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Smith BL, Lu CP, Cornic M, Alvarado Bremer JR. High-throughput identification of tuna (Thunnus spp.) larvae in the Gulf of Mexico using unlabelled-probe high-resolution melting analysis. JOURNAL OF FISH BIOLOGY 2023; 102:1425-1433. [PMID: 36999397 DOI: 10.1111/jfb.15391] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Accepted: 03/30/2023] [Indexed: 06/09/2023]
Abstract
The genus Thunnus (family Scombridae) comprises eight species of tunas of which all but one are targeted by industrialized fisheries. Although intact individuals of these species can be distinguished by morphological characteristics, researchers and managers often rely on dressed, frozen, juvenile or larval fish samples, which often necessitates the identification of molecular species. Here the authors investigate short amplicon (SA) and unlabelled probe high-resolution melting analysis (UP-HRMA) as a low-cost, high-throughput molecular genotyping assay capable of distinguishing between albacore tuna (Thunnus alalunga), blackfin tuna (Thunnus atlanticus), bigeye tuna (Thunnus obesus), Atlantic bluefin tuna (Thunnus thynnus) and yellowfin tuna (Thunnus albacares) in the Gulf of Mexico. Although SA-HRMA of variable regions in the NADH dehydrogenase subunit 4 (ND4) and subunit 5 (ND5), and subunit 6 (ND6) of the mtDNA genome did yield some species-specific diagnostic melting curves (e.g., ND4 assay can reliably distinguish Atlantic bluefin tuna), genotype masking produced excessive variation in melting curves for reliable multi-species identification. To minimize the genotyping masking of SA-HRMA a 26 base pair long UP containing four SNPs was developed within a 133 bp segment of ND4. The UP-HRMA is able to reliably distinguish Gulf of Mexico species T. thynnus, T. obesus, T. albacares and T. atlanticus by UP melting temperature at 67, 62, 59 and 57°C, respectively. The developed UP-HRMA assay is a lower-cost, higher-throughput, alternative to previously published molecular assays for tuna identification that can be easily automated for large data sets, including ichthyological larval surveys, fisheries specimens lacking distinguishing morphological characteristics or detection of fraudulent trading of tuna species.
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Affiliation(s)
- Brad L Smith
- Faculty of Science, Brigham Young University, Laie, Hawaii, USA
| | | | - Maëlle Cornic
- Department of Oceanography and Coastal Sciences, Louisiana State University, Baton Rouge, Louisiana, USA
| | - Jaime R Alvarado Bremer
- Department of Marine Biology, Texas A&M University at Galveston, Galveston, Texas, USA
- Department of Ecology and Conservation Biology, Texas A&M University, College Station, Texas, USA
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Olmedo-Velarde A, Ochoa-Corona FM, Larrea-Sarmiento AE, Elbeaino T, Flores F. In-silico prediction of RT-qPCR-high resolution melting for broad detection of emaraviruses. PLoS One 2023; 18:e0272980. [PMID: 37155676 PMCID: PMC10166557 DOI: 10.1371/journal.pone.0272980] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Accepted: 07/30/2022] [Indexed: 05/10/2023] Open
Abstract
Twenty-four species of RNA viruses contain members infecting economically important crops that are classified within the genus Emaravirus, family Fimoviridae. There are at least two other non-classified species that may be added. Some of these viruses are spreading rapidly and cause economically important diseases on several crops, raising a need for a sensitive diagnostic technique for taxonomic and quarantine purposes. High-resolution melting (HRM) has shown to be reliable for the detection, discrimination, and diagnosis of several diseases of plants, animals, and humans. This research aimed to explore the ability to predict HRM outputs coupled to reverse transcription-quantitative polymerase chain reaction (RT-qPCR). To approach this goal a pair of degenerate genus-specific primers were designed for endpoint RT-PCR and RT-qPCR-HRM and the species in the genus Emaravirus were selected to framework the development of the assays. Both nucleic acid amplification methods were able to detect in-vitro several members of seven Emaravirus species with sensitivity up to one fg of cDNA. Specific parameters for in-silico prediction of the melting temperatures of each expected emaravirus amplicon are compared to the data obtained in-vitro. A very distinct isolate of the High Plains wheat mosaic virus was also detected. The high-resolution DNA melting curves of the RT-PCR products predicted in-silico using uMeltSM allowed saving time while designing and developing the RT-qPCR-HRM assay since the approach avoided extensive searching for optimal HRM assay regions and rounds of HRM tests in-vitro for optimization. The resultant assay provides sensitive detection and reliable diagnosis for potentially any emaravirus, including new species or strains.
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Affiliation(s)
- Alejandro Olmedo-Velarde
- Institute for Biosecurity and Microbial Forensics, Oklahoma State University, Stillwater, OK, United States of America
- Department of Entomology and Plant Pathology, Oklahoma State University, Stillwater, OK, United States of America
- Departamento de Ciencias de la Vida y de la Agricultura, Universidad de las Fuerzas Armadas ESPE, Sangolqui, Ecuador
| | - Francisco M Ochoa-Corona
- Institute for Biosecurity and Microbial Forensics, Oklahoma State University, Stillwater, OK, United States of America
- Department of Entomology and Plant Pathology, Oklahoma State University, Stillwater, OK, United States of America
| | - Adriana E Larrea-Sarmiento
- Institute for Biosecurity and Microbial Forensics, Oklahoma State University, Stillwater, OK, United States of America
- Department of Entomology and Plant Pathology, Oklahoma State University, Stillwater, OK, United States of America
| | - Toufic Elbeaino
- Istituto Agronomico Mediterraneo di Bari, Valenzano, BA, Italy
| | - Francisco Flores
- Departamento de Ciencias de la Vida y de la Agricultura, Universidad de las Fuerzas Armadas ESPE, Sangolqui, Ecuador
- Centro de Investigación de Alimentos, CIAL, Facultad de Ciencias de la Ingeniería e Industrias, Universidad UTE, Quito, Ecuador
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Paula DP, Barros SKA, Pitta RM, Barreto MR, Togawa RC, Andow DA. Metabarcoding versus mapping unassembled shotgun reads for identification of prey consumed by arthropod epigeal predators. Gigascience 2022; 11:6554098. [PMID: 35333301 PMCID: PMC8952265 DOI: 10.1093/gigascience/giac020] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2021] [Revised: 12/07/2021] [Accepted: 02/09/2022] [Indexed: 12/19/2022] Open
Abstract
Background A central challenge of DNA gut content analysis is to identify prey in a highly degraded DNA community. In this study, we evaluated prey detection using metabarcoding and a method of mapping unassembled shotgun reads (Lazaro). Results In a mock prey community, metabarcoding did not detect any prey, probably owing to primer choice and/or preferential predator DNA amplification, while Lazaro detected prey with accuracy 43–71%. Gut content analysis of field-collected arthropod epigeal predators (3 ants, 1 dermapteran, and 1 carabid) from agricultural habitats in Brazil (27 samples, 46–273 individuals per sample) revealed that 64% of the prey species detections by either method were not confirmed by melting curve analysis and 87% of the true prey were detected in common. We hypothesized that Lazaro would detect fewer true- and false-positive and more false-negative prey with greater taxonomic resolution than metabarcoding but found that the methods were similar in sensitivity, specificity, false discovery rate, false omission rate, and accuracy. There was a positive correlation between the relative prey DNA concentration in the samples and the number of prey reads detected by Lazaro, while this was inconsistent for metabarcoding. Conclusions Metabarcoding and Lazaro had similar, but partially complementary, detection of prey in arthropod predator guts. However, while Lazaro was almost 2× more expensive, the number of reads was related to the amount of prey DNA, suggesting that Lazaro may provide quantitative prey information while metabarcoding did not.
