Distinct core promoter codes drive transcription initiation at key developmental transitions in a marine chordate

BACKGROUND: Development is largely driven by transitions between transcriptional programs. The initiation of transcription at appropriate sites in the genome is a key component of this and yet few rules governing selection are known. Here, we used cap analysis of gene expression (CAGE) to generate bp-resolution maps of transcription start sites (TSSs) across the genome of Oikopleura dioica, a member of the closest living relatives to vertebrates. RESULTS: Our TSS maps revealed promoter features in common with vertebrates, as well as striking differences, and uncovered key roles for core promoter elements in the regulation of development. During spermatogenesis there is a genome-wide shift in mode of transcription initiation characterized by a novel core promoter element. This element was associated with > 70% of male-specific transcription, including the use of cryptic internal promoters within operons. In many cases this led to the exclusion of trans-splice sites, revealing a novel mechanism for regulating which mRNAs receive the spliced leader. Binding of the cell cycle regulator, E2F1, is enriched at the TSS of maternal genes in endocycling nurse nuclei. In addition, maternal promoters lack the TATA-like element found in zebrafish and have broad, rather than sharp, architectures with ordered nucleosomes. Promoters of ribosomal protein genes lack the highly conserved TCT initiator. We also report an association between DNA methylation on transcribed gene bodies and the TATA-box. CONCLUSIONS: Our results reveal that distinct functional promoter classes and overlapping promoter codes are present in protochordates like in vertebrates, but show extraordinary lineage-specific innovations. Furthermore, we uncover a genome-wide, developmental stage-specific shift in the mode of TSS selection. Our results provide a rich resource for the study of promoter structure and evolution in Metazoa

Nature of fault planes in solid neutron star matter

The properties of tectonic earthquake sources are compared with those deduced here for fault planes in solid neutron-star matter. The conclusion that neutron-star matter cannot exhibit brittle fracture at any temperature or magnetic field is significant for current theories of pulsar glitches, and of the anomalous X-ray pulsars and soft-gamma repeaters.Comment: 5 AAS LaTeX pages 1 eps figur

The relationship between induced fluid structure and boundary slip in nanoscale polymer films

The molecular mechanism of slip at the interface between polymer melts and weakly attractive smooth surfaces is investigated using molecular dynamics simulations. In agreement with our previous studies on slip flow of shear-thinning fluids, it is shown that the slip length passes through a local minimum at low shear rates and then increases rapidly at higher shear rates. We found that at sufficiently high shear rates, the slip flow over atomically flat crystalline surfaces is anisotropic. It is demonstrated numerically that the friction coefficient at the liquid-solid interface (the ratio of viscosity and slip length) undergoes a transition from a constant value to the power-law decay as a function of the slip velocity. The characteristic velocity of the transition correlates well with the diffusion velocity of fluid monomers in the first fluid layer near the solid wall at equilibrium. We also show that in the linear regime, the friction coefficient is well described by a function of a single variable, which is a product of the magnitude of surface-induced peak in the structure factor and the contact density of the adjacent fluid layer. The universal relationship between the friction coefficient and induced fluid structure holds for a number of material parameters of the interface: fluid density, chain length, wall-fluid interaction energy, wall density, lattice type and orientation, thermal or solid walls.Comment: 33 pages, 14 figure

Slip boundary conditions for shear flow of polymer melts past atomically flat surfaces

Molecular dynamics simulations are carried out to investigate the dynamic behavior of the slip length in thin polymer films confined between atomically smooth thermal surfaces. For weak wall-fluid interactions, the shear rate dependence of the slip length acquires a distinct local minimum followed by a rapid growth at higher shear rates. With increasing fluid density, the position of the local minimum is shifted to lower shear rates. We found that the ratio of the shear viscosity to the slip length, which defines the friction coefficient at the liquid/solid interface, undergoes a transition from a nearly constant value to the power law decay as a function of the slip velocity. In a wide range of shear rates and fluid densities, the friction coefficient is determined by the product of the value of surface induced peak in the structure factor and the contact density of the first fluid layer near the solid wall.Comment: 27 pages, 11 figure

Electrodynamics of Magnetars IV: Self-Consistent Model of the Inner Accelerator, with Implications for Pulsed Radio Emission

