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Prevalence and Molecular Characterization of Ascaridoid Parasites of Philippine Decapterus species. J Nematol 2022; 54:20220030. [PMID: 36060477 PMCID: PMC9400525 DOI: 10.2478/jofnem-2022-0030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Indexed: 11/21/2022] Open
Abstract
There are relatively few studies on parasite fauna of marine fishes in Philippine waters. This study aimed to determine the prevalence of marine ascaridoid infection in Decapterus species in Balayan Bay and Tayabas Bay. A total of 371 fishes belonging to three different species of Decapterus (D. tabl [n = 130], D. macrosoma [n = 121], and D. maruadsi [n = 120]) were collected. Ascaridoid parasite larvae were found in all fish host species, with an overall fish infection rate of 22%. The highest infection rate was observed in D. tabl (27.69%), followed by D. macrosoma (19%), and then D. maruadsi (17.50%). Moreover, a higher prevalence of infection was detected in Tayabas Bay (27.57%) than in Balayan Bay (15.59%). Molecular analyses based on the ITS2 and 18S rRNA gene supported the identification of the larvae into two species: Anisakis typica and Raphidascaris (Ichthyascaris) lophii. This is the first report of the genetic identification of these two helminth parasites in Decapterus fish species in the Philippines. Paucity in the database of Philippine marine fish parasites warrants more research efforts, especially concerning economically important fish species with implications to food safety and food security.
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Specification and DNA Barcoding of Thai Traditional Remedy for Chronic Kidney Disease: Pikad Tri-phol-sa-mut-than. PLANTS 2021; 10:plants10102023. [PMID: 34685831 PMCID: PMC8540904 DOI: 10.3390/plants10102023] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Revised: 09/15/2021] [Accepted: 09/20/2021] [Indexed: 11/17/2022]
Abstract
The Pikad Tri-phol-sa-mut-than (TS) remedy, a Thai traditional medicine, is officially recorded in Tamra Paetsart Sonkrau Chabub Anurak for its capabilities in treating kidney deficiency. TS remedy is composed of three fruit species—Aegle marmelos (L.) Corrêa., Coriandrum sativum L., and Morinda citrifolia L.—in an equal part by weight. The quality of the raw material is one of the essential factors that can affect the effectiveness and safety of treatment by herbal remedy. The pharmacognostic evaluation and DNA barcode of the three fruit species and TS remedy were performed in this study to authenticate them from contamination, and to provide the scientific database for further uses. Macroscopic and microscopic examination, chemical profile by TLC, and DNA barcoding were employed to positively identify the raw materials bought from the herbal market, especially the powder form. Consequently, the outcomes of this investigation can be used to develop an essential and effective tool for the authentication of crude drugs and herbal remedies.
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Yanaso S, Phrutivorapongkul A, Hongwiset D, Piyamongkol S, Intharuksa A. Verification of Thai ethnobotanical medicine "Kamlang Suea Khrong" driven by multiplex PCR and powerful TLC techniques. PLoS One 2021; 16:e0257243. [PMID: 34534243 PMCID: PMC8448358 DOI: 10.1371/journal.pone.0257243] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Accepted: 08/26/2021] [Indexed: 11/18/2022] Open
Abstract
Kamlang Suea Khrong (KSK) crude drug, a traditional Thai medicine used for oral tonic and analgesic purposes, is obtained from three origins: the inner stem bark of Betula alnoides (BA) or the stems of Strychnos axillaris (SA) or Ziziphus attopensis (ZA). According to the previous reports, SA contains strychnine-type alkaloids that probably cause poisoning; however, only organoleptic approaches are insufficient to differentiate SA from the other plant materials. To ensure the botanical origin of KSK crude drug, powerful and reliable tools are desperately needed. Therefore, molecular and chemical identification methods, DNA barcoding and thin-layer chromatography (TLC), were investigated. Reference databases, i.e., the ITS region and phytochemical profile of the authentic plant species, were conducted. In case of molecular analysis, multiplex polymerase chain reaction (PCR) based on species-specific primers was applied. Regarding species-specific primers designation, the suitability of three candidate barcode regions (ITS, ITS1, and ITS2) was evaluated by genetic distance using K2P model. ITS2 presented the highest interspecific variability was verified its discrimination power by tree topology. Accordingly, ITS2 was used to create primers that successfully specified plant species of authentic samples. For chemical analysis, TLC with toluene:ethyl acetate:ammonia (1:9:0.025) and hierarchical clustering were operated to identify the authentic crude drugs. The developed multiplex PCR and TLC methods were then applied to identify five commercial KSK crude drugs (CK1-CK5). Both methods correspondingly indicated that CK1-CK2 and CK3-CK5 were originated from BA and ZA, respectively. Molecular and chemical approaches are convenient and effective identification methods that can be performed for the routine quality-control of the KSK crude drugs for consumer reliance. According to chemical analysis, the results indicated BA, SA, and ZA have distinct chemical profiles, leading to differences in pharmacological activities. Consequently, further scientific investigations are required to ensure the quality and safety of Thai ethnobotanical medicine known as KSK.
