cis-acting sequences and trans-acting factors in the localization of mRNA for mitochondrial ribosomal proteins

mRNA localization is a conserved post-transcriptional process crucial for a variety of systems. Although several mechanisms have been identified, emerging evidence suggests that most transcripts reach the protein functional site by moving along cytoskeleton elements. We demonstrated previously that mRNA for mitochondrial ribosomal proteins are asymmetrically distributed in the cytoplasm, and that localization in the proximity of mitochondria is mediated by the 3′-UTR. Here we show by biochemical analysis that these mRNA transcripts are associated with the cytoskeleton through the microtubule network. Cytoskeleton association is functional for their intracellular localization near the mitochondrion, and the 3′-UTR is involved in this cytoskeleton-dependent localization. To identify the minimal elements required for localization, we generated DNA constructs containing, downstream from the GFP gene, deletion mutants of mitochondrial ribosomal protein S12 3′-UTR, and expressed them in HeLa cells. RT-PCR analysis showed that the localization signals responsible for mRNA localization are located in the first 154 nucleotides. RNA pulldown assays, mass spectrometry, and RNP immunoprecipitation assay experiments, demonstrated that mitochondrial ribosomal protein S12 3′-UTR interacts specifically with TRAP1 (tumor necrosis factor receptor-associated protein1), hnRNPM4 (heterogeneous nuclear ribonucleoprotein M4), Hsp70 and Hsp60 (heat shock proteins 70 and 60), and α-tubulin in vitro and in vivo

Different domains cooperate to target the human ribosomal L7a protein to the nucleus and to the nucleoli.

The human ribosomal protein L7a is a component of the major ribosomal subunit. We transiently expressed in HeLa cells L7a-β-galactosidase fusion proteins and studied their subcellular localization by indirect immunofluorescence staining with anti-β-galactosidase antibodies. We have identified three distinct domains responsible for the nuclear targeting of the protein: domain I, amino acids 23-51; domain II, amino acids 52-100; domain III, amino acids 101-220, each of which contains at least one nuclear localization signal (NLS). Through subcellular localization analysis of deletion mutants of L7a-β-galactosidase chimeras, we demonstrate that domain II plays a special role because it is necessary, although not sufficient, to target the chimeric β-galactosidase to the nucleoli. In fact, we demonstrate that the nucleolar targeting process requires the presence of domain II plus an additional basic domain that can be represented by an NLS or a basic stretch of amino acids without NLS activity. Thus, when multiple NLS are present, each NLS exerts distinct functions. Domain II drives nucleolar accumulation of a reporter protein with the cooperative action of a short basic amino acid sequence, suggesting a mechanism requiring protein-protein or protein-nucleic acid interactions

Using Event Calculus to Formalise Policy Specification and Analysis

As the interest in using policy-based approaches for systems management grows, it is becoming increasingly important to develop methods for performing analysis and refinement of policy specifications. Although this is an area that researchers have devoted some attention to, none of the proposed solutions address the issues of analysing specifications that combine authorisation and management policies; analysing policy specifications that contain constraints on the applicability of the policies; and performing a priori analysis of the specification that will both detect the presence of inconsistencies and explain the situations in which the conflict will occur. We present a method for transforming both policy and system behaviour specifications into a formal notation that is based on event calculus. Additionally it describes how this formalism can be used in conjunction with abductive reasoning techniques to perform a priori analysis of policy specifications for the various conflict types identified in the literature. Finally, it presents some initial thoughts on how this notation and analysis technique could be used to perform policy refinement

GKW representation theorem and linear BSDEs under restricted information. An application to risk-minimization

In this paper we provide Galtchouk-Kunita-Watanabe representation results in the case where there are restrictions on the available information. This allows to prove existence and uniqueness for linear backward stochastic differential equations driven by a general c\`adl\`ag martingale under partial information. Furthermore, we discuss an application to risk-minimization where we extend the results of F\"ollmer and Sondermann (1986) to the partial information framework and we show how our result fits in the approach of Schweizer (1994).Comment: 22 page

