Transmission of Digitaria Streak Virus by the Maize Streak Virus Leafhopper Vector Cicadulina Mbila Naude

An unpublished account of possible trans-encapsidation of one mastrevirus by another, allowing transmission of both by a vector that normally only transmits one

Two-photon transitions in primordial hydrogen recombination

The subject of cosmological hydrogen recombination has received much attention recently because of its importance to predictions for and cosmological constraints from CMB observations. While the central role of the two-photon decay 2s->1s has been recognized for many decades, high-precision calculations require us to consider two-photon decays from the higher states ns,nd->1s (n>=3). Simple attempts to include these processes in recombination calculations have suffered from physical problems associated with sequences of one-photon decays, e.g. 3d->2p->1s, that technically also produce two photons. These correspond to resonances in the two-photon spectrum that are optically thick, necessitating a radiative transfer calculation. We derive the appropriate equations, develop a numerical code to solve them, and verify the results by finding agreement with analytic approximations to the radiative transfer equation. The related processes of Raman scattering and two-photon recombination are included using similar machinery. Our results show that early in recombination the two-photon decays act to speed up recombination, reducing the free electron abundance by 1.3% relative to the standard calculation at z=1300. However we find that some photons between Ly-alpha and Ly-beta are produced, mainly by 3d->1s two-photon decay and 2s->1s Raman scattering. At later times these photons redshift down to Ly-alpha, excite hydrogen atoms, and act to slow recombination. Thus the free electron abundance is increased by 1.3% relative to the standard calculation at z=900. The implied correction to the CMB power spectrum is neligible for the recently released WMAP and ACBAR data, but at Fisher matrix level will be 7 sigma for Planck. [ABRIDGED]Comment: Matches PRD accepted version. 28 pages, 12 figure

Physical Parameters Of The Relativistic Shock Waves In GRBs: The Case Of 30 GRBs

Using the modified internal shock wave model we fit the gamma ray burst (GRB) light and spectral curves of 30 GRBs observed with BATSE. From the best fitting we obtain basic parameters of the relativistic shells which are in good agreement with predictions given earlier. We compare measured GRB parameters with those obtained from the model and discuss connections between them in the frame of the physical processes laying behind GRB events.Comment: 18 pages, 30 figures, 2 tables, Accepted for publication in IJMP

Viable chimaeric viruses confirm the biological importance of sequence specific maize streak virus movement protein and coat protein interactions

Background. A variety of interactions between up to three different movement proteins (MPs), the coat protein (CP) and genomic DNA mediate the inter- and intra-cellular movement of geminiviruses in the genus Begomovirus. Although movement of viruses in the genus Mastrevirus is less well characterized, direct interactions between a single MP and the CP of these viruses is also clearly involved in both intra- and intercellular trafficking of virus genomic DNA. However, it is currently unknown how specific these MP-CP interactions are, nor how disruption of these interactions might impact on virus viability. Results. Using chimaeric genomes of two strains of Maize streak virus (MSV) we adopted a genetic approach to investigate the gross biological effects of interfering with interactions between virus MP and CP homologues derived from genetically distinct MSV isolates. MP and CP genes were reciprocally exchanged, individually and in pairs, between maize (MSV-Kom)- and Setaria sp. (MSV-Set)-adapted isolates sharing 78% genome-wide sequence identity. All chimaeras were infectious in Zea mays c.v. Jubilee and were characterized in terms of symptomatology and infection efficiency. Compared with their parental viruses, all the chimaeras were attenuated in symptom severity, infection efficiency, and the rate at which symptoms appeared. The exchange of individual MP and CP genes resulted in lower infection efficiency and reduced symptom severity in comparison with exchanges of matched MP-CP pairs. Conclusion. Specific interactions between the mastrevirus MP and CP genes themselves and/or their expression products are important determinants of infection efficiency, rate of symptom development and symptom severity. © 2008 van der Walt et al; licensee BioMed Central Ltd

Measuring the Small-Scale Power Spectrum of Cosmic Density Fluctuations Through 21 cm Tomography Prior to the Epoch of Structure Formation

The thermal evolution of the cosmic gas decoupled from that of the cosmic microwave background (CMB) at a redshift z~200. Afterwards and before the first stars had formed, the cosmic neutral hydrogen absorbed the CMB flux at its resonant 21cm spin-flip transition. We calculate the evolution of the spin temperature for this transition and the resulting anisotropies that are imprinted on the CMB sky due to linear density fluctuations during this epoch. These anisotropies at an observed wavelength of 10.56[(1+z)/50] meters, contain an amount of information that is orders of magnitude larger than any other cosmological probe. Their detection, although challenging, could tightly constrain any possible running of the spectral index from inflation (as suggested by WMAP), small deviations from Gaussianity, or any significant contribution from neutrinos or warm dark matter to the cosmic mass budget.Comment: 4 pages, 3 figures, accepted for publication in Physical Review Letter

On particle acceleration and trapping by Poynting flux dominated flows

Using particle-in-cell (PIC) simulations, we study the evolution of a strongly magnetized plasma slab propagating into a finite density ambient medium. Like previous work, we find that the slab breaks into discrete magnetic pulses. The subsequent evolution is consistent with diamagnetic relativistic pulse acceleration of \cite{liangetal2003}. Unlike previous work, we use the actual electron to proton mass ratio and focus on understanding trapping vs. transmission of the ambient plasma by the pulses and on the particle acceleration spectra. We find that the accelerated electron distribution internal to the slab develops a double-power law. We predict that emission from reflected/trapped external electrons will peak after that of the internal electrons. We also find that the thin discrete pulses trap ambient electrons but allow protons to pass through, resulting in less drag on the pulse than in the case of trapping of both species. Poynting flux dominated scenarios have been proposed as the driver of relativistic outflows and particle acceleration in the most powerful astrophysical jets.Comment: 25 pages, Accepted by Plasma Physics and Controlled Fusio

