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Akhter G, Ahmed I, Ahmad SM. Comparative Study of Two Himalayan Snow Trouts, Schizothorax esocinus and Schizothorax curvifrons Within the Schizothoracinae and Other Nearest Relatives of Cyprinidae, Inferred from Mitochondrial Sequences of Cytochrome b (Cyt-b) and Cytochrome Oxidase I (Co-I) Gene. Biochem Genet 2024:10.1007/s10528-024-10862-x. [PMID: 38896378 DOI: 10.1007/s10528-024-10862-x] [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: 10/31/2023] [Accepted: 06/06/2024] [Indexed: 06/21/2024]
Abstract
The Himalayan region encompasses varied aquatic ecosystems, characterized by the presence of diverse ichthyofauna, particularly represented by members of the Schizothorax genus, commonly referred to as snow trout. The primary objective of this work was to examine the molecular phylogeny of Schizothoracinae, specifically focusing on the two species, Schizothorax esocinus and Schizothorax curvifrons, which are known to inhabit the northern and north-eastern regions of the Himalayas. This investigation was conducted by analyzing the entire mitochondrial Cyt-b and Co-I gene sequences. The aligned Cyt-b and Co-I sequences for S. esocinus, S. curvifrons, and related members within the subfamily Schizothoracinae, spanned 1130 to 1141 and 1536 to 1551 base pairs, respectively. Using these gene, phylogenetic trees were created to compare Schizothoracinae species to other subfamilies of the family Cyprinidae (Barbinae, Alburninae, Leuciscinae, Xenocyprinae, Cyprininae, and Cultrinae). Genetic distances for Cyt-b and Co-I sequence at three hierarchical levels shows significant disparities in their average score. For Cyt-b, average p-distances for intraspecies, intragenus, and intrafamily were 2.13%, 4.1%, and 15.23%, respectively. Similarly, for Co-I, average p-distances were 1.19%, 3.6%, and 13.8% for intraspecies, intragenus, and intrafamily, respectively. Total number of haplotypes (h) based on Cyt-b and Co-I gene were 6 and 12 within the target Schizothorax spp. In the present study, the observed range of haplotype diversity (hd) for the Cyt-b gene varied from 0.00 to 0.847, with an average haplotype diversity of 0.847 ± 0.034. Similarly, for the Co-I gene, the observed haplotype diversity ranged from 0.00 to 0.931, with an average value of haplotype diversity estimated to be 0.931 ± 0.024. The results of the present study clearly shows that the representative species exhibited close affinities with members of Barbinae and Cyprininae, while other subfamilies formed distinct groups. The findings of the study also indicated that the Cyt-b and Co-I gene exhibits polymorphism and has the potential to serve as a marker for identifying genetic differentiation among populations based on ecological habitats. Mitochondrial Cyt-b and Co-I have been established as a universally accepted and validated genetic marker within a comprehensive bio-identification system at the species level.
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Affiliation(s)
- G Akhter
- Fish Nutrition Research Laboratory, Department of Zoology, University of Kashmir, Hazratbal, Srinagar, 190 006, Jammu and Kashmir, India
| | - I Ahmed
- Fish Nutrition Research Laboratory, Department of Zoology, University of Kashmir, Hazratbal, Srinagar, 190 006, Jammu and Kashmir, India.
| | - S M Ahmad
- Division of Biotechnology, Faculty of Veterinary Sciences & Animal Husbandry, Sher-E-Kashmir University of Agricultural Sciences and Technology, Srinagar, India
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Mukantayev K, Kanayev D, Zhumabekova S, Shevtsov A, Tursunov K, Mukanov K, Ramankulov Y. Optimization of polymerase chain reaction for the identification of Roe deer, Saiga, and Siberian stag living in Kazakhstan. Vet World 2022; 15:2067-2071. [PMID: 36313838 PMCID: PMC9615498 DOI: 10.14202/vetworld.2022.2067-2071] [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: 04/21/2022] [Accepted: 07/20/2022] [Indexed: 11/16/2022] Open
Abstract
Background and Aim: One of the reasons for the decline in the number of wild species of artiodactyls is poaching and the illegal trading of animal products. Molecular genetic identification of animals from a biological sample effectively proves poaching cases and illegal trade of animal products. This study aimed to develop a polymerase chain reaction (PCR) test that allows for species identification of artiodactyl animals that are most often subject to poaching. Materials and Methods: Genomic DNA was extracted from meat and blood samples of animals killed by poachers using commercial kits. Three pairs of primers were designed and used to amplify the cytochrome b gene fragment of Roe deer, Saiga antelope, and Siberian stag. Results: The proposed protocol allows amplification of specific PCR products of 542 bp with Roe deer DNA, 587 bp with Saiga DNA, and 525 bp with Siberian stag DNA. Specificity analysis showed no cross activity with DNA from other animal species. The detection limit of PCR ranged from 15.6 pg to 1.9 pg of DNA in 25 mL of the reaction mixture. Conclusion: Sequencing the amplified products and subsequent comparison with the corresponding reference sequence showed a similarity ranging from 99.99% to 100%. The PCR based on the developed primers demonstrated high sensitivity and specificity when using DNA from homogeneous and heterogeneous animals.
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Affiliation(s)
- Kanatbek Mukantayev
- Laboratory of Immunochemistry and Immunobiotechnology, National Center for Biotechnology, Nur-Sultan, Kazakhstan
| | - Darkhan Kanayev
- Laboratory of Immunochemistry and Immunobiotechnology, National Center for Biotechnology, Nur-Sultan, Kazakhstan
| | - Sholpan Zhumabekova
- Laboratory of Immunochemistry and Immunobiotechnology, National Center for Biotechnology, Nur-Sultan, Kazakhstan
| | - Alexander Shevtsov
- Laboratory of Applied Genetics, National Center for Biotechnology, Nur-Sultan, Kazakhstan
| | - Kanat Tursunov
- Laboratory of Immunochemistry and Immunobiotechnology, National Center for Biotechnology, Nur-Sultan, Kazakhstan
| | - Kasim Mukanov
- Laboratory of Applied Genetics, National Center for Biotechnology, Nur-Sultan, Kazakhstan
| | - Yerlan Ramankulov
- Laboratory of Applied Genetics, National Center for Biotechnology, Nur-Sultan, Kazakhstan
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Ghemrawi M, Fischinger F, Duncan G, Dukes MJ, Guilliano M, McCord B. Developmental validation of SpeID: A pyrosequencing-based assay for species identification. Forensic Sci Int Genet 2021; 55:102560. [PMID: 34507077 DOI: 10.1016/j.fsigen.2021.102560] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2021] [Revised: 06/16/2021] [Accepted: 06/30/2021] [Indexed: 11/19/2022]
Abstract
In crime scenes, biological exhibits are often human in origin, yet biological stains from other fauna may also be present at a crime scene, creating confusion during an investigation. Furthermore, identifying the source of a biological sample can be critical during an investigation. To identify the presence of biological material from non-human sources, it is common to use genetic markers within mitochondrial DNA such as cytochrome b, 16S rRNA, and 12S rRNA genes. This process usually requires DNA sequencing, a process that is neither quick nor easy. In general, a faster, more standardized method for species identification from tissue and body fluids is desirable.For this reason, we have developed a vertebrate specific real-time quantitation method that is followed by an automated pyrosequencing-based procedure that sequences a short fragment within the 12S rRNA gene. Using no more than 35 bases, the assay can distinguish between 32 different species commonly found in and around a household with a turnaround time of 6 h from extraction to sequencing. -Using this procedure, up to 48 samples can be run at a time without the need for expensive reagents or bioinformatic skills.
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Affiliation(s)
- Mirna Ghemrawi
- Department of Chemistry and Biochemistry, Florida International University, Miami, FL 33199, United States
| | | | - George Duncan
- Nova Southeastern University, Dania Beach, Fl 33004, United State
| | | | | | - Bruce McCord
- Department of Chemistry and Biochemistry, Florida International University, Miami, FL 33199, United States.
