Characterization of Peeling-Ballooning Stability Limits on the Pedestal

This report describes the Characterization of Peeling-Ballooning Stability Limits on the Pedestal

Phylogenomics reveals the basis of adaptation of Pseudorhizobium species to extreme environments and supports a taxonomic revision of the genus

The family Rhizobiaceae includes many genera of soil bacteria, often isolated for their association with plants. Herein, we investigate the genomic diversity of a group of Rhizobium species and unclassified strains isolated from atypical environments, including seawater, rock matrix or polluted soil. Based on whole-genome similarity and core genome phylogeny, we show that this group corresponds to the genus Pseudorhizobium. We thus reclassify Rhizobium halotolerans, R. marinum, R. flavum and R. endolithicum as P. halotolerans sp. nov., P. marinum comb. nov., P. flavum comb. nov. and P. endolithicum comb. nov., respectively, and show that P. pelagicum is a synonym of P. marinum. We also delineate a new chemolithoautotroph species, P. banfieldiae sp. nov., whose type strain is NT-26T (=DSM 106348T=CFBP 8663T). This genome-based classification was supported by a chemotaxonomic comparison, with increasing taxonomic resolution provided by fatty acid, protein and metabolic profiles. In addition, we used a phylogenetic approach to infer scenarios of duplication, horizontal transfer and loss for all genes in the Pseudorhizobium pangenome. We thus identify the key functions associated with the diversification of each species and higher clades, shedding light on the mechanisms of adaptation to their respective ecological niches. Respiratory proteins acquired at the origin of Pseudorhizobium were combined with clade-specific genes to enable different strategies for detoxification and nutrition in harsh, nutrient-poor environments

Silicate dust in the environment of RS Ophiuchi following the 2006 eruption

We present further Spitzer Space Telescope observations of the recurrent nova RS Ophiuchi, obtained over the period 208-430 days after the 2006 eruption. The later Spitzer IRS data show that the line emission and free-free continuum emission reported earlier is declining, revealing incontrovertible evidence for the presence of silicate emission features at 9.7 and 18microns. We conclude that the silicate dust survives the hard radiation impulse and shock blast wave from the eruption. The existence of the extant dust may have significant implications for understanding the propagation of shocks through the red giant wind and likely wind geometry.Comment: 12 pages, 4 figures, accepted for publication in ApJ (Letters

The discovery of an evolving dust scattered X-ray halo around GRB 031203

We report the first detection of a time-dependent, dust-scattered X-ray halo around a gamma-ray burst. GRB 031203 was observed by XMM-Newton starting six hours after the burst. The halo appeared as concentric ring-like structures centered on the GRB location. The radii of these structures increased with time as t^{1/2}, consistent with small-angle X-ray scattering caused by a large column of dust along the line of sight to a cosmologically distant GRB. The rings are due to dust concentrated in two distinct slabs in the Galaxy located at distances of 880 and 1390 pc, consistent with known Galactic features. The halo brightness implies an initial soft X-ray pulse consistent with the observed GRB.Comment: 4 pages. 4 figures. Accepted for publication in ApJ Letter

Design principles for riboswitch function

Scientific and technological advances that enable the tuning of integrated regulatory components to match network and system requirements are critical to reliably control the function of biological systems. RNA provides a promising building block for the construction of tunable regulatory components based on its rich regulatory capacity and our current understanding of the sequence–function relationship. One prominent example of RNA-based regulatory components is riboswitches, genetic elements that mediate ligand control of gene expression through diverse regulatory mechanisms. While characterization of natural and synthetic riboswitches has revealed that riboswitch function can be modulated through sequence alteration, no quantitative frameworks exist to investigate or guide riboswitch tuning. Here, we combined mathematical modeling and experimental approaches to investigate the relationship between riboswitch function and performance. Model results demonstrated that the competition between reversible and irreversible rate constants dictates performance for different regulatory mechanisms. We also found that practical system restrictions, such as an upper limit on ligand concentration, can significantly alter the requirements for riboswitch performance, necessitating alternative tuning strategies. Previous experimental data for natural and synthetic riboswitches as well as experiments conducted in this work support model predictions. From our results, we developed a set of general design principles for synthetic riboswitches. Our results also provide a foundation from which to investigate how natural riboswitches are tuned to meet systems-level regulatory demands

The XMM-Newton Serendipitous Source Catalogue

We describe the production, properties and scientific potential of the XMM-Newton catalogue of serendipitous X-ray sources. The first version of this catalogue is nearing completion and is planned to be released before the end of 2002.Comment: Proceedings of the "X-ray surveys, in the light of the new observatories" workshop, Astronomische Nachrichten, in the press (4 pages, 3 eps figures, uses an.cls

Multi-wavelength observations of the energetic GRB 080810: detailed mapping of the broadband spectral evolution

