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Grazina L, Amaral JS, Mafra I. Botanical origin authentication of dietary supplements by DNA‐based approaches. Compr Rev Food Sci Food Saf 2020; 19:1080-1109. [DOI: 10.1111/1541-4337.12551] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2019] [Revised: 01/22/2020] [Accepted: 02/06/2020] [Indexed: 12/14/2022]
Affiliation(s)
- Liliana Grazina
- REQUIMTE‐LAQV, Faculdade de FarmáciaUniversidade do Porto Porto Portugal
| | - Joana S. Amaral
- Centro de Investigação de Montanha (CIMO)Instituto Politécnico de Bragança Bragança Portugal
| | - Isabel Mafra
- REQUIMTE‐LAQV, Faculdade de FarmáciaUniversidade do Porto Porto Portugal
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Study on the Multitarget Synergistic Effects of Kai-Xin-San against Alzheimer's Disease Based on Systems Biology. OXIDATIVE MEDICINE AND CELLULAR LONGEVITY 2019; 2019:1707218. [PMID: 31976026 PMCID: PMC6955139 DOI: 10.1155/2019/1707218] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/29/2019] [Revised: 11/10/2019] [Accepted: 11/29/2019] [Indexed: 01/07/2023]
Abstract
Kai-Xin-San (KXS), a classical Chinese traditional prescription, was widely applied in the treatment of Alzheimer's disease (AD), while its functional mechanisms still remain unclear. By using systems biology approaches at animal, cellular, and molecular levels, the improvement of KXS on cognitive impairment was achieved by inhibiting abnormal acetylcholinesterase. The function on the nerve skeleton was performed by regulating the Tau phosphorylation pathway. Its antioxidant, anti-inflammatory, and antiapoptotic effects by modulating the aberrant upregulation of ROS, proinflammatory factors, and apoptosis-related proteins in the brain were studied to reveal the synergistic therapeutic efficacy of KXS. Then, formula dismantling in vitro indicated that ginseng was the principal herb, whereas three other herbs served adjuvant roles to achieve the best effect. After that, the in vivo analysis of components into plasma and brain of AD rats showed that 8 of 23 components in blood and 4 of 10 components in brain were from ginseng, respectively, further verifying the principal status of ginseng and the synergistic effects of the formula. Thus, the anti-AD effects of KXS were achieved by multitargets and multichannels. The systems biology approaches presented here provide a novel way in traditional herbal medicine research.
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53
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Lo YT, Shaw PC. Application of next-generation sequencing for the identification of herbal products. Biotechnol Adv 2019; 37:107450. [DOI: 10.1016/j.biotechadv.2019.107450] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2019] [Revised: 09/10/2019] [Accepted: 09/10/2019] [Indexed: 12/17/2022]
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54
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Zhu X, Wu HY, Shaw PC, Peng W, Su W. Specific DNA identification of Pheretima in the Naoxintong capsule. Chin Med 2019; 14:41. [PMID: 31583012 PMCID: PMC6767644 DOI: 10.1186/s13020-019-0264-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2019] [Accepted: 09/23/2019] [Indexed: 12/28/2022] Open
Abstract
Background Pheretima is a minister drug in Naoxintong capsule (NXTC), a well-known traditional Chinese medicine (TCM) formula for the treatment of cardiovascular and cerebrovascular diseases. Owing to the loss of morphological and microscopic characteristics and the lack of recognized chemical marker, it is difficult to identify Pheretima in NXTC. This study aims to evaluate the feasibility of using DNA techniques to authenticate Pheretima, especially when it is processed into NXTC. Methods DNA was extracted from crude drugs of the genuine and adulterant species, as well as nine batches of NXTCs. Based on mitochondrial cytochrome c oxidase subunit I (COI) gene, specific primers were designed for two genera of genuine species, Metaphire and Amynthas, respectively. PCR amplification was performed with the designed primers on crude drugs of Pheretima and NXTCs. The purified PCR products were sequenced and the obtained sequences were identified to species level with top hit of similarity with BLAST against GenBank nucleotide database. Results Primers MF2R2 and AF3R1 could amplify specific DNA fragments with sizes around 230–250 bp, both in crude drugs and NXTC. With sequencing and the BLAST search, identities of the tested samples were found. Conclusion This study indicated that the molecular approach is effective for identifying Pheretima in NXTC. Therefore, DNA identification may contribute to the quality control and assurance of NXTC.
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Affiliation(s)
- Xiaoxiao Zhu
- 1Guangdong Engineering and Technology Research Center for Quality and Efficacy Reevaluation of Post-Market Traditional Chinese Medicine, Guangdong Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275 China
| | - Hoi-Yan Wu
- 2Li Dak Sum Yip Yio Chin R & D Centre for Chinese Medicine, The Chinese University of Hong Kong, Shatin, N.T., Hong Kong China
| | - Pang-Chui Shaw
- 2Li Dak Sum Yip Yio Chin R & D Centre for Chinese Medicine, The Chinese University of Hong Kong, Shatin, N.T., Hong Kong China.,3Institute of Chinese Medicine, The Chinese University of Hong Kong, Shatin, N.T., Hong Kong China.,4School of Life Sciences, The Chinese University of Hong Kong, Shatin, N.T., Hong Kong China
| | - Wei Peng
- 1Guangdong Engineering and Technology Research Center for Quality and Efficacy Reevaluation of Post-Market Traditional Chinese Medicine, Guangdong Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275 China
| | - Weiwei Su
- 1Guangdong Engineering and Technology Research Center for Quality and Efficacy Reevaluation of Post-Market Traditional Chinese Medicine, Guangdong Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275 China
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55
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Haynes E, Jimenez E, Pardo MA, Helyar SJ. The future of NGS (Next Generation Sequencing) analysis in testing food authenticity. Food Control 2019. [DOI: 10.1016/j.foodcont.2019.02.010] [Citation(s) in RCA: 46] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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56
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Frequency of Anti-HCV, HBsAg, HIV1-p24 Antigen, Acid Fast Bacilli and Plasmodium spp., in Herbal Home and Hospital Patients with Elevated TNFα (≥ 5.0 pg/ml) in Saki, West Nigeria. JOURNAL OF PURE AND APPLIED MICROBIOLOGY 2019. [DOI: 10.22207/jpam.13.2.19] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
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57
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58
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Moore MK, Frazier K. Humans Are Animals, Too: Critical Commonalities and Differences Between Human and Wildlife Forensic Genetics. J Forensic Sci 2019; 64:1603-1621. [DOI: 10.1111/1556-4029.14066] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2018] [Revised: 03/10/2019] [Accepted: 04/08/2019] [Indexed: 12/31/2022]
Affiliation(s)
- M. Katherine Moore
- Forensic Laboratory Conservation Biology Division Northwest Fisheries Science Center, National Marine Fisheries Service National Oceanic and Atmospheric Administration 219 Fort Johnson Road Charleston SC29412
| | - Kim Frazier
- Wyoming Game and Fish Wildlife Forensic and Fish Health Laboratory 1212 South Adams Street Laramie WY 82070
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Zhang P, Liu C, Zheng X, Wu L, Liu Z, Liao B, Shi Y, Li X, Xu J, Chen S. Full-Length Multi-Barcoding: DNA Barcoding from Single Ingredient to Complex Mixtures. Genes (Basel) 2019; 10:E343. [PMID: 31067783 PMCID: PMC6562688 DOI: 10.3390/genes10050343] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2019] [Revised: 04/22/2019] [Accepted: 04/29/2019] [Indexed: 11/22/2022] Open
Abstract
DNA barcoding has been used for decades, although it has mostly been applied to somesingle-species. Traditional Chinese medicine (TCM), which is mainly used in the form ofcombination-one type of the multi-species, identification is crucial for clinical usage.Next-generation Sequencing (NGS) has been used to address this authentication issue for the pastfew years, but conventional NGS technology is hampered in application due to its short sequencingreads and systematic errors. Here, a novel method, Full-length multi-barcoding (FLMB) vialong-read sequencing, is employed for the identification of biological compositions in herbalcompound formulas in adequate and well controlled studies. By directly sequencing the full-lengthamplicons of ITS2 and psbA-trnH through single-molecule real-time (SMRT) technology, thebiological composition of a classical prescription Sheng-Mai-San (SMS) was analyzed. At the sametime, clone-dependent Sanger sequencing was carried out as a parallel control. Further, anotherformula-Sanwei-Jili-San (SJS)-was analyzed with genes of ITS2 and CO1. All the ingredients inthe samples of SMS and SJS were successfully authenticated at the species level, and 11 exogenousspecies were also checked, some of which were considered as common contaminations in theseproducts. Methodology analysis demonstrated that this method was sensitive, accurate andreliable. FLMB, a superior but feasible approach for the identification of biological complexmixture, was established and elucidated, which shows perfect interpretation for DNA barcodingthat could lead its application in multi-species mixtures.
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Affiliation(s)
- Peng Zhang
- School of Chinese Materia Medica, Beijing University of Chinese Medicine, Beijing 102488, China.
- Key Laboratory of Beijing for Identification and Safety Evaluation of Chinese Medicine, Institute of ChineseMateria Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China.
| | - Chunsheng Liu
- School of Chinese Materia Medica, Beijing University of Chinese Medicine, Beijing 102488, China.
| | - Xiasheng Zheng
- Guangdong Provincial Key Laboratory of New Drug Development and Research of Chinese Medicine, Guangzhou University of Chinese Medicine, Guangzhou 510006, China.
| | - Lan Wu
- Key Laboratory of Beijing for Identification and Safety Evaluation of Chinese Medicine, Institute of ChineseMateria Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China.
| | - Zhixiang Liu
- Key Laboratory of Beijing for Identification and Safety Evaluation of Chinese Medicine, Institute of ChineseMateria Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China.
| | - Baosheng Liao
- Key Laboratory of Beijing for Identification and Safety Evaluation of Chinese Medicine, Institute of ChineseMateria Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China.
| | - Yuhua Shi
- Key Laboratory of Beijing for Identification and Safety Evaluation of Chinese Medicine, Institute of ChineseMateria Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China.
| | - Xiwen Li
- Key Laboratory of Beijing for Identification and Safety Evaluation of Chinese Medicine, Institute of ChineseMateria Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China.
| | - Jiang Xu
- Key Laboratory of Beijing for Identification and Safety Evaluation of Chinese Medicine, Institute of ChineseMateria Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China.
| | - Shilin Chen
- Key Laboratory of Beijing for Identification and Safety Evaluation of Chinese Medicine, Institute of ChineseMateria Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China.
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Zhou Q, Pei J, Poon J, Lau AY, Zhang L, Wang Y, Liu C, Huang L. Worldwide research trends on aristolochic acids (1957-2017): Suggestions for researchers. PLoS One 2019; 14:e0216135. [PMID: 31048858 PMCID: PMC6497264 DOI: 10.1371/journal.pone.0216135] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2018] [Accepted: 04/15/2019] [Indexed: 12/24/2022] Open
Abstract
Aristolochic acids and their derivatives are components of many traditional medicines that have been used for thousands of years, particularly in Asian countries. To study the trends of research into aristolochic acids and provide suggestions for future study, we performed the following work. In this paper, we performed a bibliometric analysis using CiteSpace and HistCite software. We reviewed the three phases of the development of aristolochic acids by using bibliometrics. In addition, we performed a longitudinal review of published review articles over 60 years: 1,217 articles and 189 review articles on the history of aristolochic acid research published between 1957 and 2017 were analyzed. The performances of relevant countries, institutions, and authors are presented; the evolutionary trends of different categories are revealed; the history of research into aristolochic acids is divided into three phases, each of which has unique characteristics; and a roadmap of the historical overview of aristolochic acid research is finally established. Finally, five pertinent suggestions for future research into aristolochic acid are offered: (1) The study of the antitumor efficacy of aristolochic acids is of value; (2) The immune activity of aristolochic acids should be explored further; (3) Researchers should perform a thorough overview of the discovery of naturally occurring aristolochic acids; (4) More efforts should be directed toward exploring the correlation between aristolochic acid mutational signature and various cancers; (5) Further efforts should be devoted to the research and review work related to analytical chemistry. Our study is expected to benefit researchers in shaping future research directions.
