Functional interplay between NTP leaving group and base pair recognition during RNA polymerase II nucleotide incorporation revealed by methylene substitution.

RNA polymerase II (pol II) utilizes a complex interaction network to select and incorporate correct nucleoside triphosphate (NTP) substrates with high efficiency and fidelity. Our previous 'synthetic nucleic acid substitution' strategy has been successfully applied in dissecting the function of nucleic acid moieties in pol II transcription. However, how the triphosphate moiety of substrate influences the rate of P-O bond cleavage and formation during nucleotide incorporation is still unclear. Here, by employing β,γ-bridging atom-'substituted' NTPs, we elucidate how the methylene substitution in the pyrophosphate leaving group affects cognate and non-cognate nucleotide incorporation. Intriguingly, the effect of the β,γ-methylene substitution on the non-cognate UTP/dT scaffold (∼3-fold decrease in kpol) is significantly different from that of the cognate ATP/dT scaffold (∼130-fold decrease in kpol). Removal of the wobble hydrogen bonds in U:dT recovers a strong response to methylene substitution of UTP. Our kinetic and modeling studies are consistent with a unique altered transition state for bond formation and cleavage for UTP/dT incorporation compared with ATP/dT incorporation. Collectively, our data reveals the functional interplay between NTP triphosphate moiety and base pair hydrogen bonding recognition during nucleotide incorporation

Chemical Abundances in the Secondary Star in the Black Hole Binary A0620-00

Using a high resolution spectrum of the secondary star in the black hole binary A0620-00, we have derived the stellar parameters and veiling caused by the accretion disk in a consistent way. We have used a chi^2 minimization procedure to explore a grid of 800 000 LTE synthetic spectra computed for a plausible range of both stellar and veiling parameters. Adopting the best model parameters found, we have determined atmospheric abundances of Fe, Ca, Ti, Ni and Al. The Fe abundance of the star is [Fe/H]=0.14 +- 0.20. Except for Ca, we found the other elements moderately over-abundant as compared with stars in the solar neighborhood of similar iron content. Taking into account the small orbital separation, the mass transfer rate and the mass of the convection zone of the secondary star, a comparison with element yields in supernova explosion models suggests a possible explosive event with a mass cut comparable to the current mass of the compact object. We have also analyzed the Li abundance, which is unusually high for a star of this spectral type and relatively low mass.Comment: 32 pages, 5 tables and 11 figures, uses rotate.st

Reversed-phase liquid chromatography coupled on-line to estrogen receptor bioaffinity detection based on fluorescence polarization

We describe the development and validation of a high-resolution screening (HRS) platform which couples gradient reversed-phase high-performance liquid chromatography (RP-HPLC) on-line to estrogen receptor α (ERα) affinity detection using fluorescence polarization (FP). FP, which allows detection at high wavelengths, limits the occurrence of interference from the autofluorescence of test compounds in the bioassay. A fluorescein-labeled estradiol derivative (E2-F) was synthesized and a binding assay was optimized in platereader format. After subsequent optimization in flow-injection analysis (FIA) mode, the optimized parameters were translated to the on-line HRS bioassay. Proof of principle was demonstrated by separating a mixture of five compounds known to be estrogenic (17β-estradiol, 17α-ethinylestradiol and the phytoestrogens coumestrol, coumarol and zearalenone), followed by post-column bioaffinity screening of the individual affinities for ERα. Using the HRS-based FP setup, we were able to screen affinities of off-line-generated metabolites of zearalenone for ERα. It is concluded that the on-line FP-based bioassay can be used to screen for the affinity of compounds without the disturbing occurrence of autofluorescence