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Affiliation(s)
- Suthira Yanaso
- Department of Pharmaceutical Sciences, Faculty of Pharmacy, Chiang Mai University, Mueang, Chiang Mai, Thailand
- Department of Pharmaceutical Chemistry and Pharmacognosy, Faculty of Pharmaceutical Sciences, Huachiew Chalermprakiet University, Bang Phli, Samutprakan, Thailand
| | - Ampai Phrutivorapongkul
- Department of Pharmaceutical Sciences, Faculty of Pharmacy, Chiang Mai University, Mueang, Chiang Mai, Thailand
| | - Darunee Hongwiset
- Department of Pharmaceutical Sciences, Faculty of Pharmacy, Chiang Mai University, Mueang, Chiang Mai, Thailand
| | - Sirivipa Piyamongkol
- Department of Pharmaceutical Sciences, Faculty of Pharmacy, Chiang Mai University, Mueang, Chiang Mai, Thailand
| | - Aekkhaluck Intharuksa
- Department of Pharmaceutical Sciences, Faculty of Pharmacy, Chiang Mai University, Mueang, Chiang Mai, Thailand
- * E-mail:
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Yang RS, Ni MY, Gu YJ, Xu JS, Jin Y, Zhang JH, Wang Y, Qin L. Newly Emerging Pest in China, Rhynchaenusmaculosus (Coleoptera: Curculionidae): Morphology and Molecular Identification with DNA Barcoding. INSECTS 2021; 12:insects12060568. [PMID: 34205814 PMCID: PMC8235397 DOI: 10.3390/insects12060568] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Revised: 06/16/2021] [Accepted: 06/18/2021] [Indexed: 11/16/2022]
Abstract
The oak flea weevil, Rhynchaenusmaculosus Yang et Zhang 1991, is a newly emerging pest that severely damages oak (genus Quercus) in China. The first R. maculosus outbreak occurred in 2020 and caused spectacular damage to all oak forests in Jilin province, northeast China. The lack of key morphological characters complicates the identification of this native pest, especially in larva and pupa stages. This is problematic because quick and accurate species identification is crucial for early monitoring and intervention during outbreaks. Here, we provided the first detailed morphological description of R. maculosus at four life stages. Additionally, we used DNA barcodes from larva and pupa specimens collected from three remote locations for molecular identification. The average pairwise divergence of all sequences in this study was 0.51%, well below the 2% to 3% (K-2-parameter) threshold set for one species. All sample sequences matched the R. maculosus morphospecies (KX657706.1 and KX657707.1), with 99.23% to 100% (sequence identity, E value: 0.00) matching success. The tree based on barcodes placed the specimens into the Rhynchaenus group, and the phylogenetic relationship between 62 sequences (30 samples and 32 from GeneBank) had high congruence with the morphospecies taxa. The traditional DNA barcodes were successfully transformed into quick response codes with larger coding capacity for information storage. The results showed that DNA barcoding is reliable for R. maculosus identification. The integration of molecular and morphology-based methods contributes to accurate species identification of this newly emerging oak pest.
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Affiliation(s)
- Rui-Sheng Yang
- College of Bioscience and Biotechnology, Shenyang Agricultural University, Shenyang 110866, China; (M.-Y.N.); (Y.-J.G.); (Y.W.)
- Correspondence: (R.-S.Y.); (L.Q.); Tel.: +86-024-8848-7163 (R.-S.Y.)
| | - Ming-Yang Ni
- College of Bioscience and Biotechnology, Shenyang Agricultural University, Shenyang 110866, China; (M.-Y.N.); (Y.-J.G.); (Y.W.)
| | - Yu-Jian Gu
- College of Bioscience and Biotechnology, Shenyang Agricultural University, Shenyang 110866, China; (M.-Y.N.); (Y.-J.G.); (Y.W.)
| | - Jia-Sheng Xu
- School of Life and Environmental Sciences, Gannan Normal University, Ganzhou 341000, China;
| | - Ying Jin
- Jilin Provincial Sericulture Institution, Agriculture Committee of Jilin Province, Jilin 132012, China; (Y.J.); (J.-H.Z.)
| | - Ji-Hui Zhang
- Jilin Provincial Sericulture Institution, Agriculture Committee of Jilin Province, Jilin 132012, China; (Y.J.); (J.-H.Z.)
| | - Yong Wang
- College of Bioscience and Biotechnology, Shenyang Agricultural University, Shenyang 110866, China; (M.-Y.N.); (Y.-J.G.); (Y.W.)
| | - Li Qin
- College of Bioscience and Biotechnology, Shenyang Agricultural University, Shenyang 110866, China; (M.-Y.N.); (Y.-J.G.); (Y.W.)
- Correspondence: (R.-S.Y.); (L.Q.); Tel.: +86-024-8848-7163 (R.-S.Y.)
