Analysis of codon usage patterns in Bupleurum falcatum chloroplast genome.

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.

Analysis of synonymous codon usage of transcriptome database in Rheum palmatum.

BACKGROUND: Rheum palmatum is an endangered and important medicinal plant in Asian countries, especially in China. However, there is little knowledge about the codon usage bias for R. palmatum CDSs. In this project, codon usage bias was determined based on the R. palmatum 2,626 predicted CDSs from R. palmatum transcriptome. METHODS: In this study, all codon usage bias parameters and nucleotide compositions were calculated by Python script, Codon W, DNA Star, CUSP of EMBOSS. RESULTS: The average GC and GC3 content are 46.57% and 46.6%, respectively, the results suggested that there exists a little more AT than GC in the R. palmatum genes, and the codon bias of R. palmatum genes preferred to end with A/T. We concluded that the codon bias in R. palmatum was affect by nucleotide composition, mutation pressure, natural selection, gene expression levels, and the mutation pressure is the prominent factor. In addition, we figured out 28 optimal codons and most of them ended with A or U. The project here can offer important information for further studies on enhancing the gene expression using codon optimization in heterogeneous expression system, predicting the genetic and evolutionary mechanisms in R. palmatum.

Eleucanainones A and B: Two Dimeric Structures from the Bulbs of Eleutherine americana with Anti-MRSA Activity.

Two naphthoquinone-derived heterodimers with unprecedented carbon skeletons, eleucanainones A (1) and B (2), were isolated from the bulbs of Eleutherine americana. Their structures were elucidated by comprehensive spectroscopic methods. The structures of 1 and 2 were determined to be the first examples of dibenzofuran- and naphthalenone-containing naphthoquinone dimers. Compound 1 exhibited significant anti-MRSA activity in vitro with minimum inhibitory concentration (MIC) values of 0.78 µg/mL by downregulation of basal expression of agrA, cidA, icaA and sarA in methicillin-resistant S. aureus (MRSA).

Characteristics and Diversity of Endophytic Bacteria in Endangered Chinese Herb Glehnia littoralis Based on Illumina Sequencing.

Glehnia littoralis is an endangered medicinal plant growing in the coastal ecological environment and plays an important role in coastal ecosystems. The endophytes in the plant have a significant role in promoting plant growth and enhancing plant stress resistance. However, the endophytic bacterial structure associated with halophyte G. littoralis is still not revealed. In this project, the construction and diversity of endophytic bacterial consortium associated with different tissues of G. littoralis were illustrated with high throughput sequencing of the V3-V4 region of the bacterial 16S rRNA. The results resolved that the diversity and richness of endophytic bacteria were significantly higher in root than in leaf and stem. The operational taxonomic units (OTU) analysis demonstrated that the Actinobacteria and Proteobacteria were dominant in all the samples at the phylum level, and Pseudomonas, Bacillus, Rhizobium were the dominant genera. Our results unraveled that the bacterial communities differed among different tissues of G. littoralis. Endophytic bacterial communities in leaf and stem shared more similarity than that in the root. Furthermore, the difference of bacteria community and structure among different tissues were also detected by principal coordinate analysis. Taken altogether, we can conclude that the bacterial communities of different tissues are unique, which could facilitate understanding the diversity of endophytic bacteria in G. littoralis.

The complete chloroplast genome sequence of Rheum tanguticum, an endangered Chinese medicinal plant (Polygonaceae).

Rheum tanguticum is a valuable medicinal plant endemic to the Qinghai-Tibetan Plateau. It has been listed classified under the IUCN Red List categories of Vulnerable due to the low reproductive rate and heavy exploitation. In this study, the complete chloroplast (cp) genome of R. tanguticum has been assembled using data from the whole-genome Illumina sequencing. The cp genome is 161,515 bp in size and contains two inverted repeat regions of 30,823 bp each, which is separated by a large single-copy region of 86,675 bp and a small single-copy region of 13,194 bp. The cp genome contains 87 protein-coding genes, 37 tRNA genes, and 8 rRNA genes. Phylogenetic analysis revealed that the cp genome of R. tanguticum was closely related to that of the R. palmatum.

