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Rai S, Omar AF, Rehan M, Al-Turki A, Sagar A, Ilyas N, Sayyed RZ, Hasanuzzaman M. Crop microbiome: their role and advances in molecular and omic techniques for the sustenance of agriculture. PLANTA 2022; 257:27. [PMID: 36583789 DOI: 10.1007/s00425-022-04052-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Accepted: 12/11/2022] [Indexed: 06/17/2023]
Abstract
This review is an effort to provide in-depth knowledge of microbe's interaction and its role in crop microbiome using combination of advanced molecular and OMICS technology to translate this information for the sustenance of agriculture. Increasing population, climate change and exhaustive agricultural practices either influenced nutrient inputs of soil or generating biological and physico-chemical deterioration of the soils and affecting the agricultural productivity and agro-ecosystems. Alarming concerns toward food security and crop production claim for renewed attention in microbe-based farming practices. Microbes are omnipresent (soil, water, and air) and their close association with plants would help to accomplish sustainable agriculture goals. In the last few decades, the search for beneficial microbes in crop production, soil fertilization, disease management, and plant growth promotion is the thirst for eco-friendly agriculture. The crop microbiome opens new paths to utilize beneficial microbes and manage pathogenic microbes through integrated advanced biotechnology. The crop microbiome helps plants acquire nutrients, growth, resilience against phytopathogens, and tolerance to abiotic stresses, such as heat, drought, and salinity. Despite the emergent functionality of the crop microbiome as a complicated constituent of the plant fitness, our understanding of how the functionality of microbiome influenced by numerous factors including genotype of host, climatic conditions, mobilization of minerals, soil composition, nutrient availability, interaction between nexus of microbes, and interactions with other external microbiomes is partially understood. However, the structure, composition, dynamics, and functional contribution of such cultured and uncultured crop microbiome are least explored. The advanced biotechnological approaches are efficient tools for acquiring the information required to investigate the microbiome and extract data to develop high yield producing and resistant variety crops. This knowledge fills the fundamental gap between the theoretical concepts and the operational use of these advanced tools in crop microbiome studies. Here, we review (1) structure and composition of crop microbiome, (2) microbiome-mediated role associated with crops fitness, (3) Molecular and -omics techniques for exploration of crop microbiome, and (4) current approaches and future prospectives of crop microbiome and its exploitation for sustainable agriculture. Recent -omic approaches are influential tool for mapping, monitoring, modeling, and management of crops microbiome. Identification of crop microbiome, using system biology and rhizho-engineering, can help to develop future bioformulations for disease management, reclamation of stressed agro-ecosystems, and improved productivity of crops. Nano-system approaches combined with triggering molecules of crop microbiome can help in designing of nano-biofertilizers and nano-biopesticides. This combination has numerous merits over the traditional bioinoculants. They stimulate various defense mechanisms in plants facing stress conditions; provide bioavailability of nutrients in the soil, helps mitigate stress conditions; and enhance chances of crops establishment.
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Affiliation(s)
- Shalini Rai
- Department of Biotechnology, SHEPA, Varanasi, India.
| | - Ayman F Omar
- Department of Plant Production and Protection, College of Agriculture and Veterinary Medicine, Qassim University, Buraydah, 51452, Saudi Arabia.
- Department of Plant Pathology, Plant Pathology and Biotechnology Laboratory and EPCRS Excellence Center, Faculty of Agriculture, Kafrelsheikh University, Kafr El-Sheikh, 33516, Egypt.
| | - Medhat Rehan
- Department of Plant Production and Protection, College of Agriculture and Veterinary Medicine, Qassim University, Buraydah, 51452, Saudi Arabia
- Department of Genetics, College of Agriculture, Kafrelsheikh University, Kafr El-Sheikh, 33516, Egypt
| | - Ahmad Al-Turki
- Department of Plant Production and Protection, College of Agriculture and Veterinary Medicine, Qassim University, Buraydah, 51452, Saudi Arabia
| | - Alka Sagar
- Department of Microbiology, MIET, Meerut, India
| | - Noshin Ilyas
- Department of Botany, PMAS Arid Agriculture University, Rawalpindi, 46300, Pakistan
| | - R Z Sayyed
- Asian PGPR Society, Auburn Venture, Auburn, AL, USA.
| | - Mirza Hasanuzzaman
- Department of Agronomy, Faculty of Agriculture, Sher-E-Bangla Agricultural University (SAU), Sher-E-Bangla Nagar, Dhaka, 1207, Bangladesh
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LAMAS A, BARREIRO R, REGAL P, VÁZQUEZ B, MIRANDA JM, CEPEDA A, FRANCO CM. Development and validation of a SNPs panel used for beef traceability throughout the food chain. FOOD SCIENCE AND TECHNOLOGY 2022. [DOI: 10.1590/fst.07221] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Podbiel D, Laermer F, Zengerle R, Hoffmann J. Fusing MEMS technology with lab-on-chip: nanoliter-scale silicon microcavity arrays for digital DNA quantification and multiplex testing. MICROSYSTEMS & NANOENGINEERING 2020; 6:82. [PMID: 34567692 PMCID: PMC8433415 DOI: 10.1038/s41378-020-00187-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/20/2020] [Revised: 05/31/2020] [Accepted: 06/07/2020] [Indexed: 05/18/2023]
Abstract
We report on the development of a microfluidic multiplexing technology for highly parallelized sample analysis via quantitative polymerase chain reaction (PCR) in an array of 96 nanoliter-scale microcavities made from silicon. This PCR array technology features fully automatable aliquoting microfluidics, a robust sample compartmentalization up to temperatures of 95 °C, and an application-specific prestorage of reagents within the 25 nl microcavities. The here presented hybrid silicon-polymer microfluidic chip allows both a rapid thermal cycling of the liquid compartments and a real-time fluorescence read-out for a tracking of the individual amplification reactions taking place inside the microcavities. We demonstrate that the technology provides very low reagent carryover of prestored reagents < 6 × 10-2 and a cross talk rate < 1 × 10-3 per PCR cycle, which facilitate a multi-targeted sample analysis via geometric multiplexing. Furthermore, we apply this PCR array technology to introduce a novel digital PCR-based DNA quantification method: by taking the assay-specific amplification characteristics like the limit of detection into account, the method allows for an absolute gene target quantification by means of a statistical analysis of the amplification results.
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Affiliation(s)
- Daniel Podbiel
- Robert Bosch GmbH, Corporate Sector Research, Microsystems and Nanotechnologies, Robert-Bosch-Campus 1, 71272 Renningen, Germany
| | - Franz Laermer
- Robert Bosch GmbH, Corporate Sector Research, Microsystems and Nanotechnologies, Robert-Bosch-Campus 1, 71272 Renningen, Germany
| | - Roland Zengerle
- IMTEK - Department of Microsystems Engineering, University of Freiburg Georges-Koehler-Allee 103, 79110 Freiburg, Germany
| | - Jochen Hoffmann
- Robert Bosch GmbH, Corporate Sector Research, Microsystems and Nanotechnologies, Robert-Bosch-Campus 1, 71272 Renningen, Germany
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High-Resolution Melting (HRM) Curve Assay for the Identification of Eight Fusarium Species Causing Ear Rot in Maize. Pathogens 2020; 9:pathogens9040270. [PMID: 32272731 PMCID: PMC7238191 DOI: 10.3390/pathogens9040270] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2020] [Revised: 04/03/2020] [Accepted: 04/05/2020] [Indexed: 11/16/2022] Open
Abstract
Maize plants are often infected with fungal pathogens of the genus Fusarium. Taxonomic characterization of these species by microscopic examination of pure cultures or assignment to mating populations is time-consuming and requires specific expertise. Reliable taxonomic assignment may be strengthened by the analysis of DNA sequences. Species-specific PCR assays are available for most Fusarium pathogens, but the number of species that infect maize increases the labor and costs required for analysis. In this work, a diagnostic assay for major Fusarium pathogens of maize based on the analysis of melting curves of PCR amplicons was established. Short segments of genes RPB2 and TEF-1α, which have been widely used in molecular taxonomy of Fusarium, were amplified with universal primers in a real-time thermocycler and high-resolution melting (HRM) curves of the products were recorded. Among major Fusarium pathogens of maize ears, F. cerealis, F. culmorum, F. graminearum, F. equiseti, F. poae, F. temperatum, F. tricinctum, and F. verticillioides, all species except for the pair F. culmorum/F. graminearum could be distinguished by HRM analysis of a 304 bp segment of the RPB2 gene. The latter two species could be differentiated by HRM analysis of a 247 bp segment of the TEF-1α gene. The assay was validated with DNA extracted from pure cultures of fungal strains, successfully applied to total DNA extracted from infected maize ears and also to fungal mycelium that was added directly to the PCR master mix ("colony PCR"). HRM analysis thus offers a cost-efficient method suitable for the diagnosis of multiple fungal pathogens.
