Translational selection on codon usage in the genus Aspergillus

Aspergillus is a genus of mold fungi that includes more than 200 described species. Many members of the group are relevant pathogens and other species are economically important. Only one species has been analyzed for codon usage, and this was performed with a small number of genes. In this paper, we report the codon usage patterns of eight completely sequenced genomes which belong to this genus. The results suggest that selection for translational efficiency and accuracy are the major factors shaping codon usage in all of the species studied so far, and therefore they were active in the last common ancestor of the group. Composition and molecular distances analyses show that highly expressed genes evolve slower at synonymous sites. We identified a conserved core of translationally optimal codons and study the tRNA gene pool in each genome. We found that the great majority of preferred triplets match the respective cognate tRNA with more copies in the respective genome. We discuss the possible scenarios that can explain the observed differences among the species analyzed. Finally we highlight the biotechnological application of this research regarding heterologous protein expression.     

Growth rate of <Emphasis Type="Italic">Daphnia</Emphasis> feeding on seston in a Siberian reservoir: the role of essential fatty acid

Specific growth rates (based on biomass increment in unit time) of Daphnia fed natural reservoir seston from a eutrophic Siberian reservoir were studied during four vegetation seasons in a laboratory flow-through system. Concentrations of particulate C, N, and P in reservoir seston <115 μm were comparatively high, 1.9, 0.2, and 0.05 mg l⁻¹, respectively; maximum C:P ratio was 259 mol:mol. According to conventional thresholds, concentrations of elements and their stoichiometry did not limit the growth rate of Daphnia. Eicosapentaenoic acid (EPA) in seston significantly effected the growth rates at concentrations up to ∼13 μg l⁻¹ (regression ANOVAR F-test value was 7.91), but not above this concentration. Thus, we consider this concentration of EPA in seston <115 μm to be the limiting concentration of EPA for the growth of Daphnia (longispina group), i.e., below this concentration EPA was the best single predictor of the growth of Daphnia.     

inSPIRE: An Open-Source Tool for Increased Mass Spectrometry Identification Rates Using Prosit Spectral Prediction

Rescoring of mass spectrometry (MS) search results using spectral predictors can strongly increase peptide spectrum match (PSM) identification rates. This approach is particularly effective when aiming to search MS data against large databases, for example, when dealing with nonspecific cleavage in immunopeptidomics or inflation of the reference database for noncanonical peptide identification. Here, we present inSPIRE (in silico Spectral Predictor Informed REscoring), a flexible and performant open-source rescoring pipeline built on Prosit MS spectral prediction, which is compatible with common database search engines. inSPIRE allows large-scale rescoring with data from multiple MS search files, increases sensitivity to minor differences in amino acid residue position, and can be applied to various MS sample types, including tryptic proteome digestions and immunopeptidomes. inSPIRE boosts PSM identification rates in immunopeptidomics, leading to better performance than the original Prosit rescoring pipeline, as confirmed by benchmarking of inSPIRE performance on ground truth datasets. The integration of various features in the inSPIRE backbone further boosts the PSM identification in immunopeptidomics, with a potential benefit for the identification of noncanonical peptides.     

The comparison of the estimation of enzyme kinetic parameters by fitting reaction curve to the integrated Michaelis-Menten rate equations of different predictor variables