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Affiliation(s)
- Débora Pires Paula
- Embrapa Genetic Resources and Biotechnology, Brasília-DF, 70770-917, Brazil
| | | | | | | | | | - David A Andow
- Department of Entomology, University of Minnesota, MN, 55108, St. Paul, USA
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Olmedo-Velarde A, Ochoa-Corona FM, Larrea-Sarmiento AE, Elbeaino T, Flores F. Exploring in-silico prediction for the development of a RT-qPCR-high resolution melting assay for the broad detection of emaraviruses. J Virol Methods 2021:114425. [PMID: 34902460 DOI: 10.1016/j.jviromet.2021.114425] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2020] [Revised: 03/09/2021] [Accepted: 12/09/2021] [Indexed: 01/13/2023]
Abstract
High-resolution melting (HRM) has shown to be reliable for the detection, discrimination, and diagnosis of several diseases of plants, animals, and humans. The aim of this research was to explore the ability to predict HRM outputs when coupled to reverse transcription quantitative polymerase chain reaction (RT-qPCR). This research used the species in the Emaravirus genus as model to framework the development of genus-specific RT-qPCR-HRM assays. A pair of degenerate genus-specific primers were designed for use in endpoint RT-PCR and RT-qPCR-HRM detection of emaraviruses. Eleven species of RNA viruses infecting economically important crops are classified within the genus Emaravirus, family Fimoviridae. There are at least fifteen other non-classified species that may be added. Some of these viruses are spreading rapidly and cause economically important diseases on several crops, raising a need for a sensitive diagnostic technique for taxonomic and quarantine purposes. RT-PCR and RT-qPCR-HRM were able to detect seven emaravirus species in-vitro with sensitivity up to one fg of cDNA. Specific parameters for prediction in-silico of the melting temperatures of each expected emaravirus amplicon are provided and compared to the data obtained in-vitro. A very distinct isolate of the High Plains wheat mosaic virus was also detected. The prediction in-silico of fluorescence of high-resolution DNA melting curves of predicted RT-PCR products using uMeltSM speeded the design and development of RT-qPCR-HRM assay. This approach avoided rounds of HRM tests in-vitro when searching for the optimal regions that provides accurate diagnosis. The resultant assay provided sensitive detection and reliable diagnosis for potentially any emaravirus, including new species or strains.
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Affiliation(s)
- Alejandro Olmedo-Velarde
- Oklahoma State University, Institute for Biosecurity and Microbial Forensics, Stillwater, OK, USA; Oklahoma State University, Department of Entomology and Plant Pathology, Stillwater, OK, USA; Universidad de las Fuerzas Armadas ESPE, Departamento de Ciencias de la Vida y de la Agricultura, Sangolqui, Ecuador
| | - Francisco M Ochoa-Corona
- Oklahoma State University, Institute for Biosecurity and Microbial Forensics, Stillwater, OK, USA; Oklahoma State University, Department of Entomology and Plant Pathology, Stillwater, OK, USA.
| | - Adriana E Larrea-Sarmiento
- Oklahoma State University, Institute for Biosecurity and Microbial Forensics, Stillwater, OK, USA; Oklahoma State University, Department of Entomology and Plant Pathology, Stillwater, OK, USA
| | - Toufic Elbeaino
- Istituto Agronomico Mediterraneo di Bari, Valenzano, BA, Italy
| | - Francisco Flores
- Universidad de las Fuerzas Armadas ESPE, Departamento de Ciencias de la Vida y de la Agricultura, Sangolqui, Ecuador; Universidad UTE, Centro de Investigación de Alimentos, CIAL, Facultad de Ciencias de la Ingeniería e Industrias, Quito, Ecuador
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del Rio-Lavín A, Jiménez E, Pardo MÁ. SYBR-Green real-time PCR assay with melting curve analysis for the rapid identification of Mytilus species in food samples. Food Control 2021. [DOI: 10.1016/j.foodcont.2021.108257] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
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Development of DNA Melt Curve Analysis for the Identification of Lepidopteran Pests in Almonds and Pistachios. INSECTS 2021; 12:insects12060553. [PMID: 34203602 PMCID: PMC8232234 DOI: 10.3390/insects12060553] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Revised: 06/04/2021] [Accepted: 06/09/2021] [Indexed: 11/17/2022]
Abstract
Simple Summary Almonds and pistachios are fed upon by a diverse assemblage of lepidopteran insects, several of which are economically important pests. Unfortunately, identification of these pests can be difficult, as specimens are frequently damaged during collection, occur in traps with non-target species, and are morphologically similar up to their third instar. Here, we present a quantitative PCR based melt curve analysis for simple, rapid, and accurate identification of six lepidopteran pests of almonds and pistachios: navel orangeworm, peach twig borer, oriental fruit moth, obliquebanded leafroller, raisin moth, and Indian meal moth. We demonstrate that the dissociation or the “melt” temperature(s) of a 658 bp section of cytochrome c oxidase subunit 1 provides unambiguous species level identification of these six species and is reproducible in field specimens collected following conventional orchard practices. The melt curve’s simplicity allows it to be performed in any basic molecular biology laboratory with a quantitative PCR. Abstract Almonds and pistachios are fed upon by a diverse assemblage of lepidopteran insects, several of which are economically important pests. Unfortunately, identification of these pests can be difficult, as specimens are frequently damaged during collection, occur in traps with non-target species, and are morphologically similar up to their third instar. Here, we present a quantitative PCR based melt curve analysis for simple, rapid, and accurate identification of six lepidopteran pests of almonds and pistachios: navel orangeworm (Amyelois transitella), peach twig borer (Anarsia lineatella), oriental fruit moth (Grapholita molesta), obliquebanded leafroller (Choristoneura rosaceana), raisin moth (Cadra figulilella), and Indian meal moth (Plodia interpunctella). In this approach, the dissociation (melt) temperature(s) of a 658 bp section of cytochrome c oxidase subunit 1 was determined using quantitative PCR (qPCR). Within these six species, the distribution and the number of melt peak temperatures provide an unambiguous species level identification that is reproducible when unsheared DNA can be extracted. The test is robust across a variety of sampling approaches including insects removed from sticky card traps, museum specimens, and samples that were left in the field for up to 7 days. The melt curve’s simplicity allows it to be performed in any basic molecular biology laboratory with a quantitative PCR.
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Assessing the Use of Molecular Barcoding and qPCR for Investigating the Ecology of Prorocentrum minimum (Dinophyceae), a Harmful Algal Species. Microorganisms 2021; 9:microorganisms9030510. [PMID: 33670984 PMCID: PMC7997176 DOI: 10.3390/microorganisms9030510] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Revised: 02/12/2021] [Accepted: 02/19/2021] [Indexed: 01/04/2023] Open
Abstract
Prorocentrum minimum is a species of marine dinoflagellate that occurs worldwide and can be responsible for harmful algal blooms (HABs). Some studies have reported it to produce tetrodotoxin; however, results have been inconsistent. qPCR and molecular barcoding (amplicon sequencing) using high-throughput sequencing have been increasingly applied to quantify HAB species for ecological analyses and monitoring. Here, we isolated a strain of P. minimum from eastern Australian waters, where it commonly occurs, and developed and validated a qPCR assay for this species based on a region of ITS rRNA in relation to abundance estimates from the cultured strain as determined using light microscopy. We used this tool to quantify and examine ecological drivers of P. minimum in Botany Bay, an estuary in southeast Australia, for over ~14 months in 2016–2017. We compared abundance estimates using qPCR with those obtained using molecular barcoding based on an 18S rRNA amplicon. There was a significant correlation between the abundance estimates from amplicon sequencing and qPCR, but the estimates from light microscopy were not significantly correlated, likely due to the counting method applied. Using amplicon sequencing, ~600 unique actual sequence variants (ASVs) were found, much larger than the known phytoplankton diversity from this region. P. minimum abundance in Botany Bay was found to be significantly associated with lower salinities and higher dissolved CO2 levels.
