associated microbial communities in general and those of sponges in particular. In the present study, we used an endogenous plasmid isolation method to obtain plasmids from bacterial symbionts of the marine sponges Stylissa carteri and Paratetilla sp. and investigated the genomic composition, putative ecological relevance and biotechnological potential of these plasmids. In total, we isolated and characterized three complete plasmids, three plasmid prophages and one incomplete plasmid. Our results highlight the importance of plasmids to transfer relevant genetic traits putatively involved in microbial symbiont adaptation and host-microbe and microbe-microbe interactions. For example, putative genes involved in bacterial response to chemical stress, competition, metabolic versatility and mediation of bacterial colonization and pathogenicity were detected. Genes coding for enzymes and toxins of biotechnological potential were also detected. Most plasmid prophage coding sequences were, however, hypothetical proteins with unknown functions. Overall, this study highlights the ecological relevance of plasmids in the marine sponge microbiome and provides evidence that plasmids of sponge bacterial symbionts may represent an untapped resource of genes of biotechnological interest.
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Complete Genome Sequence of a Novel Monopartite Mastrevirus, Soybean Geminivirus B, Isolated from Soybean (Glycine max (L.) Merrill). PLANTS 2022; 11:plants11131768. [PMID: 35807721 PMCID: PMC9269612 DOI: 10.3390/plants11131768] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Revised: 06/28/2022] [Accepted: 06/29/2022] [Indexed: 11/17/2022]
Abstract
Soybean is one of the most important crops in Korea. To identify the viruses infecting soybean, we conducted RNA sequencing with samples displaying symptoms of viral disease. A contig displaying sequence similarity to the known Geminivirus was identified. A polymerase chain reaction (PCR) using two different pairs of back-to-back primers and rolling circle amplification (RCA) confirmed the complete genome of a novel virus named soybean geminivirus B (SGVB), consisting of a circular monopartite DNA genome measuring 2616 nucleotides (nt) in length. SGVB contains four open reading frames (ORFs) and three intergenic regions (IRs). IR1 includes a nonanucleotide origin of replication in the stem-loop structure. Phylogenetic and BLAST analyses demonstrated that SGVB could be a novel virus belonging to the genus Mastrevirus in the family Geminiviridae. We generated infectious clones for SGVB by adding a copy of the IR1 region of SGVB, comparing the V-ori in addition to the full-length genome of SGVB. Using the infectious clones, we observed chlorosis and leaf curling with a latent infection in the inoculated Nicotiana benthamiana plants, while none of the inoculated soybean plants showed any visible symptoms of disease. This study provides the complete genome sequence and infectious clones of a novel Mastrevirus referred to as SGVB from soybean in Korea.
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Diversity of CRESS DNA Viruses in Squamates Recapitulates Hosts Dietary and Environmental Sources of Exposure. Microbiol Spectr 2022; 10:e0078022. [PMID: 35616383 PMCID: PMC9241739 DOI: 10.1128/spectrum.00780-22] [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] [Indexed: 11/22/2022] Open
Abstract
Replication-associated protein (Rep)-encoding single-stranded (CRESS) DNA viruses comprise viruses with covalently closed, circular, single-stranded DNA (ssDNA) genomes, and are considered the smallest known autonomously replicating, capsid-encoding animal pathogens. CRESS DNA viruses (phylum Cressdnaviricota) encompass several viral families including Circoviridae. Circoviruses are classified into two genera, Circovirus and Cyclovirus, and they are known to cause fatal diseases in birds and pigs. Circoviruses have also been identified in human stools, blood, and cerebrospinal fluid (CSF), as well as in various wild and domestic vertebrates, including reptiles. The synanthropic presence of Squamata reptiles has increased in the last century due to the anthropic pressure, which has shifted forested animal behavior to an urban and peri-urban adaptation. In this paper, we explored the diversity of CRESS DNA viruses in Squamata reptiles from different Italian areas representative of the Mediterranean basin. CRESS DNA viruses were detected in 31.7% (33/104) of sampled lizards and geckoes. Different CRESS DNA viruses likely reflected dietary composition or environmental contamination and included avian-like (n = 3), dog (n = 4), bat-like (n = 1), goat-like (n = 1), rodent-like (n = 4), and insect-like (n = 2) viruses. Rep sequences of at least two types of human-associated cycloviruses (CyV) were identified consistently, regardless of geographic location, namely, TN9-like (n = 11) and TN12-like (n = 6). A third human-associated CyV, TN25-like, was detected in a single sample. The complete genome of human-like CyVs, of a rodent-like, insect-like, and of a bat-like virus were generated. Collectively, the results recapitulate hosts dietary and environmental sources of exposure and may suggest unexpected ecological niches for some CRESS DNA viruses. IMPORTANCE CRESS DNA viruses are significant pathogens of birds and pigs and have been detected repeatedly in human samples (stools, serum, and cerebrospinal fluid), both from healthy individuals and from patients with neurological disease, eliciting in 2013 a risk assessment by the European Centre for Disease Prevention and Control (ECDC). Sequences of CRESS DNA viruses previously reported in humans (TN9, TN12, and TN25), and detected in different animal species (e.g., birds, dogs, and bats) were herein detected in fecal samples of synanthropic squamates (geckos and lizards). The complete genome sequence of six viruses was generated. This study extends the information on the genetic diversity and ecology of CRESS DNA viruses. Because geckos and lizards are synanthropic animals, a role in sustaining CRESS DNA virus circulation and increasing viral pressure in the environment is postulated.
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Fanelli A, Pellegrini F, Camero M, Catella C, Buonavoglia D, Fusco G, Martella V, Lanave G. Genetic Diversity of Porcine Circovirus Types 2 and 3 in Wild Boar in Italy. Animals (Basel) 2022; 12:ani12080953. [PMID: 35454199 PMCID: PMC9031215 DOI: 10.3390/ani12080953] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Revised: 04/04/2022] [Accepted: 04/05/2022] [Indexed: 01/27/2023] Open
Abstract
Simple Summary Porcine circoviruses (PCVs) are major viral agents of farmed swine, causing relevant economic impact due to direct losses and control measures expenses. Wild boar may serve as a PCVs reservoir for the domestic pigs, thus threatening for production efficiency in pig farms. PCV infection in both domestic pigs and wild boar has been chiefly studied in Northern Italy, a densely populated area with a highly developed pork industry. However, data on circulation of PCV are scarce in other Italian areas. For the above reasons, along with the increasing sanitary relevance of wildlife as host of many livestock diseases, we carried out an epidemiological study to assess the prevalence and genetic characteristics of the PCVs circulating in wild boar in Basilicata region (Southern Italy), characterized by large forested areas with limited anthropic presence. A high prevalence was detected, suggesting that PCVs infection is endemic in the study population. These findings are of particular interest as the pig production system of the study area involves local breeds raised outdoor for the production of high-quality cured meat, thus having a high risk of being in contact with infected wild boar. Abstract Porcine circovirus (PCV) infection is associated with relevant economic impact to the pig industry. To date, four species of PCV (PCV1 to 4) have been identified but only PCV2 has been associated firmly with disease in pigs. The objective of this study was to assess the prevalence of PCV2 and PCV3 in the wild boar population in Basilicata region, Southern Italy, since this region is characterized by large forested and rural areas and the anthropic pressure is lower than in other Italian regions. Liver samples from 82 hunted wild boar were collected in 2021 from 3 different hunting districts. Sixty (73%, 95%CI: 63–82) samples tested positive for PCVs by quantitative PCR. In detail, 22 (27%, 95%CI: 18–37) were positive for PCV2, 58 (71%, 95%CI: 60–79) for PCV3, and 20 (24.4%, 95%CI 16–35) for both PCV2 and PCV3. On genome sequencing, different types and sub-types of PCV2 and PCV3 were identified, remarking a genetic diversity and hinting to a global circulation for the identified PCV strains. Overall, the high prevalence suggests that PCV2 and PCV3 infections are endemic in the wild boar population, posing risks for semi-intensive and free-range pig farming, typical of this region, due to contact with PCV-infected wild boar.
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Affiliation(s)
- Angela Fanelli
- Department of Veterinary Medicine, University Aldo Moro of Bari, 70010 Valenzano, BA, Italy; (F.P.); (M.C.); (C.C.); (D.B.); (V.M.)
- Correspondence: (A.F.); (G.L.)
| | - Francesco Pellegrini
- Department of Veterinary Medicine, University Aldo Moro of Bari, 70010 Valenzano, BA, Italy; (F.P.); (M.C.); (C.C.); (D.B.); (V.M.)
| | - Michele Camero
- Department of Veterinary Medicine, University Aldo Moro of Bari, 70010 Valenzano, BA, Italy; (F.P.); (M.C.); (C.C.); (D.B.); (V.M.)
| | - Cristiana Catella
- Department of Veterinary Medicine, University Aldo Moro of Bari, 70010 Valenzano, BA, Italy; (F.P.); (M.C.); (C.C.); (D.B.); (V.M.)
| | - Domenico Buonavoglia
- Department of Veterinary Medicine, University Aldo Moro of Bari, 70010 Valenzano, BA, Italy; (F.P.); (M.C.); (C.C.); (D.B.); (V.M.)
| | - Giovanna Fusco
- Istituto Zooprofilattico Sperimentale del Mezzogiorno, 80055 Portici, NA, Italy;
| | - Vito Martella
- Department of Veterinary Medicine, University Aldo Moro of Bari, 70010 Valenzano, BA, Italy; (F.P.); (M.C.); (C.C.); (D.B.); (V.M.)
| | - Gianvito Lanave
- Department of Veterinary Medicine, University Aldo Moro of Bari, 70010 Valenzano, BA, Italy; (F.P.); (M.C.); (C.C.); (D.B.); (V.M.)
- Correspondence: (A.F.); (G.L.)
