Cyclic Variability of the Circumstellar Disc of the Be Star ζ\zeta Tau. II. Testing the 2D Global Disc Oscillation Model

Aims. In this paper we model, in a self-consistent way, polarimetric, photometric, spectrophotometric and interferometric observations of the classical Be star $\zeta$ Tauri. Our primary goal is to conduct a critical quantitative test of the global oscillation scenario. Methods. We have carried out detailed three-dimensional, NLTE radiative transfer calculations using the radiative transfer code HDUST. For the input for the code we have used the most up-to-date research on Be stars to include a physically realistic description for the central star and the circumstellar disc. We adopt a rotationally deformed, gravity darkened central star, surrounded by a disc whose unperturbed state is given by a steady-state viscous decretion disc model. We further assume that disc is in vertical hydrostatic equilibrium. Results. By adopting a viscous decretion disc model for $\zeta$ Tauri and a rigorous solution of the radiative transfer, we have obtained a very good fit of the time-average properties of the disc. This provides strong theoretical evidence that the viscous decretion disc model is the mechanism responsible for disc formation. With the global oscillation model we have successfully fitted spatially resolved VLTI/AMBER observations and the temporal V/R variations of the H$\alpha$ and Br$\gamma$ lines. This result convincingly demonstrates that the oscillation pattern in the disc is a one-armed spiral. Possible model shortcomings, as well as suggestions for future improvements, are also discussed.Comment: 14 pages, 9 figures, accepted to A&

Collective pulsational velocity broadening due to gravity modes as a physical explanation for macroturbulence in hot massive stars

We aimed at finding a physical explanation for the occurrence of macroturbulence in the atmospheres of hot massive stars, a phenomenon found in observations since more than a decade but yet unexplained. We computed time series of line profiles for evolved massive stars broadened by rotation and by hundreds of low-amplitude nonradial gravity-mode pulsations which are predicted to be excited for evolved massive stars. In general, line profiles based on macrotubulent broadening can mimic those subject to pulsational broadening. In several cases, though, good fits require macroturbulent velocities that pass the speed of sound for realistic pulsation amplitudes. Moreover, we find that the rotation velocity can be seriously underestimated by using a simple parameter description for macroturbulence rather than an appropriate pulsational model description to fit the line profiles. We conclude that macroturbulence is a likely signature of the collective effect of pulsations. We provide line diagnostics and their typical values to decide whether or not pulsational broadening is present in observed line profiles, as well as a procedure to avoid an inaccurate estimation of the rotation velocity.Comment: 12 pages, 9 figures, accepted for publication by Astronomy and Astrophysic

Solution structure of the N-terminal dsRBD of Drosophila ADAR and interaction studies with RNA

Adenosine deaminases that act on RNA (ADAR) catalyze adenosine to inosine (A-to-I) editing in double-stranded RNA (dsRNA) substrates. Inosine is read as guanosine by the translation machinery; therefore A-to-I editing events in coding sequences may result in recoding genetic information. Whereas vertebrates have two catalytically active enzymes, namely ADAR1 and ADAR2, Drosophila has a single ADAR protein (dADAR) related to ADAR2. The structural determinants controlling substrate recognition and editing of a specific adenosine within dsRNA substrates are only partially understood. Here, we report the solution structure of the N-terminal dsRNA binding domain (dsRBD) of dADAR and use NMR chemical shift perturbations to identify the protein surface involved in RNA binding. Additionally, we show that Drosophila ADAR edits the R/G site in the mammalian GluR-2 pre-mRNA which is naturally modified by both ADAR1 and ADAR2. We then constructed a model showing how dADAR dsRBD1 binds to the GluR-2 R/G stem-loop. This model revealed that most side chains interacting with the RNA sugar-phosphate backbone need only small displacement to adapt for dsRNA binding and are thus ready to bind to their dsRNA target. It also predicts that dADAR dsRBD1 would bind to dsRNA with less sequence specificity than dsRBDs of ADAR2. Altogether, this study gives new insights into dsRNA substrate recognition by Drosophila ADAR

