Multifluid magnetohydrodynamic turbulent decay

It is generally believed that turbulence has a significant impact on the dynamics and evolution of molecular clouds and the star formation which occurs within them. Non-ideal magnetohydrodynamic effects are known to influence the nature of this turbulence. We present the results of a suite of 512-cubed resolution simulations of the decay of initially super-Alfvenic and supersonic fully multifluid MHD turbulence. We find that ambipolar diffusion increases the rate of decay of the turbulence while the Hall effect has virtually no impact. The decay of the kinetic energy can be fitted as a power-law in time and the exponent is found to be -1.34 for fully multifluid MHD turbulence. The power spectra of density, velocity and magnetic field are all steepened significantly by the inclusion of non-ideal terms. The dominant reason for this steepening is ambipolar diffusion with the Hall effect again playing a minimal role except at short length scales where it creates extra structure in the magnetic field. Interestingly we find that, at least at these resolutions, the majority of the physics of multifluid turbulence can be captured by simply introducing fixed (in time and space) resistive terms into the induction equation without the need for a full multifluid MHD treatment. The velocity dispersion is also examined and, in common with previously published results, it is found not to be power-law in nature.Comment: 16 pages, 15 figures, Accepted for publication in Ap

Phenotypic variation in the sexual attractiveness pheromone of the red-sided garter snake, Thamnophis sirtalis parietalis

Pheromones are chemical cues produced by organisms that affect the behavior and/or physiology of conspecifics. The orchestration of reproductive behaviors in many animals depends on the expression of sex pheromones. In insects, intraspecific variation in sex pheromone expression is commonly observed and often influences social interactions between individuals. To what extent similar variation is present in vertebrate sex pheromone systems is not well understood. This thesis investigated the occurrence and significance of phenotypic variation in the sexual attractiveness pheromone of the red-sided garter snake, Thamnophis sirtalis parietalis. Composed of a homologous series of saturated and unsaturated methyl ketones sequestered in the skin lipids of females, this pheromone elicits male courtship behaviors during the breeding season. Variation in the expression of the sexual attractiveness pheromone was examined at three levels: seasonal, individual and populational. Seasonal variation in pheromone expression was examined with respect to trailing behavior. In field experiments, males followed female trails during the breeding season but not during the non-breeding season. Skin lipid analysis revealed marked differences in pheromone composition between the two seasons, suggesting a role for this pheromone in regulating male trailing behavior. Individual variation in pheromone expression was examined with respect to mate choice. In arena trials, males displayed a courtship preference for larger females and continued to demonstrate this preference when visual, tactile, and behavioral cues from the females were removed through the use of skin lipid extracts. Analysis of pheromone profiles from individual females showed size-specific variation in composition, demonstrating that this pheromone can function as a reliable indicator of female size. Finally, populational variation in pheromone expression was examined with respect to sexual isolation among hibernacula. In arena and trailing experiments, males preferred to court and trail resident (same den) females over non-resident (distant den) females. Chemical analysis showed significant inter-den variation in pheromone composition, suggesting that this pheromone represents the cue that males use to identify females from their own population. In summary, these studies demonstrate that significant variation exists in the female sexual attractiveness pheromone of the red-sided garter snake and suggest that this variation has functional significance for this species

Perivascular Adipose Tissue Diminishes Nitric Oxide Bioavailability in Metabolic Syndrome

Please refer to the pdf version of the abstract located adjacent to the title

Trend analysis of in-situ spectral reflectance data from the Thermal Control Surfaces Experiment (TCSE)