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He Z, Su Y, Li S, Long P, Zhang P, Chen Z. Development and Evaluation of Isothermal Amplification Methods for Rapid Detection of Lethal Amanita Species. Front Microbiol 2019; 10:1523. [PMID: 31338080 PMCID: PMC6626908 DOI: 10.3389/fmicb.2019.01523] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2019] [Accepted: 06/18/2019] [Indexed: 12/04/2022] Open
Abstract
In the present work, loop-mediated isothermal amplification (LAMP) and hyperbranched rolling circle amplification (HRCA) methods were developed to detect and distinguish different lethal Amanita species. Specific LAMP primers and HRCA padlock probes for species-specific identification and a set of universal LAMP primers for lethal Amanita species were designed and tested. The results indicated that the LAMP-based assay was able to discriminate introclade lethal Amanita species but was not able to discriminate intraclade species perfectly, while the HRCA-based assay could discriminate whether introclade or intraclade species. The universal LAMP primers were positive for 10 lethal species of Amanita section Phalloideae and negative for 16 species of Amanita outside section Phalloideae. The detection limits of LMAP and HRCA were 10 and 1 pg of genomic DNA per reaction, respectively. In conclusion, the two methods could be rapid, specific, sensitive and low-cost tools for the identification of lethal Amanita species.
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Affiliation(s)
- Zhengmi He
- College of Life Sciences, Hunan Normal University, Changsha, China
| | - Yuting Su
- College of Life Sciences, Hunan Normal University, Changsha, China
| | - Sainan Li
- College of Life Sciences, Hunan Normal University, Changsha, China
| | - Pan Long
- College of Life Sciences, Hunan Normal University, Changsha, China
| | - Ping Zhang
- College of Life Sciences, Hunan Normal University, Changsha, China
| | - Zuohong Chen
- College of Life Sciences, Hunan Normal University, Changsha, China
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Wei M, Xu C, Xu X, Zhu C, Li J, Lv G. Characteristics of atmospheric bacterial and fungal communities in PM 2.5 following biomass burning disturbance in a rural area of North China Plain. THE SCIENCE OF THE TOTAL ENVIRONMENT 2019; 651:2727-2739. [PMID: 30463127 DOI: 10.1016/j.scitotenv.2018.09.399] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/25/2018] [Revised: 09/29/2018] [Accepted: 09/30/2018] [Indexed: 05/23/2023]
Abstract
Biomass burning (BB) in North China Plain has been urgent issue in recent years due to the severe environmental impaction. Bacteria and fungi are ubiquitous in particulate matter. Their taxonomic composition, concentration, ecophysiological functions have potentially important implications in atmospheric biochemical cycle and human health. However, current knowledge about airborne microbes during biomass burning period is scant. Here we investigated bacterial and fungal community composition, abundance and potential function in Yucheng, the center of the North China Plain during summer harvest season in 2014. Monthly field observation suggested serious pollution with high concentration of PM2.5 and water-soluble ions during biomass burning period. Elevated total bacterial and fungal concentration determined by real-time quantitative PCR was observed for samples during burning events. The predominant bacterial taxa were gram-negative, e.g. Acinetobacter, Cyanobacterium, Janthinobacterium, Massilia, Pseudomonas, accounted for 70.9% of total bacteria. The filamentous fungi Alternaria, Aspergillus, Cladosporium and Penicillium were predominant fungal genera. Metastats analysis showed significant disparity in terms of carbohydrate, amino acids metabolism, human and plant disease predicted by PICRUSt analysis between BB and non-BB events. Microbial community structure were mainly influenced by organic carbon and water-soluble ions (magnesium and potassium) suggested by redundancy analysis (RDA) and co-occurrence analysis. Our data yielded insights into microbial community dynamics following biomass burning disturbance. This study may provide potentially important reference for environmental, agricultural and health management.
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Affiliation(s)
- Min Wei
- College of Geography and Environment, Shandong Normal University, Ji'nan 250014, China; Environment Research Institute, School of Environmental Science and Engineering, Shandong University, Ji'nan 250100, China.
| | - Caihong Xu
- Environment Research Institute, School of Environmental Science and Engineering, Shandong University, Ji'nan 250100, China
| | - Xianmang Xu
- Environment Research Institute, School of Environmental Science and Engineering, Shandong University, Ji'nan 250100, China
| | - Chao Zhu
- Environment Research Institute, School of Environmental Science and Engineering, Shandong University, Ji'nan 250100, China
| | - Jiarong Li
- Environment Research Institute, School of Environmental Science and Engineering, Shandong University, Ji'nan 250100, China
| | - Ganglin Lv
- Environment Research Institute, School of Environmental Science and Engineering, Shandong University, Ji'nan 250100, China
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Lau HY, Botella JR. Advanced DNA-Based Point-of-Care Diagnostic Methods for Plant Diseases Detection. FRONTIERS IN PLANT SCIENCE 2017; 8:2016. [PMID: 29375588 PMCID: PMC5770625 DOI: 10.3389/fpls.2017.02016] [Citation(s) in RCA: 88] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/14/2017] [Accepted: 11/13/2017] [Indexed: 05/07/2023]
Abstract
Diagnostic technologies for the detection of plant pathogens with point-of-care capability and high multiplexing ability are an essential tool in the fight to reduce the large agricultural production losses caused by plant diseases. The main desirable characteristics for such diagnostic assays are high specificity, sensitivity, reproducibility, quickness, cost efficiency and high-throughput multiplex detection capability. This article describes and discusses various DNA-based point-of care diagnostic methods for applications in plant disease detection. Polymerase chain reaction (PCR) is the most common DNA amplification technology used for detecting various plant and animal pathogens. However, subsequent to PCR based assays, several types of nucleic acid amplification technologies have been developed to achieve higher sensitivity, rapid detection as well as suitable for field applications such as loop-mediated isothermal amplification, helicase-dependent amplification, rolling circle amplification, recombinase polymerase amplification, and molecular inversion probe. The principle behind these technologies has been thoroughly discussed in several review papers; herein we emphasize the application of these technologies to detect plant pathogens by outlining the advantages and disadvantages of each technology in detail.