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Teltscher F, Bouvaine S, Gibson G, Dyer P, Guest J, Young S, Hopkins RJ. Understanding mosquito host-choice behaviour: a new and low-cost method of identifying the sex of human hosts from mosquito blood meals. Parasit Vectors 2021; 14:75. [PMID: 33482889 PMCID: PMC7825230 DOI: 10.1186/s13071-021-04577-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Accepted: 01/01/2021] [Indexed: 12/03/2022] Open
Abstract
Background Mosquito-borne diseases are a global health problem, causing hundreds of thousands of deaths per year. Pathogens are transmitted by mosquitoes feeding on the blood of an infected host and then feeding on a new host. Monitoring mosquito host-choice behaviour can help in many aspects of vector-borne disease control. Currently, it is possible to determine the host species and an individual human host from the blood meal of a mosquito by using genotyping to match the blood profile of local inhabitants. Epidemiological models generally assume that mosquito biting behaviour is random; however, numerous studies have shown that certain characteristics, e.g. genetic makeup and skin microbiota, make some individuals more attractive to mosquitoes than others. Analysing blood meals and illuminating host-choice behaviour will help re-evaluate and optimise disease transmission models. Methods We describe a new blood meal assay that identifies the sex of the person that a mosquito has bitten. The amelogenin locus (AMEL), a sex marker located on both X and Y chromosomes, was amplified by polymerase chain reaction in DNA extracted from blood-fed Aedes aegypti and Anopheles coluzzii. Results AMEL could be successfully amplified up to 24 h after a blood meal in 100% of An. coluzzii and 96.6% of Ae. aegypti, revealing the sex of humans that were fed on by individual mosquitoes. Conclusions The method described here, developed using mosquitoes fed on volunteers, can be applied to field-caught mosquitoes to determine the host species and the biological sex of human hosts on which they have blood fed. Two important vector species were tested successfully in our laboratory experiments, demonstrating the potential of this technique to improve epidemiological models of vector-borne diseases. This viable and low-cost approach has the capacity to improve our understanding of vector-borne disease transmission, specifically gender differences in exposure and attractiveness to mosquitoes. The data gathered from field studies using our method can be used to shape new transmission models and aid in the implementation of more effective and targeted vector control strategies by enabling a better understanding of the drivers of vector-host interactions. ![]()
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Affiliation(s)
- Fiona Teltscher
- Natural Resources Institute, University of Greenwich, Central Avenue, Chatham Maritime, Kent, ME4 4TB, UK.
| | - Sophie Bouvaine
- Natural Resources Institute, University of Greenwich, Central Avenue, Chatham Maritime, Kent, ME4 4TB, UK
| | - Gabriella Gibson
- Natural Resources Institute, University of Greenwich, Central Avenue, Chatham Maritime, Kent, ME4 4TB, UK
| | - Paul Dyer
- Anglia Ruskin University, East Road, Cambridge, CB1 1PT, UK
| | - Jennifer Guest
- Home Office, Lunar House, 40 Wellesley Road, Croydon, CR9 2BY, UK
| | - Stephen Young
- Natural Resources Institute, University of Greenwich, Central Avenue, Chatham Maritime, Kent, ME4 4TB, UK
| | - Richard J Hopkins
- Natural Resources Institute, University of Greenwich, Central Avenue, Chatham Maritime, Kent, ME4 4TB, UK
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Sinha K, Sharma P, Som Chaudhury S, Das Mukhopadhyay C, Ruidas B. Species detection using probe technology. FOOD TOXICOLOGY AND FORENSICS 2021:313-346. [DOI: 10.1016/b978-0-12-822360-4.00012-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/19/2023]
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10
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Torres-Corral Y, Santos Y. Development of a real-time PCR assay for detection and quantification of Streptococcus iniae using the lactate permease gene. JOURNAL OF FISH DISEASES 2021; 44:53-61. [PMID: 32959452 DOI: 10.1111/jfd.13267] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/21/2020] [Revised: 08/21/2020] [Accepted: 08/24/2020] [Indexed: 06/11/2023]
Abstract
The aim of this study is the development and evaluation of a rapid and accurate quantitative PCR (qPCR)-based protocol for detection of zoonotic pathogen Streptococcus iniae in bacterial cultures and tissues of diseased fish. For this purpose, the lactate permease-encoding (lldY) gene was selected as a target for the design of S. iniae-specific primers based on comparative genomic analysis using 45 sequences retrieved from NCBI genome database. Specificity and applicability of these primers were tested using 115 bacterial strains and fish tissues infected with S. iniae. Sensitivity, reproducibility and efficiency of qPCR assay were also determined. The developed qPCR assay showed 100% specificity with pure bacterial cultures or DNA extracted from S. iniae or tissues of fish infected with the bacterium. The method has high sensitivity with a detection limit of 1.12 × 101 amplicon copies per assay (equivalent to 2 × 10-9 ng/µl) using bacterial DNA and of 1.44 × 101 gene copies in tissues of fish infected with S. iniae. In conclusion, this qPCR protocol provides an accurate and sensitive alternative for the identification of S. iniae and its detection on fish tissues that can be implemented as a routine tool in microbiological laboratories.
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Affiliation(s)
- Yolanda Torres-Corral
- Departamento de Microbiología y Parasitología, Instituto de Análisis Químico y Biológico (IAQBUS), Universidad de Santiago de Compostela, Santiago de Compostela, Spain
| | - Ysabel Santos
- Departamento de Microbiología y Parasitología, Instituto de Análisis Químico y Biológico (IAQBUS), Universidad de Santiago de Compostela, Santiago de Compostela, Spain
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Espinoza GJ, Alvarado Bremer JR. Genetic species identification of ecologically important planthoppers (Prokelisia spp.) of coastal Spartina saltmarshes using High Resolution Melting Analysis (HRMA). Sci Rep 2019; 9:20073. [PMID: 31882766 PMCID: PMC6934748 DOI: 10.1038/s41598-019-56518-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2018] [Accepted: 12/11/2019] [Indexed: 11/29/2022] Open
Abstract
Phloem-feeding planthoppers of the genus Prokelisia rank among the most abundant and ecologically important browsers of coastal saltmarsh grasses of eastern North America and the Caribbean. Along the Spartina marshes of the northern Gulf of Mexico, the sympatric species P. marginata and P. dolus are the most abundant, but are difficult to distinguish from each other based solely on morphology. This study seeks to design a molecular assay based on High Resolution Melting Analysis (HRMA) as a fast, cost-effective alternative to differentiate these species. A 450 base pairs (bp) segment of cytochrome c oxidase subunit I (COI) was amplified and sequenced for representative samples of both species, and a short amplicon (SA) HRMA was designed based on the presence of fixed nucleotide differences between species found along a 60 bp segment of COI. The unambiguous identification of individual specimens of P. marginata or P. dolus was possible due to easily discernable differences in the melting temperatures of the two species along this mini barcode. This assay may prove useful for future genetic studies involving these species by preventing the overestimation of genetic diversity via inclusion of conspecifics, and in ecological studies by improving data on the effects of individual species of Prokelisia.
