RNAmute: RNA secondary structure mutation analysis tool

BACKGROUND: RNAMute is an interactive Java application that calculates the secondary structure of all single point mutations, given an RNA sequence, and organizes them into categories according to their similarity with respect to the wild type predicted structure. The secondary structure predictions are performed using the Vienna RNA package. Several alternatives are used for the categorization of single point mutations: Vienna's RNAdistance based on dot-bracket representation, as well as tree edit distance and second eigenvalue of the Laplacian matrix based on Shapiro's coarse grain tree graph representation. RESULTS: Selecting a category in each one of the processed tables lists all single point mutations belonging to that category. Selecting a mutation displays a graphical drawing of the single point mutation and the wild type, and includes basic information such as associated energies, representations and distances. RNAMute can be used successfully with very little previous experience and without choosing any parameter value alongside the initial RNA sequence. The package runs under LINUX operating system. CONCLUSION: RNAMute is a user friendly tool that can be used to predict single point mutations leading to conformational rearrangements in the secondary structure of RNAs. In several cases of substantial interest, notably in virology, a point mutation may lead to a loss of important functionality such as the RNA virus replication and translation initiation because of a conformational rearrangement in the secondary structure

Principles of mRNA transport in yeast

mRNA localization and localized translation is a common mechanism by which cellular asymmetry is achieved. In higher eukaryotes the mRNA transport machinery is required for such diverse processes as stem cell division and neuronal plasticity. Because mRNA localization in metazoans is highly complex, studies at the molecular level have proven to be cumbersome. However, active mRNA transport has also been reported in fungi including Saccharomyces cerevisiae, Ustilago maydis and Candida albicans, in which these events are less difficult to study. Amongst them, budding yeast S. cerevisiae has yielded mechanistic insights that exceed our understanding of other mRNA localization events to date. In contrast to most reviews, we refrain here from summarizing mRNA localization events from different organisms. Instead we give an in-depth account of ASH1 mRNA localization in budding yeast. This approach is particularly suited to providing a more holistic view of the interconnection between the individual steps of mRNA localization, from transcriptional events to cytoplasmic mRNA transport and localized translation. Because of our advanced mechanistic understanding of mRNA localization in yeast, the present review may also be informative for scientists working, for example, on mRNA localization in embryogenesis or in neurons

Nitrogen speciation in upper mantle fluids and the origin of Earth's nitrogen-rich atmosphere

Volatile elements stored in the mantles of terrestrial planets escape through volcanic degassing, and thereby influence planetary atmospheric evolution and habitability. Compared with the atmospheres of Venus and Mars, Earth's atmosphere is nitrogen-rich relative to primordial noble gas concentrations1, 2, 3. The compatibility of volatile elements in mantle minerals versus melts and fluids controls how readily these elements are degassed. However, the speciation of nitrogen in mantle fluids is not well constrained4, 5, 6. Here we present thermodynamic calculations that establish the speciation of nitrogen in aqueous fluids under upper mantle conditions. We find that, under the relatively oxidized conditions of Earth's mantle wedges at convergent plate margins7, 8, 9, nitrogen is expected to exist predominantly as N2 in fluids and, therefore, be degassed easily. In contrast, under more reducing conditions elsewhere in the Earth's upper mantle and in the mantles of Venus and Mars, nitrogen is expected predominantly in the form of ammonium (NH4+) in aqueous fluids. Ammonium is moderately compatible in upper mantle minerals10, 11 and unconducive to nitrogen degassing. We conclude that Earth's oxidized mantle wedge conditions—a result of subduction and hence plate tectonics—favour the development of a nitrogen-enriched atmosphere, relative to the primordial noble gases, whereas the atmospheres of Venus and Mars have less nitrogen because they lack plate tectonics.</p