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Affiliation(s)
- Han Yih Lau
- Biotechnology and Nanotechnology Research Centre, Malaysian Agricultural Research and Development Institute, Serdang, Malaysia
| | - Jose R. Botella
- Plant Genetic Engineering Laboratory, School of Agriculture and Food Sciences, University of Queensland, Brisbane, QLD, Australia
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8
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Gene expression studies of reference genes for quantitative real-time PCR: an overview in insects. Biotechnol Lett 2017; 40:227-236. [DOI: 10.1007/s10529-017-2465-4] [Citation(s) in RCA: 57] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2017] [Accepted: 10/23/2017] [Indexed: 12/29/2022]
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Lin H, Jiang X, Yi J, Wang X, Zuo R, Jiang Z, Wang W, Zhou E. Molecular identification of Neofabraea species associated with bull's-eye rot on apple using rolling-circle amplification of partial EF-1α sequence. Can J Microbiol 2017; 64:57-68. [PMID: 29084390 DOI: 10.1139/cjm-2017-0448] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
A rolling-circle amplification (RCA) method with padlock probes targeted on EF-1α regions was developed for rapid detection of apple bull's-eye rot pathogens, including Neofabraea malicorticis, N. perennans, N. kienholzii, and N. vagabunda (synonym: N. alba). Four padlock probes (PLP-Nm, PLP-Np, PLP-Nk, and PLP-Nv) were designed and tested against 28 samples, including 22 BER pathogen cultures, 4 closely related species, and 2 unrelated species that may cause serious apple decays. The assay successfully identified all the bull's-eye rot pathogenic fungi at the level of species, while no cross-reaction was observed in all target species and no false-positive reaction was observed with all strains used for reference. This study showed that the use of padlock probes and the combination of probe signal amplification by RCA provided an effective and sensitive method for the rapid identification of Neofabraea spp. The method could therefore be a useful tool for monitoring bull's-eye rot pathogens in port quarantine and orchard epidemiological studies.
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Affiliation(s)
- Huijiao Lin
- a Guangdong Province Key Laboratory of Microbial Signals and Disease Control, College of Agriculture, South China Agricultural University, Guangzhou 510642, China.,b Inspection and Test Center, Huangpu Entry-Exit Inspection and Quarantine Bureau, Guangzhou 510730, China
| | - Xiang Jiang
- b Inspection and Test Center, Huangpu Entry-Exit Inspection and Quarantine Bureau, Guangzhou 510730, China
| | - Jianping Yi
- c Technical Center for Animal, Plant and Food Inspection and Quarantine, Shanghai Entry-Exit Inspection and Quarantine Bureau, Shanghai 200135, China
| | - Xinguo Wang
- b Inspection and Test Center, Huangpu Entry-Exit Inspection and Quarantine Bureau, Guangzhou 510730, China
| | - Ranling Zuo
- b Inspection and Test Center, Huangpu Entry-Exit Inspection and Quarantine Bureau, Guangzhou 510730, China
| | - Zide Jiang
- a Guangdong Province Key Laboratory of Microbial Signals and Disease Control, College of Agriculture, South China Agricultural University, Guangzhou 510642, China
| | - Weifang Wang
- d Guangdong Key Laboratory of Import and Export Technical Measures of Animal, Plant and Food, Guangdong Inspection and Quarantine Technology Center, Guangzhou 510623, China
| | - Erxun Zhou
- a Guangdong Province Key Laboratory of Microbial Signals and Disease Control, College of Agriculture, South China Agricultural University, Guangzhou 510642, China
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Osman F, Dang T, Bodaghi S, Vidalakis G. One-step multiplex RT-qPCR detects three citrus viroids from different genera in a wide range of hosts. J Virol Methods 2017; 245:40-52. [PMID: 28300606 DOI: 10.1016/j.jviromet.2017.03.007] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2016] [Revised: 02/27/2017] [Accepted: 03/10/2017] [Indexed: 01/23/2023]
Abstract
A one-step multiplex reverse transcription real-time quantitative polymerase chain reaction (RT-qPCR) based on species-specific minor groove binding (MGB) probes, was developed for the simultaneous detection, identification, and quantification of three citrus viroids belonging to different genera. Citrus exocortis viroid (Pospiviroid), Hop stunt viroid (Hostuviroid), and Citrus bark cracking viroid (Cocadviroid) cause a variety of maladies in agriculturally significant crops. Therefore, reliable assays for their detection are essential tools for various government and industry organizations implementing disease management programs. Singleplex qPCR primers and MGB probes were designed individually for the detection of the three targeted viroids, and subsequently combined in a one-step multiplex RT-qPCR reaction. A wide host range of woody plants, including citrus, grapevines, apricots, plums and herbaceous plants such as tomato, cucumber, eggplant and chrysanthemum different world regions were used to validate the assay. Single, double and triple viroid infections were identified in the tested samples. The developed multiplex RT-qPCR assay was compared with a previously reported SYBR Green I RT-qPCR for the universal detection of citrus viroids. Both assays accurately identified all citrus viroid infected samples. The multiplex assay complemented the SYBR Green I universal detection assay by differentiating among citrus viroid species in the positive samples. The developed multiplex RT-qPCR assay has the potential to simultaneously detect each targeted viroid and could be used in high throughput screenings for citrus viroids in field surveys, germplasm banks, nurseries and other viroid disease management programs.
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Affiliation(s)
- Fatima Osman
- Department of Plant Pathology, University of California, Davis, CA 95616, USA
| | - Tyler Dang
- Department of Plant Pathology and Microbiology, University of California, Riverside, CA 92521, USA
| | - Sohrab Bodaghi
- Department of Plant Pathology and Microbiology, University of California, Riverside, CA 92521, USA
| | - Georgios Vidalakis
- Department of Plant Pathology and Microbiology, University of California, Riverside, CA 92521, USA.
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Xu C, Wei M, Chen J, Wang X, Zhu C, Li J, Zheng L, Sui G, Li W, Wang W, Zhang Q, Mellouki A. Bacterial characterization in ambient submicron particles during severe haze episodes at Ji'nan, China. THE SCIENCE OF THE TOTAL ENVIRONMENT 2017; 580:188-196. [PMID: 28017418 DOI: 10.1016/j.scitotenv.2016.11.145] [Citation(s) in RCA: 51] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/29/2016] [Revised: 11/12/2016] [Accepted: 11/21/2016] [Indexed: 05/14/2023]
Abstract
In January 2014, severe haze episodes which sweep across Chinese cities have attracted public concern and interest at home and abroad. In addition to the physicochemical properties of air pollutants, bacteria are thought to be responsible for the spread of respiratory diseases and various allergies. We attempted the bacterial characterization of submicron particles (PM0.18-0.32, PM0.32-0.56, and PM0.56-1) under severe haze episodes using high-throughput sequencing and real-time quantitative PCR detecting system based on 21 samples collected from January to March 2014 at Ji'nan, China. The high bacterial concentration in PM0.32-0.56 (7314cells m-3), PM0.18-0.32 (7212cells m-3), and PM0.56-1 (6982cells m-3) showed significant negative correlations with SO2, NO2, and O3. Under sufficient sequencing depth, 37 phyla, 71 classes, 137 orders, 236 families, and 378 genera were classified, and the bacterial community structure varied significantly in different size fractions. For example, Holophagaceae (Acidobacteria) in PM0.32-0.56 showed 6-fold higher abundance than that in PM0.18-0.32. Moreover, functional categories and bacterial species (Lactococcus piscium, Pseudomonas fragi, Streptococcus agalactiae, and Pseudomonas cichorii) that may potentially be responsible for infections and allergies were also discovered. Source track analysis showed that the ambient bacteria mainly originated from soils, leaf surfaces, and feces. Our results highlighted the importance of airborne microbial communities by understanding the concentration, structure, ecological and health effects, especially those in submicron particles during haze episodes.