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Affiliation(s)
- G Janelle Espinoza
- Texas A&M University at Galveston, Department of Marine Biology, 1001 Texas Clipper Road, Galveston, TX, 77554-2888, USA.
| | - Jaime R Alvarado Bremer
- Texas A&M University at Galveston, Department of Marine Biology, 1001 Texas Clipper Road, Galveston, TX, 77554-2888, USA.,Texas A&M University, Department of Wildlife and Fisheries Sciences, 210 Nagle Hall, Texas A&M University, College Station, TX, 77843-2258, USA
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Torres-Corral Y, Fernández-Álvarez C, Santos Y. High-throughput identification and quantification of Vagococcus salmoninarum by SYBR Green I-based real-time PCR combined with melting curve analysis. JOURNAL OF FISH DISEASES 2019; 42:1359-1368. [PMID: 31359457 DOI: 10.1111/jfd.13053] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/15/2019] [Revised: 06/14/2019] [Accepted: 06/17/2019] [Indexed: 06/10/2023]
Abstract
This work describes a primer pair and a high-throughput SYBR Green I-based real-time PCR protocol combined with melting curve analysis for identification and quantification of Vagococcus salmoninarum in bacterial cultures and infected fish tissues. The 16S rRNA gene was selected for the design of the primer pair (SalF and SalR). The sensitivity and specificity of this primer pair were compared with other previously designed for conventional PCR. Although both primer pairs showed 100% specificity using pure bacterial cultures or DNA extracted from bacteria or fish tissues, the primer pairs designed in this study showed the highest sensitivity with a detection limit of 0.034 × 100 amplicon copies per assay (equivalent to 2 × 10-11 ng/µl, Cq value of 30.49 ± 1.71). The developed qPCR protocol allowed the detection of V. salmoninarum in non-lethal and lethal fish samples with detection levels of 0.17 × 100 gene copies in tissues artificially infected and 0.02 × 100 in tissues of fish experimentally infected with V. salmoninarum. The high sensitivity of the developed method suggests that it could be considered as a useful tool for diagnosis of vagococcosis and the detection of V. salmoninarum in asymptomatic or carrier fish.
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Affiliation(s)
- Yolanda Torres-Corral
- Departamento de Microbiología y Parasitología, Instituto de Investigación y Análisis Alimentario, Universidad de Santiago de Compostela, Santiago de Compostela, Spain
| | - Clara Fernández-Álvarez
- Departamento de Microbiología y Parasitología, Instituto de Investigación y Análisis Alimentario, Universidad de Santiago de Compostela, Santiago de Compostela, Spain
| | - Ysabel Santos
- Departamento de Microbiología y Parasitología, Instituto de Investigación y Análisis Alimentario, Universidad de Santiago de Compostela, Santiago de Compostela, Spain
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Analysis of enhanced nitrogen removal mechanisms in a validation wastewater treatment plant containing anammox bacteria. Appl Microbiol Biotechnol 2018; 103:1255-1265. [PMID: 30539255 DOI: 10.1007/s00253-018-9495-2] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2018] [Revised: 09/27/2018] [Accepted: 10/31/2018] [Indexed: 01/26/2023]
Abstract
Anammox bacteria have attracted attention due to their apparent importance in saving energy and reducing organic chemical demands. Here, we report the detection and quantification of anammox bacteria with an improved primer set in a validation wastewater treatment plant. The improved primer set was shown to detect a broad range of anammox bacteria (47.3%) facilitating more accurate analyses of nitrogen removal mechanisms. Nitrogen removal efficiency and dominant nitrogen removal mechanisms were compared in the modification-Johannesburg (Mod-JHB), modified Ludzack-Ettinger (MLE) single-feed, and anoxic-oxic-anoxic-oxic (AOAO) step-feed modes. In the Mod-JHB configuration, simultaneous nitrification and denitrification (SND) and anammox were found to be responsible for more than 80% of total inorganic nitrogen (TIN) removal (98.5 ± 0.8% of TIN removal). Decrease of anoxic SRT from 5 to 2.5 days did not have any obvious effect on nitrogen removal or the abundance of functional microorganisms. Microbial batch tests demonstrated that both partial nitrification and dissimilatory nitrate reduction to ammonium (DNRA) were responsible for maintaining the anammox process. Short SRT (2 days) in the aerobic zone may explain the presence of partial nitrification. This study provides insights to the analysis of nitrogen removal mechanisms in validation wastewater treatment plants (WWTPs) aiming for high nitrogen removal efficiency.
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Nadai C, Bovo B, Giacomini A, Corich V. New rapid
PCR
protocol based on high‐resolution melting analysis to identify
Saccharomyces cerevisiae
and other species within its genus. J Appl Microbiol 2018; 124:1232-1242. [DOI: 10.1111/jam.13709] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2017] [Revised: 01/08/2018] [Accepted: 01/15/2018] [Indexed: 12/16/2022]
Affiliation(s)
- C. Nadai
- Department of Agronomy Food Natural resources Animals and Environment (DAFNAE) University of Padova Legnaro PD Italy
| | - B. Bovo
- Department of Agronomy Food Natural resources Animals and Environment (DAFNAE) University of Padova Legnaro PD Italy
| | - A. Giacomini
- Department of Agronomy Food Natural resources Animals and Environment (DAFNAE) University of Padova Legnaro PD Italy
- Interdepartmental Centre for Research in Viticulture and Enology (CIRVE) University of Padova Conegliano TV Italy
| | - V. Corich
- Department of Agronomy Food Natural resources Animals and Environment (DAFNAE) University of Padova Legnaro PD Italy
- Interdepartmental Centre for Research in Viticulture and Enology (CIRVE) University of Padova Conegliano TV Italy
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15
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Richards NK, Mansfield S, Townsend RJ, Ferguson CM. Genetic variation within species and haplotypes of the Wiseana (Lepidoptera: Hepialidae) complex and development of non-sequenced based identification tools to aid field studies. PEST MANAGEMENT SCIENCE 2017; 73:2334-2344. [PMID: 28544267 DOI: 10.1002/ps.4620] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2016] [Revised: 05/10/2017] [Accepted: 05/16/2017] [Indexed: 06/07/2023]
Abstract
BACKGROUND Porina is the common name used to describe moths and caterpillars of the seven endemic species and three haplotypes of Wiseana in New Zealand. Several species have adapted to eating introduced pasture plants; however, a paucity of defining morphological characteristics has meant that porina are grouped as indistinguishable species within a complex. This study aimed to develop non-sequencing identification methods for porina species. RESULTS We sequenced 1718 bp of the mitochondrial cytochrome oxidase genes for all Wiseana species and haplotypes using 75 specimens collected from 42 sites throughout New Zealand. Two identification methods were developed; the high-resolution melt method uses 106 bp of the cytochrome oxidase I gene, and the restriction fragment polymorphism method uses a larger 700 bp region from the same gene. Validation was performed on a further 275 specimens. Melt curve profiles varied more with population heterogeneity than digest results. In both methods, W. mimica and W. jocosa were inseparable. W. fuliginea grouped with W. mimica and W. jocosa in the restriction method, but the melt curve profile differed. CONCLUSION Until now, ecological studies of porina at the species level have been implausible. Our non-sequencing based methods allow rapid identification of moths and caterpillars to species and haplotype level, paving the way for ecological studies of pasture pest species and the development of species-specific mitigation strategies. © 2017 Society of Chemical Industry.