GRB 080810 was one of the first bursts to trigger both Swift and the Fermi Gamma-ray Space Telescope. It was subsequently monitored over the X-ray and UV/optical bands by Swift, in the optical by ROTSE and a host of other telescopes and was detected in the radio by the VLA. The redshift of z= 3.355 +/- 0.005 was determined by Keck/HIRES and confirmed by RTT150 and NOT. The prompt gamma/X-ray emission, detected over 0.3-10^3 keV, systematically softens over time, with E_peak moving from ~600 keV at the start to ~40 keV around 100 s after the trigger; alternatively, this spectral evolution could be identified with the blackbody temperature of a quasithermal model shifting from ~60 keV to ~3 keV over the same time interval. The first optical detection was made at 38 s, but the smooth, featureless profile of the full optical coverage implies that this originated from the afterglow component, not the pulsed/flaring prompt emission. Broadband optical and X-ray coverage of the afterglow at the start of the final X-ray decay (~8 ks) reveals a spectral break between the optical and X-ray bands in the range 10^15 - 2x10^16 Hz. The decay profiles of the X-ray and optical bands show that this break initially migrates blueward to this frequency and then subsequently drifts redward to below the optical band by ~3x10^5 s. GRB 080810 was very energetic, with an isotropic energy output for the prompt component of 3x10^53 erg and 1.6x10^52 erg for the afterglow; there is no evidence for a jet break in the afterglow up to six days following the burst.Comment: 15 pages, 9 figures, 4 in colour. Accepted for publication in MNRA

High intensity neutrino oscillation facilities in Europe

The EUROnu project has studied three possible options for future, high intensity neutrino oscillation facilities in Europe. The first is a Super Beam, in which the neutrinos come from the decay of pions created by bombarding targets with a 4 MW proton beam from the CERN High Power Superconducting Proton Linac. The far detector for this facility is the 500 kt MEMPHYS water Cherenkov, located in the Fréjus tunnel. The second facility is the Neutrino Factory, in which the neutrinos come from the decay of μ+ and μ− beams in a storage ring. The far detector in this case is a 100 kt magnetized iron neutrino detector at a baseline of 2000 km. The third option is a Beta Beam, in which the neutrinos come from the decay of beta emitting isotopes, in particular He6 and Ne18, also stored in a ring. The far detector is also the MEMPHYS detector in the Fréjus tunnel. EUROnu has undertaken conceptual designs of these facilities and studied the performance of the detectors. Based on this, it has determined the physics reach of each facility, in particular for the measurement of CP violation in the lepton sector, and estimated the cost of construction. These have demonstrated that the best facility to build is the Neutrino Factory. However, if a powerful proton driver is constructed for another purpose or if the MEMPHYS detector is built for astroparticle physics, the Super Beam also becomes very attractive

A Universal Decline Law of Classical Novae

We calculate many different nova light curves for a variety of white dwarf masses and chemical compositions, with the assumption that free-free emission from optically thin ejecta dominates the continuum flux. We show that all these light curves are homologous and a universal law can be derived by introducing a ``time scaling factor.'' The template light curve for the universal law has a slope of the flux, F \propto t^{-1.75}, in the middle part (from ~2 to ~6 mag below the optical maximum), but it declines more steeply, F \propto t^{-3.5}, in the later part (from ~6 to ~10 mag). This break on the light curve is due to a quick decrease in the wind mass-loss rate. The nova evolutions are approximately scaled by the time of break. Once the time of break is observationally determined, we can derive the various timescales of novae such as the period of a UV burst phase, the duration of optically thick wind phase, and the turnoff date of hydrogen shell-burning. We have applied our template light curve model to the three well-observed novae, V1500 Cyg, V1668 Cyg, and V1974 Cyg. Our theoretical light curves show excellent agreement with the optical y and infrared J, H, K light curves. The WD mass is estimated, from the light curve fitting, to be 1.15 M_\sun for V1500 Cyg, 0.95 ~M_\sun for V1668 Cyg, and 0.95-1.05 M_\sun for V1974 Cyg.Comment: To appear in ApJS, vol.167, 23 pages including 24 figure

Regulation of mammary gland branching morphogenesis by the extracellular matrix and its remodeling enzymes.

A considerable body of research indicates that mammary gland branching morphogenesis is dependent, in part, on the extracellular matrix (ECM), ECM-receptors, such as integrins and other ECM receptors, and ECM-degrading enzymes, including matrix metalloproteinases (MMPs) and their inhibitors, tissue inhibitors of metalloproteinases (TIMPs). There is some evidence that these ECM cues affect one or more of the following processes: cell survival, polarity, proliferation, differentiation, adhesion, and migration. Both three-dimensional culture models and genetic manipulations of the mouse mammary gland have been used to study the signaling pathways that affect these processes. However, the precise mechanisms of ECM-directed mammary morphogenesis are not well understood. Mammary morphogenesis involves epithelial 'invasion' of adipose tissue, a process akin to invasion by breast cancer cells, although the former is a highly regulated developmental process. How these morphogenic pathways are integrated in the normal gland and how they become dysregulated and subverted in the progression of breast cancer also remain largely unanswered questions