The Thermal Control Surfaces Experiment (TCSE) on the LDEF was a comprehensive experiment that combined in-space measurements with extensive pre- and post-flight analyses of thermal control surfaces to determine the effects of exposure to the low earth orbit (LEO) space environment. The TCSE is the first space experiment to directly measure in-situ total hemispherical reflectance of thermal control surfaces in the same way they are routinely measured in the laboratory. In-space optical measurements performed by the TCSE provide the unique opportunity for trend analysis of the performance of materials in the space environment. Such trend analysis of flight data offers the potential to develop an empirical life time prediction model for several thermal control surfaces. For material research, trend analysis of the TCSE flight data, particularly the spectral data, can provide insight into the damage mechanisms of space exposure. Trend analysis for the TCSE samples has been limited to those materials that were not significantly eroded by the atomic oxygen (AO) environment. The performance of several materials on the LDEF mission was dominated by AO effects. Trend analysis was performed on both the detailed spectral reflectance measurements (in-space, pre-flight, and post-flight) and on the integrated solar absorptance. Results of this analysis for the five selected TCSE materials are presented along with the spectral flight data. Possible degradation and effects mechanisms will be discussed to better understand and predict the behavior of these materials in the LEO space environment

Simulating Supersonic Turbulence in Magnetized Molecular Clouds

We present results of large-scale three-dimensional simulations of weakly magnetized supersonic turbulence at grid resolutions up to 1024^3 cells. Our numerical experiments are carried out with the Piecewise Parabolic Method on a Local Stencil and assume an isothermal equation of state. The turbulence is driven by a large-scale isotropic solenoidal force in a periodic computational domain and fully develops in a few flow crossing times. We then evolve the flow for a number of flow crossing times and analyze various statistical properties of the saturated turbulent state. We show that the energy transfer rate in the inertial range of scales is surprisingly close to a constant, indicating that Kolmogorov's phenomenology for incompressible turbulence can be extended to magnetized supersonic flows. We also discuss numerical dissipation effects and convergence of different turbulence diagnostics as grid resolution refines from 256^3 to 1024^3 cells.Comment: 10 pages, 3 figures, to appear in the proceedings of the DOE/SciDAC 2009 conferenc

Driven Multifluid MHD Molecular Cloud Turbulence

It is believed that turbulence may have a significant impact on star formation and the dynamics and evolution of the molecular clouds in which this occurs. It is also known that non-ideal magnetohydrodynamic effects influence the nature of this turbulence. We present the results of a numerical study of 4-fluid MHD turbulence in which the dynamics of electrons, ions, charged dust grains and neutrals and their interactions are followed. The parameters describing the fluid being simulated are based directly on observations of molecular clouds. We find that the velocity and magnetic field power spectra are strongly influenced by multifluid effects on length-scales at least as large as 0.05 pc. The PDFs of the various species in the system are all found to be close to log-normal, with charged species having a slightly less platykurtic (flattened) distribution than the neutrals. We find that the introduction of multifluid effects does not significantly alter the structure functions of the centroid velocity increment.Comment: 15 pages, 14 figures, 5 tables. Accepted for publication in MNRA

Co-directional replication-transcription conflicts lead to replication restart

August 24, 2011Head-on encounters between the replication and transcription machineries on the lagging DNA strand can lead to replication fork arrest and genomic instability1, 2. To avoid head-on encounters, most genes, especially essential and highly transcribed genes, are encoded on the leading strand such that transcription and replication are co-directional. Virtually all bacteria have the highly expressed ribosomal RNA genes co-directional with replication3. In bacteria, co-directional encounters seem inevitable because the rate of replication is about 10–20-fold greater than the rate of transcription. However, these encounters are generally thought to be benign2, 4, 5, 6, 7, 8, 9. Biochemical analyses indicate that head-on encounters10 are more deleterious than co-directional encounters8 and that in both situations, replication resumes without the need for any auxiliary restart proteins, at least in vitro. Here we show that in vivo, co-directional transcription can disrupt replication, leading to the involvement of replication restart proteins. We found that highly transcribed rRNA genes are hotspots for co-directional conflicts between replication and transcription in rapidly growing Bacillus subtilis cells. We observed a transcription-dependent increase in association of the replicative helicase and replication restart proteins where head-on and co-directional conflicts occur. Our results indicate that there are co-directional conflicts between replication and transcription in vivo. Furthermore, in contrast to the findings in vitro, the replication restart machinery is involved in vivo in resolving potentially deleterious encounters due to head-on and co-directional conflicts. These conflicts probably occur in many organisms and at many chromosomal locations and help to explain the presence of important auxiliary proteins involved in replication restart and in helping to clear a path along the DNA for the replisome.Biotechnology and Biological Sciences Research Council (Great Britain) (Grant BB/E006450/1)Wellcome Trust (London, England) (Grant 091968/Z/10/Z)National Institutes of Health (U.S.) (Grant GM41934)National Institutes of Health (U.S.) (Postdoctoral Fellowship GM093408)Biotechnology and Biological Sciences Research Council (Great Britain) (Sabbatical Visit