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Abstract
Hepadnaviruses have been identified in several animal species. The hepadnavirus prototype, human hepatitis B virus (HBV), is a major public health problem associated with chronic liver diseases and hepatocellular carcinoma. Recently, a novel hepadnavirus, similar to HBV, was identified in domestic cats. Since several pathogens can be shared between cats and dogs, we hypothesized that dogs could also harbor hepadnaviruses and we tested a collection of canine sera with multiple molecular strategies. Overall, hepadnavirus DNA was identified in 6.3% (40/635) of canine serum samples, although the viral load in positive sera was low (geometric mean of 2.70 × 102 genome copies per mL, range min 1.36 × 102—max 4.03 × 104 genome copies per mL). On genome sequencing, the canine hepadnaviruses revealed high nucleotide identity (about 98%) and similar organization to the domestic cat hepadnavirus. Altered hepatic markers were found in hepadnavirus-positive dogs, although the role of hepadnavirus in canine health remains to be elucidated.
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Rodríguez-Verástegui LL, Ramírez-Zavaleta CY, Capilla-Hernández MF, Gregorio-Jorge J. Viruses Infecting Trees and Herbs That Produce Edible Fleshy Fruits with a Prominent Value in the Global Market: An Evolutionary Perspective. PLANTS (BASEL, SWITZERLAND) 2022; 11:203. [PMID: 35050091 PMCID: PMC8778216 DOI: 10.3390/plants11020203] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2021] [Revised: 09/20/2021] [Accepted: 09/23/2021] [Indexed: 05/12/2023]
Abstract
Trees and herbs that produce fruits represent the most valuable agricultural food commodities in the world. However, the yield of these crops is not fully achieved due to biotic factors such as bacteria, fungi, and viruses. Viruses are capable of causing alterations in plant growth and development, thereby impacting the yield of their hosts significantly. In this work, we first compiled the world's most comprehensive list of known edible fruits that fits our definition. Then, plant viruses infecting those trees and herbs that produce fruits with commercial importance in the global market were identified. The identified plant viruses belong to 30 families, most of them containing single-stranded RNA genomes. Importantly, we show the overall picture of the host range for some virus families following an evolutionary approach. Further, the current knowledge about plant-virus interactions, focusing on the main disorders they cause, as well as yield losses, is summarized. Additionally, since accurate diagnosis methods are of pivotal importance for viral diseases control, the current and emerging technologies for the detection of these plant pathogens are described. Finally, the most promising strategies employed to control viral diseases in the field are presented, focusing on solutions that are long-lasting.
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Affiliation(s)
| | - Candy Yuriria Ramírez-Zavaleta
- Cuerpo Académico Procesos Biotecnológicos, Universidad Politécnica de Tlaxcala, Av. Universidad Politécnica 1, San Pedro Xalcaltzinco 90180, Mexico; (C.Y.R.-Z.); (M.F.C.-H.)
| | - María Fernanda Capilla-Hernández
- Cuerpo Académico Procesos Biotecnológicos, Universidad Politécnica de Tlaxcala, Av. Universidad Politécnica 1, San Pedro Xalcaltzinco 90180, Mexico; (C.Y.R.-Z.); (M.F.C.-H.)
| | - Josefat Gregorio-Jorge
- Consejo Nacional de Ciencia y Tecnología, Universidad Politécnica de Tlaxcala, Av. Insurgentes Sur 1582, Col. Crédito Constructor, Ciudad de Mexico 03940, Mexico
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Gao YP, Huang KJ, Wang FT, Hou YY, Xu J, Li G. Recent advances in biological detection with rolling circle amplification: design strategy, biosensing mechanism, and practical applications. Analyst 2022; 147:3396-3414. [DOI: 10.1039/d2an00556e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Rolling circle amplification (RCA) is a simple and isothermal DNA amplification technique that is used to generate thousands of repeating DNA sequences using circular templates under the catalysis of DNA polymerase.
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Affiliation(s)
- Yong-ping Gao
- International Joint Research Laboratory of New Energy Materials and Devices of Henan Province, School of Physics and Electronics, Henan University, Kaifeng, 475004, PR China
- Analysis and Testing Center, Xinyang College, Xinyang 464000, PR China
| | - Ke-Jing Huang
- Key Laboratory of Guangxi Colleges and Universities for Food Safety and Pharmaceutical Analytical Chemistry, School of Chemistry and Chemical and Engineering, Guangxi Minzu University, Nanning 530008, PR China
| | - Fu-Ting Wang
- College of Chemistry and Chemical Engineering, Xinyang Normal University, Xinyang 464000, PR China
| | - Yang-Yang Hou
- College of Chemistry and Chemical Engineering, Xinyang Normal University, Xinyang 464000, PR China
| | - Jing Xu
- College of Chemistry and Chemical Engineering, Xinyang Normal University, Xinyang 464000, PR China
| | - Guoqiang Li
- International Joint Research Laboratory of New Energy Materials and Devices of Henan Province, School of Physics and Electronics, Henan University, Kaifeng, 475004, PR China
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20
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Aimone CD, Hoyer JS, Dye AE, Deppong DO, Duffy S, Carbone I, Hanley-Bowdoin L. An experimental strategy for preparing circular ssDNA virus genomes for next-generation sequencing. J Virol Methods 2021; 300:114405. [PMID: 34896458 DOI: 10.1016/j.jviromet.2021.114405] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Revised: 08/26/2021] [Accepted: 12/07/2021] [Indexed: 10/19/2022]
Abstract
The ability of begomoviruses to evolve rapidly threatens many crops and underscores the importance of detecting these viruses quickly and to understand their genome diversity. This study presents an improved protocol for the enhanced amplification and enrichment of begomovirus DNA for use in next generation sequencing of the viral genomes. An enhanced rolling circle amplification (RCA) method using EquiPhi29 polymerase was combined with size selection to generate a cost-effective, short-read sequencing method. This improved short-read sequencing produced at least 50 % of the reads mapping to the target viral reference genomes, African cassava mosaic virus and East African cassava mosaic virus. This study provided other insights into common misconceptions about RCA and lessons that could be learned from the sequencing of single-stranded DNA virus genomes. This protocol can be used to examine the viral DNA as it moves from host to vector, thus producing valuable information for viral DNA population studies, and would likely work well with other circular Rep-encoding ssDNA viruses (CRESS) DNA viruses.
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Affiliation(s)
- Catherine D Aimone
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC, 27695, USA.
| | - J Steen Hoyer
- Department of Ecology, Evolution, and Natural Resources, Rutgers University, New Brunswick, NJ, 08901, USA
| | - Anna E Dye
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC, 27695, USA
| | - David O Deppong
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC, 27695, USA
| | - Siobain Duffy
- Department of Ecology, Evolution, and Natural Resources, Rutgers University, New Brunswick, NJ, 08901, USA
| | - Ignazio Carbone
- Center for Integrated Fungal Research, Department of Entomology and Plant Pathology, North Carolina State University, Raleigh, NC, 27695, USA
| | - Linda Hanley-Bowdoin
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC, 27695, USA
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21
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Soares RRG, Madaboosi N, Nilsson M. Rolling Circle Amplification in Integrated Microsystems: An Uncut Gem toward Massively Multiplexed Pathogen Diagnostics and Genotyping. Acc Chem Res 2021; 54:3979-3990. [PMID: 34637281 PMCID: PMC8567418 DOI: 10.1021/acs.accounts.1c00438] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The development of robust methods allowing the precise detection of specific nucleic acid sequences is of major societal relevance, paving the way for significant advances in biotechnology and biomedical engineering. These range from a better understanding of human disease at a molecular level, allowing the discovery and development of novel biopharmaceuticals and vaccines, to the improvement of biotechnological processes providing improved food quality and safety, efficient green fuels, and smart textiles. Among these applications, the significance of pathogen diagnostics as the main focus of this Account has become particularly clear during the recent SARS-CoV-2 pandemic. In this context, while RT-PCR is the gold standard method for unambiguous detection of genetic material from pathogens, other isothermal amplification alternatives circumventing rapid heating-cooling cycles up to ∼95 °C are appealing to facilitate the translation of the assay into point-of-care (PoC) analytical platforms. Furthermore, the possibility of routinely multiplexing the detection of tens to hundreds of target sequences with single base pair specificity, currently not met by state-of-the-art methods available in clinical laboratories, would be instrumental along the path to tackle emergent viral variants and antimicrobial resistance genes. Here, we advocate that padlock probes (PLPs), first reported by Nilsson et al. in 1994, coupled with rolling circle amplification (RCA), termed here as PLP-RCA, is an underexploited technology in current arena of isothermal nucleic acid amplification tests (NAATs) providing an unprecedented degree of multiplexing, specificity, versatility, and amenability to integration in miniaturized PoC platforms. Furthermore, the intrinsically digital amplification of PLP-RCA retains spatial information and opens new avenues in the exploration of pathogenesis with spatial multiomics analysis of infected cells and tissue.The Account starts by introducing PLP-RCA in a nutshell focusing individually on the three main assay steps, namely, (1) PLP design and ligation mechanism, (2) RCA after probe ligation, and (3) detection of the RCA products. Each subject is touched upon succinctly but with sufficient detail for the reader to appreciate some assay intricacies and degree of versatility depending on the analytical challenge at hand. After familiarizing the reader with the method, we discuss specific examples of research in our group and others using PLP-RCA for viral, bacterial, and fungal diagnostics in a variety of clinical contexts, including the genotyping of antibiotic resistance genes and viral subtyping. Then, we dissect key developments in the miniaturization and integration of PLP-RCA to minimize user input, maximize analysis throughput, and expedite the time to results, ultimately aiming at PoC applications. These developments include molecular enrichment for maximum sensitivity, spatial arrays to maximize analytical throughput, automation of liquid handling to streamline the analytical workflow in miniaturized devices, and seamless integration of signal transduction to translate RCA product titers (and ideally spatial information) into a readable output. Finally, we position PLP-RCA in the current landscape of NAATs and furnish a systematic Strengths, Weaknesses, Opportunities and Threats analysis to shine light upon unpolished edges to uncover the gem with potential for ubiquitous, precise, and unbiased pathogen diagnostics.