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Affiliation(s)
- Qiang Zhou
- Engineering Research Center of Chinese Medicine Resource, Ministry of Education, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Jin Pei
- College of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu, Sichuan, China
| | - Josiah Poon
- School of Information Technologies, The University of Sydney, Sydney, Australia.,Analytic and Clinical Cooperative Laboratory of Integrative Medicine, Chinese University of Hong Kong and The University of Sydney, Sydney, Australia
| | - Alexander Y Lau
- Analytic and Clinical Cooperative Laboratory of Integrative Medicine, Chinese University of Hong Kong and The University of Sydney, Sydney, Australia.,Department of Medicine and Therapeutics, Chinese University of Hong Kong, Hong Kong SAR, China
| | - Li Zhang
- College of Science, Sichuan Agricultural University, Yaan, Sichuan, China
| | - Yuhua Wang
- College of Pharmacy, Inner Mongolia Medical University, Hohhot, Inner Mongolia, China
| | - Chang Liu
- Engineering Research Center of Chinese Medicine Resource, Ministry of Education, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Linfang Huang
- Engineering Research Center of Chinese Medicine Resource, Ministry of Education, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
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61
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Biological ingredient complement chemical ingredient in the assessment of the quality of TCM preparations. Sci Rep 2019; 9:5853. [PMID: 30971728 PMCID: PMC6458136 DOI: 10.1038/s41598-019-42341-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2018] [Accepted: 03/28/2019] [Indexed: 12/12/2022] Open
Abstract
Traditional Chinese Medicine (TCM) preparations have been used in China for thousands of years. Quality evaluation for TCM preparations could be conducted based on chemical ingredients or biological ingredients. To date, the overwhelming majority of researches have focused on chemical ingredients while few studies were reported for biological ingredients. It is only recently that the assessments based on biological ingredients have drawn broader attentions. In this work, we have established a method for quality evaluation of TCM preparations by combination of chemical ingredients determined by HPLC fingerprint and biological ingredients obtained by high-throughput sequencing. This proof-of-concept method has been evaluated and compared with existing methods on Liuwei Dihuang Wan, a classical TCM preparation in China. By comparison of this method with those only based on chemical or biological ingredients, it is suggested that (1) Biological ingredient could complement chemical ingredient in separating TCM preparation from different manufacturers and batches with high accuracy; (2) classification of samples based on selected features would always out-perform those based on all features (either chemical or biological or both). By rationally selecting representative biological and chemical features, we have proven that these two types of features could complement each other for the assessment of ingredient consistencies and differences among various TCM samples, which is helpful to ensure the effectiveness, safety and legality of TCM preparations.
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62
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DNA Authentication of St John's Wort ( Hypericum perforatum L.) Commercial Products Targeting the ITS Region. Genes (Basel) 2019; 10:genes10040286. [PMID: 30970623 PMCID: PMC6523358 DOI: 10.3390/genes10040286] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2019] [Revised: 04/03/2019] [Accepted: 04/03/2019] [Indexed: 11/17/2022] Open
Abstract
There is considerable potential for the use of DNA barcoding methods to authenticate raw medicinal plant materials, but their application to testing commercial products has been controversial. A simple PCR test targeting species-specific sequences within the nuclear ribosomal internal transcribed spacer (ITS) region was adapted to screen commercial products for the presence of Hypericum perforatum L. material. DNA differing widely in amount and extent of fragmentation was detected in a number of product types. Two assays were designed to further analyse this DNA using a curated database of selected Hypericum ITS sequences: A qPCR assay based on a species-specific primer pair spanning the ITS1 and ITS2 regions, using synthetic DNA reference standards for DNA quantitation and a Next Generation Sequencing (NGS) assay separately targeting the ITS1 and ITS2 regions. The ability of the assays to detect H. perforatum DNA sequences in processed medicines was investigated. Out of twenty different matrices tested, both assays detected H. perforatum DNA in five samples with more than 103 ITS copies µL−1 DNA extract, whilst the qPCR assay was also able to detect lower levels of DNA in two further samples. The NGS assay confirmed that H. perforatum was the major species in all five positive samples, though trace contaminants were also detected.
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63
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Ahmad Nizar NN, Hossain M, Sultana S, Ahamad MN, Johan MR, Ali ME. Quantitative duplex real-time polymerase chain reaction assay with TaqMan probe detects and quantifies Crocodylus porosus in food chain and traditional medicines. Food Addit Contam Part A Chem Anal Control Expo Risk Assess 2019; 36:825-835. [DOI: 10.1080/19440049.2019.1584407] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Nina Naquiah Ahmad Nizar
- Nanotechnology and Catalysis Research Centre (NANOCAT), University of Malaya, Kuala Lumpur, Malaysia
| | - Motalib Hossain
- Nanotechnology and Catalysis Research Centre (NANOCAT), University of Malaya, Kuala Lumpur, Malaysia
| | - Sharmin Sultana
- Nanotechnology and Catalysis Research Centre (NANOCAT), University of Malaya, Kuala Lumpur, Malaysia
| | - Mohamad Nasiruddin Ahamad
- Nanotechnology and Catalysis Research Centre (NANOCAT), University of Malaya, Kuala Lumpur, Malaysia
| | - Mohd Rafie Johan
- Nanotechnology and Catalysis Research Centre (NANOCAT), University of Malaya, Kuala Lumpur, Malaysia
| | - Md. Eaqub Ali
- Nanotechnology and Catalysis Research Centre (NANOCAT), University of Malaya, Kuala Lumpur, Malaysia
- Centre for Research in Biotechnology for Agriculture (CEBAR), University of Malaya, Kuala Lumpur, Malaysia
- Institute of Halal Research (IHRUM), University of Malaya, Kuala Lumpur, Malaysia
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64
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Morello L, Braglia L, Gavazzi F, Gianì S, Breviario D. Tubulin-Based DNA Barcode: Principle and Applications to Complex Food Matrices. Genes (Basel) 2019; 10:genes10030229. [PMID: 30889932 PMCID: PMC6471244 DOI: 10.3390/genes10030229] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2019] [Revised: 03/14/2019] [Accepted: 03/14/2019] [Indexed: 12/13/2022] Open
Abstract
The DNA polymorphism diffusely present in the introns of the members of the Eukaryotic beta-tubulin gene families, can be conveniently used to establish a DNA barcoding method, named tubulin-based polymorphism (TBP), that can reliably assign specific genomic fingerprintings to any plant or/and animal species. Similarly, many plant varieties can also be barcoded by TBP. The method is based on a simple cell biology concept that finds a conveniently exploitable molecular basis. It does not depend on DNA sequencing as the most classically established DNA barcode strategies. Successful applications, diversified for the different target sequences or experimental purposes, have been reported in many different plant species and, of late, a new a version applicable to animal species, including fishes, has been developed. Also, the TBP method is currently used for the genetic authentication of plant material and derived food products. Due to the use of a couple of universal primer pairs, specific for plant and animal organisms, respectively, it is effective in metabarcoding a complex matrix allowing an easy and rapid recognition of the different species present in a mixture. A simple, dedicated database made up by the genomic profile of reference materials is also part of the analytical procedure. Here we will provide some example of the TBP application and will discuss its features and uses in comparison with the DNA sequencing-based methods.
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Key Words
- The DNA polymorphism diffusely present in the introns of the members of the Eukaryotic beta-tubulin gene families, can be conveniently used to establish a DNA barcoding method, named tubulin-based polymorphism (TBP), that can reliably assign specific genomic fingerprintings to any plant or/and animal species. Similarly, many plant varieties can also be barcoded by TBP. The method is based on a simple cell biology concept that finds a conveniently exploitable molecular basis. It does not depend on DNA sequencing as the most classically established DNA barcode strategies. Successful applications, diversified for the different target sequences or experimental purposes, have been reported in many different plant species and, of late, a new a version applicable to animal species, including fishes, has been developed. Also, the TBP method is currently used for the genetic authentication of plant material and derived food products. Due to the use of a couple of universal primer pairs, specific for plant and animal organisms, respectively, it is effective in metabarcoding a complex matrix allowing an easy and rapid recognition of the different species present in a mixture. A simple, dedicated database made up by the genomic profile of reference materials is also part of the analytical procedure. Here we will provide some example of the TBP application and will discuss its features and uses in comparison with the DNA sequencing-based methods.
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Affiliation(s)
- Laura Morello
- Istituto Biologia e Biotecnologia Agraria, Via Adolfo Corti 12, 20131 Milano, Italy.
| | - Luca Braglia
- Istituto Biologia e Biotecnologia Agraria, Via Adolfo Corti 12, 20131 Milano, Italy.
| | - Floriana Gavazzi
- Istituto Biologia e Biotecnologia Agraria, Via Adolfo Corti 12, 20131 Milano, Italy.
| | - Silvia Gianì
- Istituto Biologia e Biotecnologia Agraria, Via Adolfo Corti 12, 20131 Milano, Italy.
| | - Diego Breviario
- Istituto Biologia e Biotecnologia Agraria, Via Adolfo Corti 12, 20131 Milano, Italy.
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Seethapathy GS, Raclariu-Manolica AC, Anmarkrud JA, Wangensteen H, de Boer HJ. DNA Metabarcoding Authentication of Ayurvedic Herbal Products on the European Market Raises Concerns of Quality and Fidelity. FRONTIERS IN PLANT SCIENCE 2019; 10:68. [PMID: 30804961 PMCID: PMC6370972 DOI: 10.3389/fpls.2019.00068] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/12/2018] [Accepted: 01/17/2019] [Indexed: 05/30/2023]
Abstract
Ayurveda is one of the oldest systems of medicine in the world, but the growing commercial interest in Ayurveda based products has increased the incentive for adulteration and substitution within this herbal market. Fraudulent practices such as the use of undeclared fillers and use of other species of inferior quality is driven both by the increased as well as insufficient supply capacity of especially wild plant species. Developing novel strategies to exhaustively assess and monitor both the quality of raw materials and final marketed herbal products is a challenge in herbal pharmacovigilance. Seventy-nine Ayurvedic herbal products sold as tablets, capsules, powders, and extracts were randomly purchased via e-commerce and pharmacies across Europe, and DNA metabarcoding was used to assess the ability of this method to authenticate these products. Our analysis reveals that only two out of 12 single ingredient products contained only one species as labeled, eight out of 27 multiple ingredient products contained none of the species listed on the label, and the remaining 19 products contained 1 to 5 of the species listed on the label along with many other species not specified on the label. The fidelity for single ingredient products was 67%, the overall ingredient fidelity for multi ingredient products was 21%, and for all products 24%. The low level of fidelity raises concerns about the reliability of the products, and detection of threatened species raises further concerns about illegal plant trade. The study highlights the necessity for quality control of the marketed herbal products and shows that DNA metabarcoding is an effective analytical approach to authenticate complex multi ingredient herbal products. However, effort needs to be done to standardize the protocols for DNA metabarcoding before this approach can be implemented as routine analytical approaches for plant identification, and approved for use in regulated procedures.
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Affiliation(s)
- Gopalakrishnan Saroja Seethapathy
- Natural History Museum, University of Oslo, Oslo, Norway
- Department of Pharmaceutical Chemistry, School of Pharmacy, University of Oslo, Oslo, Norway
| | - Ancuta-Cristina Raclariu-Manolica
- Natural History Museum, University of Oslo, Oslo, Norway
- Stejarul Research Centre for Biological Sciences, National Institute of Research and Development for Biological Sciences, Piatra Neamt, Romania
| | | | - Helle Wangensteen
- Department of Pharmaceutical Chemistry, School of Pharmacy, University of Oslo, Oslo, Norway
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Verrez-Bagnis V, Sotelo CG, Mendes R, Silva H, Kappel K, Schröder U. Methods for Seafood Authenticity Testing in Europe. BIOACTIVE MOLECULES IN FOOD 2019. [DOI: 10.1007/978-3-319-78030-6_69] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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67
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Tnah L, Lee S, Tan A, Lee C, Ng K, Ng C, Nurul Farhanah Z. DNA barcode database of common herbal plants in the tropics: a resource for herbal product authentication. Food Control 2019. [DOI: 10.1016/j.foodcont.2018.08.022] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
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68
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Adulterants and Contaminants in Psychotropic Herbal Medicines Detected with Mass Spectrometry and Next-Generation DNA Sequencing. Pharmaceut Med 2018. [DOI: 10.1007/s40290-018-0252-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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69
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Establishment of widely applicable DNA extraction methods to identify the origins of crude drugs derived from animals using molecular techniques. J Nat Med 2018; 73:173-178. [PMID: 30374697 DOI: 10.1007/s11418-018-1261-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2018] [Accepted: 10/17/2018] [Indexed: 10/28/2022]
Abstract
We established widely applicable DNA extraction methods to identify the origins of crude drugs derived from animals. Twenty-one samples including 17 kinds of crude drug derived from animals were examined. DNA was extracted from most of the crude drugs by adjustment of the QIAamp® DNA Mini Kit. DNA extraction was performed successfully using phenol to remove impurities after applying a proteinase treatment. DNA extraction was performed successfully by decalcification treatment using ethylenediaminetetraacetic acid (EDTA), before applying the proteinase treatment for crude drugs having high calcium content, such as those from oyster shell and cuttlefish bone. DNA could not be extracted from sea-ear shell using the EDTA decalcification treatment, but was extracted successfully using a TBONE EX KIT. The mitochondrial 16S ribosomal RNA (rRNA) gene region was amplified, and Basic Local Alignment Search Tool (BLAST) analysis was performed after sequencing. Polymerase chain reaction (PCR) products of approximately 600 bp in length were obtained from all samples except donkey glue, one of the two seahorses, and longgu. Drug origins were determined in all samples by sequence analysis based on the BLAST results, and match rates were >97 %. Moreover, 16 samples had a match rate >99 %. Our DNA extraction methods were widely applicable to evaluation of many crude drugs derived from animals, and proved very useful for identifying the origins of such drugs.
