A compendium of Caenorhabditis elegans regulatory transcription factors: a resource for mapping transcription regulatory networks

Background Transcription regulatory networks are composed of interactions between transcription factors and their target genes. Whereas unicellular networks have been studied extensively, metazoan transcription regulatory networks remain largely unexplored. Caenorhabditis elegans provides a powerful model to study such metazoan networks because its genome is completely sequenced and many functional genomic tools are available. While C. elegans gene predictions have undergone continuous refinement, this is not true for the annotation of functional transcription factors. The comprehensive identification of transcription factors is essential for the systematic mapping of transcription regulatory networks because it enables the creation of physical transcription factor resources that can be used in assays to map interactions between transcription factors and their target genes. Results By computational searches and extensive manual curation, we have identified a compendium of 934 transcription factor genes (referred to as wTF2.0). We find that manual curation drastically reduces the number of both false positive and false negative transcription factor predictions. We discuss how transcription factor splice variants and dimer formation may affect the total number of functional transcription factors. In contrast to mouse transcription factor genes, we find that C. elegans transcription factor genes do not undergo significantly more splicing than other genes. This difference may contribute to differences in organism complexity. We identify candidate redundant worm transcription factor genes and orthologous worm and human transcription factor pairs. Finally, we discuss how wTF2.0 can be used together with physical transcription factor clone resources to facilitate the systematic mapping of C. elegans transcription regulatory networks. Conclusion wTF2.0 provides a starting point to decipher the transcription regulatory networks that control metazoan development and function

Evolution and nucleosynthesis of helium-rich asymptotic giant branch models

There is now strong evidence that some stars have been born with He mass fractions as high as $Y \approx 0.40$ (e.g., in $\omega$ Centauri). However, the advanced evolution, chemical yields, and final fates of He-rich stars are largely unexplored. We investigate the consequences of He-enhancement on the evolution and nucleosynthesis of intermediate-mass asymptotic giant branch (AGB) models of 3, 4, 5, and 6 M$_\odot$ with a metallicity of $Z = 0.0006$ ([Fe/H] $\approx -1.4$). We compare models with He-enhanced compositions ($Y=0.30, 0.35, 0.40$) to those with primordial He ($Y=0.24$). We find that the minimum initial mass for C burning and super-AGB stars with CO(Ne) or ONe cores decreases from above our highest mass of 6 M$_\odot$ to $\sim$ 4-5 M$_\odot$ with $Y=0.40$. We also model the production of trans-Fe elements via the slow neutron-capture process (s-process). He-enhancement substantially reduces the third dredge-up efficiency and the stellar yields of s-process elements (e.g., 90% less Ba for 6 M$_\odot$, $Y=0.40$). An exception occurs for 3 M$_\odot$, where the near-doubling in the number of thermal pulses with $Y=0.40$ leads to $\sim$ 50% higher yields of Ba-peak elements and Pb if the $^{13}$C neutron source is included. However, the thinner intershell and increased temperatures at the base of the convective envelope with $Y=0.40$ probably inhibit the $^{13}$C neutron source at this mass. Future chemical evolution models with our yields might explain the evolution of s-process elements among He-rich stars in $\omega$ Centauri.Comment: 21 pages, 16 figures, accepted for publication by MNRAS. Stellar yields included as online data table

A chemical signature from fast-rotating low-metallicity massive stars: ROA 276 in ω Centauri

© 2017. The American Astronomical Society. All rights reserved. We present a chemical abundance analysis of a metal-poor star, ROA 276, in the stellar system ω Centauri. We confirm that this star has an unusually high [Sr/Ba] abundance ratio. Additionally, ROA 276 exhibits remarkably high abundance ratios, [X/Fe] , for all elements from Cu to Mo along with normal abundance ratios for the elements from Ba to Pb. The chemical abundance pattern of ROA 276, relative to a primordial ω Cen star ROA 46, is best fit by a fast-rotating low-metallicity massive stellar model of 20 , [Fe/H] = -1.8, and an initial rotation 0.4 times the critical value; no other nucleosynthetic source can match the neutron-capture element distribution. ROA 276 arguably offers the most definitive proof to date that fast-rotating massive stars contributed to the production of heavy elements in the early universe

Using late-time optical and near-infrared spectra to constrain Type Ia supernova explosion properties

The late-time spectra of Type Ia supernovae (SNe Ia) are powerful probes of the underlying physics of their explosions. We investigate the late-time optical and near-infrared spectra of seven SNe Ia obtained at the VLT with XShooter at $>$200 d after explosion. At these epochs, the inner Fe-rich ejecta can be studied. We use a line-fitting analysis to determine the relative line fluxes, velocity shifts, and line widths of prominent features contributing to the spectra ([Fe II], [Ni II], and [Co III]). By focussing on [Fe II] and [Ni II] emission lines in the ~7000-7500 \AA\ region of the spectrum, we find that the ratio of stable [Ni II] to mainly radioactively-produced [Fe II] for most SNe Ia in the sample is consistent with Chandrasekhar-mass delayed-detonation explosion models, as well as sub-Chandrasekhar mass explosions that have metallicity values above solar. The mean measured Ni/Fe abundance of our sample is consistent with the solar value. The more highly ionised [Co III] emission lines are found to be more centrally located in the ejecta and have broader lines than the [Fe II] and [Ni II] features. Our analysis also strengthens previous results that SNe Ia with higher Si II velocities at maximum light preferentially display blueshifted [Fe II] 7155 \AA\ lines at late times. Our combined results lead us to speculate that the majority of normal SN Ia explosions produce ejecta distributions that deviate significantly from spherical symmetry.Comment: 17 pages, 12 figure, accepted for publication in MNRA

