Dataset Information

Identification of Acorus gramineus, A. calamus, and A. tatarinowii using sequence characterized amplified regions (SCAR) primers for monitoring of Acori graminei rhizoma in Korean markets.

ABSTRACT: Acori Graminei Rhizoma (AGR), widely used in traditional herbal medicine, is composed of the roots of Acorus gramineus Soland. The family Acoraceae includes A. gramineus, A. calamus, and A. tatarinowii, among others. We compared genomic DNA sequences of AGR for polymorphisms. The sequences of the internal transcribed spacer (ITS) regions of nuclear ribosomal DNA, the rbcL region of chloroplast DNA from A. gramineus, A. calamus, and A. tatarinowii were compared. We designed primers specific to the ITS region of A. calamus and A. tatarinowii (A. cataF4/R4) and the internal primer Araceae Radix (IntAcoF2/R4). Random amplification of polymorphic DNA (RAPD) analysis showed a difference in A. calamus using the UBC 681 primer. A specific primer (Aca681-F/R) amplified 138 base pairs of A. calamus. The primers designed for this study (A. cataF4/R4, Aca681-F/R, and IntAcoF2/R2) can be used for multiplex PCR to distinguish the three species of Acorus. An allelic discrimination assay was conducted using commercially available AGR. We used sequence-characterized amplified region (SCAR) markers to confirm whether AGR purchased at a market was A. gramineus. Our study indicated the SCAR markers could be used as molecular evidence to distinguish Araceae Radix.

SUBMITTER: Ryuk JA

PROVIDER: S-EPMC4211751 | biostudies-literature | 2014

REPOSITORIES: biostudies-literature

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Identification of Acorus gramineus, A. calamus, and A. tatarinowii using sequence characterized amplified regions (SCAR) primers for monitoring of Acori graminei rhizoma in Korean markets.

Ryuk Jin Ah JA Kim Young Seon YS Lee Hye Won HW Ko Byoung Seob BS

International journal of clinical and experimental medicine 20140915 9

Acori Graminei Rhizoma (AGR), widely used in traditional herbal medicine, is composed of the roots of Acorus gramineus Soland. The family Acoraceae includes A. gramineus, A. calamus, and A. tatarinowii, among others. We compared genomic DNA sequences of AGR for polymorphisms. The sequences of the internal transcribed spacer (ITS) regions of nuclear ribosomal DNA, the rbcL region of chloroplast DNA from A. gramineus, A. calamus, and A. tatarinowii were compared. We designed primers specific to th ...[more]

PMID: 25356101

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Project description:Explore Acori Tatarinowii Rhizoma (ATR) and Polygalae Radix (PR) mechanisms in Alzheimer's disease (AD) treatment through network pharmacology. ATR-PR was investigated in the Traditional Chinese Medicine Systems Pharmacology (TCMSP) database, Batman, and Traditional Chinese Medicines Integrated Database (TCMID) to gather information on its chemical components and target proteins. Target genes associated with AD were retrieved from the GeneCards and National Center for Biotechnology Information (NCBI) databases. The integration of these datasets with potential targets facilitated the construction of an AD and ATR-PR protein-protein interaction (PPI) network using the STRING database. The resulting network identified the core active ingredients and main targets of ATR-PR in AD treatment. Cluster analysis of the PPI network was performed using Cytoscape 3.7.1. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses were conducted using the Metascape database. Molecular docking simulations revealed potential interactions between the main active ingredients and core targets. Our analysis identified 8 putative components and 455 targets of ATR-PR. We systematically searched for 1306 genes associated with AD, conducted Venn diagram analysis resulting in 156 common targets, and constructed a PPI network with 57 key targets. GO functional analysis highlighted the primary biological processes associated with oxidative stress. KEGG pathway enrichment analysis revealed the involvement of 64 signaling pathways, with the PI3K/Akt signaling pathway playing a key role. Molecular docking analysis indicated a high affinity between the potential targets of ATR-PR and the main compounds of AD. This study sheds light on the complex network of interactions involving ATR-PR in the context of AD. The identified targets, pathways, and interactions provide a foundation for understanding the potential therapeutic mechanisms. The involvement of oxidative stress-related processes and the crucial role of the PI3K/Akt signaling pathway suggest avenues for targeted therapeutic interventions in Alzheimer's disease treatment. Our proposition of the combined use of ATR-PR has emerged as a potential treatment strategy for AD, supported by a network pharmacology approach. This framework provides a robust foundation for future clinical applications and experimental research in the pursuit of effective Alzheimer's disease treatments.

Project description:BACKGROUND:Acori Tatarinowii Rhizoma (ATR; rhizome of Acorus tatarinowii Schott) (Shi Chang Pu) is widely used in Chinese medicine (CM) to resuscitate, calm the mind, resolve shi (dampness) and harmonize the wei (stomach). Seven different species have been identified as belonging to the genus Acorus, all of which can be found in China. However, it can be difficult to distinguish the different species of Acorus because of their morphological similarities. The aim of this study was to authenticate Acorus species using macroscopic and microscopic techniques, chemical analysis and DNA authentication and to compare the resolution power and reliability of these different methods. METHODS:Four batches of ATR, Acori Graminei Rhizoma (AGR), Acori Calami Rhizoma (ACR) and Anemones Altaicae Rhizoma (AAR) (totaling 16 samples) were collected from Hong Kong and mainland China. The major characteristic features of these Acorus species were identified by macroscopic and microscopic examination. The identified samples were also analyzed by UHPLC analysis. Principal component analysis (PCA) and hierarchal clustering analysis (HCA) on UHPLC results were used to differentiate between the samples. An internal transcribed spacer (ITS) was selected as a molecular probe and a modified DNA extraction method was developed to obtain trace amounts of DNA from the different Acorus species. All extracted DNA sequences were edited by Bioedit and aligned with the ClustalW. And the sequence distances were calculated using the Maximum Parsimony method. RESULTS:Macroscopic and microscopic analyses allowed for AAR to be readily distinguished from ATR, AGR and ACR. However, it was difficult to distinguish between ATR, AGR and ACR because of their similar morphological features. Chemical profiling revealed that ?- and ?-asarone were only found in the ATR, AGR and ACR samples, but not in the AAR samples. Furthermore, PCA and HCA allowed for the differentiation of these three species based on their asarone contents. Morphological authentication and chemical profiling allowed for the partial differentiation of ATR, AGR ACR and AAR. DNA analysis was the only method capable of accurately differentiating between all four species. CONCLUSION:DNA authentication exhibited higher resolution power and reliability than conventional morphological identification and UHPLC in differentiating between different Acorus species.

Dataset Information

Identification of Acorus gramineus, A. calamus, and A. tatarinowii using sequence characterized amplified regions (SCAR) primers for monitoring of Acori graminei rhizoma in Korean markets.

Publications

Identification of Acorus gramineus, A. calamus, and A. tatarinowii using sequence characterized amplified regions (SCAR) primers for monitoring of Acori graminei rhizoma in Korean markets.

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