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Evaluation of an early twentieth century Afghan herbalist’s preparations. Forensic Sci Med Pathol 2018; 15:314-318. [DOI: 10.1007/s12024-018-0027-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/17/2018] [Indexed: 12/27/2022]
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New Contributions to Asarum Powder on Immunology Related Toxicity Effects in Lung. EVIDENCE-BASED COMPLEMENTARY AND ALTERNATIVE MEDICINE 2018; 2018:1054032. [PMID: 30245729 PMCID: PMC6139235 DOI: 10.1155/2018/1054032] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/03/2018] [Revised: 06/25/2018] [Accepted: 07/10/2018] [Indexed: 01/11/2023]
Abstract
Objective. Asarum is widely used in clinical practice of Chinese medicine in the treatment of respiratory diseases. Many toxic ingredients (safrole, etc.) had been found in Asarum that show multiple visceral toxicities. In this study, we performed systematic investigation of expression profiles of genes to take a new insight into unclear mechanism of Asarum toxicities in lung. Methods. mRNAs were extracted from lungs of rats after intragastric administration with/without Asarum powders, and microarray assays were applied to investigate gene expression profiles. Differentially expressed genes with significance were selected to carry out GO analysis. Subsequently, quantitative PCRs were performed to verify the differential expression of Tmprss6, Prkag3, Nptx2, Antxr11, Klk11, Rag2, Olr77, Cd7, Il20, LOC69, C6, Ccl20, LOC68, and Cd163 in lung. Changes of Ampk, Bcl2, Caspase 3, Il1, Il20, Matriptase2, Nfκb, Nptx2, and Rag2 in the lung on protein level were verified by western blotting and immunohistochemistry. Results. Compared with control group, the estimated organ coefficients were relatively increased in Asarum group. Results of GO analysis showed that a group of immune related genes in lung were expressed abnormally. The result of PCRs showed that Ccl20 was downregulated rather than other upregulated genes in the Asarum group. Western blotting and immunohistochemistry images showed that Asarum can upregulate the expression of Ampk, Caspase 3, Il1, Il20, Matriptase2, Nfκb, and Rag2 and downregulate the expression of Bcl2 in lung. Conclusion. Our data suggest that expressions of immune related genes in lung were selectively altered by Asarum. Therefore, inflammatory response was active, by regulating Caspase 3, Il1, Il20, Matriptase2, Nfκb, Rag2, Tmprss6, Prkag3, Nptx2, Antxr1, Klk11, Olr77, Cd7, LOC69, C6, LOC68, Cd163, Ampk, Bcl2, and Ccl20. Our study indicated that inflammatory factors take effect in lung toxicity caused by Asarum, which provides a new insight into molecular mechanism of Asarum toxicities in lung.
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Ahmad Nizar NN, Sultana S, Hossain MM, Johan MR, Ali ME. Double gene targeting multiplex PCR-RFLP detects Crocodylus porosus in chicken meatball and traditional medicine. INTERNATIONAL JOURNAL OF FOOD PROPERTIES 2018. [DOI: 10.1080/10942912.2018.1508164] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Affiliation(s)
- Nina Naquiah Ahmad Nizar
- Nanotechnology and Catalysis Research Centre, Institute of Postgraduate Studies, University of Malaya, Kuala Lumpur, Malaysia
| | - Sharmin Sultana
- Nanotechnology and Catalysis Research Centre, Institute of Postgraduate Studies, University of Malaya, Kuala Lumpur, Malaysia
| | - M.A. Motalib Hossain
- Nanotechnology and Catalysis Research Centre, Institute of Postgraduate Studies, University of Malaya, Kuala Lumpur, Malaysia
| | - Mohd Rafie Johan
- Nanotechnology and Catalysis Research Centre, Institute of Postgraduate Studies, University of Malaya, Kuala Lumpur, Malaysia
| | - Md. Eaqub Ali
- Nanotechnology and Catalysis Research Centre, Institute of Postgraduate Studies, University of Malaya, Kuala Lumpur, Malaysia
- Centre for Research in Biotechnology for Agriculture (CEBAR), University of Malaya, Kuala Lumpur, Malaysia
- University of Malaya Halal Research Centre (UMHRC), University of Malaya, Kuala Lumpur, Malaysia
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Li H, Wang Z, Zhang J, Wang Y, Yu C, Zhang J, Song X, Lv C. Feifukang ameliorates pulmonary fibrosis by inhibiting JAK-STAT signaling pathway. Altern Ther Health Med 2018; 18:234. [PMID: 30092799 PMCID: PMC6085667 DOI: 10.1186/s12906-018-2297-3] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2018] [Accepted: 07/26/2018] [Indexed: 12/20/2022]
Abstract
Background Feifukang (FFK) is a traditional Chinese medicine composed of herbs that protect lung function. However, difficulty arises regarding the clinical application of FFK due to the complex mechanism of Chinese medicines. This study aimed to investigate the efficacy of FFK and explore its targeted genes and pathways. Methods Histopathological changes and collagen deposition were measured to evaluate the effect of FFK on bleomycin-induced pulmonary fibrosis in mice. The differentially expressed targeted genes and pathways were first screened using RNA sequencing. Then network pharmacology and other experiments were conducted to confirm RNA sequencing data. Results FFK treatment reduced the pathological score and collagen deposition, with a decrease in α-SMA and collagen. RNA sequencing and network pharmacology results all showed that FFK can ameliorate pulmonary fibrosis through multi-genes and multi-pathways. The targeted genes in JAK-STAT signaling pathway are some of the most notable components of these multi-genes and multi-pathways. Further experiments illustrated that FFK regulated phosphorylation of SMAD3, STAT3 and JAK1, and their co-expressed lncRNAs, which all are the important genes in JAK-STAT signaling pathway. Conclusion FFK can ameliorate pulmonary fibrosis by inhibiting JAK-STAT signaling pathway and has potential therapeutic value for lung fibrosis treatment. Our study provides a new idea for the study of traditional Chinese medicine.
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Xin T, Su C, Lin Y, Wang S, Xu Z, Song J. Precise species detection of traditional Chinese patent medicine by shotgun metagenomic sequencing. PHYTOMEDICINE : INTERNATIONAL JOURNAL OF PHYTOTHERAPY AND PHYTOPHARMACOLOGY 2018; 47:40-47. [PMID: 30166107 DOI: 10.1016/j.phymed.2018.04.048] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2017] [Revised: 03/19/2018] [Accepted: 04/17/2018] [Indexed: 05/22/2023]
Abstract
BACKGROUND Current quality control methods for traditional Chinese patent medicines (TCPMs), e.g., microscopy, thin-layer chromatography (TLC), and high-performance liquid chromatography (HPLC), cannot detect herbal species composition with adequate precision. To address this issue, more effective detection methods should be explored. HYPOTHESIS/PURPOSE We hypothesized that shotgun metagenomic sequencing can fulfill the requirements for the species detection of multi-ingredient TCPMs. METHODS Longdan Xiegan Wan (LDXGW), once thought to be the chief culprit in aristolochic acid nephropathy (AAN), was selected to establish the method. It was used for both reference and commercial LDXGW samples. The precision authentication of herbal species contained in multi-ingredient TCPM is based on the shotgun metagenomic sequencing of genomic DNA without PCR amplification. Chemical analyses were also conducted as a contrast test. RESULTS Over 100 G of raw data was obtained, and this value represented more than 0.75 billion reads. After assembling and filtering all the reads, a total of 261 contigs were obtained, which belonged to the ITS2, psbA-trnH, and matK regions of the reference and commercial samples. Because the homology of the rbcL region was high, it was not analyzed in the HTS data. Bioinformatics analysis indicated that the ITS2 region, as a DNA barcode, showed the highest identification efficiency. It could successfully detect all prescribed species, including four processed herbal ingredients, in the lab-made reference samples. The commercial samples all met the requirements of the Chinese Pharmacopoeia according to the TLC and HPLC tests. However, the shotgun metagenomic sequencing detected the substitution of Akebiae Caulis (Mutong) in the commercial samples, while the chemical analyses could not distinguish. CONCLUSION The results highlight that shotgun metagenomic sequencing is a complementary method for the precise species detection of TCPMs.
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Affiliation(s)
- Tianyi Xin
- Key Lab of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of the People's Republic of China, Institute of Medicinal Plant Development, Peking Union Medical College & Chinese Academy of Medical Sciences, No.151, Malianwa North Road, Haidian District, Beijing 100193, PR China
| | - Chang Su
- Shenzhen Institute for Drug Control, Shenzhen 518057, PR China
| | - Yulin Lin
- Key Lab of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of the People's Republic of China, Institute of Medicinal Plant Development, Peking Union Medical College & Chinese Academy of Medical Sciences, No.151, Malianwa North Road, Haidian District, Beijing 100193, PR China
| | - Shuhong Wang
- Shenzhen Institute for Drug Control, Shenzhen 518057, PR China
| | - Zhichao Xu
- Key Lab of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of the People's Republic of China, Institute of Medicinal Plant Development, Peking Union Medical College & Chinese Academy of Medical Sciences, No.151, Malianwa North Road, Haidian District, Beijing 100193, PR China.
| | - Jingyuan Song
- Key Lab of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of the People's Republic of China, Institute of Medicinal Plant Development, Peking Union Medical College & Chinese Academy of Medical Sciences, No.151, Malianwa North Road, Haidian District, Beijing 100193, PR China.
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Seethapathy GS, Tadesse M, Urumarudappa SKJ, V Gunaga S, Vasudeva R, Malterud KE, Shaanker RU, de Boer HJ, Ravikanth G, Wangensteen H. Authentication of Garcinia fruits and food supplements using DNA barcoding and NMR spectroscopy. Sci Rep 2018. [PMID: 30002410 DOI: 10.1038/s41598-018-28635] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/10/2023] Open
Abstract
Garcinia L. (Clusiaceae) fruits are a rich source of (-)-hydroxycitric acid, and this has gained considerable attention as an anti-obesity agent and a popular weight loss food supplement. In this study, we assessed adulteration of morphologically similar samples of Garcinia using DNA barcoding, and used NMR to quantify the content of (-)-hydroxycitric acid and (-)-hydroxycitric acid lactone in raw herbal drugs and Garcinia food supplements. DNA barcoding revealed that mostly G. gummi-gutta (previously known as G. cambogia) and G. indica were traded in Indian herbal markets, and there was no adulteration. The content of (-)-hydroxycitric acid and (-)-hydroxycitric acid lactone in the two species varied from 1.7% to 16.3%, and 3.5% to 20.7% respectively. Analysis of ten Garcinia food supplements revealed a large variation in the content of (-)-hydroxycitric acid, from 29 mg (4.6%) to 289 mg (50.6%) content per capsule or tablet. Only one product contained quantifiable amounts of (-)-hydroxycitric acid lactone. Furthermore the study demonstrates that DNA barcoding and NMR could be effectively used as a regulatory tool to authenticate Garcinia fruit rinds and food supplements.
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Affiliation(s)
- Gopalakrishnan Saroja Seethapathy
- Department of Pharmaceutical Chemistry, School of Pharmacy, University of Oslo, P.O. Box 1068, Blindern, 0316, Oslo, Norway
- Ashoka Trust for Research in Ecology and the Environment (ATREE), Royal Enclave, Srirampura, Jakkur Post, Bangalore, 560064, India
- Natural History Museum, University of Oslo, P.O. Box 1172, 0318, Oslo, Norway
| | - Margey Tadesse
- Department of Pharmaceutical Chemistry, School of Pharmacy, University of Oslo, P.O. Box 1068, Blindern, 0316, Oslo, Norway
| | - Santhosh Kumar J Urumarudappa
- Department of Crop Physiology, School of Ecology and Conservation, University of Agricultural Sciences, Gandhi Krishi Vigyan Kendra, Bangalore, 560065, India
| | - Srikanth V Gunaga
- Department of Forest Biology, College of Forestry, University of Agricultural Sciences, Sirsi, 581401, India
| | - Ramesh Vasudeva
- Department of Forest Biology, College of Forestry, University of Agricultural Sciences, Sirsi, 581401, India
| | - Karl Egil Malterud
- Department of Pharmaceutical Chemistry, School of Pharmacy, University of Oslo, P.O. Box 1068, Blindern, 0316, Oslo, Norway
| | - Ramanan Uma Shaanker
- Ashoka Trust for Research in Ecology and the Environment (ATREE), Royal Enclave, Srirampura, Jakkur Post, Bangalore, 560064, India
- Department of Crop Physiology, School of Ecology and Conservation, University of Agricultural Sciences, Gandhi Krishi Vigyan Kendra, Bangalore, 560065, India
| | - Hugo J de Boer
- Natural History Museum, University of Oslo, P.O. Box 1172, 0318, Oslo, Norway
| | - Gudasalamani Ravikanth
- Ashoka Trust for Research in Ecology and the Environment (ATREE), Royal Enclave, Srirampura, Jakkur Post, Bangalore, 560064, India.
| | - Helle Wangensteen
- Department of Pharmaceutical Chemistry, School of Pharmacy, University of Oslo, P.O. Box 1068, Blindern, 0316, Oslo, Norway.