New polyoxypregnane glycosides from Aspidopterys obcordata vines with antitumor activity.

Nine new polyoxypregnane glycosides, obcordatas A-I (1-9), were isolated from Aspidopterys obcordata Hemsl vines. Their structures were elucidated by extensive spectroscopic methods. Separated compounds were evaluated for antitumor activities against the human cancer cell lines AGS, SW480, HuH-7 and MCF-7, and compounds 1-6 and 9 showed selective cytotoxicity against HuH-7 cells with IC50 values of 8.7, 10.2, 7.5, 12.1, 16.5, 14.3, and 17.4 µM, respectively. Flow cytometry experiments showed that the effects of compound 1 on the cell cycle were attributable to cell cycle arrest at G1/S phase.

NF-κB and Nrf2 pathways contribute to the protective effect of Licochalcone A on dextran sulphate sodium-induced ulcerative colitis in mice.

Licochalcone A (Lico A) is a characteristic chalcone isolated from licorice root which is widely recognized in traditional Chinese medicine for the ability of anti-inflammatory, antioxidant, anti-parasitic and anti-cancer. The present study was aimed to investigate the effect of Lico A on dextran sulphate sodium (DSS)-induced ulcerative colitis (UC) in a mouse model which was induced by administration of 3% DSS in drinking water. Mice were then treated with Lico A (20, 40 and 80 mg/kg, p.o.) or 0.9% saline (20 ml/kg, p.o.) for 17 days. The results showed that treatment with Lico A significantly reduced the colon length, histological damage scores, and colonic myeloperoxidase (MPO) activity in a dose-dependent manner as compared to the UC control group. Besides, Lico A significantly decreased the oxidative stress and pro-inflammatory cytokines, downregulated nuclear transcription factor kappa B (NF-κB) pathway and upregulated nuclear factor erythroid 2-related factor 2 (Nrf2) pathway. Collectively, Lico A is effective in alleviating DSS-induced colitis in mice and the mechanism is associated with its inhibition of NF-κB-regulated pro-inflammatory signaling and activation of Nrf2-regulated cytoprotective protein expression.

Hepatoprotective Effect of Aqueous Extract from the Seeds of Orychophragmus violaceus against Liver Injury in Mice and HepG2 Cells.

Orychophragmus violaceus (O. violaceus) is a kind of edible wild herb in north China and its seeds have medical potential, however, the effect of O. violaceus seeds on liver injury and the mechanism of action remains poorly understood. Thus, the purpose of the present study is to investigate the effect of O. violaceus seeds on liver injury and further explore the molecular mechanism of the beneficial effects using aqueous extract from the seeds of O. violaceus (AEOV). Mice were orally administrated with saline, AEOV, and biphenyldicarboxylate for 4 days, and were then injected subcutaneously with 0.1% carbon tetrachloride (CCl4) dissolved in corn oil. Sixteen hours later, mice were sacrificed and blood samples were collected. Then, the serum was separated and used for biochemical assay. Livers were excised and were routinely processed for histological examinations. Enzyme activities and protein levels in liver homogenates were detected using commercial kits or by western blot analysis. Additionally, the hepatoprotective effect of AEOV in vitro was evaluated using epigoitrin, the major alkaloid compound isolated from AEOV. We found that AEOV attenuated liver injury induced by CCl4 as evidenced by decreased levels of alanine aminotransferase (ALT) and aminotransferase (AST) in serum, improvement of liver histopathological changes, and substantial attenuation of oxidative stress and inflammation via regulation of nuclear factor-erythroid 2-related factor-2 (Nrf2) and nuclear factor κB (NFκB) pathways. These effects of AEOV were comparable to that of biphenyldicarboxylate which was commonly used as a hepatoprotective reference. Moreover, pretreatment of HepG2 cells with epigoitrin improved cell viability, decreased lactate dehydrogenase (LDH) and malondialdehyde (MDA) levels, increased superoxide dismutase (SOD) and glutathione peroxidase (GSH-Px) activity, attenuated the NFκB pathway, and elevated the Nrf2 pathway after exposure to H2O2. These results suggest that AEOV could effectively prevent CCl4-induced liver injury in mice via regulating the Nrf2 and NFκB pathways, and reveal the cytoprotective effects of epigoitrin against H2O2-induced oxidative stress in HepG2 cells.

