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Mück F, Scotti F, Mauvisseau Q, Thorbek BLG, Wangensteen H, de Boer HJ. Three-tiered authentication of herbal traditional Chinese medicine ingredients used in women's health provides progressive qualitative and quantitative insight. Front Pharmacol 2024; 15:1353434. [PMID: 38375033 PMCID: PMC10875096 DOI: 10.3389/fphar.2024.1353434] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2023] [Accepted: 01/16/2024] [Indexed: 02/21/2024] Open
Abstract
Traditional Chinese Medicine (TCM) herbal products are increasingly used in Europe, but prevalent authentication methods have significant gaps in detection. In this study, three authentication methods were tested in a tiered approach to improve accuracy on a collection of 51 TCM plant ingredients obtained on the European market. We show the relative performance of conventional barcoding, metabarcoding and standardized chromatographic profiling for TCM ingredients used in one of the most diagnosed disease patterns in women, endometriosis. DNA barcoding using marker ITS2 and chromatographic profiling are methods of choice reported by regulatory authorities and relevant national pharmacopeias. HPTLC was shown to be a valuable authentication tool, combined with metabarcoding, which gives an increased resolution on species diversity, despite dealing with highly processed herbal ingredients. Conventional DNA barcoding as a recommended method was shown to be an insufficient tool for authentication of these samples, while DNA metabarcoding yields an insight into biological contaminants. We conclude that a tiered identification strategy can provide progressive qualitative and quantitative insight in an integrative approach for quality control of processed herbal ingredients.
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Affiliation(s)
- Felicitas Mück
- Section for Pharmaceutical Chemistry, Department of Pharmacy, University of Oslo, Oslo, Norway
| | - Francesca Scotti
- Department of Pharmaceutical and Biological Chemistry, School of Pharmacy, University College London, London, United Kingdom
| | | | | | - Helle Wangensteen
- Section for Pharmaceutical Chemistry, Department of Pharmacy, University of Oslo, Oslo, Norway
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Quatela AS, Cangren P, Jafari F, Michel T, de Boer HJ, Oxelman B. Retrieval of long DNA reads from herbarium specimens. AOB PLANTS 2023; 15:plad074. [PMID: 38130422 PMCID: PMC10735254 DOI: 10.1093/aobpla/plad074] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Accepted: 11/06/2023] [Indexed: 12/23/2023]
Abstract
High-throughput sequencing of herbarium specimens' DNA with short-read platforms has helped explore many biological questions. Here, for the first time, we investigate the potential of using herbarium specimens as a resource for long-read DNA sequencing technologies. We use target capture of 48 low-copy nuclear loci in 12 herbarium specimens of Silene as a basis for long-read sequencing using SMRT PacBio Sequel. The samples were collected between 1932 and 2019. A simple optimization of size selection protocol enabled the retrieval of both long DNA fragments (>1 kb) and long on-target reads for nine of them. The limited sampling size does not enable statistical evaluation of the influence of specimen age to the DNA fragmentation, but our results confirm that younger samples, that is, collected after 1990, are less fragmented and have better sequencing success than specimens collected before this date. Specimens collected between 1990 and 2019 yield between 167 and 3403 on-target reads > 1 kb. They enabled recovering between 34 loci and 48 (i.e. all loci recovered). Three samples from specimens collected before 1990 did not yield on-target reads > 1 kb. The four other samples collected before this date yielded up to 144 reads and recovered up to 25 loci. Young herbarium specimens seem promising for long-read sequencing. However, older ones have partly failed. Further exploration would be necessary to statistically test and understand the potential of older material in the quest for long reads. We would encourage greatly expanding the sampling size and comparing different taxonomic groups.