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Tan WH, Chai LC, Chin CF. Efficacy of DNA barcode internal transcribed spacer 2 (ITS 2) in phylogenetic study of Alpinia species from Peninsular Malaysia. PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2020; 26:1889-1896. [PMID: 32943824 PMCID: PMC7468033 DOI: 10.1007/s12298-020-00868-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/18/2020] [Revised: 08/01/2020] [Accepted: 08/14/2020] [Indexed: 05/20/2023]
Abstract
Alpinia belongs to a large genus with many species found in Peninsular Malaysia. Several species of Alpinia exhibit important medicinal potential. However, progressive studies on the genus Alpinia were hampered by difficulties encountered in species identification. With the advancement achieved in genomic technology, more sensitive tools such as DNA barcoding were developed, which can be used for species identification. Internal Transcribe Spacer 2 (ITS2) is a DNA barcode which has proven to be a promising tool for species identification. The criterions of ITS2 efficacy namely universality and efficacy for species identification were tested on Alpinia species collected from Peninsular Malaysia. The results showed that a success rate of 96.97% was achieved using ITS2 for screening 11 species of Alpinia and an outgroup sample (Zingiber specatabile). Combined with 15 additional sequences from the Genbank for five Alpinia species, ITS2 demonstrated high species identification efficacy with 88.2% of species identified using phylogenetic and distance analysis. The analysis was further improved with the use of ITS2 secondary structure. The results of both criterions demonstrated the ability of ITS2 to successfully discriminate Alpinia species, which will help to improve species identification of Alpinia species in Peninsular Malaysia.
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Affiliation(s)
- Wei Harn Tan
- University of Nottingham Malaysia Campus, Semenyih, Malaysia
| | - Li Chin Chai
- University of Nottingham Malaysia Campus, Semenyih, Malaysia
| | - Chiew Foan Chin
- University of Nottingham Malaysia Campus, Semenyih, Malaysia
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DNA barcodes for delineating Clerodendrum species of North East India. Sci Rep 2020; 10:13490. [PMID: 32778674 PMCID: PMC7417596 DOI: 10.1038/s41598-020-70405-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2020] [Accepted: 07/06/2020] [Indexed: 01/06/2023] Open
Abstract
The diversified genus of Clerodendrum with its complex evolutionary history leads to taxonomic mystification. Unlike traditional taxonomic methods, DNA barcoding could be a promising tool for the identification and conservation of Clerodendrum species. This study was attempted to develop an efficient barcode locus in Clerodendrum species of North East India. We evaluated four barcode candidates (ITS2, matK, rbcL, ycf1) and its combinations in different Clerodendrum species. The reliability of barcodes to distinguish the species were calculated using genetic pairwise distances, intra- and inter-specific diversity, barcode gap, and phylogenetic tree-based methods. The results exemplify that matK posse’s maximum number of variables and parsimony-informative sites (103/100), intra- (0.021 ± 0.001) and inter- (0.086 ± 0.005) specific divergences and species resolution rate (89.1%) followed by ITS2, ycf1, and rbcL. Among the combinatorial locus, ITS2 + matK showed the best species discrimination with distinctive barcode gaps. Therefore, we tentatively suggest that the combination of ITS2 + matK as core barcode for Clerodendrum and converted into quick response (QR) code. Hence, this finding indicates that DNA barcoding could provide consistent resources for species discrimination and resolve taxonomic controversies of the genus as well as set a preliminary assessment toward its biodiversity.
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Prieto JAF, Rodríguez JMA, Sanna M, Cires E. Phylogeographical patterns of Campanula gr. arvatica, an endemic group of the Cantabrian mountains (NW Iberian Peninsula), based on plastid and nuclear DNA polymorphisms. SYST BIODIVERS 2020. [DOI: 10.1080/14772000.2020.1783715] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Affiliation(s)
- José Antonio Fernández Prieto
- Departamento de Biología de Organismos y Sistemas, Universidad de Oviedo, Área de Botánica, C/Catedrático Rodrigo Uría s/n, Oviedo, 33071, Spain
- Instituto de Recursos Naturales y Ordenación del Territorio (INDUROT), Campus de Mieres, C/Gonzalo Gutiérrez Quirós s/n, Mieres, 33600, Spain
| | - Jose M. Arjona Rodríguez
- Field Crops Program, IRTA (Institute for Food and Agricultural Research and Technology), Rovira Roure, Lleida, 191, 25198, Spain
| | - Mauro Sanna
- Instituto de Recursos Naturales y Ordenación del Territorio (INDUROT), Campus de Mieres, C/Gonzalo Gutiérrez Quirós s/n, Mieres, 33600, Spain
| | - Eduardo Cires
- Departamento de Biología de Organismos y Sistemas, Universidad de Oviedo, Área de Botánica, C/Catedrático Rodrigo Uría s/n, Oviedo, 33071, Spain
- Instituto de Recursos Naturales y Ordenación del Territorio (INDUROT), Campus de Mieres, C/Gonzalo Gutiérrez Quirós s/n, Mieres, 33600, Spain
- Instituto Universitario de Biotecnología de Asturias, Campus El Cristo, Edificio Santiago Gascón 2a planta, Oviedo, 33006, Spain
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Tang G, Chen L, Wang Z, Gao S, Qu Q, Xiong R, Braeckmans K, De Smedt SC, Zhang YS, Huang C. Faithful Fabrication of Biocompatible Multicompartmental Memomicrospheres for Digitally Color-Tunable Barcoding. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2020; 16:e1907586. [PMID: 32390312 DOI: 10.1002/smll.201907586] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/25/2019] [Revised: 03/24/2020] [Accepted: 03/26/2020] [Indexed: 06/11/2023]
Abstract
Barcodes have attracted widespread attention, especially for the multiplexed bioassays and anti-counterfeiting used toward medical and biomedical applications. An enabling gas-shearing approach is presented for generating 10-faced microspherical barcodes with precise control over the properties of each compartment. As such, the color of each compartment could be programmatically adjusted in the 10-faced memomicrospheres by using pregel solutions containing different combinations of fluorescent nanoparticles. During the process, three primary colors (red, green, and blue) are adopted to obtain up to seven merged fluorescent colors for constituting a large amount of coding as well as a magnetic compartment, capable of effective and robust high-throughput information-storage. More importantly, by using the biocompatible sodium alginate to construct the multicolor microspherical barcodes, the proposed technology is likely to advance the fields of food and pharmaceutics anti-counterfeiting. These remarkable properties point to the potential value of gas-shearing in engineering microspherical barcodes for biomedical applications in the future.
