DNA metabarcoding analysis of fungal community on surface of four root herbs / 中草药·英文版

OBJECTIVE@#Angelicae Sinensis Radix (ASR, Danggui in Chinese), Cistanches Herba (CH, Roucongrong in Chinese), Ginseng Radix et Rhizoma (PG, Renshen in Chinese), and Panacis Quinquefolii Radix (PQ, Xiyangshen in Chinese), widely used as medicine and dietary supplement around the world, are susceptible to fungal and mycotoxin contamination. In this study, we aim to analyze their fungal community by DNA metabarcoding.@*METHODS@#A total of 12 root samples were collected from three main production areas in China. The samples were divided into four groups based on herb species, including ASR, CH, PG, and PQ groups. The fungal community on the surface of four root groups was investigated through DNA metabarcoding via targeting the internal transcribed spacer 2 region (ITS2).@*RESULTS@#All the 12 samples were detected with fungal contamination. Rhizopus (13.04%-74.03%), Aspergillus (1.76%-23.92%), and Fusarium (0.26%-15.27%) were the predominant genera. Ten important fungi were identified at the species level, including two potential toxigenic fungi (Penicillium citrinum and P. oxalicum) and eight human pathogenic fungi (Alternaria infectoria, Candida sake, Hyphopichia burtonii, Malassezia globosa, M. restricta, Rhizopus arrhizus, Rhodotorula mucilaginosa, and Ochroconis tshawytschae). Fungal community in ASR and CH groups was significantly different from other groups, while fungal community in PG and PQ groups was relatively similar.@*CONCLUSION@#DNA metabarcoding revealed the fungal community in four important root herbs. This study provided an important reference for preventing root herbs against fungal and mycotoxin contamination.

Discussion on the botanical origin of isatidis radix and Isatidis folium based on DNA barcoding / 药学学报

This paper aimed to investigate the botanical origins of Isatidis Radix and Isatidis Folium, and clarify the confusion of its classification. The second internal transcribed spacer (ITS2) of ribosomal DNA, the chloroplast matK gene of 22 samples from some major production areas were amplified and sequenced. Sequence assembly and consensus sequence generation were performed using the CodonCode Aligner. Phylogenetic study was performed using MEGA 4.0 software in accordance with the Kimura 2-Parameter (K2P) model, and the phylogenetic tree was constructed using the neighbor-joining methods. The results showed that the length of ITS2 sequence of the botanical origins of Isatidis Radix and Isatidis Folium was 191 bp. The sequence showed that some samples had several SNP sites, and some samples had heterozygosis sites. In the NJ tree, based on ITS2 sequence, the studied samples were separated into two groups, and one of them was gathered with Isatis tinctoria L. The studied samples also were divided into two groups obviously based on the chloroplast matK gene. In conclusion, our results support that the botanical origins of Isatidis Radix and Isatidis Folium are Isatis indigotica Fortune, and Isatis indigotica and Isatis tinctoria are two distinct species. This study doesn't support the opinion about the combination of these two species in Flora of China.

Identification of Codonopsis Radix and Its Adulterants Using the ITS/ITS2 Barcodes / 世界科学技术-中医药现代化

The ITS/ITS2 barcodes were used to simply and effectively identify Codonopsis Radix and its adulter-ants. In this study, ITS (internal transcribed spacer of unclear ribosomal DNA) regions were amplified using PCR (polymerase chain reaction) from thirty-three samples of Codonopsis Radix and ITS2 regions were obtained from the ITS sequences using the hidden Markov model (HMMer)-based annotation methods. The sequences of ITS/ITS2 regions were aligned and the genetic distances were computed by MEGA5.0. Species identification efficiency of ITS/ITS2 sequences were evaluated using BLAST1 and nearest distance methods. The results indicated that The sequences lengths of ITS regions of Codonopsis Radix were 654-655 bp, and the lengths of ITS2 regions were 239 bp. The intraspecific genetic distances among Codonopsis Radix were obviously lower than the interspecific genetic distance between Codonopsis Radix and its adulterants. Therefore, ITS/ITS2 regions can stably and accu-rately distinguish Codonopsis Radix and its adulterants.

Advances of studies on new technology and method for identifying traditional Chinese medicinal materials / 中国中药杂志

In this review, the authors summarized the new technologies and methods for identifying traditional Chinese medicinal materials, including molecular identification, chemical identification, morphological identification, microscopic identification and identification based on biological effects. The authors introduced the principle, characteristics, application and prospect on each new technology or method and compared their advantages and disadvantages. In general, new methods make the result more objective and accurate. DNA barcoding technique and spectroscopy identification have their owner obvious strongpoint in universality and digitalization. In the near future, the two techniques are promising to be the main trend for identifying traditional Chinese medicinal materials. The identification techniques based on microscopy, liquid chromatography, PCR, biological effects and DNA chip will be indispensable supplements. However, the bionic identification technology is just placed in the developing stage at present.

