Structural determination of archaeal UDP-N-acetylglucosamine 4-epimerase from Methanobrevibacter ruminantium M1 in complex with the bacterial cell wall intermediate UDP-N-acetylmuramic acid

The crystal structure of UDP-N-acetylglucosamine 4-epimerase (UDP-GlcNAc 4-epimerase; WbpP; EC 5.1.3.7), from the archaeal methanogen Methanobrevibacter ruminantium strain M1, was determined to a resolution of 1.65 Å. The structure, with a single monomer in the crystallographic asymmetric unit, contained a conserved N-terminal Rossmann fold for nucleotide binding and an active site positioned in the C-terminus. UDP-GlcNAc 4-epimerase is a member of the short-chain dehydrogenase/reductase superfamily, sharing sequence motifs and structural elements characteristic of this family of oxidoreductases and bacterial 4-epimerases. The protein was co-crystallized with coenzyme NADH and UDP-N-acetylmuramic acid, the latter an unintended inclusion and well known product of the bacterial enzyme MurB and a critical intermediate for bacterial cell wall synthesis. This is a non-native UDP sugar amongst archaea and was most likely incorporated from the Eschericha coli expression host during purification of the recombinant enzyme

Spectral Mapping Reconstruction of Extended Sources

Three dimensional spectroscopy of extended sources is typically performed with dedicated integral field spectrographs. We describe a method of reconstructing full spectral cubes, with two spatial and one spectral dimension, from rastered spectral mapping observations employing a single slit in a traditional slit spectrograph. When the background and image characteristics are stable, as is often achieved in space, the use of traditional long slits for integral field spectroscopy can substantially reduce instrument complexity over dedicated integral field designs, without loss of mapping efficiency -- particularly compelling when a long slit mode for single unresolved source followup is separately required. We detail a custom flux-conserving cube reconstruction algorithm, discuss issues of extended source flux calibration, and describe CUBISM, a tool which implements these methods for spectral maps obtained with ther Spitzer Space Telescope's Infrared Spectrograph.Comment: 11 pages, 8 figures, accepted by PAS

The Infra‐Red Absorption Spectra of Ethylene and Tetra‐Deutero‐Ethylene under High Resolution

The fine structure of several infra‐red absorption bands of C2H4 and C2D4 have been resolved. From the rotational constants so found, the C☒C and C☒H distances in this molecule were calculated to be 1.353 and 1.071A, and the H☒C☒H angle to be 119°55′. An assignment of fundamental frequencies has been made which is consistent with the observed data.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/69770/2/JCPSA6-10-2-88-1.pd

On the observability of T Tauri accretion shocks in the X-ray band

Context. High resolution X-ray observations of classical T Tauri stars (CTTSs) show a soft X-ray excess due to high density plasma (n_e=10^11-10^13 cm^-3). This emission has been attributed to shock-heated accreting material impacting onto the stellar surface. Aims. We investigate the observability of the shock-heated accreting material in the X-ray band as a function of the accretion stream properties (velocity, density, and metal abundance) in the case of plasma-beta<<1 in the post-shock zone. Methods. We use a 1-D hydrodynamic model describing the impact of an accretion stream onto the chromosphere, including the effects of radiative cooling, gravity and thermal conduction. We explore the space of relevant parameters and synthesize from the model results the X-ray emission in the [0.5-8.0] keV band and in the resonance lines of O VII (21.60 Ang) and Ne IX (13.45 Ang), taking into account the absorption from the chromosphere. Results. The accretion stream properties influence the temperature and the stand-off height of the shocked slab and its sinking in the chromosphere, determining the observability of the shocked plasma. Our model predicts that X-ray observations preferentially detect emission from low density and high velocity shocked accretion streams due to the large absorption of dense post-shock plasma. In all the cases examined, the post-shock zone exhibits quasi-periodic oscillations due to thermal instabilities, but in the case of inhomogeneous streams and beta<<1, the shock oscillations are hardly detectable. Conclusions. We suggest that, if accretion streams are inhomogeneous, the selection effect introduced by the absorption on observable plasma components may explain the discrepancy between the accretion rate measured by optical and X-ray data as well as the different densities measured using different He-like triplets in the X-ray band.Comment: 12 pages, 7 figures. Accepted for publication on A&

X-ray emitting MHD accretion shocks in classical T Tauri stars. Case for moderate to high plasma-beta values

AIMS. We investigate the stability and dynamics of accretion shocks in CTTSs, considering the case of beta >= 1 in the post-shock region. In these cases the 1D approximation is not valid and a multi-dimensional MHD approach is necessary. METHODS. We model an accretion stream propagating through the atmosphere of a CTTS and impacting onto its chromosphere, by performing 2D axisymmetric MHD simulations. The model takes into account the stellar magnetic field, the gravity, the radiative cooling, and the thermal conduction (including the effects of heat flux saturation). RESULTS. The dynamics and stability of the accretion shock strongly depends on the plasma beta. In the case of shocks with beta > 10, violent outflows of shock-heated material (and possibly MHD waves) are generated at the base of the accretion column and strongly perturb the surrounding stellar atmosphere and the accretion column itself (modifying, therefore, the dynamics of the shock). In shocks with beta ~ 1, the post-shock region is efficiently confined by the magnetic field. The shock oscillations induced by cooling instability are strongly influenced by beta: for beta > 10, the oscillations may be rapidly dumped by the magnetic field, approaching a quasi-stationary state, or may be chaotic with no obvious periodicity due to perturbation of the stream induced by the post-shock plasma itself; for beta ~ 1 the oscillations are quasi-periodic, although their amplitude is smaller and the frequency higher than those predicted by 1D models.Comment: 12 pages, 10 Figures; accepted for publication on A&A. Version with full resolution images can be found at http://www.astropa.unipa.it/~orlando/PREPRINTS/sorlando_13565.pd

