Ganoderma lucidum is a widely used medicinal macrofungus in traditional Chinese medicine that creates a diverse set of bioactive compounds. Here we report its 43.3-Mb genome, encoding 16,113 ...predicted genes, obtained using next-generation sequencing and optical mapping approaches. The sequence analysis reveals an impressive array of genes encoding cytochrome P450s (CYPs), transporters and regulatory proteins that cooperate in secondary metabolism. The genome also encodes one of the richest sets of wood degradation enzymes among all of the sequenced basidiomycetes. In all, 24 physical CYP gene clusters are identified. Moreover, 78 CYP genes are coexpressed with lanosterol synthase, and 16 of these show high similarity to fungal CYPs that specifically hydroxylate testosterone, suggesting their possible roles in triterpenoid biosynthesis. The elucidation of the G. lucidum genome makes this organism a potential model system for the study of secondary metabolic pathways and their regulation in medicinal fungi.
Internal transcribed spacer of nuclear ribosomal DNA (nrDNA) is already one of the most popular phylogenetic and DNA barcoding markers. However, the existence of its multiple copies has complicated ...such usage and a detailed characterization of intra-genomic variations is critical to address such concerns.
In this study, we used sequence-tagged pyrosequencing and genome-wide analyses to characterize intra-genomic variations of internal transcribed spacer 2 (ITS2) regions from 178 plant species. We discovered that mutation of ITS2 is frequent, with a mean of 35 variants per species. And on average, three of the most abundant variants make up 91% of all ITS2 copies. Moreover, we found different congeneric species share identical variants in 13 genera. Interestingly, different species across different genera also share identical variants. In particular, one minor variant of ITS2 in Eleutherococcus giraldii was found identical to the ITS2 major variant of Panax ginseng, both from Araliaceae family. In addition, DNA barcoding gap analysis showed that the intra-genomic distances were markedly smaller than those of the intra-specific or inter-specific variants. When each of 5543 variants were examined for its species discrimination efficiency, a 97% success rate was obtained at the species level.
Identification of identical ITS2 variants across intra-generic or inter-generic species revealed complex species evolutionary history, possibly, horizontal gene transfer and ancestral hybridization. Although intra-genomic multiple variants are frequently found within each genome, the usage of the major variants alone is sufficient for phylogeny construction and species determination in most cases. Furthermore, the inclusion of minor variants further improves the resolution of species identification.
Camptotheca acuminata is a Nyssaceae plant, often called the "happy tree", which is indigenous in Southern China. C. acuminata produces the terpenoid indole alkaloid, camptothecin (CPT), which ...exhibits clinical effects in various cancer treatments. Despite its importance, little is known about the transcriptome of C. acuminata and the mechanism of CPT biosynthesis, as only few nucleotide sequences are included in the GenBank database.
From a constructed cDNA library of young C. acuminata leaves, a total of 30,358 unigenes, with an average length of 403 bp, were obtained after assembly of 74,858 high quality reads using GS De Novo assembler software. Through functional annotation, a total of 21,213 unigenes were annotated at least once against the NCBI nucleotide (Nt), non-redundant protein (Nr), Uniprot/SwissProt, Kyoto Encyclopedia of Genes and Genomes (KEGG), and Arabidopsis thaliana proteome (TAIR) databases. Further analysis identified 521 ESTs representing 20 enzyme genes that are involved in the backbone of the CPT biosynthetic pathway in the library. Three putative genes in the upstream pathway, including genes for geraniol-10-hydroxylase (CaPG10H), secologanin synthase (CaPSCS), and strictosidine synthase (CaPSTR) were cloned and analyzed. The expression level of the three genes was also detected using qRT-PCR in C. acuminata. With respect to the branch pathway of CPT synthesis, six cytochrome P450s transcripts were selected as candidate transcripts by detection of transcript expression in different tissues using qRT-PCR. In addition, one glucosidase gene was identified that might participate in CPT biosynthesis. For CPT transport, three of 21 transcripts for multidrug resistance protein (MDR) transporters were also screened from the dataset by their annotation result and gene expression analysis.
This study produced a large amount of transcriptome data from C. acuminata by 454 pyrosequencing. According to EST annotation, catalytic features prediction, and expression analysis, novel putative transcripts involved in CPT biosynthesis and transport were discovered in C. acuminata. This study will facilitate further identification of key enzymes and transporter genes in C. acuminata.
Pu-erh tea: A review of a healthful brew Jia, Wei; Rajani, Cynthia; Lv, Aiping ...
Journal of Traditional Chinese Medical Sciences,
04/2022, Volume:
9, Issue:
2
Journal Article
Peer reviewed
Open access
Pu-erh tea has been used for thousands of years to treat metabolic diseases. Recognized in Shen Nong's Herbal Classic, a compendium kept by the first traditional Chinese practitioners, it is still ...highly valued for its hypocholesterolemic and hypolipidemic effects. This review reports the processing and bioactive components of pu-erh tea. Recent human and animal studies of pu-erh tea and its potential therapeutic mechanisms have also been summarized. The interaction of liver and gut microbiome regulates the pu-erh tea biotransformation and endogenous metabolism, and thus contributes to the health benefits.
Aptamers, which are selected
by a technology known as the systematic evolution of ligands by exponential enrichment (SELEX), represent a crucial recognition element in molecular sensing. With ...advantages such as good biocompatibility, facile functionalization, and special optical and physical properties, various nanomaterials can protect aptamers from enzymatic degradation and nonspecific binding in living systems and thus provide a preeminent platform for biochemical applications. Coupling aptamers with various nanomaterials offers many opportunities for developing highly sensitive and selective sensing systems. Here, we focus on the recent applications of aptamer-assembled nanomaterials in fluorescent sensing and imaging. Different types of nanomaterials are examined along with their advantages and disadvantages. Finally, we look toward the future of aptamer-assembled nanomaterials.