Optical variabilities in Be/X-ray binary system:GRO J2058+42

We present an analysis of long-term optical monitoring observations and optical spectroscopic observations of the counterpart to CXOU J205847.5+414637 (high mass X-ray binary system). We search for a variability in the light curve of Be star. We used differential magnitudes in the time series analysis. The variability search in the optical light curve was made by using different algorithms. The reduction and analysis of spectra were done by using MIDAS and its suitable packages. We have performed a frequency search which gave us the value 2.404 1/day. This value is attributed to the non-radial pulsation of Be star. H alpha emission line profiles always show double-peaked emissions with a mean equivalent width of 2.31 \pm 0.19 \AA ~and a peak separation of 516 \pm 45 km/s. This suggests that Be star disk is still present. CXOU J205847.5+414637 is in X-ray quiescent state.Comment: 8 pages, 9 figures. To appear at Astronomy and Astrophysic

Beta Cephei stars in the ASAS-3 data. I. Long-term variations of periods and amplitudes

We analysed V-filter ASAS-3 photometry of 41 known Beta Cephei-type stars. The ASAS-3 photometry was combined with the archival data, if available, to determine long-term stability of periods and amplitudes of excited modes. We detected amplitude changes in three Beta Cephei stars, BW Cru, V836 Cen, and V348 Nor. Period changes were found in KK Vel and V836 Cen. Our analysis shows that intrinsic period changes are more common among multiperiodic stars, apparently because they are caused by some kind of mode interaction. In addition, we found new modes for seven stars, and for ten others we provide new solutions or remove ambiguities in the detected frequencies. One candidate hybrid Beta Cephei/SPB star, HD133823, is discovered.Comment: 22 pages, 11 figures, accepted for publication in A&

Weak Glycolipid Binding of a Microdomain-Tracer Peptide Correlates with Aggregation and Slow Diffusion on Cell Membranes

10.1371/journal.pone.0051222PLoS ONE712

Low potency toxins reveal dense interaction networks in metabolism

Background The chemicals of metabolism are constructed of a small set of atoms and bonds. This may be because chemical structures outside the chemical space in which life operates are incompatible with biochemistry, or because mechanisms to make or utilize such excluded structures has not evolved. In this paper I address the extent to which biochemistry is restricted to a small fraction of the chemical space of possible chemicals, a restricted subset that I call Biochemical Space. I explore evidence that this restriction is at least in part due to selection again specific structures, and suggest a mechanism by which this occurs. Results Chemicals that contain structures that our outside Biochemical Space (UnBiological groups) are more likely to be toxic to a wide range of organisms, even though they have no specifically toxic groups and no obvious mechanism of toxicity. This correlation of UnBiological with toxicity is stronger for low potency (millimolar) toxins. I relate this to the observation that most chemicals interact with many biological structures at low millimolar toxicity. I hypothesise that life has to select its components not only to have a specific set of functions but also to avoid interactions with all the other components of life that might degrade their function. Conclusions The chemistry of life has to form a dense, self-consistent network of chemical structures, and cannot easily be arbitrarily extended. The toxicity of arbitrary chemicals is a reflection of the disruption to that network occasioned by trying to insert a chemical into it without also selecting all the other components to tolerate that chemical. This suggests new ways to test for the toxicity of chemicals, and that engineering organisms to make high concentrations of materials such as chemical precursors or fuels may require more substantial engineering than just of the synthetic pathways involved

Environmental factors modulating the stability and enzymatic activity of the Petrotoga mobilis Esterase (PmEst)

Enzymes isolated from thermophilic organisms found in oil reservoirs can find applications in many fields, including the oleochemical, pharmaceutical, bioenergy, and food/dairy industries. In this study, in silico identification and recombinant production of an esterase from the extremophile bacteria Petrotoga mobilis (designated PmEst) were performed. Then biochemical, bioinformatics and structural characterizations were undertaken using a combination of synchrotron radiation circular dichroism (SRCD) and fluorescence spectroscopies to correlate PmEst stability and hydrolytic activity on different substrates. The enzyme presented a high Michaelis-Menten constant (KM 0.16 mM) and optimum activity at ~55°C for p-nitrophenyl butyrate. The secondary structure of PmEst was preserved at acid pH, but not under alkaline conditions. PmEst was unfolded at high concentrations of urea or guanidine through apparently different mechanisms. The esterase activity of PmEst was preserved in the presence of ethanol or propanol and its melting temperature increased ~8°C in the presence of these organic solvents. PmEst is a mesophilic esterase with substrate preference towards short-to medium-length acyl chains. The SRCD data of PmEst is in agreement with the prediction of an α/β protein, which leads us to assume that it displays a typical fold of esterases from this family. The increased enzyme stability in organic solvents may enable novel applications for its use in synthetic biology. Taken together, our results demonstrate features of the PmEst enzyme that indicate it may be suitable for applications in industrial processes, particularly, when the use of polar organic solvents is required