A metagenome for lacustrine Cladophora (Cladophorales) reveals remarkable diversity of eukaryotic epibionts and genes relevant to materials cycling

Periphyton dominated by the cellulose-rich filamentous green alga Cladophora forms conspicuous growths along rocky marine and freshwater shorelines worldwide, providing habitat for diverse epibionts. Bacterial epibionts have been inferred to display diverse functions of biogeochemical significance: N-fixation and other redox reactions, phosphorus accumulation, and organic degradation. Here, we report taxonomic diversity of eukaryotic and prokaryotic epibionts and diversity of genes associated with materials cycling in a Cladophora metagenome sampled from Lake Mendota, Dane Co., WI, USA, during the growing season of 2012. A total of 1,060 distinct 16S, 173 18S, and 351 28S rRNA operational taxonomic units, from which >220 genera or species of bacteria (~60), protists (~80), fungi (6), and microscopic metazoa (~80), were distinguished with the use of reference databases. We inferred the presence of several algal taxa generally associated with marine systems and detected Jaoa, a freshwater periphytic ulvophyte previously thought endemic to China. We identified six distinct nifH gene sequences marking nitrogen fixation, >25 bacterial and eukaryotic cellulases relevant to sedimentary C-cycling and technological applications, and genes encoding enzymes in aerobic and anaerobic pathways for vitamin B12 biosynthesis. These results emphasize the importance of Cladophora in providing habitat for microscopic metazoa, fungi, protists, and bacteria that are often inconspicuous, yet play important roles in ecosystem biogeochemistry

PTF11kx: A Type Ia Supernova with Hydrogen Emission Persisting After 3.5 Years

The optical transient PTF11kx exhibited both the characteristic spectral features of Type Ia supernovae (SNe Ia) and the signature of ejecta interacting with circumstellar material (CSM) containing hydrogen, indicating the presence of a nondegenerate companion. We present an optical spectrum at $1342$ days after peak from Keck Observatory, in which the broad component of H$\alpha$ emission persists with a similar profile as in early-time observations. We also present $Spitzer$ IRAC detections obtained $1237$ and $1818$ days after peak, and an upper limit from $HST$ ultraviolet imaging at $2133$ days. We interpret our late-time observations in context with published results - and reinterpret the early-time observations - in order to constrain the CSM's physical parameters and compare to theoretical predictions for recurrent nova systems. We find that the CSM's radial extent may be several times the distance between the star and the CSM's inner edge, and that the CSM column density may be two orders of magnitude lower than previous estimates. We show that the H$\alpha$ luminosity decline is similar to other SNe with CSM interaction, and demonstrate how our infrared photometry is evidence for newly formed, collisionally heated dust. We create a model for PTF11kx's late-time CSM interaction and find that X-ray reprocessing by photoionization and recombination cannot reproduce the observed H$\alpha$ luminosity, suggesting that the X-rays are thermalized and that H$\alpha$ radiates from collisional excitation. Finally, we discuss the implications of our results regarding the progenitor scenario and the geometric properties of the CSM for the PTF11kx system.Comment: 15 pages, 8 figures, 3 tables; submitted to Ap

Constraining the Progenitor Companion of the Nearby Type Ia SN 2011fe with a Nebular Spectrum at +981 Days

We present an optical nebular spectrum of the nearby Type Ia supernova 2011fe, obtained 981 days after explosion. SN 2011fe exhibits little evolution since the +593 day optical spectrum, but there are several curious aspects in this new extremely late-time regime. We suggest that the persistence of the $\sim5800$~\AA\ feature is due to Na I D, and that a new emission feature at $\sim7300$~\AA\ may be [Ca II]. Also, we discuss whether the new emission feature at $\sim6400$~\AA\ might be [Fe I] or the high-velocity hydrogen predicted by Mazzali et al. The nebular feature at 5200~\AA\ exhibits a linear velocity evolution of $\sim350$ $\rm km\ s^{-1}$ per 100 days from at least +220 to +980 days, but the line's shape also changes in this time, suggesting that line blending contributes to the evolution. At $\sim 1000$ days after explosion, flux from the SN has declined to a point where contribution from a luminous secondary could be detected. In this work we make the first observational tests for a post-impact remnant star and constrain its temperature and luminosity to $T \gtrsim 10^4$ $\rm K$ and $L \lesssim 10^4$ $\rm L_{\odot}$. Additionally, we do not see any evidence for narrow H$\alpha$ emission in our spectrum. We conclude that observations continue to strongly exclude many single-degenerate scenarios for SN 2011fe.Comment: 11 pages, 10 figures, published by MNRA

