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Oliveira PV, de Almeida FAN, Lugon MD, Britto KB, Oliveira-Costa J, Santos AR, Paneto GG. Using high-resolution melting to identify Calliphoridae (blowflies) species from Brazil. PeerJ 2020; 8:e9680. [PMID: 33335803 PMCID: PMC7713596 DOI: 10.7717/peerj.9680] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2020] [Accepted: 07/17/2020] [Indexed: 01/22/2023] Open
Abstract
Forensic entomology is the study of insects and other arthropods used in the solution of crimes. Most of entomological evidences strongly depend on accurate species identification. Therefore, new methods are being developed due to difficulties in morphological identification, including molecular methods such as High-Resolution Melting. In this study, we reported a new HRM primer set to identify forensically important Calliphoridae (blowflies) from Brazil. For such purpose, Calliphoridae species of forensic importance in Brazil were listed and confirmed by specialists. Mitochondrial COI sequences of those species were downloaded from databases and aligned, and polymorphic variations were selected for distinction between species. Based on it, HRM primers were designed. Forty-three fly samples representing six species were tested in the HRM assay. All samples had the COI gene sequenced to validate the result. Identifying and differentiating the six species proposed using a combination of two amplicons was possible. The protocol was effective even for old insect specimens, collected and preserved dried for more than ten years, unlike the DNA sequencing technique that failed for those samples. The HRM technique proved to be an alternative tool to DNA sequencing, with advantage of amplifying degraded samples and being fast and cheaper than the sequencing technique.
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Affiliation(s)
- Pablo Viana Oliveira
- Programa de Pós-Graduação em Biotecnologia, Universidade Federal do Espírito Santo, Vitória, Espírito Santo, Brazil
| | | | - Magda Delorence Lugon
- Programa de Pós-Graduação em Biotecnologia, Universidade Federal do Espírito Santo, Vitória, Espírito Santo, Brazil
| | - Karolinni Bianchi Britto
- Programa de Pós-Graduação em Biotecnologia, Universidade Federal do Espírito Santo, Vitória, Espírito Santo, Brazil
| | - Janyra Oliveira-Costa
- Polícia Civil do Estado do Rio de Janeiro, Instituto Médico Legal Afrânio Peixoto, Rio de Janeiro, Rio de Janeiro, Brazil
| | - Alexandre Rosa Santos
- Centro de Ciências Agrárias e Engenharias, Universidade Federal do Espírito Santo, Alegre, Espírito Santo, Brazil
| | - Greiciane Gaburro Paneto
- Programa de Pós-Graduação em Biotecnologia, Universidade Federal do Espírito Santo, Vitória, Espírito Santo, Brazil
- Centro de Ciências Exatas, Naturais e da Saúde, Universidade Federal do Espírito Santo, Alegre, Espírito Santo, Brazil
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2
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Application of HRM-PCR (high resolution melting PCR) for identification of forensically important Coleoptera species. FORENSIC SCIENCE INTERNATIONAL GENETICS SUPPLEMENT SERIES 2019. [DOI: 10.1016/j.fsigss.2019.09.051] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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3
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George K, Masters A, Dawnay N. Development of HyBeacon® probes for the forensic detection of Panthera, rhinoceros, and pangolin species. Mol Cell Probes 2019; 48:101450. [PMID: 31563668 DOI: 10.1016/j.mcp.2019.101450] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2019] [Revised: 08/14/2019] [Accepted: 09/16/2019] [Indexed: 10/25/2022]
Abstract
The Illegal Wildlife Trade (IWT) represents a multi-billion dollar black-market industry whereby wild species are illegally taken from their natural environment and sold. A common question asked by wildlife forensic scientists pertains to species and/or genus identity, which currently requires multi-step processing. Our work details the development of three HyBeacon® probes, used for the presumptive detection of rhinoceros, pangolin and key target species in the Panthera genus. The approach can be performed in a single tube using melt curve analysis and provide rapid assessment of sample identity. Using synthetic DNA of representative species, early data suggest the approach is sensitive enough to achieve species identification with <10 cells. Future development and assay validation can allow the rapid screening of multiple seized items before confirmatory DNA sequencing.