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Affiliation(s)
- Guosheng Tang
- Joint Laboratory of Advanced Biomedical Technology (NFU-UGent), College of Chemical Engineering, Nanjing Forestry University (NFU), Nanjing, 210037, P. R. China
- Division of Engineering in Medicine, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Cambridge, MA, 02139, USA
| | - Long Chen
- Joint Laboratory of Advanced Biomedical Technology (NFU-UGent), College of Chemical Engineering, Nanjing Forestry University (NFU), Nanjing, 210037, P. R. China
| | - Zixuan Wang
- Division of Engineering in Medicine, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Cambridge, MA, 02139, USA
| | - Shuting Gao
- Joint Laboratory of Advanced Biomedical Technology (NFU-UGent), College of Chemical Engineering, Nanjing Forestry University (NFU), Nanjing, 210037, P. R. China
| | - Qingli Qu
- Joint Laboratory of Advanced Biomedical Technology (NFU-UGent), College of Chemical Engineering, Nanjing Forestry University (NFU), Nanjing, 210037, P. R. China
| | - Ranhua Xiong
- Laboratory of General Biochemistry and Physical Pharmacy, Faculty of Pharmaceutical Sciences, Ghent University, Ottergemsesteenweg, 460, Ghent, 9000, Belgium
| | - Kevin Braeckmans
- Laboratory of General Biochemistry and Physical Pharmacy, Faculty of Pharmaceutical Sciences, Ghent University, Ottergemsesteenweg, 460, Ghent, 9000, Belgium
| | - Stefaan C De Smedt
- Joint Laboratory of Advanced Biomedical Technology (NFU-UGent), College of Chemical Engineering, Nanjing Forestry University (NFU), Nanjing, 210037, P. R. China
- Laboratory of General Biochemistry and Physical Pharmacy, Faculty of Pharmaceutical Sciences, Ghent University, Ottergemsesteenweg, 460, Ghent, 9000, Belgium
| | - Yu Shrike Zhang
- Division of Engineering in Medicine, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Cambridge, MA, 02139, USA
| | - Chaobo Huang
- Joint Laboratory of Advanced Biomedical Technology (NFU-UGent), College of Chemical Engineering, Nanjing Forestry University (NFU), Nanjing, 210037, P. R. China
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Abstract
INTRODUCTION In Saudi Arabia, Rhazya stricta is a widely used folkloric plant because of its various therapeutic properties. It is sold in herbal markets as a dried powder; however, the absence of visible phenotypic traits in the powder can mask its authenticity. Potential misidentification of this substance threatens consumer health. DNA barcoding could accurately identify this plant regardless of its physical state, however barcoding presents the challenge of variations in marker loci. OBJECTIVES The objective of this work was to assess barcode markers from the chloroplast and nuclear regions to determine their taxonomic accuracy in R. stricta barcoding, and select the best marker for this species that could fulfill the authentication test for its fresh and dried samples. METHOD In this study, we assessed seven barcode markers from the chloroplast (psbA-trnH, matK, rbcL, rpoB, and rpoC1) and nuclear regions (ITS1and ITS2). We compared DNA sequences of R. stricta from 50 fresh locally collected samples and 10 dried ground samples from the herbal market with the database sequences of R. stricta, R. orientalis, and eight other related species as controls. We utilized three methods (BLAST, nearest distance, and neighbor-joining tree) in this analysis. RESULT With the exception of psbA-trnH, all the chloroplast markers determined high similarity with other taxa. However, nuclear ITS2 best distinguished between R. stricta, R. orientalis, and other related species because of its secondary structures, which allowed for more accurate distinctions. A two-locus marker of ITS1 + ITS2 sequences also showed promising results. A two-dimensional image of our proposed marker was generated to more easily handle DNA barcoding applications. CONCLUSION Our study indicates that ITS2 is a cost-effective barcoding marker capable of verifying the authenticity of R. stricta and other medicinal plants in order to protect consumer health.
