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Wang N, Zhao Z, Gao J, Tian E, Yu W, Li H, Zhang J, Xie R, Zhao X, Chen A. Rapid and Visual Identification of Chlorophyllum molybdites With Loop-Mediated Isothermal Amplification Method. Front Microbiol 2021; 12:638315. [PMID: 33815325 PMCID: PMC8013719 DOI: 10.3389/fmicb.2021.638315] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2020] [Accepted: 02/10/2021] [Indexed: 11/14/2022] Open
Abstract
Chlorophyllum molybdites is a kind of common poisonous mushroom in China that is widely distributed in different areas. Food poisoning caused by accidentally eating C. molybdites has become more frequent in recent years. In 2019, there were 55 food poisoning incidents caused by eating this mushroom in China. Mushroom poisoning continues to be a common health issue of global concern. When mushroom poisoning occurs, an effective, simple, and rapid detection method is required for accurate clinical treatment or forensic analysis. For the first time, we established a loop-mediated isothermal amplification (LAMP) assay for the visual detection of C. molybdites. A set of specific LAMP primers was designed, and the specificity was confirmed against 43 different mushroom species. The LAMP method could detect as low as 1 pg of genomic DNA. Boiled mushrooms and artificial gastric-digested mushroom samples were prepared to test the applicability of the method, and the results showed that as low as 1% C. molybdites in boiled and digested samples could be successfully detected. The LAMP method can also be completed within 45 min, and the reaction results could be directly observed based on a color change under daylight by the naked eye. Therefore, the LAMP assay established in this study provides an accurate, sensitive, rapid, and low-cost method for the detection of C. molybdites.
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Affiliation(s)
- Nan Wang
- Institute of Quality Standard and Testing Technology for Agro-Products, Key Laboratory of Agro-product Quality and Safety, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Zhiyong Zhao
- Institute for Agri-food Standards and Testing Technology, Shanghai Academy of Agricultural Sciences, Shanghai, China
| | - Jie Gao
- Institute of Quality Standard and Testing Technology for Agro-Products, Key Laboratory of Agro-product Quality and Safety, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Enjing Tian
- Institute of Mycology, Engineering Research Center of Chinese Ministry of Education for Edible and Medicinal Fungi, Jilin Agricultural University, Jilin, China
| | - Wenjie Yu
- Institute of Quality Standard and Testing Technology for Agro-Products, Key Laboratory of Agro-product Quality and Safety, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Hui Li
- Institute of Quality Standard and Testing Technology for Agro-Products, Key Laboratory of Agro-product Quality and Safety, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Juan Zhang
- Institute of Quality Standard and Testing Technology for Agro-Products, Key Laboratory of Agro-product Quality and Safety, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Ruibin Xie
- Institute of Quality Standard and Testing Technology for Agro-Products, Key Laboratory of Agro-product Quality and Safety, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Xiaoyan Zhao
- Institute for Agri-food Standards and Testing Technology, Shanghai Academy of Agricultural Sciences, Shanghai, China
| | - Ailiang Chen
- Institute of Quality Standard and Testing Technology for Agro-Products, Key Laboratory of Agro-product Quality and Safety, Chinese Academy of Agricultural Sciences, Beijing, China
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Species identification of white false hellebore (Veratrum album subsp. oxysepalum) by loop-mediated isothermal amplification (LAMP). Forensic Toxicol 2019. [DOI: 10.1007/s11419-018-00461-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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3
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Kröll AK, Wetter C, Schmidt P, Schäfer N. Tödlicher berufsspezifischer Suizid mit Eibennadeln. Rechtsmedizin (Berl) 2017. [DOI: 10.1007/s00194-017-0169-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Kikkawa HS, Tsuge K, Kubota S, Aragane M, Ohta H, Sugita R. Species identification of white false hellebore (Veratrum album subsp. oxysepalum) using real-time PCR. Forensic Sci Int 2017; 275:160-166. [PMID: 28366623 DOI: 10.1016/j.forsciint.2017.02.002] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2016] [Revised: 12/30/2016] [Accepted: 02/02/2017] [Indexed: 10/19/2022]
Abstract
Food poisoning is frequently caused by the accidental ingestion of toxic plants that possess strong morphological similarities to edible plants. False helleborine (Veratrum album) is one of the most common plants involved in such accidents. In cases of poisoning by toxic plants, rapid and accurate identification, usually based on the morphological or chemical analysis of plant parts, is required for appropriate medical treatment or forensic investigation. However, morphological examinations require experience in systematic botany because the samples are fragmentary, and chemical analysis of natural compounds can be difficult. In this study, we developed a TaqMan real-time PCR method using trnH-psbA and trnL-trnF that could be carried out in 30-60min. The lower detection limit was less than 10pg of DNA and the primer sets were specific to V. album and Veratrum stamineum. Mixed samples, cooked samples, and simulated gastric contents were successfully identified, and a multiplex assay of two regions was also possible. These results indicate that the TaqMan real-time PCR analysis is a very effective method to detect small samples of V. album and V. stamineum accurately and rapidly in poisoning cases.