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Biteye B, Fall AG, Seck MT, Ciss M, Diop M, Gimonneau G. Host-feeding patterns of Aedes (Aedimorphus) vexans arabiensis, a Rift Valley Fever virus vector in the Ferlo pastoral ecosystem of Senegal. PLoS One 2019; 14:e0215194. [PMID: 31584948 PMCID: PMC6777780 DOI: 10.1371/journal.pone.0215194] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2019] [Accepted: 09/20/2019] [Indexed: 12/02/2022] Open
Abstract
Background Host-vector contact is a key factor in vectorial capacity assessment and thus the transmission of mosquito-borne viruses such as Rift Valley Fever (RVF), an emerging zoonotic disease of interest in West Africa. The knowledge of the host-feeding patterns of vector species constitutes a key element in the assessment of their epidemiological importance in a given environment. The aim of this work was to identify the blood meal origins of the mosquito Aedes vexans arabiensis, the main vector of RVF virus in the Ferlo pastoral ecosystem of Senegal. Methodology/principal findings Engorged female mosquitoes were collected in Younouféré in the pastoral ecosystem in the Ferlo region during the 2014 rainy season. CO2-baited CDC light traps were set at six points for two consecutive nights every month from July to November. Domestic animals present around traps were identified and counted for each trapping session. Blood meal sources of engorged mosquitoes were identified using a vertebrate-specific multiplexed primer set based on cytochrome b. Blood meal sources were successfully identified for 319 out of 416 blood-fed females (76.68%), of which 163 (51.1%) were single meals, 146 (45.77%) mixed meals from two different hosts and 10 (3.13%) mixed meals from three different hosts. Aedes vexans arabiensis fed preferentially on mammals especially on horse compared to other hosts (FR = 46.83). Proportions of single and mixed meals showed significant temporal and spatial variations according to the availability of the hosts. Conclusion Aedes vexans arabiensis shows an opportunistic feeding behavior depending on the host availability. This species fed preferentially on mammals especially on horses (primary hosts) and ruminants (secondary hosts).
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Affiliation(s)
- Biram Biteye
- Institut Sénégalais de Recherches Agricoles/Laboratoire National de l’Elevage et de Recherches Vétérinaires BP 2057 Dakar-Hann, Sénégal
- * E-mail:
| | - Assane Gueye Fall
- Institut Sénégalais de Recherches Agricoles/Laboratoire National de l’Elevage et de Recherches Vétérinaires BP 2057 Dakar-Hann, Sénégal
| | - Momar Talla Seck
- Institut Sénégalais de Recherches Agricoles/Laboratoire National de l’Elevage et de Recherches Vétérinaires BP 2057 Dakar-Hann, Sénégal
| | - Mamadou Ciss
- Institut Sénégalais de Recherches Agricoles/Laboratoire National de l’Elevage et de Recherches Vétérinaires BP 2057 Dakar-Hann, Sénégal
| | - Mariame Diop
- Institut Sénégalais de Recherches Agricoles/Laboratoire National de l’Elevage et de Recherches Vétérinaires BP 2057 Dakar-Hann, Sénégal
| | - Geoffrey Gimonneau
- CIRAD, UMR INTERTRYP, Montpellier, France
- Centre International de Recherche–Développement sur l’Elevage en zone subhumide, Bobo-Dioulasso 01, Burkina Faso
- INTERTRYP, Univ Montpellier, CIRAD, IRD, Montpellier, France
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Bowman S, McNevin D, Venables SJ, Roffey P, Richardson A, Gahan ME. Species identification using high resolution melting (HRM) analysis with random forest classification. AUST J FORENSIC SCI 2017. [DOI: 10.1080/00450618.2017.1315835] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Affiliation(s)
- Sorelle Bowman
- National Centre for Forensic Studies, University of Canberra, Bruce, Australia
| | - Dennis McNevin
- National Centre for Forensic Studies, University of Canberra, Bruce, Australia
| | | | - Paul Roffey
- Forensics, Specialist Operations, Australian Federal Police, Canberra, Australia
| | - Alice Richardson
- National Centre for Epidemiology & Population Health, Australian National University, Canberra, Australia
| | - Michelle E. Gahan
- National Centre for Forensic Studies, University of Canberra, Bruce, Australia
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Lopez-Oceja A, Gamarra D, Borragan S, Jiménez-Moreno S, de Pancorbo MM. New cyt b gene universal primer set for forensic analysis. Forensic Sci Int Genet 2016; 23:159-165. [PMID: 27206224 DOI: 10.1016/j.fsigen.2016.05.001] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2016] [Revised: 05/03/2016] [Accepted: 05/04/2016] [Indexed: 11/28/2022]
Abstract
Analysis of mitochondrial DNA, and in particular the cytochrome b gene (cyt b), has become an essential tool for species identification in routine forensic practice. In cases of degraded samples, where the DNA is fractionated, universal primers that are highly efficient for the amplification of the target region are necessary. Therefore, in the present study a new universal cyt b primer set with high species identification capabilities, even in samples with highly degraded DNA, has been developed. In order to achieve this objective, the primers were designed following the alignment of complete sequences of the cyt b from 751 species from the Class of Mammalia listed in GenBank. A highly variable region of 148bp flanked by highly conserved sequences was chosen for placing the primers. The effectiveness of the new pair of primers was examined in 63 animal species belonging to 38 Families from 14 Orders and 5 Classes (Mammalia, Aves, Reptilia, Actinopterygii, and Malacostraca). Species determination was possible in all cases, which shows that the fragment analyzed provided a high capability for species identification. Furthermore, to ensure the efficiency of the 148bp fragment, the intraspecific variability was analyzed by calculating the concordance between individuals with the BLAST tool from the NCBI (National Center for Biotechnological Information). The intraspecific concordance levels were superior to 97% in all species. Likewise, the phylogenetic information from the selected fragment was confirmed by obtaining the phylogenetic tree from the sequences of the species analyzed. Evidence of the high power of phylogenetic discrimination of the analyzed fragment of the cyt b was obtained, as 93.75% of the species were grouped within their corresponding Orders. Finally, the analysis of 40 degraded samples with small-size DNA fragments showed that the new pair of primers permits identifying the species, even when the DNA is highly degraded as it is very common in forensic samples.
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Affiliation(s)
- A Lopez-Oceja
- BIOMICS Research Group, University of the Basque Country, UPV/EHU, 01006, Vitoria-Gasteiz, Spain
| | - D Gamarra
- BIOMICS Research Group, University of the Basque Country, UPV/EHU, 01006, Vitoria-Gasteiz, Spain
| | - S Borragan
- Parque de la Naturaleza de Cabárceno, 39693, Obregón, Cantabria, Spain
| | - S Jiménez-Moreno
- Area of Forensic and Legal Medicine, Pathology and Surgery Dept., Miguel Hernández University of Elche, 03550, Elche, Alicante, Spain
| | - M M de Pancorbo
- BIOMICS Research Group, University of the Basque Country, UPV/EHU, 01006, Vitoria-Gasteiz, Spain.