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76
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Authentication of Garcinia fruits and food supplements using DNA barcoding and NMR spectroscopy. Sci Rep 2018; 8:10561. [PMID: 30002410 PMCID: PMC6043575 DOI: 10.1038/s41598-018-28635-z] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2018] [Accepted: 06/26/2018] [Indexed: 12/27/2022] Open
Abstract
Garcinia L. (Clusiaceae) fruits are a rich source of (−)-hydroxycitric acid, and this has gained considerable attention as an anti-obesity agent and a popular weight loss food supplement. In this study, we assessed adulteration of morphologically similar samples of Garcinia using DNA barcoding, and used NMR to quantify the content of (−)-hydroxycitric acid and (−)-hydroxycitric acid lactone in raw herbal drugs and Garcinia food supplements. DNA barcoding revealed that mostly G. gummi-gutta (previously known as G. cambogia) and G. indica were traded in Indian herbal markets, and there was no adulteration. The content of (−)-hydroxycitric acid and (−)-hydroxycitric acid lactone in the two species varied from 1.7% to 16.3%, and 3.5% to 20.7% respectively. Analysis of ten Garcinia food supplements revealed a large variation in the content of (−)-hydroxycitric acid, from 29 mg (4.6%) to 289 mg (50.6%) content per capsule or tablet. Only one product contained quantifiable amounts of (−)-hydroxycitric acid lactone. Furthermore the study demonstrates that DNA barcoding and NMR could be effectively used as a regulatory tool to authenticate Garcinia fruit rinds and food supplements.
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Arulandhu AJ, Staats M, Hagelaar R, Voorhuijzen MM, Prins TW, Scholtens I, Costessi A, Duijsings D, Rechenmann F, Gaspar FB, Barreto Crespo MT, Holst-Jensen A, Birck M, Burns M, Haynes E, Hochegger R, Klingl A, Lundberg L, Natale C, Niekamp H, Perri E, Barbante A, Rosec JP, Seyfarth R, Sovová T, Van Moorleghem C, van Ruth S, Peelen T, Kok E. Development and validation of a multi-locus DNA metabarcoding method to identify endangered species in complex samples. Gigascience 2018; 6:1-18. [PMID: 29020743 PMCID: PMC5632295 DOI: 10.1093/gigascience/gix080] [Citation(s) in RCA: 53] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2017] [Accepted: 08/15/2017] [Indexed: 11/19/2022] Open
Abstract
DNA metabarcoding provides great potential for species identification in complex samples such as food supplements and traditional medicines. Such a method would aid Convention on International Trade in Endangered Species of Wild Fauna and Flora (CITES) enforcement officers to combat wildlife crime by preventing illegal trade of endangered plant and animal species. The objective of this research was to develop a multi-locus DNA metabarcoding method for forensic wildlife species identification and to evaluate the applicability and reproducibility of this approach across different laboratories. A DNA metabarcoding method was developed that makes use of 12 DNA barcode markers that have demonstrated universal applicability across a wide range of plant and animal taxa and that facilitate the identification of species in samples containing degraded DNA. The DNA metabarcoding method was developed based on Illumina MiSeq amplicon sequencing of well-defined experimental mixtures, for which a bioinformatics pipeline with user-friendly web-interface was developed. The performance of the DNA metabarcoding method was assessed in an international validation trial by 16 laboratories, in which the method was found to be highly reproducible and sensitive enough to identify species present in a mixture at 1% dry weight content. The advanced multi-locus DNA metabarcoding method assessed in this study provides reliable and detailed data on the composition of complex food products, including information on the presence of CITES-listed species. The method can provide improved resolution for species identification, while verifying species with multiple DNA barcodes contributes to an enhanced quality assurance.
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Affiliation(s)
- Alfred J Arulandhu
- RIKILT Wageningen University & Research, P.O. Box 230, 6700 AE Wageningen, The Netherlands.,Food Quality and Design Group, Wageningen University and Research, P.O. Box 8129, 6700 EV Wageningen, The Netherlands
| | - Martijn Staats
- RIKILT Wageningen University & Research, P.O. Box 230, 6700 AE Wageningen, The Netherlands
| | - Rico Hagelaar
- RIKILT Wageningen University & Research, P.O. Box 230, 6700 AE Wageningen, The Netherlands
| | - Marleen M Voorhuijzen
- RIKILT Wageningen University & Research, P.O. Box 230, 6700 AE Wageningen, The Netherlands
| | - Theo W Prins
- RIKILT Wageningen University & Research, P.O. Box 230, 6700 AE Wageningen, The Netherlands
| | - Ingrid Scholtens
- RIKILT Wageningen University & Research, P.O. Box 230, 6700 AE Wageningen, The Netherlands
| | | | - Danny Duijsings
- Baseclear B. V, Einsteinweg 5, 2333 CC Leiden, The Netherlands
| | - François Rechenmann
- GenoStar Bioinformatics Solutions, 60 rue Lavoisier, 38330 Montbonnot Saint Martin, France
| | - Frédéric B Gaspar
- iBET, Instituto de Biologia Experimental e Tecnológica, Apartado 12, 2780-901 Oeiras, Portugal
| | | | - Arne Holst-Jensen
- Norwegian Veterinary Institute, Ullevaalsveien 68, P.O. Box 750 Sentrum, 0106 Oslo, Norway
| | - Matthew Birck
- U.S. Customs and Border Protection Laboratory, 1100 Raymond Blvd Newark, NJ 07102 USA
| | - Malcolm Burns
- LGC, Queens Road, Teddington, Middlesex, TW11 0LY, UK
| | | | - Rupert Hochegger
- Austrian Agency for Health and Food Safety, Spargelfeldstrasse 191, 1220 Vienna, Austria
| | - Alexander Klingl
- Generalzolldirektion, Direktion IX, Bildungs- und Wissenschaftszentrum der Bundesfinanzverwaltung, Dienstort Hamburg, Baumacker 3, D-22523 Hamburg, Germany
| | - Lisa Lundberg
- Livsmedelsverket, Att. Lisa Lundberg, Strandbodgatan 4, SE 75323 Uppsala, Sweden
| | - Chiara Natale
- AGENZIA DELLE DOGANE E DEI MONOPOLI, Laboratori e servizi chimici - Laboratorio Chimico di Genova, 16126 Genova, Via Rubattino n. 6, Italy
| | - Hauke Niekamp
- Eurofins GeneScan GmbH, Engesserstrasse 4 79108 Freiburg, Germany
| | - Elena Perri
- CREA-SCS sede di Tavazzano - Laboratorio via Emilia, Km 307, 26838 Tavazzano, Italy
| | - Alessandra Barbante
- CREA-SCS sede di Tavazzano - Laboratorio via Emilia, Km 307, 26838 Tavazzano, Italy
| | - Jean-Philippe Rosec
- Service Commun des Laboratoires, Laboratoire de Montpellier, Parc Euromédecine, 205 rue de la Croix Verte, 34196 Montpellier Cedex 5, France
| | - Ralf Seyfarth
- Biolytix AG, Benkenstrasse 254, 4108 Witterswil, Switzerland
| | - Tereza Sovová
- Crop Research Institute, Department of Molecular Genetics, Drnovská 507, 161 06 Prague, Czech Republic
| | | | - Saskia van Ruth
- RIKILT Wageningen University & Research, P.O. Box 230, 6700 AE Wageningen, The Netherlands.,Food Quality and Design Group, Wageningen University and Research, P.O. Box 8129, 6700 EV Wageningen, The Netherlands
| | - Tamara Peelen
- Dutch Customs Laboratory, Kingsfordweg 1, 1043 GN, Amsterdam, The Netherlands
| | - Esther Kok
- RIKILT Wageningen University & Research, P.O. Box 230, 6700 AE Wageningen, The Netherlands
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Li Q, Sun Y, Guo H, Sang F, Ma H, Peng H, Zheng N, Xu L. Quality control of the traditional Chinese medicine Ruyi jinhuang powder based on high-throughput sequencing and real-time PCR. Sci Rep 2018; 8:8261. [PMID: 29844337 PMCID: PMC5974330 DOI: 10.1038/s41598-018-26520-3] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2018] [Accepted: 05/11/2018] [Indexed: 11/09/2022] Open
Abstract
Traditional Chinese medicine (TCM) has been practiced for thousands of years, although concerns about the efficacy, legality, and safety of TCM continue to be raised. Chromatographic studies have detected the presence of heavy metals and plant toxins within some TCM preparations. However, chromatography is not able to identify all of the compounds of TCM, particularly those items that are not clearly labeled on the packaging. The present study aimed to establish a supplemental method that better assesses the ingredient components of TCM preparations.We established an effective approach to screen the biological and toxical composition of TCM based on high-throughput sequencing (HTS), as well as fast detection and validation of the toxical species by real-time PCR, based on ITS2 DNA barcoding. Ruyi jinhuang powder (RHP), a classical herbal prescription containing the toxical herb Arisaematis rhizoma, was chosen to test the method. This method could determine whether the Arisaematis Rhizoma had been replaced by Pinellia pedatisecta in the RHP. The results were validated by real-time PCR. 90% compositions of RHP were identified by ITS2 DNA barcoding, suggesting that more DNA barcoding markers are needed for TCM identification. The strategy of high-throughput sequencing has the potential for comprehensive ingredient profiling for TCM preparations. Real-time PCR provides a expeditious metehod for monitoring the safety and legality of TCM preparations.
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Affiliation(s)
- Qiang Li
- Department of Acquired Immune Deficiency Syndrome Treatment and Research Center, the First Affiliated Hospital, Henan University of Chinese Medicine, Zhengzhou, 450000, China.,Key Laboratory of Viral Diseases Prevention and Treatment of Traditional Chinese Medicine of Henan Province, Zhengzhou, 450000, China
| | - Ying Sun
- Gansu Institute for Drug Control, Yinan Road No. 7, Lanzhou, 730070, China
| | - Huijun Guo
- Department of Acquired Immune Deficiency Syndrome Treatment and Research Center, the First Affiliated Hospital, Henan University of Chinese Medicine, Zhengzhou, 450000, China.,Key Laboratory of Viral Diseases Prevention and Treatment of Traditional Chinese Medicine of Henan Province, Zhengzhou, 450000, China
| | - Feng Sang
- Department of Acquired Immune Deficiency Syndrome Treatment and Research Center, the First Affiliated Hospital, Henan University of Chinese Medicine, Zhengzhou, 450000, China.,Key Laboratory of Viral Diseases Prevention and Treatment of Traditional Chinese Medicine of Henan Province, Zhengzhou, 450000, China
| | - Hongyu Ma
- Thermo Fisher Scientific, Building 6, No. 27, Xin Jinqiao Rd., Pudong, Shanghai, 201206, China
| | - Hai Peng
- Institute for Systems Biology, Jianghan University, Wuhan, Hubei, 430056, China
| | - Na Zheng
- Thermo Fisher Scientific, Building 6, No. 27, Xin Jinqiao Rd., Pudong, Shanghai, 201206, China.
| | - Liran Xu
- Department of Acquired Immune Deficiency Syndrome Treatment and Research Center, the First Affiliated Hospital, Henan University of Chinese Medicine, Zhengzhou, 450000, China. .,Key Laboratory of Viral Diseases Prevention and Treatment of Traditional Chinese Medicine of Henan Province, Zhengzhou, 450000, China.
