Structural modeling and functional analysis of the essential ribosomal processing protease Prp from Staphylococcus aureus

In Firmicutes and related bacteria, ribosomal large subunit protein L27 is encoded with a conserved N-terminal extension that is removed to expose residues critical for ribosome function. Bacteria encoding L27 with this N-terminal extension also encode a sequence-specific cysteine protease, Prp, which carries out this cleavage. In this work, we demonstrate that L27 variants with an un-cleavable N-terminal extension, or lacking the extension (pre-cleaved), are unable to complement an L27 deletion in Staphylococcus aureus. This indicates that N-terminal processing of L27 is not only essential but possibly has a regulatory role. Prp represents a new clade of previously uncharacterized cysteine proteases, and the dependence of S. aureus on L27 cleavage by Prp validates the enzyme as a target for potential antibiotic development. To better understand the mechanism of Prp activity, we analyzed Prp enzyme kinetics and substrate preference using a fluorogenic peptide cleavage assay. Molecular modeling and site-directed mutagenesis implicate several residues around the active site in catalysis and substrate binding, and support a structural model in which rearrangement of a flexible loop upon binding of the correct peptide substrate is required for the active site to assume the proper conformation. These findings lay the foundation for the development of antimicrobials that target this novel, essential pathway

RUST: A Retargetable Usability Testbed for Website Authentication Technologies

Website authentication technologies attempt to make the identity of a website clear to the user, by supplying information about the identity of the website. In practice however, usability issues can prevent users from correctly identifying the websites they are interacting with. To help identify usability issues we present RUST, a Retargetable USability Testbed for website authentication technologies. RUST is a testbed that consists of a test harness, which provides the ability to easily configure the environment for running usability study sessions, and a usability study design that evaluates usability based on spoofability, learnability, and acceptability. We present data collected by RUST and discuss preliminary results for two authentication technologies, Microsoft CardSpace and Verisign Secure Letterhead. Based on the data collected, we conclude that the testbed is useful for gathering data on a variety of technologies

Effects of Experimentally Elevated Traffic Noise on Nestling White-Crowned Sparrow Stress Physiology, Immune Function and Life History

Roads have been associated with behavioral and physiological changes in wildlife. In birds, roads decrease reproductive success and biodiversity and increase physiological stress. Although the consequences of roads on individuals and communities have been well described, the mechanisms through which roads affect birds remain largely unexplored. Here, we examine one mechanism through which roads could affect birds: traffic noise. We exposed nestling mountain white-crowned sparrows (Zonotrichia leucophrys oriantha) to experimentally elevated traffic noise for 5 days during the nestling period. Following exposure to traffic noise we measured nestling stress physiology, immune function, body size, condition and survival. Based on prior studies, we expected the traffic noise treatment to result in elevated stress hormones (glucocorticoids), and declines in immune function, body size, condition and survival. Surprisingly, nestlings exposed to traffic noise had lower glucocorticoid levels and improved condition relative to control nests. These results indicate that traffic noise does affect physiology and development in white-crowned sparrows, but not at all as predicted. Therefore, when evaluating the mechanisms through which roads affect avian populations, other factors (e.g. edge effects, pollution and mechanical vibration) may be more important than traffic noise in explaining elevated nestling stress responses in this species

Mapping The Interstellar Medium With Near-Infrared Diffuse Interstellar Bands

We map the distribution and properties of the Milky Way's interstellar medium as traced by diffuse interstellar bands (DIBs) detected in near-infrared stellar spectra from the SDSS-III/APOGEE survey. Focusing exclusively on the strongest DIB in the H band, at lambda similar to 1.527 mu m, we present a projected map of the DIB absorption field in the Galactic plane, using a set of about 60,000 sightlines that reach up to 15 kpc from the Sun and probe up to 30 mag of visual extinction. The strength of this DIB is linearly correlated with dust reddening over three orders of magnitude in both DIB equivalent width (Wpm) and extinction, with a power law index of 1.01 +/- 0.01, a mean relationship of W-DIB/A(v) = 0.1 angstrom mag(-1) and a dispersion of similar to 0.05 angstrom mag(-1) at extinctions characteristic of the Galactic midplane. These properties establish this DIB as a powerful, independent probe of dust extinction over a wide range of Av values. The subset of about 14,000 robustly detected DIB features have a W-DIB distribution that follows an exponential trend. We empirically determine the intrinsic rest wavelength of this transition to be lambda(0) = 15 272.42 angstrom and use it to calculate absolute radial velocities of the carrier, which display the kinematical signature of the rotating Galactic disk. We probe the DIB carrier distribution in three dimensions and show that it can be characterized by an exponential disk model with a scale height of about 100 pc and a scale length of about 5 kpc. Finally, we show that the DIB distribution also traces large-scale Galactic structures, including the Galactic long bar and the warp of the outer disk.NSF Astronomy & Astrophysics Postdoctoral Fellowship AST-1203017NSF AST-1109665Alfred P. Sloan FoundationNational Science FoundationU.S. Department of Energy Office of ScienceUniversity of ArizonaBrazilian Participation GroupBrookhaven National LaboratoryUniversity of CambridgeCarnegie Mellon UniversityUniversity of FloridaFrench Participation GroupGerman Participation GroupHarvard UniversityInstituto de Astrofisica de CanariasMichigan State/Notre Dame/JINA Participation GroupJohns Hopkins UniversityLawrence Berkeley National LaboratoryMax Planck Institute for AstrophysicsMax Planck Institute for Extraterrestrial PhysicsNew Mexico State UniversityNew York UniversityOhio State UniversityPennsylvania State UniversityUniversity of PortsmouthPrinceton UniversitySpanish Participation GroupUniversity of TokyoUniversity of UtahVanderbilt UniversityUniversity of VirginiaUniversity of WashingtonYale UniversitySpanish Ministry of Economy and Competitiveness AYA-2011-27754McDonald Observator