Flavonoids Extracted from Licorice Prevents Colitis-Associated Carcinogenesis in AOM/DSS Mouse Model.

Inflammatory bowel disease (IBD) is generally considered as a major risk factor in the progression of colitis-associated carcinogenesis (CAC). Thus, it is well accepted that ameliorating inflammation creates a potential to achieve an inhibitory effect on CAC. Licorice flavonoids (LFs) possess strong anti-inflammatory activity, making it possible to investigate its pharmacologic role in suppressing CAC. The purpose of the present study was to evaluate the anti-tumor potential of LFs, and further explore the underlying mechanisms. Firstly, an azoxymethane (AOM)/dextran sulfate sodium (DSS)-induced mouse model was established and administered with or without LFs for 10 weeks, and then the severity of CAC was examined macroscopically and histologically. Subsequently, the effects of LFs on expression of proteins associated with apoptosis and proliferation, levels of inflammatory cytokine, expression of phosphorylated-Janus kinases 2 (p-Jak2) and phosphorylated-signal transducer and activator of transcription 3 (p-Stat3), and activation of nuclear factor-κB (NFκB) and P53 were assessed. We found that LFs could significantly reduce tumorigenesis induced by AOM/DSS. Further study revealed that LFs treatment substantially reduced activation of NFκB and P53, and subsequently suppressed production of inflammatory cytokines and phosphorylation of Jak2 and Stat3 in AOM/DSS-induced mice. Taken together, LFs treatment alleviated AOM/DSS induced CAC via P53 and NFκB/IL-6/Jak2/Stat3 pathways, highlighting the potential of LFs in preventing CAC.

Adjuvant properties of water extractable arabinoxylans with different structural features from wheat flour against model antigen ovalbumin.

Despite the numerous benefits of AX on the immune system and gut bacteria, the potential adjuvant activity of WEAX on immune responses has not been adequately investigated. In the present study, three kinds of WEAX with different structural features were obtained and their adjuvant potential on the specific cellular and humoral immune responses in ovalbumin (OVA) immunized mice were assessed. Our data demonstrated that WEAX had potent effects on innate and acquired immune responses through up-regulating the NK cell activation and promoting the Th2 type immune response. Furthermore, this study also elucidated the possible relationship between the adjuvant activity of WEAX and the structure. Compared with the other characteristics of the WEAX, we found that the immunomodulatory activity may be related to their content of ferulic acid, and not to the molecular weight.

Antiinflammatory and Analgesic Activities of Ethanol Extract and Isolated Compounds from Millettia pulchra.

The plant Millettia pulchra was commonly used in folk medicine for the management of inflammation. However, there was no scientific rationale for these effects and the mechanism of action remained incompletely understood. The present study was designed to investigate the antiinflammatory and analgesic activities of an ethanol extract of the stem of M. pulchra (EMP) in vivo, and to explore the antiinflammatory activity of compounds isolated from EMP in vitro. We found that EMP reduced xylene-induced ear edema and relieved both acetic acid-induced pain and pain in the hot plate test. Additionally, a significant decrease in nitric oxide (NO) production was observed in cells treated with the isolated compounds. Lanceolatin B, which showed the greatest inhibition of NO synthesis among the compounds tested, also reduced levels of interleukin-1 beta (IL-1ß), IL-6, tumor necrosis factor-alpha (TNF-α), cyclooxygenase-2 (COX-2), inducible nitric oxide synthase (iNOS), nuclear factor-kappa B (NF-κB), and phosphorylation inhibitory kappa B alpha (p-IκBα) in a dose-dependent manner. These findings provide convincing evidence that EMP and the individual isolated compounds possess significant antiinflammatory and analgesic activities.