Splice variants in apoptotic pathway

Elimination of superfluous or mutated somatic cells is provided by various mechanisms including apoptosis, and deregulation of apoptotic signaling pathways contributes to oncogenesis. 40 years have passed since the term “apoptosis” was introduced by Kerr et al. in 1972; among the programmed cell death, a variety of therapeutic strategies especially targeting apoptotic pathways have been investigated. Alternative precursor messenger RNA splicing, by which the process the exons of pre-mRNA are spliced in different arrangements to produce structurally and functionally distinct mRNA and proteins, is another field in progress, and it has been recognized as one of the most important mechanisms that maintains genomic and functional diversity. A variety of apoptotic genes are regulated through alternative pre-mRNA splicing as well, some of which have important functions as pro-apoptotic and anti-apoptotic factors. In this article we summarized splice variants of some of the apoptotic genes including BCL2L1, BIRC5, CFLAR, and MADD, as well as the regulatory mechanisms of alternative splicing of these genes. If the information of the apoptosis and aberrant splicing in each of malignancies is integrated, it will become possible to target proper variants for apoptosis, and the trans-elements themselves can become specific targets of cancer therapy as well. This article is part of a Special Issue entitled “Apoptosis: Four Decades Later”

Time-dependent Turbulence in Stars

Three-dimensional (3D) hydrodynamic simulations of shell oxygen burning (Meakin and Arnett 2007) exhibit bursty, recurrent fluctuations in turbulent kinetic energy. These are shown to be due to a global instability in the convective region, which has been suppressed in calculations of stellar evolution which use mixing-length theory (MLT). Quantitatively similar behavior occurs in the model of a convective roll (cell) of Lorenz (1963), which is known to have a strange attractor that gives rise to random fluctuations in time.An extension of the Lorenz model, which includes Kolmogorov damping and nuclear burning, is shown to exhibit bursty, recurrent fluctuations like those seen in the 3D simulations. A simple model of a convective layer (composed of multiple Lorenz cells) gives luminosity fluctuations which are suggestive of irregular variables (red giants and supergiants, Schwarzschild 1975). Apparent inconsistencies between Arnett, Meakin, and Young (2009) and Nordlund, Stein, and Asplund (2009) on the nature of convective driving have been resolved, and are discussed.Comment: 8 pages, 2 figures, IAU Symposium 271 "Astrophysical Dynamics: From Galaxies to Stars", Nice, FR, 201

Improved Fokker-Planck Equation for Resonance Line Scattering

A new Fokker-Planck equation is developed for treating resonance line scattering, especially relevant to the treatment of Lyman alpha in the early universe. It is a "corrected" form of the equation of Rybicki & Dell'Antonio that now obeys detailed balance, so that the approach to thermal equilibrium is properly described. The new equation takes into account the energy changes due to scattering off moving particles, the recoil term of Basko, and stimulated scattering. One result is a surprising unification of the equation for resonance line scattering and the Kompaneets equation. An improved energy exchange formula due to resonance line scattering is derived. This formula is compared to previous formulas of Madau, Meikson, & Rees (1997) and Chen & Miralda-Escud\'e (2004).Comment: 10 pages, no figures, submitted to Ap

Crustal Oscillations of Slowly Rotating Relativistic Stars

We study low-amplitude crustal oscillations of slowly rotating relativistic stars consisting of a central fluid core and an outer thin solid crust. We estimate the effect of rotation on the torsional toroidal modes and on the interfacial and shear spheroidal modes. The results compared against the Newtonian ones for wide range of neutron star models and equations of state.Comment: 15 page

Impact of neutron star oscillations on the accelerating electric field in the polar cap of pulsar: or could we see oscillations of the neutron star after the glitch in pulsar?

Pulsar "standard model", that considers a pulsar as a rotating magnetized conducting sphere surrounded by plasma, is generalized to the case of oscillating star. We developed an algorithm for calculation of the Goldreich-Julian charge density for this case. We consider distortion of the accelerating zone in the polar cap of pulsar by neutron star oscillations. It is shown that for oscillation modes with high harmonic numbers (l,m) changes in the Goldreich-Julian charge density caused by pulsations of neutron star could lead to significant altering of an accelerating electric field in the polar cap of pulsar. In the moderately optimistic scenario, that assumes excitation of the neutron star oscillations by glitches, it could be possible to detect altering of the pulsar radioemission due to modulation of the accelerating field.Comment: 7 pages, 8 figures. Presented at the conference "Isolated Neutron Stars: from the Interior to the Surface", London, April 24-28, 2006; to appear in Astrophysics and Space Scienc

