Dissecting apoptosis the omics way

A combined analysis of transcription, translation and protein degradation reveals the global effects of an anticancer drug on tumour cells

Single polymer dynamics: coil-stretch transition in a random flow

By quantitative studies of statistics of polymer stretching in a random flow and of a flow field we demonstrate that the stretching of polymer molecules in a 3D random flow occurs rather sharply via the coil-stretch transition at the value of the criterion close to theoretically predicted.Comment: 4 pages, 5 figure

Translation inhibitors cause abnormalities in ribosome profiling experiments

Ribosome profiling and high-throughput sequencing provide unprecedented opportunities for the analysis of mRNA translation. Using this novel method, several studies have demonstrated the widespread role of short upstream reading frames in translational control as well as slower elongation at the beginning of open reading frames in response to stress. Based on the initial studies, the importance of adding or omitting translation inhibitors, such as cycloheximide, was noted as it markedly affected ribosome coverage profiles. For that reason, many recent studies omitted translation inhibitors in the culture medium. Here, we investigate the influence of ranging cycloheximide concentrations on ribosome profiles in Saccharomyces cerevisiae and demonstrate that increasing the drug concentration can overcome some of the artifacts. We subjected cells to various manipulations and show that neither oxidative stress nor heat shock nor amino acid starvation affect translation elongation. Instead, the observations in the initial studies are the result of cycloheximide-inflicted artifacts. Likewise, we find little support for short upstream reading frames to be involved in widespread protein synthesis regulation under stress conditions. Our study highlights the need for better standardization of ribosome profiling methods

Hypersensitive transport in a phase model with multiplicative stimulus

In a simple system with periodic symmetric potential, the phase model under effect of strong multiplicative noise or periodic square wave, we found a giant response, in the form of directed flux, to an ultrasmall dc signal. The resulting flux demonstrates a bell-shaped dependence on multiplicative noise correlation time and occurs even in the case of large (compared to the signal) additive noise.Comment: 3 EPS figures, submitted to Phys.Lett.