101
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Giusti A, Tinacci L, Sotelo CG, Marchetti M, Guidi A, Zheng W, Armani A. Seafood Identification in Multispecies Products: Assessment of 16SrRNA, cytb, and COI Universal Primers' Efficiency as a Preliminary Analytical Step for Setting up Metabarcoding Next-Generation Sequencing Techniques. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2017; 65:2902-2912. [PMID: 28290697 DOI: 10.1021/acs.jafc.6b05802] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Few studies applying NGS have been conducted in the food inspection field, particularly on multispecies seafood products. A preliminary study screening the performance and the potential application in NGS analysis of 14 "universal primers" amplifying 16SrRNA, cytb, and COI genes in fish and cephalopods was performed. Species used in surimi preparation were chosen as target. An in silico analysis was conducted to test primers' coverage capacity by assessing mismatches (number and position) with the target sequences. The 9 pairs showing the best coverage capacity were tested in PCR on DNA samples of 53 collected species to assess their amplification performance (amplification rate and amplicon concentration). The results confirm that primers designed for the 16SrRNA gene amplification are the most suitable for NGS analysis also for identification of multispecies seafood products. In particular, the primer pair of Chapela et al. (2002) is the best candidate.
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Affiliation(s)
- Alice Giusti
- FishLab, Department of Veterinary Sciences, University of Pisa , Via delle Piagge 2, 56124 Pisa, Italy
| | - Lara Tinacci
- FishLab, Department of Veterinary Sciences, University of Pisa , Via delle Piagge 2, 56124 Pisa, Italy
| | - Carmen G Sotelo
- Instituto de Investigaciones Marinas (IIM-CSIC) , Eduardo Cabello 6, 36208 Vigo, Spain
| | - Martina Marchetti
- FishLab, Department of Veterinary Sciences, University of Pisa , Via delle Piagge 2, 56124 Pisa, Italy
| | - Alessandra Guidi
- FishLab, Department of Veterinary Sciences, University of Pisa , Via delle Piagge 2, 56124 Pisa, Italy
| | - Wenjie Zheng
- Tianjin Entry-Exit Inspection and Quarantine Bureau of the People's Republic of China , Jingmen Road 158, Free trade Zone, Tianjin Port, 300461 Tianjin, China
| | - Andrea Armani
- FishLab, Department of Veterinary Sciences, University of Pisa , Via delle Piagge 2, 56124 Pisa, Italy
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102
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Hoban C, Nash C, Musgrave IF, Byard RW. An analysis of Vietnamese traditional herbal medicines for prescription and non-prescription drugs, herbicides and pesticides. AUST J FORENSIC SCI 2017. [DOI: 10.1080/00450618.2017.1296187] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Affiliation(s)
- Claire Hoban
- School of Medicine, The University of Adelaide , Adelaide, Australia
| | - Christine Nash
- Department of Toxicology, Forensic Science SA , Adelaide, Australia
| | - Ian F. Musgrave
- School of Medicine, The University of Adelaide , Adelaide, Australia
| | - Roger W. Byard
- School of Medicine, The University of Adelaide , Adelaide, Australia
- Department of Toxicology, Forensic Science SA , Adelaide, Australia
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103
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Martel J, Ojcius DM, Chang CJ, Lin CS, Lu CC, Ko YF, Tseng SF, Lai HC, Young JD. Anti-obesogenic and antidiabetic effects of plants and mushrooms. Nat Rev Endocrinol 2017; 13:149-160. [PMID: 27636731 DOI: 10.1038/nrendo.2016.142] [Citation(s) in RCA: 184] [Impact Index Per Article: 26.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Obesity is reaching global epidemic proportions as a result of factors such as high-calorie diets and lack of physical exercise. Obesity is now considered to be a medical condition, which not only contributes to the risk of developing type 2 diabetes mellitus, cardiovascular disease and cancer, but also negatively affects longevity and quality of life. To combat this epidemic, anti-obesogenic approaches are required that are safe, widely available and inexpensive. Several plants and mushrooms that are consumed in traditional Chinese medicine or as nutraceuticals contain antioxidants, fibre and other phytochemicals, and have anti-obesogenic and antidiabetic effects through the modulation of diverse cellular and physiological pathways. These effects include appetite reduction, modulation of lipid absorption and metabolism, enhancement of insulin sensitivity, thermogenesis and changes in the gut microbiota. In this Review, we describe the molecular mechanisms that underlie the anti-obesogenic and antidiabetic effects of these plants and mushrooms, and propose that combining these food items with existing anti-obesogenic approaches might help to reduce obesity and its complications.
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Affiliation(s)
- Jan Martel
- Center for Molecular and Clinical Immunology, Chang Gung University, 259 Wen-Hua First Road, Taoyuan 33302, Taiwan, Republic of China
- Chang Gung Immunology Consortium, Linkou Chang Gung Memorial Hospital, 5 Fu-Hsing Street, Taoyuan 33305, Taiwan, Republic of China
| | - David M Ojcius
- Center for Molecular and Clinical Immunology, Chang Gung University, 259 Wen-Hua First Road, Taoyuan 33302, Taiwan, Republic of China
- Chang Gung Immunology Consortium, Linkou Chang Gung Memorial Hospital, 5 Fu-Hsing Street, Taoyuan 33305, Taiwan, Republic of China
- Department of Biomedical Sciences, University of the Pacific, Arthur Dugoni School of Dentistry, 155 Fifth Street, San Francisco, California 94103, USA
| | - Chih-Jung Chang
- Center for Molecular and Clinical Immunology, Chang Gung University, 259 Wen-Hua First Road, Taoyuan 33302, Taiwan, Republic of China
- Chang Gung Immunology Consortium, Linkou Chang Gung Memorial Hospital, 5 Fu-Hsing Street, Taoyuan 33305, Taiwan, Republic of China
- Department of Medical Biotechnology and Laboratory Science, College of Medicine, Chang Gung University, 259 Wen-Hua First Road, Taoyuan 33302, Taiwan, Republic of China
- Department of Microbiology and Immunology, Chang Gung University, 259 Wen-Hua First Road, Taoyuan 33302, Taiwan, Republic of China
- Research Center of Bacterial Pathogenesis, Chang Gung University, 259 Wen-Hua First Road, Taoyuan 33302, Taiwan, Republic of China
| | - Chuan-Sheng Lin
- Center for Molecular and Clinical Immunology, Chang Gung University, 259 Wen-Hua First Road, Taoyuan 33302, Taiwan, Republic of China
- Chang Gung Immunology Consortium, Linkou Chang Gung Memorial Hospital, 5 Fu-Hsing Street, Taoyuan 33305, Taiwan, Republic of China
- Department of Medical Biotechnology and Laboratory Science, College of Medicine, Chang Gung University, 259 Wen-Hua First Road, Taoyuan 33302, Taiwan, Republic of China
- Department of Microbiology and Immunology, Chang Gung University, 259 Wen-Hua First Road, Taoyuan 33302, Taiwan, Republic of China
- Research Center of Bacterial Pathogenesis, Chang Gung University, 259 Wen-Hua First Road, Taoyuan 33302, Taiwan, Republic of China
| | - Chia-Chen Lu
- Department of Respiratory Therapy, Fu Jen Catholic University, 510 Zhong-Zheng Street, New Taipei City 24205, Taiwan, Republic of China
| | - Yun-Fei Ko
- Chang Gung Immunology Consortium, Linkou Chang Gung Memorial Hospital, 5 Fu-Hsing Street, Taoyuan 33305, Taiwan, Republic of China
- Chang Gung Biotechnology Corporation, 201 Tung-Hua North Road, Taipei 10508, Taiwan, Republic of China
- Biochemical Engineering Research Center, Ming Chi University of Technology, 84 Gungjuan Road, New Taipei City 24301, Taiwan, Republic of China
| | - Shun-Fu Tseng
- Chang Gung Immunology Consortium, Linkou Chang Gung Memorial Hospital, 5 Fu-Hsing Street, Taoyuan 33305, Taiwan, Republic of China
- Research Center of Bacterial Pathogenesis, Chang Gung University, 259 Wen-Hua First Road, Taoyuan 33302, Taiwan, Republic of China
| | - Hsin-Chih Lai
- Center for Molecular and Clinical Immunology, Chang Gung University, 259 Wen-Hua First Road, Taoyuan 33302, Taiwan, Republic of China
- Chang Gung Immunology Consortium, Linkou Chang Gung Memorial Hospital, 5 Fu-Hsing Street, Taoyuan 33305, Taiwan, Republic of China
- Department of Medical Biotechnology and Laboratory Science, College of Medicine, Chang Gung University, 259 Wen-Hua First Road, Taoyuan 33302, Taiwan, Republic of China
- Department of Microbiology and Immunology, Chang Gung University, 259 Wen-Hua First Road, Taoyuan 33302, Taiwan, Republic of China
- Research Center of Bacterial Pathogenesis, Chang Gung University, 259 Wen-Hua First Road, Taoyuan 33302, Taiwan, Republic of China
- Department of Laboratory Medicine, Linkou Chang Gung Memorial Hospital, 5 Fu-Hsing Street, Taoyuan 33305, Taiwan, Republic of China
- Research Center for Industry of Human Ecology, College of Human Ecology, Chang Gung University of Science and Technology, 261 Wen-Hua First Road, Taoyuan 33303, Taiwan, Republic of China
- Graduate Institute of Health Industry and Technology, College of Human Ecology, Chang Gung University of Science and Technology, 261 Wen-Hua First Road, Taoyuan 33303, Taiwan, Republic of China
| | - John D Young
- Center for Molecular and Clinical Immunology, Chang Gung University, 259 Wen-Hua First Road, Taoyuan 33302, Taiwan, Republic of China
- Chang Gung Immunology Consortium, Linkou Chang Gung Memorial Hospital, 5 Fu-Hsing Street, Taoyuan 33305, Taiwan, Republic of China
- Chang Gung Biotechnology Corporation, 201 Tung-Hua North Road, Taipei 10508, Taiwan, Republic of China
- Biochemical Engineering Research Center, Ming Chi University of Technology, 84 Gungjuan Road, New Taipei City 24301, Taiwan, Republic of China
- Laboratory of Cellular Physiology and Immunology, Rockefeller University, 1230 York Avenue, New York, New York 10021, USA
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104
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Shi Y, Zhao M, Yao H, Yang P, Xin T, Li B, Sun W, Chen S. Rapidly discriminate commercial medicinal Pulsatilla chinensis (Bge.) Regel from its adulterants using ITS2 barcoding and specific PCR-RFLP assay. Sci Rep 2017; 7:40000. [PMID: 28059130 PMCID: PMC5216359 DOI: 10.1038/srep40000] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2015] [Accepted: 12/01/2016] [Indexed: 12/18/2022] Open
Abstract
Pulsatillae radix is a conventional traditional Chinese medicine (TCM) with common name Baitouweng, and has notable effects on inflammation and dysentery. Pulsatilla chinensis (Bge.) Regel is the only source plant of Baitouweng recorded in Chinese Pharmacopoeia, but its adulteration often occurs in the market that possibly affects medicinal efficacy and safety. We have established an internal transcribed spacer 2 (ITS2) barcode library based on 105 plant samples from 12 Pulsatilla species and 10 common adulterants. Results indicate that ITS2 barcoding can accurately distinguish Pulsatilla species from their adulterants. Pulsatilla chinensis can be discriminated from 11 congeneric species by two stable single nucleotide polymorphisms (SNPs) in the ITS2 region. Additionally, a quick specific PCR-RFLP identification assay based on the ITS2 barcode was developed. Using specific primers ITS2/PR1 combined with restriction enzyme Bgl I, Pu. chinensis can rapidly be differentiated from other species via simple and low-cost test procedures. Furthermore, 30 commercial Baitouweng products were tested and only two products were derived from authentic Pu. chinensis. Thus, these two molecular approaches provide practical tools for quick identification of commercial Baitouweng products and can help ensure the safe use of this TCM product.
