Analysis of synonymous codon usage patterns in the genus Rhizobium

The codon usage patterns of rhizobia have received increasing attention. However, little information is available regarding the conserved features of the codon usage patterns in a typical rhizobial genus. The codon usage patterns of six completely sequenced strains belonging to the genus Rhizobium were analysed as model rhizobia in the present study. The relative neutrality plot showed that selection pressure played a role in codon usage in the genus Rhizobium. Spearman’s rank correlation analysis combined with correspondence analysis (COA) showed that the codon adaptation index and the effective number of codons (ENC) had strong correlation with the first axis of the COA, which indicated the important role of gene expression level and the ENC in the codon usage patterns in this genus. The relative synonymous codon usage of Cys codons had the strongest correlation with the second axis of the COA. Accordingly, the usage of Cys codons was another important factor that shaped the codon usage patterns in Rhizobium genomes and was a conserved feature of the genus. Moreover, the comparison of codon usage between highly and lowly expressed genes showed that 20 unique preferred codons were shared among Rhizobium genomes, revealing another conserved feature of the genus. This is the first report of the codon usage patterns in the genus Rhizobium.     

Genome-wide identification and expression profiling of ankyrin-repeat gene family in maize

Members of the ankyrin repeats (ANK) gene family encode ANK domain that are common in diverse organisms and play important roles in cell growth and development, such as cell-cell signal transduction and cell cycle regulation. Recently, genome-wide identification and evolutionary analyses of the ANK gene family have been carried out in Arabidopsis and rice. However, little is known regarding the ANK genes in the entire maize genome. In this study, we described the identification and structural characterization of 71 ANK genes in maize (ZmANK). Then, comprehensive bioinformatics analyses of ZmANK genes family were performed including phylogenetic, domain and motif analysis, chromosomal localization, intron/exon structural patterns, gene duplications and expression profiling. Domain composition analyses showed that ZmANK genes formed ten subfamilies. Five tandem duplications and 14 segmental duplications were identified in ZmANK genes. Furthermore, we took comparative analysis of the total ANK gene family in Arabidopsis, rice and maize, ZmANKs were more closely paired with OsANKs than with AtANKs. At last, expression profile analyses were performed. Forty-one members of ZmANK genes held EST sequences records. Semi-quantitative expression and microarray data analysis of these 41 ZmANK genes demonstrated that ZmANK genes exhibit a various expression pattern, suggesting that functional diversification of ZmANK genes family. The results will present significant insights to explore ANK genes expression and function in future studies in maize.     

Biodegradation of high concentration of nitrobenzene by Pseudomonas corrugata embedded in peat-phosphate esterified polyvinyl alcohol

Efficiency on biodegradation of high concentration of nitrobenzene (NB) by peat-phosphate esterified polyvinyl alcohol-embedded NB-degrading bacteria Pseudomonas corrugata was conducted compared to free bacteria cells. Its biodegradation kinetics, reuse ability, degradation effect in the absence of the essential element needed for the growth of bacteria and degradation efficiency of the raw water from the contaminated site were also invested. Results show that the degradation rate when the concentration of NB was at 600, 750, and 900 mg/L reached 91.02, 83.23, and 55.9 %, which was higher than that observed in free bacteria at the same concentration levels. Biodegradation kinetics of the material could be well described by first- and zero-order kinetics when the concentration of NB was at 300, 450 mg/L and 600, 750, 900 mg/L, respectively. Stable degradation activity (stayed at a level of approximately 70 %) was displayed during the 11th repeat-batch experiment. The affect of absence of phosphorus in the medium can be abated ascribed to the addition of peat, which contributes with organic matter and other elements such as nitrogen and phosphorus necessary to maintain metabolically active the microorganisms. Effective biodegradation of the raw water from the experimental site revealed that the material can be a potential candidate for treating NB-contaminated wastewater in the practical setting.     

Optimization of soluble human interferon-γ production in Escherichia coli using SUMO fusion partner

Interferon-γ (IFN-γ) is a broad-spectrum antiviral glycoprotein that produced by lymphatic T cells and natural killer cells those who had stimulated by antigen. Human IFN-γ (hIFN-γ) often used in clinical research and practice because of its bioactivity, for example, antivirus, antitumor, controlling cell apoptosis, and the strict selectivity. However, due to the difficulties of Escherichia coli expression system meet in protein folding, the hIFN-γ often existed as inclusion body. The production of soluble hIFN-γ can be developed to shorten the production cycle and decrease the cost. In this study, small ubiquitin-related modifier fusion technology was used to express and purify recombinant hIFN-γ. Expression induced by adding 50 mM arginine and 1 % (w/v) glycerol into the culture at 24 °C existed as a soluble form of 70 % in total protein. Finally, about 62 mg recombinant hIFN-γ was obtained from 1 L fermentation culture with no less than 96 % purity. Determined by cytopathic effect inhibition assay, the specific activity of the recombinant hIFN-γ achieved at 7.78 × 10⁵ IU/mL.     