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Han SH, Oh HS, Cho IC. Identifying the species of origin in commercial sausages in South Korea. JOURNAL OF APPLIED ANIMAL RESEARCH 2016. [DOI: 10.1080/09712119.2015.1124334] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Affiliation(s)
- Sang-Hyun Han
- Department of Science Education, Jeju National University, Jeju, South Korea
- Educational Science Research Institute, Jeju National University, Jeju, South Korea
| | - Hong-Shik Oh
- Department of Science Education, Jeju National University, Jeju, South Korea
| | - In-Cheol Cho
- Subtropical Animal Experiment Station, National Institute of Animal Science, RDA, Jeju, South Korea
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Ciavaglia S, Donnellan S, Henry J, Linacre A. Species identification of protected carpet pythons suitable for degraded forensic samples. Forensic Sci Med Pathol 2014; 10:295-305. [DOI: 10.1007/s12024-014-9573-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/05/2014] [Indexed: 10/25/2022]
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Identification of human DNA in forensic evidence by loop-mediated isothermal amplification combined with a colorimetric gold nanoparticle hybridization probe. Int J Legal Med 2014; 128:923-31. [PMID: 24827529 DOI: 10.1007/s00414-014-1018-9] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2013] [Accepted: 04/30/2014] [Indexed: 10/25/2022]
Abstract
A DNA test based on loop-mediated isothermal amplification (LAMP) and colorimetric gold nanoparticle (AuNP) hybridization probe to detect the presence of human DNA in forensic evidence was developed. The LAMP primer set targeted eight regions of the human cytochrome b, and its specificity was verified against the DNA of 11 animal species, which included animals closely related to humans, such as chimpanzee and orangutan. By using the AuNP probe, sequence-specific LAMP product could be detected and the test result could be visualized through the change in color. The limit of detection was demonstrated with reproducibility to be as low as 718 fg of genomic DNA, which is equivalent to approximately 100 plasmid DNA copies containing the cytochrome b DNA target region. A simple DNA extraction method for the commonly found forensic biological samples was also devised to streamline the test process. This LAMP-AuNP human DNA test showed to be a robust, specific, and cost-effective tool for the forensic identification of human specimens without requiring sophisticated laboratory instruments.
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Species identification through mitochondrial rRNA genetic analysis. Sci Rep 2014; 4:4089. [PMID: 24522485 PMCID: PMC5379257 DOI: 10.1038/srep04089] [Citation(s) in RCA: 73] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2013] [Accepted: 01/27/2014] [Indexed: 12/22/2022] Open
Abstract
Inter-species and intraspecific variations in mitochondrial DNA (mtDNA) were observed in a bioinformatics analysis of the mitochondrial genomic sequences of 11 animal species. Some highly conserved regions were identified in the mitochondrial 12S and 16S ribosomal RNA (rRNA) genes of these species. To test whether these sequences are universally conserved, primers were designed to target the conserved regions of these two genes and were used to amplify DNA from 21 animal tissues, including two of unknown origin. By sequencing these PCR amplicons and aligning the sequences to a database of non-redundant nucleotide sequences, it was confirmed that these amplicons aligned specifically to mtDNA sequences from the expected species of origin. This molecular technique, when combined with bioinformatics, provides a reliable method for the taxonomic classification of animal tissues.
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11
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Authentication of animal signatures in traditional Chinese medicine of Lingyang Qingfei Wan using routine molecular diagnostic assays. Mol Biol Rep 2014; 41:2485-91. [PMID: 24445529 DOI: 10.1007/s11033-014-3105-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2013] [Accepted: 01/06/2014] [Indexed: 10/25/2022]
Abstract
Lingyang Qingfei Wan produced by Beijing TongRenTang is a long-standing and popular medicine in China and international pharmaceutical markets. Concerns continue to be raised about the legality of usage of saiga antelope, which was defined as endangered species by Convention on International Trade in Endangered Species of Wild Fauna and Flora legislation and internal legislation in China. Therefore, the alternative pill in which substitutes saiga antelope with goat in the formula of Lingyang Qingfei Wan was developed. In order to authenticate the origin of animal contents in Lingyang Qingfei Wan and its alternative pill, molecular diagnostic assay was utilized by mtDNA polymorphism analysis. Four universal primer pairs containing mtDNA 12SrRNA, 16SrRNA, cytochrome b gene and cytochrome oxidase I were employed to obtain species-specific sequences of saiga antelope and goat, and multiple species-specific primer pairs for saiga antelope and goat were used to identify the animal origin in patent pills according to nucleotide polymorphisms between the two species. In additions, alternative techniques were attempted surrounding dilemmas of low concentration of target DNAs and presence of PCR-inhibitory substances in organic ingredients within complex pill. Results revealed that all species-specific primers could be successfully used for authentication of animal origin within complex pill, and sample preprocessing was critical during experimental manipulation. Internal positive control was an efficient and cost-effective way to assist in monitoring the potential interference from inhibitory substances which existed in the highly processed pills.
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Xie J, Zhu W, Zhou Y, Liu Z, Chen Y, Zhao Z. Identification of mammalian species using the short and highly variable regions of mitochondrial DNA. ACTA ACUST UNITED AC 2014; 26:550-4. [PMID: 24438314 DOI: 10.3109/19401736.2013.873892] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
The mitochondrial DNA (mtDNA) typing is useful for the species determination of degraded samples and the nucleotide diversity of target fragments across species is crucial for the discrimination. In this study, the short and highly polymorphic regions flanked by two conserved termini were sought by the sequence alignment of mtDNA across species and two target regions located at 12S rRNA gene were characterized. Two universal primer sets were developed that appear to be effective for a wide variety of mammalian species, even for domestic birds. The two target regions could be efficiently amplified using their universal primer sets on degraded samples and provide sufficient information for species determination. Therefore, the two short and highly variable target regions might provide a high discriminative capacity and should be suitable for the species determination of degraded samples.
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Affiliation(s)
- Jianhui Xie
- Department of Forensic Medicine, Shanghai Medical College, Fudan University , Shanghai , China
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Grisafi D, Pozzobon M, Dedja A, Vanzo V, Tomanin R, Porzionato A, Macchi V, Salmaso R, Scarpa M, Cozzi E, Fassina A, Navaglia F, Maran C, Onisto M, Caenazzo L, De Coppi P, De Caro R, Chiandetti L, Zaramella P. Human amniotic fluid stem cells protect rat lungs exposed to moderate hyperoxia. Pediatr Pulmonol 2013; 48:1070-80. [PMID: 23533160 DOI: 10.1002/ppul.22791] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/18/2012] [Accepted: 02/17/2013] [Indexed: 01/24/2023]
Abstract
BACKGROUND Treatment of bronchopulmonary dysplasia (BPD) remains as yet an unmet clinical need and recently stem cells have been proposed as a therapeutic tool in animal models. We investigated the role of amniotic fluid stem cells (AFS) in an adult rat model of hyperoxia lung injury. METHODS Fifty Sprague-Dawley rats were, at birth, randomly exposed to moderate hyperoxia or room air for 14 days and a single dose of human amniotic fluid stem (hAFS) or human Fibroblasts (hF), cells was delivered intratracheally (P21). At P42 animals were euthanized and lung tissue examined using histology, immunohistochemistry, PCR, and ELISA. hAFS cells characterization and homing were studied by immunofluorescence. RESULTS In rats treated with hAFS and hF cells 16S human rRNA fragment was detected. Despite a low level of pulmonary hAFS cell retention (1.43 ± 0.2% anti-human-mitochondria-positive cells), the lungs of the treated animals revealed higher secondary crest numbers and lower mean linear intercept and alveolar size, than those exposed to hyperoxia, those left untreated or treated with hF cells. Except for those treated with hAFS cells, moderate hyperoxia induced an increase in protein content of IL-6, IL-1β, as well as IF-γ and TGF-1β in lung tissues. High VEGF expression and arrangement of capillary architecture in hAFS cell group were also detected. CONCLUSIONS Treatment with hAFS cells has a reparative potential through active involvement of cells in alveolarization and angiogenesis. A downstream paracrine action was also taken into account, in order to understand the immunodulatory response.