Until now the overlapping and diverse pharmacological protective mechanisms of different compounds in the treatment of cerebral ischemia, both on the signaling pathway and network levels have not ...been revealed. In order to find differential pathway networks from gene expression profiles of hippocampus of ischemic mice treated with baicalin (BA), ursodeoxycholic acid (UA) and jasminoidin (JA), a microarray comprising 16,463 genes, FDA Arraytrack software and Ingenuity Pathway Analysis, was employed. A total of 5, 8, 11, 9 networks and 6, 7, 40, 16 pathways were found in vehicle (vs sham), BA, UA and JA (vs vehicle), respectively. Only 4 and 7 overlapping pathways were shared between BA and UA, UA and JA, accounting for 9.3% and 14.3% of the total number of all pathways, respectively. BA, UA and JA all acted on Ca(2+)-dependent signaling cascades in diverse links. BA intervened in arachidonic acid metabolism. UA affected eicosanoid, cyclin-dependent kinase 5, nuclear factor-kB, and T-helper 1 cell cytokine production. It was found that JA might decrease oxidative damage via nuclear factor erythroid 2-related factor 2-mediated antioxidant response. Compared to vehicle, no overlapping pathways were found among three groups. However, the total of 60 (71.4%) overlapping functions could be approximately divided into diseases and disorders, molecular and cellular functions, physiological system development and function as categories with ratio of 1:1:1. Analysis of network functions and known pathways may be two complementary paradigms for revealing potential pharmacological mechanisms based on the same phenotype variation.
This study was aimed at exploring the rules of Chinese patent medicine and Western medicine, as well as their combination rules used in the treatment of osteoporosis by text mining. Data on ...osteoporosis were queried and downloaded from SinoMed in March 2011. After transferring semi-structured data into the Microsoft SQL Server, the algorithm of data slicing based on frequency analysis was applied. A few simple, meaningful networks were achieved. The data of these networks were imported into Cytoscape and visualized. The results showed that in the treatment of osteoporosis, Chinese patent medicines, such as Zuogui pills, Liuwei Dihuang pills, Gusongbao granules, Yougui pills, and Shengu capsules, are widely used in the clinical practice. Chinese herbal medicines, such as Herba Epimedii, Radix Rehmannia, Radix Astragali, Rhizoma Drynariae, Salvia Miltiorrhiza, Fructus Psoraleae, Radix Puerariae, Radix Angelica, and Cortex Eucommiae, are frequently dealt with in articles on osteoporosis. Herba Epimedii and Radix Rehmannia are major herbal medicines that are most frequently used in the herbal combination. The most important treatment method of treating osteoporosis is by strengthening the kidney and spleen by activating and nourishing blood. Among all Western medicines, estrogen agents, Vitamin D, calcium, and thyrocalcitonin are the most frequently used in the treatment of osteoporosis. In this article, the rules pertaining to Chinese patent medicine and Western medicine used in the treatment of osteoporosis were described. The combination of Chinese patent medicine and Western medicine was also calculated for the clinical application and basic research reference.
Huang-Lian-Jie-Du-Tang is a famous Traditional Chinese medicine consisting of Rhizoma coptidis (Coptis chinensis Franch, Ranunculaceae), Radix scutellariae (Scutellaria baicalensis Georgi, Labiatae), ...Cortex phellodendri (Phellodendron amurense Rupr. Rutaceae) and Fructus gardeniae (Gardenia jasminoide Ellis, Rubiaceae) in a weight ratio of 3:2:2:3.This formula was described by Wang Tao (in the Chinese Tang Dynasty) in his treatise “Wai Tai Mi Yao”. It has been used to treat inflammation, hypertension, gastrointestinal disorders, and liver and cerebrovascular diseases in the clinical practice of Traditional Chinese medicine, especially in treating inflammation for nearly two thousand years. However, the essential compounds in it have not been identified, and the mechanisms remain to be addressed. To investigate the protective effects of HLJDT and its component group (HLJDT–CG) on collagen-induced arthritis in rats.
CIA was established in male Wistar rats with subcutaneous injection of type II bovine collagen at the base of the tail of animals. CIA rats were treated daily with oral administration of HLJDT aqueous extracts (270mg/kg) or HLJDT–CG (40mg/kg) once per day from day 6 to day 28. Rats in normal and vehicle control groups were given an equal volume of vehicle (0.9% saline) and 0.025mg/kg Dexamethasone was given to the Standard group at the same time. The protective effect of them were assessed by measuring arthritis index, swelling, the cytokines such as TNF-α, IFN-γ and IL-17 in serum, type II collagen antibodies, splenocyte proliferation and so on.
The results demonstrated that treatment of CIA rat with either HLJDT aqueous extracts or HLJDT–CG not only ameliorated the symptoms of arthritis, prevented joint damage but also reduced the serum levels of TNF-α, IFN-γ and IL-17 in CIA rats. Anti-CII antibodies showed the similar trend except that of IgG1. Furthermore, HLJDT aqueous extracts and HLJDT–CG administration also suppressed CII-induced proliferative response of splenocytes. More importantly, HLJDT–CG exhibited similar pharmacological activities as HLJDT aqueous extracts in all aforementioned experiments.
HLJDT aqueous extracts and HLJDT–CG could effectively ameliorate CII-induced arthritis and significantly suppress the immune response against CII with similar pharmacological efficacy. These findings suggest that HLJDT has therapeutic potential in RA treatment and HLJDT–CG can represent the effective-composite of HLJDT.
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