Packaging signals in single-stranded RNA viruses: nature’s alternative to a purely electrostatic assembly mechanism

The formation of a protective protein container is an essential step in the life-cycle of most viruses. In the case of single-stranded (ss)RNA viruses, this step occurs in parallel with genome packaging in a co-assembly process. Previously, it had been thought that this process can be explained entirely by electrostatics. Inspired by recent single-molecule fluorescence experiments that recapitulate the RNA packaging specificity seen in vivo for two model viruses, we present an alternative theory, which recognizes the important cooperative roles played by RNA–coat protein interactions, at sites we have termed packaging signals. The hypothesis is that multiple copies of packaging signals, repeated according to capsid symmetry, aid formation of the required capsid protein conformers at defined positions, resulting in significantly enhanced assembly efficiency. The precise mechanistic roles of packaging signal interactions may vary between viruses, as we have demonstrated for MS2 and STNV. We quantify the impact of packaging signals on capsid assembly efficiency using a dodecahedral model system, showing that heterogeneous affinity distributions of packaging signals for capsid protein out-compete those of homogeneous affinities. These insights pave the way to a new anti-viral therapy, reducing capsid assembly efficiency by targeting of the vital roles of the packaging signals, and opens up new avenues for the efficient construction of protein nanocontainers in bionanotechnology

A novel approach to isolating improved industrial interspecific wine yeasts using chromosomal mutations as potential markers for increased fitness

Wine yeast breeding programs utilizing interspecific hybridization deliver cost-effective tools to winemakers looking to differentiate their wines through the development of new wine styles. The addition of a non-Saccharomyces cerevisiae genome to a commercial wine yeast can generate novel phenotypes ranging from wine flavor and aroma diversity to improvements in targeted fermentation traits. In the current study we utilized a novel approach to screen isolates from an evolving population for increased fitness in a S. cerevisiae × S. uvarum interspecific hybrid previously generated to incorporate the targeted phenotype of lower volatile acidity production. Sequential grape-juice fermentations provided a selective environment from which to screen isolates. Chromosomal markers were used in a novel approach to identify isolates with potential increased fitness. A strain with increased fitness relative to its parents was isolated from an early timepoint in the evolving population, thereby minimizing the risk of introducing collateral mutations and potentially undesirable phenotypes. The evolved strain retained the desirable fermentation trait of reduced volatile acidity production, along with other winemaking traits of importance while exhibiting improved fermentation kinetics.Jennifer R. Bellon, Christopher M. Ford, Anthony R. Borneman and Paul J. Chamber

The relative importance of electron-electron interactions compared to disorder in the two-dimensional "metallic" state

The effect of substrate bias and surface gate voltage on the low temperature resistivity of a Si-MOSFET is studied for electron concentrations where the resistivity increases with increasing temperature. This technique offers two degrees of freedom for controlling the electron concentration and the device mobility, thereby providing a means to evaluate the relative importance of electron-electron interactions and disorder in this so-called ``metallic'' regime. For temperatures well below the Fermi temperature, the data obey a scaling law where the disorder parameter ($k_{\rm{F}}l$), and not the concentration, appears explicitly. This suggests that interactions, although present, do not alter the Fermi-liquid properties of the system fundamentally. Furthermore, this experimental observation is reproduced in results of calculations based on temperature-dependent screening, in the context of Drude-Boltzmann theory.Comment: 5 pages, 6 figure

Search for the Rare Decay KL --> pi0 ee

The KTeV/E799 experiment at Fermilab has searched for the rare kaon decay KL--> pi0ee. This mode is expected to have a significant CP violating component. The measurement of its branching ratio could support the Standard Model or could indicate the existence of new physics. This letter reports new results from the 1999-2000 data set. One event is observed with an expected background at 0.99 +/- 0.35 events. We set a limit on the branching ratio of 3.5 x 10^(-10) at the 90% confidence level. Combining the results with the dataset taken in 1997 yields the final KTeV result: BR(KL --> pi0 ee) < 2.8 x 10^(-10) at 90% CL.Comment: 4 pages, three figure

