Background Ganoderma lucidum (Reishi or Ling Zhi) is one of the most famous Traditional Chinese Medicines and has been widely used in the treatment of various human diseases in Asia countries. It is also a fungus with strong wood degradation ability with potential in bioenergy production. However, genes, pathways and mechanisms of these functions are still unknown.Methodology/Principal FindingsThe genome of G. lucidum was sequenced and assembled into a 39.9 megabases (Mb) draft genome, which encoded 12,080 protein-coding genes and ∼83% of them were similar to public sequences. We performed comprehensive annotation for G. lucidum genes and made comparisons with genes in other fungi genomes. Genes in the biosynthesis of the main G. lucidum active ingredients, ganoderic acids (GAs), were characterized. Among the GAs synthases, we identified a fusion gene, the N and C terminal of which are homologous to two different enzymes. Moreover, the fusion gene was only found in basidiomycetes. As a white rot fungus with wood degradation ability, abundant carbohydrate-active enzymes and ligninolytic enzymes were identified in the G. lucidum genome and were compared with other fungi.Conclusions/SignificanceThe genome sequence and well annotation of G. lucidum will provide new insights in function analyses including its medicinal mechanism. The characterization of genes in the triterpene biosynthesis and wood degradation will facilitate bio-engineering research in the production of its active ingredients and bioenergy.

Apoptosis is the main form of β-cell death in diabetes. Ginseng has been used as an anti-diabetic herb for several thousand years in Asia with ginsenoside Rg1 and ginsenoside Rb1 as important active ingredients. In this study, we demonstrated ginsenoside Rg1 and Rb1 protect β-cells from high glucose/cytokine-induced pancreatic β-cell apoptosis via inhibiting nitric oxide (NO) production and regulating apoptosis-related genes. Among these genes, Bax, Fas and Caspase-3 gene expressions were up-regulated by high glucose, whereas only Bax and Caspase-3 gene expression were elevated by cytokines. In these two stimuli-induced apoptotic cells, Rg1 down-regulated Fas gene expression, while Rb1 decreased Caspase-3 gene expression. As a conclusion, Fas signal pathway and mitochondria stress is mostly related to anti-diabetes function of ginsenoside Rg1, while Caspase-3 pathway is essential when Rb1 is present.

Single molecule, real-time (SMRT) sequencing was used to characterize mitochondrial (mt) genome of Ophiocordyceps sinensis and to analyze the mt genome-wide pattern of epigenetic DNA modification. The complete mt genome of O. sinensis, with a size of 157,539 bp, is the fourth largest Ascomycota mt genome sequenced to date. It contained 14 conserved protein-coding genes (PCGs), 1 intronic protein rps3, 27 tRNAs and 2 rRNA subunits, which are common characteristics of the known mt genomes in Hypocreales. A phylogenetic tree inferred from 14 PCGs in Pezizomycotina fungi supports O. sinensis as most closely related to Hirsutella rhossiliensis in Ophiocordycipitaceae. A total of 36 sequence sites in rps3 were under positive selection, with dN/dS >1 in the 20 compared fungi. Among them, 16 sites were statistically significant. In addition, the mt genome-wide base modification pattern of O. sinensis was determined in this study, especially DNA methylation. The methylations were located in coding and uncoding regions of mt PCGs in O. sinensis, and might be closely related to the expression of PCGs or the binding affinity of transcription factor A to mtDNA. Consequently, these methylations may affect the enzymatic activity of oxidative phosphorylation and then the mt respiratory rate; or they may influence mt biogenesis. Therefore, methylations in the mitogenome of O. sinensis might be a genetic feature to adapt to the cold and low PO2 environment at high altitude, where O. sinensis is endemic. This is the first report on epigenetic modifications in a fungal mt genome.

Probiotics have been reported to be associated with the alleviation of constipation. The aim of this study was to detect and determine the effect of Bifidobacterium animalis subsp. lactis MN-Gup (MN-Gup) on the alleviation of constipation in BALB/c mice and humans, and to elucidate the mechanisms underlying its effect by measuring changes in the concentration of short-chain fatty acids and the composition of microbes in human faeces. BALB/c mice were given MN-Gup by gavage for 14 days. On the 8th day of this treatment, constipation was induced by the application of diphenoxylate via gavage. The results showed that MN-Gup significantly decreased the first black stool defecation time, and significantly increased black faecal wet weight, black faecal number and the gastric-intestinal transit rate (P<0.05), thereby relieving constipation. In humans, a randomised, double-blind, placebo-controlled trial was performed to investigate the effect of MN-Gup in adults with functional constipation. After 4 weeks of intervention with placebo or MN-Gup yogurt, constipation-related symptoms (including defecation frequency, stool consistency, straining and incomplete feeling during defecation) in the constipated subjects were significantly improved in the two groups, but not different between the groups at the end of the intervention. The concentration of acetate increased significantly in the MN-Gup group compared to the placebo group and before ingestion. Significant changes in the composition of gut microbiota were found after intake of MN-Gup yogurt when compared to placebo. The relative abundances of acetate-producing Bifidobacterium, Ruminoccaceae_UCG-002 and Ruminoccaceae_UCG-005 were significantly increased after intake of MN-Gup yogurt. These results showed that MN-Gup could relieve constipation related to increased acetate-producing Bifidobacterium, Ruminoccaceae_UCG-002 and Ruminoccaceae_UCG-005.

BackgroundExcessive apoptosis of β-cell is closely related to diabetes mellitus. Chronic exposure to high glucose causes β-cell dysfunction and apoptosis in diabetes. Thorn grape (Vitis davidii Foex.) has been used to treat diabetes in Traditional Chinese medicine for many years. In our previous research, thorn grape seeds oil (TGSO) showed promising anti-diabetic effects in animal models. However, it is unknown whether TGSO played an anti-apoptotic role in the anti-diabetic effects and the mechanism regarding signal transduction pathway is unclear either.MethodsThe rattus pancreatic β-cell line RIN-m5F was treated with/without TGSO which was extracted by supercritical carbon dioxide (CO2) fluid extraction and analyzed by Gas Chromatography/Mass Spectrometry (GC/MS). Cell apoptosis was detected by fluorescence activated cell sorting (FACS), insulin secretion was assayed by Enzyme-Linked Immunosorbent Assay (ELISA), and the apoptosis-related genes expressions were evaluated by quantitative Reverse Transcription Polymerase Chain Reaction (qRT-PCR).ResultsTGSO, containing 87.02% unsaturated fatty acids (UFAs), significantly reduced pancreatic β-cell apoptosis and protected the insulin secretion impaired by high glucose. The expressions of pro-apoptotic genes such as iNOS, Caspase-3, ATF-3, JNK, p38 and Fas were down-regulated while the anti-apoptotic genes Akt and Bcl-2/Bax were up-regulated.ConclusionsThe results indicated that TGSO protected β-cells from high glucose-induced apoptosis and its protective activity may be linked to mitochondrial pathway, endoplasmic reticulum (ER) stress pathway and Fas signal pathway, which implied that TGSO might be an effective complementary or alternative medicine to reduce β-cell apoptosis and dysfunction.