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Affiliation(s)
- Kimberley George
- School of Pharmacy and Biomolecular Sciences, Liverpool John Moores University, Byrom Street, Liverpool, L3 3AF, UK
| | - Alice Masters
- School of Pharmacy and Biomolecular Sciences, Liverpool John Moores University, Byrom Street, Liverpool, L3 3AF, UK
| | - Nick Dawnay
- School of Pharmacy and Biomolecular Sciences, Liverpool John Moores University, Byrom Street, Liverpool, L3 3AF, UK.
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4
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Gemmellaro MD, Hamilton GC, Ware JL. Review of Molecular Identification Techniques for Forensically Important Diptera. JOURNAL OF MEDICAL ENTOMOLOGY 2019; 56:887-902. [PMID: 31173634 DOI: 10.1093/jme/tjz040] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/01/2018] [Indexed: 06/09/2023]
Abstract
The medico-legal section of forensic entomology focuses on the analysis of insects associated with a corpse. Such insects are identified, and their life history characteristics are evaluated to provide information related to the corpse, such as postmortem interval and time of colonization. Forensically important insects are commonly identified using dichotomous keys, which rely on morphological characteristics. Morphological identifications can pose a challenge as local keys are not always available and can be difficult to use, especially when identifying juvenile stages. If a specimen is damaged, certain keys cannot be used for identification. In contrast, molecular identification can be a better instrument to identify forensically important insects, regardless of life stage or specimen completeness. Despite more than 20 yr since the first use of molecular data for the identification of forensic insects, there is little overlap in gene selection or phylogenetic methodology among studies, and this inconsistency reduces efficiency. Several methods such as genetic distance, reciprocal monophyly, or character-based methods have been implemented in forensic identification studies. It can be difficult to compare the results of studies that employ these different methods. Here we present a comprehensive review of the published results for the molecular identification of Diptera of forensic interest, with an emphasis on evaluating variation among studies in gene selection and phylogenetic methodology.
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Affiliation(s)
| | | | - Jessica L Ware
- Department of Entomology, Rutgers University, New Brunswick, NJ
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5
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Wing measurement can be used to identify European blow flies (Diptera: Calliphoridae) of forensic importance. Forensic Sci Int 2019; 296:1-8. [DOI: 10.1016/j.forsciint.2019.01.001] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2018] [Revised: 12/27/2018] [Accepted: 01/02/2019] [Indexed: 01/04/2023]
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6
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A bibliometric analysis of forensic entomology trends and perspectives worldwide over the last two decades (1998–2017). Forensic Sci Int 2019; 295:72-82. [DOI: 10.1016/j.forsciint.2018.12.002] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2018] [Revised: 11/30/2018] [Accepted: 12/03/2018] [Indexed: 12/11/2022]
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7
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Parada R, Malewski T, Jaszczak K, Kawka M. Alternative Transcription of Peroxisome Proliferator-Activated Receptor Gamma in the Liver Is Associated with Fatness of Chickens. BRAZILIAN JOURNAL OF POULTRY SCIENCE 2018. [DOI: 10.1590/1806-9061-2017-0661] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- R Parada
- Polish Academy of Sciences, Poland
| | | | | | - M Kawka
- Polish Academy of Sciences, Poland
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8
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Cowan AF, Elkins KM. Detection and Identification of Psilocybe cubensis DNA Using a Real-Time Polymerase Chain Reaction High Resolution Melt Assay. J Forensic Sci 2017; 63:1500-1505. [PMID: 29194645 DOI: 10.1111/1556-4029.13714] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2017] [Revised: 10/03/2017] [Accepted: 11/14/2017] [Indexed: 12/20/2022]
Abstract
Psilocybe cubensis, or "magic mushroom," is the most common species of fungus with psychedelic characteristics. Two primer sets were designed to target Psilocybe DNA using web-based software and NBCI gene sequences. DNA was extracted from eighteen samples, including twelve mushroom species, using the Qiagen DNeasy® Plant Mini Kit. The DNA was amplified by the polymerase chain reaction (PCR) using the primers and a master mix containing either a SYBR® Green I, Radiant™ Green, or LCGreen Plus® intercalating dye; amplicon size was determined using agarose gel electrophoresis. The PCR assays were tested for amplifiability, specificity, reproducibility, robustness, sensitivity, and multiplexing with primers that target marijuana. The observed high resolution melt (HRM) temperatures for primer sets 1 and 7 were 78.85 ± 0.31°C and 73.22 ± 0.61°C, respectively, using SYBR® Green I dye and 81.67 ± 0.06°C and 76.04 ± 0.11°C, respectively, using Radiant™ Green dye.