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Affiliation(s)
- Hitomi S Kikkawa
- National Research Institute of Police Science, 6-3-1 Kashiwanoha, Kashiwa, Chiba 277-0882, Japan.
| | - Kouichiro Tsuge
- National Research Institute of Police Science, 6-3-1 Kashiwanoha, Kashiwa, Chiba 277-0882, Japan
| | - Satoshi Kubota
- National Research Institute of Police Science, 6-3-1 Kashiwanoha, Kashiwa, Chiba 277-0882, Japan
| | - Masako Aragane
- Medical Plant Garden, Tokyo Metropolitan Institute of Public Health, 21-1 Nakajimacho, Kodaira, Tokyo 187-0033, Japan
| | - Hikoto Ohta
- National Research Institute of Police Science, 6-3-1 Kashiwanoha, Kashiwa, Chiba 277-0882, Japan
| | - Ritsuko Sugita
- National Research Institute of Police Science, 6-3-1 Kashiwanoha, Kashiwa, Chiba 277-0882, Japan
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Tobe SS, Swaran YC, Dennany L, Sibbing U, Schulze Johann K, Welch L, Vennemann M. A proof of principal study on the use of direct PCR of semen and spermatozoa and development of a differential isolation protocol for use in cases of alleged sexual assault. Int J Legal Med 2016; 131:87-94. [DOI: 10.1007/s00414-016-1461-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2016] [Accepted: 10/05/2016] [Indexed: 11/29/2022]
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Cheng T, Xu C, Lei L, Li C, Zhang Y, Zhou S. Barcoding the kingdom Plantae: new PCR primers for ITS regions of plants with improved universality and specificity. Mol Ecol Resour 2015; 16:138-49. [PMID: 26084789 DOI: 10.1111/1755-0998.12438] [Citation(s) in RCA: 152] [Impact Index Per Article: 16.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2014] [Revised: 04/20/2015] [Accepted: 06/09/2015] [Indexed: 01/22/2023]
Abstract
The internal transcribed spacer (ITS) of nuclear ribosomal DNA is one of the most commonly used DNA markers in plant phylogenetic and DNA barcoding analyses, and it has been recommended as a core plant DNA barcode. Despite this popularity, the universality and specificity of PCR primers for the ITS region are not satisfactory, resulting in amplification and sequencing difficulties. By thoroughly surveying and analysing the 18S, 5.8S and 26S sequences of Plantae and Fungi from GenBank, we designed new universal and plant-specific PCR primers for amplifying the whole ITS region and a part of it (ITS1 or ITS2) of plants. In silico analyses of the new and the existing ITS primers based on these highly representative data sets indicated that (i) the newly designed universal primers are suitable for over 95% of plants in most groups; and (ii) the plant-specific primers are suitable for over 85% of plants in most groups without amplification of fungi. A total of 335 samples from 219 angiosperm families, 11 gymnosperm families, 24 fern and lycophyte families, 16 moss families and 17 fungus families were used to test the performances of these primers. In vitro PCR produced similar results to those from the in silico analyses. Our new primer pairs gave PCR improvements up to 30% compared with common-used ones. The new universal ITS primers will find wide application in both plant and fungal biology, and the new plant-specific ITS primers will, by eliminating PCR amplification of nonplant templates, significantly improve the quality of ITS sequence information collections in plant molecular systematics and DNA barcoding.