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Affiliation(s)
- Davide Grisafi
- Neonatal Intensive Care Unit, Women's and Children's Health Department, University Padova Hospital, Padova, Italy; Gene Therapy Laboratory, Women's and Children's Health Department, University of Padova, Padova, Italy
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Ablimit A, Qin W, Shan W, Wu W, Ling F, Ling KH, Zhao C, Zhang F, Ma Z, Zheng X. Genetic diversities of cytochrome B in Xinjiang Uyghur unveiled its origin and migration history. BMC Genet 2013; 14:100. [PMID: 24103151 PMCID: PMC3852047 DOI: 10.1186/1471-2156-14-100] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2012] [Accepted: 10/04/2013] [Indexed: 11/19/2022] Open
Abstract
Background Uyghurs are one of the many populations of Central Eurasia that is considered to be genetically related to Eastern and Western Eurasian populations. However, there are some different opinions on the relative importance of the degree of Eastern and Western Eurasian genetic influence. In addition, the genetic diversity of the Uyghur in different geographic locations has not been clearly studied. Results In this study, we are the first to report on the DNA polymorphism of cytochrome B in the Uyghur population located in Xinjiang in northwest China. We observed a total of 102 mutant sites in the 240 samples that were studied. The average number of mutated nucleotides in the samples was 5.126. A total of 93 different haplotypes were observed. The gene diversity and discrimination power were 0.9480 and 0.9440, respectively. There were founder and bottleneck haplotypes observed in Xinjiang Uyghurs. Xinjiang Uyghurs are more genetically related to Chinese population in genetics than to Caucasians. Moreover, there was genetic diversity between Uyghurs from the southern and northern regions. There was significance in genetic distance between the southern Xinjiang Uyghurs and Chinese population, but not between the northern Xinjiang Uyghurs and Chinese. The European vs. East Asian contribution to the ten regional Uyghur groups varies among the groups and the European contribution to the Uyghur increases from north to south geographically. Conclusion This study is the first report on DNA polymorphisms of cytochrome B in the Uyghur population. The study also further confirms that there are significant genetic differences among the Uyghurs in different geographical locations.
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Affiliation(s)
- Abdurahman Ablimit
- Life science and technology, Xinjiang University, Xinjiang Key Laboratory of Biological Resources and Genetic Engineering, Urumqi 830046, China.
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Wozney KM, Wilson PJ. Real-time PCR detection and quantification of elephantid DNA: Species identification for highly processed samples associated with the ivory trade. Forensic Sci Int 2012; 219:106-12. [DOI: 10.1016/j.forsciint.2011.12.006] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2011] [Revised: 12/12/2011] [Accepted: 12/18/2011] [Indexed: 10/14/2022]
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Corato S, Giuliodori A, Ponzano E, Novelli E, Rodriguez D, Caenazzo L. Two 16S rRNA mitochondrial markers for species identification in forensic science. FORENSIC SCIENCE INTERNATIONAL GENETICS SUPPLEMENT SERIES 2011. [DOI: 10.1016/j.fsigss.2011.09.053] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/15/2022]
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17
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Rosli MKA, Zamzuriada AS, Syed-Shabthar SMF, Mahani MC, Abas-Mazni O, Md-Zain BM. Optimization of PCR conditions to amplify Cyt b, COI and 12S rRNA gene fragments of Malayan gaur (Bos gaurus hubbacki) mtDNA. GENETICS AND MOLECULAR RESEARCH 2011; 10:2554-68. [PMID: 22033937 DOI: 10.4238/2011.october.19.2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
PCR has been extensively used for amplification of DNA sequences. We conducted a study to obtain the best amplification conditions for cytochrome b (Cyt b), cytochrome c oxidase I (COI) and 12S rRNA (12S) gene fragments of Malayan gaur mtDNA. DNA from seven Malayan gaur samples were extracted for PCR amplification. Various trials and combinations were tested to determine the best conditions of PCR mixture and profile to obtain the best PCR products for sequencing purposes. Four selected target factors for enhancing PCR, annealing temperature, concentration of primer pairs, amount of Taq polymerase, and PCR cycle duration, were optimized by keeping the amount of DNA template (50 ng/μL) and concentration of PCR buffer (1X), MgCl(2) (2.5 mM) and dNTP mixture (200 μM each) constant. All genes were successfully amplified, giving the correct fragment lengths, as assigned for both forward and reverse primers. The optimal conditions were determined to be: 0.1 μM primers for Cyt b and COI, 0.3 μM primers for 12S, 1 U Taq polymerase for all genes, 30 s of both denaturation and annealing cycles for Cyt b, 1 min of both stages for 12S and COI and annealing temperature of 58.4 ° C for Cyt b, 56.1 ° C for 12S and 51.3 ° C for COI. PCR products obtained under these conditions produced excellent DNA sequences.
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Affiliation(s)
- M K A Rosli
- School of Environmental and Natural Resource Sciences, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, Bangi, Selangor, Malaysia
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Discrimination between human and animal DNA: application of a duplex polymerase chain reaction to forensic identification. Am J Forensic Med Pathol 2011; 32:180-2. [PMID: 21263288 DOI: 10.1097/paf.0b013e31820c2bba] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Identification of a report's species is one of the basic analyses in forensic laboratories. The authors report the case of 6 bone fragments recovered in a wooded area, which were not attributable to 1 animal species on the basis of morphologic examination. The aim of this study was to develop a duplex polymerase chain reaction (PCR) to discriminate human and animal origin of bone fragments. The method is based on the PCR amplification of cytochrome b and a 16S ribosomal mitochondrial DNA fragment, which has never been tested up to now. Our protocol combines a single-round PCR with direct visualization of amplicons in agarose gel, without sequencing analysis of the PCR products. The presence of a single band (359 bp) indicates a nonhuman origin of the sample, whereas 2 bands (157 and 359 bp) indicate a human biologic sample.This method revealed to be useful for forensic purposes because the 16S ribosomal mitochondrial DNA is a small human-specific fragment that is easily amplifiable even with degraded DNA from biologic materials such as old bones.
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Li B, Xu YC, Ma Y, Elmeros M, Lan TM, Bai SY. A PCR-RFLP-based method to distinguish sable (Martes zibellina) and pine marten (Martes martes). ACTA ACUST UNITED AC 2011. [DOI: 10.1007/s13364-011-0027-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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20
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A DNA microarray for species identification of cetacean animals in Korean water. BIOCHIP JOURNAL 2010. [DOI: 10.1007/s13206-010-4306-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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21
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Kim W, Kim S, Choi H, Truong ND, Thong LM, Kim JH, Xiao R, Park KK, Seo K, Lee H, Kim BS, Yoo MH, Park C. Discrimination of animal species using polymorphisms of the nuclear gene zinc finger protein 238. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2010; 58:2398-2402. [PMID: 20085280 DOI: 10.1021/jf9036968] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
We screened 3750 single exonic genes listed in the intronless genes in the eukaryotes (SEGE) database and performed bioinformatic analyses to identify candidate genes for new species-specific markers. A set of PCR primers for the conserved regions of ZNF238 was developed and used to amplify the 823 bp DNA fragment. We compared nucleotide variations of the PCR products among 20 species plus two subspecies of animals, which led to the identification of interspecies nucleotide variations. To establish a simple method for the analysis of species-specific DNA polymorphisms using ZNF238, we developed a PCR-RFLP method using HhaI and HpyCH4IV restriction enzymes for 13 species. For the remaining species, the direct sequencing of PCR products provided additional SNPs, enabling precise species classification. As a result, we report here that a new nuclear DNA marker, ZNF238, can be used to increase the accuracy of species identification among euteleostomi (bony vertebrates).
