Isolation of pigment cell specific genes in the sea urchin embryo by differential macroarray screening

New secondary mesenchyme specific genes, expressed exclusively in pigment cells, were isolated from sea urchin embryos using a differential screening of a macroarray cDNA library. The comparison was performed between mRNA populations of embryos having an expansion of the endo-mesodermal territory and embryos blocked in secondary mesenchyme specification. To be able to isolate transcripts with a prevalence down to five copies per cell, a subtractive hybridization procedure was employed. About 400 putative positive clones were identified and sequenced from the 5' end. Gene expression analysis was carried out on a subset of 66 clones with real time quantitative PCR and 40 clones were positive. This group of clones contained sequences highly similar to: the transcription factor glial cells missing (gcm); the polyketide synthase gene cluster (pks-gc); three different members of the flavin-containing monooxygenase gene family (fmo); and a sulfotransferase gene (sult). Using whole mount in situ hybridization, it was shown that these genes are specifically expressed in pigment cells. A functional analysis of the S. purpuratus pks and of one S. purpuratus fmo was carried out using antisense technology and it was shown that their expression is necessary for the biosynthesis of the sea urchin pigment echinochrome. The results suggest that S. purpuratus pks, fmo and sult could belong to a differentiation gene battery of pigment cells

Single-particle dispersion in stably stratified turbulence

We present models for single-particle dispersion in vertical and horizontal directions of stably stratified flows. The model in the vertical direction is based on the observed Lagrangian spectrum of the vertical velocity, while the model in the horizontal direction is a combination of a continuous-time eddy-constrained random walk process with a contribution to transport from horizontal winds. Transport at times larger than the Lagrangian turnover time is not universal and dependent on these winds. The models yield results in good agreement with direct numerical simulations of stratified turbulence, for which single-particle dispersion differs from the well studied case of homogeneous and isotropic turbulence

Expansion of the Supergranular Magnetic Network through the Solar Atmosphere

The solar magnetic field has its footpoints in the photosphere, extends through the chromosphere, and is thought to expand through the transition region and into the corona. It is organized by fluid motions to form strong flux concentrations within the boundaries of the supergranular convection cells. These boundaries are the network lanes observed in line emission, and they display increasing width with height through the solar atmosphere. The network field concentrations are surrounded by a mixed-polarity internetwork magnetic field on the scale of granulation. We use a potential magnetic field extrapolation of synthetic photospheric magnetograms to study the magnetic network topology and the effects of a mixed-polarity background field on the network expansion with height through the solar atmosphere.We find that the expansion of the network boundary with height deviates significantly from the funnel expansion model. Moreover, we find that the background magnetic field has a considerable effect on the filling factor of the network area with height, even though the background flux is strictly equal to zero

The Intensity Profile of the Solar Supergranulation

We have measured the average radial (cell center to network boundary) profile of the continuum intensity contrast associated with supergranular flows using data from the Precision Solar Photometric Telescope (PSPT) at the Mauna Loa Solar Observatory (MLSO). After removing the contribution of the network flux elements by the application of masks based on Ca II K intensity and averaging over more than 10^5 supergranular cells, we find a ~ 0.1% decrease in red and blue continuum intensity from the supergranular cell centers outward, corresponding to a ~ 1.0 K decrease in brightness temperature across the cells. The radial intensity profile may be caused either by the thermal signal associated with the supergranular flows or a variation in the packing density of unresolved magnetic flux elements. These are not unambiguously distinguished by the observations, and we raise the possibility that the network magnetic fields play an active role in supergranular scale selection by enhancing the radiative cooling of the deep photosphere at the cell boundaries.Comment: Accepted to Ap

The Role of Subsurface Flows in Solar Surface Convection: Modeling the Spectrum of Supergranular and Larger Scale Flows

We model the solar horizontal velocity power spectrum at scales larger than granulation using a two-component approximation to the mass continuity equation. The model takes four times the density scale height as the integral (driving) scale of the vertical motions at each depth. Scales larger than this decay with height from the deeper layers. Those smaller are assumed to follow a Kolomogorov turbulent cascade, with the total power in the vertical convective motions matching that required to transport the solar luminosity in a mixing length formulation. These model components are validated using large scale radiative hydrodynamic simulations. We reach two primary conclusions: 1. The model predicts significantly more power at low wavenumbers than is observed in the solar photospheric horizontal velocity spectrum. 2. Ionization plays a minor role in shaping the observed solar velocity spectrum by reducing convective amplitudes in the regions of partial helium ionization. The excess low wavenumber power is also seen in the fully nonlinear three-dimensional radiative hydrodynamic simulations employing a realistic equation of state. This adds to other recent evidence suggesting that the amplitudes of large scale convective motions in the Sun are significantly lower than expected. Employing the same feature tracking algorithm used with observational data on the simulation output, we show that the observed low wavenumber power can be reproduced in hydrodynamic models if the amplitudes of large scale modes in the deep layers are artificially reduced. Since the large scale modes have reduced amplitudes, modes on the scale of supergranulation and smaller remain important to convective heat flux even in the deep layers, suggesting that small scale convective correlations are maintained through the bulk of the solar convection zone.Comment: 36 pages, 6 figure