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Affiliation(s)
- Ruben R. G. Soares
- Department of Biochemistry and Biophysics, Science for Life Laboratory, Stockholm University, 17165 Solna, Sweden
- Division of Nanobiotechnology, Department of Protein Science, Science for Life Laboratory, KTH Royal Institute of Technology, 17165 Solna, Sweden
| | - Narayanan Madaboosi
- Department of Biochemistry and Biophysics, Science for Life Laboratory, Stockholm University, 17165 Solna, Sweden
- Department of Biotechnology, Indian Institute of Technology Madras, Chennai, 600036 Tamil Nadu, India
| | - Mats Nilsson
- Department of Biochemistry and Biophysics, Science for Life Laboratory, Stockholm University, 17165 Solna, Sweden
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22
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Chen CA, Huang YJ, Yi-Ju Ho N, Huang TH, Tsai TT. Smartphone-assisted fluorescent analysis of polyT-Cu-nanoprobes using nucleic acid amplification test for the diagnosis of tuberculosis. Anal Biochem 2021; 630:114340. [PMID: 34411550 DOI: 10.1016/j.ab.2021.114340] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2021] [Revised: 08/09/2021] [Accepted: 08/13/2021] [Indexed: 11/28/2022]
Abstract
Tuberculosis is one of devastating infectious diseases in the world, and early diagnosis and treatment can help overcome this global burden. In this work, a new detection platform combining smartphone-assisted fluorescent analysis and highly sensitive fluorescent copper nanoprobes (CuNPs) in a specific nucleic acid amplification test (NAAT) for the diagnosis of tuberculosis (TB) was demonstrated and validated using clinical samples. To enhance the precision and accuracy of detection, polymerase chain reaction (PCR), padlock probe (PLP) ligation, and rolling circle amplification (RCA) were combined. Long poly(thymine) (polyT) single-stranded DNA was synthesized through RCA, and polyT-CuNPs were formed by adding copper(II) ions and sodium ascorbate as reducing agents; subsequently, the results were visualized through the excitation from a UV transilluminator and quantified with just a smartphone. After optimization, this proposed platform was validated by testing 18 residual DNA samples after TB PCR, including 8 TB-negative and 10 TB-positive samples, and exhibited a detection limit of 5 fg/μL. The findings indicate the potential of this platform for practical application, where it can be combined with a smartphone for image analysis to achieve accurate on-site detection of TB, especially in resource-limited settings.
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Affiliation(s)
- Chung-An Chen
- Department of Orthopaedic Surgery, Bone and Joint Research Center, Chang Gung Memorial Hospital at Linkou and Chang Gung University College of Medicine, Taoyuan 333, Taiwan, R.O.C
| | - Yu-Jui Huang
- Department of Orthopaedic Surgery, Bone and Joint Research Center, Chang Gung Memorial Hospital at Linkou and Chang Gung University College of Medicine, Taoyuan 333, Taiwan, R.O.C
| | - Natalie Yi-Ju Ho
- Department of Orthopaedic Surgery, Bone and Joint Research Center, Chang Gung Memorial Hospital at Linkou and Chang Gung University College of Medicine, Taoyuan 333, Taiwan, R.O.C
| | - Tse-Hao Huang
- Department of Orthopaedic Surgery, Bone and Joint Research Center, Chang Gung Memorial Hospital at Linkou and Chang Gung University College of Medicine, Taoyuan 333, Taiwan, R.O.C
| | - Tsung-Ting Tsai
- Department of Orthopaedic Surgery, Bone and Joint Research Center, Chang Gung Memorial Hospital at Linkou and Chang Gung University College of Medicine, Taoyuan 333, Taiwan, R.O.C..
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23
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Sauthier JT, Daudt C, da Silva FRC, Alves CDBT, Mayer FQ, Bianchi RM, Driemeier D, Streit RSA, Staats CC, Canal CW, Weber MN. The genetic diversity of "papillomavirome" in bovine teat papilloma lesions. Anim Microbiome 2021; 3:51. [PMID: 34321106 PMCID: PMC8317299 DOI: 10.1186/s42523-021-00114-3] [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: 04/16/2021] [Accepted: 07/21/2021] [Indexed: 12/25/2022] Open
Abstract
Background Papillomaviruses are small nonenveloped, circular double-stranded DNA viruses that belong to the Papillomaviridae family. To date, 29 Bos taurus papillomavirus (BPV) types have been described. Studies involving mixed BPV infections have rarely been reported in contrast to human papillomavirus (HPV), which is commonly described in numerous studies showing coinfections. Moreover, previous studies had shown that HPV coinfections increase the risk of carcinogenesis. In the present study, we used rolling-circle amplification followed by a high-throughput sequencing (RCA-HTS) approach in 23 teat papillomas from southern Brazil.
Results Eleven well-characterized BPV types and 14 putative new BPV types were genetically characterized into the Xi, Epsilon and Dyoxipapillomavirus genera according to phylogenetic analysis of the L1 gene, which expands the previous 29 BPV types to 43. Moreover, BPV coinfections were detected in the majority (56.3%) of the papilloma lesions analyzed, suggesting a genetic diverse “papillomavirome” in bovine teat warts. Conclusions The data generated in this study support the possibility that a wide range of BPV is probably underdetected by conventional molecular detection tools, and that BPV coinfections are underestimated and probably genetic diverse. Additionally, 14 new BPV types were characterized, increasing the knowledge regarding BPV genetic diversity. Supplementary Information The online version contains supplementary material available at 10.1186/s42523-021-00114-3.
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Affiliation(s)
- Jéssica Tatiane Sauthier
- Laboratório de Virologia Veterinária, Faculdade de Veterinária, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, RS, Brazil
| | - Cíntia Daudt
- Laboratório de Virologia Geral eParasitologia, Centro de Ciências Biológicas e da Natureza, Universidade Federal do Acre, Rio Branco, AC, Brazil
| | - Flavio Roberto Chaves da Silva
- Laboratório de Virologia Geral eParasitologia, Centro de Ciências Biológicas e da Natureza, Universidade Federal do Acre, Rio Branco, AC, Brazil
| | | | - Fabiana Quoos Mayer
- Laboratório de Biologia Molecular, Instituto de Pesquisas Veterinárias Desidério Finamor, Fundação Estadual de Pesquisa Agropecuária, Eldorado do Sul, RS, Brazil
| | - Ronaldo Michel Bianchi
- Setor de Patologia Veterinária, Faculdade de Veterinária, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, RS, Brazil
| | - David Driemeier
- Setor de Patologia Veterinária, Faculdade de Veterinária, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, RS, Brazil
| | | | - Charley Christian Staats
- Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, RS, Brazil
| | - Cláudio Wageck Canal
- Laboratório de Virologia Veterinária, Faculdade de Veterinária, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, RS, Brazil
| | - Matheus Nunes Weber
- Laboratório de Microbiologia Molecular, Instituto de Ciências da Saúde, Universidade Feevale, Novo Hamburgo, RS, Brazil.
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24
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Jain S, Dandy DS, Geiss BJ, Henry CS. Padlock probe-based rolling circle amplification lateral flow assay for point-of-need nucleic acid detection. Analyst 2021; 146:4340-4347. [PMID: 34106115 PMCID: PMC8294176 DOI: 10.1039/d1an00399b] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Sensitive, reliable and cost-effective detection of pathogens has wide ranging applications in clinical diagnostics and therapeutics, water and food safety, environmental monitoring, biosafety and epidemiology. Nucleic acid amplification tests (NAATs) such as PCR and isothermal amplification methods provide excellent analytical performance and significantly faster turnaround times than conventional culture-based methods. However, the inherent cost and complexity of NAATs limit their application in resource-limited settings and the developing world. To help address this urgent need, we have developed a sensitive method for nucleic acid analysis based on padlock probe rolling circle amplification (PLRCA), nuclease protection (NP) and lateral flow detection (LFA), referred to as PLAN-LFA, that can be used in resource-limited settings. The assay involves solution-phase hybridization of a padlock probe to target, sequence-specific ligation of the probe to form a circular template that undergoes isothermal rolling circle amplification in the presence of a polymerase and a labeled probe DNA. The RCA product is a long, linear concatenated single-stranded DNA that contains binding sites for the labeled probe. The sample is then exposed to a nuclease which selectively cleaves single-stranded DNA, the double-stranded labeled probe is protected from nuclease digestion and detected in a lateral flow immunoassay format to provide a visual, colorimetric readout of results. We have developed specific assays targeting beta-lactamase resistance gene for monitoring of antimicrobial resistance and Severe Acute Respiratory Syndrome-Coronavirus-2 (SARS-CoV-2, the novel coronavirus discovered in 2019) using the PLAN-LFA platform. The assay provides a limit of detection of 1.1 pM target DNA (or 1.3 × 106 copies per reaction). We also demonstrate the versatility and robustness of the method by performing analysis on DNA and RNA targets, and perform analysis in complex sample matrices like saliva, plant tissue extract and bacterial culture without any sample pretreatment steps.