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Affiliation(s)
- Ashley F Cowan
- Chemistry Department, Forensic Science Program, Towson University, 8000 York Rd, Towson, MD, 21252
| | - Kelly M Elkins
- Chemistry Department, Forensic Science Program, Towson University, 8000 York Rd, Towson, MD, 21252
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Arenas M, Pereira F, Oliveira M, Pinto N, Lopes AM, Gomes V, Carracedo A, Amorim A. Forensic genetics and genomics: Much more than just a human affair. PLoS Genet 2017; 13:e1006960. [PMID: 28934201 PMCID: PMC5608170 DOI: 10.1371/journal.pgen.1006960] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
While traditional forensic genetics has been oriented towards using human DNA in criminal investigation and civil court cases, it currently presents a much wider application range, including not only legal situations sensu stricto but also and, increasingly often, to preemptively avoid judicial processes. Despite some difficulties, current forensic genetics is progressively incorporating the analysis of nonhuman genetic material to a greater extent. The analysis of this material-including other animal species, plants, or microorganisms-is now broadly used, providing ancillary evidence in criminalistics in cases such as animal attacks, trafficking of species, bioterrorism and biocrimes, and identification of fraudulent food composition, among many others. Here, we explore how nonhuman forensic genetics is being revolutionized by the increasing variety of genetic markers, the establishment of faster, less error-burdened and cheaper sequencing technologies, and the emergence and improvement of models, methods, and bioinformatics facilities.
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Affiliation(s)
- Miguel Arenas
- Department of Biochemistry, Genetics and Immunology, University of Vigo, Vigo, Spain
- Instituto de Investigação e Inovação em Saúde (i3S), University of Porto, Porto, Portugal
- Institute of Molecular Pathology and Immunology of the University of Porto (IPATIMUP), Porto, Portugal
| | - Filipe Pereira
- Instituto de Investigação e Inovação em Saúde (i3S), University of Porto, Porto, Portugal
- Interdisciplinary Centre of Marine and Environmental Research (CIIMAR), University of Porto, Porto, Portugal
| | - Manuela Oliveira
- Instituto de Investigação e Inovação em Saúde (i3S), University of Porto, Porto, Portugal
- Institute of Molecular Pathology and Immunology of the University of Porto (IPATIMUP), Porto, Portugal
- Faculty of Sciences, University of Porto, Porto, Portugal
| | - Nadia Pinto
- Instituto de Investigação e Inovação em Saúde (i3S), University of Porto, Porto, Portugal
- Institute of Molecular Pathology and Immunology of the University of Porto (IPATIMUP), Porto, Portugal
- Centre of Mathematics of the University of Porto, Porto, Portugal
| | - Alexandra M. Lopes
- Instituto de Investigação e Inovação em Saúde (i3S), University of Porto, Porto, Portugal
- Institute of Molecular Pathology and Immunology of the University of Porto (IPATIMUP), Porto, Portugal
| | - Veronica Gomes
- Instituto de Investigação e Inovação em Saúde (i3S), University of Porto, Porto, Portugal
- Institute of Molecular Pathology and Immunology of the University of Porto (IPATIMUP), Porto, Portugal
| | - Angel Carracedo
- Institute of Forensic Sciences Luis Concheiro, University of Santiago de Compostela, Santiago de Compostela, Spain
