Characterization of White bream virus reveals a novel genetic cluster of nidoviruses.

The order Nidovirales comprises viruses from the families Coronaviridae (genera Coronavirus and Torovirus), Roniviridae (genus Okavirus), and Arteriviridae (genus Arterivirus). In this study, we characterized White bream virus (WBV), a bacilliform plus-strand RNA virus isolated from fish. Analysis of the nucleotide sequence, organization, and expression of the 26.6-kb genome provided conclusive evidence for a phylogenetic relationship between WBV and nidoviruses. The polycistronic genome of WBV contains five open reading frames (ORFs), called ORF1a, -1b, -2, -3, and -4. In WBV-infected cells, three subgenomic RNAs expressing the structural proteins S, M, and N were identified. The subgenomic RNAs were revealed to share a 42-nucleotide, 5' leader sequence that is identical to the 5'-terminal genome sequence. The data suggest that a conserved nonanucleotide sequence, CA(G/A)CACUAC, located downstream of the leader and upstream of the structural protein genes acts as the core transcription-regulating sequence element in WBV. Like other nidoviruses with large genomes (>26 kb), WBV encodes in its ORF1b an extensive set of enzymes, including putative polymerase, helicase, ribose methyltransferase, exoribonuclease, and endoribonuclease activities. ORF1a encodes several membrane domains, a putative ADP-ribose 1"-phosphatase, and a chymotrypsin-like serine protease whose activity was established in this study. Comparative sequence analysis revealed that WBV represents a separate cluster of nidoviruses that significantly diverged from toroviruses and, even more, from coronaviruses, roniviruses, and arteriviruses. The study adds to the amazing diversity of nidoviruses and appeals for a more extensive characterization of nonmammalian nidoviruses to better understand the evolution of these largest known RNA viruses.

Detection of the icaADBC gene cluster and biofilm formation in Staphylococcus epidermidis isolates from catheter-related urinary tract infections.

Cho SH, Naber K, Hacker J, Ziebuhr W. Institut für Molekulare Infektionsbiologie, Röntgenring 11, D-97070 Würzburg, Germany. Biofilm production in Staphylococcus epidermidis is an important virulence factor that is mediated by the expression of the icaADBC operon. In this study 41 S. epidermidis isolates obtained from catheter-related urinary tract infections were analyzed for the presence of the icaADBC operon and biofilm formation. Eighteen of 41 isolates (44%) were shown to carry ica-specific DNA, but only 11 isolates (27%) produced biofilms spontaneously under normal growth conditions. Upon induction by external stress or antibiotics, biofilm formation could be stimulated in five of seven ica-positive, biofilm-negative isolates, indicating that the icaADBC expression was down-regulated in these strains. Genetic analyses of the ica gene clusters of the remaining two ica-positive, biofilm-negative strains revealed a spontaneous ICAC::IS256 insertion in one strain. Insertion of the element caused a target site duplication of seven base pairs and a biofilm-negative phenotype. After repeated passages the insertion mutant was able to revert to a biofilm-forming phenotype which was due to the precise excision of IS256 from the icaC gene. The data show that icaC::IS256 integrations occur during S. epidermidis polymer-related infections and the results highlight the biological relevance of the IS256-mediated phase variation of biofilm production in S. epidermidis during an infection.

Intense-field dissociation dynamics of D2+ molecular ions using ultrafast laser pulses

The dynamics of dissociation of pre-ionized D2+ molecules using intense (10^12–10^15 W cm-2), ultrashort (50 fs), infrared (? = 790 nm) laser pulses are examined. Use of an intensity selective scan technique has allowed the deuterium energy spectrum to be measured over a broad range of intensity. It is found that the dominant emission shifts to lower energies as intensity is increased, in good agreement with corresponding wavepacket simulations. The results are consistent with an interpretation in terms of bond softening, which at high intensity (approximately >3 × 10^14 W cm-2) becomes dominated by dissociative ionization. Angular distribution measurements reveal the presence of slow molecular dissociation, an indication that vibrational trapping mechanisms occur in this molecule.