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Affiliation(s)
- Sidhartha Jain
- School of Biomedical Engineering, Colorado State University, Fort Collins, CO 80523, USA.
| | - David S Dandy
- School of Biomedical Engineering, Colorado State University, Fort Collins, CO 80523, USA. and Department of Chemical and Biological Engineering, Colorado State University, Fort Collins, CO 80523, USA
| | - Brian J Geiss
- School of Biomedical Engineering, Colorado State University, Fort Collins, CO 80523, USA. and Department of Microbiology, Immunology, and Pathology, Colorado State University, Fort Collins, CO 80523, USA
| | - Charles S Henry
- School of Biomedical Engineering, Colorado State University, Fort Collins, CO 80523, USA. and Department of Chemistry, Colorado State University, Fort Collins, CO 80523, USA
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25
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Circular Rep-Encoding Single-Stranded DNA Sequences in Milk from Water Buffaloes ( Bubalus arnee f. bubalis). Viruses 2021; 13:v13061088. [PMID: 34200389 PMCID: PMC8228113 DOI: 10.3390/v13061088] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2021] [Revised: 05/26/2021] [Accepted: 06/03/2021] [Indexed: 02/06/2023] Open
Abstract
Isolation and characterization of circular replicase-encoding single-stranded (ss) DNA from animal, plant and environmental samples are rapidly evolving in virology. We detected 21 circular DNA elements, including one genomoviral sequence, in individual milk samples from domesticated Asian water buffaloes (Bubalus arnee f. bubalis). Most of the obtained genomes are related to Sphinx 1.76 and Sphinx 2.36 sequences and share a high degree of similarity to recently published circular DNAs—named BMMF (bovine meat and milk factors)—that have been isolated from commercial milk, as well as from bovine serum. Characteristic features such as rep genes, tandem repeats and inverted repeats were detected. These BMMF have recently been found to be present in taurine-type dairy cattle breeds descending from the aurochs (Bos primigenius). Importantly, the occurrence of BMMF has been linked to the higher incidence of colorectal and breast cancer in North America and Western Europe compared with Asia. This is the first report of circular ssDNA detected in milk from the domesticated form of the wild Asian water buffalo (B. arnee) belonging to the subfamily Bovinae. This novelty should be taken into account in view of the above-mentioned cancer hypothesis.
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26
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Janik M, Hamidi SV, Koba M, Perreault J, Walsh R, Bock WJ, Smietana M. Real-time isothermal DNA amplification monitoring in picoliter volumes using an optical fiber sensor. LAB ON A CHIP 2021; 21:397-404. [PMID: 33331382 DOI: 10.1039/d0lc01069c] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Rolling circle amplification (RCA) of DNA can be considered as a great alternative to the gold standard polymerase chain reaction (PCR), especially during this pandemic period, where rapid, sensitive, and reliable test results for hundreds of thousands of samples are required daily. This work presents the first research to date on direct, real-time and label-free isothermal DNA amplification monitoring using a microcavity in-line Mach-Zehnder interferometer (μIMZI) fabricated in an optical fiber. The solution based on μIMZI offers a great advantage over many other sensing concepts - making possible optical analysis in just picoliter sample volumes. The selectivity of the biosensor is determined by DNA primers immobilized on the microcavity's surface that act as selective biorecognition elements and trigger initiation of the DNA amplification process. In this study, we verified the sensing concept using circular DNA designed to target the H5N1 influenza virus. The developed biosensor exhibits an ultrahigh refractive index sensitivity reaching 14 000 nm per refractive index unit and a linear detection range between 9.4 aM and 94 pM of the target DNA sequence. Within a 30 min period, the amplification of as little as 9.4 aM DNA can be effectively detected, with a calculated limit of detection of as low as 0.2 aM DNA, suggesting that this methodology holds great promise in practical disease diagnosis applications in the future.
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Affiliation(s)
- Monika Janik
- Warsaw University of Technology, Institute of Microelectronics and Optoelectronics, Koszykowa 75, 00-662, Warszawa, Poland.
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27
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Identification of Extrachromosomal Circular Forms of Active Transposable Elements Using Mobilome-Seq. Methods Mol Biol 2021; 2250:87-93. [PMID: 33900594 DOI: 10.1007/978-1-0716-1134-0_7] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Abstract
Active transposable elements (TEs) generate insertion polymorphisms that can be detected through genome resequencing strategies. However, these techniques may have limitations for organisms with large genomes or for somatic insertions. Here, we present a method that takes advantage of the extrachromosomal circular DNA (eccDNA) forms of actively transposing TEs in order to detect and characterize active TEs in any plant or animal tissue. Mobilome-seq consists in selectively amplifying and sequencing eccDNAs. It relies on linear digestion of genomic DNA followed by rolling circle amplification of circular DNA. Both active DNA transposons and retrotransposons can be identified using this technique.
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28
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Xu L, Duan J, Chen J, Ding S, Cheng W. Recent advances in rolling circle amplification-based biosensing strategies-A review. Anal Chim Acta 2020; 1148:238187. [PMID: 33516384 DOI: 10.1016/j.aca.2020.12.062] [Citation(s) in RCA: 77] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2020] [Revised: 12/09/2020] [Accepted: 12/28/2020] [Indexed: 01/12/2023]
Abstract
Rolling circle amplification (RCA) is an efficient enzymatic isothermal reaction that using circular probe as a template to generate long tandem single-stranded DNA or RNA products under the initiation of short DNA or RNA primers. As a simplified derivative of natural rolling circle replication which synthesizes copies of circular nucleic acids molecules such as plasmids, RCA amplifies the circular template rapidly without thermal cycling and finds various applications in molecular biology. Compared with other amplification strategies, RCA has many obvious advantages. Firstly, because of the strict complementarity required in ligation of a padlock probe, it endows the RCA reaction with high specificity and can even be utilized to distinguish single base mismatches. Secondly, through the introduction of multiple primers, exponential amplification can be achieved easily and leads to a good sensitivity. Thirdly, RCA products can be customized by manipulating circular templates to generate functional nucleic acids such as aptamer, DNAzymes and restriction enzyme sites. Moreover, the RCA has good biocompatibility and is especially suitable for in situ detection. Therefore, RCA has attracted considerable attention as an efficient and potential tool for highly sensitive detection of biomarkers. Herein, we comprehensively introduce the fundamental principles of RCA technology, summarize it from three aspects including initiation mode, amplification mode and signal output mode, and discuss the recent application of RCA-based biosensor in this review.
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Affiliation(s)
- Lulu Xu
- The Center for Clinical Molecular Medical Detection, The First Affiliated Hospital of Chongqing Medical University, Chongqing, 400016, PR China
| | - Jiaxin Duan
- The Center for Clinical Molecular Medical Detection, The First Affiliated Hospital of Chongqing Medical University, Chongqing, 400016, PR China
| | - Junman Chen
- Key Laboratory of Clinical Laboratory Diagnostics (Ministry of Education), College of Laboratory Medicine, Chongqing Medical University, Chongqing, 400016, PR China
| | - Shijia Ding
- Key Laboratory of Clinical Laboratory Diagnostics (Ministry of Education), College of Laboratory Medicine, Chongqing Medical University, Chongqing, 400016, PR China.
| | - Wei Cheng
- The Center for Clinical Molecular Medical Detection, The First Affiliated Hospital of Chongqing Medical University, Chongqing, 400016, PR China.
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29
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Wang L, Song K, Qu Y, Chang Y, Li Z, Dong C, Liu M, Brennan JD, Li Y. Engineering Micrometer-Sized DNA Tracks for High-Speed DNA Synthesis and Biosensing. Angew Chem Int Ed Engl 2020; 59:22947-22951. [PMID: 33007137 DOI: 10.1002/anie.202010693] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Revised: 09/22/2020] [Indexed: 01/07/2023]
Abstract
φ29 DNA polymerase (Polφ29) is capable of synthesizing long-chain single-stranded (ss) DNA molecules by copying the sequence of a small ss circular DNA template (ssCDT) in a process known as rolling circle amplification (RCA). The use of a ssCDT in RCA, however, comes with a key drawback: the rate of DNA synthesis is significantly reduced. We hypothesize that this issue can be overcome using a very long linear ssDNA template with a repeating sequence. To test this idea, we engineered a DNA assembly, which we denote "micrometer-sized DNA track" (μDT). This μDT, with an average length of ≈13.5 μm, is made of a long chain DNA with a primer-binding domain at its 3' end and ≈1000 repeating sequence units at its 5' end, each carrying a DNA anchor. We find that Polφ29 copies μDT at a speed ≈5-time faster than it does a related ssCDT. We use this to design a simple all-in-one printed paper device for rapid and sensitive detection of microRNA let-7. This paper sensor is capable of detecting 1 pM let-7a in 10 minutes.