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Affiliation(s)
- Nicola K Richards
- AgResearch, Lincoln Science Centre, Lincoln, Canterbury, New Zealand
| | - Sarah Mansfield
- AgResearch, Lincoln Science Centre, Lincoln, Canterbury, New Zealand
| | | | - Colin M Ferguson
- AgResearch, Invermay Agricultural Centre, Mosgiel, Dunedin, New Zealand
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16
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Satta E, Nanni IM, Contaldo N, Collina M, Poveda JB, Ramírez AS, Bertaccini A. General phytoplasma detection by a q-PCR method using mycoplasma primers. Mol Cell Probes 2017; 35:1-7. [PMID: 28558918 DOI: 10.1016/j.mcp.2017.05.008] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2017] [Revised: 05/24/2017] [Accepted: 05/24/2017] [Indexed: 11/24/2022]
Abstract
Phytoplasmas and mycoplasmas are bacteria belonging to the class Mollicutes. In this study, a fine tuning of quantitative polymerase chain reaction (qPCR) with a universal mycoplasma primer pair (GPO3F/MGSO) targeting the 16S rRNA gene was carried out on phytoplasmas. The dissociation curves of DNAs from Catharanthus roseus phytoplasma-infected micropropagated shoots and from phytoplasma field-infected plant samples showed a single peak at 82.5 °C (±0.5) specifically detecting phytoplasmas belonging to several ribosomal groups. Assay specificity was determined with DNA of selected bacteria: 'Candidatus Liberibacter solanacearum', Xylella fastidiosa, Ralstonia solanacearum and Clavibacter michiganensis. No amplification curves were observed with any of these tested bacteria except 'Ca. L. solanacearum' that was amplified with a melting temperature at 85 °C. Absolute quantification of phytoplasma titer was calculated using standard curves prepared from serial dilutions of plasmids containing the cloned fragment GPO3F/MGSO from European stone fruit yellows phytoplasma. Phytoplasma copy number ranged from 106 to 103 according with the sample. The sensitivity evaluated comparing plasmid serial dilutions resulted 10-6 for conventional PCR and 10-7 for qPCR. The latter method resulted therefore able to detect very low concentrations of phytoplasma in plant material.
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Affiliation(s)
- Eleonora Satta
- Department of Agricultural Sciences, Plant Pathology, Alma Mater Studiorum - University of Bologna, Bologna, Italy.
| | - Irene M Nanni
- Department of Agricultural Sciences, Plant Pathology, Alma Mater Studiorum - University of Bologna, Bologna, Italy
| | - Nicoletta Contaldo
- Department of Agricultural Sciences, Plant Pathology, Alma Mater Studiorum - University of Bologna, Bologna, Italy
| | - Marina Collina
- Department of Agricultural Sciences, Plant Pathology, Alma Mater Studiorum - University of Bologna, Bologna, Italy
| | - José B Poveda
- Unidad de Epidemiologia y Medicina Preventiva, Universidad de Las Palmas de Gran Canaria, (IUSA), Arucas, Spain
| | - Ana S Ramírez
- Unidad de Epidemiologia y Medicina Preventiva, Universidad de Las Palmas de Gran Canaria, (IUSA), Arucas, Spain
| | - Assunta Bertaccini
- Department of Agricultural Sciences, Plant Pathology, Alma Mater Studiorum - University of Bologna, Bologna, Italy
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17
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Ajamma YU, Mararo E, Omondi D, Onchuru T, Muigai AWT, Masiga D, Villinger J. Rapid and high throughput molecular identification of diverse mosquito species by high resolution melting analysis. F1000Res 2016; 5:1949. [PMID: 27703667 PMCID: PMC5031131 DOI: 10.12688/f1000research.9224.1] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 07/25/2016] [Indexed: 01/08/2023] Open
Abstract
Mosquitoes are a diverse group of invertebrates, with members that are among the most important vectors of diseases. The correct identification of mosquitoes is paramount to the control of the diseases that they transmit. However, morphological techniques depend on the quality of the specimen and often unavailable taxonomic expertise, which may still not be able to distinguish mosquitoes among species complexes (sibling and cryptic species). High resolution melting (HRM) analyses, a closed-tube, post-polymerase chain reaction (PCR) method used to identify variations in nucleic acid sequences, has been used to differentiate species within the
Anopheles gambiae and
Culex pipiens complexes. We validated the use of PCR-HRM analyses to differentiate species within
Anopheles and within each of six genera of culicine mosquitoes, comparing primers targeting cytochrome b (
cyt b), NADH dehydrogenase subunit 1 (ND1), intergenic spacer region (IGS) and cytochrome c oxidase subunit 1 (
COI) gene regions. HRM analyses of amplicons from all the six primer pairs successfully differentiated two or more mosquito species within one or more genera (
Aedes (
Ae. vittatus from
Ae. metallicus),
Culex (
Cx. tenagius from
Cx. antennatus,
Cx. neavei from
Cx. duttoni, cryptic
Cx. pipiens species),
Anopheles (
An. gambiae s.s. from
An. arabiensis) and
Mansonia (
Ma. africana from
Ma. uniformis)) based on their HRM profiles. However, PCR-HRM could not distinguish between species within
Aedeomyia (
Ad. africana and
Ad. furfurea),
Mimomyia (
Mi. hispida and
Mi. splendens) and
Coquillettidia (
Cq. aurites,
Cq. chrysosoma,
Cq. fuscopennata,
Cq. metallica,
Cq. microannulatus,
Cq. pseudoconopas and
Cq. versicolor) genera using any of the primers. The IGS and COI barcode region primers gave the best and most definitive separation of mosquito species among anopheline and culicine mosquito genera, respectively, while the other markers may serve to confirm identifications of closely related sub-species. This approach can be employed for rapid identification of mosquitoes.
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Affiliation(s)
- Yvonne Ukamaka Ajamma
- Martin Lüscher Emerging Infectious Diseases (ML-EID) Laboratory, International Centre of Insect Physiology and Ecology, Nairobi, Kenya; Department of Botany (Genetics), Jomo Kenyatta University of Agriculture and Technology, Juja, Kenya
| | - Enock Mararo
- Martin Lüscher Emerging Infectious Diseases (ML-EID) Laboratory, International Centre of Insect Physiology and Ecology, Nairobi, Kenya
| | - David Omondi
- Martin Lüscher Emerging Infectious Diseases (ML-EID) Laboratory, International Centre of Insect Physiology and Ecology, Nairobi, Kenya; Biochemistry and Molecular Biology Department, Egerton University, Egerton, Kenya; Molecular Biology and Virology Laboratory, Department of Medical Biosciences, University of Western Cape, South Africa
| | - Thomas Onchuru
- Martin Lüscher Emerging Infectious Diseases (ML-EID) Laboratory, International Centre of Insect Physiology and Ecology, Nairobi, Kenya; Insect Symbiosis Research Group, Max Planck Institute for Chemical Ecology (MPI-CE), Jena, Germany; Department for Evolutionary Ecology, Institute for Zoology, Johannes Gutenberg University, Mainz, Germany
| | - Anne W T Muigai
- Department of Botany (Genetics), Jomo Kenyatta University of Agriculture and Technology, Juja, Kenya
| | - Daniel Masiga
- Martin Lüscher Emerging Infectious Diseases (ML-EID) Laboratory, International Centre of Insect Physiology and Ecology, Nairobi, Kenya
| | - Jandouwe Villinger
- Martin Lüscher Emerging Infectious Diseases (ML-EID) Laboratory, International Centre of Insect Physiology and Ecology, Nairobi, Kenya
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Dobhal S, Olson JD, Arif M, Garcia Suarez JA, Ochoa-Corona FM. A simplified strategy for sensitive detection of Rose rosette virus compatible with three RT-PCR chemistries. J Virol Methods 2016; 232:47-56. [PMID: 26850142 DOI: 10.1016/j.jviromet.2016.01.013] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2015] [Revised: 12/12/2015] [Accepted: 01/31/2016] [Indexed: 11/29/2022]
Abstract
Rose rosette disease is a disorder associated with infection by Rose rosette virus (RRV), a pathogen of roses that causes devastating effects on most garden cultivated varieties, and the wild invasive rose especially Rosa multiflora. Reliable and sensitive detection of this disease in early phases is needed to implement proper control measures. This study assesses a single primer-set based detection method for RRV and demonstrates its application in three different chemistries: Endpoint RT-PCR, TaqMan-quantitative RT-PCR (RT-qPCR) and SYBR Green RT-qPCR with High Resolution Melting analyses. A primer set (RRV2F/2R) was designed from consensus sequences of the nucleocapsid protein gene p3 located in the RNA 3 region of RRV. The specificity of primer set RRV2F/2R was validated in silico against published GenBank sequences and in-vitro against infected plant samples and an exclusivity panel of near-neighbor and other viruses that commonly infect Rosa spp. The developed assay is sensitive with a detection limit of 1fg from infected plant tissue. Thirty rose samples from 8 different states of the United States were tested using the developed methods. The developed methods are sensitive and reliable, and can be used by diagnostic laboratories for routine testing and disease management decisions.
