Low-density genotype panel for both parentage verification and discovery in a multi-breed sheep population

peer-reviewedThe generally low usage of artificial insemination and single-sire mating in sheep, compounded by mob lambing (and lambing outdoors), implies that parentage assignment in sheep is challenging. The objective here was to develop a low-density panel of single nucleotide polymorphisms (SNPs) for accurate parentage verification and discovery in sheep. Of particular interest was where SNP selection was limited to only a subset of chromosomes, thereby eliminating the ability to accurately impute genome-wide denser marker panels. Data used consisted of 10,933 candidate SNPs on 9,390 purebred sheep. These data consisted of 1,876 validated genotyped sire–offspring pairs and 2,784 validated genotyped dam–offspring pairs. The SNP panels developed consisted of 87 SNPs to 500 SNPs. Parentage verification and discovery were undertaken using 1) exclusion, based on the sharing of at least one allele between candidate parent–offspring pairs, and 2) a likelihood-based approach. Based on exclusion, allowing for one discordant offspring–parent genotype, a minimum of 350 SNPs was required when the goal was to unambiguously identify the true sire or dam from all possible candidates. Results suggest that, if selecting SNPs across the entire genome, a minimum of 250 carefully selected SNPs are required to ensure that the most likely selected parent (based on the likelihood approach) was, in fact, the true parent. If restricting the SNPs to just a subset of chromosomes, the recommendation is to use at least a 300-SNP panel from at least six chromosomes, with approximately an equal number of SNPs per chromosome

Is turbulent mixing a self convolution process ?

Experimental results for the evolution of the probability distribution function (PDF) of a scalar mixed by a turbulence flow in a channel are presented. The sequence of PDF from an initial skewed distribution to a sharp Gaussian is found to be non universal. The route toward homogeneization depends on the ratio between the cross sections of the dye injector and the channel. In link with this observation, advantages, shortcomings and applicability of models for the PDF evolution based on a self-convolution mechanisms are discussed.Comment: 4 page

Systematic Errors in the Estimation of Black Hole Masses by Reverberation Mapping

The mass of the central black hole in many active galactic nuclei has been estimated on the basis of the assumption that the dynamics of the broad emission line gas are dominated by the gravity of the black hole. The most commonly-employed method is to estimate a characteristic size-scale $r_*$ from reverberation mapping experiments and combine it with a characteristic velocity $v_*$ taken from the line profiles; the inferred mass is then estimated by $r_* v_*^2/G$. We critically discuss the evidence supporting the assumption of gravitational dynamics and find that the arguments are still inconclusive. We then explore the range of possible systematic error if the assumption of gravitational dynamics is granted. Inclination relative to a flattened system may cause a systematic underestimate of the central mass by a factor $\sim (h/r)^2$, where $h/r$ is the aspect ratio of the flattening. The coupled effects of a broad radial emissivity distribution, an unknown angular radiation pattern of line emission, and sub-optimal sampling in the reverberation experiment can cause additional systematic errors as large as a factor of 3 or more in either direction.Comment: 19 pages, 4 figures, AASLaTeX, accepted by Ap

Dynamics of the Lyman alpha and C IV emitting gas in 3C 273

In this paper we study the variability properties of the Lyman alpha and C IV emission lines in 3C273 using archival IUE observations. Our data show for the first time the existence of variability on time scales of several years. We study the spatial distribution and the velocity field of the emitting gas by performing detailed analyses on the line variability using correlations, 1D and 2D response functions, and principal component analysis. In both lines we find evidence for two components, one which has the dynamic properties of gas in Keplerian motion around a black hole with a mass of the order of 10^9 Mo, and one which is characterized by high, blue-shifted velocities at large lag. There is no indication of the presence of optically thick emission medium neither in the Lya, nor in the Civ response functions. The component characterized by blue-shifted velocities, which is comparatively much stronger in Civ than in Lya, is more or less compatible with being the result of gas falling towards the central black hole with free-fall acceleration. We propose however that the line emission at high, blue-shifted velocities is better explained in terms of entrainment of gas clouds by the jet. This gas is therefore probably collisionally excited as a result of heating due to the intense infrared radiation from the jet, which would explain the strength of this component in Civ relative to Lya. This phenomenon might be a signature of disk-jet interaction.Comment: 16 pages, 10 figures. Accepted for publication in ApJ. Uses aaste

