Single-molecule microscopy reveals new insights into nucleotide selection by DNA polymerase I.

The mechanism by which DNA polymerases achieve their extraordinary accuracy has been intensely studied because of the linkage between this process and mutagenesis and carcinogenesis. Here, we have used single-molecule fluorescence microscopy to study the process of nucleotide selection and exonuclease action. Our results show that the binding of Escherichia coli DNA polymerase I (Klenow fragment) to a primer-template is stabilized by the presence of the next correct dNTP, even in the presence of a large excess of the other dNTPs and rNTPs. These results are consistent with a model where nucleotide selection occurs in the open complex prior to the formation of a closed ternary complex. Our assay can also distinguish between primer binding to the polymerase or exonuclease domain and, contrary to ensemble-averaged studies, we find that stable exonuclease binding only occurs with a mismatched primer terminus

Solving the kilo-second QPO problem of the intermediate polar GK Persei

We detect the likely optical counterpart to previously reported X-ray QPOs in spectrophotometry of the intermediate polar GK Persei during the 1996 dwarf nova outburst. The characteristic timescales range between 4000--6000 s. Although the QPOs are an order of magnitude longer than those detected in the other dwarf novae we show that a new QPO model is not required to explain the long timescale observed. We demonstrate that the observations are consistent with oscillations being the result of normal-timescale QPOs beating with the spin period of the white dwarf. We determine the spectral class of the companion to be consistent with its quiescent classification and find no significant evidence for irradiation over its inner face. We detect the white dwarf spin period in line fluxes, V/R ratios and Doppler-broadened emission profiles.Comment: 14 pages, 11 figures. Accepted for publication in MNRA

Fundamental Frequencies in the Schwarzschild Spacetime

We consider the Keplerian, radial and vertical fundamental frequencies in the Schwarzschild spacetime to study the so-called kilohertz quasi-periodic oscillations from low-mass X-ray binary systems. We show that, within the Relativistic Precession Model, the interpretation of observed kilohertz quasi-periodic oscillations in terms of the fundamental frequencies of test particles in the Schwarzschild spacetime, allows one to infer the total mass $M$ of the central object, the internal $R_{in}$ and external $R_{ex}$ radii of accretion disks, and innermost stable circular orbits $r_{ISCO}$ for test particles in a low-mass X-ray binary system. By constructing the relation between the upper and lower frequencies and exploiting the quasi-periodic oscillation data of the Z and Atoll sources we perform the non-linear model fit analysis and estimate the mass of the central object. Knowing the value of the mass we calculate the internal $R_{in}$ and external $R_{ex}$ radii of accretion disks and show that they are larger than $r_{ISCO}$, what was expected.Comment: 7 pages, 6 figures, 1 tabl

The mass and radius of the M-dwarf in the short period eclipsing binary RR Caeli

We present new photometry and spectroscopy of the eclipsing white dwarf - M-dwarf binary star RR Cae. We use timings of the primary eclipse from white-light photo-electric photometry to derive a new ephemeris for the eclipses. We find no evidence for any period change greater than Pdot/P ~ 5E-12 over a timescale of 10 years. We have measured the effective temperature of the white dwarf, T_WD, from an analysis of two high resolution spectra of RR Cae and find T_WD = (7540 +- 175)K. We estimate a spectral type of M4 for the companion from the same spectra. We have combined new spectroscopic orbits for the white dwarf and M-dwarf with an analysis of the primary eclipse and cooling models for helium white dwarfs to measure the mass and radius of the M-dwarf. The mass of the M-dwarf is (0.182 - 0.183) +- 0.013 Msun and the radius is (0.203 - 0.215) +- 0.013 Rsun, where the ranges quoted for these values reflect the range of white dwarf models used. In contrast to previous studies, which lacked a spectroscopic orbit for the white dwarf, we find that the mass and radius of the M-dwarf are normal for an M4 dwarf. The mass of the white dwarf is (0.440 +-0.022) Msun. With these revised masses and radii we find that RR Cae will become a cataclysmic variable star when the orbital period is reduced from its current value of 7.3 hours to 121 minutes by magnetic braking in 9-20 Gyr. We note that there is night-to-night variability of a few seconds in the timing of primary eclipse caused by changes to the shape of the primary eclipse. We speculate as to the possible causes of this phenomenon. (Abridged)Comment: Accepted for publication in MNRAS. The paper contains 10 figures and 3 table

When is the Haar measure a Pietsch measure for nonlinear mappings?

We show that, as in the linear case, the normalized Haar measure on a compact topological group $G$ is a Pietsch measure for nonlinear summing mappings on closed translation invariant subspaces of $C(G)$. This answers a question posed to the authors by J. Diestel. We also show that our result applies to several well-studied classes of nonlinear summing mappings. In the final section some problems are proposed

Tracing the spiral arms in IP Pegasi

We report the analysis of time-resolved spectroscopy of IP Pegasi in outburst with eclipse mapping techniques to investigate the location and geometry of the observed spiral structures. We were able to obtain an improved view of the spiral structures with the aid of light curves extracted in velocity bins matching the observed range of velocities of the spiral arms combined with a double default map tailored for reconstruction of asymmetric structures. Two-armed spiral structures are clearly seen in all eclipse maps. The arms are located at different distances from the disc centre. The “blue” arm is farther out in the disc (R = 0.55 ± 0.05 R L1 ) than the “red” arm (R = 0.30 ± 0.05 R L1 ). There is evidence that the velocity of the emitting gas along the spiral pattern is lower than the Keplerian velocity for the same disc radius. The discrepancy is smaller in the outer arm (measured velocities 10–15 per cent lower than Keplerian) and is more significant in the inner arm (observed velocities up to 40 per cent lower than Keplerian). We measured the opening angle of the spirals from the azimuthal intensity distribution of the eclipse maps to be φ = 25◦ ± 3◦ . A comparison with similar measurements on data at different outburst stages reveals that the opening angle of the spiral arms in IP Peg decreases while the outbursting accretion disc cools and shrinks, in agreement with the expected evolution of a tidally driven spiral wave. The sub-Keplerian velocities along the spiral pattern and the clear correlation between the opening angle of the spirals and the outburst stage favors the interpretation of these asymmetric structures as tidally-induced spiral shocks