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Affiliation(s)
- Won Kim
- Department of Animal Biotechnology, Konkuk University, Seoul 143-701, South Korea
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Active trachoma and ocular Chlamydia trachomatis infection in two Gambian regions: on course for elimination by 2020? PLoS Negl Trop Dis 2009; 3:e573. [PMID: 20027217 PMCID: PMC2791206 DOI: 10.1371/journal.pntd.0000573] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2009] [Accepted: 11/13/2009] [Indexed: 11/24/2022] Open
Abstract
Background Trachoma has been endemic in The Gambia for decades. National trachoma control activities have been in place since the mid-1980's, but with no mass antibiotic treatment campaign. We aimed to assess the prevalence of active trachoma and of actual ocular Chlamydia trachomatis infection as measured by polymerase chain reaction (PCR) in the two Gambian regions that had had the highest prevalence of trachoma in the last national survey in 1996 prior to planned national mass antibiotic treatment distribution in 2006. Methodology/Principal Findings Two stage random sampling survey in 61 randomly selected Enumeration Areas (EAs) in North Bank Region (NBR) and Lower River Region (LRR). Fifty randomly selected children aged under 10 years were examined per EA for clinical signs of trachoma. In LRR, swabs were taken to test for ocular C. trachomatis infection. Unadjusted prevalences of active trachoma were calculated, as would be done in a trachoma control programme. The prevalence of trachomatous inflammation, follicular (TF) in the 2777 children aged 1–9 years was 12.3% (95% CI 8.8%–17.0%) in LRR and 10.0% (95% CI 7.7%–13.0%) in NBR, with significant variation within divisions (p<0.01), and a design effect of 3.474. Infection with C. trachomatis was found in only 0.3% (3/940) of children in LRR. Conclusions/Significance This study shows a large discrepancy between the prevalence of trachoma clinical signs and ocular C. trachomatis infection in two Gambian regions. Assessment of trachoma based on clinical signs alone may lead to unnecessary treatment, since the prevalence of active trachoma remains high but C. trachomatis infection has all but disappeared. Assuming that repeated infection is required for progression to blinding sequelae, blinding trachoma is on course for elimination by 2020 in The Gambia. Trachoma is the leading infectious cause of blindness worldwide, and is mainly found in tropical and poor countries. It is caused by infection of the eyes with the bacterium Chlamydia trachomatis. However, sometimes the clinical signs of disease can be present without infection being detected. Control efforts involve surgery, antibiotic treatment, face washing, and environmental improvement for better hygiene. Surveys of trachoma help countries to know whether and where they should implement control interventions. The Gambia is found in West Africa and has suffered from trachoma for decades. We conducted a survey of two Gambian regions to look at how much trachoma disease and C. trachomatis infection there is in the eyes. We found that although there was enough disease (≥10%) to warrant antibiotic treatment for everyone in the regions, there was nearly no infection (0.3%). This means that using clinical signs alone to make treatment decisions in low prevalence settings like The Gambia can lead to the waste of scarce resources. Our results also suggest that since less than 1% of children are infected with C. trachomatis, The Gambia is on course to achieve the World Health Organization's aim of eliminating blinding trachoma by the year 2020.
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Ma G, Chang H, Li S, Chen H, Ji D, Geng R, Chang C, Li Y. Phylogenetic relationships and status quo of colonies for gayal based on analysis of cytochrome B gene partial sequences. J Genet Genomics 2009; 34:413-9. [PMID: 17560527 DOI: 10.1016/s1673-8527(07)60045-9] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2006] [Accepted: 11/23/2006] [Indexed: 10/23/2022]
Abstract
Thirty-three mutations and four different haplotypes were found when cytochrome b(Cytb) gene partial sequences of 12 gayals were analyzed. Together with sequences of Bos indicus, Bos taurus, Bos grunniens and Bos gaurus with Bubalus bubalis as the out group, the partial sequences of Cytb gene of gayals were aligned and base composition and nucleotide variation of Cytb gene were analyzed. The phylogenetic trees were constructed by the NJ method and the MP method respectively, both supporting almost the same topology. Gayal is an independent species of Bos from Bos indicus, Bos taurus and Bos gaurus. The results also indicate that a great proportion of gayal bloodline was invaded by other species, and the protection of gayal is facing a formidable situation.
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Affiliation(s)
- Guolong Ma
- Animal Science and Technology College, Yangzhou University, Yangzhou 225009, China
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24
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Forensic species identification based on size variation of mitochondrial DNA hypervariable regions. Int J Legal Med 2008; 123:177-84. [PMID: 19052767 DOI: 10.1007/s00414-008-0306-7] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2008] [Accepted: 11/17/2008] [Indexed: 10/21/2022]
Abstract
In this study, two new systems for species identification were developed based on size variation of mitochondrial DNA hypervariable regions among animals: one was a conventional method using non-fluorescent primer sets and agarose gel electrophoresis and the other was an automatic method using fluorescent primer sets and capillary electrophoresis. DNA samples from 18 mammal, four birds, and 19 fish species were amplified using three primer sets specific for mammals, birds, and fishes, respectively. The differences in the sizes of the polymerase chain reaction (PCR) products, ranging from about 350 to 900 bp, permitted us to identify species. These systems were successfully applied to various specimens from several criminal cases. In unknown samples, which were different in size from reference DNA markers, sequencing of the PCR products and subsequent BLAST analysis helped to identify species. Furthermore, the sequence data provided us with information on individuals. Because these species identification methods are very simple, easy, rapid, and exact, they are useful in the field of forensic science.
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Díaz S, Kienast ME, Villegas-Castagnasso EE, Pena NL, Manganare MM, Posik D, Peral-García P, Giovambattista G. Substitution of Human for Horse Urine Disproves an Accusation of Doping*. J Forensic Sci 2008; 53:1145-8. [DOI: 10.1111/j.1556-4029.2008.00797.x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Caenazzo L, Ceola F, Ponzano E, Novelli E. Human identification analysis to forensic purposes with two mitochondrial markers in polyacrilamide mini gel. FORENSIC SCIENCE INTERNATIONAL GENETICS SUPPLEMENT SERIES 2008. [DOI: 10.1016/j.fsigss.2007.12.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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Tobe SS, Linacre AMT. A multiplex assay to identify 18 European mammal species from mixtures using the mitochondrial cytochrome b gene. Electrophoresis 2008; 29:340-7. [PMID: 18080254 DOI: 10.1002/elps.200700706] [Citation(s) in RCA: 77] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
A novel species-specific multiplex to identify 18 common European mammalian species (badger, cat, cow, dog, donkey, fox, goat, guinea pig, harvest mouse, hedgehog, horse, house mouse, human, pig, rabbit, rat, red deer and sheep), many of which are often associated with forensic investigations, has been developed. The assay is based on the mitochondrial cytochrome b gene, which is commonly used in species identification and phylogeny studies. Areas of homology and variation were identified and were used to create universal and species-specific primers. The species-specific primers were designed such that they will only react with the species for which they were designed. Two primer sets were designed for each species making the test self-confirmatory. All primer sets produced the expected results. The multiplex was balanced at template concentration of 40 000 copies (approximately 1.36 pg). Validation was accomplished by analysing the same sample ten times to determine run variation and several samples for each species to determine between-sample variation. Twenty-eight additional mammalian species were reacted with the multiplex. The multiplex provides, for the first time, a definitive method for identification of species in a forensic context.
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Affiliation(s)
- Shanan S Tobe
- Department of Pure and Applied Chemistry, University of Strathclyde, Glasgow, UK.
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Melton T, Holland C. Routine forensic use of the mitochondrial 12S ribosomal RNA gene for species identification. J Forensic Sci 2007; 52:1305-7. [PMID: 17868265 DOI: 10.1111/j.1556-4029.2007.00553.x] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Since July 2004, Mitotyping Technologies has been amplifying and sequencing a approximately 150 base pair fragment of mitochondrial DNA (mtDNA) that codes for 12S ribosomal RNA, to identify the species origin of nonhuman casework samples. The approximately 100 base pair sequence product is searched at http://www.ncbi.nlm.nih.gov/BLAST and the species match is reported. The use of this assay has halved the number of samples for which no mtDNA results are obtained and is especially useful on hairs and degraded samples. The availability of species determination may aid forensic investigators in opening or closing off lines of inquiry where a highly probative but challenging sample has been collected.
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Affiliation(s)
- Terry Melton
- Mitotyping Technologies, 2565 Park Center Boulevard, Suite 200, State College, PA 16801, USA.
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Pepe T, Trotta M, Di Marco I, Anastasio A, Bautista JM, Cortesi ML. Fish species identification in surimi-based products. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2007; 55:3681-5. [PMID: 17417868 DOI: 10.1021/jf063321o] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/14/2023]
Abstract
Whole fish morphologically identified as belonging to Theragra chalcogramma, Merluccius merluccius, Merluccius hubbsi, and Merluccius capensis and 19 fish products commercialized as surimi with different commercial brands and labeled as T. chalcogramma were analyzed by direct sequence analysis of the cytochrome b gene. A phylogenetic analysis of surimi products was performed as well. Results demonstrated that mislabeling is a large-scale phenomenon, since 84.2% of surimi-based fish products sold as T. chalcogramma (16/19) were prepared with species different from the one declared. In fact, only three samples (samples 15-17) were found to belong to T. chalcogramma. In the remaining samples, Merluccidae (samples 4-14), Gadidae (samples 18 and 19), Sparidae (sample 1), and Pomacentridae (samples 2 and 3) families were detected. A phylogenetic tree was constructed, and the bootstrap value was calculated. According to this methodology, 11 samples were grouped in the same clade as Merluccius spp.