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Affiliation(s)
- Liying Wang
- School of Environmental Science and Technology, Key Laboratory of Industrial Ecology and Environmental Engineering, (Ministry of Education), Dalian University of Technology, Dalian, 116024, China
| | - Kaiyun Song
- School of Environmental Science and Technology, Key Laboratory of Industrial Ecology and Environmental Engineering, (Ministry of Education), Dalian University of Technology, Dalian, 116024, China
| | - Yuanyuan Qu
- School of Environmental Science and Technology, Key Laboratory of Industrial Ecology and Environmental Engineering, (Ministry of Education), Dalian University of Technology, Dalian, 116024, China
| | - Yangyang Chang
- School of Environmental Science and Technology, Key Laboratory of Industrial Ecology and Environmental Engineering, (Ministry of Education), Dalian University of Technology, Dalian, 116024, China
| | - Zhongping Li
- Institute of Environmental Science, Shanxi University, Taiyuan, 030006, China
| | - Chuan Dong
- Institute of Environmental Science, Shanxi University, Taiyuan, 030006, China
| | - Meng Liu
- School of Environmental Science and Technology, Key Laboratory of Industrial Ecology and Environmental Engineering, (Ministry of Education), Dalian University of Technology, Dalian, 116024, China
| | - John D Brennan
- Biointerfaces Institute, McMaster University, 1280 Main Street West, Hamilton, Ontario, L8S4O3, Canada
| | - Yingfu Li
- Department of Biochemistry and Biomedical Sciences, McMaster University, 1280 Main Street West, Hamilton, Ontario, L8S4K1, Canada
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30
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Wang L, Song K, Qu Y, Chang Y, Li Z, Dong C, Liu M, Brennan JD, Li Y. Engineering Micrometer‐Sized DNA Tracks for High‐Speed DNA Synthesis and Biosensing. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202010693] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Liying Wang
- School of Environmental Science and Technology Key Laboratory of Industrial Ecology and Environmental Engineering, (Ministry of Education) Dalian University of Technology Dalian 116024 China
| | - Kaiyun Song
- School of Environmental Science and Technology Key Laboratory of Industrial Ecology and Environmental Engineering, (Ministry of Education) Dalian University of Technology Dalian 116024 China
| | - Yuanyuan Qu
- School of Environmental Science and Technology Key Laboratory of Industrial Ecology and Environmental Engineering, (Ministry of Education) Dalian University of Technology Dalian 116024 China
| | - Yangyang Chang
- School of Environmental Science and Technology Key Laboratory of Industrial Ecology and Environmental Engineering, (Ministry of Education) Dalian University of Technology Dalian 116024 China
| | - Zhongping Li
- Institute of Environmental Science Shanxi University Taiyuan 030006 China
| | - Chuan Dong
- Institute of Environmental Science Shanxi University Taiyuan 030006 China
| | - Meng Liu
- School of Environmental Science and Technology Key Laboratory of Industrial Ecology and Environmental Engineering, (Ministry of Education) Dalian University of Technology Dalian 116024 China
| | - John D. Brennan
- Biointerfaces Institute McMaster University 1280 Main Street West Hamilton Ontario L8S4O3 Canada
| | - Yingfu Li
- Department of Biochemistry and Biomedical Sciences McMaster University 1280 Main Street West Hamilton Ontario L8S4K1 Canada
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31
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Li F, Zhou Y, Yin H, Ai S. Recent advances on signal amplification strategies in photoelectrochemical sensing of microRNAs. Biosens Bioelectron 2020; 166:112476. [DOI: 10.1016/j.bios.2020.112476] [Citation(s) in RCA: 65] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Revised: 07/22/2020] [Accepted: 07/24/2020] [Indexed: 01/23/2023]
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32
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Zhang Q, Hao T, Hu D, Guo Z, Wang S, Hu Y. RNA aptamer-driven ECL biosensing for tracing histone acetylation based on nano-prism substrate and cascade DNA amplification strategy. Electrochim Acta 2020. [DOI: 10.1016/j.electacta.2020.136828] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
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33
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Oliveira V, Polónia ARM, Cleary DFR, Huang YM, de Voogd NJ, da Rocha UN, Gomes NCM. Characterization of putative circular plasmids in sponge-associated bacterial communities using a selective multiply-primed rolling circle amplification. Mol Ecol Resour 2020; 21:110-121. [PMID: 32866335 DOI: 10.1111/1755-0998.13248] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2020] [Revised: 07/22/2020] [Accepted: 08/14/2020] [Indexed: 11/28/2022]
Abstract
Plasmid transfers among bacterial populations can directly influence the ecological adaptation of these populations and their interactions with host species and environment. In this study, we developed a selective multiply-primed rolling circle amplification (smRCA) approach to enrich and characterize circular plasmid DNA from sponge microbial symbionts via high-throughput sequencing (HTS). DNA (plasmid and total community DNA) obtained from sponge (Cinachyrella sp.) samples and a bacterial symbiont (Vibrio sp. CyArs1) isolated from the same sponge species (carrying unknown plasmids) were used to develop and validate our methodology. The smRCA was performed during 16 hr with 141 plasmid-specific primers covering all known circular plasmid groups. The amplified products were purified and subjected to a reamplification with random hexamer primers (2 hr) and then sequenced using Illumina MiSeq. The developed method resulted in the successful amplification and characterization of the sponge plasmidome and allowed us to detect plasmids associated with the bacterial symbiont Vibrio sp. CyArs1 in the sponge host. In addition to this, a large number of small (<2 kbp) and cryptic plasmids were also amplified in sponge samples. Functional analysis identified proteins involved in the control of plasmid partitioning, maintenance and replication. However, most plasmids contained unknown genes, which could potentially serve as a resource of unknown genetic information and novel replication systems. Overall, our results indicate that the smRCA-HTS approach developed here was able to selectively enrich and characterize plasmids from bacterial isolates and sponge host microbial communities, including plasmids larger than 20 kbp.
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Affiliation(s)
- Vanessa Oliveira
- Department of Biology and Centre for Environmental and Marine Studies (CESAM), University of Aveiro, Aveiro, Portugal
| | - Ana R M Polónia
- Department of Biology and Centre for Environmental and Marine Studies (CESAM), University of Aveiro, Aveiro, Portugal
| | - Daniel F R Cleary
- Department of Biology and Centre for Environmental and Marine Studies (CESAM), University of Aveiro, Aveiro, Portugal
| | - Yusheng M Huang
- Tropical Island Sustainable Development Research Center, National Penghu University of Science and Technology, Magong City Penghu, Taiwan.,Department of Marine Recreation, National Penghu University of Science and Technology, Magong City Penghu, Taiwan
| | - Nicole J de Voogd
- Marine Biodiversity, Naturalis Biodiversity Center, Leiden, The Netherlands.,Institute of Environmental Sciences (CML), Leiden University, Leiden, The Netherlands
| | - Ulisses N da Rocha
- Department of Environmental Microbiology, Helmholtz Centre for Environmental Research-UFZ, Leipzig, Germany
| | - Newton C M Gomes
- Department of Biology and Centre for Environmental and Marine Studies (CESAM), University of Aveiro, Aveiro, Portugal
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Kim J, Ahn JK, Kim JS, Choi BR, Cho J, Lee H. Highly selective detection of single nucleotide polymorphism (SNP) using a dumbbell DNA probe with a gap-filling approach. J IND ENG CHEM 2020. [DOI: 10.1016/j.jiec.2020.03.028] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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35
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Maeda R, Kami D, Maeda H, Shikuma A, Gojo S. High throughput single cell analysis of mitochondrial heteroplasmy in mitochondrial diseases. Sci Rep 2020; 10:10821. [PMID: 32616755 PMCID: PMC7331593 DOI: 10.1038/s41598-020-67686-z] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2019] [Accepted: 06/11/2020] [Indexed: 12/21/2022] Open
Abstract
Mitochondrial heteroplasmy, which fundamentally means intracellular heterogeneity of mitochondrial DNA (mtDNA), has been measured in a group of cells, regardless of intercellular heterogeneity. Ordinal methods for mitochondrial heteroplasmy cannot discriminate between an intercellular homogenic population composed of cells with similar intracellular heterogeneity for mtDNA and an intercellular heterogenic population composed of cells with different rates of mutated mtDNA. A high-throughput method to determine mitochondrial heteroplasmy in a single cell was developed by using droplet digital PCR with TaqMan polymerase in this study. This technique revealed that there are three different cell populations of cultured fibroblasts derived from patients with mitochondrial disease carrying a mutation in the mtDNA; cells with homoplasmy of either mutated or healthy mtDNA; and cells mixed with mutated and healthy mtDNA. The presence of intercellular heterogeneity, even in uniformed cultured fibroblasts, suggests that heterogeneity should exist among different kinds of cells. The diagnosis of intercellular heterogeneity with respect to mitochondrial heteroplasmy by this methodology could provide novel insight into developing a treatment strategy for mitochondrial diseases.
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Affiliation(s)
- Ryotaro Maeda
- Department of Cardiovascular Medicine, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, 465, Kajii cho, Kamigyo ku, Kyoto, 802-8566, Japan
| | - Daisuke Kami
- Department of Regenerative Medicine, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, 465, Kajii cho, Kamigyo ku, Kyoto, 802-8566, Japan
| | - Hideki Maeda
- Department of Cardiovascular Medicine, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, 465, Kajii cho, Kamigyo ku, Kyoto, 802-8566, Japan
| | - Akira Shikuma
- Department of Cardiovascular Medicine, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, 465, Kajii cho, Kamigyo ku, Kyoto, 802-8566, Japan
| | - Satoshi Gojo
- Department of Regenerative Medicine, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, 465, Kajii cho, Kamigyo ku, Kyoto, 802-8566, Japan.
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Draft Genome Sequence of an Adomavirus Associated with Raised Mucoid Skin Lesions on Smallmouth Bass (Micropterus dolomieu). Microbiol Resour Announc 2020; 9:9/14/e01479-19. [PMID: 32241864 PMCID: PMC7118190 DOI: 10.1128/mra.01479-19] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Raised mucoid skin lesions have been observed on smallmouth bass (Micropterus dolomieu) for years. Here, we report the draft genome of a novel adomavirus (Micropterus dolomieu adomavirus 2) associated with this disease. The circular genome is 17,561 bp and most similar to that of alpha-adomaviruses. Raised mucoid skin lesions have been observed on smallmouth bass (Micropterus dolomieu) for years. Here, we report the draft genome of a novel adomavirus (Micropterus dolomieu adomavirus 2) associated with this disease. The circular genome is 17,561 bp and most similar to that of alpha-adomaviruses.
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38
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Metagenomic Detection of Two Vientoviruses in a Human Sputum Sample. Viruses 2020; 12:v12030327. [PMID: 32197299 PMCID: PMC7150755 DOI: 10.3390/v12030327] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2020] [Revised: 03/06/2020] [Accepted: 03/17/2020] [Indexed: 02/02/2023] Open
Abstract
We used metagenomics to analyze one sputum sample from a patient with symptoms of a respiratory infection that yielded negative results for all pathogens tested. We detected two viral genomes that could be assembled and showed sequence similarity to redondoviruses, a recently described group within the CRESS-DNA viruses. One hundred sputum samples were screened for the presence of these viruses using specific primers. One sample was positive for the same two viruses, and another was positive for one of them. These findings raise questions about a possible role of redondoviruses in respiratory infections in humans.
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Hao M, Qiao J, Qi H. Current and Emerging Methods for the Synthesis of Single-Stranded DNA. Genes (Basel) 2020; 11:E116. [PMID: 31973021 PMCID: PMC7073533 DOI: 10.3390/genes11020116] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2020] [Revised: 01/16/2020] [Accepted: 01/18/2020] [Indexed: 12/21/2022] Open
Abstract
Methods for synthesizing arbitrary single-strand DNA (ssDNA) fragments are rapidly becoming fundamental tools for gene editing, DNA origami, DNA storage, and other applications. To meet the rising application requirements, numerous methods have been developed to produce ssDNA. Some approaches allow the synthesis of freely chosen user-defined ssDNA sequences to overcome the restrictions and limitations of different length, purity, and yield. In this perspective, we provide an overview of the representative ssDNA production strategies and their most significant challenges to enable the readers to make informed choices of synthesis methods and enhance the availability of increasingly inexpensive synthetic ssDNA. We also aim to stimulate a broader interest in the continued development of efficient ssDNA synthesis techniques and improve their applications in future research.