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Affiliation(s)
- Yuhua Shi
- Key Laboratory of Beijing for Identification and Safety Evaluation of Chinese Medicine, Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China
| | - Mingming Zhao
- Key Laboratory of Beijing for Identification and Safety Evaluation of Chinese Medicine, Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China
| | - Hui Yao
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences &Peking Union Medical College, Beijing 100193, China
| | - Pei Yang
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences &Peking Union Medical College, Beijing 100193, China
| | - Tianyi Xin
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences &Peking Union Medical College, Beijing 100193, China
| | - Bin Li
- Xi'an Botanical Garden of Shanxi Province, Xi'an 710061, China
| | - Wei Sun
- Key Laboratory of Beijing for Identification and Safety Evaluation of Chinese Medicine, Institute of Chinese Materia 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 Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China
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105
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Chen JF, Liu T, Huang DP, He QD, Chen ZG, Yao MC. Developmental Toxicity and Potential Teratogenicity of Compound Danshen Tablet, Angong Niuhuang Pill, and Lidan Paishi Tablet in Zebrafish Embryos. CHINESE HERBAL MEDICINES 2017. [DOI: 10.1016/s1674-6384(17)60079-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022] Open
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106
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Jia J, Xu Z, Xin T, Shi L, Song J. Quality Control of the Traditional Patent Medicine Yimu Wan Based on SMRT Sequencing and DNA Barcoding. FRONTIERS IN PLANT SCIENCE 2017; 8:926. [PMID: 28620408 PMCID: PMC5449480 DOI: 10.3389/fpls.2017.00926] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/20/2017] [Accepted: 05/17/2017] [Indexed: 05/22/2023]
Abstract
Substandard traditional patent medicines may lead to global safety-related issues. Protecting consumers from the health risks associated with the integrity and authenticity of herbal preparations is of great concern. Of particular concern is quality control for traditional patent medicines. Here, we establish an effective approach for verifying the biological composition of traditional patent medicines based on single-molecule real-time (SMRT) sequencing and DNA barcoding. Yimu Wan (YMW), a classical herbal prescription recorded in the Chinese Pharmacopoeia, was chosen to test the method. Two reference YMW samples were used to establish a standard method for analysis, which was then applied to three different batches of commercial YMW samples. A total of 3703 and 4810 circular-consensus sequencing (CCS) reads from two reference and three commercial YMW samples were mapped to the ITS2 and psbA-trnH regions, respectively. Moreover, comparison of intraspecific genetic distances based on SMRT sequencing data with reference data from Sanger sequencing revealed an ITS2 and psbA-trnH intergenic spacer that exhibited high intraspecific divergence, with the sites of variation showing significant differences within species. Using the CCS strategy for SMRT sequencing analysis was adequate to guarantee the accuracy of identification. This study demonstrates the application of SMRT sequencing to detect the biological ingredients of herbal preparations. SMRT sequencing provides an affordable way to monitor the legality and safety of traditional patent medicines.
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107
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The application of metabolomics for herbal medicine pharmacovigilance: a case study on ginseng. Essays Biochem 2016; 60:429-435. [PMID: 27980093 DOI: 10.1042/ebc20160030] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2016] [Revised: 10/12/2016] [Accepted: 10/14/2016] [Indexed: 11/17/2022]
Abstract
Herbal medicines are growing in popularity, use and commercial value; however, there remain problems with the quality and consequently safety of these products. Adulterated, contaminated and fraudulent products are often found on the market, a risk compounded by the fact that these products are available to consumers with little or no medical advice. Current regulations and quality control methods are lacking in their ability to combat these serious problems. Metabolomics is a biochemical profiling tool that may help address these issues if applied to quality control of both raw ingredients and final products. Using the example of the popular herbal medicine, ginseng, this essay offers an overview of the potential use of metabolomics for quality control in herbal medicines and also highlights where more research is needed.
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108
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From market to food plate: Current trusted technology and innovations in halal food analysis. Trends Food Sci Technol 2016. [DOI: 10.1016/j.tifs.2016.10.024] [Citation(s) in RCA: 50] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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109
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Ghorbani A, Gravendeel B, Selliah S, Zarré S, de Boer H. DNA barcoding of tuberous Orchidoideae: a resource for identification of orchids used in Salep. Mol Ecol Resour 2016; 17:342-352. [DOI: 10.1111/1755-0998.12615] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2016] [Revised: 08/26/2016] [Accepted: 09/06/2016] [Indexed: 12/15/2022]
Affiliation(s)
- Abdolbaset Ghorbani
- Department of Organismal Biology; Evolutionary Biology Centre; Uppsala University; Norbyvägen 18D SE-75236 Uppsala Sweden
- Traditional Medicine and Materia Medica Research Center; Shahid Beheshti University of Medical Sciences; No 19, Tavanir Street, Hemmat Highway P.O. Box 14155-6153 Tehran Iran
| | - Barbara Gravendeel
- Naturalis Biodiversity Center; Darwinweg 2 2333 CR Leiden The Netherlands
- University of Applied Sciences Leiden; Zernikedreef 11 2333 CK Leiden The Netherlands
| | - Sugirthini Selliah
- The Natural History Museum; University of Oslo; P.O. Box 1172 Blindern 0318 Oslo Norway
| | - Shahin Zarré
- Department of Plant Sciences; School of Biology; College of Science; University of Tehran; 14155-6455 Tehran Iran
| | - Hugo de Boer
- Department of Organismal Biology; Evolutionary Biology Centre; Uppsala University; Norbyvägen 18D SE-75236 Uppsala Sweden
- Naturalis Biodiversity Center; Darwinweg 2 2333 CR Leiden The Netherlands
- The Natural History Museum; University of Oslo; P.O. Box 1172 Blindern 0318 Oslo Norway
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110
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Poisonous or non-poisonous plants? DNA-based tools and applications for accurate identification. Int J Legal Med 2016; 131:1-19. [PMID: 27796590 DOI: 10.1007/s00414-016-1460-y] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2016] [Accepted: 10/05/2016] [Indexed: 11/25/2022]
Abstract
Plant exposures are among the most frequently reported cases to poison control centres worldwide. This is a growing condition due to recent societal trends oriented towards the consumption of wild plants as food, cosmetics, or medicine. At least three general causes of plant poisoning can be identified: plant misidentification, introduction of new plant-based supplements and medicines with no controls about their safety, and the lack of regulation for the trading of herbal and phytochemical products. Moreover, an efficient screening for the occurrence of plants poisonous to humans is also desirable at the different stages of the food supply chain: from the raw material to the final transformed product. A rapid diagnosis of intoxication cases is necessary in order to provide the most reliable treatment. However, a precise taxonomic characterization of the ingested species is often challenging. In this review, we provide an overview of the emerging DNA-based tools and technologies to address the issue of poisonous plant identification. Specifically, classic DNA barcoding and its applications using High Resolution Melting (Bar-HRM) ensure high universality and rapid response respectively, whereas High Throughput Sequencing techniques (HTS) provide a complete characterization of plant residues in complex matrices. The pros and cons of each approach have been evaluated with the final aim of proposing a general user's guide to molecular identification directed to different stakeholder categories interested in the diagnostics of poisonous plants.
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111
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Fluorescence Visual Detection of Herbal Product Substitutions at Terminal Herbal Markets by CCP-based FRET technique. Sci Rep 2016; 6:35540. [PMID: 27765955 PMCID: PMC5073245 DOI: 10.1038/srep35540] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2016] [Accepted: 09/19/2016] [Indexed: 11/25/2022] Open
Abstract
Inaccurate labeling of materials used in herbal products may compromise the therapeutic efficacy and may pose a threat to medicinal safety. In this paper, a rapid (within 3 h), sensitive and visual colorimetric method for identifying substitutions in terminal market products was developed using cationic conjugated polymer-based fluorescence resonance energy transfer (CCP-based FRET). Chinese medicinal materials with similar morphology and chemical composition were clearly distinguished by the single-nucleotide polymorphism (SNP) genotyping method. Assays using CCP-based FRET technology showed a high frequency of adulterants in Lu-Rong (52.83%) and Chuan-Bei-Mu (67.8%) decoction pieces, and patented Chinese drugs (71.4%, 5/7) containing Chuan-Bei-Mu ingredients were detected in the terminal herbal market. In comparison with DNA sequencing, this protocol simplifies procedures by eliminating the cumbersome workups and sophisticated instruments, and only a trace amount of DNA is required. The CCP-based method is particularly attractive because it can detect adulterants in admixture samples with high sensitivity. Therefore, the CCP-based detection system shows great potential for routine terminal market checks and drug safety controls.
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112
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Hansen TA, Mollerup S, Nguyen NP, White NE, Coghlan M, Alquezar-Planas DE, Joshi T, Jensen RH, Fridholm H, Kjartansdóttir KR, Mourier T, Warnow T, Belsham GJ, Bunce M, Willerslev E, Nielsen LP, Vinner L, Hansen AJ. High diversity of picornaviruses in rats from different continents revealed by deep sequencing. Emerg Microbes Infect 2016; 5:e90. [PMID: 27530749 PMCID: PMC5034103 DOI: 10.1038/emi.2016.90] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2016] [Revised: 05/30/2016] [Accepted: 06/13/2016] [Indexed: 12/02/2022]
Abstract
Outbreaks of zoonotic diseases in humans and livestock are not uncommon, and an important component in containment of such emerging viral diseases is rapid and reliable diagnostics. Such methods are often PCR-based and hence require the availability of sequence data from the pathogen. Rattus norvegicus (R. norvegicus) is a known reservoir for important zoonotic pathogens. Transmission may be direct via contact with the animal, for example, through exposure to its faecal matter, or indirectly mediated by arthropod vectors. Here we investigated the viral content in rat faecal matter (n=29) collected from two continents by analyzing 2.2 billion next-generation sequencing reads derived from both DNA and RNA. Among other virus families, we found sequences from members of the Picornaviridae to be abundant in the microbiome of all the samples. Here we describe the diversity of the picornavirus-like contigs including near-full-length genomes closely related to the Boone cardiovirus and Theiler's encephalomyelitis virus. From this study, we conclude that picornaviruses within R. norvegicus are more diverse than previously recognized. The virome of R. norvegicus should be investigated further to assess the full potential for zoonotic virus transmission.