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Affiliation(s)
- Tao Cheng
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - Chao Xu
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - Li Lei
- Department of Plant Pathology, Kansas State University, Manhattan, KS, 66506, USA
| | - Changhao Li
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - Yu Zhang
- Beijing Botanic Gardens, Beijing, 100093, China
| | - Shiliang Zhou
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
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Hünniger T, Felbinger C, Wessels H, Mast S, Hoffmann A, Schefer A, Märtlbauer E, Paschke-Kratzin A, Fischer M. Food Targeting: A Real-Time PCR Assay Targeting 16S rDNA for Direct Quantification of Alicyclobacillus spp. Spores after Aptamer-Based Enrichment. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2015; 63:4291-4296. [PMID: 25880790 DOI: 10.1021/acs.jafc.5b00874] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Spore-forming Alicyclobacillus spp. are able to form metabolites that induce even in small amounts an antiseptical or medicinal off-flavor in fruit juices. Microbial contaminations could occur by endospores, which overcame the pasteurization process. The current detection method for Alicyclobacillus spp. can take up to 1 week because of microbiological enrichment. In a previous study, DNA aptamers were selected and characterized for an aptamer-driven rapid enrichment of Alicyclobacillus spp. spores from orange juice by magnetic separation. In the present work, a direct quantification assay for Alicyclobacillus spp. spores was developed to complete the two-step approach of enrichment and detection. After mechanical treatment of the spores, the isolated DNA was quantified in a real-time PCR-assay targeting 16S rDNA. The assay was evaluated by the performance requirements of the European Network of Genetically Modified Organisms Laboratories (ENGL). Hence, the presented method is applicable for direct spore detection from orange juice in connection with an enrichment step.
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Affiliation(s)
- Tim Hünniger
- †Hamburg School of Food Science, Institute of Food Chemistry, University of Hamburg, Grindelallee 117, 20146 Hamburg, Germany
| | - Christine Felbinger
- †Hamburg School of Food Science, Institute of Food Chemistry, University of Hamburg, Grindelallee 117, 20146 Hamburg, Germany
| | - Hauke Wessels
- †Hamburg School of Food Science, Institute of Food Chemistry, University of Hamburg, Grindelallee 117, 20146 Hamburg, Germany
| | - Sophia Mast
- ‡Lehrstuhl für Hygiene und Technologie der Milch, Tierärtzliche Fakultät, Ludwig-Maximilians-Universität, Schönleutnerstraße 8/219, 85764 Oberschleißheim, Germany
| | - Antonia Hoffmann
- †Hamburg School of Food Science, Institute of Food Chemistry, University of Hamburg, Grindelallee 117, 20146 Hamburg, Germany
| | - Anna Schefer
- †Hamburg School of Food Science, Institute of Food Chemistry, University of Hamburg, Grindelallee 117, 20146 Hamburg, Germany
| | - Erwin Märtlbauer
- ‡Lehrstuhl für Hygiene und Technologie der Milch, Tierärtzliche Fakultät, Ludwig-Maximilians-Universität, Schönleutnerstraße 8/219, 85764 Oberschleißheim, Germany
| | - Angelika Paschke-Kratzin
- †Hamburg School of Food Science, Institute of Food Chemistry, University of Hamburg, Grindelallee 117, 20146 Hamburg, Germany
| | - Markus Fischer
- †Hamburg School of Food Science, Institute of Food Chemistry, University of Hamburg, Grindelallee 117, 20146 Hamburg, Germany
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Poczai P, Varga I, Hyvönen J. Internal transcribed spacer (ITS) evolution in populations of the hyperparasitic European mistletoe pathogen fungus, Sphaeropsis visci (Botryosphaeriaceae): The utility of ITS2 secondary structures. Gene 2014; 558:54-64. [PMID: 25536165 DOI: 10.1016/j.gene.2014.12.042] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2014] [Revised: 11/29/2014] [Accepted: 12/19/2014] [Indexed: 01/18/2023]
Abstract
We investigated patterns of nucleotide polymorphism in the internal transcribed spacer (ITS) region for Sphaeropsis visci, a hyperparasitic fungus that causes the leaf spot disease of the hemiparasite European mistletoe (Viscum album). Samples of S. visci were obtained from Hungary covering all major infected forest areas. For obtaining PCR products we used a fast and efficient direct PCR approach based on a high fidelity DNA polymerase. A total of 140 ITS sequences were subjected to an array of complementary sequence analyses, which included analyses of secondary structure stability, nucleotide polymorphism patterns, GC content, and presence of conserved motifs. Analysed sequences exhibited features of functional rRNAs. Overall, polymorphism was observed within less conserved motifs, such as loops and bulges, or, alternatively, as non-canonical G-U pairs within conserved regions of double stranded helices. The secondary structure of ITS2 provides new opportunities for obtaining further valuable information, which could be used in phylogenetic analyses, or at population level as demonstrated in our study. This is due to additional information provided by secondary structures and their models. The combined score matrix was used with the methods implemented in the programme 4SALE. Besides the pseudoprotein coding method of 4SALE, the molecular morphometric character coding also has potential for gaining further information for phylogenetic analyses based on the geometric features of the sub-structural elements of the ITS2 RNA transcript.