Absolute single and multiple charge exchange cross sections for highly charged C, O, and Ne ions on H2O, CO, and CO2

Reported herein are measured absolute single, double, and triple charge exchange (CE) cross sections for the highly charged ions (HCIs) Cq+ (q=5,6), Oq+ (q=6,7,8), and Neq+ (q=7,8) colliding with the molecular species H2O, CO, and CO2. Present data can be applied to interpreting observations of x-ray emissions from comets as they interact with the solar wind. As such, the ion impact energies of 7.0q keV (1.62–3.06 keV/amu) are representative of the fast solar wind, and data at 1.5q keV for O6+ (0.56 keV/amu) on CO and CO2 and 3.5q keV for O5+ (1.09 keV/amu) on CO provide checks of the energy dependence of the cross sections at intermediate and typical slow solar wind velocities. The HCIs are generated within a 14 GHz electron cyclotron resonance ion source. Absolute CE measurements are made using a retarding potential energy analyzer, with measurement of the target gas cell pressure and incident and final ion currents. Trends in the cross sections are discussed in light of the classical overbarrier model (OBM), extended OBM, and with recent results of the classical trajectory Monte Carlo theory.

Quantum revivals in ultrashort intense field dissociation of molecular ions

Ultrashort (<15 fs) high intensity (1014-1016 W cm-2) laser pulses have provided novel methods for investigation of the dynamics of simple molecular ions such as H2+ and D2+. In this paper we report on simulations carried out for the D2+ molecular ion, within the Born- Oppenheimer and two-state approximations. These simulations allow one to investigate the dissociation dynamics of the D2+ molecular ion when subjected to such ultrashort, intense laser pulses. In particular, these simulations are compared to the results from recent pump-probe experiments, in which, the nuclear vibrational motion of D2+ has been imaged. Simulations suggest that the nature of the dissociation process, be it 1- or 2-photon, may be influenced by the tuning of the pump-probe delay time.

Multiple ionization of ions and atoms by intense ultrafast laser pulses

Non-sequential processes in the multiple ionization of Xe and Xe+ targets subject to intense femtosecond laser pulses have been investigated. A precise ratio has been determined for the direct comparison of ionization using circular and linear polarized fields. Suppression of non-sequential effects where an ionic target is compared to a neutral atom target has been confirmed.

Atomic and molecular ions in intense ultra-fast laser fields

The interaction of a 60 fs 790 nm laser pulse with beams of Ar+, C+, H2+, HD+ and D2+ are discussed. Intensities up to 10^16 Wcm-2 are employed. An experimental z-scanning technique is used to resolve the intensity dependent processes in the confocal volume.

Fast-beam study of H2+ ions in an intense femtosecond laser field

A fast beam of H-2(+) ions, produced from a low energy ion accelerator, has been used for the first time in intense laser field experiments. The technique has enabled neutral dissociation products to be analysed and detected for the first time in such studies. Energy spectra of neutral and ionized fragments, product yields as a function of focused laser intensity and angular distributions of neutral dissociation products have been measured. Significant differences are observed between the present results and those obtained from experiments involving neutral H-2 molecules. These differences are indicative of the precursor H-2 molecule playing an important and hitherto neglected formative role in the laser-induced fragmentation processes.

Electron and laser interactions with positive ions

Recent progress in laboratory-based electron-ion scattering is reviewed, and the sensitivity of observed interference structure as a probe of collision dynamics is discussed. The extension of our use of positive ions as scattering targets to photon-ion interactions is demonstrated with the first ion-beam measurements for the fragmentation of a molecular ion, H-2(+), using intense femtosecond laser pulses.

Short pulse laser interaction with positive ions

The viability of using beams of molecular ions as a target for strong field fragmentation studies using intense ultra-short laser pulses is demonstrated. In this way the production mechanism for multiply charged ions in strong fields may be elucidated.

Elastic scattering of electrons from argon ions

A crossed-beams energy-loss spectrometer has been used to investigate angular distributions for electron scattering from Ar2+ and Ar3+ ions, at a collision energy of 16 eV. Results are compared with the predictions of a partial waves calculation based on a semi-empirical potential, and with the classical Rutherford formula.