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Cui X, Li W, Wei J, Qi Y, Li R, Yang Y, Shi Y, Meng X, Mi Y, Huot T, Sun W, Zheng X. Assessing the Identity of Commercial Herbs From a Cambodian Market Using DNA Barcoding. Front Pharmacol 2020; 11:244. [PMID: 32265692 PMCID: PMC7105672 DOI: 10.3389/fphar.2020.00244] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2019] [Accepted: 02/21/2020] [Indexed: 12/21/2022] Open
Abstract
In Cambodia, medicinal plants are often used to treat various illnesses. However, the identities of many medicinal plants remain unknown. In this study, we collected 50 types of traditional Cambodian medicinal plants that could not be identified by their appearance from a domestic market. We utilized the DNA barcoding technique, combined with the literature survey, to trace their identities. In the end, 33 species were identified at the species level and 7 species were identified at the genus level. The ethnopharmacological information of 33 medicinal plants was documented. The DNA barcoding technique is useful in the identification of medicinal plants with no previous information.
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Affiliation(s)
- Xinyun Cui
- Hainan Provincial Key Laboratory of Resources Conservation and Development of Southern Medicine, Hainan Branch of the Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Haikou, China
| | - Weijie Li
- Hainan Provincial Key Laboratory of Resources Conservation and Development of Southern Medicine, Hainan Branch of the Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Haikou, China
| | - Jianhe Wei
- Hainan Provincial Key Laboratory of Resources Conservation and Development of Southern Medicine, Hainan Branch of the Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Haikou, China.,Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Yaodong Qi
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Rongtao Li
- Hainan Provincial Key Laboratory of Resources Conservation and Development of Southern Medicine, Hainan Branch of the Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Haikou, China
| | - Yun Yang
- Hainan Provincial Key Laboratory of Resources Conservation and Development of Southern Medicine, Hainan Branch of the Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Haikou, China
| | - Yuhua Shi
- Key Laboratory of Beijing for Identification and Safety Evaluation of Chinese Medicine, Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
| | - Xiangxiao Meng
- Key Laboratory of Beijing for Identification and Safety Evaluation of Chinese Medicine, Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
| | - Yaolei Mi
- Key Laboratory of Beijing for Identification and Safety Evaluation of Chinese Medicine, Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
| | - Theang Huot
- National Center of Traditional Medicine, Ministry of Health of Cambodia, Phnom Penh, Cambodia
| | - 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, China
| | - Xilong Zheng
- Hainan Provincial Key Laboratory of Resources Conservation and Development of Southern Medicine, Hainan Branch of the Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Haikou, China
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Vu HT, Vu QL, Nguyen TD, Tran N, Nguyen TC, Luu PN, Tran DD, Nguyen TK, Le L. Genetic Diversity and Identification of Vietnamese Paphiopedilum Species Using DNA Sequences. BIOLOGY 2019; 9:E9. [PMID: 31906128 PMCID: PMC7168009 DOI: 10.3390/biology9010009] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/14/2019] [Revised: 12/20/2019] [Accepted: 12/20/2019] [Indexed: 12/23/2022]
Abstract
Paphiopedilum is among the most popular ornamental orchid genera due to its unique slipper flowers and attractive leaf coloration. Most of the Paphiopedilum species are in critical danger due to over-exploitation. They were listed in Appendix I of the Convention on International Trade in Endangered Species of Wild Fauna and Flora, which prevents their being traded across borders. While most Paphiopedilum species are distinctive, owing to their respective flowers, their vegetative features are more similar and undistinguished. Hence, the conservation of these species is challenging, as most traded specimins are immature and non-flowered. An urgent need exists for effective identification methods to prevent further illegal trading of Paphiopedilum species. DNA barcoding is a rapid and sensitive method for species identification, at any developmental stage, using short DNA sequences. In this study, eight loci, i.e., ITS, LEAFY, ACO, matK, trnL, rpoB, rpoC1, and trnH-psbA, were screened for potential barcode sequences on the Vietnamese Paphiopedilum species. In total, 17 out of 22 Paphiopedilum species were well identified. The studied DNA sequences were deposited to GenBank, in which Paphiopedilum dalatense accessions were introduced for the first time. ACO, LEAFY, and trnH-psbA were limited in amplification rate for Paphiopedilum. ITS was the best single barcode. Single ITS could be used along with nucleotide polymorphism characteristics for species discrimination. The combination of ITS + matK was the most efficient identification barcode for Vietnamese Paphiopedilum species. This barcode also succeeded in recognizing misidentified or wrongly-named traded samples. Different bioinformatics programs and algorithms for establishing phylogenetic trees were also compared in the study to propose quick, simple, and effective tools for practical use. It was proved that both the Bayesian Inference method in the MRBAYES program and the neighbor-joining method in the MEGA software met the criteria. Our study provides a barcoding database of Vietnamese Paphiopedilum which may significantly contribute to the control and conservation of these valuable species.
