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

Long-lived Charginos in the Focus-point Region of the MSSM Parameter Space

We analyse the possibility to get light long-lived charginos within the framework of the MSSM with gravity mediated SUSY breaking. We find out that this possibility can be realized in the so-called focus-point region of parameter space. The mass degeneracy of higgsino-like chargino and two higgsino-like neutralinos is the necessary condition for a long lifetime. It requires the fine-tuning of parameters, but being a single additional constraint in the whole parameter space it can be fulfilled in the Constrained MSSM along the border line where radiative electroweak symmetry breaking fails. In a narrow band close to the border line the charginos are long-lived particles. The cross-sections of their production and co-production at the LHC via electroweak interaction reach a few tenth of pb.Comment: LaTeX, 11 pages, 11 eps figure

Coupling running through the Looking-Glass of dimensional Reduction

The dimensional reduction, in a form of transition from four to two dimensions, was used in the 90s in a context of HE Regge scattering. Recently, it got a new impetus in quantum gravity where it opens the way to renormalizability and finite short-distance behavior. We consider a QFT model $g\,\varphi^4\,$ with running coupling defined in both the two domains of different dimensionality; the \gbar(Q^2)\, evolutions being duly conjugated at the reduction scale $\,Q\sim M.$ Beyond this scale, in the deep UV 2-dim region, the running coupling does not increase any more. Instead, it {\it slightly decreases} and tends to a finite value \gbar_2(\infty) \,< \, \gbar_2(M^2)\, from above. As a result, the global evolution picture looks quite peculiar and can propose a base for the modified scenario of gauge couplings behavior with UV fixed points provided by dimensional reduction instead of leptoquarks.Comment: 8 pages, 4 figures,Version to match the one which (besides the Appendix) will appear in "Particles and Nuclei (PEPAN), Letters", v.7, No 6(162) 2010 pp 625-631. Slightly edited, one more reference and related numerical estimate adde

Reduced reliance on the trace element selenium during evolution of mammals

Evolution from fish to mammals was accompanied by decreased use of selenocysteine, raising questions about the need for selenium dietary supplements when pathology is not imminent

SECISearch3 and Seblastian: new tools for prediction of SECIS elements and selenoproteins

Selenoproteins are proteins containing an uncommon amino acid selenocysteine (Sec). Sec is inserted by a specific translational machinery that recognizes a stem-loop structure, the SECIS element, at the 3′ UTR of selenoprotein genes and recodes a UGA codon within the coding sequence. As UGA is normally a translational stop signal, selenoproteins are generally misannotated and designated tools have to be developed for this class of proteins. Here, we present two new computational methods for selenoprotein identification and analysis, which we provide publicly through the web servers at http://gladyshevlab.org/SelenoproteinPredictionServer or http://seblastian.crg.es. SECISearch3 replaces its predecessor SECISearch as a tool for prediction of eukaryotic SECIS elements. Seblastian is a new method for selenoprotein gene detection that uses SECISearch3 and then predicts selenoprotein sequences encoded upstream of SECIS elements. Seblastian is able to both identify known selenoproteins and predict new selenoproteins. By applying these tools to diverse eukaryotic genomes, we provide a ranked list of newly predicted selenoproteins together with their annotated cysteine-containing homologues. An analysis of a representative candidate belonging to the AhpC family shows how the use of Sec in this protein evolved in bacterial and eukaryotic lineages

Pyrrolysine and Selenocysteine Use Dissimilar Decoding Strategies

Selenocysteine (Sec) and pyrrolysine (Pyl) are known as the 21st and 22nd amino acids in protein. Both are encoded by codons that normally function as stop signals. Sec specification by UGA codons requires the presence of a cis-acting selenocysteine insertion sequence (SECIS) element. Similarly, it is thought that Pyl is inserted by UAG codons with the help of a putative pyrrolysine insertion sequence (PYLIS) element. Herein, we analyzed the occurrence of Pyl-utilizing organisms, Pyl-associated genes, and Pyl-containing proteins. The Pyl trait is restricted to several microbes, and only one organism has both Pyl and Sec. We found that methanogenic archaea that utilize Pyl have few genes that contain in-frame UAG codons, and many of these are followed with nearby UAA or UGA codons. In addition, unambiguous UAG stop signals could not be identified. This bias was not observed in Sec-utilizing organisms and non-Pyl-utilizing archaea, as well as with other stop codons. These observations as well as analyses of the coding potential of UAG codons, overlapping genes, and release factor sequences suggest that UAG is not a typical stop signal in Pyl-utilizing archaea. On the other hand, searches for conserved Pyl-containing proteins revealed only four protein families, including methylamine methyltransferases and transposases. Only methylamine methyltransferases matched the Pyl trait and had conserved Pyl, suggesting that this amino acid is used primarily by these enzymes. These findings are best explained by a model wherein UAG codons may have ambiguous meaning and Pyl insertion can effectively compete with translation termination for UAG codons obviating the need for a specific PYLIS structure. Thus, Sec and Pyl follow dissimilar decoding and evolutionary strategies

Supersymmetry and LHC

The motivation for introduction of supersymmetry in high energy physics as well as a possibility for supersymmetry discovery at LHC (Large Hadronic Collider) are discussed. The main notions of the Minimal Supersymmetric Standard Model (MSSM) are introduced. Different regions of parameter space are analyzed and their phenomenological properties are compared. Discovery potential of LHC for the planned luminosity is shown for different channels. The properties of SUSY Higgs bosons are studied and perspectives of their observation at LHC are briefly outlined.Comment: Lectures given at the 9th Moscow International School of Physics (XXXIV ITEP Winter School of Physics

Identification of Trace Element-Containing Proteins in Genomic Databases

Development of bioinformatics tools provided researchers with the ability to identify full sets of trace element–containing proteins in organisms for which complete genomic sequences are available. Recently, independent bioinformatics methods were used to identify all, or almost all, genes encoding selenocysteine-containing proteins in human, mouse, and Drosophila genomes, characterizing entire selenoproteomes in these organisms. It also should be possible to search for entire sets of other trace element–associated proteins, such as metal-containing proteins, although methods for their identification are still in development