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Affiliation(s)
- Shefali Dobhal
- National Institute for Microbial Forensics & Food and Agricultural Biosecurity, Stillwater, OK, USA; Department of Entomology and Plant Pathology, Oklahoma State University, Stillwater, OK, USA
| | - Jennifer D Olson
- Department of Entomology and Plant Pathology, Oklahoma State University, Stillwater, OK, USA
| | - Mohammad Arif
- National Institute for Microbial Forensics & Food and Agricultural Biosecurity, Stillwater, OK, USA; Department of Entomology and Plant Pathology, Oklahoma State University, Stillwater, OK, USA
| | - Johnny A Garcia Suarez
- National Institute for Microbial Forensics & Food and Agricultural Biosecurity, Stillwater, OK, USA; Department of Entomology and Plant Pathology, Oklahoma State University, Stillwater, OK, USA; Departamento de Ciencias de la Vida y de la Agricultura, Universidad de las Fuerzas Armadas ESPE, Sangolquí, Ecuador
| | - Francisco M Ochoa-Corona
- National Institute for Microbial Forensics & Food and Agricultural Biosecurity, Stillwater, OK, USA; Department of Entomology and Plant Pathology, Oklahoma State University, Stillwater, OK, USA.
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Pereyra VA, Gomez CA, La Manna L, Roux G, Lanteri AA, Vallejos NC, Marvaldi AE. Introduction and Establishment of Pissodes castaneus (Coleoptera: Curculionidae) in the Andean Patagonia of Argentina. JOURNAL OF ECONOMIC ENTOMOLOGY 2016; 109:222-231. [PMID: 26511982 DOI: 10.1093/jee/tov304] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/17/2015] [Accepted: 09/28/2015] [Indexed: 06/05/2023]
Abstract
The pine weevils that occur in plantations of Pinus spp. in Andean Patagonia of Argentina belong to the species Pissodes castaneus (De Geer), a Eurasian endemic species, according to the identification based on molecular and morphological characters. Sequences of the mitochondrial Cytochrome oxidase subunit I and nuclear genes (28 S rDNA and ITS2) were obtained for individuals of 13 afforestations, covering the entire distribution area of the established populations in the Andean Patagonia of Argentina. Sequence comparison with representative species of the genus (European, North American, and Chinese species) shows that Patagonian specimens are conspecific to those of P. castaneus sequenced from Europe. Phylogenetic analyses indicate that all terminals from Patagonia form a monophyletic unit without evident subclades, eliminating the possibility of existence of more than one species of Pissodes Germar in this area, including cryptic ones. Moreover, the very low genetic divergence between the Patagonian populations suggests that it is plausible that P. castaneus was introduced into Patagonia from just one location. Mitochondrial DNA analysis shows that Patagonian terminals group together with a French haplotype and are clearly separated from other P. castaneus individuals represented in our sample, and reveal that established populations in Andean Patagonia originated via a limited introduction.
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Affiliation(s)
- V A Pereyra
- Instituto Argentino de Investigaciones de las Zonas Áridas, CCT-CONICET Mendoza, CC 507 5500 Provincia de Mendoza, Argentina (; ), División Entomología, Facultad de Ciencias Naturales y Museo, Universidad Nacional de La Plata, Paseo del Bosque s/n 1900 La Plata, Provincia de Buenos Aires, Argentina (; ; ),
| | - C A Gomez
- LEAI, Facultad de Ingeniería, Sede Esquel, Universidad Nacional de la Patagonia San Juan Bosco, CP9200, Esquel, Provincia de Chubut, Argentina (; )
| | - L La Manna
- Instituto Argentino de Investigaciones de las Zonas Áridas, CCT-CONICET Mendoza, CC 507 5500 Provincia de Mendoza, Argentina (; ), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET) (; ; )
| | - G Roux
- INRA, UR633 Zoologie Forestière, F-45075 Orléans, Université d'Orléans, France , and
| | - A A Lanteri
- División Entomología, Facultad de Ciencias Naturales y Museo, Universidad Nacional de La Plata, Paseo del Bosque s/n 1900 La Plata, Provincia de Buenos Aires, Argentina (; ; ), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET) (; ; )
| | - N C Vallejos
- Facultad de Ingeniería, Sede Esquel, Universidad Nacional de la Patagonia San Juan Bosco, CP9200, Esquel, Provincia de Chubut, Argentina
| | - A E Marvaldi
- Instituto Argentino de Investigaciones de las Zonas Áridas, CCT-CONICET Mendoza, CC 507 5500 Provincia de Mendoza, Argentina (; ), LEAI, Facultad de Ingeniería, Sede Esquel, Universidad Nacional de la Patagonia San Juan Bosco, CP9200, Esquel, Provincia de Chubut, Argentina (; ), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET) (; ; )
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20
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Dawnay N, Hughes R, Court DS, Duxbury N. Species detection using HyBeacon(®) probe technology: Working towards rapid onsite testing in non-human forensic and food authentication applications. Forensic Sci Int Genet 2015; 20:103-111. [PMID: 26561743 DOI: 10.1016/j.fsigen.2015.10.006] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2015] [Revised: 10/05/2015] [Accepted: 10/15/2015] [Indexed: 10/22/2022]
Abstract
Identifying individual species or determining species' composition in an unknown sample is important for a variety of forensic applications. Food authentication, monitoring illegal trade in endangered species, forensic entomology, sexual assault case work and counter terrorism are just some of the fields that can require the detection of the biological species present. Traditional laboratory based approaches employ a wide variety of tools and technologies and exploit a number of different species specific traits including morphology, molecular differences and immuno-chemical analyses. A large number of these approaches require laboratory based apparatus and results can take a number of days to be returned to investigating authorities. Having a presumptive test for rapid identification could lead to savings in terms of cost and time and allow sample prioritisation if confirmatory testing in a laboratory is required later. This model study describes the development of an assay using a single HyBeacon(®) probe and melt curve analyses allowing rapid screening and authentication of food products labelled as Atlantic cod (Gadus morhua). Exploiting melt curve detection of species specific SNP sites on the COI gene the test allows detection of a target species (Atlantic cod) and closely related species which may be used as substitutes. The assay has been designed for use with the Field Portable ParaDNA system, a molecular detection platform for non-expert users. The entire process from sampling to result takes approximately 75min. Validation studies were performed on both single source genomic DNA, mixed genomic DNA and commercial samples. Data suggests the assay has a lower limit of detection of 31 pg DNA. The specificity of the assay to Atlantic cod was measured by testing highly processed food samples including frozen, defrosted and cooked fish fillets as well as fish fingers, battered fish fillet and fish pie. Ninety-six (92.7%) of all Atlantic cod food products, tested, provided a correct single species result with the remaining samples erroneously identified as containing non-target species. The data shows that the assay was quick to design and characterise and is also capable of yielding results that would be beneficial in a variety of fields, not least the authentication of food.