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Affiliation(s)
- Thomas Arn Hansen
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, DK-1350 Copenhagen, Denmark
| | - Sarah Mollerup
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, DK-1350 Copenhagen, Denmark
| | - Nam-Phuong Nguyen
- Carl R. Woese Institute for Genomic Biology, The University of Illinois at Urbana-Champaign, Urbana, IL 61801-2302, USA
| | - Nicole E White
- Trace and Environmental DNA Lab and Australian Wildlife Forensic Services, Curtin University, Perth, Western Australia 6102, Australia
| | - Megan Coghlan
- Trace and Environmental DNA Lab and Australian Wildlife Forensic Services, Curtin University, Perth, Western Australia 6102, Australia
| | - David E Alquezar-Planas
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, DK-1350 Copenhagen, Denmark
| | - Tejal Joshi
- Center for Biological Sequence Analysis, Department of Systems Biology, Technical University of Denmark, Kemitorvet, DK-2800 Kongens Lyngby, Denmark
| | - Randi Holm Jensen
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, DK-1350 Copenhagen, Denmark
| | - Helena Fridholm
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, DK-1350 Copenhagen, Denmark.,Virus Research and Development, Statens Serum Institut, DK-2300 Copenhagen, Denmark
| | - Kristín Rós Kjartansdóttir
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, DK-1350 Copenhagen, Denmark
| | - Tobias Mourier
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, DK-1350 Copenhagen, Denmark
| | - Tandy Warnow
- Departments of Bioengineering and Computer Science, The University of Illinois at Urbana-Champaign, Urbana, IL 61801-2302, USA
| | - Graham J Belsham
- National Veterinary Institute, Technical University of Denmark, Lindholm, DK-4771 Kalvehave, Denmark
| | - Michael Bunce
- Trace and Environmental DNA Lab and Australian Wildlife Forensic Services, Curtin University, Perth, Western Australia 6102, Australia
| | - Eske Willerslev
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, DK-1350 Copenhagen, Denmark
| | - Lars Peter Nielsen
- Department of Autoimmunology and Biomarkers, Statens Serum Institut, DK-2300 Copenhagen, Denmark
| | - Lasse Vinner
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, DK-1350 Copenhagen, Denmark
| | - Anders Johannes Hansen
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, DK-1350 Copenhagen, Denmark
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113
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Sharma S, Shrivastava N. Renaissance in phytomedicines: promising implications of NGS technologies. PLANTA 2016; 244:19-38. [PMID: 27002972 DOI: 10.1007/s00425-016-2492-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/08/2015] [Accepted: 02/19/2016] [Indexed: 06/05/2023]
Abstract
Medicinal plant research is growing significantly in faith to discover new and more biologically compatible phytomedicines. Deposition of huge genome/trancriptome sequence data assisted by NGS technologies has revealed the new possibilities for producing upgraded bioactive molecules in medicinal plants. Growing interest of investors and consumers in the herbal drugs raises the need for extensive research to open the facts and details of every inch of life canvas of medicinal plants to produce improved quality of phytomedicines. As in agriculture crops, knowledge emergence from medicinal plant's genome/transcriptome, can be used to assure their amended quality and these improved varieties are then transported to the fields for cultivation. Genome studies generate huge sequence data which can be exploited further for obtaining information regarding genes/gene clusters involved in biosynthesis as well as regulation. This can be achieved rapidly at a very large scale with NGS platforms. Identification of new RNA molecules has become possible, which can lead to the discovery of novel compounds. Sequence information can be combined with advanced phytochemical and bioinformatics tools to discover functional herbal drugs. Qualitative and quantitative analysis of small RNA species put a light on the regulatory aspect of biosynthetic pathways for phytomedicines. Inter or intra genomic as well as transcriptomic interactive processes for biosynthetic pathways can be elucidated in depth. Quality management of herbal material will also become rapid and high throughput. Enrichment of sequence information will be used to engineer the plants to get more efficient phytopharmaceuticals. The present review comprises of role of NGS technologies to boost genomic studies of pharmaceutically important plants and further, applications of sequence information aiming to produce enriched phytomedicines. Emerging knowledge from the medicinal plants genome/transcriptome can give birth to deep understanding of the processes responsible for biosynthesis of medicinally important compounds.
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Affiliation(s)
- Sonal Sharma
- B.V. Patel Pharmaceutical Education and Research Development (PERD) Centre, Sarkhej - Gandhinagar Highway, Ahmedabad, Gujarat, India
- Nirma University, Ahmedabad, Gujarat, India
| | - Neeta Shrivastava
- B.V. Patel Pharmaceutical Education and Research Development (PERD) Centre, Sarkhej - Gandhinagar Highway, Ahmedabad, Gujarat, India.
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114
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Staats M, Arulandhu AJ, Gravendeel B, Holst-Jensen A, Scholtens I, Peelen T, Prins TW, Kok E. Advances in DNA metabarcoding for food and wildlife forensic species identification. Anal Bioanal Chem 2016; 408:4615-30. [PMID: 27178552 PMCID: PMC4909793 DOI: 10.1007/s00216-016-9595-8] [Citation(s) in RCA: 112] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2016] [Revised: 04/19/2016] [Accepted: 04/20/2016] [Indexed: 12/18/2022]
Abstract
Species identification using DNA barcodes has been widely adopted by forensic scientists as an effective molecular tool for tracking adulterations in food and for analysing samples from alleged wildlife crime incidents. DNA barcoding is an approach that involves sequencing of short DNA sequences from standardized regions and comparison to a reference database as a molecular diagnostic tool in species identification. In recent years, remarkable progress has been made towards developing DNA metabarcoding strategies, which involves next-generation sequencing of DNA barcodes for the simultaneous detection of multiple species in complex samples. Metabarcoding strategies can be used in processed materials containing highly degraded DNA e.g. for the identification of endangered and hazardous species in traditional medicine. This review aims to provide insight into advances of plant and animal DNA barcoding and highlights current practices and recent developments for DNA metabarcoding of food and wildlife forensic samples from a practical point of view. Special emphasis is placed on new developments for identifying species listed in the Convention on International Trade of Endangered Species (CITES) appendices for which reliable methods for species identification may signal and/or prevent illegal trade. Current technological developments and challenges of DNA metabarcoding for forensic scientists will be assessed in the light of stakeholders' needs.
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Affiliation(s)
- Martijn Staats
- RIKILT Wageningen UR, P.O. Box 230, 6700 AE, Wageningen, The Netherlands.
| | - Alfred J Arulandhu
- RIKILT Wageningen UR, P.O. Box 230, 6700 AE, Wageningen, The Netherlands
| | - Barbara Gravendeel
- Naturalis Biodiversity Center, Sylviusweg 72, P.O. Box 9517, Leiden, The Netherlands
| | - Arne Holst-Jensen
- Norwegian Veterinary Institute, Ullevaalsveien 68, P.O. Box 750, Sentrum, 0106, Oslo, Norway
| | - Ingrid Scholtens
- RIKILT Wageningen UR, P.O. Box 230, 6700 AE, Wageningen, The Netherlands
| | - Tamara Peelen
- Dutch Customs Laboratory, Kingsfordweg 1, 1043 GN, Amsterdam, The Netherlands
| | - Theo W Prins
- RIKILT Wageningen UR, P.O. Box 230, 6700 AE, Wageningen, The Netherlands
| | - Esther Kok
- RIKILT Wageningen UR, P.O. Box 230, 6700 AE, Wageningen, The Netherlands
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115
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A strategy for screening active lead compounds and functional compound combinations from herbal medicines based on pharmacophore filtering and knockout/knockin chromatography. J Chromatogr A 2016; 1456:176-86. [DOI: 10.1016/j.chroma.2016.06.009] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2016] [Revised: 05/30/2016] [Accepted: 06/02/2016] [Indexed: 11/19/2022]
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116
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117
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Ivanova NV, Kuzmina ML, Braukmann TWA, Borisenko AV, Zakharov EV. Authentication of Herbal Supplements Using Next-Generation Sequencing. PLoS One 2016; 11:e0156426. [PMID: 27227830 PMCID: PMC4882080 DOI: 10.1371/journal.pone.0156426] [Citation(s) in RCA: 70] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2016] [Accepted: 05/14/2016] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND DNA-based testing has been gaining acceptance as a tool for authentication of a wide range of food products; however, its applicability for testing of herbal supplements remains contentious. METHODS We utilized Sanger and Next-Generation Sequencing (NGS) for taxonomic authentication of fifteen herbal supplements representing three different producers from five medicinal plants: Echinacea purpurea, Valeriana officinalis, Ginkgo biloba, Hypericum perforatum and Trigonella foenum-graecum. Experimental design included three modifications of DNA extraction, two lysate dilutions, Internal Amplification Control, and multiple negative controls to exclude background contamination. Ginkgo supplements were also analyzed using HPLC-MS for the presence of active medicinal components. RESULTS All supplements yielded DNA from multiple species, rendering Sanger sequencing results for rbcL and ITS2 regions either uninterpretable or non-reproducible between the experimental replicates. Overall, DNA from the manufacturer-listed medicinal plants was successfully detected in seven out of eight dry herb form supplements; however, low or poor DNA recovery due to degradation was observed in most plant extracts (none detected by Sanger; three out of seven-by NGS). NGS also revealed a diverse community of fungi, known to be associated with live plant material and/or the fermentation process used in the production of plant extracts. HPLC-MS testing demonstrated that Ginkgo supplements with degraded DNA contained ten key medicinal components. CONCLUSION Quality control of herbal supplements should utilize a synergetic approach targeting both DNA and bioactive components, especially for standardized extracts with degraded DNA. The NGS workflow developed in this study enables reliable detection of plant and fungal DNA and can be utilized by manufacturers for quality assurance of raw plant materials, contamination control during the production process, and the final product. Interpretation of results should involve an interdisciplinary approach taking into account the processes involved in production of herbal supplements, as well as biocomplexity of plant-plant and plant-fungal biological interactions.
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Affiliation(s)
- Natalia V. Ivanova
- Centre for Biodiversity Genomics, Biodiversity Institute of Ontario, University of Guelph, Guelph, Ontario, Canada
| | - Maria L. Kuzmina
- Centre for Biodiversity Genomics, Biodiversity Institute of Ontario, University of Guelph, Guelph, Ontario, Canada
| | - Thomas W. A. Braukmann
- Centre for Biodiversity Genomics, Biodiversity Institute of Ontario, University of Guelph, Guelph, Ontario, Canada
| | - Alex V. Borisenko
- Centre for Biodiversity Genomics, Biodiversity Institute of Ontario, University of Guelph, Guelph, Ontario, Canada
| | - Evgeny V. Zakharov
- Centre for Biodiversity Genomics, Biodiversity Institute of Ontario, University of Guelph, Guelph, Ontario, Canada
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118
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Abstract
Pharmacovigilance of herbal medicines relies on the product label information regarding the ingredients and the adherence to good manufacturing practices along the commercialisation chain. Several studies have shown that substitution of plant species occurs in herbal medicines, and this in turn poses a challenge to herbal pharmacovigilance as adverse reactions might be due to adulterated or added ingredients. Authentication of constituents in herbal medicines using analytical chemistry methods can help detect contaminants and toxins, but are often limited or incapable of detecting the source of the contamination. Recent developments in molecular plant identification using DNA sequence data enable accurate identification of plant species from herbal medicines using defined DNA markers. Identification of multiple constituent species from compound herbal medicines using amplicon metabarcoding enables verification of labelled ingredients and detection of substituted, adulterated and added species. DNA barcoding is proving to be a powerful method to assess species composition in herbal medicines and has the potential to be used as a standard method in herbal pharmacovigilance research of adverse reactions to specific products.