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Affiliation(s)
- Anne-Sophie Quatela
- Department of Biological and Environmental Sciences, University of Gothenburg, Box 463, 405 30, Gothenburg, Sweden
- Gothenburg Global Biodiversity Center, Gothenburg, Box 463, 405 30, Sweden
| | - Patrik Cangren
- Department of Biological and Environmental Sciences, University of Gothenburg, Box 463, 405 30, Gothenburg, Sweden
| | - Farzaneh Jafari
- Department of Biology, Faculty of Basic Sciences, Lorestan University, P.O. BOX 6815144316, Khorramabad, Iran
- Department of Plant Science, Center of Excellence in Phylogeny of Living Organisms, School of Biology, College of Science, University of Tehran, P.O. Box 14155-6455, Tehran, Iran
| | - Thibauld Michel
- Tropical Diversity Research Department, Royal Botanic Garden of Edinburgh, 20A Inverleith Row, Edinburgh, EH3 5LRUK
| | - Hugo J de Boer
- Natural History Museum, University of Oslo, P.O. Box 1172 Blindern, 0318 Oslo, Norway
| | - Bengt Oxelman
- Department of Biological and Environmental Sciences, University of Gothenburg, Box 463, 405 30, Gothenburg, Sweden
- Gothenburg Global Biodiversity Center, Gothenburg, Box 463, 405 30, Sweden
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Pezzini FF, Ferrari G, Forrest LL, Hart ML, Nishii K, Kidner CA. Target capture and genome skimming for plant diversity studies. APPLICATIONS IN PLANT SCIENCES 2023; 11:e11537. [PMID: 37601316 PMCID: PMC10439825 DOI: 10.1002/aps3.11537] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Revised: 06/16/2023] [Accepted: 07/10/2023] [Indexed: 08/22/2023]
Abstract
Recent technological advances in long-read high-throughput sequencing and assembly methods have facilitated the generation of annotated chromosome-scale whole-genome sequence data for evolutionary studies; however, generating such data can still be difficult for many plant species. For example, obtaining high-molecular-weight DNA is typically impossible for samples in historical herbarium collections, which often have degraded DNA. The need to fast-freeze newly collected living samples to conserve high-quality DNA can be complicated when plants are only found in remote areas. Therefore, short-read reduced-genome representations, such as target capture and genome skimming, remain important for evolutionary studies. Here, we review the pros and cons of each technique for non-model plant taxa. We provide guidance related to logistics, budget, the genomic resources previously available for the target clade, and the nature of the study. Furthermore, we assess the available bioinformatic analyses, detailing best practices and pitfalls, and suggest pathways to combine newly generated data with legacy data. Finally, we explore the possible downstream analyses allowed by the type of data generated using each technique. We provide a practical guide to help researchers make the best-informed choice regarding reduced genome representation for evolutionary studies of non-model plants in cases where whole-genome sequencing remains impractical.
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Affiliation(s)
| | - Giada Ferrari
- Royal Botanic Garden Edinburgh Edinburgh United Kingdom
| | | | | | - Kanae Nishii
- Royal Botanic Garden Edinburgh Edinburgh United Kingdom
| | - Catherine A Kidner
- Royal Botanic Garden Edinburgh Edinburgh United Kingdom
- School of Biological Sciences University of Edinburgh Edinburgh United Kingdom
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Raclariu-Manolică AC, Mauvisseau Q, de Boer HJ. Horizon scan of DNA-based methods for quality control and monitoring of herbal preparations. Front Pharmacol 2023; 14:1179099. [PMID: 37214460 PMCID: PMC10193163 DOI: 10.3389/fphar.2023.1179099] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Accepted: 04/20/2023] [Indexed: 05/24/2023] Open
Abstract
Herbal medicines and preparations are widely used in healthcare systems globally, but concerns remain about their quality and safety. New herbal products are constantly being introduced to the market under varying regulatory frameworks, with no global consensus on their definition or characterization. These biologically active mixtures are sold through complex globalized value chains, which create concerns around contamination and profit-driven adulteration. Industry, academia, and regulatory bodies must collaborate to develop innovative strategies for the identification and authentication of botanicals and their preparations to ensure quality control. High-throughput sequencing (HTS) has significantly improved our understanding of the total species diversity within DNA mixtures. The standard concept of DNA barcoding has evolved over the last two decades to encompass genomic data more broadly. Recent research in DNA metabarcoding has focused on developing methods for quantifying herbal product ingredients, yielding meaningful results in a regulatory framework. Techniques, such as loop-mediated isothermal amplification (LAMP), DNA barcode-based Recombinase Polymerase Amplification (BAR-RPA), DNA barcoding coupled with High-Resolution Melting (Bar-HRM), and microfluidics-based methods, offer more affordable tests for the detection of target species. While target capture sequencing and genome skimming are considerably increasing the species identification resolution in challenging plant clades, ddPCR enables the quantification of DNA in samples and could be used to detect intended and unwanted ingredients in herbal medicines. Here, we explore the latest advances in emerging DNA-based technologies and the opportunities they provide as taxa detection tools for evaluating the safety and quality of dietary supplements and herbal medicines.