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Affiliation(s)
- Caihong Xu
- Environment Research Institute, School of Environmental Science and Engineering, Shandong University, Ji'nan 250100, China
| | - Min Wei
- Environment Research Institute, School of Environmental Science and Engineering, Shandong University, Ji'nan 250100, China
| | - Jianmin Chen
- Environment Research Institute, School of Environmental Science and Engineering, Shandong University, Ji'nan 250100, China; Shanghai Key Laboratory of Atmospheric Particle Pollution and Prevention (LAP), Fudan Tyndall Centre, Department of Environmental Science & Engineering, Fudan University, Shanghai 200433, China.
| | - Xinfeng Wang
- Environment Research Institute, School of Environmental Science and Engineering, Shandong University, Ji'nan 250100, China
| | - Chao Zhu
- Environment Research Institute, School of Environmental Science and Engineering, Shandong University, Ji'nan 250100, China
| | - Jiarong Li
- Environment Research Institute, School of Environmental Science and Engineering, Shandong University, Ji'nan 250100, China
| | - Lulu Zheng
- Shanghai Key Laboratory of Atmospheric Particle Pollution and Prevention (LAP), Fudan Tyndall Centre, Department of Environmental Science & Engineering, Fudan University, Shanghai 200433, China
| | - Guodong Sui
- Shanghai Key Laboratory of Atmospheric Particle Pollution and Prevention (LAP), Fudan Tyndall Centre, Department of Environmental Science & Engineering, Fudan University, Shanghai 200433, China
| | - Weijun Li
- Environment Research Institute, School of Environmental Science and Engineering, Shandong University, Ji'nan 250100, China
| | - Wenxing Wang
- Environment Research Institute, School of Environmental Science and Engineering, Shandong University, Ji'nan 250100, China
| | - Qingzhu Zhang
- Environment Research Institute, School of Environmental Science and Engineering, Shandong University, Ji'nan 250100, China
| | - Abdelwahid Mellouki
- Environment Research Institute, School of Environmental Science and Engineering, Shandong University, Ji'nan 250100, China; Institut de Combustion, Aérothermique, Réactivité et Environnement, CNRS, 45071 Orléans cedex 02, France
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Lau HY, Wang Y, Wee EJH, Botella JR, Trau M. Field Demonstration of a Multiplexed Point-of-Care Diagnostic Platform for Plant Pathogens. Anal Chem 2016; 88:8074-81. [PMID: 27403651 DOI: 10.1021/acs.analchem.6b01551] [Citation(s) in RCA: 71] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
Effective disease management strategies to prevent catastrophic crop losses require rapid, sensitive, and multiplexed detection methods for timely decision making. To address this need, a rapid, highly specific and sensitive point-of-care method for multiplex detection of plant pathogens was developed by taking advantage of surface-enhanced Raman scattering (SERS) labeled nanotags and recombinase polymerase amplification (RPA), which is a rapid isothermal amplification method with high specificity. In this study, three agriculturally important plant pathogens (Botrytis cinerea, Pseudomonas syringae, and Fusarium oxysporum) were used to demonstrate potential translation into the field. The RPA-SERS method was faster, more sensitive than polymerase chain reaction, and could detect as little as 2 copies of B. cinerea DNA. Furthermore, multiplex detection of the three pathogens was demonstrated for complex systems such as the Arabidopsis thaliana plant and commercial tomato crops. To demonstrate the potential for on-site field applications, a rapid single-tube RPA/SERS assay was further developed and successfully performed for a specific target outside of a laboratory setting.
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Affiliation(s)
- Han Yih Lau
- Centre for Personalized Nanomedicine, Australian Institute for Bioengineering and Nanotechnology, The University of Queensland , Brisbane QLD 4072, Australia.,Plant Genetic Engineering Laboratory, School of Agriculture and Food Sciences, The University of Queensland , Brisbane QLD 4072, Australia
| | - Yuling Wang
- Centre for Personalized Nanomedicine, Australian Institute for Bioengineering and Nanotechnology, The University of Queensland , Brisbane QLD 4072, Australia
| | - Eugene J H Wee
- Centre for Personalized Nanomedicine, Australian Institute for Bioengineering and Nanotechnology, The University of Queensland , Brisbane QLD 4072, Australia
| | - Jose R Botella
- Plant Genetic Engineering Laboratory, School of Agriculture and Food Sciences, The University of Queensland , Brisbane QLD 4072, Australia
| | - Matt Trau
- Centre for Personalized Nanomedicine, Australian Institute for Bioengineering and Nanotechnology, The University of Queensland , Brisbane QLD 4072, Australia.,School of Chemistry and Molecular Biosciences, The University of Queensland , Brisbane QLD 4072, Australia
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Álvarez SP, López NEL, Lozano JM, Negrete EAR, Cervantes MES. Plant Fungal Disease Management Using Nanobiotechnology as a Tool. ADVANCES AND APPLICATIONS THROUGH FUNGAL NANOBIOTECHNOLOGY 2016. [DOI: 10.1007/978-3-319-42990-8_8] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
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14
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Development and validation of a multiplex reverse transcription quantitative PCR (RT-qPCR) assay for the rapid detection of Citrus tristeza virus, Citrus psorosis virus, and Citrus leaf blotch virus. J Virol Methods 2015; 220:64-75. [PMID: 25907469 DOI: 10.1016/j.jviromet.2015.04.013] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2013] [Revised: 04/07/2015] [Accepted: 04/09/2015] [Indexed: 11/20/2022]
Abstract
A single real-time multiplex reverse transcription quantitative polymerase chain reaction (RT-qPCR) assay for the simultaneous detection of Citrus tristeza virus (CTV), Citrus psorosis virus (CPsV), and Citrus leaf blotch virus (CLBV) was developed and validated using three different fluorescently labeled minor groove binding qPCR probes. To increase the detection reliability, coat protein (CP) genes from large number of different isolates of CTV, CPsV and CLBV were sequenced and a multiple sequence alignment was generated with corresponding CP sequences from the GenBank and a robust multiplex RT-qPCR assay was designed. The capacity of the multiplex RT-qPCR assay in detecting the viruses was compared to singleplex RT-qPCR designed specifically for each virus and was assessed using multiple virus isolates from diverse geographical regions and citrus species as well as graft-inoculated citrus plants infected with various combination of the three viruses. No significant difference in detection limits was found and specificity was not affected by the inclusion of the three assays in a multiplex RT-qPCR reaction. Comparison of the viral load for each virus using singleplex and multiplex RT-qPCR assays, revealed no significant differences between the two assays in virus detection. No significant difference in Cq values was detected when using one-step and two-step multiplex RT-qPCR detection formats. Optimizing the RNA extraction technique for citrus tissues and testing the quality of the extracted RNA using RT-qPCR targeting the cytochrome oxidase citrus gene as an RNA specific internal control proved to generate better diagnostic assays. Results showed that the developed multiplex RT-qPCR can streamline viruses testing of citrus nursery stock by replacing three separate singleplex assays, thus reducing time and labor while retaining the same sensitivity and specificity. The three targeted RNA viruses are regulated pathogens for California's mandatory "Section 3701: Citrus Nursery Stock Pest Cleanliness Program". Adopting a compatible multiplex RT-qPCR testing protocol for these viruses as well as other RNA and DNA regulated pathogens will provide a valuable alternative tool for virus detection and efficient program implementation.
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Wei M, Yu Z, Zhang H. Molecular characterization of microbial communities in bioaerosols of a coal mine by 454 pyrosequencing and real-time PCR. J Environ Sci (China) 2015; 30:241-251. [PMID: 25872733 DOI: 10.1016/j.jes.2014.07.035] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2014] [Revised: 06/25/2014] [Accepted: 07/24/2014] [Indexed: 06/04/2023]
Abstract
Microbial diversity and abundance in bioaerosols of a coal mine were analyzed based on 454 pyrosequencing and real-time polymerase chain reaction (PCR). A total of 37,191 high quality sequences were obtained and could be classified into 531, 1730 and 448 operational taxonomic units respectively for archaea, bacteria and fungi at 97% sequence similarity. The Shannon diversity index for archaea, bacteria and fungi was respectively 4.71, 6.29 and 3.86, indicating a high diversity in coal mine bioaerosols. Crenarchaeota, Proteobacteria and Ascomycota were the dominant phyla for archaea, bacteria and fungi, respectively. The concentrations of total archaea, bacteria and fungi were 1.44×10(8), 1.02×10(8) and 9.60×10(4) cells/m3, respectively. Methanotrophs observed in bioaerosols suggested possible methane oxidation in the coal mine. The identified potential pathogens to coal miners, such as Acinetobacter schindleri, Aeromonas cavernicola, Alternaria alternata, Aspergillus penicillioides, Cladosporium cladosporioides, and Penicillium brevicompactum were also observed. This was the first investigation of microbial diversity and abundance in coal mine bioaerosols. The investigation of microbial communities would be favorable in promoting the progress of methane control based on microbial technique and concern on coal miners' health.