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119
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Review and future prospects for DNA barcoding methods in forensic palynology. Forensic Sci Int Genet 2016; 21:110-6. [DOI: 10.1016/j.fsigen.2015.12.010] [Citation(s) in RCA: 60] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2015] [Revised: 10/19/2015] [Accepted: 12/15/2015] [Indexed: 11/18/2022]
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120
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Osathanunkul M, Suwannapoom C, Osathanunkul K, Madesis P, de Boer H. Evaluation of DNA barcoding coupled high resolution melting for discrimination of closely related species in phytopharmaceuticals. PHYTOMEDICINE : INTERNATIONAL JOURNAL OF PHYTOTHERAPY AND PHYTOPHARMACOLOGY 2016; 23:156-65. [PMID: 26926177 DOI: 10.1016/j.phymed.2015.11.018] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/06/2015] [Revised: 10/11/2015] [Accepted: 11/12/2015] [Indexed: 05/06/2023]
Abstract
BACKGROUND Phytopharmaceuticals are increasingly popular as alternative medicines, but poorly regulated in many countries. The manufacturers of these products should be subject to strict controls regarding each product's quality and constituents. Routine testing and identification of raw materials should be performed to ensure that the raw materials used in pharmaceutical products are suitable for their intended use. HYPOTHESIS/PURPOSE We have applied DNA Barcoding - High Resolution Melting (Bar-HRM), an emerging method for identifying of medicinal plant species based on DNA dissociation kinetics and DNA barcoding, for the authentication of medicinal plant species. STUDY DESIGN Commonly commercialized Thai medicinal plants that are widely used for medicinal purposes were used in this study. Publicly available sequences of four plastid markers were used for universal primer design. Species discrimination efficiency of the designed primers was evaluated as single and multi-locus analyses by using the primers sets. METHODS HRM analysis was performed in triplicate on each of the 26 taxa to establish the Tm for each primer set (matK, rbcLA, rbcLB, rbcLC, rpoC1, and trnL). The shapes of the melting curves were analyzed to distinguish the different plant species. Bar-HRM species identification success rates were assessed for each single-locus as well as for multi-locus combinations to establish the optimal combination of primer sets. RESULTS In single locus analysis the rpoC1 primer set gave the highest discrimination (58%), and in multi locus analysis this could be increased from 87% to 99% depending on the total number of regions included. Different combinations proved to be more or less effective at discrimination, depending on the genus or family examined. CONCLUSIONS Bar-HRM has proven to be a cost-effective and reliable method for the identification of species in this study of Thai medicinal plants, and results show an identification success rate of 99% among species in the test set.
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Affiliation(s)
- Maslin Osathanunkul
- Department of Biology, Faculty of Science, Chiang Mai University, 239 Huay Kaew Rd., Suthep, Muang, Chiang Mai 50200, Thailand.
| | - Chatmongkon Suwannapoom
- State Key Laboratory of Genetic Resources and Evolution State, and Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China; School of Agriculture and Natural Resources, University of Phayao, Phayao 56000, Thailand
| | - Kitisak Osathanunkul
- Department of Computer Science, Faculty of Science, Maejo University, Chiang Mai 50290, Thailand
| | - Panagiotis Madesis
- Institute of Applied Biosciences, Centre for Research & Technology Hellas (CERTH), Thessaloniki, Greece
| | - Hugo de Boer
- Department of Organismal Biology, Evolutionary Biology Centre, Uppsala University, Norbyvägen 18D, SE-75236 Uppsala, Sweden; The Natural History Museum, University of Oslo, P.O. Box 1172, NO-0318 Oslo, Norway
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Angers-Loustau A, Petrillo M, Paracchini V, Kagkli DM, Rischitor PE, Puertas Gallardo A, Patak A, Querci M, Kreysa J. Towards Plant Species Identification in Complex Samples: A Bioinformatics Pipeline for the Identification of Novel Nuclear Barcode Candidates. PLoS One 2016; 11:e0147692. [PMID: 26807711 PMCID: PMC4725681 DOI: 10.1371/journal.pone.0147692] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2015] [Accepted: 01/07/2016] [Indexed: 11/25/2022] Open
Abstract
Monitoring of the food chain to fight fraud and protect consumer health relies on the availability of methods to correctly identify the species present in samples, for which DNA barcoding is a promising candidate. The nuclear genome is a rich potential source of barcode targets, but has been relatively unexploited until now. Here, we show the development and use of a bioinformatics pipeline that processes available genome sequences to automatically screen large numbers of input candidates, identifies novel nuclear barcode targets and designs associated primer pairs, according to a specific set of requirements. We applied this pipeline to identify novel barcodes for plant species, a kingdom for which the currently available solutions are known to be insufficient. We tested one of the identified primer pairs and show its capability to correctly identify the plant species in simple and complex samples, validating the output of our approach.
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Affiliation(s)
- Alexandre Angers-Loustau
- Molecular Biology and Genomic Unit, Institute for Health and Consumer Protection, Joint Research Center, European Commission, Ispra, Italy
| | - Mauro Petrillo
- Molecular Biology and Genomic Unit, Institute for Health and Consumer Protection, Joint Research Center, European Commission, Ispra, Italy
| | - Valentina Paracchini
- Molecular Biology and Genomic Unit, Institute for Health and Consumer Protection, Joint Research Center, European Commission, Ispra, Italy
| | - Dafni M. Kagkli
- Molecular Biology and Genomic Unit, Institute for Health and Consumer Protection, Joint Research Center, European Commission, Ispra, Italy
| | - Patricia E. Rischitor
- Molecular Biology and Genomic Unit, Institute for Health and Consumer Protection, Joint Research Center, European Commission, Ispra, Italy
| | - Antonio Puertas Gallardo
- Molecular Biology and Genomic Unit, Institute for Health and Consumer Protection, Joint Research Center, European Commission, Ispra, Italy
| | - Alex Patak
- Molecular Biology and Genomic Unit, Institute for Health and Consumer Protection, Joint Research Center, European Commission, Ispra, Italy
| | - Maddalena Querci
- Molecular Biology and Genomic Unit, Institute for Health and Consumer Protection, Joint Research Center, European Commission, Ispra, Italy
| | - Joachim Kreysa
- Molecular Biology and Genomic Unit, Institute for Health and Consumer Protection, Joint Research Center, European Commission, Ispra, Italy
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122
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Traditional medicines and species extinction: another side to forensic wildlife investigation. Forensic Sci Med Pathol 2016; 12:125-7. [PMID: 26798031 DOI: 10.1007/s12024-016-9742-8] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/04/2016] [Indexed: 02/04/2023]
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123
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An authenticity survey of herbal medicines from markets in China using DNA barcoding. Sci Rep 2016; 6:18723. [PMID: 26740340 PMCID: PMC4703975 DOI: 10.1038/srep18723] [Citation(s) in RCA: 86] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2015] [Accepted: 11/25/2015] [Indexed: 11/08/2022] Open
Abstract
Adulterant herbal materials are a threat to consumer safety. In this study, we used DNA barcoding to investigate the proportions and varieties of adulterant species in traditional Chinese medicine (TCM) markets. We used a DNA barcode database of TCM (TCMD) that was established by our group to investigate 1436 samples representing 295 medicinal species from 7 primary TCM markets in China. The results indicate that ITS2 barcodes could be generated for most of the samples (87.7%) using a standard protocol. Of the 1260 samples, approximately 4.2% were identified as adulterants. The adulterant focused on medicinal species such as Ginseng Radix et Rhizoma (Renshen), Radix Rubi Parvifolii (Maomeigen), Dalbergiae odoriferae Lignum (Jiangxiang), Acori Tatarinowii Rhizoma (Shichangpu), Inulae Flos (Xuanfuhua), Lonicerae Japonicae Flos (Jinyinhua), Acanthopanacis Cortex (Wujiapi) and Bupleuri Radix (Chaihu). The survey revealed that adulterant species are present in the Chinese market, and these adulterants pose a risk to consumer health. Thus, regulatory measures should be adopted immediately. We suggest that a traceable platform based on DNA barcode sequences be established for TCM market supervision.
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124
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Combined DNA, toxicological and heavy metal analyses provides an auditing toolkit to improve pharmacovigilance of traditional Chinese medicine (TCM). Sci Rep 2015; 5:17475. [PMID: 26658160 PMCID: PMC4675079 DOI: 10.1038/srep17475] [Citation(s) in RCA: 77] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2015] [Accepted: 10/30/2015] [Indexed: 11/25/2022] Open
Abstract
Globally, there has been an increase in the use of herbal remedies including traditional Chinese medicine (TCM). There is a perception that products are natural, safe and effectively regulated, however, regulatory agencies are hampered by a lack of a toolkit to audit ingredient lists, adulterants and constituent active compounds. Here, for the first time, a multidisciplinary approach to assessing the molecular content of 26 TCMs is described. Next generation DNA sequencing is combined with toxicological and heavy metal screening by separation techniques and mass spectrometry (MS) to provide a comprehensive audit. Genetic analysis revealed that 50% of samples contained DNA of undeclared plant or animal taxa, including an endangered species of Panthera (snow leopard). In 50% of the TCMs, an undeclared pharmaceutical agent was detected including warfarin, dexamethasone, diclofenac, cyproheptadine and paracetamol. Mass spectrometry revealed heavy metals including arsenic, lead and cadmium, one with a level of arsenic >10 times the acceptable limit. The study showed 92% of the TCMs examined were found to have some form of contamination and/or substitution. This study demonstrates that a combination of molecular methodologies can provide an effective means by which to audit complementary and alternative medicines.
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125
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Guillot G, Jónsson H, Hinge A, Manchih N, Orlando L. Accurate continuous geographic assignment from low- to high-density SNP data. Bioinformatics 2015; 32:1106-8. [DOI: 10.1093/bioinformatics/btv703] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2015] [Accepted: 11/25/2015] [Indexed: 11/12/2022] Open
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126
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Xue M, Yang L, Shi DZ, Radauer C, Breiteneder H, Ma Y. Qualitative analysis of xinyue capsules by high-performance liquid chromatography: Preliminary evaluation of drug quality in a Sino-Austrian joint study. Chin J Integr Med 2015; 21:772-7. [PMID: 26525548 DOI: 10.1007/s11655-015-2311-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2014] [Indexed: 10/22/2022]
Abstract
OBJECTIVE To develop a reliable method to assess the stability of xinyue capsules containing Panax quinquefolius saponins according to European quality standards. METHODS An efficient high-performance liquid chromatography ultraviolet (HPLC-UV) method was established to analyse six main ginsenosides (Rb1, Rb2, Rc, Rd, Re and Rg1) in six different batches (120 capsules/batch) from the same lot of xinyue capsules and in one batch measured six times within one day. The six ginsenosides were separated on a Hypersil BDS-C18 column (3 μm, 100 mm×3 mm) at a flow rate of 0.5 mL/min. Gradient elution was performed using a mobile phase gradient of acetonitrile-water modified with 0.01% formic acid. The HPLC chromatograms were analyzed with "LC data comparison" using Lab Solutions software. RESULTS The HPLC peaks were identified by comparing their retention times (Rg1: 23.44 min, Re: 23.77 min, Rb1: 35.24 min, Rc: 36.18 min, Rb2: 38.55 min and Rd: 40.88 min) with those of the standards under the same chromatographic conditions, which showed similar results among the samples of six different batches and among the samples from one batch detected six times within one day. CONCLUSIONS Xinyue capsules have good drug intra-day consistency at room temperature and exhibit a consistent quality between different batches. This study established a reliable method to assess the stability of xinyue capsules, which is suitable for further qualitative analysis and may assist in promoting the safe and effective use of Chinese herbal medicine.