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Affiliation(s)
- Ancuța Cristina Raclariu-Manolică
- Stejarul Research Centre for Biological Sciences, National Institute of Research and Development for Biological Sciences, Piatra Neamț, Romania
- Natural History Museum, University of Oslo, Oslo, Norway
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Wang Q, Liu W, Peng B, Gong X, Shi J, Zhang K, Li B, Tu P, Li J, Jiang J, Zhao Y, Song Y. Two-dimensional code enables visibly mapping herbal medicine chemome: an application in Ganoderma lucidum. Chin Med 2023; 18:6. [PMID: 36635742 PMCID: PMC9837956 DOI: 10.1186/s13020-022-00702-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2022] [Accepted: 12/14/2022] [Indexed: 01/14/2023] Open
Abstract
BACKGROUND Chemical profile provides the pronounced evidence for herbal medicine (HM) authentication; however, the chemome is extremely sophisticated. Fortunately, two-dimensional (2D) code, as a quick response means, is conceptually able to store abundant information, exactly fulfilling the chemical information storage demands of HMs. METHODS We here attempted to denote both MS[Formula: see text] and MS[Formula: see text] dataset of HM with a single 2D-code chart. Measurement of Ganoderma lucidum that is one of the most famous HMs with LC-MS/MS was employed to illustrate the "coding-decoding" workflow for the conversion amongst MS/MS dataset, 2D-code, and chemical profile, and to evaluate the applicability as well. After data acquisition, and m/z value of each deprotonated molecular signal was divided into integer and decimal portions, corresponding to x and y coordinates of 2D-plot, respectively. On the other side, m/z values of all its fragment ions were exactly assigned to serial x values sharing an identical y value being equal to the precursor ion. 2D-code was thereafter produced by plotting these defined dots at a 2D-chart. Regarding a given 2D-code map, the entire chart (x coordinate: 0-600; y coordinate: 0-600) was fragmented into two regions by the line of y=x. MS[Formula: see text] spectral signals always located below the line, whereas all fragment ions lay at the left zone. After extracting information from the edges of each square frame, m/z values of both precursor ion and fragment ions could be harvested and putatively deciphered to a compound through applying some empirical mass fragmentation rules. RESULTS The entire code of Ganoderma lucidum fruit bodies therefore corresponded exactly to a compound set. The elution program, even the employment of direct infusion, couldn't significantly impact the code, and dramatical differences occurred between different species and amongst different parts of Ganoderma lucidum as well. Not only ganoderic acid cluster but also certain primary metabolites served as the diagnostic compounds towards species differentiation. CONCLUSION 2D-code might be a meaningful, practical visual way for rapid HM recognition because it is convenient to achieve the conversion amongst MS/MS dataset, 2D-barcode plot, and the chemome.
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Affiliation(s)
- Qian Wang
- grid.24695.3c0000 0001 1431 9176Modern Research Center for Traditional Chinese Medicine, School of Chinese Materia Medica, Beijing University of Chinese Medicine, Beijing, China
| | - Wenjing Liu
- grid.24695.3c0000 0001 1431 9176Modern Research Center for Traditional Chinese Medicine, School of Chinese Materia Medica, Beijing University of Chinese Medicine, Beijing, China
| | - Bo Peng
- Amway (China) Botanical Research Center, Wuxi, China
| | - Xingcheng Gong
- grid.24695.3c0000 0001 1431 9176Modern Research Center for Traditional Chinese Medicine, School of Chinese Materia Medica, Beijing University of Chinese Medicine, Beijing, China
| | - Jingjing Shi
- grid.24695.3c0000 0001 1431 9176Modern Research Center for Traditional Chinese Medicine, School of Chinese Materia Medica, Beijing University of Chinese Medicine, Beijing, China
| | - Ke Zhang
- grid.24695.3c0000 0001 1431 9176Modern Research Center for Traditional Chinese Medicine, School of Chinese Materia Medica, Beijing University of Chinese Medicine, Beijing, China
| | - Bo Li
- Amway (Shanghai) Innovation & Science Co., Ltd., Shanghai, China
| | - Pengfei Tu