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Affiliation(s)
- Min Wei
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100049, China.
| | - Zhisheng Yu
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100049, China.
| | - Hongxun Zhang
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100049, China
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16
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Cloning and validation of reference genes for normalization of gene expression studies in pearl millet [Pennisetum glaucum (L.) R. Br.] by quantitative real-time PCR. ACTA ACUST UNITED AC 2015. [DOI: 10.1016/j.plgene.2015.02.001] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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17
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Lau HY, Palanisamy R, Trau M, Botella JR. Molecular inversion probe: a new tool for highly specific detection of plant pathogens. PLoS One 2014; 9:e111182. [PMID: 25343255 PMCID: PMC4208852 DOI: 10.1371/journal.pone.0111182] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2014] [Accepted: 09/28/2014] [Indexed: 11/18/2022] Open
Abstract
Highly specific detection methods, capable of reliably identifying plant pathogens are crucial in plant disease management strategies to reduce losses in agriculture by preventing the spread of diseases. We describe a novel molecular inversion probe (MIP) assay that can be potentially developed into a robust multiplex platform to detect and identify plant pathogens. A MIP has been designed for the plant pathogenic fungus Fusarium oxysporum f.sp. conglutinans and the proof of concept for the efficiency of this technology is provided. We demonstrate that this methodology can detect as little as 2.5 ng of pathogen DNA and is highly specific, being able to accurately differentiate Fusarium oxysporum f.sp. conglutinans from other fungal pathogens such as Botrytis cinerea and even pathogens of the same species such as Fusarium oxysporum f.sp. lycopersici. The MIP assay was able to detect the presence of the pathogen in infected Arabidopsis thaliana plants as soon as the tissues contained minimal amounts of pathogen. MIP methods are intrinsically highly multiplexable and future development of specific MIPs could lead to the establishment of a diagnostic method that could potentially screen infected plants for hundreds of pathogens in a single assay.
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Affiliation(s)
- Han Yih Lau
- Plant Genetic Engineering Laboratory, School of Agriculture and Food Sciences, University of Queensland, Brisbane, Queensland, Australia
- Australian Institute for Bioengineering and Nanotechnology, University of Queensland, Brisbane, Queensland, Australia
| | - Ramkumar Palanisamy
- Australian Institute for Bioengineering and Nanotechnology, University of Queensland, Brisbane, Queensland, Australia
| | - Matt Trau
- Australian Institute for Bioengineering and Nanotechnology, University of Queensland, Brisbane, Queensland, Australia
| | - Jose R. Botella
- Plant Genetic Engineering Laboratory, School of Agriculture and Food Sciences, University of Queensland, Brisbane, Queensland, Australia
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18
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Osman F, Hodzic E, Omanska-Klusek A, Olineka T, Rowhani A. Development and validation of a multiplex quantitative PCR assay for the rapid detection of Grapevine virus A, B and D. J Virol Methods 2013; 194:138-45. [DOI: 10.1016/j.jviromet.2013.07.046] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2013] [Revised: 07/26/2013] [Accepted: 07/26/2013] [Indexed: 10/26/2022]
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19
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Florschütz K, Schröter A, Schmieder S, Chen W, Schweizer P, Sonntag F, Danz N, Baronian K, Kunze G. 'Phytochip': on-chip detection of phytopathogenic RNA viruses by a new surface plasmon resonance platform. J Virol Methods 2013; 189:80-6. [PMID: 23391824 DOI: 10.1016/j.jviromet.2013.01.008] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2012] [Revised: 12/21/2012] [Accepted: 01/14/2013] [Indexed: 10/27/2022]
Abstract
The surface plasmon resonance (SPR) based 'Phytochip' was developed to distinguish virus-infected plants from non-infected plants. The system detects DNA-RNA hybridization to show the presence of phytopathogenic viruses such as the RNA virus barley stripe mosaic virus (BSMV) in wheat leaves. To achieve this BSMV and wheat specific oligonucleotides, and a negative control yeast oligonucleotide, were immobilized on a SPR gold surface chip. After optimization of the hybridization parameters with purified wheat samples, wheat infected with BSMV resulted in detectable signals with both the BSMV and the wheat probes. In contrast, a hybridization reaction was not be detected with the negative probe. The method is fast and sensitive with a detection time of 3000s (50min), a detection limit of 14.7pgμl(-1) BSMV RNA and a measuring range of 14.7-84pgμl(-1) BSMV RNA (1.323-7.56ng BSMV RNA per 90μl sample). These characteristics, combined with the high throughput design, make it suitable for application in plant breeding and virus control.
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Affiliation(s)
- Kristina Florschütz
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstr. 3, D-06466 Gatersleben, Germany
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20
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Ritari J, Koskinen K, Hultman J, Kurola JM, Kymäläinen M, Romantschuk M, Paulin L, Auvinen P. Molecular analysis of meso- and thermophilic microbiota associated with anaerobic biowaste degradation. BMC Microbiol 2012; 12:121. [PMID: 22727142 PMCID: PMC3408363 DOI: 10.1186/1471-2180-12-121] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2011] [Accepted: 06/22/2012] [Indexed: 12/25/2022] Open
Abstract
BACKGROUND Microbial anaerobic digestion (AD) is used as a waste treatment process to degrade complex organic compounds into methane. The archaeal and bacterial taxa involved in AD are well known, whereas composition of the fungal community in the process has been less studied. The present study aimed to reveal the composition of archaeal, bacterial and fungal communities in response to increasing organic loading in mesophilic and thermophilic AD processes by applying 454 amplicon sequencing technology. Furthermore, a DNA microarray method was evaluated in order to develop a tool for monitoring the microbiological status of AD. RESULTS The 454 sequencing showed that the diversity and number of bacterial taxa decreased with increasing organic load, while archaeal i.e. methanogenic taxa remained more constant. The number and diversity of fungal taxa increased during the process and varied less in composition with process temperature than bacterial and archaeal taxa, even though the fungal diversity increased with temperature as well. Evaluation of the microarray using AD sample DNA showed correlation of signal intensities with sequence read numbers of corresponding target groups. The sensitivity of the test was found to be about 1%. CONCLUSIONS The fungal community survives in anoxic conditions and grows with increasing organic loading, suggesting that Fungi may contribute to the digestion by metabolising organic nutrients for bacterial and methanogenic groups. The microarray proof of principle tests suggest that the method has the potential for semiquantitative detection of target microbial groups given that comprehensive sequence data is available for probe design.
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Affiliation(s)
- Jarmo Ritari
- Institute of Biotechnology, University of Helsinki, Viikinkaari 4, 00790, Helsinki, Finland.