Methyl-β-cyclodextrin potentiates the BITC-induced anti-cancer effect through modulation of the Akt phosphorylation in human colorectal cancer cells

ABSTRACT

Methyl-β-cyclodextrin (MβCD) is an effective agent for the removal of plasma membrane cholesterol. In this study, we investigated the modulating effects of MβCD on the antiproliferation induced by benzyl isothiocyanate (BITC), an ITC compound mainly derived from papaya seeds. We confirmed that MβCD dose-dependently increased the cholesterol level in the medium, possibly through its removal from the plasma membrane of human colorectal cancer cells. The pretreatment with a non-toxic concentration (2.5 mM) of MβCD significantly enhanced the BITC-induced cytotoxicity and apoptosis induction, which was counteracted by the cholesterol supplementation. Although BITC activated the phosphoinositide 3-kinase (PI3K)/Akt pathway, MβCD dose-dependently inhibited the phosphorylation level of Akt. On the contrary, the treatment of MβCD enhanced the phosphorylation of mitogen activated protein kinases, but did not potentiate their BITC-induced phosphorylation. These results suggested that MβCD might potentiate the BITC-induced anti-cancer by cholesterol depletion and thus inhibition of the PI3K/Akt-dependent survival pathway.

Abbreviations: CDs: cyclodextrins; MβCD: methyl-β-cyclodextrin; ITCs: isothiocyanates; BITC: benzyl isothiocyanate; PI3K: phosphoinositide 3-kinase; PDK1: phosphoinositide-dependent kinase-1; MAPK: mitogen activated protein kinase; ERK1/2: extracellular signal-regulated kinase1/2; JNK: c-Jun N-terminal kinase; PI: propidium iodide; FBS: fatal bovine serum; TLC: thin-layer chromatography; PBS(-): phosphate-buffered saline without calcium and magnesium; MEK: MAPK/ERK kinase; PIP2: phosphatidylinositol-4,5-bisphosphate; PIP3: phosphatidylinositol-3,4,5-trisphosphate     

藏药毛蕊杜鹃挥发油化学成分的GC-MS分析

目的：通过研究毛蕊杜鹃挥发油的化学成分,为毛蕊杜鹃的药用及开发利用提供依据.方法：采用水蒸气蒸馏法提取毛蕊杜鹃挥发油,用GC毛细管柱进行分离,归一化法测其相对含量,并用气相色谱-质谱法对化学成分进行鉴定.结果：共鉴定出38个化合物,鉴定出的化合物含量占总挥发油的92.96％.结论：毛蕊杜鹃挥发油主要成分为δ-杜松烯（相对含量为15.90％）;胡萝卜醇（15.09％）;α-杜松醇（15.02％）;τ-杜松醇（9.66％）;α-衣兰油烯（4.25％）;1,2,3,4,4a,5,6,8a-八氢-7-甲基-4-亚甲基-1-[1-甲基乙基]-萘（4.14％）;1,7-二甲基-4-异丙基-2,7-环癸二烯-1-羟基（3.27％）;石竹烯（2.86％）;5-甲基-9-亚甲基-2-异丙基-二环[4.4.0]癸-1-烯（2.62％）;1,4-二甲基-3-[2-甲基-1-丙烯-1-基]-4-乙烯基-1-环庚烯（2.42％）;γ-衣兰油烯（2.21％）;愈创醇（1.50％）;β-古芸烯（1.34％）.     

Myostatin induces mitochondrial metabolic alteration and typical apoptosis in cancer cells

Myostatin, a member of the transforming growth factor-β superfamily, regulates the glucose metabolism of muscle cells, while dysregulated myostatin activity is associated with a number of metabolic disorders, including muscle cachexia, obesity and type II diabetes. We observed that myostatin induced significant mitochondrial metabolic alterations and prolonged exposure of myostatin induced mitochondria-dependent apoptosis in cancer cells addicted to glycolysis. To address the underlying mechanism, we found that the protein levels of Hexokinase II (HKII) and voltage-dependent anion channel 1 (VDAC1), two key regulators of glucose metabolisms as well as metabolic stress-induced apoptosis, were negatively correlated. In particular, VDAC1 was dramatically upregulated in cells that are sensitive to myostatin treatment whereas HKII was downregulated and dissociated from mitochondria. Myostatin promoted the translocation of Bax from cytosol to mitochondria, and knockdown of VDAC1 inhibited myostatin-induced Bax translocation and apoptosis. These apoptotic changes can be partially rescued by repletion of ATP, or by ectopic expression of HKII, suggesting that perturbation of mitochondrial metabolism is causally linked with subsequent apoptosis. Our findings reveal novel function of myostatin in regulating mitochondrial metabolism and apoptosis in cancer cells.     

Comparative phylogeography of two sympatric beeches in subtropical China: Species‐specific geographic mosaic of lineages

In subtropical China, large‐scale phylogeographic comparisons among multiple sympatric plants with similar ecological preferences are scarce, making generalizations about common response to historical events necessarily tentative. A phylogeographic comparison of two sympatric Chinese beeches (Fagus lucida and F. longipetiolata, 21 and 28 populations, respectively) was conducted to test whether they have responded to historical events in a concerted fashion and to determine whether their phylogeographic structure is exclusively due to Quaternary events or it is also associated with pre‐Quaternary events. Twenty‐three haplotypes were recovered for F. lucida and F. longipetiolata (14 each one and five shared). Both species exhibited a species‐specific mosaic distribution of haplotypes, with many of them being range‐restricted and even private to populations. The two beeches had comparable total haplotype diversity but F. lucida had much higher within‐population diversity than F. longipetiolata. Molecular dating showed that the time to most recent common ancestor of all haplotypes was 6.36 Ma, with most haplotypes differentiating during the Quaternary. [Correction added on 14 October 2013, after first online publication: the time unit has been corrected to ‘6.36’.] Our results support a late Miocene origin and southwards colonization of Chinese beeches when the aridity in Central Asia intensified and the monsoon climate began to dominate the East Asia. During the Quaternary, long‐term isolation in subtropical mountains of China coupled with limited gene flow would have lead to the current species‐specific mosaic distribution of lineages.