- grid.24695.3c0000 0001 1431 9176Modern Research Center for Traditional Chinese Medicine, School of Chinese Materia Medica, Beijing University of Chinese Medicine, Beijing, China
| | - Jun Li
- grid.24695.3c0000 0001 1431 9176Modern Research Center for Traditional Chinese Medicine, School of Chinese Materia Medica, Beijing University of Chinese Medicine, Beijing, China
| | - Jun Jiang
- grid.495496.3Shandong Institute for Food and Drug Control, Ji’nan, China
| | - Yunfang Zhao
- grid.24695.3c0000 0001 1431 9176Modern Research Center for Traditional Chinese Medicine, School of Chinese Materia Medica, Beijing University of Chinese Medicine, Beijing, China
| | - Yuelin Song
- grid.24695.3c0000 0001 1431 9176Modern Research Center for Traditional Chinese Medicine, School of Chinese Materia Medica, Beijing University of Chinese Medicine, Beijing, China
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Ahmad RW, Al Khader W, Jayaraman R, Salah K, Antony J, Swarnakar V. Integrating Lean Six Sigma with blockchain technology for quality management – a scoping review of current trends and future prospects. TQM JOURNAL 2022. [DOI: 10.1108/tqm-06-2022-0181] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
PurposeThe purpose of this research is to study and analyze the literature that integrates Lean Six Sigma (LSS) approach with blockchain technology in different sectors for improved quality management.Design/methodology/approachThis study presents a scoping review on the application of integrated LSS and blockchain technology in the manufacturing and healthcare sector. Further, the authors examined existing blockchain-based solutions on a variety of dimensions, including application area, technical approach, methodology, application scenario, various blockchain platforms, purpose, and monitoring parameters. The authors study LSS approaches in detail, as well as the key benefits that blockchain technology can enable. Finally, the authors discuss significant research problems to be addressed in order to develop a highly efficient, resilient, and secure quality management framework using blockchain technology.FindingsIt has been observed that the adoption of blockchain technology for quality management and assurance is influenced by several factors such as transaction execution speed, throughput, latency. Also, prior blockchain-based solutions have neglected to leverage the benefits of LSS methodologies for effective quality management.Originality/valueThis is the first study to explores the influence of blockchain technology on quality management and assurance in manufacturing and healthcare industry. Furthermore, prior research has not examined how integrating the LSS methodology with blockchain technology can aid in the control of product quality management.
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Hua Z, Jiang C, Song S, Tian D, Chen Z, Jin Y, Zhao Y, Zhou J, Zhang Z, Huang L, Yuan Y. Accurate identification of taxon-specific molecular markers in plants based on DNA signature sequence. Mol Ecol Resour 2022; 23:106-117. [PMID: 35951477 DOI: 10.1111/1755-0998.13697] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Revised: 08/02/2022] [Accepted: 08/03/2022] [Indexed: 11/30/2022]
Abstract
Accurate identification of plants remains a significant challenge for taxonomists and is the basis for plant diversity conservation. Although DNA barcoding methods are commonly used for plant identification, these are limited by the low amplification success and low discriminative power of selected genomic regions. In this study, we developed a k-mer-based approach, the DNA signature sequence (DSS), to accurately identify plant taxon-specific markers, especially at the species level. DSS is a constant-length nucleotide sequence capable of identifying a taxon and distinguishing it from other taxa. In this study, we performed the first large-scale study of DSS markers in plants. DSS candidates of 3,899 angiosperm plant species were calculated based on a chloroplast dataset with 4,356 assemblies. Using Sanger sequencing of PCR amplicons and high-throughput sequencing, DSSs were validated in four and 165 species, respectively. Based on this, the universality of the DSSs was over 79.38%. Several indicators influencing DSS marker identification and detection have also been evaluated, and common criteria for DSS application in plant identification have been proposed.
