Features of 80S mammalian ribosome and its subunits

It is generally believed that basic features of ribosomal functions are universally valid, but a systematic test still stands out for higher eukaryotic 80S ribosomes. Here we report: (i) differences in tRNA and mRNA binding capabilities of eukaryotic and bacterial ribosomes and their subunits. Eukaryotic 40S subunits bind mRNA exclusively in the presence of cognate tRNA, whereas bacterial 30S do bind mRNA already in the absence of tRNA. 80S ribosomes bind mRNA efficiently in the absence of tRNA. In contrast, bacterial 70S interact with mRNA more productively in the presence rather than in the absence of tRNA. (ii) States of initiation (Pi), pre-translocation (PRE) and post-translocation (POST) of the ribosome were checked and no significant functional differences to the prokaryotic counterpart were observed including the reciprocal linkage between A and E sites. (iii) Eukaryotic ribosomes bind tetracycline with an affinity 15 times lower than that of bacterial ribosomes (Kd 30 μM and 1–2 μM, respectively). The drug does not effect enzymatic A-site occupation of 80S ribosomes in contrast to non-enzymatic tRNA binding to the A-site. Both observations explain the relative resistance of eukaryotic ribosomes to this antibiotic

Fast Algorithms For Josephson Junction Arrays : Bus--bars and Defects

We critically review the fast algorithms for the numerical study of two--dimensional Josephson junction arrays and develop the analogy of such systems with electrostatics. We extend these procedures to arrays with bus--bars and defects in the form of missing bonds. The role of boundaries and of the guage choice in determing the Green's function of the system is clarified. The extension of the Green's function approach to other situations is also discussed.Comment: Uuencoded 1 Revtex file (11 Pages), 3 Figures : Postscript Uuencode

Development and characterization of promoterless helper RNAs for the production of alphavirus replicon particle

Alphavirus-based replicon systems are frequently used as preclinical vectors and as antigen discovery tools, and they have recently been assessed in clinical vaccine trials. Typically, alphavirus replicon RNAs are delivered within virus-like replicon particles (VRP) that are produced following transfection of replicon RNA and two helper RNAs into permissive cells in vitro. The non-structural proteins expressed from the replicon RNA amplify the replicon RNA in cis and the helper RNAs in trans, the latter providing the viral structural proteins necessary to package the replicon RNA into VRP. Current helper RNA designs incorporate the alphavirus 26S promoter to direct the transcription of high levels of structural gene mRNAs. We demonstrate here that the 26S promoter is not required on helper RNAs to produce VRP and propose that such promoterless helper RNAs, by design, reduce the probability of generating replication-competent virus that may otherwise result from RNA recombination

HIV controls the selective packaging of genomic, spliced viral and cellular RNAs into virions through different mechanisms

In addition to genomic RNA, HIV-1 particles package cellular and spliced viral RNAs. In order to determine the encapsidation mechanisms of these RNAs, we determined the packaging efficiencies and specificities of genomic RNA, singly and fully spliced HIV mRNAs and different host RNAs species: 7SL RNA, U6 snRNA and GAPDH mRNA using RT-QPCR. Except GAPDH mRNA, all RNAs are selectively encapsidated. Singly spliced RNAs, harboring the Rev-responsible element, and fully spliced viral RNAs, which do not contain this motif, are enriched in virions to similar levels, even though they are exported from the nucleus by different routes. Deletions of key motifs (SL1 and/or SL3) of the packaging signal of genomic RNA indicate that HIV and host RNAs are encapsidated through independent mechanisms, while genomic and spliced viral RNA compete for the same trans-acting factor due to the presence of the 5′ common exon containing the TAR, poly(A) and U5-PBS hairpins. Surprisingly, the RNA dimerization initiation site (DIS/SL1) appears to be the main packaging determinant of genomic RNA, but is not involved in packaging of spliced viral RNAs, suggesting a functional interaction with intronic sequences. Active and selective packaging of host and spliced viral RNAs provide new potential functions to these RNAs in the early stages of the virus life cycle

Size Dependence of Current-Voltage Properties in Coulomb Blockade Networks

We theoretically investigate the current-voltage (I-V) property of two-dimensional Coulomb blockade (CB) arrays by conducting Monte Carlo simulations. The I-V property can be divided into three regions and we report the dependence of the aspect ratio delta (namely, the lateral size N_{y} over the longitudinal one N_{x}). We show that the average CB threshold obeys a power-law decay as a function of delta. Its exponent gamma corresponds to a sensitivity of the threshold depending on delta, and is inversely proportional to N_{x} (i.e., delta at fixed N_{y}). Further, the power-law exponent zeta, characterizing the nonlinearity of the I-V property in the intermediate region, logarithmically increases as delta increases. Our simulations describe the experimental result zeta=2.25 obtained by Parthasarathy et al. [Phys. Rev. Lett. 87 (2001) 186807]. In addition, the asymptotic I-V property of one-dimensional arrays obtained by Bascones et al. [Phys. Rev. B. 77 (2008) 245422] is applied to two-dimensional arrays. The asymptotic equation converges to the Ohm's law at the large voltage limit, and the combined tunneling-resistance is inversely proportional to delta. The extended asymptotic equation with the first-order perturbation well describes the experimental result obtained by Kurdak et al. [Phys. Rev. B 57 (1998) R6842]. Based on our asymptotic equation, we can estimate physical values that it is hard to obtain experimentally.Comment: 21 pages, 10 figures, accepted for publication in Journal of the Physical Society of Japa

The Astrovirus Capsid: A Review

Astroviruses are enterically transmitted viruses that cause infections in mammalian and avian species. Astroviruses are nonenveloped, icosahedral viruses comprised of a capsid protein shell and a positive-sense, single-stranded RNA genome. The capsid protein undergoes dramatic proteolytic processing both inside and outside of the host cell, resulting in a coordinated maturation process that affects cellular localization, virus structure, and infectivity. After maturation, the capsid protein controls the initial phases of virus infection, including virus attachment, endocytosis, and genome release into the host cell. The astrovirus capsid is the target of host antibodies including virus-neutralizing antibodies. The capsid protein also mediates the binding of host complement proteins and inhibits complement activation. Here, we will review our knowledge on the astrovirus capsid protein (CP), with particular attention to the recent structural, biochemical, and virological studies that have advanced our understanding of the astrovirus life cycle