The estimation of enzyme kinetic parameters by nonlinear fitting reaction curve to the integrated Michaelis-Menten rate equation ln(S(0)/S)+(S(0)-S)/K(m)=(V(m)/K(m))xt was investigated and compared to that by fitting to (S(0)-S)/t=V(m)-K(m)x[ln(S(0)/S)/t] (Atkins GL, Nimmo IA. The reliability of Michaelis-Menten constants and maximum velocities estimated by using the integrated Michaelis-Menten equation. Biochem J 1973;135:779-84) with uricase as the model. Uricase reaction curve was simulated with random absorbance error of 0.001 at 0.075 mmol/l uric acid. Experimental reaction curve was monitored by absorbance at 293 nm. For both CV and deviation <20% by simulation, K(m) from 5 to 100 micromol/l was estimated with Eq. (1) while K(m) from 5 to 50 micromol/l was estimated with Eq. (2). The background absorbance and the error in the lag time of steady-state reaction resulted in negative K(m) with Eq. (2), but did not affect K(m) estimated with Eq. (1). Both equations gave better estimation of V(m). The computation time and the goodness of fit with Eq. (1) were 40-fold greater than those with Eq. (2). By experimentation, Eq. (1) yielded K(m) consistent with the Lineweaver-Burk plot analysis, but Eq. (2) gave many negative parameters. Apparent K(m) by Eq. (1) linearly increased, while V(m) were constant, vs. xanthine concentrations, and the inhibition constant was consistent with the Lineweaver-Burk plot analysis. These results suggested that the integrated rate equation that uses the predictor variable of reaction time was reliable for the estimation of enzyme kinetic parameters and applicable for the characterization of enzyme inhibitors.     

Movements during sleep reveal the developmental emergence of a cerebellar-dependent internal model in motor thalamus

1. Download : Download high-res image (173KB)
2. Download : Download full-size image

     

Discriminatory power of different arthropod data sets for the biological monitoring of anthropogenic disturbance in tropical forests

Arthropods were monitored by local parataxonomists at 12 sites of increasing anthropogenic disturbance (old and young secondary forests, savanna and cultivated gardens) at Gamba, Gabon. We report on the discriminatory power of different data sets with regard to the classification of sites along the disturbance gradient, using preliminary data accounting for 13 surveys and 142425 arthropods collected by Malaise, pitfall and yellow-pan traps. We compared the performance of different data sets. These were based upon ordinal, familial and guild composition, or upon 22 target taxa sorted to morphospecies and either considered in toto or grouped within different functional guilds. Finally we evaluated predictor sets made up of a few families or other target taxa, selected on the basis of their indicator value index. Although the discriminatory power of data sets based on ordinal categories and guilds was low, that of target taxa belonging to chewers, parasitoids and predators was much higher. The data sets that best discriminated among sites of differing degrees of disturbance were the restricted sets of indicator families and target taxa. This validates the concept of predictor sets for species-rich tropical systems. Including or excluding rare taxa in the analyses did not alter these conclusions. We conclude that calibration studies similar to ours are needed elsewhere in the tropics and that this strategy will allow to devise a representative and efficient biotic index for the biological monitoring of terrestrial arthropod assemblages in the tropics.     

The predictive value of the first-trimester maternal serum chemerin level for pre-eclampsia

Chemerin is a novel adipokine linked to inflammation. The cross-sectional studies have reported that maternal chemerin serum concentrations are significantly increased in pre-eclampsia. However, limited data are available regarding the cause-effect relationship between chemerin and pre-eclampsia. The aim of this prospective observational study was to evaluate predictive significance of the first-trimester maternal serum chemerin levels for pre-eclampsia and to further confirm the hypothesis that chemerin is an important causative factor in the pathogenesis of pre-eclampsia. 518 pregnancy women were recruited. The first-trimester maternal serum chemerin levels were determined using enzyme-linked immunosorbent assay. The first-trimester maternal serum chemerin levels were statistically significantly elevated in women with pre-eclampsia compared with those without pre-eclampsia and in severe pre-eclampsia women compared with mild pre-eclampsia women. Serum chemerin levels remained positively associated with plasma C-reactive protein levels using a linear regression model. A logistic-regression analysis demonstrated that body mass index and serum chemerin levels appeared to be the independent predictors of pre-eclampsia. A receiver–operating characteristic curve analysis identified that serum chemerin levels predicted pre-eclampsia with high predictive value. The predictive value of the chemerin concentrations was similar to that of body mass index. Chemerin improved the predictive value of body mass index statistically significantly. Thus, our results suggest that high serum chemerin levels are associated with inflammation and pre-eclampsia independently, as well as chemerin may play a role as predictive biomarker for pre-eclampsia and be an important causative factor in the pathogenesis of pre-eclampsia.