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Affiliation(s)
- Zhongyi Hua
- National Resource Center for Chinese Materia Medica, Chinese Academy of Chinese Medical Sciences (CACMS), Beijing 100700, China
| | - Chao Jiang
- National Resource Center for Chinese Materia Medica, Chinese Academy of Chinese Medical Sciences (CACMS), Beijing 100700, China
| | - Shuhui Song
- China National Center for Bioinformation, 100101, Beijing, China.,National Genomics Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences (CAS), Beijing 100101, China
| | - Dongmei Tian
- China National Center for Bioinformation, 100101, Beijing, China.,National Genomics Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences (CAS), Beijing 100101, China
| | - Ziyuan Chen
- National Resource Center for Chinese Materia Medica, Chinese Academy of Chinese Medical Sciences (CACMS), Beijing 100700, China
| | - Yan Jin
- National Resource Center for Chinese Materia Medica, Chinese Academy of Chinese Medical Sciences (CACMS), Beijing 100700, China
| | - Yuyang Zhao
- National Resource Center for Chinese Materia Medica, Chinese Academy of Chinese Medical Sciences (CACMS), Beijing 100700, China
| | - Junhui Zhou
- National Resource Center for Chinese Materia Medica, Chinese Academy of Chinese Medical Sciences (CACMS), Beijing 100700, China
| | - Zhang Zhang
- China National Center for Bioinformation, 100101, Beijing, China.,National Genomics Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences (CAS), Beijing 100101, China
| | - Luqi Huang
- National Resource Center for Chinese Materia Medica, Chinese Academy of Chinese Medical Sciences (CACMS), Beijing 100700, China
| | - Yuan Yuan
- National Resource Center for Chinese Materia Medica, Chinese Academy of Chinese Medical Sciences (CACMS), Beijing 100700, China
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Le HTT, Nguyen LN, Pham HLB, Le HTM, Luong TD, Huynh HTT, Nguyen VT, Nong HV, Teixidor-Toneu I, De Boer HJ, Manzanilla V. Target Capture Reveals the Complex Origin of Vietnamese Ginseng. FRONTIERS IN PLANT SCIENCE 2022; 13:814178. [PMID: 35909770 PMCID: PMC9326450 DOI: 10.3389/fpls.2022.814178] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/12/2021] [Accepted: 06/21/2022] [Indexed: 05/30/2023]
Abstract
The global market of the medicinal plant ginseng is worth billions of dollars. Many ginseng species are threatened in the wild and effective sustainable development initiatives are necessary to preserve biodiversity at species and genetic level whilst meeting the demand for medicinal produce. This is also the case of Panax vietnamensis Ha & Grushv., an endemic and threatened ginseng species in Vietnam that is locally cultivated at different scales and has been the object of national breeding programs. To investigate the genetic diversity within cultivated and wild populations of P. vietnamensis we captured 353 nuclear markers using the Angiosperm-353 probe set. Genetic diversity and population structure were evaluated for 319 individuals of Vietnamese ginseng across its area of distribution and from wild and a varying range of cultivated areas. In total, 319 individuals were sampled. After filtering, 1,181 SNPs were recovered. From the population statistics, we observe high genetic diversity and high genetic flow between populations. This is also supported by the STRUCTURE analysis. The intense gene flow between populations and very low genetic differentiation is observed regardless of the populations' wild or cultivated status. High levels of admixture from two ancestral populations exist in both wild and cultivated samples. The high gene flow between populations can be attributed to ancient and on-going practices of cultivation, which exist in a continuum from understorey, untended breeding to irrigated farm cultivation and to trade and exchange activities. These results highlight the importance of partnering with indigenous peoples and local communities and taking their knowledge into account for biodiversity conservation and sustainable development of plants of high cultural value.
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Affiliation(s)
- Hien Thi Thu Le
- Institute of Genome Research, Vietnam Academy of Science and Technology, Hanoi, Vietnam
- Graduate University of Science and Technology, Vietnam Academy Science and Technology, Hanoi, Vietnam
| | - Linh Nhat Nguyen
- Institute of Genome Research, Vietnam Academy of Science and Technology, Hanoi, Vietnam
| | - Hang Le Bich Pham
- Institute of Genome Research, Vietnam Academy of Science and Technology, Hanoi, Vietnam
| | - Hao Thi My Le
- Soils and Fertilizers Research Institute, Vietnam Academy of Agricultural Sciences, Hanoi, Vietnam
| | - Toan Duc Luong
- Soils and Fertilizers Research Institute, Vietnam Academy of Agricultural Sciences, Hanoi, Vietnam
| | - Hue Thi Thu Huynh
- Institute of Genome Research, Vietnam Academy of Science and Technology, Hanoi, Vietnam
- Graduate University of Science and Technology, Vietnam Academy Science and Technology, Hanoi, Vietnam
| | - Van Tuong Nguyen
- Institute of Biotechnology, Vietnam Academy of Science and Technology, Hanoi, Vietnam
| | - Hai Van Nong
- Institute of Genome Research, Vietnam Academy of Science and Technology, Hanoi, Vietnam
- Graduate University of Science and Technology, Vietnam Academy Science and Technology, Hanoi, Vietnam
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