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Affiliation(s)
- Mei Xue
- Center of Cardiology, Xiyuan Hospital, China Academy of Chinese Medical Sciences, Beijing, 100091, China
| | - Lin Yang
- Center of Cardiology, Xiyuan Hospital, China Academy of Chinese Medical Sciences, Beijing, 100091, China
| | - Da-zhuo Shi
- Center of Cardiology, Xiyuan Hospital, China Academy of Chinese Medical Sciences, Beijing, 100091, China.
| | - Christian Radauer
- Molecular Research in Traditional Chinese Medicine Group, Department of Pathophysiology and Allergy Research, Center of Pathophysiology, Infectiology & Immunology, Medical University of Vienna, Vienna, Austria
| | - Heimo Breiteneder
- Molecular Research in Traditional Chinese Medicine Group, Department of Pathophysiology and Allergy Research, Center of Pathophysiology, Infectiology & Immunology, Medical University of Vienna, Vienna, Austria
| | - Yan Ma
- Molecular Research in Traditional Chinese Medicine Group, Department of Pathophysiology and Allergy Research, Center of Pathophysiology, Infectiology & Immunology, Medical University of Vienna, Vienna, Austria
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127
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Evidence chain-based causality identification in herb-induced liver injury: exemplification of a well-known liver-restorative herb Polygonum multiflorum. Front Med 2015; 9:457-67. [PMID: 26459430 DOI: 10.1007/s11684-015-0417-8] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2015] [Accepted: 07/07/2015] [Indexed: 12/12/2022]
Abstract
Herbal medicines have recently been recognized as the second most common cause of drug-induced liver injury (DILI) in the United States. However, reliable methods to identify the DILI causality of some herbs, such as Heshouwu (dried root of Polygonum multiflorum), remain lacking. In this study, a total of 12 307 inpatients with liver dysfunction and 147 literature-reported cases of Heshouwu DILI were screened. A general algorithm indicated that only 22.5% (9/40) and 30.6% (45/147) of all hospitalization and literature case reports, respectively, demonstrate the high probability of DILI causality of Heshouwu. By contrast, 95% (19/20) of all cases prospectively investigated by pharmacognosy, phytochemistry, and metabolomic tests exhibited highly probable causality, including a patient who was previously incorrectly attributed and a case that was excluded from Heshouwu causality by pharmacognostic evidence. Toxin (heavy metals, pesticides, and mycotoxins) contamination was also excluded from Heshouwu DILI causality. The objectivity of these screening methods for Heshouwu DILI diagnosis addresses safety concerns regarding stilbene-containing herbal medicines and dietary supplements.
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128
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Krüger M, Teste FP, Laliberté E, Lambers H, Coghlan M, Zemunik G, Bunce M. The rise and fall of arbuscular mycorrhizal fungal diversity during ecosystem retrogression. Mol Ecol 2015; 24:4912-30. [DOI: 10.1111/mec.13363] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2014] [Revised: 08/12/2015] [Accepted: 08/21/2015] [Indexed: 02/05/2023]
Affiliation(s)
- Manuela Krüger
- Institute of Botany; Academy of Sciences of the Czech Republic; Zámek 1 CZ-252 43 Průhonice Czech Republic
| | - François P. Teste
- School of Plant Biology; The University of Western Australia; 35 Stirling Highway, Crawley Perth WA 6009 Australia
- Grupo de Estudios Ambientales; IMASL-CONICET & Universidad Nacional de San Luis; Av. Ejercito de los Andes 950 (5700) San Luis Argentina
| | - Etienne Laliberté
- School of Plant Biology; The University of Western Australia; 35 Stirling Highway, Crawley Perth WA 6009 Australia
- Institut de recherche en biologie végétale; Département de sciences biologiques; Université de Montréal; 4101 Sherbrooke Est Montréal QC H1X 2B2 Canada
| | - Hans Lambers
- School of Plant Biology; The University of Western Australia; 35 Stirling Highway, Crawley Perth WA 6009 Australia
| | - Megan Coghlan
- Trace and Environmental DNA Laboratory; Department of Environment and Agriculture; Curtin University; Kent Street Perth WA 6845 Australia
| | - Graham Zemunik
- School of Plant Biology; The University of Western Australia; 35 Stirling Highway, Crawley Perth WA 6009 Australia
- Smithsonian Tropical Research Institute; Apartado 0843-03092 Balboa Ancon Republic of Panama
| | - Michael Bunce
- Trace and Environmental DNA Laboratory; Department of Environment and Agriculture; Curtin University; Kent Street Perth WA 6845 Australia
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129
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Osathanunkul M, Suwannapoom C, Ounjai S, Rora JA, Madesis P, de Boer H. Refining DNA Barcoding Coupled High Resolution Melting for Discrimination of 12 Closely Related Croton Species. PLoS One 2015; 10:e0138888. [PMID: 26406615 PMCID: PMC4583236 DOI: 10.1371/journal.pone.0138888] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2015] [Accepted: 09/04/2015] [Indexed: 11/24/2022] Open
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 Croton (Euphorbiaceae), one of the largest genera of plants with over 1,200 species. Seven primer pairs were evaluated (matK, rbcL1, rbcL2, rbcL3, rpoC, trnL and ITS1) from four plastid regions, matK, rbcL, rpoC, and trnL, and the nuclear ribosomal marker ITS1. The primer pair derived from the ITS1 region was the single most effective region for the identification of the tested species, whereas the rbcL1 primer pair gave the lowest resolution. 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. Our Bar-HRM results here also provide further support for the hypothesis that both sequence and base composition affect DNA duplex stability.
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Affiliation(s)
- Maslin Osathanunkul
- Department of Biology, Faculty of Science, Chiang Mai University, Chiang Mai 50200, Thailand
- * E-mail:
| | - Chatmongkon Suwannapoom
- State Key Laboratory of Genetic Resources and Evolution and Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China
- Science and Technology Research Institute, Chiang Mai University, Chiang Mai, 50200, Thailand
| | - Sarawut Ounjai
- Department of Biology, Faculty of Science, Chiang Mai University, Chiang Mai 50200, Thailand
| | - Jantarika A. Rora
- Department of Biology, Faculty of Science, Chiang Mai University, Chiang Mai 50200, Thailand
| | - Panagiotis Madesis
- Institute of Applied Biosciences, Centre for Research & Technology Hellas, Thessaloniki, Greece
| | - Hugo de Boer
- Department of Organismal Biology, Evolutionary Biology Centre, Uppsala University, Norbyvägen 18D, SE-75236 Uppsala, Sweden
- The Natural History Museum, University of Oslo, P.O. Box 1172, NO-0318 Oslo, Norway
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130
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Wei Y, Chen Y, Huang Y, Liu J, Liang Y. Molecular authentication and quantitative analysis of Sarcandra glabra and adulterated chloranthus products using SNP markers. Mitochondrial DNA A DNA Mapp Seq Anal 2015; 27:3618-25. [PMID: 26358522 DOI: 10.3109/19401736.2015.1079826] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
BACKGROUND Sarcandra glabra (Thunb.) Nakai is one of the most popular and valuable plant species in the oriental medicinal herb market. Chloranthus (Chloranthaceae) species are the most widely used adulterants, but they are known to have hepatotoxicity effects and different medicinal values. OBJECTIVE The aim of this study is to develop a robust and accurate DNA marker for the qualitative and quantitative analyses of their products. MATERIALS AND METHODS Four single nucleotide polymorphism (SNP) sites specific to Sarcandra glabra, Chloranthus spicatus, Chloranthus serratus and Chloranthus henryi were exploited from the trnL-F region in chloroplast DNA, which have a higher copy number in the products than the nuclear DNA. Based on the SNP sites, specific primers were designed to identify the products of Sarcandra glabra, Chloranthus spicatus, Chloranthus serratus and Chloranthus henryi in mixed solutions via multiplexed PCR. The primers were also used to quantitatively analyse the ratio of chloroplast DNA in the mixed products using real-time PCR. RESULTS The established multiplexed-PCR and real-time PCR methods were determined to be effective for the authentication and relative quantitative assessments of the products of Sarcandra glabra, its adulterants, and their mixtures. CONCLUSION We therefore present an effective method for monitoring the quality of these products.
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Affiliation(s)
- Yicong Wei
- a College of Pharmacy, Fujian University of Traditional Chinese Medicine , Fuzhou , China and
| | - Ying Chen
- b College of Landscape Architecture, Fujian Agriculture and Forestry University , Fujian Fouzhou , China
| | - Youkai Huang
- a College of Pharmacy, Fujian University of Traditional Chinese Medicine , Fuzhou , China and
| | - Jinping Liu
- a College of Pharmacy, Fujian University of Traditional Chinese Medicine , Fuzhou , China and
| | - Yichi Liang
- a College of Pharmacy, Fujian University of Traditional Chinese Medicine , Fuzhou , China and
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131
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MacDonald AJ, Sarre SD. Species assignment from trace DNA sequences: anin silicoassessment of the test used to survey for foxes in Tasmania. J Appl Ecol 2015. [DOI: 10.1111/1365-2664.12506] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Affiliation(s)
- Anna J. MacDonald
- Institute for Applied Ecology; University of Canberra; Canberra ACT 2601 Australia
| | - Stephen D. Sarre
- Institute for Applied Ecology; University of Canberra; Canberra ACT 2601 Australia
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132
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Saslis-Lagoudakis CH, Bruun-Lund S, Iwanycki NE, Seberg O, Petersen G, Jäger AK, Rønsted N. Identification of common horsetail (Equisetum arvense L.; Equisetaceae) using Thin Layer Chromatography versus DNA barcoding. Sci Rep 2015; 5:11942. [PMID: 26165523 PMCID: PMC4499799 DOI: 10.1038/srep11942] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2015] [Accepted: 05/11/2015] [Indexed: 11/09/2022] Open
Abstract
The global herbal products market has grown in recent years, making regulation of these products paramount for public healthcare. For instance, the common horsetail (Equisetum arvense L.) is used in numerous herbal products, but it can be adulterated with closely related species, especially E. palustre L. that can produce toxic alkaloids. As morphology-based identification is often difficult or impossible, the identification of processed material can be aided by molecular techniques. In this study, we explore two molecular identification techniques as methods of testing the purity of these products: a Thin Layer Chromatography approach (TLC-test) included in the European Pharmacopoeia and a DNA barcoding approach, used in recent years to identify material in herbal products. We test the potential of these methods for distinguishing and identifying these species using material from herbarium collections and commercial herbal products. We find that both methods can discriminate between the two species and positively identify E. arvense. The TLC-test is more cost- and time-efficient, but DNA barcoding is more powerful in determining the identity of adulterant species. Our study shows that, although DNA barcoding presents certain advantages, other established laboratory methods can perform as well or even better in confirming species' identity in herbal products.
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Affiliation(s)
- C. Haris Saslis-Lagoudakis
- Evolutionary Genomics Section, Natural History Museum of Denmark, Sølvgade 83S, Copenhagen, DK-1307, Denmark
| | - Sam Bruun-Lund
- Evolutionary Genomics Section, Natural History Museum of Denmark, Sølvgade 83S, Copenhagen, DK-1307, Denmark
| | - Natalie E. Iwanycki
- Evolutionary Genomics Section, Natural History Museum of Denmark, Sølvgade 83S, Copenhagen, DK-1307, Denmark
| | - Ole Seberg
- Evolutionary Genomics Section, Natural History Museum of Denmark, Sølvgade 83S, Copenhagen, DK-1307, Denmark
| | - Gitte Petersen
- Evolutionary Genomics Section, Natural History Museum of Denmark, Sølvgade 83S, Copenhagen, DK-1307, Denmark
| | - Anna K. Jäger
- Natural Products Research, Department of Drug Design and Pharmacology, University of Copenhagen, Universitetsparken 2, Copenhagen, DK-2100, Denmark
| | - Nina Rønsted
- Evolutionary Genomics Section, Natural History Museum of Denmark, Sølvgade 83S, Copenhagen, DK-1307, Denmark
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133
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Osathanunkul M, Madesis P, de Boer H. Bar-HRM for Authentication of Plant-Based Medicines: Evaluation of Three Medicinal Products Derived from Acanthaceae Species. PLoS One 2015; 10:e0128476. [PMID: 26011474 PMCID: PMC4444109 DOI: 10.1371/journal.pone.0128476] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2015] [Accepted: 04/27/2015] [Indexed: 12/05/2022] Open
Abstract
Medicinal plants are used as a popular alternative to synthetic drugs, both in developed and developing countries. The economic importance of the herbal and natural supplement industry is increasing every year. As the herbal industry grows, consumer safety is one issue that cannot be overlooked. Herbal products in Thai local markets are commonly sold without packaging or labels. Plant powders are stored in large bags or boxes, and therefore buying local herbal products poses a high risk of acquiring counterfeited, substituted and/or adulterated products. Due to these issues, a reliable method to authenticate products is needed. Here DNA barcoding was used in combination with High Resolution Melting analysis (Bar-HRM) to authenticate three medicinal Acanthaceae species (Acanthus ebracteatus, Andrographis paniculata and Rhinacanthus nasutus) commonly used in Thailand. The rbcL barcode was selected for use in primers design for HRM analysis to produce standard melting profiles of the selected species. Melting data from the HRM assay using the designed rbcL primers showed that the three chosen species could be distinguished from each other. HRM curves of all fifteen test samples indicated that three of tested products did not contain the indicated species. Two closely related species (A. paniculata and R. nasutus), which have a high level of morphological similarity, were interchanged with one another in three tested products. Incorrect information on packaging and labels of the tested herbal products was the cause of the results shown here. Morphological similarity among the species of interest also hindered the collection process. The Bar-HRM method developed here proved useful in aiding in the identification and authentication of herbal species in processed samples. In the future, species authentication through Bar-HRM could be used to promote consumer trust, as well as raising the quality of herbal products.