Confinement and Chiral Symmetry Breaking via Domain-Like Structures in the QCD Vacuum

A qualitative mechanism for the emergence of domain structured background gluon fields due to singularities in gauge field configurations is considered, and a model displaying a type of mean field approximation to the QCD partition function based on this mechanism is formulated. Estimation of the vacuum parameters (gluon condensate, topological susceptibility, string constant and quark condensate) indicates that domain-like structures lead to an area law for the Wilson loop, nonzero topological susceptibility and spontaneous breakdown of chiral symmetry. Gluon and ghost propagators in the presence of domains are calculated explicitly and their analytical properties are discussed. The Fourier transforms of the propagators are entire functions and thus describe confined dynamical fields.Comment: RevTeX, 48 pages (32 pages + Appendices A-E), new references added [1,2,4,5] and minor formulae corrected for typographical error

On a Light Spinless Particle Coupled to Photons

A pseudoscalar or scalar particle $\phi$ that couples to two photons but not to leptons, quarks and nucleons would have effects in most of the experiments searching for axions, since these are based on the $a \gamma \gamma$ coupling. We examine the laboratory, astrophysical and cosmological constraints on $\phi$ and study whether it may constitute a substantial part of the dark matter. We also generalize the $\phi$ interactions to possess $SU(2) \times U(1)$ gauge invariance, and analyze the phenomenological implications.Comment: LaTex, 20p., 6 figures. Changes in sections 4, 5 and figure 2, our bounds are now more stringent. To be published in Physical Review

Applications of scalar attractor solutions to Cosmology

We develop a framework to study the phase space of a system consisting of a scalar field rolling down an arbitrary potential with varying slope and a background fluid, in a cosmological setting. We give analytical approximate solutions of the field evolution and discuss applications of its features to the issues of quintessence, moduli stabilisation and quintessential inflation.Comment: 9 pages, 7 figures. Accepted for publication in PR

Quantitative Treatment of Decoherence

We outline different approaches to define and quantify decoherence. We argue that a measure based on a properly defined norm of deviation of the density matrix is appropriate for quantifying decoherence in quantum registers. For a semiconductor double quantum dot qubit, evaluation of this measure is reviewed. For a general class of decoherence processes, including those occurring in semiconductor qubits, we argue that this measure is additive: It scales linearly with the number of qubits.Comment: Revised version, 26 pages, in LaTeX, 3 EPS figure

On exact solutions for quintessential (inflationary) cosmological models with exponential potentials

We first study dark energy models with a minimally-coupled scalar field and exponential potentials, admitting exact solutions for the cosmological equations: actually, it turns out that for this class of potentials the Einstein field equations exhibit alternative Lagrangians, and are completely integrable and separable (i.e. it is possible to integrate the system analytically, at least by quadratures). We analyze such solutions, especially discussing when they are compatible with a late time quintessential expansion of the universe. As a further issue, we discuss how such quintessential scalar fields can be connected to the inflationary phase, building up, for this class of potentials, a quintessential inflationary scenario: actually, it turns out that the transition from inflation toward late-time exponential quintessential tail admits a kination period, which is an indispensable ingredient of this kind of theoretical models. All such considerations have also been done by including radiation into the model.Comment: Revtex4, 10 figure

Electromagnetic Casimir densities for a wedge with a coaxial cylindrical shell

Vacuum expectation values of the field square and the energy-momentum tensor for the electromagnetic field are investigated for the geometry of a wedge with a coaxal cylindrical boundary. All boundaries are assumed to be perfectly conducting and both regions inside and outside the shell are considered. By using the generalized Abel-Plana formula, the vacuum expectation values are presented in the form of the sum of two terms. The first one corresponds to the geometry of the wedge without the cylindrical shell and the second term is induced by the presence of the shell. The vacuum energy density induced by the shell is negative for the interior region and is positive for the exterior region. The asymptotic behavior of the vacuum expectation values are investigated in various limiting cases. It is shown that the vacuum forces acting on the wedge sides due to the presence of the cylindrical boundary are always attractive.Comment: 21 pages, 7 figure