Crystal structure of Schmallenberg orthobunyavirus nucleoprotein-RNA complex reveals a novel RNA sequestration mechanism

Schmallenberg virus (SBV) is a newly emerged orthobunyavirus (family Bunyaviridae) that has caused severe disease in the offspring of farm animals across Europe. Like all orthobunyaviruses, SBV contains a tripartite negative-sense RNA genome that is encapsidated by the viral nucleocapsid (N) protein in the form of a ribonucleoprotein complex (RNP). We recently reported the three-dimensional structure of SBV N that revealed a novel fold. Here we report the crystal structure of the SBV N protein in complex with a 42-nt-long RNA to 2.16 Å resolution. The complex comprises a tetramer of N that encapsidates the RNA as a cross-shape inside the protein ring structure, with each protomer bound to 11 ribonucleotides. Eight bases are bound in the positively charged cleft between the N- and C-terminal domains of N, and three bases are shielded by the extended N-terminal arm. SBV N appears to sequester RNA using a different mechanism compared with the nucleoproteins of other negative-sense RNA viruses. Furthermore, the structure suggests that RNA binding results in conformational changes of some residues in the RNA-binding cleft and the N- and C-terminal arms. Our results provide new insights into the novel mechanism of RNA encapsidation by orthobunyaviruses

Mass spectrometer tube construction

Work performed for the construction and delivery of four RF mass spectrometer tubes is reported

Effects of geometric anisotropy on local field distribution: Ewald-Kornfeld formulation

We have applied the Ewald-Kornfeld formulation to a tetragonal lattice of point dipoles, in an attempt to examine the effects of geometric anisotropy on the local field distribution. The various problems encountered in the computation of the conditionally convergent summation of the near field are addressed and the methods of overcoming them are discussed. The results show that the geometric anisotropy has a significant impact on the local field distribution. The change in the local field can lead to a generalized Clausius-Mossotti equation for the anisotropic case.Comment: Accepted for publications, Journal of Physics: Condensed Matte

H_2 Absorption and Fluorescence for Gamma Ray Bursts in Molecular Clouds

If a gamma ray burst with strong UV emission occurs in a molecular cloud, there will be observable consequences resulting from excitation of the surrounding H2. The UV pulse from the GRB will pump H2 into vibrationally-excited levels which produce strong absorption at wavelengths < 1650 A. As a result, both the prompt flash and later afterglow will exhibit strong absorption shortward of 1650 A, with specific spectroscopic features. Such a cutoff in the emission from GRB 980329 may already have been observed by Fruchter et al.; if so, GRB 980329 was at redshift 3.0 < z < 4.4 . BVRI photometry of GRB 990510 could also be explained by H2 absorption if GRB 990510 is at redshift 1.6 < z < 2.3. The fluorescence accompanying the UV pumping of the H2 will result in UV emission from the GRB which can extend over days or months, depending on parameters of the ambient medium and beaming of the GRB flash. The 7.5-13.6 eV fluorescent luminosity is \sim 10^{41.7} erg/s for standard estimates of the parameters of the GRB and the ambient medium. Spectroscopy can distinguish this fluorescent emission from other possible sources of transient optical emission, such as a supernova.Comment: 13 pages, including 4 figures. submitted to Ap.J.(Letters

Field-induced structure transformation in electrorheological solids

We have computed the local electric field in a body-centered tetragonal (BCT) lattice of point dipoles via the Ewald-Kornfeld formulation, in an attempt to examine the effects of a structure transformation on the local field strength. For the ground state of an electrorheological solid of hard spheres, we identified a novel structure transformation from the BCT to the face-centered cubic (FCC) lattices by changing the uniaxial lattice constant c under the hard sphere constraint. In contrast to the previous results, the local field exhibits a non-monotonic transition from BCT to FCC. As c increases from the BCT ground state, the local field initially decreases rapidly towards the isotropic value at the body-centered cubic lattice, decreases further, reaching a minimum value and increases, passing through the isotropic value again at an intermediate lattice, reaches a maximum value and finally decreases to the FCC value. An experimental realization of the structure transformation is suggested. Moreover, the change in the local field can lead to a generalized Clausius-Mossotti equation for the BCT lattices.Comment: Submitted to Phys. Rev.

Monte-Carlo simulations of thermal/nonthermal radiation from a neutron-star magnetospheric accretion shell

We discuss the space-and-time-dependent Monte Carlo code we have developed to simulate the relativistic radiation output from compact astrophysical objects, coupled to a Fokker-Planck code to determine the self-consistent lepton populations. We have applied this code to model the emission from a magnetized neutron star accretion shell near the Alfven radius, reprocessing the radiation from the neutron sar surface. We explore the parameter space defined by the accretion rate, stellar surface field and the level of wave turbulence in the shell. Our results are relevant to the emission from atoll sources, soft-X-ray transient X-ray binaries containing weakly magnetized neutron stars, and to recently suggested models of accretion-powered emission from anomalous X-ray pulsars.Comment: 24 pages, including 7 figures; uses epsf.sty. final version, accepted for publication in ApJ. Extended introduction and discussio

Multiepoch Mulitwavelength Spectra and Models for Blazar 3C 279

Peer reviewe

Questions on uncertainties in parton distributions

A discussion is presented of the manner in which uncertainties in parton distributions and related quantities are determined. One of the central problems is the criteria used to judge what variation of the parameters describing a set of partons is acceptable within the context of a global fit. Various ways of addressing this question are outlined