- Genomics Medicine Group, CIBERER, University of Santiago de Compostela, Santiago de Compostela, Spain
| | - Antonio Amorim
- Instituto de Investigação e Inovação em Saúde (i3S), University of Porto, Porto, Portugal
- Institute of Molecular Pathology and Immunology of the University of Porto (IPATIMUP), Porto, Portugal
- Faculty of Sciences, University of Porto, Porto, Portugal
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10
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Debode F, Marien A, Gérard A, Francis F, Fumière O, Berben G. Development of real-time PCR tests for the detection of Tenebrio molitor in food and feed. Food Addit Contam Part A Chem Anal Control Expo Risk Assess 2017; 34:1421-1426. [DOI: 10.1080/19440049.2017.1320811] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Affiliation(s)
- Frédéric Debode
- Unit Traceability and Authentication, Walloon Agricultural Research Center (CRA-W), Gembloux, Belgium
| | - Aline Marien
- Unit Traceability and Authentication, Walloon Agricultural Research Center (CRA-W), Gembloux, Belgium
- European Union Reference Laboratory for Animal Proteins in feedingstuffs (EURL-AP), Gembloux, Belgium
| | - Amaury Gérard
- Unit Traceability and Authentication, Walloon Agricultural Research Center (CRA-W), Gembloux, Belgium
- Functional and Evolutionary Entomology, Gembloux Agro-Bio Tech – University of Liège (ULg), Gembloux, Belgium
| | - Frédéric Francis
- Functional and Evolutionary Entomology, Gembloux Agro-Bio Tech – University of Liège (ULg), Gembloux, Belgium
| | - Olivier Fumière
- Unit Traceability and Authentication, Walloon Agricultural Research Center (CRA-W), Gembloux, Belgium
- European Union Reference Laboratory for Animal Proteins in feedingstuffs (EURL-AP), Gembloux, Belgium
| | - Gilbert Berben
- Unit Traceability and Authentication, Walloon Agricultural Research Center (CRA-W), Gembloux, Belgium
- European Union Reference Laboratory for Animal Proteins in feedingstuffs (EURL-AP), Gembloux, Belgium
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11
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Mehta B, Daniel R, McNevin D. HRM and SNaPshot as alternative forensic SNP genotyping methods. Forensic Sci Med Pathol 2017; 13:293-301. [PMID: 28523436 DOI: 10.1007/s12024-017-9874-5] [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] [Accepted: 04/17/2017] [Indexed: 01/25/2023]
Abstract
Single nucleotide polymorphisms (SNPs) have been widely used in forensics for prediction of identity, biogeographical ancestry (BGA) and externally visible characteristics (EVCs). Single base extension (SBE) assays, most notably SNaPshot® (Thermo Fisher Scientific), are commonly used for forensic SNP genotyping as they can be employed on standard instrumentation in forensic laboratories (e.g. capillary electrophoresis). High resolution melt (HRM) analysis is an alternative method and is a simple, fast, single tube assay for low throughput SNP typing. This study compares HRM and SNaPshot®. HRM produced reproducible and concordant genotypes at 500 pg, however, difficulties were encountered when genotyping SNPs with high GC content in flanking regions and differentiating variants of symmetrical SNPs. SNaPshot® was reproducible at 100 pg and is less dependent on SNP choice. HRM has a shorter processing time in comparison to SNaPshot®, avoids post PCR contamination risk and has potential as a screening tool for many forensic applications.