Chemical Cartography with APOGEE: Large-scale Mean Metallicity Maps of the Milky Way

We present Galactic mean metallicity maps derived from the first year of the SDSS-III APOGEE experiment. Mean abundances in different zones of Galactocentric radius (0 < R < 15 kpc) at a range of heights above the plane (0 < |z| < 3 kpc), are derived from a sample of nearly 20,000 stars with unprecedented coverage, including stars in the Galactic mid-plane at large distances. We also split the sample into subsamples of stars with low and high-[{\alpha}/M] abundance ratios. We assess possible biases in deriving the mean abundances, and find they are likely to be small except in the inner regions of the Galaxy. A negative radial gradient exists over much of the Galaxy; however, the gradient appears to flatten for R < 6 kpc, in particular near the Galactic mid-plane and for low-[{\alpha}/M] stars. At R > 6 kpc, the gradient flattens as one moves off of the plane, and is flatter at all heights for high-[{\alpha}/M] stars than for low-[{\alpha}/M] stars. Alternatively, these gradients can be described as vertical gradients that flatten at larger Galactocentric radius; these vertical gradients are similar for both low and high-[{\alpha}/M] populations. Stars with higher [{\alpha}/M] appear to have a flatter radial gradient than stars with lower [{\alpha}/M]. This could suggest that the metallicity gradient has grown steeper with time or, alternatively, that gradients are washed out over time by migration of stars.Comment: 16 pages, 12 figures, submitted to A

Sodium and Oxygen Abundances in the Open Cluster NGC 6791 from APOGEE H-Band Spectroscopy

The open cluster NGC 6791 is among the oldest, most massive and metal-rich open clusters in the Galaxy. High-resolution $H$-band spectra from the Apache Point Observatory Galactic Evolution Experiment (APOGEE) of 11 red giants in NGC 6791 are analyzed for their chemical abundances of iron, oxygen, and sodium. The abundances of these three elements are found to be homogeneous (with abundance dispersions at the level of $\sim$ 0.05 - 0.07 dex) in these cluster red giants, which span much of the red-giant branch (T$_{\rm eff}$ $\sim$ 3500K - 4600K), and include two red-clump giants. From the infrared spectra, this cluster is confirmed to be among the most metal-rich clusters in the Galaxy ($$ = 0.34 $\pm$ 0.06), and is found to have a roughly solar value of [O/Fe] and slightly enhanced [Na/Fe]. Non-LTE calculations for the studied Na I lines in the APOGEE spectral region ($\lambda$16373.86\AA\ and $\lambda$16388.85\AA) indicate only small departures from LTE ($\leq$ 0.04 dex) for the parameter range and metallicity of the studied stars. The previously reported double population of cluster members with different Na abundances is not found among the studied sample.Comment: Accepted for publication at ApJ Letter