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Affiliation(s)
- Tiziana Pepe
- Dipartimento di Scienze Zootecniche e Ispezione degli Alimenti, Sezione Ispezione, Falcoltà di Medicina Veterinaria, Università Federico II, Napoli, Italy
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Alonso A, Albarran C, Martín P, García P, Capilla J, García O, de la Rua C, Izaguirre N, Pereira F, Pereira L, Amorim A, Sancho M. Usefulness of microchip electrophoresis for the analysis of mitochondrial DNA in forensic and ancient DNA studies. Electrophoresis 2006; 27:5101-9. [PMID: 17120261 DOI: 10.1002/elps.200600331] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
We evaluate the usefulness of a commercially available microchip CE (MCE) device in different genetic identification studies performed with mitochondrial DNA (mtDNA) targets, including the haplotype analysis of HVR1 and HVR2 and the study of interspecies diversity of cytochrome b (Cyt b) and 16S ribosomal RNA (16S rRNA) mitochondrial genes in forensic and ancient DNA samples. The MCE commercial system tested in this study proved to be a fast and sensitive detection method of length heteroplasmy in cytosine stretches produced by 16 189T>C transitions in HVR1 and by 309.1 and 309.2 C-insertions in HVR2. Moreover, the quantitative analysis of PCR amplicons performed by LIF allowed normalizing the amplicon input in the sequencing reactions, improving the overall quality of sequence data. These quantitative data in combination with the quantification of genomic mtDNA by real-time PCR has been successfully used to evaluate the PCR efficiency and detection limit of full sequencing methods of different mtDNA targets. The quantification of amplicons also provided a method for the rapid evaluation of PCR efficiency of multiplex-PCR versus singleplex-PCR to amplify short HV1 amplicons (around 100 bp) from severely degraded ancient DNA samples. The combination of human-specific (Cyt b) and universal (16S rRNA) mtDNA primer sets in a single PCR reaction followed by MCE detection offers a very rapid and simple screening test to differentiate between human and nonhuman hair forensic samples. This method was also very efficient with degraded DNA templates from forensic hair and bone samples, because of its applicability to detect small amplicon sizes. Future possibilities of MCE in forensic DNA typing, including nuclear STRs and SNP profiling are suggested.
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MESH Headings
- Animals
- Bone and Bones/chemistry
- Cattle
- Cytochromes b/genetics
- DNA Fingerprinting/methods
- DNA, Mitochondrial/analysis
- DNA, Mitochondrial/genetics
- Dogs
- Electrophoresis, Microchip/methods
- Forensic Anthropology/methods
- Forensic Genetics/methods
- Hair/chemistry
- Haplotypes
- Humans
- Mice
- RNA, Ribosomal, 16S/genetics
- Rats
- Receptors, Vasoactive Intestinal Peptide, Type II/genetics
- Receptors, Vasoactive Intestinal Polypeptide, Type I/genetics
- Sequence Analysis, DNA
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Affiliation(s)
- Antonio Alonso
- Instituto Nacional de Toxicología y Ciencias Forenses, Servicio de Biología, Madrid, Spain.
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Imaizumi K, Akutsu T, Miyasaka S, Yoshino M. Development of species identification tests targeting the 16S ribosomal RNA coding region in mitochondrial DNA. Int J Legal Med 2006; 121:184-91. [PMID: 17109160 DOI: 10.1007/s00414-006-0127-5] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2006] [Accepted: 09/06/2006] [Indexed: 11/24/2022]
Abstract
This report describes the development of a species testing system based on the diversity of nucleotide sequences in mitochondrial DNA (mtDNA) among species. Five species, human, cow, pig, dog, and cat, were considered. The partial nucleotide sequences in 16S ribosomal RNA coding region were chosen as the target for discriminating the species. The sequence diversities of this approximately 400 bp long region ranged from 15.7 to 24.1% among the five species. Sequencing analysis of this target on 50 individuals of each species (53 for dogs) revealed that the nucleotide sequences were well preserved within species. Species-specific PCR for each species was also designed, and satisfactory results with regard to both sensitivity and specificity were obtained. A validation study with DNA extracted from bovine bone exposed to the environment revealed that the PCRs designed in this study worked correctly. From the results obtained, it was shown that this testing system could be a good tool for species identification. One successful case report is also demonstrated.
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Affiliation(s)
- Kazuhiko Imaizumi
- National Research Institute of Police Science, Kashiwa, Chiba, Japan.
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YANG DONGYAY, SPELLER CAMILLAF. Co-amplification of cytochrome b and D-loop mtDNA fragments for the identification of degraded DNA samples. ACTA ACUST UNITED AC 2006. [DOI: 10.1111/j.1471-8286.2006.01370.x] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Laird R, Gaudieri S, Berry J, Williamson J, Yang JS, Dawkins R. Vertebrate species profiling in one step using a single primer. Forensic Sci Med Pathol 2006; 2:165-72. [PMID: 25868694 DOI: 10.1007/s12024-006-0005-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/10/2006] [Indexed: 10/23/2022]
Abstract
Current species profiling techniques usually require several steps to identify an unknown species in quarantine cases and other forensic applications. Here we have developed a species profiling test that produces unique profiles for all vertebrate species tested using a single primer in a polymerase chain reaction. Samples tested included a range of mammals and other vertebrates such as fish and marsupials; a group of animals yet to be characterized with molecular speciation techniques. Species-specific profiles were shown to be reproducible and able to be generated from less than 10 ng of total DNA, comparable to DNA quantities used in conventional species profiling techniques. A case study demonstrates the utility of the technique by distinguishing between commercial and protected species of the Macropodidae (kangaroo) superfamily.
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Affiliation(s)
- Rebecca Laird
- Centre for Forensic Science School of Anatomy and Human Biology M420, University of Western Australia, 35 Stirling Highway, 6009, Crawley, Western Australia,
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Kitano T, Umetsu K, Tian W, Osawa M. Two universal primer sets for species identification among vertebrates. Int J Legal Med 2006; 121:423-7. [PMID: 16845543 DOI: 10.1007/s00414-006-0113-y] [Citation(s) in RCA: 147] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2006] [Accepted: 06/07/2006] [Indexed: 11/29/2022]
Abstract
The aim of this study was to develop a simple method using universal primers for species identification based on direct PCR sequencing. Two primer sets were designed based on the conserved regions of the 12S and 16S rRNA loci detected by the comprehensive sequence comparison among 30 mammalian whole mitochondrial genomes. In humans, the expected sizes of PCR products of the 12S and 16S rRNAs were 215 and 244 bp, respectively. Both primer sets successfully amplified the expected PCR products from various kinds of vertebrates including mammals, birds, reptiles, amphibians, and fish, and the sequenced segments contained sufficient nucleotide differences to identify each animal species. A case example of the identification of a piece of buried bone of unknown species is presented, and the species was identified as a pig by this method.
