RNA-Seq Analysis Reveals a Six-Gene SoxR Regulon in Streptomyces coelicolor

The redox-regulated transcription factor SoxR is conserved in diverse bacteria, but emerging studies suggest that this protein plays distinct physiological roles in different bacteria. SoxR regulates a global oxidative stress response (involving \u3e100 genes) against exogenous redox-cycling drugs in Escherichia coli and related enterics. In the antibiotic producers Streptomyces coelicolor and Pseudomonas aeruginosa, however, SoxR regulates a smaller number of genes that encode membrane transporters and proteins with homology to antibiotic-tailoring enzymes. In both S. coelicolor and P. aeruginosa, SoxR-regulated genes are expressed in stationary phase during the production of endogenously-produced redox-active antibiotics. These observations suggest that SoxR evolved to sense endogenous secondary metabolites and activate machinery to process and transport them in antibiotic-producing bacteria. Previous bioinformatics analysis that searched the genome for SoxR-binding sites in putative promoters defined a five-gene SoxR regulon in S. coelicolor including an ABC transporter, two oxidoreductases, a monooxygenase and an epimerase/dehydratase. Since this in silico screen may have missed potential SoxR-targets, we conducted a whole genome transcriptome comparison of wild type S. coelicolor and a soxR-deficient mutant in stationary phase using RNA-Seq. Our analysis revealed a sixth SoxR-regulated gene in S. coelicolor that encodes a putative quinone oxidoreductase. Knowledge of the full complement of genes regulated by SoxR will facilitate studies to elucidate the function of this regulatory molecule in antibiotic producers

Filling the holes: Evolving excised binary black hole initial data with puncture techniques

We follow the inspiral and merger of equal-mass black holes (BHs) by the moving puncture technique and demonstrate that both the exterior solution and the asymptotic gravitational waveforms are unchanged when the initial interior solution is replaced by constraint-violating ``junk'' initial data. We apply this result to evolve conformal thin-sandwich (CTS) binary BH initial data by filling their excised interiors with arbitrary, but smooth, initial data and evolving with standard puncture gauge choices. The waveforms generated for both puncture and filled-CTS initial data are remarkably similar, and there are only minor differences between irrotational and corotational CTS BH binaries. Even the interior solutions appear to evolve to the same constraint-satisfying solution at late times, independent of the initial data.Comment: 5 pages, 5 figures, accepted by PRD Rapid Communications, RevTe

Quasiequilibrium sequences of black-hole--neutron-star binaries in general relativity

We construct quasiequilibrium sequences of black hole-neutron star binaries for arbitrary mass ratios by solving the constraint equations of general relativity in the conformal thin-sandwich decomposition. We model the neutron star as a stationary polytrope satisfying the relativistic equations of hydrodynamics, and account for the black hole by imposing equilibrium boundary conditions on the surface of an excised sphere (the apparent horizon). In this paper we focus on irrotational configurations, meaning that both the neutron star and the black hole are approximately nonspinning in an inertial frame. We present results for a binary with polytropic index n=1, mass ratio M_{irr}^{BH}/M_{B}^{NS}=5 and neutron star compaction M_{ADM,0}^{NS}/R_0=0.0879, where M_{irr}^{BH} is the irreducible mass of the black hole, M_{B}^{NS} the neutron star baryon rest-mass, and M_{ADM,0}^{NS} and R_0 the neutron star Arnowitt-Deser-Misner mass and areal radius in isolation, respectively. Our models represent valid solutions to Einstein's constraint equations and may therefore be employed as initial data for dynamical simulations of black hole-neutron star binaries.Comment: 5 pages, 1 figure, revtex4, published in Phys.Rev.

Quasiequilibrium black hole-neutron star binaries in general relativity

We construct quasiequilibrium sequences of black hole-neutron star binaries in general relativity. We solve Einstein's constraint equations in the conformal thin-sandwich formalism, subject to black hole boundary conditions imposed on the surface of an excised sphere, together with the relativistic equations of hydrostatic equilibrium. In contrast to our previous calculations we adopt a flat spatial background geometry and do not assume extreme mass ratios. We adopt a Gamma=2 polytropic equation of state and focus on irrotational neutron star configurations as well as approximately nonspinning black holes. We present numerical results for ratios of the black hole's irreducible mass to the neutron star's ADM mass in isolation of M_{irr}^{BH}/M_{ADM,0}^{NS} = 1, 2, 3, 5, and 10. We consider neutron stars of baryon rest mass M_B^{NS}/M_B^{max} = 83% and 56%, where M_B^{max} is the maximum allowed rest mass of a spherical star in isolation for our equation of state. For these sequences, we locate the onset of tidal disruption and, in cases with sufficiently large mass ratios and neutron star compactions, the innermost stable circular orbit. We compare with previous results for black hole-neutron star binaries and find excellent agreement with third-order post-Newtonian results, especially for large binary separations. We also use our results to estimate the energy spectrum of the outgoing gravitational radiation emitted during the inspiral phase for these binaries.Comment: 17 pages, 15 figures, published in Phys. Rev.