Very Metal-poor Stars in the Outer Galactic Bulge Found by the Apogee Survey

Despite its importance for understanding the nature of early stellar generations and for constraining Galactic bulge formation models, at present little is known about the metal-poor stellar content of the central Milky Way. This is a consequence of the great distances involved and intervening dust obscuration, which challenge optical studies. However, the Apache Point Observatory Galactic Evolution Experiment (APOGEE), a wide-area, multifiber, high-resolution spectroscopic survey within Sloan Digital Sky Survey III (SDSS-III), is exploring the chemistry of all Galactic stellar populations at infrared wavelengths, with particular emphasis on the disk and the bulge. An automated spectral analysis of data on 2,403 giant stars in twelve fields in the bulge obtained during APOGEE commissioning yielded five stars with low metallicity([Fe/H]$\le-1.7$), including two that are very metal-poor [Fe/H]$\sim-2.1$ by bulge standards. Luminosity-based distance estimates place the five stars within the outer bulge, where other 1,246 of the analyzed stars may reside. A manual reanalysis of the spectra verifies the low metallicities, and finds these stars to be enhanced in the $\alpha$-elements O, Mg, and Si without significant $\alpha$-pattern differences with other local halo or metal-weak thick-disk stars of similar metallicity, or even with other more metal-rich bulge stars. While neither the kinematics nor chemistry of these stars can yet definitively determine which, if any, are truly bulge members, rather than denizens of other populations co-located with the bulge, the newly-identified stars reveal that the chemistry of metal-poor stars in the central Galaxy resembles that of metal-weak thick-disk stars at similar metallicity.Comment: 6 pages, 3 figures, 2 table

Mucosal Priming of Simian Immunodeficiency Virus-Specific Cytotoxic T-Lymphocyte Responses in Rhesus Macaques by the \u3ci\u3eSalmonella\u3c/i\u3e Type III Secretion Antigen Delivery System

Nearly all human immunodeficiency virus (HIV) infections are acquired mucosally, and the gut-associated lymphoid tissues are important sites for early virus replication. Thus, vaccine strategies designed to prime virus-specific cytotoxic T lymphocyte (CTL) responses that home to mucosal compartments may be particularly effective at preventing or containing HIV infection. The Salmonella type III secretion system has been shown to be an effective approach for stimulating mucosal CTL responses in mice. We therefore tested ∆phoP-phoQ attenuated strains of Salmonella enterica serovar Typhimurium and S. enterica serovar Typhi expressing fragments of the simian immunodeficiency virus (SIV) Gag protein fused to the type III-secreted SopE protein for the ability to prime virus-specific CTL responses in rhesus macaques. Mamu-A*01+ macaques were inoculated with three oral doses of recombinant Salmonella, followed by a peripheral boost with modified vaccinia virus Ankara expressing SIV Gag (MVA Gag). Transient low-level CTL responses to the Mamu-A*01 Gag181-189 epitope were detected following each dose of Salmonella. After boosting with MVA Gag, strong Gag-specific CTL responses were consistently detected, and tetramer staining revealed the expansion of Gag181-189-specific CD8+ T-cell responses in peripheral blood. A significant percentage of the Gag181-189- specific T-cell population in each animal also expressed the intestinal homing receptor α4β7. Additionally, Gag181-189-specific CD8+ T cells were detected in lymphocytes isolated from the colon. Yet, despite these responses, Salmonella-primed/MVA-boosted animals did not exhibit improved control of virus replication following a rectal challenge with SIVmac239. Nevertheless, this study demonstrates the potential of mucosal priming by the Salmonella type III secretion system to direct SIV-specific cellular immune responses to the gastrointestinal mucosa in a primate model

Testing the Asteroseismic Mass Scale Using Metal-Poor Stars Characterized with APOGEE and Kepler

Fundamental stellar properties, such as mass, radius, and age, can be inferred using asteroseismology. Cool stars with convective envelopes have turbulent motions that can stochastically drive and damp pulsations. The properties of the oscillation frequency power spectrum can be tied to mass and radius through solar-scaled asteroseismic relations. Stellar properties derived using these scaling relations need verification over a range of metallicities. Because the age and mass of halo stars are well-constrained by astrophysical priors, they provide an independent, empirical check on asteroseismic mass estimates in the low-metallicity regime. We identify nine metal-poor red giants (including six stars that are kinematically associated with the halo) from a sample observed by both the Kepler space telescope and the Sloan Digital Sky Survey-III APOGEE spectroscopic survey. We compare masses inferred using asteroseismology to those expected for halo and thick-disk stars. Although our sample is small, standard scaling relations, combined with asteroseismic parameters from the APOKASC Catalog, produce masses that are systematically higher (=0.17+/-0.05 Msun) than astrophysical expectations. The magnitude of the mass discrepancy is reduced by known theoretical corrections to the measured large frequency separation scaling relationship. Using alternative methods for measuring asteroseismic parameters induces systematic shifts at the 0.04 Msun level. We also compare published asteroseismic analyses with scaling relationship masses to examine the impact of using the frequency of maximum power as a constraint. Upcoming APOKASC observations will provide a larger sample of ~100 metal-poor stars, important for detailed asteroseismic characterization of Galactic stellar populations.Comment: 4 figures; 1 table. Accepted to ApJ