Predicting RNA Secondary Structure Using Profile Stochastic Context-Free Grammars and Phylogenic Analysis

Stochastic context-free grammars （SCFGs） have been applied to predicting RNA secondary structure. The prediction of RNA secondary structure can be facilitated by incorporating with comparative sequence analysis. However, most of existing SCFG-based methods lack explicit phylogenic analysis of homologous RNA sequences, which is probably the reason why these methods are not ideal in practical application. Hence, we present a new SCFG-based method by integrating phylogenic analysis with the newly defined profile SCFG. The method can be summarized as： 1） we define a new profile SCFG, M, to depict consensus secondary structure of multiple RNA sequence alignment; 2） we introduce two distinct hidden Markov models, λ and λ＇, to perform phylogenic analysis of homologous RNA sequences. Here, λ＇ is for non-structural regions of the sequence and λ＇ is for structural regions of the sequence; 3） we merge λ and λ＇ into M to devise a combined model for prediction of RNA secondary structure. We tested our method on data sets constructed from the Rfam database. The sensitivity and specificity of our method are more accurate than those of the predictions by Pfold.

Analysis of Saccharina japonica transcriptome using the high-throughput DNA sequencing technique and its vanadium-dependent haloperoxidase gene

Saccharina is one of the most important cold-water living marine brown algal genera. In this study we ana-lyzed the transcriptome of S. japonica, which belongs to the 1 000 Plants （OneKP） Project, by using a next-generation high-throughput DNA sequencing technique. About 5.16 GB of raw data were generated, and 65 536 scaffolds with an average length of 454 bp were assembled with SOAP de novo assembly method. In total, 19 040 unigenes were identified by BLAST;25 734 scaffolds were clustered into 37 Gene ontology functional groups;6 760 scaffolds were classified into 25 COG categories, as well as 2 665 scaffolds that were assigned to 306 KEGG pathways. Majority of the unigenes exhibited more similarities to algae including brown algae and diatom than other cyanobacteria, marine diatom, and plant. Saccharina japonica has the outstanding capability to accumulate halogen such as Br and I via halogenation processes from seawater. We acquired 42 different vanadium-dependent haloperoxidases （vHPO） in S. japonica transcriptome data, including 5 segments of vanadium-dependent iodoperoxidase （vIPO） and 37 segments of vanadium-de-pendent bromoperoxidase （vBPO）. Complicated analyses of identified fulllength S. japonica vBPO1 and S. japonica vBPO2 revealed the importance of vBPO among species of brown algae and the strong relationship between marine algal vBPOs and vIPOs. This study will enhance our understanding of the biological charac-teristics and economic values of S. japonica species.

Effects of Salinity and Temperature on Bacterial Biodiversity in Hangu Solar Saltworks,China

1 Introduction The multi-pond solar saltworks inhabit diverse microbial groups in which a gradient of salinities range from seawater to Na Cl precipitation.Along the salinity gradient,the majority of microbial community changes

Molecular Epidemiology and Vaccine Compatibility Analysis of Seasonal Influenza Viruses in Wuhan, 2016–2019

Influenza viruses(FLUV)cause high morbidity and mortality annually in the world and pose a serious threat to the public health.Wuhan,as an important transportation hub in China,has a dense population and suitable climate,which also lays a major hidden danger for the outbreak of influenza.To survey and characterize the seasonal FLUV in Wuhan during 2016–2019,we collected 44,738 throat swabs,among which 15.5%were influenza A(FLUAV)positive,6.1%influenza B(FLUBV)and 0.3%co-infection.By monitoring FLUV in each month from June 2016 to May 2019,different with the previously seasonality pattern,only a single influenza peak was appeared in winter of 2017–2018 and 2018–2019,respectively.These data indicated that the complex circulation pattern of seasonal influenza in Wuhan.In addition,we found the age group was skewed towards 5–14 years group whose activity were mostly school based,which suggested school may be an important place for influenza outbreaks.Meanwhile,phylogenic analysis revealed that two subtypes(subclade 3C.2 a2 and 3C.2 a1b)of A(H3N2)were circulating in Wuhan and there was an obvious transition in 2018 because the two subclades were detected simultaneously.Furthermore,by estimating the vaccine effectiveness,we found that the vaccine strain of FLUAV didn’t seem to match very well the current epidemic strain,especially A(H3N2).Hence,more accurate prediction of seasonal outbreak is essential for vaccine design.Taken together,our results provided the current information about seasonal FLUV in Wuhan which form the basis for vaccine updating.