DE Canum Venaticorum : a bright, eclipsing red dwarf–white dwarf binary

Context. Close white dwarf–red dwarf binaries must have gone through a common-envelope phase during their evolution. DE CVn is a detached white dwarf–red dwarf binary with a relatively short (∼8.7 h) orbital period. Its brightness and the presence of eclipses makes this system ideal for a more detailed study. Aims. From a study of photometric and spectroscopic observations of DE CVn we derive the system parameters that we discuss in the framework of common-envelope evolution. Methods. Photometric observations of the eclipses are used to determine an accurate ephemeris. From a model fit to an average lowresolution spectrum of DE CVn, we constrain the temperature of the white dwarf and the spectral type of the red dwarf. The eclipse light curve is analysed and combined with the radial velocity curve of the red dwarf determined from time-resolved spectroscopy to derive constraints on the inclination and the masses of the components in the system. Results. The derived ephemeris is HJDmin = 2 452 784.5533(1) + 0.3641394(2) × E. The red dwarf in DE CVn has a spectral type of M3V and the white dwarf has an effective temperature of 8 000 K. The inclination of the system is 86+3◦ −2 and the mass and radius of the red dwarf are 0.41 ± 0.06 M and 0.37+0.06 −0.007 R, respectively, and the mass and radius of the white dwarf are 0.51+0.06 −0.02 M and 0.0136+0.0008 −0.0002 R, respectively. Conclusions. We found that the white dwarf has a hydrogen-rich atmosphere (DA-type). Given that DE CVn has experienced a common-envelope phase, we can reconstruct its evolution and we find that the progenitor of the white dwarf was a relatively lowmass star (M ≤ 1.6 M). The current age of this system is 3.3−7.3 × 109 years, while it will take longer than the Hubble time for DE CVn to evolve into a semi-detached system

The Formation of Cataclysmic Variables with Brown Dwarf Secondaries

The present-day formation of cataclysmic variables (CVs) with brown dwarf (BD) secondaries (0.013 M_sun < M_sec < 0.075 M_sun) is investigated using a population synthesis technique. Results from the latest, detailed models for BDs have been incorporated into the population synthesis code. For our models, we find that ZACVs with BD secondaries have orbital periods in the range 46 min to 2.5 hrs. We also find that ZACVs with BD secondaries comprise 18% of the total, present-day ZACV population. In addition, we find that 80% of ZACVs with BD secondaries have orbital periods < 78 minutes. This implies that 15% of the present-day ZACV population should have orbital periods shorter than the observed orbital period minimum for CVs. We also investigate the dependence of the present-day formation rate of CVs with BD secondaries on the assumed value of the common envelope efficiency parameter, alpha_CE, for three different assumed mass ratio distributions in ZAMS binaries. Surprisingly, we find that the common envelope process must be extremely inefficient (alpha_CE < 0.1) in order for CVs with BD secondaries not to be formed. Finally, we find that the progenitor binaries of ZACVs with BD secondaries have ZAMS orbital separations < 3 AU and ZAMS primary masses between ~1-10 M_sun, with ~75% of the primary masses less than ~1.6 M_sun. Interestingly, these ranges in orbital separation and primary mass place the majority of the progenitor binaries within the so-called ``brown dwarf desert.''Comment: preprint 27 pages 4 figures; to appear in ApJ April 1, 200

Dynamics of Warm-Absorbing Gas in Seyfert Galaxies: NGC 5548

A hydromagnetic (MHD) wind from a clumpy molecular accretion disk is invoked to explain observations of warm absorbing (WA) gas in UVX from Sy galaxies. This paper focuses on two issues: (1) compatibility of kinematics and dynamics of MHD wind with the observed properties of WAs; and (2) relationship between the UVX absorptions. We provide an in-depth comparison between the MHD model and the Sy 1 galaxy NGC 5548, which at high spectral resolution exhibits a number of discrete UV absorption components. We find that: (1) the total column densities of Ovii, Oviii and H, are reproduced by constraining the UV ion column densities of Civ and Nv in each component to lie within a factor of 2 of their observed values and optimizing over the possible sets of component ionization states and Civ column densities; (2) the WA exists in the outer part of the wind and is not a continuation of the flow in the BLR; and (3) the WA extends in radial and polar directions and is ionization-stratified. X-ray absorption is found to be heavily biased towards smaller r, and UV absorption originates at larger distances from the central continuum source. We show that the discrete absorption components along the line-of-sight are intrinsically clumpy. Density differences between kinematic components result in a range of ionization and recombination timescales. We further test the applicability of the MHD wind to WAs in general, by constructing a quasi-continuous flow model, and extending it to arbitrary aspect angles. We estimate the fraction of Sy 1s having detectable WAs with larger Ovii column density than Oviii, and the range of total H column densities. We also find that the ratio of Ovii to Oviii optical depths can serve as a new diagnostic of AGN aspect angle.Comment: Latex, 8 postscript figures. Astrophysical Journal, 536, June 10, in pres

On the Theory of Gamma Ray Bursts and Hypernovae: The Black Hole Soft X-ray Transient Sources