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Affiliation(s)
- Bhavik Mehta
- National Centre for Forensic Studies, Faculty of Education, Science, Technology & Mathematics, University of Canberra, ACT, Bruce, 2617, Australia.
| | - Runa Daniel
- Office of the Chief Forensic Scientist, Forensic Services Department, Victoria Police, 31 Forensic Drive, Macleod, VIC, 3085, Australia
| | - Dennis McNevin
- National Centre for Forensic Studies, Faculty of Education, Science, Technology & Mathematics, University of Canberra, ACT, Bruce, 2617, Australia
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12
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Kranz W, Carroll C, Dixon DA, Goodpaster JV, Picard CJ. Factors Affecting Species Identifications of Blow Fly Pupae Based upon Chemical Profiles and Multivariate Statistics. INSECTS 2017; 8:E43. [PMID: 28398264 PMCID: PMC5492057 DOI: 10.3390/insects8020043] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/23/2017] [Revised: 03/30/2017] [Accepted: 04/01/2017] [Indexed: 11/17/2022]
Abstract
Alternative methods for the identification of species of blow fly pupae have been developed over the years that consist of the analyses of chemical profiles. However, the effect of biotic and abiotic factors that could influence the predictive manner for the tests have not been evaluated. The lipids of blowfly pupae (Cochliomyia macellaria, Lucilia cuprina, Lucilia sericata, and Phormia regina) were extracted in pentane, derivatized, and analyzed by total-vaporization solid phase microextraction gas chromatography-mass spectrometry (TV-SPME GC-MS). Peak areas for 26 compounds were analyzed. Here we evaluated one biotic factor (colonization) on four species of blow flies to determine how well a model produced from lipid profiles of colonized flies predicted the species of flies of offspring of wild-caught flies and found very good species identification following 10 generations of inbreeding. When we evaluated four abiotic factors in our fly rearing protocols (temperature, humidity, pupation substrate, and diet), we found that the ability to assign the chemical profile to the correct species was greatly reduced.
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Affiliation(s)
- William Kranz
- Department of Chemistry and Chemical Biology, Indiana University Purdue University Indianapolis, Indianapolis, IN 46202, USA.
| | - Clinton Carroll
- Department of Chemistry and Chemical Biology, Indiana University Purdue University Indianapolis, Indianapolis, IN 46202, USA.
| | - Darren A Dixon
- Department of Chemistry and Chemical Biology, Indiana University Purdue University Indianapolis, Indianapolis, IN 46202, USA.
| | - John V Goodpaster
- Department of Chemistry and Chemical Biology, Indiana University Purdue University Indianapolis, Indianapolis, IN 46202, USA.
- Forensic and Investigative Sciences Program, Indiana University Purdue University Indianapolis, Indianapolis, IN 46202, USA.
| | - Christine J Picard
- Forensic and Investigative Sciences Program, Indiana University Purdue University Indianapolis, Indianapolis, IN 46202, USA.
- Department of Biology, Indiana University Purdue University Indianapolis, Indianapolis, IN 46202, USA.
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13
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Voss SC, Magni P, Dadour I, Nansen C. Reflectance-based determination of age and species of blowfly puparia. Int J Legal Med 2016; 131:263-274. [DOI: 10.1007/s00414-016-1458-5] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2016] [Accepted: 10/05/2016] [Indexed: 01/25/2023]
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14
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Schmidt U, Hulkkonen J, Naue J. Detection of a G>C single nucleotide polymorphism within a repetitive DNA sequence by high-resolution DNA melting. Int J Legal Med 2016; 130:1181-4. [PMID: 26972692 DOI: 10.1007/s00414-016-1350-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2015] [Accepted: 02/25/2016] [Indexed: 11/26/2022]
Abstract
In standard forensic DNA analysis, single base mutations within short tandem repeats (STR) mostly escape detection. In this study, high-resolution DNA melting (HRM) is compared to minisequencing and Sanger sequencing as to determine the most suitable method for detection of a G to C mutation within a repetitive DNA sequence, the STR system DXS10161. It shows an ATG/ATC polymorphism surrounded by a variable number of (TATC) and (ATCT) motifs. Neutral base changes like G:C to C:G result in very low differences in the melting temperature (T m) of the PCR amplicons. By enhanced resolution of fluorescence vs. temperature in HRM, the technique showed to be suitable for detecting a G to C transversion in this repetitive DNA sequence context. Compared to minisequencing, HRM is more time- and cost-effective. Results were confirmed by Sanger sequencing.
