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 Graph-Based Approach to Topic Clustering for Online Comments to News

This paper investigates graph-based approaches to labeled topic clustering of reader comments in online news. For graph-based clustering we propose a linear regression model of similarity between the graph nodes (comments) based on similarity features and weights trained using automatically derived training data. To label the clusters our graph-based approach makes use of DBPedia to abstract topics extracted from the clusters. We evaluate the clustering approach against gold standard data created by human annotators and compare its results against LDA – currently reported as the best method for the news comment clustering task. Evaluation of cluster labelling is set up as a retrieval task, where human annotators are asked to identify the best cluster given a cluster label. Our clustering approach significantly outperforms the LDA baseline and our evaluation of abstract cluster labels shows that graph-based approaches are a promising method of creating labeled clusters of news comments, although we still find cases where the automatically generated abstractive labels are insufficient to allow humans to correctly associate a label with its cluster

Quantum Gravitational Corrections to the Nonrelativistic Scattering Potential of Two Masses

We treat general relativity as an effective field theory, obtaining the full nonanalytic component of the scattering matrix potential to one-loop order. The lowest order vertex rules for the resulting effective field theory are presented and the one-loop diagrams which yield the leading nonrelativistic post-Newtonian and quantum corrections to the gravitational scattering amplitude to second order in G are calculated in detail. The Fourier transformed amplitudes yield a nonrelativistic potential and our result is discussed in relation to previous calculations. The definition of a potential is discussed as well and we show how the ambiguity of the potential under coordinate changes is resolved.Comment: 27 pages, 17 figure

Developments in Rare Kaon Decay Physics

We review the current status of the field of rare kaon decays. The study of rare kaon decays has played a key role in the development of the standard model, and the field continues to have significant impact. The two areas of greatest import are the search for physics beyond the standard model and the determination of fundamental standard-model parameters. Due to the exquisite sensitivity of rare kaon decay experiments, searches for new physics can probe very high mass scales. Studies of the k->pnn modes in particular, where the first event has recently been seen, will permit tests of the standard-model picture of quark mixing and CP violation.Comment: One major revision to the text is the branching ratio of KL->ppg, based on a new result from KTeV. Several references were updated, with minor modifications to the text. A total of 48 pages, with 28 figures, in LaTeX; to be published in the Annual Review of Nuclear and Particle Science, Vol. 50, December 200

K^+ -> pi^+pi^0e^+e^-: a novel short-distance probe

We study the decay K^+ -> pi^+ pi^0 e^+ e^-, currently under analysis by the NA62 Collaboration at CERN. In particular, we provide a detailed analysis of the Dalitz plot for the long-distance, gamma^*-mediated, contributions (Bremsstrahlung, direct emission and its interference). We also examine a set of asymmetries to isolate genuine short-distance effects. While we show that charge asymmetries are not required to test short distances, they provide the best environment for its detection. This constitutes by itself a strong motivation for NA62 to study K^- decays in the future. We therefore provide a detailed study of different charge asymmetries and the corresponding estimated signals. Whenever possible, we make contact with the related processes K^+ -> pi^+ pi^0 gamma and K_L -> pi^+ pi^- e^+ e^- and discuss the advantages of K^+ -> pi^+ pi^0 e^+ e^- over them.Comment: 25 pages, 6 figure

Asymptotic normalization coefficients for 8B->7Be+p from a study of 8Li->7Li+n

Asymptotic normalization coefficients (ANCs) for 8Li->7Li+n have been extracted from the neutron transfer reaction 13C(7Li,8Li)12C at 63 MeV. These are related to the ANCs in 8B->7Be+p using charge symmetry. We extract ANCs for 8B that are in very good agreement with those inferred from proton transfer and breakup experiments. We have also separated the contributions from the p_1/2 and p_3/2 components in the transfer. We find the astrophysical factor for the 7Be(p,gamma)8B reaction to be S_17(0)=17.6+/-1.7 eVb. This is the first time that the rate of a direct capture reaction of astrophysical interest has been determined through a measurement of the ANCs in the mirror system.Comment: 5 pages, 3 figures, 2 table

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

The role of a disulfide bridge in the stability and folding kinetics of Arabidopsis thaliana cytochrome c6A

Cytochrome c 6A is a eukaryotic member of the Class I cytochrome c family possessing a high structural homology with photosynthetic cytochrome c 6 from cyanobacteria, but structurally and functionally distinct through the presence of a disulfide bond and a heme mid-point redox potential of + 71 mV (vs normal hydrogen electrode). The disulfide bond is part of a loop insertion peptide that forms a cap-like structure on top of the core α-helical fold. We have investigated the contribution of the disulfide bond to thermodynamic stability and (un)folding kinetics in cytochrome c 6A from Arabidopsis thaliana by making comparison with a photosynthetic cytochrome c 6 from Phormidium laminosum and through a mutant in which the Cys residues have been replaced with Ser residues (C67/73S). We find that the disulfide bond makes a significant contribution to overall stability in both the ferric and ferrous heme states. Both cytochromes c 6A and c 6 fold rapidly at neutral pH through an on-pathway intermediate. The unfolding rate for the C67/73S variant is significantly increased indicating that the formation of this region occurs late in the folding pathway. We conclude that the disulfide bridge in cytochrome c 6A acts as a conformational restraint in both the folding intermediate and native state of the protein and that it likely serves a structural rather than a previously proposed catalytic role. © 2011 Elsevier B.V. All rights reserved

Vector-meson contributions do not explain the rate and spectrum in K_L -> pi0 gamma gamma

We analyze the recent NA48 data for the reaction K_L -> pi0 gamma gamma with and without the assumption of vector meson dominance (VMD). We find that the data is well described by a three-parameter expression inspired by O(p^6) chiral perturbation theory. We also find that it is impossible to fit the shape of the decay distribution and the overall rate simultaneously if one imposes the VMD constraints on the three parameters. We comment on the different fits and their implications for the CP-conserving component of the decay K_L -> pi0 e+ e-.Comment: Version accepted for publication on Phys. Rev. D. 19 pages, LaTeX, 8 figures, uses epsf.st

Phenomenology of the Lense-Thirring effect in the Solar System

Recent years have seen increasing efforts to directly measure some aspects of the general relativistic gravitomagnetic interaction in several astronomical scenarios in the solar system. After briefly overviewing the concept of gravitomagnetism from a theoretical point of view, we review the performed or proposed attempts to detect the Lense-Thirring effect affecting the orbital motions of natural and artificial bodies in the gravitational fields of the Sun, Earth, Mars and Jupiter. In particular, we will focus on the evaluation of the impact of several sources of systematic uncertainties of dynamical origin to realistically elucidate the present and future perspectives in directly measuring such an elusive relativistic effect.Comment: LaTex, 51 pages, 14 figures, 22 tables. Invited review, to appear in Astrophysics and Space Science (ApSS). Some uncited references in the text now correctly quoted. One reference added. A footnote adde