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Raclariu AC, Ţebrencu CE, Ichim MC, Ciupercǎ OT, Brysting AK, de Boer H. What's in the box? Authentication of Echinacea herbal products using DNA metabarcoding and HPTLC. PHYTOMEDICINE : INTERNATIONAL JOURNAL OF PHYTOTHERAPY AND PHYTOPHARMACOLOGY 2018; 44:32-38. [PMID: 29895490 DOI: 10.1016/j.phymed.2018.03.058] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2017] [Revised: 02/18/2018] [Accepted: 03/21/2018] [Indexed: 05/26/2023]
Abstract
BACKGROUND Differences in regulatory policies between countries as well as a lack of appropriate standardized methods for the authentication and quality control of herbal products directly impact their quality and safety. Echinacea products are among the top-selling herbal products in Europe and the United States with indications for a broad range of ailments. The increased use of Echinacea species has led to concerns about adulterated products resulting from challenges in morphology-based identification, due to overlapping morphological variation, frequent hybridization between species, and deliberate adulteration. PURPOSE This study addressed the need for a novel analytical strategy in the authentication of herbal products. METHODS A combination of high performance thin layer chromatography (HPTLC) and DNA metabarcoding was employed. Fifty-three Echinacea herbal products marketed across Europe were tested to evaluate the accuracy of these methods in plant identification and their potential for detecting substitutes, adulterants and other unreported plant constituents. RESULTS HPTLC provides high resolution in the detection of Echinacea phytochemical target compounds, but does not offer information on the other species within the product. Alternatively, we showed that the limitation of HPTLC in detecting non-targeted species can be overcome by the complementary use of DNA metabarcoding. Using DNA metabarcoding, Echinacea species were detected in 34 out of the 38 retained products (89%), but with a lack of discriminatory resolution at the species level due to the low level of molecular divergence within the Echinacea genus. All of the tested herbal products showed considerable discrepancies between ingredients listed on the label and the ones detected using DNA metabarcoding, registering an overall ingredient fidelity of only 43%. CONCLUSION The results confirm that DNA metabarcoding can be used to test for the presence of Echinacea species and simultaneously to detect other species present in even highly processed and multi-ingredient herbal products.
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Affiliation(s)
- Ancuta Cristina Raclariu
- Natural History Museum, University of Oslo, P.O. Box 1172 Blindern, 0318 Oslo, Norway; Stejarul Research Centre for Biological Sciences, National Institute of Research and Development for Biological Sciences, Alexandru cel Bun Street, 6, 610004 Piatra Neamt, Romania
| | - Carmen Elena Ţebrencu
- Research and Processing Center for Medicinal Plants Plantavorel S.A., Cuza Voda Street, 46, 610019, Piatra Neamt, Romania; Academy of Romanian Scientists, Splaiul Independentei, 54, 050094, Bucharest, Romania
| | - Mihael Cristin Ichim
- Stejarul Research Centre for Biological Sciences, National Institute of Research and Development for Biological Sciences, Alexandru cel Bun Street, 6, 610004 Piatra Neamt, Romania
| | - Oana Teodora Ciupercǎ
- Research and Processing Center for Medicinal Plants Plantavorel S.A., Cuza Voda Street, 46, 610019, Piatra Neamt, Romania
| | - Anne Krag Brysting
- Department of Biosciences, Centre for Ecological and Evolutionary Synthesis (CEES), University of Oslo, P.O. Box 1066 Blindern, 0316 Oslo, Norway
| | - Hugo de Boer
- Natural History Museum, University of Oslo, P.O. Box 1172 Blindern, 0318 Oslo, Norway.
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80
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Song M, Dong GQ, Zhang YQ, Liu X, Sun W. Identification of processed Chinese medicinal materials using DNA mini-barcoding. Chin J Nat Med 2018; 15:481-486. [PMID: 28807221 DOI: 10.1016/s1875-5364(17)30073-0] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2016] [Indexed: 10/19/2022]
Abstract
Most of Chinese medicinal herbs are subjected to traditional processing procedures, including stir-frying, charring, steaming, boiling, and calcining before they are released into dispensaries. The marketing and identification of processed medicinal materials is a growing issue in the marketplace. However, conventional methods of identification have limitations, while DNA mini-barcoding, based on the sequencing of a short-standardized region, has received considerable attention as a new potential means to identify processed medicinal materials. In the present study, six DNA barcode loci including ITS2, psbA-trnH, rbcL, matK, trnL (UAA) intron and its P6 loop, were employed for the authentication of 45 processed samples belonging to 15 species. We evaluated the amplification efficiency of each locus. We also examined the identification accuracy of the potential mini-barcode locus, of trnL (UAA) intron P6 loop. Our results showed that the five primary barcode loci were successfully amplified in only 8.89%-20% of the processed samples, while the amplification rates of the trnL (UAA) intron P6 loop were higher, at 75.56% successful amplification. We compared the mini-barcode sequences with Genbank using the Blast program. The analysis showed that 45.23% samples could be identified to genus level, while only one sample could be identified to the species level. We conclude that trnL (UAA) p6 loop is a candidate mini-barcode that has shown its potential and may become a universal mini-barcode as complementary barcode for authenticity testing and will play an important role in medicinal materials control.
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Affiliation(s)
- Ming Song
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China; School of Chemistry, Chemical Engineering and Life Sciences, Wuhan University of Technology, Wuhan 430070, China; Amway (China) Botanical Research and Development Center, Wuxi 214145, China
| | - Gang-Qiang Dong
- Amway (China) Botanical Research and Development Center, Wuxi 214145, China
| | - Ya-Qin Zhang
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China; School of Chemistry, Chemical Engineering and Life Sciences, Wuhan University of Technology, Wuhan 430070, China
| | - Xia Liu
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China; School of Chemistry, Chemical Engineering and Life Sciences, Wuhan University of Technology, Wuhan 430070, China.
| | - Wei Sun
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China.
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81
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Xin T, Xu Z, Jia J, Leon C, Hu S, Lin Y, Ragupathy S, Song J, Newmaster SG. Biomonitoring for traditional herbal medicinal products using DNA metabarcoding and single molecule, real-time sequencing. Acta Pharm Sin B 2018; 8:488-497. [PMID: 29881688 PMCID: PMC5990340 DOI: 10.1016/j.apsb.2017.10.001] [Citation(s) in RCA: 48] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2017] [Revised: 09/05/2017] [Accepted: 09/13/2017] [Indexed: 11/12/2022] Open
Abstract
Global concerns have been paid to the potential hazard of traditional herbal medicinal products (THMPs). Substandard and counterfeit THMPs, including traditional Chinese patent medicine, health foods, dietary supplements, etc. are potential threats to public health. Recent marketplace studies using DNA barcoding have determined that the current quality control methods are not sufficient for ensuring the presence of authentic herbal ingredients and detection of contaminants/adulterants. An efficient biomonitoring method for THMPs is of great needed. Herein, metabarcoding and single-molecule, real-time (SMRT) sequencing were used to detect the multiple ingredients in Jiuwei Qianghuo Wan (JWQHW), a classical herbal prescription widely used in China for the last 800 years. Reference experimental mixtures and commercial JWQHW products from the marketplace were used to confirm the method. Successful SMRT sequencing results recovered 5416 and 4342 circular-consensus sequencing (CCS) reads belonging to the ITS2 and psbA-trnH regions. The results suggest that with the combination of metabarcoding and SMRT sequencing, it is repeatable, reliable, and sensitive enough to detect species in the THMPs, and the error in SMRT sequencing did not affect the ability to identify multiple prescribed species and several adulterants/contaminants. It has the potential for becoming a valuable tool for the biomonitoring of multi-ingredient THMPs.
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Affiliation(s)
- Tianyi Xin
- Key Lab of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of the People's Republic of China, Institute of Medicinal Plant Development, Peking Union Medical College & Chinese Academy of Medical Sciences, Beijing 100193, China
| | - Zhichao Xu
- Key Lab of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of the People's Republic of China, Institute of Medicinal Plant Development, Peking Union Medical College & Chinese Academy of Medical Sciences, Beijing 100193, China
| | - Jing Jia
- Key Lab of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of the People's Republic of China, Institute of Medicinal Plant Development, Peking Union Medical College & Chinese Academy of Medical Sciences, Beijing 100193, China
| | - Christine Leon
- Royal Botanic Gardens, Kew, Richmond, Surrey TW9 3AB, UK
| | - Songnian Hu
- Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China
| | - Yulin Lin
- Key Lab of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of the People's Republic of China, Institute of Medicinal Plant Development, Peking Union Medical College & Chinese Academy of Medical Sciences, Beijing 100193, China
| | - Subramanyam Ragupathy
- NHP Research Alliance, Biodiversity Institute of Ontario (BIO), University of Guelph, Guelph N1G 2W1, Ontario, Canada
| | - Jingyuan Song
- Key Lab of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of the People's Republic of China, Institute of Medicinal Plant Development, Peking Union Medical College & Chinese Academy of Medical Sciences, Beijing 100193, China
| | - Steven G. Newmaster
- NHP Research Alliance, Biodiversity Institute of Ontario (BIO), University of Guelph, Guelph N1G 2W1, Ontario, Canada
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82
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Yang F, Ding F, Chen H, He M, Zhu S, Ma X, Jiang L, Li H. DNA Barcoding for the Identification and Authentication of Animal Species in Traditional Medicine. EVIDENCE-BASED COMPLEMENTARY AND ALTERNATIVE MEDICINE : ECAM 2018; 2018:5160254. [PMID: 29849709 PMCID: PMC5937547 DOI: 10.1155/2018/5160254] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/19/2017] [Accepted: 03/11/2018] [Indexed: 02/06/2023]
Abstract
Animal-based traditional medicine not only plays a significant role in therapeutic practices worldwide but also provides a potential compound library for drug discovery. However, persistent hunting and illegal trade markedly threaten numerous medicinal animal species, and increasing demand further provokes the emergence of various adulterants. As the conventional methods are difficult and time-consuming to detect processed products or identify animal species with similar morphology, developing novel authentication methods for animal-based traditional medicine represents an urgent need. During the last decade, DNA barcoding offers an accurate and efficient strategy that can identify existing species and discover unknown species via analysis of sequence variation in a standardized region of DNA. Recent studies have shown that DNA barcoding as well as minibarcoding and metabarcoding is capable of identifying animal species and discriminating the authentics from the adulterants in various types of traditional medicines, including raw materials, processed products, and complex preparations. These techniques can also be used to detect the unlabelled and threatened animal species in traditional medicine. Here, we review the recent progress of DNA barcoding for the identification and authentication of animal species used in traditional medicine, which provides a reference for quality control and trade supervision of animal-based traditional medicine.
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Affiliation(s)
- Fan Yang
- Institute of Forensic Science, Ministry of Public Security, Beijing 100038, China
- Beijing Engineering Research Center of Crime Scene Evidence Examination, Institute of Forensic Science, Beijing 100038, China
| | - Fei Ding
- Center for Bioresources & Drug Discovery and School of Biosciences & Biopharmaceutics, Guangdong Pharmaceutical University, Guangzhou, Guangdong 510006, China
| | - Hong Chen
- Center for Bioresources & Drug Discovery and School of Biosciences & Biopharmaceutics, Guangdong Pharmaceutical University, Guangzhou, Guangdong 510006, China
| | - Mingqi He
- Center for Bioresources & Drug Discovery and School of Biosciences & Biopharmaceutics, Guangdong Pharmaceutical University, Guangzhou, Guangdong 510006, China
| | - Shixin Zhu
- Center for Bioresources & Drug Discovery and School of Biosciences & Biopharmaceutics, Guangdong Pharmaceutical University, Guangzhou, Guangdong 510006, China
| | - Xin Ma
- Institute of Forensic Science, Ministry of Public Security, Beijing 100038, China
- Beijing Engineering Research Center of Crime Scene Evidence Examination, Institute of Forensic Science, Beijing 100038, China
| | - Li Jiang
- Institute of Forensic Science, Ministry of Public Security, Beijing 100038, China
- Beijing Engineering Research Center of Crime Scene Evidence Examination, Institute of Forensic Science, Beijing 100038, China
| | - Haifeng Li
- Center for Bioresources & Drug Discovery and School of Biosciences & Biopharmaceutics, Guangdong Pharmaceutical University, Guangzhou, Guangdong 510006, China
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83
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Huang T, Zhong LLD, Lin CY, Zhao L, Ning ZW, Hu DD, Zhang M, Tian K, Cheng CW, Bian ZX. Approaches in studying the pharmacology of Chinese Medicine formulas: bottom-up, top-down-and meeting in the middle. Chin Med 2018; 13:15. [PMID: 29588653 PMCID: PMC5863461 DOI: 10.1186/s13020-018-0170-4] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2017] [Accepted: 02/23/2018] [Indexed: 12/31/2022] Open
Abstract
Investigating the pharmacology is key to the modernization of Chinese Medicine (CM) formulas. However, identifying which are the active compound(s) of CM formulas, which biological entities they target, and through which signaling pathway(s) they act to modify disease symptoms, are still difficult tasks for researchers, even when equipped with an arsenal of advanced modern technologies. Multiple approaches, including network pharmacology, pharmaco-genomics, -proteomics, and -metabolomics, have been developed to study the pharmacology of CM formulas. They fall into two general categories in terms of how they tackle a problem: bottom-up and top-down. In this article, we compared these two different approaches in several dimensions by using the case of MaZiRenWan (MZRW, also known as Hemp Seed Pill), a CM herbal formula for functional constipation. Multiple hypotheses are easy to be proposed in the bottom-up approach (e.g. network pharmacology); but these hypotheses are usually false positives and hard to be tested. In contrast, it is hard to suggest hypotheses in the top-down approach (e.g. pharmacometabolomics); however, once a hypothesis is proposed, it is much easier to be tested. Merging of these two approaches could results in a powerful approach, which could be the new paradigm for the pharmacological study of CM formulas.