Near-field interaction between domain walls in adjacent Permalloy nanowires

The magnetostatic interaction between two oppositely charged transverse domain walls (DWs)in adjacent Permalloy nanowires is experimentally demonstrated. The dependence of the pinning strength on wire separation is investigated for distances between 13 and 125 nm, and depinning fields up to 93 Oe are measured. The results can be described fully by considering the interaction between the full complex distribution of magnetic charge within rigid, isolated DWs. This suggests the DW internal structure is not appreciably disturbed by the pinning potential, and that they remain rigid although the pinning strength is significant. This work demonstrates the possibility of non-contact DW trapping without DW perturbation and full continuous flexibility of the pinning potential type and strength. The consequence of the interaction on DW based data storage schemes is evaluated.Comment: 4 pages, 4 figures, 1 page supplimentary material (supporting.ps

Detection of Coronal Mass Ejections in V471 Tauri with the Hubble Space Telescope

V471 Tauri, an eclipsing system consisting of a hot DA white dwarf (WD) and a dK2 companion in a 12.5-hour orbit, is the prototype of the pre-cataclysmic binaries. The late-type component is magnetically active, due to its being constrained to rotate synchronously with the short orbital period. During a program of UV spectroscopy of V471 Tau, carried out with the Goddard High Resolution Spectrograph (GHRS) onboard the Hubble Space Telescope, we serendipitously detected two episodes in which transient absorptions in the Si III 1206 A resonance line appeared suddenly, on a timescale of <2 min. The observations were taken in a narrow spectral region around Ly-alpha, and were all obtained near the two quadratures of the binary orbit, i.e., at maximum projected separation (~3.3 Rsun) of the WD and K star. We suggest that these transient features arise when coronal mass ejections (CME's) from the K2 dwarf pass across the line of sight to the WD. Estimates of the velocities, densities, and masses of the events in V471 Tau are generally consistent with the properties of solar CME's. Given our detection of 2 events during 6.8 hr of GHRS observing, along with a consideration of the restricted range of latitudes and longitudes on the K star's surface that can give rise to trajectories passing in front of the WD as seen from Earth, we estimate that the active V471 Tau dK star emits some 100-500 CME's per day, as compared to 1-3 per day for the Sun. The K dwarf's mass-loss rate associated with CME's is at least (5-25) x 10^{-14} Msun/yr, but it may well be orders of magnitude higher if most of the silicon is in ionization states other than Si III.Comment: 24 pages AASTeX, 4 figures. Accepted by Astrophysical Journa

Modeling Variable Emission Lines in AGNs: Method and Application to NGC 5548

We present a new scheme for modeling the broad line region in active galactic nuclei (AGNs). It involves photoionization calculations of a large number of clouds, in several pre-determined geometries, and a comparison of the calculated line intensities with observed emission line light curves. Fitting several observed light curves simultaneously provides strong constraints on model parameters such as the run of density and column density across the nucleus, the shape of the ionizing continuum, and the radial distribution of the emission line clouds. When applying the model to the Seyfert 1 galaxy NGC 5548, we were able to reconstruct the light curves of four ultraviolet emission-lines, in time and in absolute flux. This has not been achieved by any previous work. We argue that the Balmer lines light curves, and possibly also the MgII2798 light curve, cannot be tested in this scheme because of the limitations of present-day photoionization codes. Our fit procedure can be used to rule out models where the particle density scales as r^{-2}, where r is the distance from the central source. The best models are those where the density scales as r^{-1} or r^{-1.5}. We can place a lower limit on the column density at a distance of 1 ld, of N_{col}(r=1) >~ 10^{23} cm^{-2} and limit the particle density to be in the range of 10^{12.5}>N(r=1)>10^{11} cm^{-3}. We have also tested the idea that the spectral energy distribution (SED) of the ionizing continuum is changing with continuum luminosity. None of the variable-shape SED tried resulted in real improvement over a constant SED case although models with harder continuum during phases of higher luminosity seem to fit better the observed spectrum. Reddening and/or different composition seem to play a minor role, at least to the extent tested in this work.Comment: 12 pages, including 9 embedded EPS figures, accepted for publication in Ap