Porto Oscillation Code (POSC)

The Porto Oscillation Code (POSC) has been developed in 1995 and improved over the years, with the main goal of calculating linear adiabatic oscillations for models of solar-type stars. It has also been used to estimate the frequencies and eigenfunctions of stars from the pre-main sequence up to the sub-giant phase, having a mass between 0.8 and 4 solar masses. The code solves the linearised perturbation equations of adiabatic pulsations for an equilibrium model using a second order numerical integration method. The possibility of using Richardson extrapolation is implemented. Several options for the surface boundary condition can be used. In this work we briefly review the key ingredients of the calculations, namely the equations, the numerical scheme and the output.Comment: Accepted for publication in Astrophysics and Space Science

On the transfer of resonant-line radiation in mesh simulations

The last decade has seen applications of Adaptive Mesh Refinement (AMR) methods for a wide range of problems from space physics to cosmology. With the advent of these methods, in which space is discretized into a mesh of many individual cubic elements, the contemporary analog of the extensively studied line radiative transfer (RT) in a semi-infinite slab is that of RT in a cube. In this study we provide an approximate solution of the RT equation, as well as analytic expressions for the probability distribution functions (pdfs) of the properties of photons emerging from a cube, and compare them with the corresponding slab problem. These pdfs can be used to perform fast resonant-line RT in optically thick AMR cells where, otherwise, it could take unrealistically long times to transfer even a handful of photons.Comment: 5 two-column pages, 2 figures; matches accepted version, to appear on Ap

The chaotic behavior of the black hole system GRS 1915+105

A modified non-linear time series analysis technique, which computes the correlation dimension $D_2$, is used to analyze the X-ray light curves of the black hole system GRS 1915+105 in all twelve temporal classes. For four of these temporal classes $D_2$ saturates to $\approx 4-5$ which indicates that the underlying dynamical mechanism is a low dimensional chaotic system. Of the other eight classes, three show stochastic behavior while five show deviation from randomness. The light curves for four classes which depict chaotic behavior have the smallest ratio of the expected Poisson noise to the variability ($< 0.05$) while those for the three classes which depict stochastic behavior is the highest ($> 0.2$). This suggests that the temporal behavior of the black hole system is governed by a low dimensional chaotic system, whose nature is detectable only when the Poisson fluctuations are much smaller than the variability.Comment: Accepted for publication in Astrophysical Journa

Oscillations of rapidly rotating relativistic stars

Non-axisymmetric oscillations of rapidly rotating relativistic stars are studied using the Cowling approximation. The oscillation spectra have been estimated by Fourier transforming the evolution equations describing the perturbations. This is the first study of its kind and provides information on the effect of fast rotation on the oscillation spectra while it offers the possibility in studying the complete problem by including spacetime perturbations. Our study includes both axisymmetric and non-axisymmetric perturbations and provides limits for the onset of the secular bar mode rotational instability. We also present approximate formulae for the dependence of the oscillation spectrum from rotation. The results suggest that it is possible to extract the relativistic star's parameters from the observed gravitational wave spectrum.Comment: this article will be published in Physical Review

Radiative Transfer Effects in He I Emission Lines

We consider the effect of optical depth of the 2 ^{3}S level on the nebular recombination spectrum of He I for a spherically symmetric nebula with no systematic velocity gradients. These calculations, using many improvements in atomic data, can be used in place of the earlier calculations of Robbins. We give representative Case B line fluxes for UV, optical, and IR emission lines over a range of physical conditions: T=5000-20000 K, n_{e}=1-10^{8} cm^{-3}, and tau_{3889}=0-100. A FORTRAN program for calculating emissivities for all lines arising from quantum levels with n < 11 is also available from the authors. We present a special set of fitting formulae for the physical conditions relevant to low metallicity extragalactic H II regions: T=12,000-20,000 K, n_{e}=1-300 cm^{-3}, and tau_{3889} < 2.0. For this range of physical conditions, the Case B line fluxes of the bright optical lines 4471 A, 5876 A, and 6678 A, are changed less than 1%, in agreement with previous studies. However, the 7065 A corrections are much smaller than those calculated by Izotov & Thuan based on the earlier calculations by Robbins. This means that the 7065 A line is a better density diagnostic than previously thought. Two corrections to the fitting functions calculated in our previous work are also given.Comment: To be published in 10 April 2002 ApJ; relevant code available at ftp://wisp.physics.wisc.edu/pub/benjamin/Heliu