Iron and s-elements abundance variations in NGC5286: comparison with anomalous globular clusters and Milky Way satellites

We present a high resolution spectroscopic analysis of 62 red giants in the Milky Way globular cluster NGC5286. We have determined abundances of representative light proton-capture, alpha, Fe-peak and neutron-capture element groups, and combined them with photometry of multiple sequences observed along the colour-magnitude diagram. Our principal results are: (i) a broad, bimodal distribution in s-process element abundance ratios, with two main groups, the s-poor and s-rich groups; (ii) substantial star-to-star Fe variations, with the s-rich stars having higher Fe, e.g. _s-rich - _s-poor ~ 0.2~dex; and (iii) the presence of O-Na-Al (anti-)correlations in both stellar groups. We have defined a new photometric index, c_{BVI}=(B-V)-(V-I), to maximise the separation in the colour-magnitude diagram between the two stellar groups with different Fe and s-element content, and this index is not significantly affected by variations in light elements (such as the O-Na anticorrelation). The variations in the overall metallicity present in NGC5286 add this object to the class of "anomalous" GCs. Furthermore, the chemical abundance pattern of NGC5286 resembles that observed in some of the anomalous GCs, e.g. M22, NGC1851, M2, and the more extreme Omega Centauri, that also show internal variations in s-elements, and in light elements within stars with different Fe and s-elements content. In view of the common variations in s-elements, we propose the term s-Fe-anomalous GCs to describe this sub-class of objects. The similarities in chemical abundance ratios between these objects strongly suggest similar formation and evolution histories, possibly associated with an origin in tidally disrupted dwarf satellites.Comment: 28 pages, 21 figures, accepted for publication in MNRA

Helium as a signature of the double detonation in Type Ia supernovae

The double detonation is a widely discussed mechanism to explain Type Ia supernovae from explosions of sub-Chandrasekhar mass white dwarfs. In this scenario, a helium detonation is ignited in a surface helium shell on a carbon/oxygen white dwarf, which leads to a secondary carbon detonation. Explosion simulations predict high abundances of unburnt helium in the ejecta, however, radiative transfer simulations have not been able to fully address whether helium spectral features would form. This is because helium can not be sufficiently excited to form spectral features by thermal processes, but can be excited by collisions with non-thermal electrons, which most studies have neglected. We carry out a full non-local thermodynamic equilibrium (non-LTE) radiative transfer simulation for an instance of a double detonation explosion model, and include a non-thermal treatment of fast electrons. We find a clear He I {\lambda} 10830 feature which is strongest in the first few days after explosion and becomes weaker with time. Initially this feature is blended with the Mg II {\lambda} 10927 feature but over time separates to form a secondary feature to the blue wing of the Mg II {\lambda} 10927 feature. We compare our simulation to observations of iPTF13ebh, which showed a similar feature to the blue wing of the Mg II {\lambda} 10927 feature, previously identified as C I. Our simulation shows a good match to the evolution of this feature and we identify it as high velocity He I {\lambda} 10830. This suggests that He I {\lambda} 10830 could be a signature of the double detonation scenario.Comment: 7 pages, accepted by MNRA

Augmented Reality in Astrophysics

Augmented Reality consists of merging live images with virtual layers of information. The rapid growth in the popularity of smartphones and tablets over recent years has provided a large base of potential users of Augmented Reality technology, and virtual layers of information can now be attached to a wide variety of physical objects. In this article, we explore the potential of Augmented Reality for astrophysical research with two distinct experiments: (1) Augmented Posters and (2) Augmented Articles. We demonstrate that the emerging technology of Augmented Reality can already be used and implemented without expert knowledge using currently available apps. Our experiments highlight the potential of Augmented Reality to improve the communication of scientific results in the field of astrophysics. We also present feedback gathered from the Australian astrophysics community that reveals evidence of some interest in this technology by astronomers who experimented with Augmented Posters. In addition, we discuss possible future trends for Augmented Reality applications in astrophysics, and explore the current limitations associated with the technology. This Augmented Article, the first of its kind, is designed to allow the reader to directly experiment with this technology.Comment: 15 pages, 11 figures. Accepted for publication in Ap&SS. The final publication will be available at link.springer.co

Self-consistent 3D radiative transfer for kilonovae: directional spectra from merger simulations

We present three-dimensional radiative transfer calculations for the ejecta from a neutron star merger that include line-by-line opacities for tens of millions of bound-bound transitions, composition from an r-process nuclear network, and time-dependent thermalization of decay products from individual $\alpha$ and $\beta^-$ decay reactions. In contrast to expansion opacities and other wavelength-binned treatments, a line-by-line treatment enables us include fluorescence effects and associate spectral features with the emitting and absorbing lines of individual elements. We find variations in the synthetic observables with both the polar and azimuthal viewing angles. The spectra exhibit blended features with strong interactions by Ce III, Sr II, Y II, and Zr II that vary with time and viewing direction. We demonstrate the importance of wavelength-calibration of atomic data using a model with calibrated Sr, Y, and Zr data, and find major differences in the resulting spectra, including a better agreement with AT2017gfo. The synthetic spectra for near-polar inclination show a feature at around 8000 A, similar to AT2017gfo. However, they evolve on a more rapid timescale, likely due to the low ejecta mass (0.005 M$_\odot$) as we take into account only the early ejecta. The comparatively featureless spectra for equatorial observers gives a tentative prediction that future observations of edge-on kilonovae will appear substantially different from AT2017gfo. We also show that 1D models obtained by spherically averaging the 3D ejecta lead to dramatically different direction-integrated luminosities and spectra compared to full 3D calculations.Comment: 12 pages, 5 figures. Accepted by ApJ