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Affiliation(s)
- Tao Huang
- 1Institute of Brain and Gut Research, School of Chinese Medicine, Hong Kong Baptist University, Room 307, Jockey Club School of Chinese Medicine, 7 Baptist University Road, Kowloon, Hong Kong, Hong Kong SAR China
| | - Linda L D Zhong
- 1Institute of Brain and Gut Research, School of Chinese Medicine, Hong Kong Baptist University, Room 307, Jockey Club School of Chinese Medicine, 7 Baptist University Road, Kowloon, Hong Kong, Hong Kong SAR China.,2Hong Kong Chinese Medicine Clinical Study Centre, Hong Kong Baptist University, Room 307, Jockey Club School of Chinese Medicine, 7 Baptist University Road, Kowloon, Hong Kong, Hong Kong SAR China
| | - Chen-Yuan Lin
- 1Institute of Brain and Gut Research, School of Chinese Medicine, Hong Kong Baptist University, Room 307, Jockey Club School of Chinese Medicine, 7 Baptist University Road, Kowloon, Hong Kong, Hong Kong SAR China.,3YMU-HKBU Joint Laboratory of Traditional Natural Medicine, Yunnan Minzu University, Kunming, 650500 China
| | - Ling Zhao
- 1Institute of Brain and Gut Research, School of Chinese Medicine, Hong Kong Baptist University, Room 307, Jockey Club School of Chinese Medicine, 7 Baptist University Road, Kowloon, Hong Kong, Hong Kong SAR China
| | - Zi-Wan Ning
- 1Institute of Brain and Gut Research, School of Chinese Medicine, Hong Kong Baptist University, Room 307, Jockey Club School of Chinese Medicine, 7 Baptist University Road, Kowloon, Hong Kong, Hong Kong SAR China
| | - Dong-Dong Hu
- 1Institute of Brain and Gut Research, School of Chinese Medicine, Hong Kong Baptist University, Room 307, Jockey Club School of Chinese Medicine, 7 Baptist University Road, Kowloon, Hong Kong, Hong Kong SAR China
| | - Man Zhang
- 1Institute of Brain and Gut Research, School of Chinese Medicine, Hong Kong Baptist University, Room 307, Jockey Club School of Chinese Medicine, 7 Baptist University Road, Kowloon, Hong Kong, Hong Kong SAR China.,4Guangzhou Research Institute of Snake Venom, Guangzhou Medical University, Guangzhou, 510000 China
| | - Ke Tian
- 1Institute of Brain and Gut Research, School of Chinese Medicine, Hong Kong Baptist University, Room 307, Jockey Club School of Chinese Medicine, 7 Baptist University Road, Kowloon, Hong Kong, Hong Kong SAR China
| | - Chung-Wah Cheng
- 2Hong Kong Chinese Medicine Clinical Study Centre, Hong Kong Baptist University, Room 307, Jockey Club School of Chinese Medicine, 7 Baptist University Road, Kowloon, Hong Kong, Hong Kong SAR China
| | - Zhao-Xiang Bian
- 1Institute of Brain and Gut Research, School of Chinese Medicine, Hong Kong Baptist University, Room 307, Jockey Club School of Chinese Medicine, 7 Baptist University Road, Kowloon, Hong Kong, Hong Kong SAR China.,2Hong Kong Chinese Medicine Clinical Study Centre, Hong Kong Baptist University, Room 307, Jockey Club School of Chinese Medicine, 7 Baptist University Road, Kowloon, Hong Kong, Hong Kong SAR China
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84
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Sapanov MK. The Influence of Natural and Climatic Factors on the Number of Saiga (Saiga tatarica Pall.) (Bovidae, Artiodactyla) between the Volga and Ural Rivers. BIOL BULL+ 2018. [DOI: 10.1134/s1062359017100132] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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85
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Raclariu AC, Heinrich M, Ichim MC, de Boer H. Benefits and Limitations of DNA Barcoding and Metabarcoding in Herbal Product Authentication. PHYTOCHEMICAL ANALYSIS : PCA 2018; 29:123-128. [PMID: 28906059 PMCID: PMC5836936 DOI: 10.1002/pca.2732] [Citation(s) in RCA: 97] [Impact Index Per Article: 16.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/07/2017] [Revised: 08/23/2017] [Accepted: 08/26/2017] [Indexed: 05/21/2023]
Abstract
INTRODUCTION Herbal medicines play an important role globally in the health care sector and in industrialised countries they are often considered as an alternative to mono-substance medicines. Current quality and authentication assessment methods rely mainly on morphology and analytical phytochemistry-based methods detailed in pharmacopoeias. Herbal products however are often highly processed with numerous ingredients, and even if these analytical methods are accurate for quality control of specific lead or marker compounds, they are of limited suitability for the authentication of biological ingredients. OBJECTIVE To review the benefits and limitations of DNA barcoding and metabarcoding in complementing current herbal product authentication. METHOD Recent literature relating to DNA based authentication of medicinal plants, herbal medicines and products are summarised to provide a basic understanding of how DNA barcoding and metabarcoding can be applied to this field. RESULTS Different methods of quality control and authentication have varying resolution and usefulness along the value chain of these products. DNA barcoding can be used for authenticating products based on single herbal ingredients and DNA metabarcoding for assessment of species diversity in processed products, and both methods should be used in combination with appropriate hyphenated chemical methods for quality control. CONCLUSIONS DNA barcoding and metabarcoding have potential in the context of quality control of both well and poorly regulated supply systems. Standardisation of protocols for DNA barcoding and DNA sequence-based identification are necessary before DNA-based biological methods can be implemented as routine analytical approaches and approved by the competent authorities for use in regulated procedures. © 2017 The Authors. Phytochemical Analysis Published by John Wiley & Sons Ltd.
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Affiliation(s)
- Ancuta Cristina Raclariu
- Natural History MuseumUniversity of OsloP.O. Box 1172, Blindern0318OsloNorway
- Stejarul Research Centre for Biological SciencesNational Institute of Research and Development for Biological SciencesAlexandru cel Bun Street, 6610004Piatra NeamtRomania
| | - Michael Heinrich
- Research Group of Pharmacognosy and Phytotherapy, Research Cluster ‘Biodiversity and Medicines’, UCL School of PharmacyUniversity of London29–39 Brunswick SqLondonWC1N 1AXUK
| | - Mihael Cristin Ichim
- Stejarul Research Centre for Biological SciencesNational Institute of Research and Development for Biological SciencesAlexandru cel Bun Street, 6610004Piatra NeamtRomania
| | - Hugo de Boer
- Natural History MuseumUniversity of OsloP.O. Box 1172, Blindern0318OsloNorway
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86
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de Boer HJ, Ghorbani A, Manzanilla V, Raclariu AC, Kreziou A, Ounjai S, Osathanunkul M, Gravendeel B. DNA metabarcoding of orchid-derived products reveals widespread illegal orchid trade. Proc Biol Sci 2018; 284:rspb.2017.1182. [PMID: 28931735 DOI: 10.1098/rspb.2017.1182] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2017] [Accepted: 08/10/2017] [Indexed: 11/12/2022] Open
Abstract
In eastern Mediterranean countries orchids continue to be collected from the wild for the production of salep, a beverage made of dried orchid tubers. In this study we used nrITS1 and nrITS2 DNA metabarcoding to identify orchid and other plant species present in 55 commercial salep products purchased in Iran, Turkey, Greece and Germany. Thirty samples yielded a total of 161 plant taxa, and 13 products (43%) contained orchid species and these belonged to 10 terrestrial species with tuberous roots. Another 70% contained the substitute ingredient Cyamopsis tetraganoloba (Guar). DNA metabarcoding using the barcoding markers nrITS1 and nrITS2 shows the potential of these markers and approach for identification of species used in salep products. The analysis of interspecific genetic distances between sequences of these markers for the most common salep orchid genera shows that species level identifications can be made with a high level of confidence. Understanding the species diversity and provenance of salep orchid tubers will enable the chain of commercialization of endangered species to be traced back to the harvesters and their natural habitats, and thus allow for targeted efforts to protect or sustainably use wild populations of these orchids.
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Affiliation(s)
- Hugo J de Boer
- Natural History Museum, University of Oslo, Oslo, Norway .,Department of Organismal Biology, Uppsala University, Uppsala, Sweden.,Naturalis Biodiversity Center, Leiden, The Netherlands
| | | | | | - Ancuta-Cristina Raclariu
- Natural History Museum, University of Oslo, Oslo, Norway.,Stejarul Research Centre for Biological Sciences, NIRDBIS, Piatra Neamt, Romania
| | | | - Sarawut Ounjai
- Department of Biology, Chiang Mai University, Chiang Mai, Thailand
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87
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Raime K, Remm M. Method for the Identification of Taxon-Specific k-mers from Chloroplast Genome: A Case Study on Tomato Plant ( Solanum lycopersicum). FRONTIERS IN PLANT SCIENCE 2018; 9:6. [PMID: 29387080 PMCID: PMC5776150 DOI: 10.3389/fpls.2018.00006] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/24/2017] [Accepted: 01/03/2018] [Indexed: 06/07/2023]
Abstract
Polymerase chain reaction and different barcoding methods commonly used for plant identification from metagenomics samples are based on the amplification of a limited number of pre-selected barcoding regions. These methods are often inapplicable due to DNA degradation, low amplification success or low species discriminative power of selected genomic regions. Here we introduce a method for the rapid identification of plant taxon-specific k-mers, that is applicable for the fast detection of plant taxa directly from raw sequencing reads without aligning, mapping or assembling the reads. We identified more than 800 Solanum lycopersicum specific k-mers (32 nucleotides in length) from 42 different chloroplast genome regions using the developed method. We demonstrated that identified k-mers are also detectable in whole genome sequencing raw reads from S. lycopersicum. Also, we demonstrated the usability of taxon-specific k-mers in artificial mixtures of sequences from closely related species. Developed method offers a novel strategy for fast identification of taxon-specific genome regions and offers new perspectives for detection of plant taxa directly from sequencing raw reads.
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88
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Liu J, Shi L, Song J, Sun W, Han J, Liu X, Hou D, Yao H, Li M, Chen S. BOKP: A DNA Barcode Reference Library for Monitoring Herbal Drugs in the Korean Pharmacopeia. Front Pharmacol 2017; 8:931. [PMID: 29326593 PMCID: PMC5742532 DOI: 10.3389/fphar.2017.00931] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2017] [Accepted: 12/11/2017] [Indexed: 11/13/2022] Open
Abstract
Herbal drug authentication is an important task in traditional medicine; however, it is challenged by the limitations of traditional authentication methods and the lack of trained experts. DNA barcoding is conspicuous in almost all areas of the biological sciences and has already been added to the British pharmacopeia and Chinese pharmacopeia for routine herbal drug authentication. However, DNA barcoding for the Korean pharmacopeia still requires significant improvements. Here, we present a DNA barcode reference library for herbal drugs in the Korean pharmacopeia and developed a species identification engine named KP-IDE to facilitate the adoption of this DNA reference library for the herbal drug authentication. Using taxonomy records, specimen records, sequence records, and reference records, KP-IDE can identify an unknown specimen. Currently, there are 6,777 taxonomy records, 1,054 specimen records, 30,744 sequence records (ITS2 and psbA-trnH) and 285 reference records. Moreover, 27 herbal drug materials were collected from the Seoul Yangnyeongsi herbal medicine market to give an example for real herbal drugs authentications. Our study demonstrates the prospects of the DNA barcode reference library for the Korean pharmacopeia and provides future directions for the use of DNA barcoding for authenticating herbal drugs listed in other modern pharmacopeias.
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Affiliation(s)
- Jinxin Liu
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
- Hebei Key Laboratory of Study and Exploitation of Chinese Medicine, Chengde Medical College, Chengde, China
| | - Linchun Shi
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
| | - Jingyuan Song
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Wei Sun
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
| | - Jianping Han
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Xia Liu
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
| | - Dianyun Hou
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Hui Yao
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Mingyue Li
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Shilin Chen
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
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89
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Osathanunkul M, Dheeranupattana S, Rotarayanont S, Sookkhee S, Osathanunkul K, Madesis P. Evaluation of suitable DNA regions for molecular identification of high value medicinal plants in genus Kaempferia. NUCLEOSIDES NUCLEOTIDES & NUCLEIC ACIDS 2017; 36:726-735. [PMID: 29215948 DOI: 10.1080/15257770.2017.1391393] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
DNA barcoding coupled high resolution melting (Bar-HRM) is an emerging method for species discrimination based on DNA dissociation kinetics. The aim of this work was to evaluate the suitability of different primer sets, derived from selected DNA regions, for Bar-HRM analysis of species in Kaempferia (Zingiberaceae). Four primer pairs were evaluated (rbcL, rpoC, trnL and ITS1). It was observed that the ITS1 barcode was the most useful DNA barcoding region overall for species discrimination out of all of the regions and primers assessed. Thus, the primer pair derived from the ITS1 region was the single most effective region for the identification of the tested species, whereas the rbcL primer pair gave the lowest resolution. Our Bar-HRM developed here would not only be useful for identification of Kaempferia plant specimens lacking essential parts for morphological identification but will be useful for authenticating products in powdered form of a high value medicinal species Kaempferia parviflora, in particular.