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Affiliation(s)
- Min Hao
- School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China; (M.H.); (J.Q.)
- Key Laboratory of Systems Bioengineering of Ministry of Education, Tianjin University, Tianjin 300072, China
- SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering, Tianjin University, Tianjin 300072, China
| | - Jianjun Qiao
- School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China; (M.H.); (J.Q.)
- Key Laboratory of Systems Bioengineering of Ministry of Education, Tianjin University, Tianjin 300072, China
- SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering, Tianjin University, Tianjin 300072, China
| | - Hao Qi
- School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China; (M.H.); (J.Q.)
- Key Laboratory of Systems Bioengineering of Ministry of Education, Tianjin University, Tianjin 300072, China
- SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering, Tianjin University, Tianjin 300072, China
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40
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Oota S. Somatic mutations - Evolution within the individual. Methods 2019; 176:91-98. [PMID: 31711929 DOI: 10.1016/j.ymeth.2019.11.002] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2018] [Revised: 10/31/2019] [Accepted: 11/07/2019] [Indexed: 02/08/2023] Open
Abstract
With the rapid advancement of sequencing technologies over the last two decades, it is becoming feasible to detect rare variants from somatic tissue samples. Studying such somatic mutations can provide deep insights into various senescence-related diseases, including cancer, inflammation, and sporadic psychiatric disorders. While it is still a difficult task to identify true somatic mutations, relentless efforts to combine experimental and computational methods have made it possible to obtain reliable data. Furthermore, state-of-the-art machine learning approaches have drastically improved the efficiency and sensitivity of these methods. Meanwhile, we can regard somatic mutations as a counterpart of germline mutations, and it is possible to apply well-formulated mathematical frameworks developed for population genetics and molecular evolution to analyze this 'somatic evolution'. For example, retrospective cell lineage tracing is a promising technique to elucidate the mechanism of pre-diseases using single-cell RNA-sequencing (scRNA-seq) data.
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Affiliation(s)
- Satoshi Oota
- Image Processing Research Team, Center for Advanced Photonics, RIKEN, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan.
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41
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Hürtgen D, Mascarenhas J, Heymann M, Murray SM, Schwille P, Sourjik V. Reconstitution and Coupling of DNA Replication and Segregation in a Biomimetic System. Chembiochem 2019; 20:2633-2642. [PMID: 31344304 PMCID: PMC6899551 DOI: 10.1002/cbic.201900299] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2019] [Revised: 07/20/2019] [Indexed: 12/30/2022]
Abstract
A biomimetic system capable of replication and segregation of genetic material constitutes an essential component for the future design of a minimal synthetic cell. Here we have used the simple T7 bacteriophage system and the plasmid-derived ParMRC system to establish in vitro DNA replication and DNA segregation, respectively. These processes were incorporated into biomimetic compartments providing an enclosed reaction space. The functional lifetime of the encapsulated segregation system could be prolonged by equipping it with ATP-regenerating and oxygen-scavenging systems. Finally, we showed that DNA replication and segregation processes could be coupled in vitro by using condensed DNA nanoparticles resulting from DNA replication. ParM spindles extended over tens of micrometers and could thus be used for segregation in compartments that are significantly longer than bacterial cell size. Overall, this work demonstrates the successful bottom-up assembly and coupling of molecular machines that mediate replication and segregation, thus providing an important step towards the development of a fully functional minimal cell.
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Affiliation(s)
- Daniel Hürtgen
- Max Planck Institute for Terrestrial Microbiology &LOEWE Center for Synthetic Microbiology (Synmikro)Karl-von-Frisch Strasse 1635043MarburgGermany
| | - Judita Mascarenhas
- Max Planck Institute for Terrestrial Microbiology &LOEWE Center for Synthetic Microbiology (Synmikro)Karl-von-Frisch Strasse 1635043MarburgGermany
| | - Michael Heymann
- Max Planck Institute of BiochemistryAm Klopferspitz 1882152MartinsriedGermany
| | - Seán M. Murray
- Max Planck Institute for Terrestrial Microbiology &LOEWE Center for Synthetic Microbiology (Synmikro)Karl-von-Frisch Strasse 1635043MarburgGermany
| | - Petra Schwille
- Max Planck Institute of BiochemistryAm Klopferspitz 1882152MartinsriedGermany
| | - Victor Sourjik
- Max Planck Institute for Terrestrial Microbiology &LOEWE Center for Synthetic Microbiology (Synmikro)Karl-von-Frisch Strasse 1635043MarburgGermany
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Li J, Lin L, Yu J, Zhai S, Liu G, Tian L. Fabrication and Biomedical Applications of “Polymer-Like” Nucleic Acids Enzymatically Produced by Rolling Circle Amplification. ACS APPLIED BIO MATERIALS 2019; 2:4106-4120. [DOI: 10.1021/acsabm.9b00622] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Jing Li
- Department of Materials Science and Engineering, Southern University of Science and Technology, 1088 Xueyuan Boulevard, Nanshan District, Shenzhen, Guangdong 518055, P. R. China
| | - Li Lin
- Department of Materials Science and Engineering, Southern University of Science and Technology, 1088 Xueyuan Boulevard, Nanshan District, Shenzhen, Guangdong 518055, P. R. China
| | - Jiantao Yu
- Department of Materials Science and Engineering, Southern University of Science and Technology, 1088 Xueyuan Boulevard, Nanshan District, Shenzhen, Guangdong 518055, P. R. China
| | - Shiyao Zhai
- Department of Materials Science and Engineering, Southern University of Science and Technology, 1088 Xueyuan Boulevard, Nanshan District, Shenzhen, Guangdong 518055, P. R. China
| | - Guoyuan Liu
- Department of Materials Science and Engineering, Southern University of Science and Technology, 1088 Xueyuan Boulevard, Nanshan District, Shenzhen, Guangdong 518055, P. R. China
| | - Leilei Tian
- Department of Materials Science and Engineering, Southern University of Science and Technology, 1088 Xueyuan Boulevard, Nanshan District, Shenzhen, Guangdong 518055, P. R. China
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Chen K, Wang G, Xiong J, Jiang C, Miao W. Exploration of Genetic Variations through Single-cell Whole-genome Sequencing in the Model Ciliate Tetrahymena thermophila. J Eukaryot Microbiol 2019; 66:954-965. [PMID: 31188517 DOI: 10.1111/jeu.12746] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2019] [Revised: 05/05/2019] [Accepted: 05/30/2019] [Indexed: 01/05/2023]
Abstract
Ciliates are unicellular eukaryotes with separate germline and somatic genomes and diverse life cycles, which make them a unique model to improve our understanding of population genetics through the detection of genetic variations. However, traditional sequencing methods cannot be directly applied to ciliates because the majority are uncultivated. Single-cell whole-genome sequencing (WGS) is a powerful tool for studying genetic variation in microbes, but no studies have been performed in ciliates. We compared the use of single-cell WGS and bulk DNA WGS to detect genetic variation, specifically single nucleotide polymorphisms (SNPs), in the model ciliate Tetrahymena thermophila. Our analyses showed that (i) single-cell WGS has excellent performance regarding mapping rate and genome coverage but lower sequencing uniformity compared with bulk DNA WGS due to amplification bias (which was reproducible); (ii) false-positive SNP sites detected by single-cell WGS tend to occur in genomic regions with particularly high sequencing depth and high rate of C:G to T:A base changes; (iii) SNPs detected in three or more cells should be reliable (an detection efficiency of 83.4-97.4% was obtained for combined data from three cells). This analytical method could be adapted to measure genetic variation in other ciliates and broaden research into ciliate population genetics.
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Affiliation(s)
- Kai Chen
- Key Laboratory of Aquatic Biodiversity and Conservation, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Guangying Wang
- Key Laboratory of Aquatic Biodiversity and Conservation, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China
| | - Jie Xiong
- Key Laboratory of Aquatic Biodiversity and Conservation, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China
| | - Chuanqi Jiang
- Key Laboratory of Aquatic Biodiversity and Conservation, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China
| | - Wei Miao
- Key Laboratory of Aquatic Biodiversity and Conservation, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China.,University of Chinese Academy of Sciences, Beijing, 100049, China.,State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China.,CAS Center for Excellence in Animal Evolution and Genetics, Kunming, 650223, China
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44
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Murall CL, Rahmoun M, Selinger C, Baldellou M, Bernat C, Bonneau M, Boué V, Buisson M, Christophe G, D’Auria G, Taroni FD, Foulongne V, Froissart R, Graf C, Grasset S, Groc S, Hirtz C, Jaussent A, Lajoie J, Lorcy F, Picot E, Picot MC, Ravel J, Reynes J, Rousset T, Seddiki A, Teirlinck M, Tribout V, Tuaillon É, Waterboer T, Jacobs N, Bravo IG, Segondy M, Boulle N, Alizon S. Natural history, dynamics, and ecology of human papillomaviruses in genital infections of young women: protocol of the PAPCLEAR cohort study. BMJ Open 2019; 9:e025129. [PMID: 31189673 PMCID: PMC6576111 DOI: 10.1136/bmjopen-2018-025129] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
Abstract
INTRODUCTION Human papillomaviruses (HPVs) are responsible for one-third of all cancers caused by infections. Most HPV studies focus on chronic infections and cancers, and we know little about the early stages of the infection. Our main objective is to better understand the course and natural history of cervical HPV infections in healthy, unvaccinated and vaccinated, young women, by characterising the dynamics of various infection-related populations (virus, epithelial cells, vaginal microbiota and immune effectors). Another objective is to analyse HPV diversity within hosts, and in the study population, in relation to co-factors (lifestyle characteristics, vaccination status, vaginal microbiota, human genetics). METHODS AND ANALYSIS The PAPCLEAR study is a single center longitudinal study following 150 women, aged 18-25 years, for up to 2 years. Visits occur every 2 or 4 months (depending on HPV status) during which several variables are measured, such as behaviours (via questionnaires), vaginal pH, HPV presence and viral load (via qPCR), local concentrations of cytokines (via MesoScale Discovery technology) and immune cells (via flow cytometry). Additional analyses are outsourced, such as titration of circulating anti-HPV antibodies, vaginal microbiota sequencing (16S and ITS1 loci) and human genotyping. To increase the statistical power of the epidemiological arm of the study, an additional 150 women are screened cross-sectionally. Finally, to maximise the resolution of the time series, participants are asked to perform weekly self-samples at home. Statistical analyses will involve classical tools in epidemiology, genomics and virus kinetics, and will be performed or coordinated by the Centre National de la Recherche Scientifique (CNRS) in Montpellier. ETHICS AND DISSEMINATION This study has been approved by the Comité de Protection des Personnes Sud Méditerranée I (reference number 2016-A00712-49); by the Comité Consultatif sur le Traitement de l'Information en matière de Recherche dans le domaine de la Santé (reference number 16.504); by the Commission Nationale Informatique et Libertés (reference number MMS/ABD/AR1612278, decision number DR-2016-488) and by the Agence Nationale de Sécurité du Médicament et des Produits de Santé (reference 20160072000007). Results will be published in preprint servers, peer-reviewed journals and disseminated through conferences. TRIAL REGISTRATION NUMBER NCT02946346; Pre-results.