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Affiliation(s)
- Maslin Osathanunkul
- Department of Biology, Faculty of Science, Chiang Mai University, Chiang Mai, Thailand
| | - Panagiotis Madesis
- Institute of Applied Biosciences, Centre for Research & Technology Hellas (CERTH), Thessaloniki, Greece
| | - Hugo de Boer
- Department of Organismal Biology, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden; Naturalis Biodiversity Center, RA Leiden, The Netherlands; The Natural History Museum, University of Oslo, Oslo, Norway
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134
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Palhares RM, Gonçalves Drummond M, dos Santos Alves Figueiredo Brasil B, Pereira Cosenza G, das Graças Lins Brandão M, Oliveira G. Medicinal plants recommended by the world health organization: DNA barcode identification associated with chemical analyses guarantees their quality. PLoS One 2015; 10:e0127866. [PMID: 25978064 PMCID: PMC4433216 DOI: 10.1371/journal.pone.0127866] [Citation(s) in RCA: 92] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2015] [Accepted: 04/20/2015] [Indexed: 12/28/2022] Open
Abstract
Medicinal plants are used throughout the world, and the regulations defining their proper use, such as identification of the correct species and verification of the presence, purity and concentration of the required chemical compounds, are widely recognized. Herbal medicines are made from vegetal drugs, the processed products of medicinal species. These processed materials present a number of challenges in terms of botanical identification, and according to the World Health Organization (WHO), the use of incorrect species is a threat to consumer safety. The samples used in this study consisted of the dried leaves, flowers and roots of 257 samples from 8 distinct species approved by the WHO for the production of medicinal herbs and sold in Brazilian markets. Identification of the samples in this study using DNA barcoding (matK, rbcL and ITS2 regions) revealed that the level of substitutions may be as high as 71%. Using qualitative and quantitative chemical analyses, this study identified situations in which the correct species was being sold, but the chemical compounds were not present. Even more troubling, some samples identified as substitutions using DNA barcoding contained the chemical compounds from the correct species at the minimum required concentration. This last situation may lead to the use of unknown species or species whose safety for human consumption remains unknown. This study concludes that DNA barcoding should be used in a complementary manner for species identification with chemical analyses to detect and quantify the required chemical compounds, thus improving the quality of this class of medicines.
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Affiliation(s)
- Rafael Melo Palhares
- Programa de Pós-graduação em Genética, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
- Myleus Biotechnology Research Team, Belo Horizonte, Brazil
- Grupo de Genômica e Biologia Computacional, Centro de Pesquisa Rene Rachou, FIOCRUZ, Belo Horizonte, Brasil
| | | | | | - Gustavo Pereira Cosenza
- Laboratório de Farmacognosia, Faculdade de Farmácia, Universidade Federal de Minas Gerais, Belo Horizonte, Brasil
| | - Maria das Graças Lins Brandão
- Laboratório de Farmacognosia, Faculdade de Farmácia, Universidade Federal de Minas Gerais, Belo Horizonte, Brasil
- CEPLAMT, Museu de História Natural e Jardim Botânico & Faculdade de Farmácia, Universidade Federal de Minas Gerais, Belo Horizonte, Brasil
| | - Guilherme Oliveira
- Grupo de Genômica e Biologia Computacional, Centro de Pesquisa Rene Rachou, FIOCRUZ, Belo Horizonte, Brasil
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135
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Chen JJ, Wang Y. Microsatellite Development and Potential Application in Authentication, Conservation, and Genetic Improvement of Chinese Medicinal Plants. CHINESE HERBAL MEDICINES 2015. [DOI: 10.1016/s1674-6384(15)60029-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
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136
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Bertolini F, Ghionda MC, D’Alessandro E, Geraci C, Chiofalo V, Fontanesi L. A next generation semiconductor based sequencing approach for the identification of meat species in DNA mixtures. PLoS One 2015; 10:e0121701. [PMID: 25923709 PMCID: PMC4414512 DOI: 10.1371/journal.pone.0121701] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2014] [Accepted: 02/14/2015] [Indexed: 11/18/2022] Open
Abstract
The identification of the species of origin of meat and meat products is an important issue to prevent and detect frauds that might have economic, ethical and health implications. In this paper we evaluated the potential of the next generation semiconductor based sequencing technology (Ion Torrent Personal Genome Machine) for the identification of DNA from meat species (pig, horse, cattle, sheep, rabbit, chicken, turkey, pheasant, duck, goose and pigeon) as well as from human and rat in DNA mixtures through the sequencing of PCR products obtained from different couples of universal primers that amplify 12S and 16S rRNA mitochondrial DNA genes. Six libraries were produced including PCR products obtained separately from 13 species or from DNA mixtures containing DNA from all species or only avian or only mammalian species at equimolar concentration or at 1:10 or 1:50 ratios for pig and horse DNA. Sequencing obtained a total of 33,294,511 called nucleotides of which 29,109,688 with Q20 (87.43%) in a total of 215,944 reads. Different alignment algorithms were used to assign the species based on sequence data. Error rate calculated after confirmation of the obtained sequences by Sanger sequencing ranged from 0.0003 to 0.02 for the different species. Correlation about the number of reads per species between different libraries was high for mammalian species (0.97) and lower for avian species (0.70). PCR competition limited the efficiency of amplification and sequencing for avian species for some primer pairs. Detection of low level of pig and horse DNA was possible with reads obtained from different primer pairs. The sequencing of the products obtained from different universal PCR primers could be a useful strategy to overcome potential problems of amplification. Based on these results, the Ion Torrent technology can be applied for the identification of meat species in DNA mixtures.
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Affiliation(s)
- Francesca Bertolini
- Department of Agricultural and Food Sciences, Division of Animal Sciences, University of Bologna, Viale Fanin 46, 40127, Bologna, Italy
| | - Marco Ciro Ghionda
- Department of Agricultural and Food Sciences, Division of Animal Sciences, University of Bologna, Viale Fanin 46, 40127, Bologna, Italy
- Department of Veterinary Sciences, Animal Production Unit, University of Messina, Polo Universitario dell'Annunziata, 98168, Messina, Italy
| | - Enrico D’Alessandro
- Department of Veterinary Sciences, Animal Production Unit, University of Messina, Polo Universitario dell'Annunziata, 98168, Messina, Italy
| | - Claudia Geraci
- Department of Agricultural and Food Sciences, Division of Animal Sciences, University of Bologna, Viale Fanin 46, 40127, Bologna, Italy
| | - Vincenzo Chiofalo
- Department of Veterinary Sciences, Animal Production Unit, University of Messina, Polo Universitario dell'Annunziata, 98168, Messina, Italy
- Meat Research Consortium, Polo Universitario dell’Annunziata, 98168, Messina, Italy
| | - Luca Fontanesi
- Department of Agricultural and Food Sciences, Division of Animal Sciences, University of Bologna, Viale Fanin 46, 40127, Bologna, Italy
- * E-mail:
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137
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Murray DC, Coghlan ML, Bunce M. From benchtop to desktop: important considerations when designing amplicon sequencing workflows. PLoS One 2015; 10:e0124671. [PMID: 25902146 PMCID: PMC4406758 DOI: 10.1371/journal.pone.0124671] [Citation(s) in RCA: 107] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2014] [Accepted: 03/16/2015] [Indexed: 02/08/2023] Open
Abstract
Amplicon sequencing has been the method of choice in many high-throughput DNA sequencing (HTS) applications. To date there has been a heavy focus on the means by which to analyse the burgeoning amount of data afforded by HTS. In contrast, there has been a distinct lack of attention paid to considerations surrounding the importance of sample preparation and the fidelity of library generation. No amount of high-end bioinformatics can compensate for poorly prepared samples and it is therefore imperative that careful attention is given to sample preparation and library generation within workflows, especially those involving multiple PCR steps. This paper redresses this imbalance by focusing on aspects pertaining to the benchtop within typical amplicon workflows: sample screening, the target region, and library generation. Empirical data is provided to illustrate the scope of the problem. Lastly, the impact of various data analysis parameters is also investigated in the context of how the data was initially generated. It is hoped this paper may serve to highlight the importance of pre-analysis workflows in achieving meaningful, future-proof data that can be analysed appropriately. As amplicon sequencing gains traction in a variety of diagnostic applications from forensics to environmental DNA (eDNA) it is paramount workflows and analytics are both fit for purpose.
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Affiliation(s)
- Dáithí C. Murray
- Trace and Environmental DNA Laboratory, Department of Environment and Agriculture, Curtin University, Perth, Western Australia, Australia
| | - Megan L. Coghlan
- Trace and Environmental DNA Laboratory, Department of Environment and Agriculture, Curtin University, Perth, Western Australia, Australia
| | - Michael Bunce
- Trace and Environmental DNA Laboratory, Department of Environment and Agriculture, Curtin University, Perth, Western Australia, Australia
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138
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Chen J, Jiang Z, Li C, Ping X, Cui S, Tang S, Chu H, Liu B. Identification of ungulates used in a traditional Chinese medicine with DNA barcoding technology. Ecol Evol 2015; 5:1818-25. [PMID: 26140198 PMCID: PMC4485963 DOI: 10.1002/ece3.1457] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2015] [Revised: 02/12/2015] [Accepted: 02/16/2015] [Indexed: 11/22/2022] Open
Abstract
Horns of Saiga antelope (Saiga tatarica) have always been an ingredient of “Lingyangjiao”, a traditional Chinese medicine (TCM). Persistent hunting for Saiga antelope has already threatened the survival of critical endangered populations in wild. To control the growing pressure, CITES and Chinese government have legislated for monitoring the trade of Saiga horns. However, similar ungulate horns are difficult to identify by their morphological characteristics, which has impeded the law enforcement. Besides Saiga antelope, other seven ungulate species which have similar horns are also sold and marked as “Lingyangjiao” in TCM markets to offset shortage of Saiga antelope horns. Such species are Gazella subgutturosa, Pantholops hodgsonii, Procapra picticaudata, Procapra gutturosa, Procapra przewalskii, Capra hircus, and Ovis aries. Our study aimed at implementing DNA barcoding technology to diagnose Saiga horns and the substitutes. We successfully extracted genomic DNA from horn samples. We recovered COI sequences of 644 bp with specific primers and 349 bp with nested PCR primers designed for degraded horn samples. The mean interspecific genetic distance of data set of the 644-bp full barcodes and the 349-bp mini-barcodes was 14.96% and 15.38%, respectively, and the mean intraspecific distance was 0.24% and 0.20%, respectively. Each species formed independent clades in neighbor-joining (NJ) phylogenetic tree of the two data sets with >99% supporting values, except P. gutturosa and P. przewalskii. The deep genetic distances gap and clear species clades in NJ tree of either full barcodes or mini-barcodes suggest that barcoding technology is an effective tool to diagnose Saiga horns and their substitutes. Barcoding diagnosis protocol developed here will simplify diagnosis of “Lingyangjiao” species and will facilitate conservation of endangered ungulates involved in TCM “Lingyangjiao” markets, especially the Saiga antelope.