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Affiliation(s)
- Maslin Osathanunkul
- a Department of Biology, Faculty of Science , Chiang Mai University , Chiang Mai , Thailand.,b Center of Excellence in Bioresources for Agriculture, Industry and Medicine , Chiang Mai University , Chiang Mai , Thailand
| | | | - Siriphron Rotarayanont
- a Department of Biology, Faculty of Science , Chiang Mai University , Chiang Mai , Thailand
| | - Siriwoot Sookkhee
- c Department of Microbiology, Faculty of Medicine , Chiang Mai University , Chiang Mai , Thailand
| | - Khukrit Osathanunkul
- d Department of Information Technology , International College, Payap University , Chiang Mai , Thailand
| | - Panagiotis Madesis
- e Institute of Applied Biosciences , Centre for Research & Technology Hellas (CERTH) , Thessaloniki , Greece
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90
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Votrubova J, Rihova P, Saskova L, Vanek D. Operation Tiger’s Eye: DNA testing of traditional Chinese medicine artifacts in the Czech Republic. FORENSIC SCIENCE INTERNATIONAL GENETICS SUPPLEMENT SERIES 2017. [DOI: 10.1016/j.fsigss.2017.09.026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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91
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Kappel K, Haase I, Käppel C, Sotelo CG, Schröder U. Species identification in mixed tuna samples with next-generation sequencing targeting two short cytochrome b gene fragments. Food Chem 2017; 234:212-219. [DOI: 10.1016/j.foodchem.2017.04.178] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2016] [Revised: 04/26/2017] [Accepted: 04/29/2017] [Indexed: 10/19/2022]
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92
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Food metagenomics: Next generation sequencing identifies species mixtures and mislabeling within highly processed cod products. Food Control 2017. [DOI: 10.1016/j.foodcont.2017.04.049] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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93
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Zheng X, Zhang P, Liao B, Li J, Liu X, Shi Y, Cheng J, Lai Z, Xu J, Chen S. A Comprehensive Quality Evaluation System for Complex Herbal Medicine Using PacBio Sequencing, PCR-Denaturing Gradient Gel Electrophoresis, and Several Chemical Approaches. FRONTIERS IN PLANT SCIENCE 2017; 8:1578. [PMID: 28955365 PMCID: PMC5601397 DOI: 10.3389/fpls.2017.01578] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/23/2017] [Accepted: 08/29/2017] [Indexed: 06/01/2023]
Abstract
Herbal medicine is a major component of complementary and alternative medicine, contributing significantly to the health of many people and communities. Quality control of herbal medicine is crucial to ensure that it is safe and sound for use. Here, we investigated a comprehensive quality evaluation system for a classic herbal medicine, Danggui Buxue Formula, by applying genetic-based and analytical chemistry approaches to authenticate and evaluate the quality of its samples. For authenticity, we successfully applied two novel technologies, third-generation sequencing and PCR-DGGE (denaturing gradient gel electrophoresis), to analyze the ingredient composition of the tested samples. For quality evaluation, we used high performance liquid chromatography assays to determine the content of chemical markers to help estimate the dosage relationship between its two raw materials, plant roots of Huangqi and Danggui. A series of surveys were then conducted against several exogenous contaminations, aiming to further access the efficacy and safety of the samples. In conclusion, the quality evaluation system demonstrated here can potentially address the authenticity, quality, and safety of herbal medicines, thus providing novel insight for enhancing their overall quality control. Highlight: We established a comprehensive quality evaluation system for herbal medicine, by combining two genetic-based approaches third-generation sequencing and DGGE (denaturing gradient gel electrophoresis) with analytical chemistry approaches to achieve the authentication and quality connotation of the samples.
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Affiliation(s)
- Xiasheng Zheng
- Key Laboratory of Beijing for Identification and Safety Evaluation of Chinese Medicine, Institute of Chinese Materia Medica, China Academy of Chinese Medical SciencesBeijing, China
- Key Laboratory of Technologies and Applications of Ultrafine Granular Powder of Herbal Medicine, State Administration of Traditional Chinese Medicine, Zhongshan Zhongzhi Pharmaceutical Group LimitedZhongshan, China
- Guangdong Provincial Key Laboratory of New Drug Development and Research of Chinese Medicine, Guangzhou University of Chinese MedicineGuangzhou, China
| | - Peng Zhang
- Key Laboratory of Beijing for Identification and Safety Evaluation of Chinese Medicine, Institute of Chinese Materia Medica, China Academy of Chinese Medical SciencesBeijing, China
- School of Chinese Materia Medica, Beijing University of Chinese MedicineBeijing, China
| | - Baosheng Liao
- Key Laboratory of Beijing for Identification and Safety Evaluation of Chinese Medicine, Institute of Chinese Materia Medica, China Academy of Chinese Medical SciencesBeijing, China
| | - Jing Li
- Traditional Chinese Medicine Gynecology Laboratory in Lingnan Medical Research Center, Guangzhou University of Chinese MedicineGuangzhou, China
| | - Xingyun Liu
- Key Laboratory of Technologies and Applications of Ultrafine Granular Powder of Herbal Medicine, State Administration of Traditional Chinese Medicine, Zhongshan Zhongzhi Pharmaceutical Group LimitedZhongshan, China
| | - Yuhua Shi
- Key Laboratory of Beijing for Identification and Safety Evaluation of Chinese Medicine, Institute of Chinese Materia Medica, China Academy of Chinese Medical SciencesBeijing, China
| | - Jinle Cheng
- Key Laboratory of Technologies and Applications of Ultrafine Granular Powder of Herbal Medicine, State Administration of Traditional Chinese Medicine, Zhongshan Zhongzhi Pharmaceutical Group LimitedZhongshan, China
| | - Zhitian Lai
- Key Laboratory of Technologies and Applications of Ultrafine Granular Powder of Herbal Medicine, State Administration of Traditional Chinese Medicine, Zhongshan Zhongzhi Pharmaceutical Group LimitedZhongshan, China
| | - Jiang Xu
- Key Laboratory of Beijing for Identification and Safety Evaluation of Chinese Medicine, Institute of Chinese Materia Medica, China Academy of Chinese Medical SciencesBeijing, China
| | - Shilin Chen
- Key Laboratory of Beijing for Identification and Safety Evaluation of Chinese Medicine, Institute of Chinese Materia Medica, China Academy of Chinese Medical SciencesBeijing, China
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94
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Chen R, Wang J, Yuan Y, Deng Y, Lai X, Du F, Dong J, Huang X, Cui X, Tang Z. Weigh Biomaterials by Quantifying Species-specific DNA with Real-time PCR. Sci Rep 2017; 7:4774. [PMID: 28684790 PMCID: PMC5500521 DOI: 10.1038/s41598-017-05083-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2017] [Accepted: 05/23/2017] [Indexed: 11/09/2022] Open
Abstract
What's on the label is not what's in the bottle, from food products to herbal medicinal products (HMPs), economically-motivated biomaterials adulteration is a long-term problem affecting the food and drug industry. Accurate identification of the biomaterial ingredients in processed commodities is highly desirable. In this field, DNA-based techniques have proved to be powerful tools to overcome qualitative challenges. However, is it possible to quantify the weight of biological materials with PCR? Therefore, a basic scientific question needs to be answered: what's the relationship between DNA content and the mass of biological materials? Is DNA content directly proportional to the mass of biological materials as most of the researchers previously thought? In this study, we firstly found that there exists a linear relation between DNA contents and the weight of biomaterials indeed when the analytical practices are fully controlled. In this case, the mass of targeted biomaterials in the highly processed commercial products can also be calculated by quantifying the species-specific DNA through classic real-time PCR with a good reproducibility.
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Affiliation(s)
- Rong Chen
- Natural Products Research Center, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, P. R. China
- Ethnomedicine College, Chengdu University of Traditional Chinese Medicine, Chengdu, 611137, P. R. China
- University of Chinese Academy of Sciences, Beijing, 100049, P. R. China
| | - Jiayu Wang
- Natural Products Research Center, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, P. R. China
| | - Yi Yuan
- Natural Products Research Center, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, P. R. China
| | - Yun Deng
- Pharmacy College, Chengdu University of Traditional Chinese Medicine, Chengdu, 611137, P. R. China
| | - Xianrong Lai
- Ethnomedicine College, Chengdu University of Traditional Chinese Medicine, Chengdu, 611137, P. R. China
| | - Feng Du
- Natural Products Research Center, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, P. R. China
| | - Juan Dong
- Natural Products Research Center, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, P. R. China
| | - Xin Huang
- Natural Products Research Center, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, P. R. China
| | - Xin Cui
- Natural Products Research Center, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, P. R. China
| | - Zhuo Tang
- Natural Products Research Center, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, P. R. China.
- University of Chinese Academy of Sciences, Beijing, 100049, P. R. China.
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95
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Nagaraj V, Skillman L, Ho G, Li D, Gofton A. Characterisation and comparison of bacterial communities on reverse osmosis membranes of a full-scale desalination plant by bacterial 16S rRNA gene metabarcoding. NPJ Biofilms Microbiomes 2017. [PMID: 28649414 PMCID: PMC5476683 DOI: 10.1038/s41522-017-0021-6] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
Microbiomes of full-scale seawater reverse osmosis membranes are complex and subject to variation within and between membrane units. The pre-existing bacterial communities of unused membranes before operation have been largely ignored in biofouling studies. This study is novel as unused membranes were used as a critical benchmark for comparison. Fouled seawater reverse osmosis membrane biofilm communities from an array of autopsied membrane samples, following a 7-year operational life-span in a full-scale desalination plant in Western Australia, were characterised by 16S rRNA gene metabarcoding using the bacterial primers 515F and 806R. Communities were then compared based on fouling severity and sampling location. Microbiomes of proteobacterial predominance were detected on control unused membranes. However, fouled membrane communities differed significantly from those on unused membranes, reflecting that operational conditions select specific bacteria on the membrane surface. On fouled membranes, Proteobacteria were also predominant but families differed from those on unused membranes, followed by Bacteriodetes and Firmicutes. Betaproteobacteria correlated with stable, mature and thick biofilms such as those in severely fouled membranes or samples from the feed end of the membrane unit, while Alpha and Gammaproteobacteria were predominantly found in biofilms on fouled but visually clean, and moderately fouled samples or those from reject ends of membrane units. Gammaproteobacteria predominated the thin, compact biofilms at the mid-feed end of membrane units. The study also supported the importance of Caulobacterales and glycosphingolipid-producing bacteria, namely Sphingomonadales, Rhizobiales and Sphingobacteriia, in primary attachment and biofilm recalcitrance. Nitrate-and-nitrite-reducing bacteria such as Rhizobiales, Burkholderiales and some Pseudomonadales were also prevalent across all fouled membranes and appeared to be critical for ecological balance and biofilm maturation. The diverse microbial populations on seawater desalination plant membranes have been characterised after full operational lifecycles. The membranes were used for seven years to purify water by reverse osmosis. Biofouling can seriously impair the efficiency of the membranes but the problem has not previously been well characterised, especially after a full life-span of membrane operation. Veena Nagaraj and colleagues at Murdoch University in Australia investigated biofilms and used genetic analysis to identify the bacteria growing on 14 used membranes, and compared the results with pre-existing contamination on unused membranes. The research revealed that operational conditions favour the growth of specific bacterial populations, predominantly Proteobacteria, but also Bacteriodetes and Firmicutes. The results should assist research to devise new methods to prevent and alleviate the biofouling of desalination plant membranes and maximise the efficiency of their operation.