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Affiliation(s)
- Ulrike Schmidt
- Institute of Legal Medicine, Freiburg University Medical Center, Albertstr. 9, 79104, Freiburg, Germany.
| | - Johannes Hulkkonen
- Institute of Legal Medicine, Freiburg University Medical Center, Albertstr. 9, 79104, Freiburg, Germany
- Department of Biology, University of Freiburg, Schänzlestr. 1, 79104, Freiburg, Germany
| | - Jana Naue
- Institute of Legal Medicine, Freiburg University Medical Center, Albertstr. 9, 79104, Freiburg, Germany
- Swammerdam Institute for Life Sciences, University of Amsterdam, Science Park 904, 1098 XH, Amsterdam, Netherlands
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15
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GilArriortua M, Saloña-Bordas MI, Cainé LM, Pinheiro F, M de Pancorbo M. Technical Note: "Mitochondrial and nuclear DNA approaches for reliable identification of Lucilia (Diptera, Calliphoridae) species of forensic interest from Southern Europe". Forensic Sci Int 2015; 257:393-397. [PMID: 26544633 DOI: 10.1016/j.forsciint.2015.10.010] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2015] [Revised: 09/01/2015] [Accepted: 10/15/2015] [Indexed: 12/11/2022]
Abstract
In forensic entomology, rapid and unambiguous identification of blowfly species is a critical prerequisite for accurately estimating the post-mortem interval (PMI). The conventional diagnosis of cadaveric entomofauna based on external characters is hampered by the morphological similarities between species, especially in immature stages. Genetic analysis has been shown to allow precise and reliable diagnosis and delimitation of insect species. Nevertheless, the taxonomy of some species remains unresolved. This study was focused on improving the effectiveness and accuracy of analysis based on the widely used cytochrome c oxidase subunit I barcode region (COI barcode, 658 bp), complemented by other mitochondrial and nuclear regions, such as cytochrome b (Cyt-b, 307 bp) and the second internal transcribed spacer (ITS2, 310-331 bp), for the identification of Southern European blowflies. We analyzed a total of 209 specimens, collected from 38 human corpses, belonging to three Calliphoridae genera and seven species: Chrysomya (Ch. albiceps), Calliphora (C. vicina and C. vomitoria), and Lucilia (L. sericata, L. ampullacea, L. caesar and L. illustris). These species are the most common PMI indicators in Portugal. The results revealed that unambiguous separation of species of the Lucilia genus requires different loci from the barcode region. Furthermore, we conclude that the ITS2 (310-331 bp) molecular marker is a promising diagnostic tool because its inter-specific discriminatory power enables unequivocal and consistent distinctions to be made, even between closely related species (L. caesar-L. illustris). This work also contributes new genetic data that may be of interest in performing species diagnosis for Southern European blowflies. Notably, to the best of our knowledge, we provide the first records of the Cyt-b (307 bp) locus for L. illustris and the ITS2 (310-331 bp) region for Iberian Peninsula Lucilia species.
