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      Comparative authentication of Hypericum perforatum herbal products using DNA metabarcoding, TLC and HPLC-MS

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          Abstract

          Many herbal products have a long history of use, but there are increasing concerns over product efficacy, safety and quality in the wake of recent cases exposing discrepancies between labeling and constituents. When it comes to St. John’s wort ( Hypericum perforatum L.) herbal products, there is limited oversight, frequent off-label use and insufficient monitoring of adverse drug reactions. In this study, we use amplicon metabarcoding (AMB) to authenticate 78 H. perforatum herbal products and evaluate its ability to detect substitution compared to standard methods using thin-layer chromatography (TLC) and high performance liquid chromatography coupled with mass spectrometry (HPLC-MS). Hypericum perforatum was detected in 68% of the products using AMB. Furthermore, AMB detected incongruence between constituent species and those listed on the label in all products. Neither TLC nor HPLC-MS could be used to unambiguously identify H. perforatum. They are accurate methods for authenticating presence of the target compounds, but have limited efficiency in detecting infrageneric substitution and do not yield any information on other plant ingredients in the products. Random post-marketing AMB of herbal products by regulatory agencies could raise awareness among consumers of substitution and would provide an incentive to manufacturers to increase quality control from raw ingredients to commercialized products.

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          Basic local alignment search tool.

          A new approach to rapid sequence comparison, basic local alignment search tool (BLAST), directly approximates alignments that optimize a measure of local similarity, the maximal segment pair (MSP) score. Recent mathematical results on the stochastic properties of MSP scores allow an analysis of the performance of this method as well as the statistical significance of alignments it generates. The basic algorithm is simple and robust; it can be implemented in a number of ways and applied in a variety of contexts including straightforward DNA and protein sequence database searches, motif searches, gene identification searches, and in the analysis of multiple regions of similarity in long DNA sequences. In addition to its flexibility and tractability to mathematical analysis, BLAST is an order of magnitude faster than existing sequence comparison tools of comparable sensitivity.
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            Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences.

            In 2001 and 2002, we published two papers (Bioinformatics, 17, 282-283, Bioinformatics, 18, 77-82) describing an ultrafast protein sequence clustering program called cd-hit. This program can efficiently cluster a huge protein database with millions of sequences. However, the applications of the underlying algorithm are not limited to only protein sequences clustering, here we present several new programs using the same algorithm including cd-hit-2d, cd-hit-est and cd-hit-est-2d. Cd-hit-2d compares two protein datasets and reports similar matches between them; cd-hit-est clusters a DNA/RNA sequence database and cd-hit-est-2d compares two nucleotide datasets. All these programs can handle huge datasets with millions of sequences and can be hundreds of times faster than methods based on the popular sequence comparison and database search tools, such as BLAST.
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              Quality control and preprocessing of metagenomic datasets

              Summary: Here, we present PRINSEQ for easy and rapid quality control and data preprocessing of genomic and metagenomic datasets. Summary statistics of FASTA (and QUAL) or FASTQ files are generated in tabular and graphical form and sequences can be filtered, reformatted and trimmed by a variety of options to improve downstream analysis. Availability and Implementation: This open-source application was implemented in Perl and can be used as a stand alone version or accessed online through a user-friendly web interface. The source code, user help and additional information are available at http://prinseq.sourceforge.net/. Contact: rschmied@sciences.sdsu.edu; redwards@cs.sdsu.edu
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                Author and article information

                Contributors
                hugo.deboer@nhm.uio.no
                Journal
                Sci Rep
                Sci Rep
                Scientific Reports
                Nature Publishing Group UK (London )
                2045-2322
                2 May 2017
                2 May 2017
                2017
                : 7
                : 1291
                Affiliations
                [1 ]ISNI 0000 0004 1936 8921, GRID grid.5510.1, Natural History Museum, , University of Oslo, ; P.O. Box 1172 Blindern, 0318 Oslo, Norway
                [2 ]NIRDBS/”Stejarul” Research Centre for Biological Sciences, Alexandru cel Bun Street, 6, 610004 Piatra, Neamt Romania
                [3 ]ISNI 0000 0004 0571 5814, GRID grid.411040.0, Department of Pharmaceutical Botany, , University of Medicine and Pharmacy “Iuliu Haţieganu”, Faculty of Pharmacy, ; Gheorghe Marinescu Street, 23, 400337 Cluj-Napoca, Romania
                [4 ]ISNI 0000 0004 0571 5814, GRID grid.411040.0, Department of Pharmaceutical Technology and Biopharmaceutics, , “Iuliu Hatieganu” University of Medicine and Pharmacy, ; Ion Creanga Street, 8-10, 400010 Cluj-Napoca, Romania
                [5 ]Department of Biosciences, Centre for Ecological and Evolutionary Synthesis (CEES), University of Oslo, P.O. Box 1066 Blindern, 0316 Oslo, Norway
                Author information
                http://orcid.org/0000-0003-1985-7859
                Article
                1389
                10.1038/s41598-017-01389-w
                5431008
                28465563
                86a18365-1db0-4139-8708-6675d908195e
                © The Author(s) 2017

                Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/.

                History
                : 8 December 2016
                : 29 March 2017
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