314 research outputs found

    Structural and functional characterization of the Redβ recombinase from bacteriophage λ

    Get PDF
    The Red system of bacteriophage λ is responsible for the genetic rearrangements that contribute to its rapid evolution and has been successfully harnessed as a research tool for genome manipulation. The key recombination component is Redβ, a ring-shaped protein that facilitates annealing of complementary DNA strands. Redβ shares functional similarities with the human Rad52 single-stranded DNA (ssDNA) annealing protein although their evolutionary relatedness is not well established. Alignment of Rad52 and Redβ sequences shows an overall low level of homology, with 15% identity in the N-terminal core domains as well as important similarities with the Rad52 homolog Sak from phage ul36. Key conserved residues were chosen for mutagenesis and their impact on oligomer formation, ssDNA binding and annealing was probed. Two conserved regions were identified as sites important for binding ssDNA; a surface basic cluster and an intersubunit hydrophobic patch, consistent with findings for Rad52. Surprisingly, mutation of Redβ residues in the basic cluster that in Rad52 are involved in ssDNA binding disrupted both oligomer formation and ssDNA binding. Mutations in the equivalent of the intersubunit hydrophobic patch in Rad52 did not affect Redβ oligomerization but did impair DNA binding and annealing. We also identified a single amino acid substitution which had little effect on oligomerization and DNA binding but which inhibited DNA annealing, indicating that these two functions of Redβ can be separated. Taken together, the results provide fresh insights into the structural basis for Redβ function and the important role of quaternary structure

    Moduli and (un)attractor black hole thermodynamics

    Get PDF
    We investigate four-dimensional spherically symmetric black hole solutions in gravity theories with massless, neutral scalars non-minimally coupled to gauge fields. In the non-extremal case, we explicitly show that, under the variation of the moduli, the scalar charges appear in the first law of black hole thermodynamics. In the extremal limit, the near horizon geometry is AdS2×S2AdS_2\times S^2 and the entropy does not depend on the values of moduli at infinity. We discuss the attractor behaviour by using Sen's entropy function formalism as well as the effective potential approach and their relation with the results previously obtained through special geometry method. We also argue that the attractor mechanism is at the basis of the matching between the microscopic and macroscopic entropies for the extremal non-BPS Kaluza-Klein black hole.Comment: 36 pages, no figures, V2: minor changes, misprints corrected, expanded references; V3: sections 4.3 and 4.5 added; V4: minor changes, matches the published versio

    Rural-urban outcome differences associated with COVID-19 hospitalizations in North Carolina

    Get PDF
    People living in rural regions in the United States face more health challenges than their non-rural counterparts which could put them at additional risks during the COVID-19 pandemic. Few studies have examined if rurality is associated with additional mortality risk among those hospitalized for COVID-19. We studied a retrospective cohort of 3,991 people hospitalized with SARS-CoV-2 infections discharged between March 1 and September 30, 2020 in one of 17 hospitals in North Carolina that collaborate as a clinical data research network. Patient demographics, comorbidities, symptoms and laboratory data were examined. Logistic regression was used to evaluate associations of rurality with a composite outcome of death/hospice discharge. Comorbidities were more common in the rural patient population as were the number of comorbidities per patient. Overall, 505 patients died prior to discharge and 63 patients were discharged to hospice. Among rural patients, 16.5% died or were discharged to hospice vs. 13.3% in the urban cohort resulting in greater odds of death/hospice discharge (OR 1.3, 95% CI 1.1, 1.6). This estimate decreased minimally when adjusted for age, sex, race/ethnicity, payer, disease comorbidities, presenting oxygen levels and cytokine levels (adjusted model OR 1.2, 95% CI 1.0, 1.5). This analysis demonstrated a higher COVID-19 mortality risk among rural residents of NC. Implementing policy changes may mitigate such disparities going forward

    Mixed Hodge polynomials of character varieties

    Full text link
    We calculate the E-polynomials of certain twisted GL(n,C)-character varieties M_n of Riemann surfaces by counting points over finite fields using the character table of the finite group of Lie-type GL(n,F_q) and a theorem proved in the appendix by N. Katz. We deduce from this calculation several geometric results, for example, the value of the topological Euler characteristic of the associated PGL(n,C)-character variety. The calculation also leads to several conjectures about the cohomology of M_n: an explicit conjecture for its mixed Hodge polynomial; a conjectured curious Hard Lefschetz theorem and a conjecture relating the pure part to absolutely indecomposable representations of a certain quiver. We prove these conjectures for n = 2.Comment: with an appendix by Nicholas M. Katz; 57 pages. revised version: New definition for homogeneous weight in Definition 4.1.6, subsequent arguments modified. Some other minor changes. To appear in Invent. Mat