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Affiliation(s)
- Huyen-Trang Vu
- Faculty of Biotechnology, Nguyen-Tat-Thanh University, 298A-300A Nguyen-Tat-Thanh Street, District 04, Hochiminh City 700000, Vietnam; (H.-T.V.); (T.-D.N.); (T.-C.N.)
- Faculty of Biotechnology, International University—Vietnam National University, Linh Trung Ward, Thu Duc District, Hochiminh City 700000, Vietnam;
| | - Quoc-Luan Vu
- Tay Nguyen Institute for Scientific Research, Vietnam Academy of Science and Technology, 116 Xo Viet Nghe Tinh, Ward 7, Da Lat City, Lam Dong province 66000, Vietnam;
| | - Thanh-Diem Nguyen
- Faculty of Biotechnology, Nguyen-Tat-Thanh University, 298A-300A Nguyen-Tat-Thanh Street, District 04, Hochiminh City 700000, Vietnam; (H.-T.V.); (T.-D.N.); (T.-C.N.)
| | - Ngan Tran
- Faculty of Biotechnology, International University—Vietnam National University, Linh Trung Ward, Thu Duc District, Hochiminh City 700000, Vietnam;
| | - Thanh-Cong Nguyen
- Faculty of Biotechnology, Nguyen-Tat-Thanh University, 298A-300A Nguyen-Tat-Thanh Street, District 04, Hochiminh City 700000, Vietnam; (H.-T.V.); (T.-D.N.); (T.-C.N.)
| | - Phuong-Nam Luu
- Faculty of Biotechnology, Nguyen-Tat-Thanh University, 298A-300A Nguyen-Tat-Thanh Street, District 04, Hochiminh City 700000, Vietnam; (H.-T.V.); (T.-D.N.); (T.-C.N.)
| | - Duy-Duong Tran
- Agricultural Genetics Institute, Pham Van Dong Street, Hanoi 100000, Vietnam; (D.-D.T.); (T.-K.N.)
| | - Truong-Khoa Nguyen
- Agricultural Genetics Institute, Pham Van Dong Street, Hanoi 100000, Vietnam; (D.-D.T.); (T.-K.N.)
| | - Ly Le
- Faculty of Biotechnology, International University—Vietnam National University, Linh Trung Ward, Thu Duc District, Hochiminh City 700000, Vietnam;
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Urumarudappa SKJ, Tungphatthong C, Sukrong S. Mitigating the Impact of Admixtures in Thai Herbal Products. Front Pharmacol 2019; 10:1205. [PMID: 31749698 PMCID: PMC6843083 DOI: 10.3389/fphar.2019.01205] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2019] [Accepted: 09/17/2019] [Indexed: 12/29/2022] Open
Abstract
Medicinal plants and their products are extensively used within indigenous healthcare systems in Thailand and several other nations. The international trade of herbal products has a noteworthy impact on the worldwide economy, and the interest in herbal products is expanding in both developing and developed countries. There has been rapid growth in the medicinal plant product market and a broadening consumer base interested in herbal products from Thailand. However, in herbal industries, ingredient substitution and admixture are typical issues wherein species of lower market value are admixed with those of a higher value. The adverse consequences of consuming adulterated drugs are invariably due to the presence of an unintended herb rather than the presence of an intended herb. It has also been argued that admixtures are intentional because of the lack of regulatory policies or centralized tests for product authentication. The consequences of species admixtures can extend from the reduced efficacy of a drug to decreased trade value. This study aims to clarify the nature and extent of species admixtures reported in the Thai herbal trade market and discuss the potential reasons for such adulteration. In the broader context of species admixtures, we strongly propose the establishment of multiple herbal crude drug repositories that can be developed to facilitate the use of comparative identity tests by industry, traders, and researchers to maintain authentic natural health product (NHP) standards and to certify the authenticity of NHPs. The proposition of the establishment of centralized testing (CT) could be a promising initiative in Thailand for the development of science and technology, and the herbal medicines produced as a result of CT could be dispensed as prescription drugs based on disease consideration instead of as health foods or nutraceuticals.