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Affiliation(s)
- Péter Poczai
- Botany Unit, Finnish Museum of Natural History, University of Helsinki, PO Box 7, Helsinki FI-00014, Finland.
| | - Ildikó Varga
- Plant Biology, Department of Biosciences, PO Box 65, FI-00014, University of Helsinki, Finland.
| | - Jaakko Hyvönen
- Plant Biology, Department of Biosciences, PO Box 65, FI-00014, University of Helsinki, Finland.
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10
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Iyengar A, Hadi S. Use of non-human DNA analysis in forensic science: a mini review. MEDICINE, SCIENCE, AND THE LAW 2014; 54:41-50. [PMID: 23929675 DOI: 10.1177/0025802413487522] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
Analysis of non-human DNA in forensic science, first reported about two decades ago, is now commonplace. Results have been used as evidence in court in a variety of cases ranging from abduction and murder to patent infringement and dog attack. DNA from diverse species, including commonly encountered pets such as dogs and cats, to plants, viruses and bacteria has been used and the sheer potential offered by such analyses has been proven. In this review, using case examples throughout, we detail the considerable literature in this field.
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Affiliation(s)
- Arati Iyengar
- School of Forensic & Investigative Sciences, University of Central Lancashire, Preston, UK
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11
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Gausterer C, Penker M, Krisai-Greilhuber I, Stein C, Stimpfl T. Rapid genetic detection of ingested Amanita phalloides. Forensic Sci Int Genet 2013; 9:66-71. [PMID: 24528582 DOI: 10.1016/j.fsigen.2013.11.002] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2013] [Revised: 11/14/2013] [Accepted: 11/17/2013] [Indexed: 11/17/2022]
Abstract
Mushrooms are often poorly digested by humans. Thus, their remains (tissues, spores) may persist in the gastrointestinal tract and can be detected in feces several days after mushroom consumption. In this report, we present protocols for the rapid PCR-based detection of fungal traces in a variety of complex samples. Novel primers were designed to amplify portions of ribosomal DNA from deadly poisonous European members of the genus Amanita, namely the death cap (A. phalloides), the destroying angel (A. virosa) and the fool's mushroom (A. verna), respectively. Assay sensitivity was sufficient to discover diluted DNA traces in amounts below the genomic content of a single target mushroom cell. Specificity testing was performed with DNA extracts from a variety of mushroom species. Template amplification was exclusively observed with intended targets and it was not compromised by a vast excess of non-target DNA (i.e. DNA from human and human fecal origin, respectively). A series of experiments was conducted with prepared specimens in order to follow the course of mushroom food processing and digestion. Amplification by direct PCR was successful with raw, fried and digested mixed mushrooms. To improve assay performance with fecal samples, a rapid protocol for sample pre-processing (including water-ether sedimentation and bead beating) and a modified PCR reaction mix were applied. Thereby, it was possible to detect the presence of A. phalloides DNA in spiked feces as well as in clinical samples (vomit, stool) from two independent cases of suspected mushroom poisoning.