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Affiliation(s)
- Takashi Kitano
- Department of Experimental and Forensic Pathology, Faculty of Medicine, Yamagata University, Yamagata, Japan
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Ward J, Peakall R, Gilmore SR, Robertson J. A molecular identification system for grasses: a novel technology for forensic botany. Forensic Sci Int 2005; 152:121-31. [PMID: 15978338 DOI: 10.1016/j.forsciint.2004.07.015] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2004] [Revised: 07/02/2004] [Accepted: 07/07/2004] [Indexed: 10/26/2022]
Abstract
Our present inability to rapidly, accurately and cost-effectively identify trace botanical evidence remains the major impediment to the routine application of forensic botany. Grasses are amongst the most likely plant species encountered as forensic trace evidence and have the potential to provide links between crime scenes and individuals or other vital crime scene information. We are designing a molecular DNA-based identification system for grasses consisting of several PCR assays that, like a traditional morphological taxonomic key, provide criteria that progressively identify an unknown grass sample to a given taxonomic rank. In a prior study of DNA sequences across 20 phylogenetically representative grass species, we identified a series of potentially informative indels in the grass mitochondrial genome. In this study we designed and tested five PCR assays spanning these indels and assessed the feasibility of these assays to aid identification of unknown grass samples. We confirmed that for our control set of 20 samples, on which the design of the PCR assays was based, the five primer combinations produced the expected results. Using these PCR assays in a 'blind test', we were able to identify 25 unknown grass samples with some restrictions. Species belonging to genera represented in our control set were all correctly identified to genus with one exception. Similarly, genera belonging to tribes in the control set were correctly identified to the tribal level. Finally, for those samples for which neither the tribal or genus specific PCR assays were designed, we could confidently exclude these samples from belonging to certain tribes and genera. The results confirmed the utility of the PCR assays and the feasibility of developing a robust full-scale usable grass identification system for forensic purposes.
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Affiliation(s)
- J Ward
- School of Botany and Zoology, Australian National University, Canberra, ACT 0200, Australia.
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Matsuda H, Seo Y, Kakizaki E, Kozawa S, Muraoka E, Yukawa N. Identification of DNA of human origin based on amplification of human-specific mitochondrial cytochrome b region. Forensic Sci Int 2005; 152:109-14. [PMID: 15978336 DOI: 10.1016/j.forsciint.2004.07.019] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2004] [Revised: 07/26/2004] [Accepted: 07/28/2004] [Indexed: 10/26/2022]
Abstract
Species-specific differences in a non-polymorphic region of the mitochondrial cytochrome b gene appear to be large enough to allow human-specific amplification of forensic DNA samples. We therefore developed a PCR-based method using newly designed primers to amplify a 157-bp portion of the human mitochondrial cytochrome b gene. The forward and reverse primers were designed to hybridize to regions of the human mitochondrial cytochrome b gene with sequences differing from those of chimpanzee by 26% (7 bp/27 bp) and 26% (6 bp/23 bp), respectively. Using this primer pair, we successfully amplified DNA extracted from blood samples of 48 healthy adults. All these human samples produced a single band of the expected size on agarose gel electrophoresis, and the sequence of the single band was shown to be identical to that of the target region (157 bp) by sequence analysis. On the other hand, no visible bands were amplified from DNA extracted from blood samples of animals including non-human primates (chimpanzee, gorilla, Japanese monkey, crab-eating monkey) and other species (cow, pig, dog, goat, rat, chicken and tuna). Thus, DNA producing a single band following PCR amplification using this primer pair can be reasonably interpreted as being of human origin. In addition, aged biological specimens comprising bloodstains, hair shafts and bones were successfully identified as being of human origin, illustrating the applicability of the present method to forensic specimens.
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Affiliation(s)
- Hirokazu Matsuda
- Department of Legal Medicine, Miyazaki Medical College, 5200 Kihara, Kiyotake-cho, Miyazaki 889-1692, Japan.
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de Mazancourt P, Pfitzinger H. [DNA and paternity testing]. GYNECOLOGIE, OBSTETRIQUE & FERTILITE 2005; 33:461-3. [PMID: 16005666 DOI: 10.1016/j.gyobfe.2005.05.019] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2004] [Accepted: 05/27/2005] [Indexed: 10/25/2022]
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Wu H, Wan QH, Fang SG, Zhang SY. Application of mitochondrial DNA sequence analysis in the forensic identification of Chinese sika deer subspecies. Forensic Sci Int 2005; 148:101-5. [PMID: 15639603 DOI: 10.1016/j.forsciint.2004.04.072] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2003] [Revised: 04/26/2004] [Accepted: 04/29/2004] [Indexed: 11/24/2022]
Abstract
As a direct and indirect consequence of human activities, only two subspecies, Cervus nippon sinchuanicus and Cervus nippon kopschi, currently subsist in the wild of China. However, a large population of Cervus nippon hortulorum and Cervus nippon nippon is raised in order to gain deer parts for Chinese traditional medicine. According to Chinese Wild Animal Conservation Law, hunting, capturing and trading of the wild sika deer are strictly banned, however, raising and trading of the domestic individual are permitted. Thus, it is very necessary to identify the subspecies of sika deer in China in forensic tests. In our study, we used mitochondrial DNA control region sequence analysis and phylogenetic analysis to identify the subspecies of sika deer. Mitochondrial DNA control region sequences analysis revealed that two haplotypes came from the unknown samples. One is the same as the haplotype that came from the samples of wild population of C. n. kopschi. Phylogenetic analysis indicated that the two haplotypes of unknown samples clustered with the haplotypes of C. n. kopschi, and had significant difference from the haplotypes of the other subspecies. These results together revealed that the unknown samples came from two individuals that belong to the wild population of C. n. kopschi living in the Qinglingfeng State Natural Reserve of Zhejiang province. Therefore, the results provide forensic evidence of illegal wild animal hunting.
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Affiliation(s)
- Hua Wu
- College of Life Sciences, Zhejiang University, Kai Xuan Road No. 268, Hangzhou, 310029 Zhejiang, PR China
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40
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Pineau P, Henry M, Suspène R, Marchio A, Dettai A, Debruyne R, Petit T, Lécu A, Moisson P, Dejean A, Wain-Hobson S, Vartanian JP. A universal primer set for PCR amplification of nuclear histone H4 genes from all animal species. Mol Biol Evol 2004; 22:582-8. [PMID: 15601889 DOI: 10.1093/molbev/msi053] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
To control the quality of genomic DNA of samples from a wide variety of animals, a heminested PCR assay specifically targeting a nuclear gene has been developed. The histone H4 gene family comprises a small number of genes considered among the most conserved genes in living organisms. Tissue samples from necropsies and from cells belonging to 43 different species were studied, eight samples from invertebrates and 35 samples from vertebrates covering all classes. Ancient DNA samples from three Siberian woolly mammoths (Mammuthus primigenius) dating between 40,000 and 49,000 years before present were also tested for PCR amplification. Performance of HIST2H4 amplification were also compared with those of previously published universal PCRs (28S rRNA, 18S rRNA, and cytochrome b). Overall, 95% of species studied yielded an amplification product, including some old samples from gorilla and chimpanzees. The data indicate that the HIST2H4 amplimers are, thus, suitable for both DNA quality testing as well as species identification in the animal kingdom.
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Affiliation(s)
- Pascal Pineau
- Unité d'Organisation Nucléaire et Oncogénèse, INSERM U579, Institut Pasteur, Paris, France.
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41
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Diagnostic polymorphisms in the mitochondrial cytochrome b gene allow discrimination between cattle, sheep, goat, roe buck and deer by PCR-RFLP. BMC Genet 2004; 5:30. [PMID: 15462674 PMCID: PMC524170 DOI: 10.1186/1471-2156-5-30] [Citation(s) in RCA: 38] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2004] [Accepted: 10/05/2004] [Indexed: 11/10/2022] Open
Abstract
Background As an alternative to direct DNA sequencing of PCR products, random PCR-RFLP is an efficient technique to discriminate between species. The PCR-RFLP-method is an inexpensive tool in forensic science, even if the template is degraded or contains only traces of DNA from various species. Results Interspecies-specific DNA sequence polymorphisms in the mitochondrial cytochrome b gene were analyzed using PCR-RFLP technology to determine the source (i.e., species) of blood traces obtained from a leaf. Conclusions The method presented can be used for the discrimination of cattle (Bos taurus), sheep (Ovis aries), goat (Capra hircus), roe buck (Capreolus capreolus) and red deer (Cervus elaphus).