Asymmetry of 13C labeled 3-pyruvate affords improved site specific labeling of RNA for NMR spectroscopy

Selective isotopic labeling provides an unparalleled window within which to study the structure and dynamics of RNAs by high resolution NMR spectroscopy. Unlike commonly used carbon sources, the asymmetry of 13C-labeled pyruvate provides selective labeling in both the ribose and base moieties of nucleotides using E. coli variants, that until now were not feasible. Here we show that an E. coli mutant strain that lacks succinate and malate dehydrogenases (DL323) and grown on [3-13C]-pyruvate affords ribonucleotides with site specific labeling at C5′ (~95%) and C1′ (~42%) and minimal enrichment elsewhere in the ribose ring. Enrichment is also achieved at purine C2 and C8 (~95%) and pyrimidine C5 (~100%) positions with minimal labeling at pyrimidine C6 and purine C5 positions. These labeling patterns contrast with those obtained with DL323 E. coli grown on [1, 3-13C]-glycerol for which the ribose ring is labeled in all but the C4′ carbon position, leading to multiplet splitting of the C1′, C2′ and C3′ carbon atoms. The usefulness of these labeling patterns is demonstrated with a 27-nt RNA fragment derived from the 30S ribosomal subunit. Removal of the strong magnetic coupling within the ribose and base leads to increased sensitivity, substantial simplification of NMR spectra, and more precise and accurate dynamic parameters derived from NMR relaxation measurements. Thus these new labels offer valuable probes for characterizing the structure and dynamics of RNA that were previously limited by the constraint of uniformly labeled nucleotides

Orbitally modulated dust formation by the WC7+O5 colliding-wind binary WR140

We present high-resolution infrared (2--18 micron) images of the archetypal periodic dust-making Wolf-Rayet binary system WR140 (HD 193793) taken between 2001 and 2005, and multi-colour (J -- [19.5]) photometry observed between 1989 and 2001. The images resolve the dust cloud formed by WR140 in 2001, allowing us to track its expansion and cooling, while the photometry allows tracking the average temperature and total mass of the dust. The combination of the two datasets constrains the optical properties of the dust. The most persistent dust features, two concentrations at the ends of a `bar' of emission to the south of the star, were observed to move with constant proper motions of 324+/-8 and 243+/-7 mas/y. Longer wavelength (4.68-micron and 12.5-micron) images shows dust emission from the corresponding features from the previous (1993) periastron passage and dust-formation episode. A third persistent dust concentration to the east of the binary (the `arm') was found to have a proper motion ~ 320 mas/y. Extrapolation of the motions of the concentrations back to the binary suggests that the eastern `arm' began expansion 4--5 months earlier than those in the southern `bar', consistent with the projected rotation of the binary axis and wind-collision region (WCR) on the sky. Comparison of model dust images and the observations constrain the intervals when the WCR was producing sufficiently compressed wind for dust nucleation in the WCR, and suggests that the distribution of this material was not uniform about the axis of the WCR, but more abundant in the following edge in the orbital plane.Comment: 21 pages, 10 figures, accepted for MNRAS. A version with higher resolution figures is available at ftp://ftp.roe.ac.uk/pub/pmw/wr140dust.ps.g