We show that a common evolutionary history can produce the black hole binaries in the Galaxy in which the black holes have masses of ~ 5-10 M_sun. In with low-mass, <~ 2.5 M_sun, ZAMS (zero age main sequence) companions, the latter remain in main sequence during the active stage of soft X-ray transients (SXTs), most of them being of K or M classification. In two intermediate cases, IL Lupi and Nova Scorpii with ZAMS ~ 2.5 M_sun companions the orbits are greatly widened because of large mass loss in the explosion forming the black hole, and whereas these companions are in late main sequence evolution, they are close to evolving. Binaries with companion ZAMS masses >~ 3 M_sun are initially "silent" until the companion begins evolving across the Herzsprung gap. We provide evidence that the narrower, shorter period binaries, with companions now in main sequence, are fossil remnants of gamma ray bursters (GRBs). We also show that the GRB is generally accompanied by a hypernova explosion (a very energetic supernova explosion). We further show that the binaries with evolved companions are good models for some of the ultraluminous X-ray sources (ULXs) recently seen by Chandra in other galaxies. The great regularity in our evolutionary history, especially the fact that most of the companions of ZAMS mass <~ 2.5 M_sun remain in main sequences as K or M stars can be explained by the mass loss in common envelope evolution to be Case C; i.g., to occur only after core He burning has finished. Since our argument for Case C mass transfer is not generally understood in the community, we add an appendix, showing that with certain assumptions which we outline we can reproduce the regularities in the evolution of black hole binaries by Case C mass transfer.Comment: 59 pages, 12 figures, review articl

The long-lived Type IIn SN 2015da: Infrared echoes and strong interaction within an extended massive shell star star star

In this paper we report the results of the first similar to four years of spectroscopic and photometric monitoring of the Type IIn supernova SN 2015da (also known as PSN J13522411+3941286, or iPTF16tu). The supernova exploded in the nearby spiral galaxy NGC 5337 in a relatively highly extinguished environment. The transient showed prominent narrow Balmer lines in emission at all times and a slow rise to maximum in all bands. In addition, early observations performed by amateur astronomers give a very well-constrained explosion epoch. The observables are consistent with continuous interaction between the supernova ejecta and a dense and extended H-rich circumstellar medium. The presence of such an extended and dense medium is difficult to reconcile with standard stellar evolution models, since the metallicity at the position of SN 2015da seems to be slightly subsolar. Interaction is likely the mechanism powering the light curve, as confirmed by the analysis of the pseudo bolometric light curve, which gives a total radiated energy greater than or similar to 10(51) erg. Modeling the light curve in the context of a supernova shock breakout through a dense circumstellar medium allowed us to infer the mass of the prexisting gas to be similar or equal to 8 M-circle dot, with an extreme mass-loss rate for the progenitor star similar or equal to 0.6 M-circle dot yr(-1), suggesting that most of the circumstellar gas was produced during multiple eruptive events. Near- and mid-infrared observations reveal a fluxexcess in these domains, similar to those observed in SN 2010jl and other interacting transients, likely due to preexisting radiatively heated dust surrounding the supernova. By modeling the infrared excess, we infer a mass greater than or similar to 0.4 x 10(-3) M-circle dot for the dustSpanish MICINN gran

Optimizing Cadences with Realistic Light Curve Filtering for Serendipitous Kilonova Discovery with Vera Rubin Observatory

Current and future optical and near-infrared wide-field surveys have the potential of finding kilonovae, the optical and infrared counterparts to neutron star mergers, independently of gravitational-wave or high-energy gamma-ray burst triggers. The ability to discover fast and faint transients such as kilonovae largely depends on the area observed, the depth of those observations, the number of re-visits per field in a given time frame, and the filters adopted by the survey; it also depends on the ability to perform rapid follow-up observations to confirm the nature of the transients. In this work, we assess kilonova detectability in existing simulations of the LSST strategy for the Vera C. Rubin Wide Fast Deep survey, with focus on comparing rolling to baseline cadences. Although currently available cadences can enable the detection of more than 300 kilonovae out to 1400 Mpc over the ten-year survey, we can expect only 3-32 kilonovae similar to GW170817 to be recognizable as fast-evolving transients. We also explore the detectability of kilonovae over the plausible parameter space, focusing on viewing angle and ejecta masses. We find that observations in redder izy bands are crucial for identification of nearby (within 300 Mpc) kilonovae that could be spectroscopically classified more easily than more distant sources. Rubin's potential for serendipitous kilonova discovery could be increased by gain of efficiency with the employment of individual 30s exposures (as opposed to 2x15s snap pairs), with the addition of red-band observations coupled with same-night observations in g- or r-bands, and possibly with further development of a new rolling-cadence strategy