Linearized Kompaneetz equation as a relativistic diffusion

We show that Kompaneetz equation describing photon diffusion in an environment of an electron gas, when linearized around its equilibrium distribution, coincides with the relativistic diffusion discussed in recent publications. The model of the relativistic diffusion is related to soluble models of imaginary time quantum mechanics. We suggest some non-linear generalizations of the relativistic diffusion equation and their astrophysical applications (in particular to the Sunyaev-Zeldovich effect).Comment: 12 page

Experimental observations of rapid Maize streak virus evolution reveal a strand-specific nucleotide substitution bias

Background. Recent reports have indicated that single-stranded DNA (ssDNA) viruses in the taxonomic families Geminiviridae, Parvoviridae and Anellovirus may be evolving at rates of ∼10-4 substitutions per site per year (subs/site/year). These evolution rates are similar to those of RNA viruses and are surprisingly high given that ssDNA virus replication involves host DNA polymerases with fidelities approximately 10 000 times greater than those of error-prone viral RNA polymerases. Although high ssDNA virus evolution rates were first suggested in evolution experiments involving the geminivirus maize streak virus (MSV), the evolution rate of this virus has never been accurately measured. Also, questions regarding both the mechanistic basis and adaptive value of high geminivirus mutation rates remain unanswered. Results. We determined the short-term evolution rate of MSV using full genome analysis of virus populations initiated from cloned genomes. Three wild type viruses and three defective artificial chimaeric viruses were maintained in planta for up to five years and displayed evolution rates of between 7.4 × 10-4 and 7.9 × 10-4 subs/site/year. Conclusion. These MSV evolution rates are within the ranges observed for other ssDNA viruses and RNA viruses. Although no obvious evidence of positive selection was detected, the uneven distribution of mutations within the defective virus genomes suggests that some of the changes may have been adaptive. We also observed inter-strand nucleotide substitution imbalances that are consistent with a recent proposal that high mutation rates in geminiviruses (and possibly ssDNA viruses in general) may be due to mutagenic processes acting specifically on ssDNA molecules. © 2008 Walt et al; licensee BioMed Central Ltd

Discovery of Interstellar Hydrogen Fluoride

We report the first detection of interstellar hydrogen fluoride. Using the Long Wavelength Spectrometer (LWS) of the Infrared Space Observatory (ISO), we have detected the 121.6973 micron J = 2 - 1 line of HF in absorption toward the far-infrared continuum source Sagittarius B2. The detection is statistically significant at the 13 sigma level. On the basis of our model for the excitation of HF in Sgr B2, the observed line equivalent width of 1.0 nm implies a hydrogen fluoride abundance of 3E-10 relative to H2. If the elemental abundance of fluorine in Sgr B2 is the same as that in the solar system, then HF accounts for ~ 2% of the total number of fluorine nuclei. We expect hydrogen fluoride to be the dominant reservoir of gas-phase fluorine in Sgr B2, because it is formed rapidly in exothermic reactions of atomic fluorine with either water or molecular hydrogen; thus the measured HF abundance suggests a substantial depletion of fluorine onto dust grains. Similar conclusions regarding depletion have previously been reached for the case of chlorine in dense interstellar clouds. We also find evidence at a lower level of statistical significance (~ 5 sigma) for an emission feature at the expected position of the 4(3,2)-4(2,3) 121.7219 micron line of water. The emission line equivalent width of 0.5 nm for the water feature is consistent with the water abundance of 5E-6 relative to H2 that has been inferred previously from observations of the hot core of Sgr B2.Comment: 11 pages (AASTeX using aaspp4.sty) plus 2 figures; to appear in ApJ Letter

HIV-1 sub-type C chimaeric VLPs boost cellular immune responses in mice

Several approaches have been explored to eradicate HIV; however, a multigene vaccine appears to be the best option, given their proven potential to elicit broad, effective responses in animal models. The Pr55Gag protein is an excellent vaccine candidate in its own right, given that it can assemble into large, enveloped, virus-like particles (VLPs) which are highly immunogenic, and can moreover be used as a scaffold for the presentation of other large non-structural HIV antigens. In this study, we evaluated the potential of two novel chimaeric HIV-1 Pr55Gag-based VLP constructs - C-terminal fusions with reverse transcriptase and a Tat::Nef fusion protein, designated GagRT and GagTN respectively - to enhance a cellular response in mice when used as boost components in two types of heterologous prime-boost vaccine strategies. A vaccine regimen consisting of a DNA prime and chimaeric HIV-1 VLP boosts in mice induced strong, broad cellular immune responses at an optimum dose of 100 ng VLPs. The enhanced cellular responses induced by the DNA prime-VLP boost were two- to three-fold greater than two DNA vaccinations. Moreover, a mixture of GagRT and GagTN VLPs also boosted antigen-specific CD8+ and CD4+ T-cell responses, while VLP vaccinations only induced predominantly robust Gag CD4+ T-cell responses. The results demonstrate the promising potential of these chimaeric VLPs as vaccine candidates against HIV-1