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Affiliation(s)
- Santhosh Kumar J Urumarudappa
- Research Unit of DNA Barcoding of Thai Medicinal Plants, Department of Pharmacognosy and Pharmaceutical Botany, Faculty of Pharmaceutical Sciences, Chulalongkorn University, Bangkok, Thailand
| | - Chayapol Tungphatthong
- Research Unit of DNA Barcoding of Thai Medicinal Plants, Department of Pharmacognosy and Pharmaceutical Botany, Faculty of Pharmaceutical Sciences, Chulalongkorn University, Bangkok, Thailand
| | - Suchada Sukrong
- Research Unit of DNA Barcoding of Thai Medicinal Plants, Department of Pharmacognosy and Pharmaceutical Botany, Faculty of Pharmaceutical Sciences, Chulalongkorn University, Bangkok, Thailand
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Mohajeri N, Imani M, Akbarzadeh A, Sadighi A, Zarghami N. An update on advances in new developing DNA conjugation diagnostics and ultra-resolution imaging technologies: Possible applications in medical and biotechnological utilities. Biosens Bioelectron 2019; 144:111633. [DOI: 10.1016/j.bios.2019.111633] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2019] [Revised: 08/21/2019] [Accepted: 08/23/2019] [Indexed: 12/15/2022]
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Frigerio J, Agostinetto G, Sandionigi A, Mezzasalma V, Berterame NM, Casiraghi M, Labra M, Galimberti A. The hidden 'plant side' of insect novel foods: A DNA-based assessment. Food Res Int 2019; 128:108751. [PMID: 31955731 DOI: 10.1016/j.foodres.2019.108751] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2019] [Revised: 10/02/2019] [Accepted: 10/04/2019] [Indexed: 11/17/2022]
Abstract
In the context of novel foods, a category for which the market demand is increasing worldwide, the consumption of edible insects and related insect-based products is expected to grow in the next years. Insects represent an important source of energy for the human diet but there is a lack of scientific knowledge about their processing to ensure safe food items to the consumer. In this study we adopted a combined DNA-based approach to verify the identity of the declared species in five categories of commercial insect-based products (mt COI DNA barcoding) and to characterize plant declared ingredients or contaminants (nu ITS2 DNA metabarcoding) with particular attention to putative elements of allergenic concern belonging, for example to the insect rearing substrate. Moreover, the same approach has been used to assess its sensitivity to cases of contamination and counterfeits to insect flour with low cost (and potentially allergenic) vegetable flours like wheat and soybean. Results show the success of insect DNA barcoding authentication even for highly processed products. Furthermore, the DNA metabarcoding analysis revealed a high efficacy as a screening method to identify both plant ingredients and vegetal traces belonging to insect farming or possible adulteration events, also acting as an early warning strategy for the occurrence of allergens of human concern. This approach could support the development of new risk assessment procedures for novel foods by regulatory authorities to ensure their quality, safety, and acceptance which will become more required in order to face the challenge of feeding the world population in the next decades.
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Affiliation(s)
| | - Giulia Agostinetto
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Piazza della Scienza 2, I-20126 Milano, Italy
| | - Anna Sandionigi
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Piazza della Scienza 2, I-20126 Milano, Italy
| | | | - Nadia Maria Berterame
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Piazza della Scienza 2, I-20126 Milano, Italy
| | - Maurizio Casiraghi
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Piazza della Scienza 2, I-20126 Milano, Italy
| | - Massimo Labra
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Piazza della Scienza 2, I-20126 Milano, Italy
| | - Andrea Galimberti
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Piazza della Scienza 2, I-20126 Milano, Italy.
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He T, Jiao L, Wiedenhoeft AC, Yin Y. Machine learning approaches outperform distance- and tree-based methods for DNA barcoding of Pterocarpus wood. PLANTA 2019; 249:1617-1625. [PMID: 30825008 DOI: 10.1007/s00425-019-03116-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2018] [Accepted: 02/20/2019] [Indexed: 05/10/2023]
Abstract
Machine-learning approaches (MLAs) for DNA barcoding outperform distance- and tree-based methods on identification accuracy and cost-effectiveness to arrive at species-level identification of wood. DNA barcoding is a promising tool to combat illegal logging and associated trade, and the development of reliable and efficient analytical methods is essential for its extensive application in the trade of wood and in the forensics of natural materials more broadly. In this study, 120 DNA sequences of four barcodes (ITS2, matK, ndhF-rpl32, and rbcL) generated in our previous study and 85 downloaded from National Center for Biotechnology Information (NCBI) were collected to establish a reference data set for six commercial Pterocarpus woods. MLAs (BLOG, BP-neural network, SMO and J48) were compared with distance- (TaxonDNA) and tree-based (NJ tree) methods based on identification accuracy and cost-effectiveness across these six species, and also were applied to discriminate the CITES-listed species Pterocarpus santalinus from its anatomically similar species P. tinctorius for forensic identification. MLAs provided higher identification accuracy (30.8-100%) than distance- (15.1-97.4%) and tree-based methods (11.1-87.5%), with SMO performing the best among the machine learning classifiers. The two-locus combination ITS2 + matK when using SMO classifier exhibited the highest resolution (100%) with the fewest barcodes for discriminating the six Pterocarpus species. The CITES-listed species P. santalinus was discriminated successfully from P. tinctorius using MLAs with a single barcode, ndhF-rpl32. This study shows that MLAs provided higher identification accuracy and cost-effectiveness for forensic application over other analytical methods in DNA barcoding of Pterocarpus wood.