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21
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Abstract
The Key to the Common Phytophthora species (Lucid v 3.4) is a matrix-based computerized identification key and includes important morphological and molecular characters that are useful for identification of 55 common species of Phytophthora. A set of 20 features are used to make a correct species identification. Once a culture is obtained, the user enters responses to known character state options into Lucid Player, and the correct species is identified. Illustrations of each character state for a feature are included in the key. The main morphological features included in the key are: asexual structures, sexual structures, and chlamydospore, hyphae, and cultural characteristics. The user can read an illustrated "Fact Sheet" on each species that includes pictures of morphological characters, disease symptoms, host range, and relevant references. A cross-linked glossary of terminology is included in each fact sheet. In addition, a DNA search function that contains a simple search of internal transcribed spacer (ITS) and Barcode of Life (BOL, 5' end of the cox 1 gene) sequences for each species can be queried. The key was created to provide teachers, diagnosticians, and regulatory personnel with easily accessible tools to distinguish common species in the genus Phytophthora based on a number of important morphological and molecular characteristics. The key is available for purchase from APS Press and should provide another useful tool for the identification of members of this destructive group of Oomycete plant pathogens.
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Affiliation(s)
- Jean Beagle Ristaino
- Department of Plant Pathology, North Carolina State University, Raleigh, NC 27695
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22
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Sikora K, Verstappen E, Mendes O, Schoen C, Ristaino J, Bonants P. A universal microarray detection method for identification of multiple Phytophthora spp. using padlock probes. PHYTOPATHOLOGY 2012; 102:635-645. [PMID: 22568817 DOI: 10.1094/phyto-11-11-0309] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
The genus Phytophthora consists of many species that cause important diseases in ornamental, agronomic, and forest ecosystems worldwide. Molecular methods have been developed for detection and identification of one or several species of Phytophthora in single or multiplex reactions. In this article, we describe a padlock probe (PLP)-based multiplex method of detection and identification for many Phytophthora spp. simultaneously. A generic TaqMan polymerase chain reaction assay, which detects all known Phytophthora spp., is conducted first, followed by a species-specific PLP ligation. A 96-well-based microarray platform with colorimetric readout is used to detect and identify the different Phytophthora spp. PLPs are long oligonucleotides containing target complementary sequence regions at both their 5' and 3' ends which can be ligated on the target into a circular molecule. The ligation is point mutation specific; therefore, closely related sequences can be differentiated. This circular molecule can then be detected on a microarray. We developed 23 PLPs to economically important Phytophthora spp. based upon internal transcribed spacer-1 sequence differences between individual Phytophthora spp. Tests on genomic DNA of many Phytophthora isolates and DNA from environmental samples showed the specificity and utility of PLPs for Phytophthora diagnostics.
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Affiliation(s)
- Katarzyna Sikora
- Forest Research Insitute, Department of Forest Protection, Sękocin Stary, Braci Leśnej 3, 05-090 Raszyn, Poland
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23
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Slinger R, Moldovan I, Barrowman N, Chan F. Successful nanolitre real-time PCR detection of respiratory pathogens in clinical specimens. Clin Microbiol Infect 2012; 18:E286-8. [PMID: 22630162 DOI: 10.1111/j.1469-0691.2012.03896.x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
We performed a proof-of-concept study to determine if human pathogens could be detected in clinical specimens using nanolitre-volume real-time PCR. Nanolitre PCR for Bordetella pertussis/B. parapertussis and respiratory syncytial virus (RSV) was performed on nasopharyngeal specimens and results compared with conventional methods. B. pertussis/B. parapertussis nanolitre PCR detection was 100% sensitive (20/20; 95% CI, 84-100%) and 100% specific (26/26; 95% CI, 87-100%). RSV nanolitre PCR was also 100% sensitive (21/21; 95% CI, 85-100%) and specific (25/25; 95%, CI 87-100%). Respiratory pathogens can be successfully detected in clinical specimens using nanolitre-volume PCR.
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Affiliation(s)
- R Slinger
- Children's Hospital of Eastern Ontario, Ottawa, ON, Canada.
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24
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Tsui CK, Woodhall J, Chen W, Lévesque CA, Lau A, Schoen CD, Baschien C, Najafzadeh MJ, de Hoog GS. Molecular techniques for pathogen identification and fungus detection in the environment. IMA Fungus 2011; 2:177-89. [PMID: 22679603 PMCID: PMC3359816 DOI: 10.5598/imafungus.2011.02.02.09] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2011] [Accepted: 11/03/2011] [Indexed: 12/25/2022] Open
Abstract
Many species of fungi can cause disease in plants, animals and humans. Accurate and robust detection and quantification of fungi is essential for diagnosis, modeling and surveillance. Also direct detection of fungi enables a deeper understanding of natural microbial communities, particularly as a great many fungi are difficult or impossible to cultivate. In the last decade, effective amplification platforms, probe development and various quantitative PCR technologies have revolutionized research on fungal detection and identification. Examples of the latest technology in fungal detection and differentiation are discussed here.
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Affiliation(s)
- Clement K.M. Tsui
- Department of Forest Sciences, The University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
| | - James Woodhall
- The Food and Environment Research Agency, Sand Hutton, York YO41 1LZ, UK
| | - Wen Chen
- Central Experimental Farm, Agriculture and Agri-Food Canada, Ottawa, Canada, K1A OC6
| | - C. André Lévesque
- Central Experimental Farm, Agriculture and Agri-Food Canada, Ottawa, Canada, K1A OC6
| | - Anna Lau
- Centre for Infectious Diseases and Microbiology and the University of Sydney, Westmead Hospital, Westmead, NSW 2145, Australia
- *Current mailing address: Department of Laboratory Medicine, 10 Center Drive, National Institutes of Health, Bethesda, MD 20892, USA
| | - Cor D. Schoen
- Plant Research International, Business Unit Bio-Interactions and Plant Health, PO Box 16, 6700 AA, Wageningen, The Netherlands
| | - Christiane Baschien
- Technische Universität Berlin, Environmental Microbiology, Sekr. FR1-2, Franklinstrasse 29, 10587 Berlin, Germany
- **Current mailing address: Federal Environment Agency Germany, Corrensplatz 1, 14195 Berlin, Germany
| | - Mohammad J. Najafzadeh
- CBS-KNAW Fungal Biodiversity Centre, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
- Department of Parasitology and Mycology, School of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - G. Sybren de Hoog
- CBS-KNAW Fungal Biodiversity Centre, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
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25
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Perspectives for nano-biotechnology enabled protection and nutrition of plants. Biotechnol Adv 2011; 29:792-803. [DOI: 10.1016/j.biotechadv.2011.06.007] [Citation(s) in RCA: 628] [Impact Index Per Article: 48.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2011] [Revised: 05/17/2011] [Accepted: 06/11/2011] [Indexed: 11/20/2022]
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26
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Peleg O, Baneth G, Eyal O, Inbar J, Harrus S. Multiplex real-time qPCR for the detection of Ehrlichia canis and Babesia canis vogeli. Vet Parasitol 2010; 173:292-9. [DOI: 10.1016/j.vetpar.2010.06.039] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2010] [Revised: 05/27/2010] [Accepted: 06/30/2010] [Indexed: 11/26/2022]
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27
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Tsui CKM, Wang B, Khadempour L, Alamouti SM, Bohlmann J, Murray BW, Hamelin RC. Rapid identification and detection of pine pathogenic fungi associated with mountain pine beetles by padlock probes. J Microbiol Methods 2010; 83:26-33. [PMID: 20650291 DOI: 10.1016/j.mimet.2010.07.016] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2010] [Revised: 07/10/2010] [Accepted: 07/10/2010] [Indexed: 11/16/2022]
Abstract
Fifteen million hectares of pine forests in western Canada have been attacked by the mountain pine beetle (Dendroctonus ponderosae; MPB), leading to devastating economic losses. Grosmannia clavigera and Leptographium longiclavatum, are two fungi intimately associated with the beetles, and are crucial components of the epidemic. To detect and discriminate these two closely related pathogens, we utilized a method based on ligase-mediated nucleotide discrimination with padlock probe technology, and signal amplification by hyperbranched rolling circle amplification (HRCA). Two padlock probes were designed to target species-specific single nucleotide polymorphisms (SNPs) located at the inter-generic spacer 2 region and large subunit of the rRNA respectively, which allows discrimination between the two species. Thirty-four strains of G. clavigera and twenty-five strains of L. longiclavatum representing a broad geographic origin were tested with this assay. The HRCA results were largely in agreement with the conventional identification based on morphology or DNA-based methods. Both probes can also efficiently distinguish the two MPB-associated fungi from other fungi in the MPB, as well as other related fungi in the order Ophiostomatales. We also tested this diagnostic method for the direct detection of these fungi from the DNA of MPB. A nested PCR approach was used to enrich amplicons for signal detection. The results confirmed the presence of these two fungi in MPB. Thus, the padlock probe assay coupled with HRCA is a rapid, sensitive and reproducible method for the identification and detection of these ophiostomatoid fungi.