The Role of miR-29 Family in TGF-β Driven Fibrosis in Glaucomatous Optic Neuropathy

Primary open angle glaucoma (POAG), a chronic optic neuropathy, remains the leading cause of irreversible blindness worldwide. It is driven in part by the pro-fibrotic cytokine transforming growth factor beta (TGF-β) and leads to extracellular matrix remodelling at the lamina cribrosa of the optic nerve head. Despite an array of medical and surgical treatments targeting the only known modifiable risk factor, raised intraocular pressure, many patients still progress and develop significant visual field loss and eventual blindness. The search for alternative treatment strategies targeting the underlying fibrotic transformation in the optic nerve head and trabecular meshwork in glaucoma is ongoing. MicroRNAs are small non-coding RNAs known to regulate post-transcriptional gene expression. Extensive research has been undertaken to uncover the complex role of miRNAs in gene expression and miRNA dysregulation in fibrotic disease. MiR-29 is a family of miRNAs which are strongly anti-fibrotic in their effects on the TGF-β signalling pathway and the regulation of extracellular matrix production and deposition. In this review, we discuss the anti-fibrotic effects of miR-29 and the role of miR-29 in ocular pathology and in the development of glaucomatous optic neuropathy. A better understanding of the role of miR-29 in POAG may aid in developing diagnostic and therapeutic strategies in glaucoma

Impact of Colonoscopy Bowel Preparation on Intestinal Microbiota

The gut microbiota is important in maintaining human health, but numerous factors have the potential to alter its composition. Our aim was to examine the impact of a standard bowel preparation on the intestinal microbiota using two different techniques. Fifteen subjects undergoing colonoscopy consumed a bowel preparation comprised of 10 mg bisacodyl and 2 L polyethylene glycol. The microbiota of stool samples, collected one month before, one week before (pre-colonoscopy), and one week, one month, and three to six months after colonoscopy (post-colonoscopy) was evaluated. Two samples were taken three to six months apart from five healthy subjects who did not undergo colonoscopy. Universal primers targeting the V2-V3 region of the 16S rRNA gene were used to PCR amplify all samples for denaturing gradient gel electrophoresis (PCR-DGGE). Pre- and post-colonoscopy samples were compared using Dice's similarity coefficients. Three samples from ten subjects who underwent colonoscopy, and both samples from the five subjects who didn't, were used for high-throughput sequencing of the V1-V3 region of the 16S rRNA gene. Samples were curated and analysed in Mothur. Results of the DGGE analyses show that the fecal microbiota of a small number of subjects had short-term changes. High-throughput sequencing results indicated that the variation between the samples of subjects who underwent colonoscopy was no greater than the variation observed between samples from subjects who did not. We conclude that bowel preparation does not have a lasting effect on the composition of the intestinal microbiota for the majority of subjects.This work was funded by an Australian Post-Graduate Award scholarship. The funders had no role in the study design, data collection and analysis, decision to publish, or preparation of the manuscript

Molecular Line Observations of Infrared Dark Clouds: Seeking the Precursors to Intermediate and Massive Star Formation

We have identified 41 infrared dark clouds from the 8 micron maps of the Midcourse Space Experiment (MSX), selected to be found within one square degree areas centered on known ultracompact HII regions. We have mapped these infrared dark clouds in N2H+(1-0), CS(2-1) and C18O(1-0) emission using the Five College Radio Astronomy Observatory. The maps of the different species often show striking differences in morphologies, indicating differences in evolutionary state and/or the presence of undetected, deeply embedded protostars. We derive an average mass for these clouds using N2H+ column densities of ~2500 solar masses, a value comparable to that found in previous studies of high mass star forming cores using other mass tracers. The linewidths of these clouds are typically ~2.0 - 2.9 km/s. Based on the fact that they are dark at 8 micron, compact, massive, and have large velocity dispersions, we suggest that these clouds may be the precursor sites of intermediate and high mass star formation.Comment: Accepted to ApJS, 22 pages, 10 pages of figures. For full-resolution images, see http://www.astro.lsa.umich.edu/~seragan/pubs/fcrao/figures.tar.g