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Verma SK, Prasad K, Nagesh N, Sultana M, Singh L. Was elusive carnivore a panther? DNA typing of faeces reveals the mystery. Forensic Sci Int 2003; 137:16-20. [PMID: 14550608 DOI: 10.1016/s0379-0738(03)00277-9] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
In this study, we report the findings of a recent case in which the officials of an Indian zoo claimed that an animal, possibly a carnivore, is periodically visiting the zoo from a nearby vast forest area and causing panic in zoo and nearby villages. They collected some elusive faecal material from the vicinity of an herbivore enclosure. Looking to the pugmarks found in that area and faecal matter ceased, the officials could not decide whether it was a lioness, a tiger or a panther. We resolved this mystery by DNA-based analysis of the faecal material, using our recently developed novel universal primers to amplify and sequence a specific fragment of mitochondrial cytochrome b gene. The findings of the DNA-based analyses were confirmed after few days when the zoo officials trapped the animal of same species as suggested in our report. The potential of our procedure to investigate the cases related to wildlife offence is discussed.
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Bellis C, Ashton KJ, Freney L, Blair B, Griffiths LR. A molecular genetic approach for forensic animal species identification. Forensic Sci Int 2003; 134:99-108. [PMID: 12850402 DOI: 10.1016/s0379-0738(03)00128-2] [Citation(s) in RCA: 75] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
This study investigated potential markers within chromosomal, mitochondrial DNA (mtDNA) and ribosomal RNA (rRNA) with the aim of developing a DNA based method to allow differentiation between animal species. Such discrimination tests may have important applications in the forensic science, agriculture, quarantine and customs fields. DNA samples from five different animal individuals within the same species for 10 species of animal (including human) were analysed. DNA extraction and quantitation followed by PCR amplification and GeneScan visualisation formed the basis of the experimental analysis. Five gene markers from three different types of genes were investigated. These included genomic markers for the beta-actin and TP53 tumor suppressor gene. Mitochondrial DNA markers, designed by Bataille et al. [Forensic Sci. Int. 99 (1999) 165], examined the Cytochrome b gene and Hypervariable Displacement Loop (D-Loop) region. Finally, a ribosomal RNA marker for the 28S rRNA gene optimised by Naito et al. [J. Forensic Sci. 37 (1992) 396] was used as a possible marker for speciation. Results showed a difference of only several base pairs between all species for the beta-actin and 28S markers, with the exception of Sus scrofa (pig) beta-actin fragment length, which produced a significantly smaller fragment. Multiplexing of Cytochrome b and D-Loop markers gave limited species information, although positive discrimination of human DNA was evident. The most specific and discriminatory results were shown using the TP53 gene since this marker produced greatest fragment size differences between animal species studied. Sample differentiation for all species was possible following TP53 amplification, suggesting that this gene could be used as a potential animal species identifier.
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Affiliation(s)
- C Bellis
- Genomics Research Centre, School of Health Science, Griffith University Gold Coast, PMB 50, GCMC, Bundall 9726, Qld, Australia
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Ngo KA, Kramer LD. Identification of mosquito bloodmeals using polymerase chain reaction (PCR) with order-specific primers. JOURNAL OF MEDICAL ENTOMOLOGY 2003; 40:215-222. [PMID: 12693851 DOI: 10.1603/0022-2585-40.2.215] [Citation(s) in RCA: 122] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
A polymerase chain reaction (PCR) protocol was developed to identify host bloodmeals from mosquitoes. Primers for the cytochrome b gene were designed to distinguish between mammalian and avian bloodmeals and further differentiate among four avian orders: passeriformes, falconiformes, columbiformes, and galliformes. The assay was validated by testing tissues from 18 species of passeriformes, three species of falconiformes, three species of columbiformes, and two species of galliformes. American crows were distinguished from other passeriformes by restriction enzyme digestion. Host bloodmeals from engorged mosquitoes collected in New York State were identified to avian order level. PCR was able to detect the mosquito bloodmeal for up to 3 d after feeding on a quail. Significantly, these studies use order-specific primers in a single PCR test to identify mosquito bloodmeals.
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Affiliation(s)
- Kiet A Ngo
- The Arbovirus Laboratories, Wadsworth Center, New York State Department of Health, 5668 State Farm Road, Slingerlands, NY 12139, USA
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Wan QH, Fang SG. Application of species-specific polymerase chain reaction in the forensic identification of tiger species. Forensic Sci Int 2003; 131:75-8. [PMID: 12505474 DOI: 10.1016/s0379-0738(02)00398-5] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Globally, tigers are considered to be endangered, and are listed on Appendix I of CITES. A simple test, using a species-specific primer pair, was developed to identify tiger meat, faeces and dried skin, and provide forensic evidence of illegal wildlife trade. The specific fragment of mitochondrial cytochrome b gene was also successfully amplified from raw DNA products extracted from single tiger hairs. This PCR-based approach opens a new avenue to forensic identification of less-than-optimal samples.
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Affiliation(s)
- Qiu-Hong Wan
- Key Laboratory of Conservation Genetics and Reproductive Biology for Endangered Wild Animals, Ministry of Education, Zhejiang, PR China
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Berti A, Virgili A, Zignale G, Serafini M, Lago G. Cyt-b analysis and hair comparison in serial robbery cases. ACTA ACUST UNITED AC 2003. [DOI: 10.1016/s0531-5131(02)00589-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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Lee SD, Lee YS, Lee JB. Polymorphism in the mitochondrial cytochrome B gene in Koreans. An additional marker for individual identification. Int J Legal Med 2002; 116:74-8. [PMID: 12056524 DOI: 10.1007/s004140100238] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
Sequencing the mitochondrial control region is very useful for individual identification when conventional DNA typing using autosomal STRs is unavailable. However, low discriminatory power is a problem and another polymorphic locus within the mitochondrial genome is necessary. The cytochrome B (MTCYB) gene, which has undergone several changes during evolution, may be a good candidate for this purpose. Here the sequencing data of the MTCYB gene of 98 unrelated Koreans is presented. A total of 30 polymorphic sites were found which were distributed evenly along the gene. All were nucleotide substitutions and no insertions/deletions were noted. A total of 22 different MTCYB lineages were revealed. Out of 22 different control region lineages with 79 samples which shared the same D-loop sequence with some others within a lineage, 10 lineages with 37 samples could be sub-grouped according to different MTCYB sequences. Some issues concerning the MTCYB gene polymorphism are discussed.
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Affiliation(s)
- Soong Deok Lee
- Department of Forensic Medicine, Seoul National University College of Medicine, Korea.
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Affiliation(s)
- T A Brettell
- Forensic Science Bureau, New Jersey State Police, West Trenton 08628, USA
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Poetsch M, Seefeldt S, Maschke M, Lignitz E. Analysis of microsatellite polymorphism in red deer, roe deer, and fallow deer -- possible employment in forensic applications. Forensic Sci Int 2001; 116:1-8. [PMID: 11118746 DOI: 10.1016/s0379-0738(00)00337-6] [Citation(s) in RCA: 52] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
DNA microsatellites play a major role in population genetics, linkage mapping, and parentage studies of mammals. In addition, they may be used for forensic purposes, if an individual identification of a specific animal is necessary. Therefore, we tested a variety of microsatellite polymorphism derived from reindeer (Rangifer tarandus) by PCR and sequencing analysis for use in red deer (Cervus elaphus), roe deer (Capreolus capreolus) and fallow deer (Dama dama). Twelve of these microsatellites were selected for further analysis. In all these microsatellite polymorphism short tandem repeats could be detected for one or all three species as shown by sequencing analysis. In red deer, more than two alleles were found in eight microsatellites, in roe deer more than two alleles could be demonstrated in seven microsatellites, whereas in fallow deer more than two alleles were found in only two microsatellite polymorphism. A comparison of sequences of PCR products from the three deer species with the sequences of reindeer revealed several differences between the four species. In six microsatellites -- selected because or their reliability in PCR and because of their polymorphic character -- we established a sequenced allelic ladder and give population data of all three species from 82 deer of the Northeast region of Germany (Vorpommern). Our results show the possibility to use microsatellite polymorphism in the identification of deer in forensic applications like poaching.
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Affiliation(s)
- M Poetsch
- Institute of Legal Medicine, Ernst-Moritz-Arndt-University, Kuhstrasse 30, D-17489 Greifswald, Germany.
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