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Affiliation(s)
- Jing Chen
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences Chaoyang District, No. 1 Beichen West Road, Beijing, 100101, China ; University of Chinese Academy of Sciences No. 19 (A) Yuquan Road, Beijing, 100049, China
| | - Zhigang Jiang
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences Chaoyang District, No. 1 Beichen West Road, Beijing, 100101, China ; University of Chinese Academy of Sciences No. 19 (A) Yuquan Road, Beijing, 100049, China ; Endangered Species Scientific Commission of the People's Republic of China Chaoyang District, No. 1 Beichen West Road, Beijing, 100101, China
| | - Chunlin Li
- School of Resources and Environmental Engineering, Anhui University No. 111 Jiu Long Road, Hefei, 230601, Anhui Province, China
| | - Xiaoge Ping
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences Chaoyang District, No. 1 Beichen West Road, Beijing, 100101, China
| | - Shaopeng Cui
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences Chaoyang District, No. 1 Beichen West Road, Beijing, 100101, China ; University of Chinese Academy of Sciences No. 19 (A) Yuquan Road, Beijing, 100049, China
| | - Songhua Tang
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences Chaoyang District, No. 1 Beichen West Road, Beijing, 100101, China
| | - Hongjun Chu
- Wildlife Conservation Office of Altay Prefecture 836500, Altay, Xinjiang, China
| | - Binwan Liu
- College of Wildlife Resources, Northeast Forestry University, No. 26 Hexing Road Xiangfang District Harbin, 150040, Heilongjiang Province, China
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139
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Flavigny RMG, Cord-Ruwisch R. Organic carbon removal from wastewater by a PHA storing biofilm using direct atmospheric air contact as oxygen supply. BIORESOURCE TECHNOLOGY 2015; 187:182-188. [PMID: 25855525 DOI: 10.1016/j.biortech.2015.03.121] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2015] [Revised: 03/24/2015] [Accepted: 03/25/2015] [Indexed: 06/04/2023]
Abstract
The principal reason for the high energy costs for biological wastewater treatment is the poor transfer efficiency of oxygen to the bulk water phase. The current paper describes a biofilm reactor in which oxygen transfer to the bulk solution is avoided by alternating anaerobic submersed (2h) and drained (1h) operation of the biofilm. During the submersed phase the biofilm enriched for glycogen accumulating organism (GAO) stored the organic carbon (acetate) as poly-hydroxy-alkanoate (PHA). After draining the reactor, this carbon stored as PHA was biologically oxidised, using oxygen directly from the atmosphere. The 12Cmmol/L (384mg/L BOD) of acetate was completely removed during long term automated operation of the reactor for 9months with a cycle length of 3.3h. As the process specifically removes dissolved organic carbon but not N or P it could possibly be coupled with novel processes such as Anammox or nutrient recovery.
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Affiliation(s)
| | - Ralf Cord-Ruwisch
- School of Engineering and IT, Murdoch University, 90 South Street, Murdoch 6150, Western Australia, Australia.
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140
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Lo YT, Li M, Shaw PC. Identification of constituent herbs in ginseng decoctions by DNA markers. Chin Med 2015; 10:1. [PMID: 25657815 PMCID: PMC4318153 DOI: 10.1186/s13020-015-0029-x] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2014] [Accepted: 01/20/2015] [Indexed: 12/02/2022] Open
Abstract
Background DNA in herbal decoctions is usually fragmented by extensive boiling and is usually regarded as unsuitable for molecular authentication. This study aims to evaluate the feasibility for molecular authentication methods by multiplex polymerase chain reaction (PCR) and DNA sequencing for decoctions. Methods The DNA extraction procedure, sample pulverization and boiling time were examined in (1) single herb decoction with Panax ginseng (“ginseng”) or P. quinquefolius (“American ginseng”), (2) decoctions of two classical ginseng prescriptions of five herbal materials (Aconitum carmichaeli, Atractylodes macrocephala, P. ginseng, Glycyrrhiza uralensis and Zingiber officinale) and (3) a commercial ready-to-serve ginseng soup. Primers were designed from 26S-18S, ITS2 and trnH-psbA region, with DNA sequences obtained from GenBank. Multiplex PCR was also employed in ginseng or American ginseng decoctions to differentiate between these two herbs. Results All six herbal species tested in this study could be identified in decoctions. We had four main observations: (1) sample pulverization before boiling improved PCR detection; (2) prolonged boiling increased the DNA concentration but decreased the intactness of DNA fragments; (3) ginseng could be differentiated from American ginseng by multiplex PCR; (4) identification of individual herbs in multi-herb decoctions with prolonged boiling time of 180 min could be achieved. Conclusions DNA could be amplified from extensively boiled ginseng decoctions, multi-herb decoctions and commercial soup although DNA degradation was critical to successful PCR. Electronic supplementary material The online version of this article (doi:10.1186/s13020-015-0029-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Yat-Tung Lo
- School of Life Sciences, The Chinese University of Hong Kong, S.A.R N.T, Shatin, Hong Kong China
| | - Ming Li
- State Key Laboratory of Phytochemistry and Plant Resources in West China (CUHK), Institute of Chinese Medicine, The Chinese University of Hong Kong, Shatin, N.T., Hong Kong China
| | - Pang-Chui Shaw
- School of Life Sciences, The Chinese University of Hong Kong, S.A.R N.T, Shatin, Hong Kong China ; State Key Laboratory of Phytochemistry and Plant Resources in West China (CUHK), Institute of Chinese Medicine, The Chinese University of Hong Kong, Shatin, N.T., Hong Kong China
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141
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Abstract
Biothreats are a high priority concern for public safety and national security. The field of microbial forensics was developed to analyze evidence associated with biological crimes in which microbes or their toxins are used as weapons. Microbial forensics is the scientific discipline dedicated to analyzing evidence from a bioterrorism act, biocrime, hoax, or inadvertent microorganism/toxin release for attribution purposes. Microbial forensics combines the practices of epidemiology with the characterization of microbial and microbial-related evidence to assist in determining the specific source of the sample, as individualizing as possible, and/or the methods, means, processes and locations involved to determine the identity of the perpetrator(s) of an attack.
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142
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Tong Y, Jiang C, Yuan Y, Jin Y, Cui ZH, Huang L. Molecular identification of antelope horn by melting curve analysis. Mitochondrial DNA A DNA Mapp Seq Anal 2014; 27:3945-3951. [PMID: 25541315 DOI: 10.3109/19401736.2014.989500] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Antelope horn is a valuable Chinese traditional medicine and widely used in clinic. However, with the deterioration of antelope's living environment and a lot of killing, the saiga population begins falling and in some places plummet. Since the increasing demand of this expensive and good bioactive medicine, the horn of artiodactyla animals is often used as the antelope horn. The adulterated or impostor not only cause damage to clinical medicine but also affect the antelope resources protection and sustainable development. Here, in order to establish a melting curve analysis (MCA) method to distinguish the antelope horn from other animal horns and identify the decoction pieces and Chinese patent medicine in a fast and easy way, animal horns and its decoction pieces, Chinese patent medicines were collected from the market and the DNA of all the collected samples were extracted. The melting curve of two universal fragments (COI and Cyt b) was scanned and Cyt b was selected as feasibility fragment for identifying authentic antelope horn from eight adulterant animal horns. After optimizing the condition for MCA, inspecting the precision and the replication of the method, a reference melting curve modern was established and we performed MCA on the antelope horns, fakes, and adulterants on a 1:1 mix, decoction pieces, and Chinese patent medicine. Thus, this study provides fast and easy methods so that MCA can detect the truth, fakes, and adulterations of antelope horns.
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Affiliation(s)
- Yuru Tong
- a State Key Laboratory Breeding Base of Dao-di Herbs, National Resource Center for Chinese Materia Medica , China Academy of Chinese Medical Sciences , Beijing , PR China and.,b School of Traditional Chinese Medicine , Capital Medical University , Beijing , PR China
| | - Chao Jiang
- a State Key Laboratory Breeding Base of Dao-di Herbs, National Resource Center for Chinese Materia Medica , China Academy of Chinese Medical Sciences , Beijing , PR China and
| | - Yuan Yuan
- a State Key Laboratory Breeding Base of Dao-di Herbs, National Resource Center for Chinese Materia Medica , China Academy of Chinese Medical Sciences , Beijing , PR China and
| | - Yan Jin
- a State Key Laboratory Breeding Base of Dao-di Herbs, National Resource Center for Chinese Materia Medica , China Academy of Chinese Medical Sciences , Beijing , PR China and
| | - Zhan-Hu Cui
- a State Key Laboratory Breeding Base of Dao-di Herbs, National Resource Center for Chinese Materia Medica , China Academy of Chinese Medical Sciences , Beijing , PR China and
| | - Luqi Huang
- a State Key Laboratory Breeding Base of Dao-di Herbs, National Resource Center for Chinese Materia Medica , China Academy of Chinese Medical Sciences , Beijing , PR China and.,b School of Traditional Chinese Medicine , Capital Medical University , Beijing , PR China
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143
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Zheng Z, Hu J, He Z. A split G-quadruplex and graphene oxide-based low-background platform for fluorescence authentication of Pseudostellaria heterophylla. SENSORS 2014; 14:22971-81. [PMID: 25479327 PMCID: PMC4299048 DOI: 10.3390/s141222971] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/14/2014] [Revised: 11/09/2014] [Accepted: 11/27/2014] [Indexed: 11/25/2022]
Abstract
A label-free split G-quadruplex and graphene oxide (GO)-based fluorescence platform has been designed to distinguish Pseudostellaria heterophylla (PH) from its adulterants based on the differences in their nrDNA ITS sequences. Herein, GO has been first introduced to capture G-rich probes with 2:2 split mode and then decrease the background signal. As T-DNA exists, the probes leave the GO surface to form double-stranded structures followed by the formation of the overhanging G-rich sequence into a G-quadruplex structure, which combines quinaldine red specifically to produce a strong fluorescence signal. In addition, this strategy allows detection of T-DNA in a wide range of concentrations from 1.0 × 10−8 to 2.0 × 10−6 mol·L−1 with a detection limit of 7.8 × 10−9 mol·L−1. We hope that the split G-quadruplex/GO platform can be utilized to further develop gene identification sensors in Traditional Chinese Medicine or other analysis areas.
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Affiliation(s)
- Zhenzhu Zheng
- Institute of Drug Research, Fujian Academy of Traditional Chinese Medicine, Fuzhou 350003, China.
| | - Juan Hu
- Institute of Drug Research, Fujian Academy of Traditional Chinese Medicine, Fuzhou 350003, China.
| | - Zhaodong He
- Institute of Drug Research, Fujian Academy of Traditional Chinese Medicine, Fuzhou 350003, China.