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Affiliation(s)
- Maite GilArriortua
- Dpto de Zoología y Biología Celular Animal. Facultad de Ciencia y Tecnología. Universidad del País Vasco/Euskal Herriko Unibertsitatea (UPV/EHU), Barrio Sarriena s/n, 48940 Leioa, Spain; BIOMICs Research Group. Universidad del País Vasco/Euskal Herriko Unibertsitatea (UPV/EHU), Centro de Investigación "Lascaray" Ikergunea, Avda. Miguel de Unamuno 3, 01006 Vitoria-Gasteiz, Spain
| | - Marta I Saloña-Bordas
- Dpto de Zoología y Biología Celular Animal. Facultad de Ciencia y Tecnología. Universidad del País Vasco/Euskal Herriko Unibertsitatea (UPV/EHU), Barrio Sarriena s/n, 48940 Leioa, Spain; BIOMICs Research Group. Universidad del País Vasco/Euskal Herriko Unibertsitatea (UPV/EHU), Centro de Investigación "Lascaray" Ikergunea, Avda. Miguel de Unamuno 3, 01006 Vitoria-Gasteiz, Spain
| | - Laura M Cainé
- Delegação do Norte do Instituto Nacional de Medicina Legal, Jardim Carrilho Videira, 4050-167 Porto, Portugal; Faculdade de Medicina da Universidade do Porto, Alameda Prof. Hernâni Monteiro, 4200-316 Porto, Portugal
| | - Fátima Pinheiro
- Delegação do Norte do Instituto Nacional de Medicina Legal, Jardim Carrilho Videira, 4050-167 Porto, Portugal
| | - Marian M de Pancorbo
- Dpto de Zoología y Biología Celular Animal. Facultad de Ciencia y Tecnología. Universidad del País Vasco/Euskal Herriko Unibertsitatea (UPV/EHU), Barrio Sarriena s/n, 48940 Leioa, Spain; BIOMICs Research Group. Universidad del País Vasco/Euskal Herriko Unibertsitatea (UPV/EHU), Centro de Investigación "Lascaray" Ikergunea, Avda. Miguel de Unamuno 3, 01006 Vitoria-Gasteiz, Spain.
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16
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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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GilArriortua M, Salona Bordas MI, Cainé LM, Pinheiro F, de Pancorbo MM. Cytochrome b as a useful tool for the identification of blowflies of forensic interest (Diptera, Calliphoridae). Forensic Sci Int 2013; 228:132-6. [DOI: 10.1016/j.forsciint.2013.02.037] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2012] [Revised: 02/20/2013] [Accepted: 02/23/2013] [Indexed: 11/26/2022]
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Swisher KD, Munyaneza JE, Crosslin JM. Temporal and spatial analysis of potato psyllid haplotypes in the United States. ENVIRONMENTAL ENTOMOLOGY 2013; 42:381-393. [PMID: 23575030 DOI: 10.1603/en12261] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
The potato psyllid, Bactericera cockerelli (Sulc) (Hemiptera: Triozidae), is an economically important pest of potato (Solanum tuberosum L.) crops across the western and central United States, as it is known to cause psyllid yellows disease and to transmit the bacterium that causes zebra chip disease. Recent genotyping of B. cockerelli collected during the 2011 potato growing season identified three psyllid haplotypes within the western and central United States according to their geographical regions: northwestern, western, and central. To understand potato psyllid population dynamics before the year 2011, high resolution melting analysis of the B. cockerelli mitochondrial cytochrome oxidase I-like gene was used to identify the haplotypes of over 450 archived psyllids collected in the western and central United States between the years 1998 and 2010. Results show that the northwestern haplotype was present in Washington State as early as 1998 and has persisted in this region since that time. Likewise, psyllids of the western haplotype have also been present in Washington and Oregon before 2011.
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Affiliation(s)
- Kylie D Swisher
- United States Department of Agriculture-Agricultural Research Service 24106 North Bunn Rd., Prosser, WA 99350, USA
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Baumjohann K, Schiwy-Bochat KH, Rothschild MA. Maggots reveal a case of antemortal insect infestation. Int J Legal Med 2011; 125:487-92. [PMID: 21534007 DOI: 10.1007/s00414-011-0571-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2010] [Accepted: 04/01/2011] [Indexed: 11/26/2022]
Affiliation(s)
- Kristina Baumjohann
- Institute of Legal Medicine, University Hospital of Cologne, Melatenguertel 60-62, 50823 Cologne, Germany.
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Winder L, Phillips C, Richards N, Ochoa-Corona F, Hardwick S, Vink CJ, Goldson S. Evaluation of DNA melting analysis as a tool for species identification. Methods Ecol Evol 2010. [DOI: 10.1111/j.2041-210x.2010.00079.x] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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