The interplay of sedimentation and crystallization in hard-sphere suspensions

We study crystal nucleation under the influence of sedimentation in a model of colloidal hard spheres via Brownian Dynamics simulations. We introduce two external fields acting on the colloidal fluid: a uniform gravitational field (body force), and a surface field imposed by pinning a layer of equilibrium particles (rough wall). We show that crystal nucleation is suppressed in proximity of the wall due to the slowing down of the dynamics, and that the spatial range of this effect is governed by the static length scale of bond orientational order. For distances from the wall larger than this length scale, the nucleation rate is greatly enhanced by the process of sedimentation, since it leads to a higher volume fraction, or a higher degree of supercooling, near the bottom. The nucleation stage is similar to the homogeneous case, with nuclei being on average spherical and having crystalline planes randomly oriented in space. The growth stage is instead greatly affected by the symmetry breaking introduced by the gravitation field, with a slowing down of the attachment rate due to density gradients, which in turn cause nuclei to grow faster laterally. Our findings suggest that the increase of crystal nucleation in higher density regions might be the cause of the large discrepancy in the crystal nucleation rate of hard spheres between experiments and simulations, on noting that the gravitational effects in previous experiments are not negligible.Comment: 16 pages, 15 figures, 2 tables; Soft Matter (2013

Delocalised oxygen as the origin of two-level defects in Josephson junctions

One of the key problems facing superconducting qubits and other Josephson junction devices is the decohering effects of bi-stable material defects. Although a variety of phenomenological models exist, the true microscopic origin of these defects remains elusive. For the first time we show that these defects may arise from delocalisation of the atomic position of the oxygen in the oxide forming the Josephson junction barrier. Using a microscopic model, we compute experimentally observable parameters for phase qubits. Such defects are charge neutral but have non-zero response to both applied electric field and strain. This may explain the observed long coherence time of two-level defects in the presence of charge noise, while still coupling to the junction electric field and substrate phonons.Comment: 5 pages, 4 figures. This version streamlines presentation and focuses on the 2D model. Also fixed embarrassing typo (pF -> fF

Strong Magnetic Limit of String Theory

We show that there exists a certain limit in type I and type II superstring theory in the presence of a suitable configuration of magnetic U(1) fields where all string excitations get an infinite mass, except for the neutral massless sector and for the boson and fermion string states lying on the leading Regge trajectory. For a supersymmetric configuration of magnetic fields in internal directions, the resulting theory after the limit is a 3+1 Lorentz invariant supersymmetric theory. Supersymmetry can be broken by introducing extra components of the magnetic field or else by finite temperature. In both cases we compute the one-loop partition function for the type I string model after taking the limit, which turns out to be different from the Yang-Mills result that arises by a direct $\alpha'\to 0$ limit. In the case of finite temperature, no Hagedorn transition appears, in consistency with the reduction of the string spectrum. In type II superstring theory, the analogous limit is constructed by starting with a configuration of Melvin twists in two or more complex planes. The resulting theory contains gravitation plus an infinite number of states of the leading Regge trajectory.Comment: 10 pages. Minor correction

Structural properties and quasiparticule energies of cubic SrO, MgO and SrTiO3

The structural properties and the band structures of the charge-transfer insulating oxides SrO, MgO and SrTiO3 are computed both within density functional theory in the local density approximation (LDA) and in the Hedin's GW scheme for self-energy corrections, by using a model dielectric function, which approximately includes local field and dynamical effects. The deep valence states are shifted by the GW method to higher binding energies, in very good agreement with photoemission spectra. Since in all of these oxides the direct gaps at high-symmetry points of the Brillouin zone may be very sensitive to the actual value of the lattice parameter a, already at the LDA level, self-energy corrections are computed both at the theoretical and the experimental a. For MgO and SrO, the values of the transition energies between the valence and the conduction bands are improved by GW corrections, while for SrTiO3 they are overestimated. The results are discussed in relation to the importance of local field effects and to the nature of the electronic states in these insulating oxides.Comment: 3 figures, accepted in J. Phys.: Condens. Matte