    The Science of Sungrazers, Sunskirters, and Other Near-Sun Comets

    Get PDF
    This review addresses our current understanding of comets that venture close to the Sun, and are hence exposed to much more extreme conditions than comets that are typically studied from Earth. The extreme solar heating and plasma environments that these objects encounter change many aspects of their behaviour, thus yielding valuable information on both the comets themselves that complements other data we have on primitive solar system bodies, as well as on the near-solar environment which they traverse. We propose clear definitions for these comets: We use the term near-Sun comets to encompass all objects that pass sunward of the perihelion distance of planet Mercury (0.307 AU). Sunskirters are defined as objects that pass within 33 solar radii of the Sun’s centre, equal to half of Mercury’s perihelion distance, and the commonly-used phrase sungrazers to be objects that reach perihelion within 3.45 solar radii, i.e. the fluid Roche limit. Finally, comets with orbits that intersect the solar photosphere are termed sundivers. We summarize past studies of these objects, as well as the instruments and facilities used to study them, including space-based platforms that have led to a recent revolution in the quantity and quality of relevant observations. Relevant comet populations are described, including the Kreutz, Marsden, Kracht, and Meyer groups, near-Sun asteroids, and a brief discussion of their origins. The importance of light curves and the clues they provide on cometary composition are emphasized, together with what information has been gleaned about nucleus parameters, including the sizes and masses of objects and their families, and their tensile strengths. The physical processes occurring at these objects are considered in some detail, including the disruption of nuclei, sublimation, and ionisation, and we consider the mass, momentum, and energy loss of comets in the corona and those that venture to lower altitudes. The different components of comae and tails are described, including dust, neutral and ionised gases, their chemical reactions, and their contributions to the near-Sun environment. Comet-solar wind interactions are discussed, including the use of comets as probes of solar wind and coronal conditions in their vicinities. We address the relevance of work on comets near the Sun to similar objects orbiting other stars, and conclude with a discussion of future directions for the field and the planned ground- and space-based facilities that will allow us to address those science topics

    Search for direct production of charginos and neutralinos in events with three leptons and missing transverse momentum in √s = 7 TeV pp collisions with the ATLAS detector

    Get PDF
    A search for the direct production of charginos and neutralinos in final states with three electrons or muons and missing transverse momentum is presented. The analysis is based on 4.7 fb−1 of proton–proton collision data delivered by the Large Hadron Collider and recorded with the ATLAS detector. Observations are consistent with Standard Model expectations in three signal regions that are either depleted or enriched in Z-boson decays. Upper limits at 95% confidence level are set in R-parity conserving phenomenological minimal supersymmetric models and in simplified models, significantly extending previous results

    Jet size dependence of single jet suppression in lead-lead collisions at sqrt(s(NN)) = 2.76 TeV with the ATLAS detector at the LHC

    Get PDF
    Measurements of inclusive jet suppression in heavy ion collisions at the LHC provide direct sensitivity to the physics of jet quenching. In a sample of lead-lead collisions at sqrt(s) = 2.76 TeV corresponding to an integrated luminosity of approximately 7 inverse microbarns, ATLAS has measured jets with a calorimeter over the pseudorapidity interval |eta| < 2.1 and over the transverse momentum range 38 < pT < 210 GeV. Jets were reconstructed using the anti-kt algorithm with values for the distance parameter that determines the nominal jet radius of R = 0.2, 0.3, 0.4 and 0.5. The centrality dependence of the jet yield is characterized by the jet "central-to-peripheral ratio," Rcp. Jet production is found to be suppressed by approximately a factor of two in the 10% most central collisions relative to peripheral collisions. Rcp varies smoothly with centrality as characterized by the number of participating nucleons. The observed suppression is only weakly dependent on jet radius and transverse momentum. These results provide the first direct measurement of inclusive jet suppression in heavy ion collisions and complement previous measurements of dijet transverse energy imbalance at the LHC.Comment: 15 pages plus author list (30 pages total), 8 figures, 2 tables, submitted to Physics Letters B. All figures including auxiliary figures are available at http://atlas.web.cern.ch/Atlas/GROUPS/PHYSICS/PAPERS/HION-2011-02

    Observation of a new chi_b state in radiative transitions to Upsilon(1S) and Upsilon(2S) at ATLAS

    Get PDF
    The chi_b(nP) quarkonium states are produced in proton-proton collisions at the Large Hadron Collider (LHC) at sqrt(s) = 7 TeV and recorded by the ATLAS detector. Using a data sample corresponding to an integrated luminosity of 4.4 fb^-1, these states are reconstructed through their radiative decays to Upsilon(1S,2S) with Upsilon->mu+mu-. In addition to the mass peaks corresponding to the decay modes chi_b(1P,2P)->Upsilon(1S)gamma, a new structure centered at a mass of 10.530+/-0.005 (stat.)+/-0.009 (syst.) GeV is also observed, in both the Upsilon(1S)gamma and Upsilon(2S)gamma decay modes. This is interpreted as the chi_b(3P) system.Comment: 5 pages plus author list (18 pages total), 2 figures, 1 table, corrected author list, matches final version in Physical Review Letter

    Search for displaced vertices arising from decays of new heavy particles in 7 TeV pp collisions at ATLAS

    Get PDF
    We present the results of a search for new, heavy particles that decay at a significant distance from their production point into a final state containing charged hadrons in association with a high-momentum muon. The search is conducted in a pp-collision data sample with a center-of-mass energy of 7 TeV and an integrated luminosity of 33 pb^-1 collected in 2010 by the ATLAS detector operating at the Large Hadron Collider. Production of such particles is expected in various scenarios of physics beyond the standard model. We observe no signal and place limits on the production cross-section of supersymmetric particles in an R-parity-violating scenario as a function of the neutralino lifetime. Limits are presented for different squark and neutralino masses, enabling extension of the limits to a variety of other models.Comment: 8 pages plus author list (20 pages total), 8 figures, 1 table, final version to appear in Physics Letters
    corecore