Analysis of codon usage patterns in Bupleurum falcatum chloroplast genome / 中草药·英文版

OBJECTIVE@#In order to distinguish the traditional Chinese medicine Bupleurum falcatum and its adulterants effectively and develop a better understanding of the factors affecting synonymous codon usage, codon usage patterns of chloroplast genome, we determine the complete chloroplast (cp) genome of B. falcatum and clarify the main factors that influence codon usage patterns of 78 genes in B. falcatum chloroplast genome.@*METHODS@#The total genomic DNA of fresh leaves from a single individual of B. falcatum was extracted with EASYspin plus Total DNA Isolation Kit and 2 μg genome DNA was sequenced using Illumina Hiseq 2500 Sequencing Platform. The cp genome of B. falcatum was reconstructed with MITObim v1.8 and annotated in the program CPGAVAS2 with default parameters. Python script and Codon W were used to calculate the codon usage bias parameters.@*RESULTS@#The full length of B. falcatum cp genome was 155 851 bp, 132 different genes were annotated in this cp genome containing 80 protein-coding genes, 30 tRNA genes, and four rRNA genes. The codon usage models tended to use A/T-ending codons. The neutrality plot, ENC plot, PR2-Bias plot and correspondence analysis showed that both compositional constraint under selection and mutation could affect the codon usage models in B. falcatum cp genome. Furthermore, three optimal codons were identified and most of these three optimal codons ended with G/U.@*CONCLUSION@#The cp genome of B. falcatum has been characterized and the codon usage bias in B. falcatum cp genome is influenced by natural selection, mutation pressure and nucleotide composition. The results will provide much more barcode information for species discrimination and lay a foundation for future research on codon optimization of exogenous genes, genetic engineering and molecular evolution in B. falcatum.

Exploration of the Mechanism about Couplet Medicine of Bupleurum falcatum-Scutellaria baicalensis Intervening in Podocyte Lesion Based on Network Pharmacology / 中国药房

OBJECTIVE：To predict the pot ential target and mechanism of Xintong Changluo Method carrier-Compund Shensu Ⅱ couplet medicine of Bupleurum falcatum-Scutellaria baicalensis intervening in podocyte lesion ，and to provide reference for the development of sequential clinical and basic research of Xintong Changluo Method in the prevention and treatment of podocyte lesion. METHODS ：Based on TCMSP database ，chemical components and target protein of B. falcatum and S. baicalensis were retrieved，and Cytoscape 3.2.1 software was used to draw a “TCM-component-target”network. The targets related to podocyte lesion were searched from OMIM database ，DrugBank database and Digsee online text ，and the intersection genes of above targets and“B. falcatum -S. baicalensis ”target were obtained by Venny 2.1.0 online mapping tool. The protein-protein interaction （PPI） network was constructed by STRING database ，and the core targets were obtained by topology analysis of the network by using CytoNCA plug-in Cytospace 3.2.1 software. With the help of DAVID database ，the fu nction of Gene Ontology （GO）was annotated and KEGG pathway was enriched ；and the enrichment results were visualized through OmicShare Tools online mapping platform. RESULTS ：Based on retrieval results of TCMSP database，44 active components were obtained ，involving 13 com of B. falcatum and 32 of S. baicalensis ； stigmasterol is common component of B. falcatum and S. baicalensis Quercetin，kaempferol and wogonin were the compounds withmain potential targets. T he target proteins wi th high node degree were prostaglandin endoperoxide synthase 2（PTGS2），PTGS1， nuclear receptor coactivator 2 and heat shock protein 90α，which were associated with 37，30，25 and 25 active components respectively. Twenty genes were obtained from the interaction between “B. falcatum -S. baicalensis ”and podocyte lesion related targets，including PTGS2，VEGFA，MMP9，TNF and IL6. PPI network diagram of the above intersection genes contained 20 nodes and 110 lines，with MMP9，VEGFA，IL6 and other genes at the core. The results of GO analysis showed that a total of 154 biological information items were obtained （P＜0.05），including 139 biological process items ，8 cell composition items and 7 molecular function items. Among them ，biological processes mainly involved in the positive regulation of NO biosynthesis process ， inflammatory response ，immune response. Cell composition mainly involved in extracellular space ，extracellular region ，external side of plasma membrane ，etc.，and molecular function mainly involved in protein binding ，cytokine activity ，growth factor activity，etc. At the same time ，47 KEGG pathways were obtained （P＜0.05），mainly including cytokine-cytokine receptor interaction，rheumatoid arthritis ，malaria，cancer signaling pathways. CONCLUSIONS ：The active components of Compund Shensu Ⅱ couplet medicine of “B. falcatum -S. baicalensis ”may act on MMP9，VEGFA，IL6，TNF and other targets through cytokine-cytokine receptor interaction ，rheumatoid arthritis ，malaria，cancer signal pathway ，so as to play its intervention effect on podocyte lesion.