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Affiliation(s)
- Clement K M Tsui
- Department of Forest Science, University of British Columbia, Vancouver, BC, Canada.
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28
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Zhang C, Xing D. Single-Molecule DNA Amplification and Analysis Using Microfluidics. Chem Rev 2010; 110:4910-47. [DOI: 10.1021/cr900081z] [Citation(s) in RCA: 115] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Chunsun Zhang
- MOE Key Laboratory of Laser Life Science & Institute of Laser Life Science, College of Biophotonics, South China Normal University, Guangzhou 510631, China
| | - Da Xing
- MOE Key Laboratory of Laser Life Science & Institute of Laser Life Science, College of Biophotonics, South China Normal University, Guangzhou 510631, China
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29
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Lee SH, Lee HJ, Kim SJ, Lee HM, Kang H, Kim YP. Identification of airborne bacterial and fungal community structures in an urban area by T-RFLP analysis and quantitative real-time PCR. THE SCIENCE OF THE TOTAL ENVIRONMENT 2010; 408:1349-1357. [PMID: 19913878 DOI: 10.1016/j.scitotenv.2009.10.061] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/30/2008] [Revised: 08/06/2009] [Accepted: 10/23/2009] [Indexed: 05/28/2023]
Abstract
This study explores the characteristics of bacterial and fungal communities of total suspended particles (TSP) in the atmosphere by using various molecular methods. TSP samples were collected on a glass fiber filter at an urban location in the middle of the Korean Peninsula (Seoul) between middle autumn and early winter in 2007. From the aerosol samples, DNA could be extracted and DNA sequences were determined for bacteria and fungi. Terminal restriction length polymorphism (T-RFLP) analysis was applied to analyze the community structure of them. To estimate the concentration of DNA originating from bacterial and fungal communities, we used the quantitative real-time polymerase chain reaction (Q-PCR). Sequence analyses were also used to determine the identity of biological organisms. The number of bacteria and fungi in the air were between 5.19x10(1) and 4.31x10(3) cellsm(-3) and from 9.56x10(1) to 4.22x10(4) cellsm(-3), respectively and bacterium/fungus ratios ranged from 0.09 to 0.76 across the seven sampling dates. Most of the bacterial sequences found in our TSP samples were from Proteobacteria, Actinobacteria, Firmicutes, and Bacteroidetes. The fungal sequences were characteristic for Ascomycota, Basidiomycota, and Glomeromycota which are known to actively discharge spores into the atmosphere. The plant sequences could be also detected. We found that large shifts in the community structure of bacteria and fungi were present in our TSP samples collected on different dates. The results demonstrated that in our TSP samples collected at the urban site; (1) there were very diverse bacterial and fungal groups including potential pathogens and allergens and (2) there were temporal shifts in both bacterial and fungal communities in terms of both diversity and abundances across an inter-seasonal period.
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Affiliation(s)
- Seung-Hoon Lee
- School of Civil and Environmental Engineering, Yonsei University, Seoul, Republic of Korea
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30
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Wu W, Tang YW. Emerging molecular assays for detection and characterization of respiratory viruses. Clin Lab Med 2010; 29:673-93. [PMID: 19892228 PMCID: PMC7130760 DOI: 10.1016/j.cll.2009.07.005] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022]
Abstract
This article describes several emerging molecular assays that have potential applications in the diagnosis and monitoring of respiratory viral infections. These techniques include direct nucleic acid detection by quantum dots, loop-mediated isothermal amplification, multiplex ligation-dependent probe amplification, amplification using arbitrary primers, target-enriched multiplexing amplification, pyrosequencing, padlock probes, solid and suspension microarrays, and mass spectrometry. Several of these systems already are commercially available to provide multiplex amplification and high-throughput detection and identification of a panel of respiratory viral pathogens. Further validation and implementation of such emerging molecular assays in routine clinical virology services will enhance the rapid diagnosis of respiratory viral infections and improve patient care.
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Affiliation(s)
- Wenjuan Wu
- Department of Pathology, Vanderbilt University Medical Center, Nashville, TN, USA
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31
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Hopp K, Weber K, Bellissimo D, Johnson ST, Pietz B. High-throughput red blood cell antigen genotyping using a nanofluidic real-time polymerase chain reaction platform. Transfusion 2010; 50:40-6. [PMID: 19761548 DOI: 10.1111/j.1537-2995.2009.02377.x] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
BACKGROUND Serologic testing of donors to obtain antigen-negative blood for transfusion is limited by availability and quality of reagents. Where sequence variant information is available, molecular typing platforms can be used to determine the presence of a variant allele and offer a high-throughput format correlated to the blood group antigen. We have investigated a flexible high-throughput platform to screen blood donors for antigen genotypes in the African American population. STUDY DESIGN AND METHODS Genomic DNA from 427 African American donors was analyzed for single-nucleotide polymorphisms responsible for red blood cell (RBC) antigens E/e, Fy(a)/Fy(b), Fy gene promoter, Jk(a)/Jk(b), Lu(a)/Lu(b), K/k, Js(a)/Js(b), Do(a)/Do(b), Jo(a), and Hy using primer/probe sets (Taqman, Applied Biosystems) on a high-throughput genotyping platform (OpenArray, BioTrove). Where available, the phenotype obtained by serologic testing was compared to genotype data. RESULTS Serologic antigen types were available for 2037 of the 4270 genotypes generated. There were five discordant results. Three resolved with repeat serologic typing, one resolved after repeat genotyping, and one discordance was clarified by confirmation of the BioTrove genotype by Sanger sequencing. Triplicate determinations were made for each sample genotype and the results were identical more than 99% of the time. CONCLUSIONS The nanofluidic genotyping platform described here provides an accurate method for predicting blood group phenotypes. The user-specified array layout provides flexibility of target selection and number of replicate determinations and is suitable for screening antigen types.
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Affiliation(s)
- Kathleen Hopp
- Diagnostic Laboratories, BloodCenter of Wisconsin, Milwaukee, Wisconsin 53233, USA
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32
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Accurate quantification of microorganisms in PCR-inhibiting environmental DNA extracts by a novel internal amplification control approach using Biotrove OpenArrays. Appl Environ Microbiol 2009; 75:7253-60. [PMID: 19801486 DOI: 10.1128/aem.00796-09] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
PCR-based detection assays are prone to inhibition by substances present in environmental samples, thereby potentially leading to inaccurate target quantification or false-negative results. Internal amplification controls (IACs) have been developed to help alleviate this problem but are generally applied in a single concentration, thereby yielding less-than-optimal results across the wide range of microbial gene target concentrations possible in environmental samples (J. Hoorfar, B. Malorny, A. Abdulmawjood, N. Cook, M. Wagner, and P. Fach, J. Clin. Microbiol. 42:1863-1868, 2004). Increasing the number of IACs for each quantitative PCR (qPCR) sample individually, however, typically reduces sensitivity and, more importantly, the reliability of quantification. Fortunately, current advances in high-throughput qPCR platforms offer the possibility of multiple reactions for a single sample simultaneously, thereby allowing the implementation of more than one IAC concentration per sample. Here, we describe the development of a novel IAC approach that is specifically designed for the state-of-the-art Biotrove OpenArray platform. Different IAC targets were applied at a range of concentrations, yielding a calibration IAC curve for each individual DNA sample. The developed IACs were optimized, tested, and validated by using more than 5,000 unique qPCR amplifications, allowing accurate quantification of microorganisms when applied to soil DNA extracts containing various levels of PCR-inhibiting compounds. To our knowledge, this is the first study using a suite of IACs at different target concentrations to monitor PCR inhibition across a wide target range, thereby allowing reliable and accurate quantification of microorganisms in PCR-inhibiting DNA extracts. The developed IAC is ideally suited for high-throughput screenings of, for example, ecological and agricultural samples on next-generation qPCR platforms.