We consider the voltage structure in the open-field circuit and outer magnetosphere of a magnetar. The standard polar-cap model for radio pulsars is modified significantly when the polar magnetic field exceeds 1.8x10^{14} G. Pairs are created by accelerated particles via resonant scattering of thermal X-rays, followed by the nearly instantaneous conversion of the scattered photon to a pair. A surface gap is then efficiently screened by e+- creation, which regulates the voltage in the inner part of the circuit to ~10^9 V. We also examine the electrostatic gap structure that can form when the magnetic field is somewhat weaker, and deduce a voltage 10-30 times larger over a range of surface temperatures. We examine carefully how the flow of charge back to the star above the gap depends on the magnitude of the current that is extracted from the surface of the star, on the curvature of the magnetic field lines, and on resonant drag. The rates of different channels of pair creation are determined self-consistently, including the non-resonant scattering of X-rays, and collisions between gamma rays and X-rays. We find that the electrostatic gap solution has too small a voltage to sustain the observed pulsed radio output of magnetars unless i) the magnetic axis is nearly aligned with the rotation axis and the light of sight; or ii) the gap is present on the closed as well as the open magnetic field lines. Several properties of the radio magnetars -- their rapid variability, broad pulses, and unusually hard radio spectra -- are consistent with a third possibility, that the current in the outer magnetosphere is strongly variable, and a very high rate of pair creation is sustained by a turbulent cascade.Comment: 32 pages, submitted to the Astrophysical Journa

Nucleation of quark matter in neutron stars cores

We consider the general conditions of quark droplets formation in high density neutron matter. The growth of the quark bubble (assumed to contain a sufficiently large number of particles) can be described by means of a Fokker-Planck equation. The dynamics of the nucleation essentially depends on the physical properties of the medium it takes place. The conditions for quark bubble formation are analyzed within the frameworks of both dissipative and non-dissipative (with zero bulk and shear viscosity coefficients) approaches. The conversion time of the neutron star to a quark star is obtained as a function of the equation of state of the neutron matter and of the microscopic parameters of the quark nuclei. As an application of the obtained formalism we analyze the first order phase transition from neutron matter to quark matter in rapidly rotating neutron stars cores, triggered by the gravitational energy released during the spinning down of the neutron star. The endothermic conversion process, via gravitational energy absorption, could take place, in a very short time interval, of the order of few tens seconds, in a class of dense compact objects, with very high magnetic fields, called magnetars.Comment: 31 pages, 2 figures, to appear in Ap

Haze in the Mars atmosphere as revealed by the Mariner 4 television data

Photometric investigation of haze in Mars atmosphere revealed by Mariner 4 television dat

Suppression of Kelvon-induced decay of quantized vortices in oblate Bose-Einstein Condensates

We study the Kelvin mode excitations on a vortex line in a three-dimensional trapped Bose-Einstein condensate at finite temperature. Our stochastic Gross-Pitaevskii simulations show that the activation of these modes can be suppressed by tightening the confinement along the direction of the vortex line, leading to a strong suppression in the vortex decay rate as the system enters a regime of two-dimensional vortex dynamics. As the system approaches the condensation transition temperature we find that the vortex decay rate is strongly sensitive to dimensionality and temperature, observing a large enhancement for quasi-two-dimensional traps. Three-dimensional simulations of the recent vortex dipole decay experiment of Neely et al. [Phys. Rev. Lett. 104, 160401 (2010)] confirm two-dimensional vortex dynamics, and predict a dipole lifetime consistent with experimental observations and suppression of Kelvon-induced vortex decay in highly oblate condensates.Comment: 8 pages, 8 figure

MLS: Airplane system modeling

Analysis, modeling, and simulations were conducted as part of a multiyear investigation of the more important airplane-system-related items of the microwave landing system (MLS). Particular emphasis was placed upon the airplane RF system, including the antenna radiation distribution, the cabling options from the antenna to the receiver, and the overall impact of the airborne system gains and losses upon the direct-path signal structure. In addition, effort was expended toward determining the impact of the MLS upon the airplane flight management system and developing the initial stages of a fast-time MLS automatic control system simulation model. Results ot these studies are presented

Neutron star matter in the quark-meson coupling model in strong magnetic fields

The effects of strong magnetic fields on neutron star matter are investigated in the quark-meson coupling (QMC) model. The QMC model describes a nuclear many-body system as nonoverlapping MIT bags in which quarks interact through self-consistent exchange of scalar and vector mesons in the mean-field approximation. The results of the QMC model are compared with those obtained in a relativistic mean-field (RMF) model. It is found that quantitative differences exist between the QMC and RMF models, while qualitative trends of the magnetic field effects on the equation of state and composition of neutron star matter are very similar.Comment: 16 pages, 4 figure