Internal Dust Correction Factors for Star Formation Rates Derived for Dusty \HII Regions and Starburst Galaxies

Star formation rates in galaxies are frequently estimated using the Balmer line fluxes. However, these can be systematically underestimated because dust competes for the absorption of Lyman continuum photons in the ionized gas. Here we present theoretical correction factors in a simple analytic form. T These factors scale as the product of the ionization parameter, ${\cal U}$, and the nebular O/H abundance ratio, both of which can now be derived from the observation of bright nebular line ratios. The correction factors are only somewhat dependent upon the photoelectron production by grains, but are very sensitive to the presence of complex PAH-like carbonaceous molecules in the ionized gas, providing that these can survive in such an environment.Comment: 13 pages, 1 figures, Accepted for publication in ApJ. (Feb 1, 2003

Observed Consequences of Presupernova Instability in Very Massive Stars

This chapter concentrates on the deaths of very massive stars, the events leading up to their deaths, and how mass loss affects the resulting death. The previous three chapters emphasized the theory of wind mass loss, eruptions, and core collapse physics, but here we emphasize mainly the observational properties of the resulting death throes. Mass loss through winds, eruptions, and interacting binaries largely determines the wide variety of different types of supernovae that are observed, as well as the circumstellar environments into which the supernova blast waves expand. Connecting these observed properties of the explosions to the initial masses of their progenitor stars is, however, an enduring challenge and is especially difficult for very massive stars. Superluminous supernovae, pair instability supernovae, gamma ray bursts, and "failed" supernovae are all end fates that have been proposed for very massive stars, but the range of initial masses or other conditions leading to each of these (if they actually occur) are still very certain. Extrapolating to infer the role of very massive stars in the early universe is essentially unencumbered by observational constraints and still quite dicey.Comment: 39 pages, 5 figures, to appear as chapter in the book "Very Massive Stars in the Local Universe", ed. J. Vin

The History and Future of the Local and Loop I Bubbles

The Local and Loop I superbubbles are the closest and best investigated supernova (SN) generated bubbles and serve as test laboratories for observations and theories of the interstellar medium. Since the morphology and dynamical evolution of bubbles depend on the ambient density and pressure distributions, a realistic modelling of the galactic environment is crucial for a detailed comparison with observations. We have performed 3D high resolution (down to 1.25 pc on a kpc-scale grid) hydrodynamic simulations of the Local Bubble (LB) and the neighbouring Loop I (L1) superbubble in a realistically evolving inhomogeneous background ISM, disturbed already by SN explosions at the Galactic rate for 200 Myr before the LB and L1 are generated. The LB is the result of 19 SNe occurring in a moving group, which passed through the present day local HI cavity. We can reproduce (i) the OVI column density in absorption within the LB in agreement with COPERNICUS and recent FUSE observations, giving N(OVI) <2 10^{13} cm^-2 and N(OVI)<7 10^{12} cm^-2, respectively, (ii) the observed sizes of the Local and Loop I superbubbles, (iii) the interaction shell between LB and L1, discovered with ROSAT, (iv) constrain the age of the LB to be 14.5+0.7/-0.4 Myr, (v) predict the merging of the two bubbles in about 3 Myr, when the interaction shell starts to fragment, (vi) the generation of blobs like the Local Cloud as a consequence of a dynamical instability. We find that evolving superbubbles strongly deviate from idealised self-similar solutions due to ambient pressure and density gradients, as well as due to turbulent mixing and mass loading. Hence, at later times the hot interior can break through the surrounding shell, which may also help to explain the puzzling energy "deficit" observed in LMC bubbles.Comment: Accepted for publication in Astronomy and Astrophysics Letters. The paper contains 5 pages and 11 figures. Fig. 1a replaced by correct figur

Investigating a genetic link between Alzheimer’s Disease and CADASIL related Cerebral Small Vessel Disease

Monogenic forms of Alzheimer’s disease (AD) have been identified through mutations in genes such as APP, PSEN1, and PSEN2, whilst other genetic markers such as the APOE ε carrier allele status have been shown to increase the likelihood of having the disease. Mutations in these genes are not limited to AD, as APP mutations can also cause an amyloid form of cerebral small vessel disease (CSVD) known as cerebral amyloid angiopathy, whilst PSEN1 and PSEN2 are involved in NOTCH3 signalling, a process known to be dysregulated in the monogenic CSVD, cerebral autosomal dominant arteriopathy with subcortical infarcts and leukoencephalopathy (CADASIL). The overlap between AD genes and causes of CSVD led to the hypothesis that mutations in other genes within the PANTHER AD–presenilin pathway may be novel causes of CSVD in a cohort of clinically suspicious CADASIL patients without a pathogenic NOTCH3 mutation. To investigate this, whole exome sequencing was performed on 50 suspected CADASIL patients with no NOTCH3 mutations, and a targeted gene analysis was completed on the PANTHER. ERN1 was identified as a novel candidate CSVD gene following predicted pathogenic gene mutation analysis. Rare variant burden testing failed to identify an association with any gene; however, it did show a nominally significant link with ERN1 and TRPC3. This study provides evidence to support a genetic overlap between CSVD and Alzheimer’s disease.</p