Genome survey analysis and SSR loci mining of Bupleurum falcatum / 中国中药杂志

Buplewrum falcatum is a traditional Chinese medicine,which is mainly used for the treatment of cold and liver protection. B. falcatum is dominantly cultivated in Japan as well as planted in China,Korea and other countries and regions. In order to determine the appropriate sequencing strategy,the genome survey before large-scale genome sequencing is needed. This survey can provide information about the size and complexity of the whole genome of the target species. In the present study,the next generation sequencing technology( Illumina Hiseq 2000) was used to analyze the genome size and complexity of B. falcatum. In addition,SSR loci were analyzed from the sequenced data. Primer 3 was used to design specific primers and 33 pairs of primers were randomly selected for PCR with template DNA of B. falcatum,and the PCR system and optimal annealing temperature were screened. A total of 288. 64 G genome sequence data was obtained,and the estimated genome size of B. falcatum was 2 119. 58 Mb. The measured genome data depth was138×; the rate of heterozygosity was 1. 84%; and the ratio of repeat sequence was 83. 89%. It is speculated that the genome of B. falcatum is complex. The preliminary assembly was performed with K-mer = 41,and the contig N50 was 224 bp,the total length 896. 97 Mb,the scaffold N50 313 bp,and the total length was 922. 67 Mb. A total of 91 377 SSR sequences were detected in the sequenced genome data which were distributed in 70 809 unigenes.The main type is dinucleotide repeats,with 49 680 sequences,accounting for70. 16%. Among the 33 pairs of primers randomly synthesized according to the obtained SSR sequences,21 pairs were successfully amplifying the target sequences. The results will be helpful for later large scale genome sequencing and SSR molecular markers development for germplasm identification and trait mapping.

Chemical Constituents from the Aerial Parts of Bupleurum falcatum L. and Biological Evidences

In this study, phytochemical investigation on the aerial parts of Bupleurum falcatum resulted in the isolation of fourteen compounds including three quinic acid derivatives (1 - 3), five flavonoids (4 - 8), three monoterpene glycosides (9 - 11), and three saikosaponins (12 - 14). Compound 1 was first isolated from nature and unambiguously determined to be 3-O-feruloyl 5-O-caffeoylquinic acid on the basis of the extensive spectroscopic evidence. Biological testing revealed that saikosaponin A (12) and saikosaponin D (13) showed moderate antiproliferative effects on HL-60 and HepG2 cancer cell lines.

<b>Study on Conditions to Increase the Domestic Production of Herbal Materials by Changing Crops Production from Tobacco </b> / 日本東洋医学雑誌

Herb supplies can become unstable because of climate change and the economic development of herb exporters. In this paper, in order to increase the self-sufficiency of herbal resources we examined the possibil ity of changing to herb crop production from tobacco, for which demand is declining. Firstly, we considered demand, quality and the price of raw herb materials to make recommendations for corrections, and selected <i>Angelica </i>(A. ) <i>acutiloba </i>and <i>Bupleurum </i>(B. ) <i>falcatum </i>Linne. Next, we compared the profitability of tobacco and the herbs. Profit margins for <i>A. acutiloba </i>were less than for tobacco. It was thought that the profitability of <i>A. acutiloba </i>could become equivalent to tobacco if an adjustment subsidy were provided. The self-sufficiency rate for <i>A. acutiloba </i>would be one hundred percent with 35 million yen in every year. Although the profitabil ity of <i>B. falcatum </i>has exceeded tobacco, its selling price was about 3 times that of imports, while the price of medical <i>B. falcatum </i>was lower than its selling price. It was thought that the price competitiveness problem of <i>B. falcatum </i>can be covered if a production subsidy is provided, and to reach a 50 percent B. falcatum self sufficiency rate with 660 million yen per year.