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      Combined DNA, toxicological and heavy metal analyses provides an auditing toolkit to improve pharmacovigilance of traditional Chinese medicine (TCM)

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          Abstract

          Globally, there has been an increase in the use of herbal remedies including traditional Chinese medicine (TCM). There is a perception that products are natural, safe and effectively regulated, however, regulatory agencies are hampered by a lack of a toolkit to audit ingredient lists, adulterants and constituent active compounds. Here, for the first time, a multidisciplinary approach to assessing the molecular content of 26 TCMs is described. Next generation DNA sequencing is combined with toxicological and heavy metal screening by separation techniques and mass spectrometry (MS) to provide a comprehensive audit. Genetic analysis revealed that 50% of samples contained DNA of undeclared plant or animal taxa, including an endangered species of Panthera (snow leopard). In 50% of the TCMs, an undeclared pharmaceutical agent was detected including warfarin, dexamethasone, diclofenac, cyproheptadine and paracetamol. Mass spectrometry revealed heavy metals including arsenic, lead and cadmium, one with a level of arsenic >10 times the acceptable limit. The study showed 92% of the TCMs examined were found to have some form of contamination and/or substitution. This study demonstrates that a combination of molecular methodologies can provide an effective means by which to audit complementary and alternative medicines.

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          Traditional Chinese medicine.

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            GenBank

            GenBank (R) is a comprehensive database that contains publicly available DNA sequences for more than 205 000 named organisms, obtained primarily through submissions from individual laboratories and batch submissions from large-scale sequencing projects. Most submissions are made using the Web-based BankIt or standalone Sequin programs and accession numbers are assigned by GenBank staff upon receipt. Daily data exchange with the EMBL Data Library in Europe and the DNA Data Bank of Japan ensures worldwide coverage. GenBank is accessible through NCBI's retrieval system, Entrez, which integrates data from the major DNA and protein sequence databases along with taxonomy, genome, mapping, protein structure and domain information, and the biomedical journal literature via PubMed. BLAST provides sequence similarity searches of GenBank and other sequence databases. Complete bimonthly releases and daily updates of the GenBank database are available by FTP. To access GenBank and its related retrieval and analysis services, go to the NCBI Homepage at .
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              An In silico approach for the evaluation of DNA barcodes

              Background DNA barcoding is a key tool for assessing biodiversity in both taxonomic and environmental studies. Essential features of barcodes include their applicability to a wide spectrum of taxa and their ability to identify even closely related species. Several DNA regions have been proposed as barcodes and the region selected strongly influences the output of a study. However, formal comparisons between barcodes remained limited until now. Here we present a standard method for evaluating barcode quality, based on the use of a new bioinformatic tool that performs in silico PCR over large databases. We illustrate this approach by comparing the taxonomic coverage and the resolution of several DNA regions already proposed for the barcoding of vertebrates. To assess the relationship between in silico and in vitro PCR, we also developed specific primers amplifying different species of Felidae, and we tested them using both kinds of PCR Results Tests on specific primers confirmed the correspondence between in silico and in vitro PCR. Nevertheless, results of in silico and in vitro PCRs can be somehow different, also because tuning PCR conditions can increase the performance of primers with limited taxonomic coverage. The in silico evaluation of DNA barcodes showed a strong variation of taxonomic coverage (i.e., universality): barcodes based on highly degenerated primers and those corresponding to the conserved region of the Cyt-b showed the highest coverage. As expected, longer barcodes had a better resolution than shorter ones, which are however more convenient for ecological studies analysing environmental samples. Conclusions In silico PCR could be used to improve the performance of a study, by allowing the preliminary comparison of several DNA regions in order to identify the most appropriate barcode depending on the study aims.
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                Author and article information

                Journal
                Sci Rep
                Sci Rep
                Scientific Reports
                Nature Publishing Group
                2045-2322
                10 December 2015
                2015
                : 5
                : 17475
                Affiliations
                [1 ]Trace and Environmental DNA laboratory, Department of Environment and Agriculture, Curtin University , Kent St, Bentley, WA, 6102, Australia
                [2 ]Separation Science and Metabolomics Laboratory and the Advanced Mass Spectrometry Facility, Murdoch University , South St, Murdoch, WA, 6150, Australia
                [3 ]School of Veterinary and Life Sciences, Murdoch University , South St, Murdoch, WA, 6150, Australia
                [4 ]School of Medical Sciences, The University of Adelaide, Frome Rd , Adelaide, SA, 5005, Australia
                [5 ]Forensic Science SA , Adelaide, SA, 5000, Australia
                [6 ]Centre for Comparative Genomics, Murdoch University , South St, Murdoch, WA, 6150, Australia
                [7 ]LotteryWest State Biomedical Facility Genomics, School of Pathology and Laboratory Medicine, University of Western Australia , 35 Stirling Hwy, Crawley, WA, 6009, Australia
                [8 ]Department of Diagnostic Genomics, Pathwest Laboratory Medicine WA, QEII Medical Centre , Hospital Ave, Nedlands, WA, 6009, Australia
                [9 ]Trace Research Advanced Clean Environment (TRACE) Facility, Department of Physics, Astronomy and Medical Radiation Sciences, Curtin University , Kent St, Bentley, WA, 6102, Australia
                Author notes
                Article
                srep17475
                10.1038/srep17475
                4675079
                26658160
                ff109ac0-297a-422d-98cc-76e7b884fb24
                Copyright © 2015, Macmillan Publishers Limited

                This work is licensed under a Creative Commons Attribution 4.0 International License. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in the credit line; if the material is not included under the Creative Commons license, users will need to obtain permission from the license holder to reproduce the material. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/

                History
                : 11 August 2015
                : 30 October 2015
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