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Affiliation(s)
- Nick Dawnay
- Product Development Group, LGC Forensics, Culham Science Centre, Abingdon OX14 3ED, UK; School of Pharmacy and Biomolecular Sciences, Liverpool John Moores University, Byrom Street, Liverpool L3 3AF, UK.
| | - Rebecca Hughes
- Department of Pharmacy and Forensic Science, King's College London, Faculty of Life Sciences and Medicine, Franklin-Wilkins Building, 150 Stamford Street, London SE1 9NH, UK
| | - Denise Syndercombe Court
- Department of Pharmacy and Forensic Science, King's College London, Faculty of Life Sciences and Medicine, Franklin-Wilkins Building, 150 Stamford Street, London SE1 9NH, UK
| | - Nicola Duxbury
- Product Development Group, LGC Forensics, Culham Science Centre, Abingdon OX14 3ED, UK
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21
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Perera OP, Allen KC, Jain D, Purcell M, Little NS, Luttrell RG. Rapid identification of Helicoverpa armigera and Helicoverpa zea (Lepidoptera: Noctuidae) using ribosomal RNA internal transcribed spacer 1. JOURNAL OF INSECT SCIENCE (ONLINE) 2015; 15:155. [PMID: 26516166 PMCID: PMC4625950 DOI: 10.1093/jisesa/iev137] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/07/2015] [Accepted: 10/10/2015] [Indexed: 05/31/2023]
Abstract
Rapid identification of invasive species is crucial for deploying management strategies to prevent establishment. Recent Helicoverpa armigera (Hübner) invasions and subsequent establishment in South America has increased the risk of this species invading North America. Morphological similarities make differentiation of H. armigera from the native Helicoverpa zea (Boddie) difficult. Characteristics of adult male genitalia and nucleotide sequence differences in mitochondrial DNA are two of the currently available methods to differentiate these two species. However, current methods are likely too slow to be employed as rapid detection methods. In this study, conserved differences in the internal transcribed spacer 1 (ITS1) of the ribosomal RNA genes were used to develop species-specific oligonucleotide primers that amplified ITS1 fragments of 147 and 334 bp from H. armigera and H. zea, respectively. An amplicon (83 bp) from a conserved region of 18S ribosomal RNA subunit served as a positive control. Melting temperature differences in ITS1 amplicons yielded species-specific dissociation curves that could be used in high resolution melt analysis to differentiate the two Helicoverpa species. In addition, a rapid and inexpensive procedure for obtaining amplifiable genomic DNA from a small amount of tissue was identified. Under optimal conditions, the process was able to detect DNA from one H. armigera leg in a pool of 25 legs. The high resolution melt analysis combined with rapid DNA extraction could be used as an inexpensive method to genetically differentiate large numbers of H. armigera and H. zea using readily available reagents.
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Affiliation(s)
| | - Kerry C Allen
- USDA-ARS Southern Insect Management Research Unit, Stoneville, MS 38776
| | - Devendra Jain
- Department of Molecular Biology and Biotechnology, Maharana Pratap University of Agriculture and Technology, Udaipur-313001, Rajasthan, India
| | - Matthew Purcell
- USDA-ARS Australian Biological Control Laboratory, CSIRO Biosecurity, GPO Box 2583 Brisbane, Queensland 4001, Australia
| | - Nathan S Little
- USDA-ARS Southern Insect Management Research Unit, Stoneville, MS 38776
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Identifying the last bloodmeal of questing sheep tick nymphs (Ixodes ricinus L.) using high resolution melting analysis. Vet Parasitol 2015; 210:194-205. [PMID: 25941127 DOI: 10.1016/j.vetpar.2015.04.007] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2014] [Revised: 04/02/2015] [Accepted: 04/07/2015] [Indexed: 11/18/2022]
Abstract
The sheep tick, Ixodes ricinus L., is an important hematophagous vector of zoonotic disease of both veterinary and public health importance in Europe. Risk models for tick-borne diseases can be improved by identifying the main hosts of this species in any given area. However, this generalist tick stays on a host for only a few days a year over its life cycle, making the study of its feeding ecology difficult. In contrast, ticks can easily be collected from vegetation when they are questing. Molecular methods have proved to be a reliable alternative to field observation, but most current methods have low sensitivity and/or low identification success (i.e. hosts are only identified to taxonomic levels higher than species). In this study we use Real-time PCR coupled with High Resolution Melting Analysis (HRMA) to identify the source of the last bloodmeal in questing tick nymphs. Twenty of the most important tick hosts were grouped taxonomically and six group-specific primer sets, targeting short mitochondrial DNA regions, were designed de novo. Firstly, we show that these primers successfully amplify target host DNA (from host tissue or engorged ticks), and that HRMA can be used to reliably identify hosts to species (or genera in the case of Sorex and Apodemus). Secondly, the new protocol was tested on field-collected questing nymphs. Bloodmeal source was identified in 65.4% of 52 individuals. In 83.3% of these, the host was identified to species or genera using HRMA alone. Moreover, the primer sets designed here can unequivocally identify mixed bloodmeals. The combination of sensitivity and identification success together with the closed-tube and single step approach that minimizes contamination, make Real-time HRMA a good alternative to current methods for bloodmeal identification.
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Przybylska A, Fiedler Ż, Kucharczyk H, Obrępalska-Stęplowska A. Detection of the quarantine species Thrips palmi by loop-mediated isothermal amplification. PLoS One 2015; 10:e0122033. [PMID: 25793743 PMCID: PMC4368663 DOI: 10.1371/journal.pone.0122033] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2014] [Accepted: 02/05/2015] [Indexed: 12/04/2022] Open
Abstract
Thrips palmi (from the order Thysanoptera) is a serious insect pest of various crops, including vegetables, fruits and ornamental plants, causing significant economic losses. Its presence constitutes a double threat; not only does T. palmi feed on the plants, it is also a vector for several plant viruses. T. palmi originated in Asia, but has spread to North and Central America, Africa, Oceania and the Caribbean in recent decades. This species has been sporadically noted in Europe and is under quarantine regulation in the European Union. For non-specialists its larval stages are indistinguishable morphologically from another widespread and serious insect pest Frankliniella occidentalis (a non-quarantine species in the European Union) as well as other frequently occurring thrips. In this study, we have developed a loop-mediated isothermal amplification protocol to amplify rDNA regions of T. palmi. The results were consistent whether isolated DNA or crushed insects were used as template, indicating that the DNA isolation step could be omitted. The described method is species-specific and sensitive and provides a rapid diagnostic tool to detect T. palmi in the field.