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Affiliation(s)
- Tuo He
- Department of Wood Anatomy and Utilization, Chinese Research Institute of Wood Industry, Chinese Academy of Forestry, Beijing, 100091, China
- Wood Collections (WOODPEDIA), Chinese Academy of Forestry, Beijing, 100091, China
- Forest Products Laboratory, Center for Wood Anatomy Research, USDA Forest Service, Madison, WI, 53726, USA
- Department of Botany, University of Wisconsin, Madison, WI, 53706, USA
| | - Lichao Jiao
- Department of Wood Anatomy and Utilization, Chinese Research Institute of Wood Industry, Chinese Academy of Forestry, Beijing, 100091, China
- Wood Collections (WOODPEDIA), Chinese Academy of Forestry, Beijing, 100091, China
| | - Alex C Wiedenhoeft
- Forest Products Laboratory, Center for Wood Anatomy Research, USDA Forest Service, Madison, WI, 53726, USA
- Department of Botany, University of Wisconsin, Madison, WI, 53706, USA
- Department of Forestry and National Resources, Purdue University, West Lafayette, IN, 47907, USA
- Ciências Biológicas (Botânica), Univesidade Estadual Paulista, Botucatu, São Paulo, Brazil
| | - Yafang Yin
- Department of Wood Anatomy and Utilization, Chinese Research Institute of Wood Industry, Chinese Academy of Forestry, Beijing, 100091, China.
- Wood Collections (WOODPEDIA), Chinese Academy of Forestry, Beijing, 100091, China.
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Gong L, Qiu XH, Huang J, Xu W, Bai JQ, Zhang J, Su H, Xu CM, Huang ZH. Constructing a DNA barcode reference library for southern herbs in China: A resource for authentication of southern Chinese medicine. PLoS One 2018; 13:e0201240. [PMID: 30044868 PMCID: PMC6059470 DOI: 10.1371/journal.pone.0201240] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2018] [Accepted: 07/11/2018] [Indexed: 11/19/2022] Open
Abstract
Southern Chinese Medicine (SCM) is an important sect of Traditional Chinese Medicine (TCM) with its own special cultural style. Species identification is essential for TCM quality control because authentic herbs are possibly substituted with adulterants that would threaten the health of the public or even cause death. Here, we provided the first local reference DNA barcode library based on the second internal transcribed spacer (ITS2) for the molecular identification of SCM. A total of 1512 specimens of southern herbs representing 359 species were collected under the instructions and identification of taxonomic experts. Genomic DNA was extracted, and the PCR reaction proceeded according to standard procedures. After Sanger sequencing, sequence assembling and annotation, a reliable ITS2 barcode library with 1276 sequences from 309 species of Southern herbs was constructed. The PCR efficiency of the whole samples was 84.39%. Characteristics of the ITS2 barcode were analyzed, including sequence lengths and GC contents in different taxa. Neighbor-joining trees based on Kimura 2-Parameter (K2P) genetic distances showed a 67.56% successful rate of species identification with ITS2 barcode. In addition, 96.57% of species could be successfully identified at the genus level by the BLAST method. Eleven plant species were discovered to be cryptic. In addition, we found that there is an incorrect sequence existing in the public database, making a reliable local DNA barcode reference more meaningful. ITS2 barcodes exhibit advantages in TCM identification. This DNA barcode reference library could be used in Southern Chinese Medicine quality control, thus contributing to protecting public health.
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Affiliation(s)
- Lu Gong
- Guangdong Provincial Hospital of Chinese Medicine, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, and China Academy of Chinese Medical Sciences Guangdong Branch, China Academy of Chinese Medical Sciences, Guangzhou, China
| | - Xiao Hui Qiu
- Guangdong Provincial Hospital of Chinese Medicine, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, and China Academy of Chinese Medical Sciences Guangdong Branch, China Academy of Chinese Medical Sciences, Guangzhou, China
- Guangdong Provincial Key Laboratory of Clinical Research on Traditional Chinese Medicine Syndrome, Guangzhou, China
| | - Juan Huang
- Guangdong Provincial Hospital of Chinese Medicine, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, and China Academy of Chinese Medical Sciences Guangdong Branch, China Academy of Chinese Medical Sciences, Guangzhou, China
| | - Wen Xu
- Guangdong Provincial Hospital of Chinese Medicine, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, and China Academy of Chinese Medical Sciences Guangdong Branch, China Academy of Chinese Medical Sciences, Guangzhou, China
| | - Jun Qi Bai
- Guangdong Provincial Hospital of Chinese Medicine, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, and China Academy of Chinese Medical Sciences Guangdong Branch, China Academy of Chinese Medical Sciences, Guangzhou, China
| | - Jing Zhang
- Guangdong Provincial Hospital of Chinese Medicine, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, and China Academy of Chinese Medical Sciences Guangdong Branch, China Academy of Chinese Medical Sciences, Guangzhou, China
| | - He Su
- Guangdong Provincial Hospital of Chinese Medicine, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, and China Academy of Chinese Medical Sciences Guangdong Branch, China Academy of Chinese Medical Sciences, Guangzhou, China
| | - Chu Mei Xu
- Guangdong Provincial Hospital of Chinese Medicine, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, and China Academy of Chinese Medical Sciences Guangdong Branch, China Academy of Chinese Medical Sciences, Guangzhou, China
| | - Zhi Hai Huang
- Guangdong Provincial Hospital of Chinese Medicine, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, and China Academy of Chinese Medical Sciences Guangdong Branch, China Academy of Chinese Medical Sciences, Guangzhou, China
- * E-mail:
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