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Affiliation(s)
- Christian Gausterer
- FDZ-Forensisches DNA Zentrallabor GmbH, Medical University of Vienna, Sensengasse 2, 1090 Vienna, Austria.
| | - Martina Penker
- FDZ-Forensisches DNA Zentrallabor GmbH, Medical University of Vienna, Sensengasse 2, 1090 Vienna, Austria; Department of Health, FH Campus Wien, University of Applied Sciences, Favoritenstraße 226, 1100 Vienna, Austria.
| | - Irmgard Krisai-Greilhuber
- Department of Systematic and Evolutionary Botany, Faculty Centre of Biodiversity, University of Vienna, Rennweg 14, 1030 Vienna, Austria.
| | - Christina Stein
- FDZ-Forensisches DNA Zentrallabor GmbH, Medical University of Vienna, Sensengasse 2, 1090 Vienna, Austria.
| | - Thomas Stimpfl
- Clinical Department of Laboratory Medicine, Medical University of Vienna, Währinger Gürtel 18-20, 1090 Vienna, Austria.
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Haase I, Brüning P, Matissek R, Fischer M. Real-time PCR assays for the quantitation of rDNA from apricot and other plant species in marzipan. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2013; 61:3414-3418. [PMID: 23495652 DOI: 10.1021/jf3052175] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
Marzipan or marzipan raw paste is a typical German sweet which is consumed directly or is used as an ingredient in the bakery industry/confectionery (e.g., in stollen) and as filling for chocolate candies. Almonds (blanched and pealed) and sugar are the only ingredients for marzipan production according to German food guidelines. Especially for the confectionery industry, the use of persipan, which contains apricot or peach kernels instead of almonds, is preferred due to its stronger aroma. In most of the companies, both raw pastes are produced, in most cases on the same production line, running the risk of an unintended cross contamination. Additionally, due to high almond market values, dilutions of marzipan with cheaper seeds may occur. Especially in the case of apricot and almond, the close relationship of both species is a challenge for the analysis. DNA based methods for the qualitative detection of apricot, peach, pea, bean, lupine, soy, cashew, pistachio, and chickpea in marzipan have recently been published. In this study, different quantitation strategies on the basis of real-time PCR have been evaluated and a relative quantitation method with a reference amplification product was shown to give the best results. As the real-time PCR is based on the high copy rDNA-cluster, even contaminations <1% can be reliably quantitated.
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Affiliation(s)
- Ilka Haase
- Hamburg School of Food Science, Institute of Food Chemistry, University of Hamburg, Hamburg, Germany.
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Ottens R, Taylor D, Abarno D, Linacre A. Successful direct amplification of nuclear markers from a single hair follicle. Forensic Sci Med Pathol 2012; 9:238-43. [PMID: 23275022 DOI: 10.1007/s12024-012-9402-6] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/15/2012] [Indexed: 11/29/2022]
Abstract
We report on successful amplification of DNA profiles from a single hair. Direct amplification was used on the root tip of both anagen and telogen hairs using a kit to amplify 15 STR loci. All 30 anagen hairs tested from five different people gave full DNA profiles after 29 cycles with no allelic drop-in or heterozygous imbalance. Six of the 30 telogen hairs tested resulted in a full DNA profile, and a further four telogen hair samples tested produced a DNA profile of five or more complete loci that could be up-loaded to the National DNA Database (Australia). A full DNA profile was also obtained from the shaft of an anagen hair. Current practice for many laboratories is that a single hair may not be subjected to DNA testing as there is little chance of success, hence this 100 % success rate from anagen hairs is a significant advancement. A full DNA profile was obtained from a 5 year-old single hair illustrating the success when using direct PCR rather than attempting an extraction prior to the amplification step. The process described deliberately uses current DNA profiling methods with no increase in cycle number, such that the methodology can be incorporated readily into operational practice. For the first time in the field of human identification, single hairs can be analyzed with confidence that a meaningful DNA profile will be generated and the data accepted by the criminal justice system.
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Affiliation(s)
- Renée Ottens
- School of Biological Sciences, Flinders University, Bedford Park, Adelaide, SA, Australia
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14
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Hao DC, Xiao PG, Ge GB, Liu M. Biological, Chemical, and Omics Research ofTaxusMedicinal Resources. Drug Dev Res 2012. [DOI: 10.1002/ddr.21040] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Affiliation(s)
- Da-Cheng Hao
- Biotechnology Institute/School of Environment; Dalian Jiaotong University; Dalian; China
| | | | - Guang-Bo Ge
- Pharmaceutical resource discovery; Dalian Institute of Chemical Physics; Chinese Academy of Sciences; Dalian; China
| | - Ming Liu
- Biotechnology Institute/School of Environment; Dalian Jiaotong University; Dalian; China
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