Black Hole-Neutron Star Binary Merger Calculations: GRB Progenitors and the Stability of Mass Transfer

We have calculated the first dynamical evolutions of merging black hole-neutron star binaries that treat the combined spacetime in a nonperturbative general relativistic framework. Using the conformal flatness approximation, we have studied how the location of the tidal disruption radius with respect to the the black hole horizon and innermost stable circular orbit (ISCO) affects the qualitative evolution of the system. Based on simple arguments, we show that for a binary mass ratio q>~0.24, tidal disruption occurs outside the ISCO, while the opposite is true for q<~0.24. When tidal disruption occurs sufficiently far outside the ISCO, mass is transferred unstably from the neutron star to the black hole, resulting in the complete disruption of the neutron star. When tidal disruption occurs slightly within the ISCO, we find that some of the mass forms an extremely hot disk around the black hole. The resulting configurations in this case are excellent candidates for the progenitors of short-hard gamma ray bursts.Comment: 8 pages, 5 figures, in Proceedings of the Albert Einstein Century International Conference, Paris, France, 2005, edited by Jean-Michel Alimi and Andre Fuzf

General Relativistic Binary Merger Simulations and Short Gamma Ray Bursts

The recent localization of some short-hard gamma ray bursts (GRBs) in galaxies with low star formation rates has lent support to the suggestion that these events result from compact object binary mergers. We discuss how new simulations in general relativity are helping to identify the central engine of short-hard GRBs. Motivated by our latest relativistic black hole-neutron star merger calculations, we discuss a scenario in which these events may trigger short-hard GRBs, and compare this model to competing relativistic models involving binary neutron star mergers and the delayed collapse of hypermassive neutron stars. Distinguishing features of these models may help guide future GRB and gravitational wave observations to identify the nature of the sources.Comment: 5 Pages, 3 figures, accepted by ApJ Let

Maintaining Treatment Fidelity of Mindfulness-Based Relapse Prevention Intervention for Alcohol Dependence: A Randomized Controlled Trial Experience

Background. Treatment fidelity is essential to methodological rigor of clinical trials evaluating behavioral interventions such as Mindfulness Meditation (MM). However, procedures for monitoring and maintenance of treatment fidelity are inconsistently applied, limiting the strength of such research. Objective. To describe the implementation and findings related to fidelity monitoring of the Mindfulness-Based Relapse Prevention for Alcohol Dependence (MBRP-A) intervention in a 26-week randomized controlled trial. Methods. 123 alcohol dependent adults were randomly assigned to MM (MBRP-A and home practice, adjunctive to usual care; N=64) or control (usual care alone; N=59). Treatment fidelity assessment strategies recommended by the National Institutes of Health Behavior Change Consortium for study/intervention design, therapist training, intervention delivery, and treatment receipt and enactment were applied. Results. Ten 8-session interventions were delivered. Therapist adherence and competence, assessed using the modified MBRP Adherence and Competence Scale, were high. Among the MM group participants, 46 attended ≥4 sessions; over 90% reported at-home MM practice at 8 weeks and 72% at 26 weeks. They also reported satisfaction with and usefulness of MM for maintaining sobriety. No adverse events were reported. Conclusions. A systematic approach to assessment of treatment fidelity in behavioral clinical trials allows determination of the degree of consistency between intended and actual delivery and receipt of intervention

Fully General Relativistic Simulations of Black Hole-Neutron Star Mergers

Black hole-neutron star (BHNS) binaries are expected to be among the leading sources of gravitational waves observable by ground-based detectors, and may be the progenitors of short-hard gamma ray bursts (SGRBs) as well. Here, we discuss our new fully general relativistic calculations of merging BHNS binaries, which use high-accuracy, low-eccentricity, conformal thin-sandwich configurations as initial data. Our evolutions are performed using the moving puncture method and include a fully relativistic, high-resolution shock-capturing hydrodynamics treatment. Focusing on systems in which the neutron star is irrotational and the black hole is nonspinning with a 3:1 mass ratio, we investigate the inspiral, merger, and disk formation in the system. We find that the vast majority of material is promptly accreted and no more than 3% of the neutron star's rest mass is ejected into a tenuous, gravitationally bound disk. We find similar results for mass ratios of 2:1 and 1:1, even when we reduce the NS compaction in the 2:1 mass ratio case. These ambient disks reach temperatures suitable for triggering SGRBs, but their masses may be too small to produce the required total energy output. We measure gravitational waveforms and compute the effective strain in frequency space, finding measurable differences between our waveforms and those produced by binary black hole mergers within the advanced LIGO band. These differences appear at frequencies corresponding to the emission that occurs when the NS is tidally disrupted and accreted by the black hole. The resulting information about the radius of the neutron star may be used to constrain the neutron star equation of state.Comment: 22 pages, 14 figures, fixed a few typo

The Central Component of Gravitational Lens Q0957+561

In 1981, a faint radio source (G') was detected near the center of the lensing galaxy of the famous "twin quasar" Q0957+561. It is still unknown whether this central radio source is a third quasar image or an active nucleus of the lensing galaxy, or a combination of both. In an attempt to resolve this ambiguity, we observed Q0957+561 at radio wavelengths of 13cm, 18cm, and 21cm, using the Very Long Baseline Array in combination with the phased Very Large Array and the Green Bank Telescope. We measured the spectrum of G' for the first time and found it to be significantly different from the spectra of the two bright quasar images. This finding suggests that the central component is primarily or entirely emission from the foreground lens galaxy, but the spectrum is also consistent with the hypothesis of a central quasar image suffering free-free absorption. In addition, we confirm the previously-reported VLBI position of G' just north of the optical center of the lens galaxy. The position slightly favors the hypothesis that G' originates in the lens, but is not conclusive. We discuss the prospects for further clarification of this issue.Comment: 18 pages, accepted for publication in A