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Affiliation(s)
| | | | | | - Monique Baldellou
- Center for Free Information, Screening and Diagnosis (CGIDD), Centre Hospitalier Universitaire de Montpellier, Montpellier, France
| | - Claire Bernat
- MIVEGEC (UMR 5290 CNRS, IRD, UM), CNRS, Montpellier, France
| | - Marine Bonneau
- Department of Obstetrics and Gynaecology, Centre Hospitalier Universitaire de Montpellier, Montpellier, France
| | - Vanina Boué
- MIVEGEC (UMR 5290 CNRS, IRD, UM), CNRS, Montpellier, France
| | - Mathilde Buisson
- Department of Research and Innovation (DRI), Centre Hospitalier Universitaire de Montpellier, Montpellier, France
| | - Guillaume Christophe
- Center for Free Information, Screening and Diagnosis (CGIDD), Centre Hospitalier Universitaire de Montpellier, Montpellier, France
| | - Giuseppe D’Auria
- CIBER en Epidemiología y Salud Pública (CIBEResp), Madrid, Spain
- Sequencing and Bioinformatics Service, Fundaciónpara el Fomento de la Investigación Sanitaria y Biomédica de laComunidad Valenciana (FISABIO-Salud Pública), Valencia, Spain
| | - Florence De Taroni
- Center for Free Information, Screening and Diagnosis (CGIDD), Centre Hospitalier Universitaire de Montpellier, Montpellier, France
| | - Vincent Foulongne
- Pathogenesis and Control of Chronic Infections, INSERM, CHU, University of Montpellier, Montpellier, France
- Department of Virology, Centre Hospitalier Universitaire de Montpellier, Montpellier, France
| | - Rémy Froissart
- MIVEGEC (UMR 5290 CNRS, IRD, UM), CNRS, Montpellier, France
| | - Christelle Graf
- Department of Obstetrics and Gynaecology, Centre Hospitalier Universitaire de Montpellier, Montpellier, France
| | - Sophie Grasset
- MIVEGEC (UMR 5290 CNRS, IRD, UM), CNRS, Montpellier, France
- Center for Free Information, Screening and Diagnosis (CGIDD), Centre Hospitalier Universitaire de Montpellier, Montpellier, France
| | - Soraya Groc
- MIVEGEC (UMR 5290 CNRS, IRD, UM), CNRS, Montpellier, France
- Department of Virology, Centre Hospitalier Universitaire de Montpellier, Montpellier, France
| | - Christophe Hirtz
- LBPC/PPC- IRMB, CHU de Montpellier and Université de Montpellier, Montpellier, France
| | - Audrey Jaussent
- Department of Medical Information (DIM), Centre Hospitalier Universitaire de Montpellier, Montpellier, France
| | - Julie Lajoie
- Department of Medical microbiology, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Frédérique Lorcy
- Department of pathology and oncobiology, Centre Hospitalier Universitaire de Montpellier, Montpellier, France
| | - Eric Picot
- Center for Free Information, Screening and Diagnosis (CGIDD), Centre Hospitalier Universitaire de Montpellier, Montpellier, France
| | - Marie-Christine Picot
- Department of Medical Information (DIM), Centre Hospitalier Universitaire de Montpellier, Montpellier, France
| | - Jacques Ravel
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - Jacques Reynes
- Department of Infectious and Tropical Diseases, Centre Hospitalier Universitaire de Montpellier, Montpellier, France
| | - Thérèse Rousset
- Department of pathology and oncobiology, Centre Hospitalier Universitaire de Montpellier, Montpellier, France
| | - Aziza Seddiki
- Department of Research and Innovation (DRI), Centre Hospitalier Universitaire de Montpellier, Montpellier, France
| | - Martine Teirlinck
- Center for Free Information, Screening and Diagnosis (CGIDD), Centre Hospitalier Universitaire de Montpellier, Montpellier, France
| | - Vincent Tribout
- Center for Free Information, Screening and Diagnosis (CGIDD), Centre Hospitalier Universitaire de Montpellier, Montpellier, France
| | - Édouard Tuaillon
- Pathogenesis and Control of Chronic Infections, INSERM, CHU, University of Montpellier, Montpellier, France
- Department of Virology, Centre Hospitalier Universitaire de Montpellier, Montpellier, France
| | - Tim Waterboer
- German Cancer Research Center (DKFZ), Infections and Cancer Epidemiology, Heidelberg, Germany
| | - Nathalie Jacobs
- GIGA-Research, Cellular and molecular immunology, University of Liège, Liège, Belgium
| | | | - Michel Segondy
- Pathogenesis and Control of Chronic Infections, INSERM, CHU, University of Montpellier, Montpellier, France
- Department of Virology, Centre Hospitalier Universitaire de Montpellier, Montpellier, France
| | - Nathalie Boulle
- Pathogenesis and Control of Chronic Infections, INSERM, CHU, University of Montpellier, Montpellier, France
- Department of pathology and oncobiology, Centre Hospitalier Universitaire de Montpellier, Montpellier, France
| | - Samuel Alizon
- MIVEGEC (UMR 5290 CNRS, IRD, UM), CNRS, Montpellier, France
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Abstract
Viruses, which are the most abundant biological entities on the planet, have been regarded as the "dark matter" of biology in the sense that despite their ubiquity and frequent presence in large numbers, their detection and analysis are not always straightforward. The majority of them are very small (falling under the limit of 0.5 μm), and collectively, they are extraordinarily diverse. In fact, the majority of the genetic diversity on the planet is found in the so-called virosphere, or the world of viruses. Furthermore, the most frequent viral agents of disease in humans display an RNA genome, and frequently evolve very fast, due to the fact that most of their polymerases are devoid of proofreading activity. Therefore, their detection, genetic characterization, and epidemiological surveillance are rather challenging. This review (part of the Curated Collection on Advances in Molecular Epidemiology of Infectious Diseases) describes many of the methods that, throughout the last few decades, have been used for viral detection and analysis. Despite the challenge of having to deal with high genetic diversity, the majority of these methods still depend on the amplification of viral genomic sequences, using sequence-specific or sequence-independent approaches, exploring thermal profiles or a single nucleic acid amplification temperature. Furthermore, viral populations, and especially those with RNA genomes, are not usually genetically uniform but encompass swarms of genetically related, though distinct, viral genomes known as viral quasispecies. Therefore, sequence analysis of viral amplicons needs to take this fact into consideration, as it constitutes a potential analytic problem. Possible technical approaches to deal with it are also described here. *This article is part of a curated collection.
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Sukal AC, Kidanemariam DB, Dale JL, Harding RM, James AP. Assessment and optimization of rolling circle amplification protocols for the detection and characterization of badnaviruses. Virology 2019; 529:73-80. [PMID: 30665100 DOI: 10.1016/j.virol.2019.01.013] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2018] [Revised: 01/13/2019] [Accepted: 01/13/2019] [Indexed: 11/15/2022]
Abstract
The genus Badnavirus is characterized by members that are genetically and serologically heterogeneous which presents challenges for their detection and characterization. The presence of integrated badnavirus-like sequences in some host species further complicates detection using PCR-based protocols. To address these challenges, we have assessed and optimized various RCA protocols including random-primed RCA (RP-RCA), primer-spiked random-primed RCA (primer-spiked RP-RCA), directed RCA (D-RCA) and specific-primed RCA (SP-RCA). Using Dioscorea bacilliform AL virus (DBALV) as an example, we demonstrate that viral DNA amplified using the optimized D-RCA and SP-RCA protocols showed an 85-fold increase in badnavirus NGS reads compared with RP-RCA. The optimized RCA techniques described here were used to detect a range of badnaviruses infecting banana, sugar cane, taro and yam demonstrating the utility of RCA for detection of diverse badnaviruses infecting a variety of host plant species.