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Eriksson R, Jobs M, Ekstrand C, Ullberg M, Herrmann B, Landegren U, Nilsson M, Blomberg J. Multiplex and quantifiable detection of nucleic acid from pathogenic fungi using padlock probes, generic real time PCR and specific suspension array readout. J Microbiol Methods 2009; 78:195-202. [DOI: 10.1016/j.mimet.2009.05.016] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2008] [Revised: 05/21/2009] [Accepted: 05/22/2009] [Indexed: 10/20/2022]
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Robust detection and identification of multiple oomycetes and fungi in environmental samples by using a novel cleavable padlock probe-based ligation detection assay. Appl Environ Microbiol 2009; 75:4185-93. [PMID: 19395562 DOI: 10.1128/aem.00071-09] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Simultaneous detection and identification of multiple pathogenic microorganisms in complex environmental samples are required in numerous diagnostic fields. Here, we describe the development of a novel, background-free ligation detection (LD) system using a single compound detector probe per target. The detector probes used, referred to as padlock probes (PLPs), are long oligonucleotides containing asymmetric target complementary regions at both their 5' and 3' ends which confer extremely specific target detection. Probes also incorporate a desthiobiotin moiety and an internal endonuclease IV cleavage site. DNA samples are PCR amplified, and the resulting products serve as potential targets for PLP ligation. Upon perfect target hybridization, the PLPs are circularized via enzymatic ligation, captured, and cleaved, allowing only the originally ligated PLPs to be visualized on a universal microarray. Unlike previous procedures, the probes themselves are not amplified, thereby allowing a simple PLP cleavage to yield a background-free assay. We designed and tested nine PLPs targeting several oomycetes and fungi. All of the probes specifically detected their corresponding targets and provided perfect discrimination against closely related nontarget organisms, yielding an assay sensitivity of 1 pg genomic DNA and a dynamic detection range of 10(4). A practical demonstration with samples collected from horticultural water circulation systems was performed to test the robustness of the newly developed multiplex assay. This novel LD system enables highly specific detection and identification of multiple pathogens over a wide range of target concentrations and should be easily adaptable to a variety of applications in environmental microbiology.
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Prins TW, van Dijk JP, Beenen HG, Van Hoef AMA, Voorhuijzen MM, Schoen CD, Aarts HJM, Kok EJ. Optimised padlock probe ligation and microarray detection of multiple (non-authorised) GMOs in a single reaction. BMC Genomics 2008; 9:584. [PMID: 19055784 PMCID: PMC2631584 DOI: 10.1186/1471-2164-9-584] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2008] [Accepted: 12/04/2008] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND To maintain EU GMO regulations, producers of new GM crop varieties need to supply an event-specific method for the new variety. As a result methods are nowadays available for EU-authorised genetically modified organisms (GMOs), but only to a limited extent for EU-non-authorised GMOs (NAGs). In the last decade the diversity of genetically modified (GM) ingredients in food and feed has increased significantly. As a result of this increase GMO laboratories currently need to apply many different methods to establish to potential presence of NAGs in raw materials and complex derived products. RESULTS In this paper we present an innovative method for detecting (approved) GMOs as well as the potential presence of NAGs in complex DNA samples containing different crop species. An optimised protocol has been developed for padlock probe ligation in combination with microarray detection (PPLMD) that can easily be scaled up. Linear padlock probes targeted against GMO-events, -elements and -species have been developed that can hybridise to their genomic target DNA and are visualised using microarray hybridisation.In a tenplex PPLMD experiment, different genomic targets in Roundup-Ready soya, MON1445 cotton and Bt176 maize were detected down to at least 1%. In single experiments, the targets were detected down to 0.1%, i.e. comparable to standard qPCR. CONCLUSION Compared to currently available methods this is a significant step forward towards multiplex detection in complex raw materials and derived products. It is shown that the PPLMD approach is suitable for large-scale detection of GMOs in real-life samples and provides the possibility to detect and/or identify NAGs that would otherwise remain undetected.
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Affiliation(s)
- Theo W Prins
- RIKILT – Institute of Food Safety (WUR), Bornsesteeg 45, 6708 PD Wageningen, the Netherlands
| | - Jeroen P van Dijk
- RIKILT – Institute of Food Safety (WUR), Bornsesteeg 45, 6708 PD Wageningen, the Netherlands
| | - Henriek G Beenen
- RIKILT – Institute of Food Safety (WUR), Bornsesteeg 45, 6708 PD Wageningen, the Netherlands
| | - AM Angeline Van Hoef
- RIKILT – Institute of Food Safety (WUR), Bornsesteeg 45, 6708 PD Wageningen, the Netherlands
| | - Marleen M Voorhuijzen
- RIKILT – Institute of Food Safety (WUR), Bornsesteeg 45, 6708 PD Wageningen, the Netherlands
| | - Cor D Schoen
- Plant Research International BV (WUR), Droevendaalsesteeg 1, 6708 PB Wageningen, the Netherlands
| | - Henk JM Aarts
- RIKILT – Institute of Food Safety (WUR), Bornsesteeg 45, 6708 PD Wageningen, the Netherlands
| | - Esther J Kok
- RIKILT – Institute of Food Safety (WUR), Bornsesteeg 45, 6708 PD Wageningen, the Netherlands
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Madico GE, Rice PA. 16S-ribosomal DNA to diagnose culture-negative endocarditis. Curr Infect Dis Rep 2008; 10:280-6. [DOI: 10.1007/s11908-008-0046-3] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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Development and experimental validation of a predictive threshold cycle equation for quantification of virulence and marker genes by high-throughput nanoliter-volume PCR on the OpenArray platform. Appl Environ Microbiol 2008; 74:3831-8. [PMID: 18424532 DOI: 10.1128/aem.02743-07] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Development of quantitative PCR (QPCR) assays typically requires extensive screening within and across a given species to ensure specific detection and lucid identification among various pathogenic and nonpathogenic strains and to generate standard curves. To minimize screening requirements, multiple virulence and marker genes (VMGs) were targeted simultaneously to enhance reliability, and a predictive threshold cycle (C(T)) equation was developed to calculate the number of starting copies based on an experimental C(T). The empirical equation was developed with Sybr green detection in nanoliter-volume QPCR chambers (OpenArray) and tested with 220 previously unvalidated primer pairs targeting 200 VMGs from 30 pathogens. A high correlation (R(2) = 0.816) was observed between the predicted and experimental C(T)s based on the organism's genome size, guanine and cytosine (GC) content, amplicon length, and stability of the primer's 3' end. The performance of the predictive C(T) equation was tested using 36 validation samples consisting of pathogenic organisms spiked into genomic DNA extracted from three environmental waters. In addition, the primer success rate was dependent on the GC content of the target organisms and primer sequences. Targeting multiple assays per organism and using the predictive C(T) equation are expected to reduce the extent of the validation necessary when developing QPCR arrays for a large number of pathogens or other targets.
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