Cardioviral RNA structure logo analysis: entropy, correlations, and prediction

In recent years, there has been an increased number of sequenced RNAs leading to the development of new RNA databases. Thus, predicting RNA structure from multiple alignments is an important issue to understand its function. Since RNA secondary structures are often conserved in evolution, developing methods to identify covariate sites in an alignment can be essential for discovering structural elements. Structure Logo is a technique established on the basis of entropy and mutual information measured to analyze RNA sequences from an alignment. We proposed an efficient Structure Logo approach to analyze conservations and correlations in a set of Cardioviral RNA sequences. The entropy and mutual information content were measured to examine the conservations and correlations, respectively. The conserved secondary structure motifs were predicted on the basis of the conservation and correlation analyses. Our predictive motifs were similar to the ones observed in the viral RNA structure database, and the correlations between bases also corresponded to the secondary structure in the database.

C, N and P regeneration by a detritivorous fish, Liza haematocheila T. & S.: effects of temperature, diet and body size

Detritus, as a nutrients reservoir, affects the trophic structure and dynamics of communities and supports a greater diversity of species and longer food chains. Detritivorous fish is an important organism to regenerate the nutrients from sediments. Despite the numerous studies on the nutrients cycle in fish, only a few attempts have been made to quantify the regenerating ability. In the present study, we chose the common detritivorous fish redeye mullet as the research object. Redeye mullet is also a common poly-culture fish in China. Diet, including a commercial diet mostly used in aquaculture and a home-made diet with contents close to detritus, was used and considered as a fixed factor. Temperature was also considered as a fixed factor as much research has shown that temperature has significant effects on fish metabolism. Moreover, body size was regarded as a covariate under analysis of covariance. Three key nutrients, namely carbon, nitrogen and phosphorus, were used to measure the nutrient-regenerating ability of redeye mullet under laboratory conditions. The results showed that the nutrient regeneration in percent of the consumption decreased with increasing temperature. Carbon and nitrogen regeneration of redeye mullet fed on commercial diet was lower than those of the home-made diet group, while the opposite was found for phosphorus. In each group, the amount of regenerated nutrients increased linearly with body size. Fed on the home-made diet, 5-g fish at 25 degrees C can regenerate 210.822 mg C, 37.533 mg N and 0.727 mg P per day.