Characterization and phylogenetic analysis of the complete chloroplast genome of Lycopus europaeus / 药学学报

We intend to study the structural characteristics of Lycopus europaeus Linn. chloroplast genome and compare the evolutionary relationship of species from Lamiaceae with similar medicinal effects. The total DNA of Lycopus europaeus was sequenced using the Illumina Hiseq 4000 Sequencing platform and was assembled using NOVOplasty software. And then we annotated and analyzed the genome using the CPGAVAS2 online tool. We constructed the phylogenetic tree using the Stellera chamaejasme and Potentilla chinensis as the outgroup. The whole length of Lycopus europaeus chloroplast genome was 152 085 bp. A total of 132 genes were annotated including 88 protein-coding genes, 8 rRNA genes and 36 tRNA genes. Among them, 8 protein-coding genes (ndhB, rps7, rps12, rps19, rpl2, rpl23, ycf2, ycf15), 7 tRNA coding genes (trnM-CAU, trnL CAA, trnN-GUU, trnE-UUC, trnV-GAC, trnA-UGC, trnR-ACG) and 4 rRNA coding genes (rrn16s, rrn23s, rrn4.5s, rrn5s) are located in the IR region. There are 13 protein coding genes [rps16, rps19 (×2), atpF, rpoC1, rpl2 (×2), petB, petD, rpl16, ndhB (×2), ndhA] each contains one intron, two protein-coding genes (ycf3, clpP) each contain two introns, and 8 tRNA coding genes each contain one intron. A total of 34 SSRs were detected in the chloroplast genome of Lycopus europaeus. Phylogenetic analysis revealed that two species in the Lycopus genus, four species in the Dracocephalum genus, Glechoma longituba, two species in the Mentha genus and Prunella vulgari, in total 10 species are most related. The complete genome sequence of Lycopus europaeus was obtained and analyzed, which clarified the evolutional relationship between the species of Lycopus europaeus and in the Lamiaceae family.

Sequence analysis of HBV in primary hepatomas patients infected with HBV / 中华实验和临床病毒学杂志

Objective@#To study the relationship between the development of hepatocellular carcinoma(HCC) and HBV gene characteristics among the HCC patients with hepatitis B virus (HBV) infection.@*Methods@#Some acute and chronic hepatitis B patients were collected as control group and HBV associated HCC patients as HCC group. Serum samples of subjects were tested for HBV serological markers. HBV DNA of those samples had been extracted and nested PCR was used to amplify the sequence of HBV DNA. Furthermore, MEGA 6.0 and Bioedit softwares were used to made phylogenetic trees and analyze the gene mutations.@*Results@#The sequences of S region and BCP/Precore region of HBV were amplified from 86 samples in study group and 39 samples in control group. The prevalence of PreS deletion, A1762T and A1762T/G1764A in HCC group were 39.53%, 74.42% and 72.09% respectively, and in control group were 20.51%, 53.85% and 53.85% respectively. The statistical differences of them were significant. The prevalence of A1762T and A1762T/G1764A in ≥ 50 years group were higher than that of < 50 years group. The prevalence of A1762T, G1764A and A1762T/G1764A of subjects who infected genotype C were higher than those infected genotype B. On the contrary, the prevalence of G1896A of subjects who infected genotype C were lower than that of genotype B. It was found that ≥ 50 years, genotype C and G1896A mutation were independently associated with HCC. The risk for suffer from HCC of ≥50 years group, genotype C group and G1896A group were 9.349, 28.875 and 7.648 times compared with < 50 years group genotype B group and without G1896A mutation group, respectively.@*Conclusions@#The population of ≥50 years or genotype C had a higher prevalence of A1762T, A1762T/G1764A, ≥50years、genotype C、G1896A were independently associated with HCC, as compared with the subjects of the control group.

Prediction of protein subcellular locations by ensemble of improved K-nearest neighbor / 生物工程学报

Adaboost algorithm with improved K-nearest neighbor classifiers is proposed to predict protein subcellular locations. Improved K-nearest neighbor classifier uses three sequence feature vectors including amino acid composition, dipeptide and pseudo amino acid composition of protein sequence. K-nearest neighbor uses Blast in classification stage. The overall success rates by the jackknife test on two data sets of CH317 and Gram1253 are 92.4% and 93.1%. Adaboost algorithm with the novel K-nearest neighbor improved by Blast is an effective method for predicting subcellular locations of proteins.

Identification and bioinformatic analysis on rhizomes of Dioscorea zingiberensis WRKY transcription factor / 中草药

Objective: To identify WRKY genes from the rhizomes of Dioscorea zingiberensis and analyze the protein characteristics and expression level of these genes. Methods: The transcriptional EST database of the rhizomes of D. zingiberensis was used to search the analogs of AtWRKY genes by BLASTn, the full-length open reading frames (ORF) of DzWRKY and its protein characteristics were studied using bioinformatic method, and the expression levels of DzWRKY genes in rhizomes and leaves were detected from transcriptional data of the rhizomes of D. zingiberensis. Results: Twenty-seven DzWRKY transcription factors family genes with full length ORF were isolated from the rhizomes of D. zingiberensis, and two WRKY domains were confirmed in six WRKY genes. All the DzWRKY proteins were predicted as hydrophilic proteins and nucleoproteins with highly conserved WRKY domains. The 27 DzWRKY and 19 AtWRKY proteins were divided into three groups by phylogenetic analysis. All DzWRKY genes showed higher expression level in the leaves compared to the rhizomes, and highly expressed genes were mainly in groups I and IId. DzWRKY proteins exhibited lower sequence identity. Conclusion: The DzWRKY genes are successfully isolated for the first time, which would provide a reference for the study on the roles of WRKY in development and active components biosynthesis of the rhizomes of D. zingiberensis.