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144
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Seethapathy GS, Ganesh D, Santhosh Kumar JU, Senthilkumar U, Newmaster SG, Ragupathy S, Uma Shaanker R, Ravikanth G. Assessing product adulteration in natural health products for laxative yielding plants, Cassia, Senna, and Chamaecrista, in Southern India using DNA barcoding. Int J Legal Med 2014; 129:693-700. [DOI: 10.1007/s00414-014-1120-z] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2014] [Accepted: 11/10/2014] [Indexed: 12/19/2022]
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145
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A renaissance in herbal medicine identification: from morphology to DNA. Biotechnol Adv 2014; 32:1237-1244. [PMID: 25087935 DOI: 10.1016/j.biotechadv.2014.07.004] [Citation(s) in RCA: 162] [Impact Index Per Article: 16.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2014] [Revised: 07/13/2014] [Accepted: 07/16/2014] [Indexed: 02/08/2023]
Abstract
Numerous adverse reactions have arisen following the use of inaccurately identified medicinal plant ingredients, resulting in conditions such as aristolochic acid nephropathy and herb-induced poisoning. This problem has prompted increased global concern over the safety of herbal medicines. DNA barcoding, a technique aiming at detecting species-specific differences in a short region of DNA, provides a powerful new tool for addressing this problem. A preliminary system for DNA barcoding herbal materials has been established based on a two-locus combination of ITS2+psbA-trnH barcodes. There are 78,847 sequences belonging to 23,262 species in the system, which include more than 95% of crude herbal drugs in pharmacopeia, such as those of China, Japan, Korea, India, USA, and Europe. The system has been widely used in traditional herbal medicine enterprises. This review summarizes recent key advances in the DNA barcoding of medicinal plant ingredients (herbal materia medica) as a contribution towards safe and efficacious herbal medicines.
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146
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Ripp F, Krombholz CF, Liu Y, Weber M, Schäfer A, Schmidt B, Köppel R, Hankeln T. All-Food-Seq (AFS): a quantifiable screen for species in biological samples by deep DNA sequencing. BMC Genomics 2014; 15:639. [PMID: 25081296 PMCID: PMC4131036 DOI: 10.1186/1471-2164-15-639] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2013] [Accepted: 07/24/2014] [Indexed: 01/16/2023] Open
Abstract
BACKGROUND DNA-based methods like PCR efficiently identify and quantify the taxon composition of complex biological materials, but are limited to detecting species targeted by the choice of the primer assay. We show here how untargeted deep sequencing of foodstuff total genomic DNA, followed by bioinformatic analysis of sequence reads, facilitates highly accurate identification of species from all kingdoms of life, at the same time enabling quantitative measurement of the main ingredients and detection of unanticipated food components. RESULTS Sequence data simulation and real-case Illumina sequencing of DNA from reference sausages composed of mammalian (pig, cow, horse, sheep) and avian (chicken, turkey) species are able to quantify material correctly at the 1% discrimination level via a read counting approach. An additional metagenomic step facilitates identification of traces from animal, plant and microbial DNA including unexpected species, which is prospectively important for the detection of allergens and pathogens. CONCLUSIONS Our data suggest that deep sequencing of total genomic DNA from samples of heterogeneous taxon composition promises to be a valuable screening tool for reference species identification and quantification in biosurveillance applications like food testing, potentially alleviating some of the problems in taxon representation and quantification associated with targeted PCR-based approaches.
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Affiliation(s)
- Fabian Ripp
- />Institute of Molecular Genetics, Johannes Gutenberg University Mainz, D55099 Mainz, Germany
| | | | - Yongchao Liu
- />Institute of Computer Science, Johannes Gutenberg University Mainz, D55099 Mainz, Germany
| | - Mathias Weber
- />Institute of Molecular Genetics, Johannes Gutenberg University Mainz, D55099 Mainz, Germany
| | - Anne Schäfer
- />Institute of Molecular Genetics, Johannes Gutenberg University Mainz, D55099 Mainz, Germany
| | - Bertil Schmidt
- />Institute of Computer Science, Johannes Gutenberg University Mainz, D55099 Mainz, Germany
| | - Rene Köppel
- />Official Food Control Authority of the Canton Zürich, Zürich, Switzerland
| | - Thomas Hankeln
- />Institute of Molecular Genetics, Johannes Gutenberg University Mainz, D55099 Mainz, Germany
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147
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Yuan QJ, Zhang B, Jiang D, Zhang WJ, Lin TY, Wang NH, Chiou SJ, Huang LQ. Identification of species and materia medica within Angelica L. (Umbelliferae) based on phylogeny inferred from DNA barcodes. Mol Ecol Resour 2014; 15:358-71. [PMID: 24961287 PMCID: PMC4344822 DOI: 10.1111/1755-0998.12296] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2013] [Revised: 06/05/2014] [Accepted: 06/20/2014] [Indexed: 11/29/2022]
Abstract
DNA barcodes have been increasingly used in authentication of medicinal plants, while their wide application in materia medica is limited in their accuracy due to incomplete sampling of species and absence of identification for materia medica. In this study, 95 leaf accessions of 23 species (including one variety) and materia medica of three Pharmacopoeia-recorded species of Angelica in China were collected to evaluate the effectiveness of four DNA barcodes (rbcL, matK, trnH-psbA and ITS). Our results showed that ITS provided the best discriminatory power by resolving 17 species as monophyletic lineages without shared alleles and exhibited the largest barcoding gap among the four single barcodes. The phylogenetic analysis of ITS showed that Levisticum officinale and Angelica sinensis were sister taxa, which indicates that L. officinale should be considered as a species of Angelica. The combination of ITS + rbcL + matK + trnH-psbA performed slight better discriminatory power than ITS, recovering 23 species without shared alleles and 19 species as monophyletic clades in ML tree. Authentication of materia medica using ITS revealed that the decoction pieces of A. sinensis and A. biserrata were partially adulterated with those of L. officinale, and the temperature around 80 °C processing A. dahurica decoction pieces obviously reduced the efficiency of PCR and sequencing. The examination of two cultivated varieties of A. dahurica from different localities indicated that the four DNA barcodes are inefficient for discriminating geographical authenticity of conspecific materia medica. This study provides an empirical paradigm in identification of medicinal plants and their materia medica using DNA barcodes.
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Affiliation(s)
- Qing-Jun Yuan
- State Key Laboratory Breeding Base of Dao-di Herbs, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, China
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148
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Zhang L, Ma L, Feng W, Zhang C, Sheng F, Zhang Y, Xu C, Dong G, Dong X, Xiao X, Yan D. Quality fluctuation detection of an herbal injection based on biological fingerprint combined with chemical fingerprint. Anal Bioanal Chem 2014; 406:5009-18. [DOI: 10.1007/s00216-014-7918-1] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2014] [Revised: 05/08/2014] [Accepted: 05/20/2014] [Indexed: 01/14/2023]
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149
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Cheng X, Su X, Chen X, Zhao H, Bo C, Xu J, Bai H, Ning K. Biological ingredient analysis of traditional Chinese medicine preparation based on high-throughput sequencing: the story for Liuwei Dihuang Wan. Sci Rep 2014; 4:5147. [PMID: 24888649 PMCID: PMC4042125 DOI: 10.1038/srep05147] [Citation(s) in RCA: 75] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2014] [Accepted: 05/06/2014] [Indexed: 01/03/2023] Open
Abstract
Although Traditional Chinese Medicine (TCM) preparations have long history with successful applications, the scientific and systematic quality assessment of TCM preparations mainly focuses on chemical constituents and is far from comprehensive. There are currently only few primitive studies on assessment of biological ingredients in TCM preparations. Here, we have proposed a method, M-TCM, for biological assessment of the quality of TCM preparations based on high-throughput sequencing and metagenomic analysis. We have tested this method on Liuwei Dihuang Wan (LDW), a TCM whose ingredients have been well-defined. Our results have shown that firstly, this method could determine the biological ingredients of LDW preparations. Secondly, the quality and stability of LDW varies significantly among different manufacturers. Thirdly, the overall quality of LDW samples is significantly affected by their biological contaminations. This novel strategy has the potential to achieve comprehensive ingredient profiling of TCM preparations.
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Affiliation(s)
- Xinwei Cheng
- Institute of Materia Medica, Shandong Academy of Medical Sciences, Jinan, Shandong, 250062, China
- School of Medicine and Life Sciences, , University of Jinan-Shandong Academy of Medical Sciences, Jinan 250062, China
- These authors contributed equally to this work
| | - Xiaoquan Su
- Shandong Key Laboratory of Energy Genetics, CAS Key Laboratory of Biofuels and Bioinformatics Group of SingleCell Center, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao266101, China
- These authors contributed equally to this work
| | - Xiaohua Chen
- Shandong Key Laboratory of Energy Genetics, CAS Key Laboratory of Biofuels and Bioinformatics Group of SingleCell Center, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao266101, China
| | - Huanxin Zhao
- Institute of Materia Medica, Shandong Academy of Medical Sciences, Jinan, Shandong, 250062, China
| | - Cunpei Bo
- Shandong Key Laboratory of Energy Genetics, CAS Key Laboratory of Biofuels and Bioinformatics Group of SingleCell Center, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao266101, China
| | - Jian Xu
- Shandong Key Laboratory of Energy Genetics, CAS Key Laboratory of Biofuels and Bioinformatics Group of SingleCell Center, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao266101, China
| | - Hong Bai
- Institute of Materia Medica, Shandong Academy of Medical Sciences, Jinan, Shandong, 250062, China
| | - Kang Ning
- Shandong Key Laboratory of Energy Genetics, CAS Key Laboratory of Biofuels and Bioinformatics Group of SingleCell Center, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao266101, China
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150
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DNA extraction protocol for biological ingredient analysis of Liuwei Dihuang Wan. GENOMICS PROTEOMICS & BIOINFORMATICS 2014; 12:137-43. [PMID: 24838067 PMCID: PMC4411345 DOI: 10.1016/j.gpb.2014.03.002] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/25/2014] [Revised: 03/29/2014] [Accepted: 03/31/2014] [Indexed: 11/23/2022]
Abstract
Traditional Chinese medicine (TCM) preparations are widely used for healthcare and clinical practice. So far, the methods commonly used for quality evaluation of TCM preparations mainly focused on chemical ingredients. The biological ingredient analysis of TCM preparations is also important because TCM preparations usually contain both plant and animal ingredients, which often include some mis-identified herbal materials, adulterants or even some biological contaminants. For biological ingredient analysis, the efficiency of DNA extraction is an important factor which might affect the accuracy and reliability of identification. The component complexity in TCM preparations is high, and DNA might be destroyed or degraded in different degrees after a series of processing procedures. Therefore, it is necessary to establish an effective protocol for DNA extraction from TCM preparations. In this study, we chose a classical TCM preparation, Liuwei Dihuang Wan (LDW), as an example to develop a TCM-specific DNA extraction method. An optimized cetyl trimethyl ammonium bromide (CTAB) method (TCM-CTAB) and three commonly-used extraction kits were tested for extraction of DNA from LDW samples. Experimental results indicated that DNA with the highest purity and concentration was obtained by using TCM-CTAB. To further evaluate the different extraction methods, amplification of the second internal transcribed spacer (ITS2) and the chloroplast genome trnL intron was carried out. The results have shown that PCR amplification was successful only with template of DNA extracted by using TCM-CTAB. Moreover, we performed high-throughput 454 sequencing using DNA extracted by TCM-CTAB. Data analysis showed that 3–4 out of 6 prescribed species were detected from LDW samples, while up to 5 contaminating species were detected, suggesting TCM-CTAB method could facilitate follow-up DNA-based examination of TCM preparations.
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