Identification of Junci Medulla using DNA barcoding technique / 中国中药杂志

<p><b>OBJECTIVE</b>To identify Junci Medulla using the ITS2 barcode.</p><p><b>METHOD</b>The ITS2 regions of Juncus effuses and its closely related species were PCR amplified and sequenced. Sequence assembly and consensus sequence generation were performed using the CodonCode Aligner. The Kimura 2-Parameter (K2P) distances were calculated using software MEGA 5.0. Identification analyses were performed using BLAST1, Nearest Distance, PWG Distance and neighbor-joining (NJ) methods.</p><p><b>RESULT</b>The intra-specific genetic distances of J. effuses were ranged from 0 to 0.005, which were far lower than inter-specific genetic distances between J. effuses and its closely related species (0.215-0.614). All the four methods showed that ITS2 could discriminate J. effuses from its closely related species correctly.</p><p><b>CONCLUSION</b>The ITS2 region is an efficient barcode for authentication of Junci Medulla, and our study further confirmed the ability of ITS2 to identify traditional Chinese medicinal materials.</p>

Applying DNA barcoding technique to identify menthae haplocalycis herba / 中国中药杂志

<p><b>OBJECTIVE</b>To identify Menthae Haplocalycis Herba and its closely related species using DNA barcoding technique.</p><p><b>METHOD</b>Total genomic DNA was isolated from Mentha canadensis and its closely related species. Nuclear DNA ITS2 sequences were amplified, and purified PCR products were sequenced. Sequence assembly and consensus sequence generation were performed using the CodonCode Aligner V3.0. The Kimura 2-Parameter (K2P) distances were calculated using software MEGA 5.0. Identification analyses were performed using BLAST1, Nearest Distance and neighbor-joining (NJ) methods.</p><p><b>RESULT</b>The intra-specific genetic distances of M. canadensis were ranged from 0 to 0.006, which were lower than inter-specific genetic distances between M. canadensis and its closely related species (0.071-0.231). All the three methods showed that ITS2 could discriminate M. canadensis from its closely related species correctly.</p><p><b>CONCLUSION</b>The ITS2 region is an efficient barcode for identification of Menthae Haplocalycis Herba, which provides a scientific basis for fast and accurate identification of the herb.</p>

Using ITS2 barcode to identify ephedrae herba / 中国中药杂志

<p><b>OBJECTIVE</b>To identify Ephedrae Herba using the ITS2 barcode and to secure its quality and safety in medication.</p><p><b>METHOD</b>Total genomic DNA was isolated from Ephedrae Herba and its closely related species. Nuclear DNA ITS2 sequences were amplified, and purified PCR products were sequenced. Sequence assembly and consensus sequence generation were performed using the CodonCode Aligner. The Kimura 2-Parameter (K2P) distances were calculated using software MEGA 5.0. Identification analyses were performed using BLAST1, Nearest Distance and neighbor-joining (NJ) methods.</p><p><b>RESULT</b>The intra-specific genetic distances of Ephedrae Herba were ranged from 0 to 0.002. The inter-specific genetic distances between Ephedrae Herba and its closely related species were ranged from 0.004 to 0.034. All the three methods showed that ITS2 could discriminate Ephedrae Herba from its closely related species correctly.</p><p><b>CONCLUSION</b>The ITS2 region is suitable to be used for authentication of Ephedrae Herba, and our study further confirmed the effectiveness of ITS2 to identify traditional Chinese medicinal materials.</p>

Review on the research progress of the role of miRNAs in gastric cancer / 生物医学工程学杂志

MicroRNAs, known as small noncoding MiRNAs, 19 to 24 nt in length, are important gene regulators and recognized as key players in carcinogenesis. The mechanism lies in that the MiRNAs can conjugate with their targeted mRNA and then lead to the targeted mRNA degradation or repress their translation. Bioinformatic analysis indicates that each MiRNA can regulate hundreds of gene targets and could serve functionally as "oncogenes" or "tumor suppressor genes", and therefore regulate multiple cellular processes relevant to carcinogenesis and cancer progression. Up to now, there have been a lot of studies about the MiRNAs which may play an important role in stomach neoplasms. The purpose of this paper is to have a review of the present studies on the MiRNAs related to stomach neoplasms, in order set basis for further study and their clinical application.

Relationship between DNA Barcoding and Chemical Classification of Salvia Medicinal Herbs / 中草药·英文版

Objective To make the identification of medicinal herbs in Salvia L. quickly and accurately. Methods In this work,DNA barcoding and chemical fingerprint were compared for the identification of herbs in Salvia L. First, the nucleotide sequences of the internal transcribed spacer region two amplified from 48 medicinal plants in Salvia L., and three other groups of medicinal plants in Lamiaceae were sequenced. A molecular phylogeny was constructed using the minimum evolution and maximum parsimony methods according to their sequence diversity. Second, the water-solution bioactive components and lipid soluble components were tested by HPLC. Then a chemical phylogeny was built using HPLC fingerprint data. Comparing the molecular and chemical phylogenetic trees revealed many similarities. Results DNA barcoding was sequencing based and could therefore provide more accurate results within a shorter time especially in large-scale studies. Conclusion The results show that ITS2 region is a novel DNA barcode for the authentication of the species in Salvia L. This is the first work to show the relationship between DNA barcoding and chemical components.