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Affiliation(s)
- Amit C Sukal
- Centre for Tropical Crops and Biocommodities (CTCB), Faculty of Science and Engineering (SEF), Queensland University of Technology (QUT), Brisbane 4001, Australia; Centre for Pacific Crops and Trees (CePaCT), Land Resource Division (LRD), Pacific Community (SPC), Suva, Fiji
| | - Dawit B Kidanemariam
- Centre for Tropical Crops and Biocommodities (CTCB), Faculty of Science and Engineering (SEF), Queensland University of Technology (QUT), Brisbane 4001, Australia
| | - James L Dale
- Centre for Tropical Crops and Biocommodities (CTCB), Faculty of Science and Engineering (SEF), Queensland University of Technology (QUT), Brisbane 4001, Australia
| | - Robert M Harding
- Centre for Tropical Crops and Biocommodities (CTCB), Faculty of Science and Engineering (SEF), Queensland University of Technology (QUT), Brisbane 4001, Australia.
| | - Anthony P James
- Centre for Tropical Crops and Biocommodities (CTCB), Faculty of Science and Engineering (SEF), Queensland University of Technology (QUT), Brisbane 4001, Australia
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Gu L, Yan W, Liu L, Wang S, Zhang X, Lyu M. Research Progress on Rolling Circle Amplification (RCA)-Based Biomedical Sensing. Pharmaceuticals (Basel) 2018; 11:E35. [PMID: 29690513 PMCID: PMC6027247 DOI: 10.3390/ph11020035] [Citation(s) in RCA: 58] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2018] [Revised: 04/10/2018] [Accepted: 04/10/2018] [Indexed: 12/26/2022] Open
Abstract
Enhancing the limit of detection (LOD) is significant for crucial diseases. Cancer development could take more than 10 years, from one mutant cell to a visible tumor. Early diagnosis facilitates more effective treatment and leads to higher survival rate for cancer patients. Rolling circle amplification (RCA) is a simple and efficient isothermal enzymatic process that utilizes nuclease to generate long single stranded DNA (ssDNA) or RNA. The functional nucleic acid unit (aptamer, DNAzyme) could be replicated hundreds of times in a short period, and a lower LOD could be achieved if those units are combined with an enzymatic reaction, Surface Plasmon Resonance, electrochemical, or fluorescence detection, and other different kinds of biosensor. Multifarious RCA-based platforms have been developed to detect a variety of targets including DNA, RNA, SNP, proteins, pathogens, cytokines, micromolecules, and diseased cells. In this review, improvements in using the RCA technique for medical biosensors and biomedical applications were summarized and future trends in related research fields described.
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Affiliation(s)
- Lide Gu
- College of Marine Life and Fisheries, Huahai Institute of Technology, Lianyungang 222005, China.
| | - Wanli Yan
- College of Marine Life and Fisheries, Huahai Institute of Technology, Lianyungang 222005, China.
| | - Le Liu
- College of Marine Life and Fisheries, Huahai Institute of Technology, Lianyungang 222005, China.
| | - Shujun Wang
- Marine Resources Development Institute of Jiangsu, Lianyungang 222005, China.
- Co-Innovation Center of Jiangsu Marine Bio-industry Technology, Huaihai Institute of Technology, Lianyungang 222005, China.
| | - Xu Zhang
- Co-Innovation Center of Jiangsu Marine Bio-industry Technology, Huaihai Institute of Technology, Lianyungang 222005, China.
- Verschuren Centre for Sustainability in Energy & the Environment, Cape Breton University, Sydney, NS B1P 6L2, Canada.
| | - Mingsheng Lyu
- College of Marine Life and Fisheries, Huahai Institute of Technology, Lianyungang 222005, China.
- Marine Resources Development Institute of Jiangsu, Lianyungang 222005, China.
- Co-Innovation Center of Jiangsu Marine Bio-industry Technology, Huaihai Institute of Technology, Lianyungang 222005, China.
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Dutta S, Robitaille A, Aubin F, Fouéré S, Galicier L, Boutboul D, Luzi F, Di Bonito P, Tommasino M, Gheit T. Identification and characterization of two novel Gammapapillomavirus genomes in skin of an immunosuppressed Epidermodysplasia Verruciformis patient. Virus Res 2018; 249:66-68. [PMID: 29526719 DOI: 10.1016/j.virusres.2018.03.003] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2017] [Revised: 03/03/2018] [Accepted: 03/04/2018] [Indexed: 01/19/2023]
Abstract
Two novel human gamma-papillomavirus genomes (HPV_MTS3, and HPV_MTS4) were isolated from the skin of an immunosuppressed, late-onset Epidermodysplasia Verruciformis patient and fully cloned. The L1 open reading frames of HPV_MTS3 and HPV_MTS4 were 77% and 91% identical to their closest HPV full genome isolates w18c39 and EV03c60, which belong to the species gamma-22and gamma-7 of the genus Gammapapillomavirus, respectively.
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Affiliation(s)
- Sankhadeep Dutta
- Infections and Cancer Biology Group, International Agency for Research on Cancer, Lyon, France
| | - Alexis Robitaille
- Infections and Cancer Biology Group, International Agency for Research on Cancer, Lyon, France
| | - François Aubin
- Dermatology Department and EA3181, Centre National de Référence HPV, Centre Hospitalier Universitaire, Université de Franche-Comté, Besançon, France
| | - Sébastien Fouéré
- STD Unit (Centre des MST) Dermatology Department (Service de Dermatologie), Saint Louis University Hospital, Paris, France
| | - Lionel Galicier
- Department of Clinical Immunology, Hôpital Saint-Louis, Assistance Publique Hôpitaux de Paris (APHP), Paris, France
| | - David Boutboul
- Department of Clinical Immunology, Hôpital Saint-Louis, Assistance Publique Hôpitaux de Paris (APHP), Paris, France
| | - Fabiola Luzi
- Plastic and Reconstructive Surgery, San Gallicano Dermatologic Institute, IRCCS, Rome, Italy
| | - Paola Di Bonito
- Department of Infectious Diseases, Istituto Superiore di Sanità, Viale Regina Elena 299, 00161 Rome, Italy
| | - Massimo Tommasino
- Infections and Cancer Biology Group, International Agency for Research on Cancer, Lyon, France
| | - Tarik Gheit
- Infections and Cancer Biology Group, International Agency for Research on Cancer, Lyon, France.
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Qi H, Yue S, Bi S, Ding C, Song W. Isothermal exponential amplification techniques: From basic principles to applications in electrochemical biosensors. Biosens Bioelectron 2018; 110:207-217. [PMID: 29625328 DOI: 10.1016/j.bios.2018.03.065] [Citation(s) in RCA: 64] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2018] [Revised: 03/16/2018] [Accepted: 03/28/2018] [Indexed: 12/12/2022]
Abstract
As a conventional amplification technique, polymerase chain reaction (PCR) has been widely applied to detect a variety of analytes with exponential amplification efficiency. However, the requirement of thermocycling procedures largely limits the application of PCR-based methods. Alternatively, several isothermal amplification techniques have been developed since the early 1990s. In particular, according to the reaction kinetics, isothermal exponential amplification techniques possess higher amplification efficiency and detection sensitivity. The isothermal exponential amplification techniques can be mainly divided into two categories: enzyme-based isothermal exponential amplification and enzyme-free isothermal exponential amplification. Considering the advantages of high sensitivity and selectivity, high signal-to-noise ratio, low cost and rapid response time, exponential amplification electrochemical biosensors have attracted considerable attention. In this review, we introduce the basic principles of isothermal exponential amplification techniques and summarize their applications in electrochemical biosensors during the past five years. We also highlighted the present challenges and further perspectives of isothermal exponential amplification-based electrochemical biosensors.
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Affiliation(s)
- Hongjie Qi
- College of Chemistry and Chemical Engineering, Shandong Demonstration Center for Experimental Chemistry Education, Qingdao University, Qingdao 266071, PR China
| | - Shuzhen Yue
- College of Chemistry and Chemical Engineering, Shandong Demonstration Center for Experimental Chemistry Education, Qingdao University, Qingdao 266071, PR China
| | - Sai Bi
- College of Chemistry and Chemical Engineering, Shandong Demonstration Center for Experimental Chemistry Education, Qingdao University, Qingdao 266071, PR China.
| | - Caifeng Ding
- Key Laboratory of Sensor Analysis of Tumor Marker, Ministry of Education, College of Chemistry and Molecular Engineering, Qingdao University of Science and Technology, Qingdao 266042, PR China
| | - Weiling Song
- Key Laboratory of Sensor Analysis of Tumor Marker, Ministry of Education, College of Chemistry and Molecular Engineering, Qingdao University of Science and Technology, Qingdao 266042, PR China
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Bömer M, Turaki AA, Rathnayake AI, Silva G, Kumar PL, Seal SE. Rolling Circle Amplification to Screen Yam Germplasm for Badnavirus Infections and to Amplify and Characterise Novel Badnavirus Genomes. Bio Protoc 2018; 8:e2672. [PMID: 34179227 DOI: 10.21769/bioprotoc.2672] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2017] [Revised: 12/11/2017] [Accepted: 12/18/2017] [Indexed: 11/02/2022] Open
Abstract
Since the first discovery of badnaviruses (family Caulimoviridae, genus Badnavirus) in yam (Dioscorea spp.) germplasm in the 1970s (Harrison and Roberts, 1973), several hundred partial badnavirus reverse transcriptase (RT)-ribonuclease H (RNaseH) sequences have been characterised ( Kenyon et al., 2008 ; Bousalem et al., 2009 ), but only a few complete Dioscorea bacilliform virus (DBV) genome sequences have been reported ( Phillips et al., 1999 ; Seal and Muller, 2007; Bömer et al., 2016 and 2017; Sukal et al., 2017 ; Umber et al., 2017 ). We have optimised a workflow involving total nucleic acid extractions and rolling circle amplification (RCA) combined with restriction enzyme analysis for the detection and amplification of DBVs present in yam germplasm. We have employed this approach successfully revealing three novel episomal yam badnaviruses ( Bömer et al., 2016 ). We proposed this to be a complementary method to denaturing gradient gel electrophoresis, which enables a rapid indication of badnavirus diversity as well as the identification of potentially integrated badnavirus sequences in the host genome ( Turaki et al., 2017 ). Here, we describe the step-by-step protocol to screen yam germplasm for badnavirus infections using RCA as an efficient research tool in the amplification and characterization of novel badnavirus genomes.
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Affiliation(s)
- Moritz Bömer
- Natural Resources Institute, University of Greenwich, London, UK
| | - Aliyu A Turaki
- Kebbi State University of Science and Technology Aliero, Birnin Kebbi, Nigeria
| | | | - Gonçalo Silva
- Natural Resources Institute, University of Greenwich, London, UK
| | - P Lava Kumar
- International Institute of Tropical Agriculture (IITA), Ibadan, Nigeria
| | - Susan E Seal
- Natural Resources Institute, University of Greenwich, London, UK
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