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Affiliation(s)
- Veena Nagaraj
- School of Engineering and Information Technology, Murdoch University, Murdoch, Western Australia 6150 Australia
| | - Lucy Skillman
- School of Engineering and Information Technology, Murdoch University, Murdoch, Western Australia 6150 Australia
| | - Goen Ho
- School of Engineering and Information Technology, Murdoch University, Murdoch, Western Australia 6150 Australia
| | - Dan Li
- School of Engineering and Information Technology, Murdoch University, Murdoch, Western Australia 6150 Australia
| | - Alexander Gofton
- School of Veterinary and Life Sciences, Murdoch University, Murdoch, Western Australia 6150 Australia
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96
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Raclariu AC, Mocan A, Popa MO, Vlase L, Ichim MC, Crisan G, Brysting AK, de Boer H. Veronica officinalis Product Authentication Using DNA Metabarcoding and HPLC-MS Reveals Widespread Adulteration with Veronica chamaedrys. Front Pharmacol 2017; 8:378. [PMID: 28674497 PMCID: PMC5474480 DOI: 10.3389/fphar.2017.00378] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2017] [Accepted: 05/31/2017] [Indexed: 11/13/2022] Open
Abstract
Studying herbal products derived from local and traditional knowledge and their value chains is one of the main challenges in ethnopharmacology. The majority of these products have a long history of use, but non-harmonized trade and differences in regulatory policies between countries impact their value chains and lead to concerns over product efficacy, safety and quality. Veronica officinalis L. (common speedwell), a member of Plantaginaceae family, has a long history of use in European traditional medicine, mainly in central eastern Europe and the Balkans. However, no specified control tests are available either to establish the quality of derived herbal products or for the discrimination of its most common substitute, V. chamaedrys L. (germander speedwell). In this study, we use DNA metabarcoding and high performance liquid chromatography coupled with mass spectrometry (HPLC-MS) to authenticate sixteen V. officinalis herbal products and compare the potential of the two approaches to detect substitution, adulteration and the use of unreported constituents. HPLC-MS showed high resolution in detecting phytochemical target compounds, but did not enable detection of specific plant species in the products. DNA metabarcoding detected V. officinalis in only 15% of the products, whereas it detected V. chamaedrys in 62% of the products. The results confirm that DNA metabarcoding can be used to test for the presence of Veronica species, and detect substitution and/or admixture of other Veronica species, as well as simultaneously detect all other species present. Our results confirm that none of the herbal products contained exactly the species listed on the label, and all included substitutes, contaminants or fillers. This study highlights the need for authentication of raw herbals along the value chain of these products. An integrative methodology can assess both the quality of herbal products in terms of target compound concentrations and species composition, as well as admixture and substitution with other chemical compounds and plants.
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Affiliation(s)
- Ancuta C Raclariu
- Plant Evolution and Metabarcoding Group, Natural History Museum, University of OsloOslo, Norway.,Stejarul Research Centre for Biological Sciences, National Institute of Research and Development for Biological Sciences (NIRDBS)Piatra Neamţ, Romania
| | - Andrei Mocan
- Department of Pharmaceutical Botany, Faculty of Pharmacy, Iuliu Hatieganu University of Medicine and PharmacyCluj-Napoca, Romania.,ICHAT and Institute for Life Sciences, University of Agricultural Sciences and Veterinary Medicine of Cluj-NapocaCluj-Napoca, Romania
| | - Madalina O Popa
- Stejarul Research Centre for Biological Sciences, National Institute of Research and Development for Biological Sciences (NIRDBS)Piatra Neamţ, Romania
| | - Laurian Vlase
- Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of OsloOslo, Norway
| | - Mihael C Ichim
- Stejarul Research Centre for Biological Sciences, National Institute of Research and Development for Biological Sciences (NIRDBS)Piatra Neamţ, Romania
| | - Gianina Crisan
- Department of Pharmaceutical Botany, Faculty of Pharmacy, Iuliu Hatieganu University of Medicine and PharmacyCluj-Napoca, Romania
| | - Anne K Brysting
- Department of Biosciences, Centre for Ecological and Evolutionary Synthesis (CEES)Oslo, Norway
| | - Hugo de Boer
- Plant Evolution and Metabarcoding Group, Natural History Museum, University of OsloOslo, Norway.,Department of Organismal Biology, Evolutionary Biology Centre, Uppsala UniversityUppsala, Sweden
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97
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Raclariu AC, Paltinean R, Vlase L, Labarre A, Manzanilla V, Ichim MC, Crisan G, Brysting AK, de Boer H. Comparative authentication of Hypericum perforatum herbal products using DNA metabarcoding, TLC and HPLC-MS. Sci Rep 2017; 7:1291. [PMID: 28465563 PMCID: PMC5431008 DOI: 10.1038/s41598-017-01389-w] [Citation(s) in RCA: 59] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2016] [Accepted: 03/29/2017] [Indexed: 12/03/2022] Open
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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Affiliation(s)
- Ancuta Cristina Raclariu
- Natural History Museum, University of Oslo, P.O. Box 1172 Blindern, 0318, Oslo, Norway.,NIRDBS/"Stejarul" Research Centre for Biological Sciences, Alexandru cel Bun Street, 6, 610004, Piatra, Neamt, Romania
| | - Ramona Paltinean
- Department of Pharmaceutical Botany, University of Medicine and Pharmacy "Iuliu Haţieganu", Faculty of Pharmacy, Gheorghe Marinescu Street, 23, 400337, Cluj-Napoca, Romania
| | - Laurian Vlase
- Department of Pharmaceutical Technology and Biopharmaceutics, "Iuliu Hatieganu" University of Medicine and Pharmacy, Ion Creanga Street, 8-10, 400010, Cluj-Napoca, Romania
| | - Aurélie Labarre
- Natural History Museum, University of Oslo, P.O. Box 1172 Blindern, 0318, Oslo, Norway
| | - Vincent Manzanilla
- Natural History Museum, University of Oslo, P.O. Box 1172 Blindern, 0318, Oslo, Norway
| | - Mihael Cristin Ichim
- NIRDBS/"Stejarul" Research Centre for Biological Sciences, Alexandru cel Bun Street, 6, 610004, Piatra, Neamt, Romania
| | - Gianina Crisan
- Department of Pharmaceutical Botany, University of Medicine and Pharmacy "Iuliu Haţieganu", Faculty of Pharmacy, Gheorghe Marinescu Street, 23, 400337, Cluj-Napoca, Romania
| | - Anne Krag Brysting
- Department of Biosciences, Centre for Ecological and Evolutionary Synthesis (CEES), University of Oslo, P.O. Box 1066 Blindern, 0316, Oslo, Norway
| | - Hugo de Boer
- Natural History Museum, University of Oslo, P.O. Box 1172 Blindern, 0318, Oslo, Norway.
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98
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Mohammed Abubakar B, Mohd Salleh F, Shamsir Omar MS, Wagiran A. Review: DNA Barcoding and Chromatography Fingerprints for the Authentication of Botanicals in Herbal Medicinal Products. EVIDENCE-BASED COMPLEMENTARY AND ALTERNATIVE MEDICINE : ECAM 2017; 2017:1352948. [PMID: 28536641 PMCID: PMC5425840 DOI: 10.1155/2017/1352948] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 11/08/2016] [Revised: 02/11/2017] [Accepted: 03/16/2017] [Indexed: 01/28/2023]
Abstract
In the last two decades, there has been a tremendous increase in the global use of herbal medicinal products (HMPs) due to their claimed health benefits. This has led to increase in their demand and consequently, also, resulted in massive adulteration. This is due to the fact that most of the traditional methods cannot identify closely related species in a process product form. Therefore the urgent need for simple and rapid identification methods resulted in the discovery of a novel technique. DNA barcoding is a process that uses short DNA sequence from the standard genome for species identification. This technique is reliable and is not affected by external factors such as climates, age, or plant part. The difficulties in isolation of DNA of high quality in addition to other factors are among the challenges encountered using the DNA barcoding in the authentication of HMP. These limitations indicated that using DNA barcoding alone may ineffectively authenticate the HMP. Therefore, the combination of DNA barcoding with chromatographic fingerprint, a popular and generally accepted technique for the assessment and quality control of HMP, will offer an efficient solution to effectively evaluate the authenticity and quality consistency of HMP. Detailed and quality information about the main composition of the HMPs will help to ascertain their efficacy and safety as these are very important for quality control.
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Affiliation(s)
- Bashir Mohammed Abubakar
- Department of Biotechnology & Medical Engineering, Faculty of Biosciences and Medical Engineering, UTM, 81310 Skudai, Johor, Malaysia
- Department of Biological Sciences, Bauchi State University Gadau, PMB 065, Bauchi, Nigeria
| | - Faezah Mohd Salleh
- Department of Biotechnology & Medical Engineering, Faculty of Biosciences and Medical Engineering, UTM, 81310 Skudai, Johor, Malaysia
| | - Mohd Shahir Shamsir Omar
- Department of Biosciences & Health Sciences, Faculty of Biosciences and Medical Engineering, UTM, 81310 Skudai, Johor, Malaysia
| | - Alina Wagiran
- Department of Biotechnology & Medical Engineering, Faculty of Biosciences and Medical Engineering, UTM, 81310 Skudai, Johor, Malaysia
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99
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Ghorbani A, Saeedi Y, de Boer HJ. Unidentifiable by morphology: DNA barcoding of plant material in local markets in Iran. PLoS One 2017; 12:e0175722. [PMID: 28419161 PMCID: PMC5395179 DOI: 10.1371/journal.pone.0175722] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2016] [Accepted: 03/30/2017] [Indexed: 11/24/2022] Open
Abstract
Local markets provide a rapid insight into the medicinal plants growing in a region as well as local traditional health concerns. Identification of market plant material can be challenging as plants are often sold in dried or processed forms. In this study, three approaches of DNA barcoding-based molecular identification of market samples are evaluated, two objective sequence matching approaches and an integrative approach that coalesces sequence matching with a priori and a posteriori data from other markers, morphology, ethnoclassification and species distribution. Plant samples from markets and herbal shops were identified using morphology, descriptions of local use, and vernacular names with relevant floras and pharmacopoeias. DNA barcoding was used for identification of samples that could not be identified to species level using morphology. Two methods based on BLAST similarity-based identification, were compared with an integrative identification approach. Integrative identification combining the optimized similarity-based approach with a priori and a posteriori information resulted in a 1.67, 1.95 and 2.00 fold increase for ITS, trnL-F spacer, and both combined, respectively. DNA barcoding of traded plant material requires objective strategies to include data from multiple markers, morphology, and traditional knowledge to optimize species level identification success.
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MESH Headings
- Amaranthus
- Cell Nucleus/genetics
- DNA Barcoding, Taxonomic/methods
- DNA, Chloroplast/chemistry
- DNA, Chloroplast/genetics
- DNA, Plant/chemistry
- DNA, Plant/genetics
- DNA, Ribosomal Spacer/chemistry
- DNA, Ribosomal Spacer/genetics
- Plants, Medicinal/anatomy & histology
- Plants, Medicinal/classification
- Plants, Medicinal/genetics
- RNA, Transfer/genetics
- Reproducibility of Results
- Sequence Analysis, DNA
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Affiliation(s)
- Abdolbaset Ghorbani
- Department of Organismal Biology, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden
- Traditional Medicine and Materia Medica Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Yousef Saeedi
- Traditional Medicine and Materia Medica Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Hugo J. de Boer
- Department of Organismal Biology, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden
- Naturalis Biodiversity Center, Leiden, The Netherlands
- The Natural History Museum, University of Oslo, Oslo, Norway
- * E-mail:
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100
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Somervuo P, Yu DW, Xu CC, Ji Y, Hultman J, Wirta H, Ovaskainen O. Quantifying uncertainty of taxonomic placement in
DNA
barcoding and metabarcoding. Methods Ecol Evol 2017. [DOI: 10.1111/2041-210x.12721] [Citation(s) in RCA: 62] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Panu Somervuo
- Department of Biosciences University of Helsinki P.O. Box 65 Helsinki FI‐00014 Finland
| | - Douglas W. Yu
- State Key Laboratory of Genetic Resources and Evolution Kunming Institute of Zoology Chinese Academy of Sciences 32 Jiaochang East Road Kunming Yunnan 650223 China
- School of Biological Sciences University of East Anglia Norwich Research Park Norwich Norfolk NR47TJ UK
| | - Charles C.Y. Xu
- State Key Laboratory of Genetic Resources and Evolution Kunming Institute of Zoology Chinese Academy of Sciences 32 Jiaochang East Road Kunming Yunnan 650223 China
- Groningen Institute for Evolutionary Life Sciences University of Groningen P.O. Box 11103 9700 CC Groningen The Netherlands
| | - Yinqiu Ji
- State Key Laboratory of Genetic Resources and Evolution Kunming Institute of Zoology Chinese Academy of Sciences 32 Jiaochang East Road Kunming Yunnan 650223 China
| | - Jenni Hultman
- Department of Food and Environmental Sciences University of Helsinki P.O. Box 56 Helsinki FI‐00014 Finland
| | - Helena Wirta
- Department of Agricultural Sciences University of Helsinki P.O. Box 27 Helsinki FI‐00014 Finland
| | - Otso Ovaskainen
- Department of Biosciences University of Helsinki P.O. Box 65 Helsinki FI‐00014 Finland
- Centre for Biodiversity Dynamics Department of Biology Norwegian University of Science and Technology N‐7491 Trondheim Norway
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