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Affiliation(s)
- Arnika Przybylska
- Interdepartmental Laboratory of Molecular Biology, Institute of Plant Protection-National Research Institute, Poznań, Poland
| | - Żaneta Fiedler
- Department of Biological Control, Institute of Plant Protection-National Research Institute, Poznań, Poland
| | - Halina Kucharczyk
- Department of Zoology, Maria Curie-Skłodowska University, Lublin, Poland
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McCarthy JK, Didham RK, Brockerhoff EG, van Bysterveldt KA, Varsani A. High-resolution DNA melt-curve analysis for cost-effective mass screening of pairwise species interactions. Mol Ecol Resour 2013; 13:908-17. [PMID: 23875939 DOI: 10.1111/1755-0998.12143] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2013] [Accepted: 06/05/2013] [Indexed: 11/28/2022]
Abstract
Ecological studies of pairwise interactions are constrained by the methods available for rapid species identification of the interacting organisms. The resolution of data required to characterize species interaction networks at multiple spatio-temporal scales can be intensive, and therefore laborious and costly to collect. We explore the utility of high-resolution DNA melt-curve analysis (HRM) as a rapid species identification method. An approach was developed to identify organisms at the pairwise interaction level, with particular application to cryptic species interactions that are traditionally difficult to study. Here, we selected a challenging application; to identify the presence/absence of pathogenic fungi (Sporothrix inflata, Ophiostoma nigrocarpum and Ophiostoma galeiforme) transported by bark beetle vectors (Hylastes ater and Hylurgus ligniperda). The technique was able to distinguish between different species of DNA within a single, pooled sample. In test applications, HRM was effective in the mass screening and identification of pathogenic fungal species carried by many individual bark beetle vectors (n = 455 beetles screened) across large geographic scales. For two of the fungal species, there was no difference in the frequency of association with either of their vectors, but for the third fungal species there was a shift in vector-pathogen associations across locations. This technique allows rapid, mass screening and characterization of species interactions at a fraction of the time and cost of traditional methods. It is anticipated that this method can be readily applied to explore other cryptic species interactions, or other studies requiring rapid generation of large data sets and/or high-throughput efficiency.
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Affiliation(s)
- James K McCarthy
- School of Biological Sciences, University of Canterbury, Private Bag 4800, Christchurch 8140, New Zealand.
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Tsykun T, Rigling D, Prospero S. A new multilocus approach for a reliable DNA-based identification of Armillaria species. Mycologia 2013; 105:1059-76. [PMID: 23449075 DOI: 10.3852/12-209] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
In this paper we highlight and critically discuss limitations to molecular methods for identification of fungi via the example of the basidiomycete genus Armillaria. We analyzed a total of 144 sequences of three DNA regions commonly used for identifying fungi (ribosomal IGS-1 and ITS regions, translation elongation factor-1 alpha gene) from 48 specimens of six Armillaria species occurring in Europe (A. cepistipes, A. ostoyae, A. gallica, A. borealis, A. mellea, A. tabescens). Species were identified by comparing newly obtained sequences with those from the NCBI database, phylogenetic analyses and PCR-RFLP analyses of the three regions considered. When analyzed separately, no single gene region could unambiguously identify all six Armillaria species because of low interspecific and high intrasequence variability. We therefore developed a multilocus approach, which involves the stepwise use of the three regions. Following this scheme, all six species could be clearly discriminated. Our study suggests that, to improve the reliability of DNA-based techniques for species identification, multiple genes or intergenic regions should be analyzed.
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Kuster CJ, Von Elert E. High-resolution melting analysis: a genotyping tool for population studies on Daphnia. Mol Ecol Resour 2012; 12:1048-57. [PMID: 22925691 DOI: 10.1111/j.1755-0998.2012.03177.x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2012] [Revised: 07/05/2012] [Accepted: 07/17/2012] [Indexed: 11/27/2022]
Abstract
Determining genetic variation at the DNA level within and between natural populations is important for understanding the role of natural selection on phenotypic traits, but many techniques of screening for genetic variation are either cost intensive, not sensitive enough or too labour- and time-consuming. Here, we demonstrate high-resolution melting analysis (HRMA) as a cost-effective and powerful tool for screening variable target genes in natural populations. HRMA is based on monitoring the melting of PCR amplicons. Owing to saturating concentrations of a dye that binds at high concentrations to double-stranded DNA, it is possible to genotype high numbers of samples rapidly and accurately. We analysed digestive trypsins of two Daphnia magna populations as an application example for HRMA. One population originated from a pond containing toxic cyanobacteria that possibly produce protease inhibitors and the other from a pond without such cyanobacteria. The hypothesis was that D. magna clones from ponds with cyanobacteria have undergone selection by these inhibitors, which has led to different trypsin alleles. We first sequenced pooled genomic PCR products of trypsins from both populations to identify variable DNA sequences of active trypsins. Second, we screened variable DNA sequences of each D. magna clone from both populations for single nucleotide polymorphisms via HRMA. The HRMA results revealed that both populations exhibited phenotypic differences in the analysed trypsins. Our results indicate that HRMA is a powerful genotyping tool for studying the variation of target genes in response to selection within and between natural Daphnia populations.
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Affiliation(s)
- C J Kuster
- Zoological Institute, Aquatic Chemical Ecology, University of Cologne, Cologne, Germany.
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Drobná Z, Del Razo LM, Garcia-Vargas G, Sánchez-Ramírez B, González-Horta C, Ballinas-Casarrubias L, Loomis D, Stýblo M. Identification of the GST-T1 and GST-M1 null genotypes using high resolution melting analysis. Chem Res Toxicol 2011; 25:216-24. [PMID: 22136492 DOI: 10.1021/tx200457u] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Glutathione S-transferases, including GST-T1 and GST-M1, are known to be involved in the phase II detoxification pathways for xenobiotics as well as in the metabolism of endogenous compounds. Polymorphisms in these genes have been linked to an increased susceptibility to carcinogenesis and associated with risk factors that predispose to certain inflammatory diseases. In addition, GST-T1 and GST-M1 null genotypes have been shown to be responsible for interindividual variations in the metabolism of arsenic, a known human carcinogen. To assess the specific GST genotypes in the Mexican population chronically exposed to arsenic, we have developed a multiplex High Resolution Melting PCR (HRM-PCR) analysis using a LightCycler480 instrument. This method is based on analysis of the PCR product melting curve that discriminates PCR products according to their lengths and base sequences. Three pairs of primers that specifically recognize GST-T1, GST-M1, and β-globin, an internal control, to produce amplicons of different length were designed and combined with LightCycler480 High Resolution Melting Master Mix containing ResoLight, a completely saturating DNA dye. Data collected from melting curve analysis were evaluated using LightCycler480 software to determine specific melting temperatures of individual melting curves representing target genes. Using this newly developed multiplex HRM-PCR analysis, we evaluated GST-T1 and GST-M1 genotypes in 504 DNA samples isolated from the blood of individuals residing in Zimapan, Lagunera, and Chihuahua regions in Mexico. We found that the Zimapan and Lagunera populations have similar GST-T1 and GST-M1 genotype frequencies which differ from those of the Chihuahua population. In addition, 14 individuals have been identified as carriers of the double null genotype, i.e., null genotypes in both GST-T1 and GST-M1 genes. Although this procedure does not distinguish between biallelic (+/+) and monoallelic (+/-) genotypes, it can be used in an automated workflow as a simple, sensitive, and time and money saving procedure for rapid identification of the GST-T1 and GST-M1 positive or null genotypes.
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Affiliation(s)
- Zuzana Drobná
- Department of Nutrition, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, North Carolina 27599-7461, United States.
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