Understanding the Role of Small-Scale Flux in Solar Spectral Irradiance Variation

Global solar spectral irradiance variations depend on changes inmagnetic flux concentrations at the smallest scales. Modeling has focused on the contributions of magnetic structures in full disk images as those contributions have strong center-to-limb dependencies, but these dependencies have never been determined radiometrically; only the photometric intensity relative to some reference ’quiet-sun’1, themagnetic structure contrast, is measurable with ground based imagery. This is problematic because unre- solved inhomogeneities influence not only the full-disk structure intensities themselves, but also the quiet-sun background against which their contrast is measured. We thus argue that, to understand the physical causes underlying solar spectral irradiance varia- tions, two fundamental questionsmust be addressed: What is the real Iλ(µ) as a function of B in full-disk images? This can only be answered by imaging the Sun radiometrically from space, and we propose a Radiometric Solar Imager design. What governs spectral irradiance changes at sub arc-second scales? This can be addressed by a combination of high resolution ground based imaging (ATST-VBI) and three dimensional radiative magnetohydrodynamic modeling, and we propose a synoptic approach. Finally, a way to account for the variance introduced by unresolved substructure in spectral irradiance modeling must be devised. This is critical, as imaging and modeling at the highest resolutions but over the full solar disk will likely remain unattainable for some time

Theoretical study of electronic relaxation processes in hydrated Gd³⁺ complexes in solutions

The EPR line widths of [Gd(H2O)(8)](3+) measured in water at various magnetic fields by Merbach's group have been reinterpreted. A theoretical model of the transverse electronic relaxation is proposed, All the terms of the static zero-field splitting (ZFS) allowed by the symmetry of the complex are included and shown to have a significant contribution. The influence of a transient distortion ZFS is also studied

Dynamic Evolution of Toll-Like Receptor Multigene Families in Echinoderms

The genome sequence of the purple sea urchin, Strongylocentrotus purpuratus, a large and long-lived invertebrate, provides a new perspective on animal immunity. Analysis of this genome uncovered a highly complex immune system in which the gene families that encode homologs of the pattern recognition receptors that form the core of vertebrate innate immunity are encoded in large multigene families. The sea urchin genome contains 253 Toll-like receptor (TLR) sequences, more than 200 Nod-like receptors and 1095 scavenger receptor cysteine-rich domains, a 10-fold expansion relative to vertebrates. Given their stereotypic protein structure and simple intron-exon architecture, the TLRs are the most tractable of these families for more detailed analysis. A role for these receptors in immune defense is suggested by their similarity to TLRs in other organisms, sequence diversity, and expression in immunologically active tissues, including phagocytes. The complexity of the sea urchin TLR multigene families is largely derived from expansions independent of those in vertebrates and protostomes, although a small family of TLRs with structure similar to that of Drosophila Toll can be traced to an ancient eumetazoan ancestor. Several other echinoderm sequences are now available, including Lytechinus variegatus, as well as partial sequences from two other sea urchin species. Here, we present an analysis of the invertebrate deuterostome TLRs with emphasis on the echinoderms. Representatives of most of the S. purpuratus TLR subfamilies and homologs of the mccTLR sequences are found in L. variegatus, although the L. variegatus TLR gene family is notably smaller (68 TLR sequences). The phylogeny of these genes within sea urchins highlights lineage-specific expansions at higher resolution than is evident at the phylum level. These analyses identify quickly evolving TLR subfamilies that are likely to have novel immune recognition functions and other, more stable, subfamilies that may function more similarly to those of vertebrates

High-resolution models of solar granulation: the 2D case

Using grid refinement, we have simulated solar granulation in 2D. The refined region measures 1.97*2.58 Mm (vertical*horizontal). Grid spacing there is 1.82*2.84 km. The downflows exhibit strong Kelvin-Helmholtz instabilities. Below the photosphere, acoustic pulses are generated. They proceed laterally (in some cases distances of at least the size of our refined domain) and may be enhanced when transversing downflows) as well as upwards where, in the photosphere they contribute significantly to 'turbulence' (velocity gradients, etc.) The acoustic pulses are ubiquitous in that at any time several of them are seen in our high-resolution domain. Their possible contributions to p-mode excitation or heating of the chromosphere needs to be investigated