Constraints on the Progenitor System of the Type Ia Supernova 2014J from Pre-Explosion Hubble Space Telescope Imaging

We constrain the properties of the progenitor system of the highly reddened Type Ia supernova (SN) 2014J in Messier 82 (M82; d ~ 3.5 Mpc). We determine the SN location using Keck-II K-band adaptive optics images, and we find no evidence for flux from a progenitor system in pre-explosion near-ultraviolet through near-infrared Hubble Space Telescope (HST) images. Our upper limits exclude systems having a bright red giant companion, including symbiotic novae with luminosities comparable to that of RS Ophiuchi. While the flux constraints are also inconsistent with predictions for comparatively cool He-donor systems (T < ~35,000 K), we cannot preclude a system similar to V445 Puppis. The progenitor constraints are robust across a wide range of R_V and A_V values, but significantly greater values than those inferred from the SN light curve and spectrum would yield proportionally brighter luminosity limits. The comparatively faint flux expected from a binary progenitor system consisting of white dwarf stars would not have been detected in the pre-explosion HST imaging. Infrared HST exposures yield more stringent constraints on the luminosities of very cool (T < 3000 K) companion stars than was possible in the case of SN Ia 2011fe.Comment: Accepted by ApJ 14 May 2014 with only minor revision

Novel DNA methylation profiles associated with key gene regulation and transcription pathways in blood and placenta of growth-restricted neonates

BB/H012494/1/ Biotechnology and Biological Sciences Research Counci

Endurance of SN 2005ip after a decade: X-rays, radio, and H-alpha like SN 1988Z require long-lived pre-supernova mass loss

SN2005ip was a TypeIIn event notable for its sustained strong interaction with circumstellar material (CSM), coronal emission lines, and IR excess, interpreted as shock interaction with the very dense and clumpy wind of an extreme red supergiant. We present a series of late-time spectra of SN2005ip and a first radio detection of this SN, plus late-time X-rays, all of which indicate that its CSM interaction is still strong a decade post-explosion. We also present and discuss new spectra of geriatric SNe with continued CSM interaction: SN1988Z, SN1993J, and SN1998S. From 3-10 yr post-explosion, SN2005ip's H-alpha luminosity and other observed characteristics were nearly identical to those of the radio-luminous SN1988Z, and much more luminous than SNe1993J and 1998S. At 10 yr after explosion, SN2005ip showed a drop in H$\alpha$ luminosity, followed by a quick resurgence over several months. We interpret this variability as ejecta crashing into a dense shell located at around 0.05 pc from the star, which may be the same shell that caused the IR echo at earlier epochs. The extreme H-alpha luminosities in SN2005ip and SN1988Z are still dominated by the forward shock at 10 yr post-explosion, whereas SN1993J and SN1998S are dominated by the reverse shock at a similar age. Continuous strong CSM interaction in SNe~2005ip and 1988Z is indicative of enhanced mass loss for about 1e3 yr before core collapse, longer than Ne, O, or Si burning phases. Instead, the episodic mass loss must extend back through C burning and perhaps even part of He burning.Comment: 14 pages, 8 figs. accepted in MNRA

Molecular-orbital-free algorithm for excited states in time-dependent perturbation theory

A non-linear conjugate gradient optimization scheme is used to obtain excitation energies within the Random Phase Approximation (RPA). The solutions to the RPA eigenvalue equation are located through a variational characterization using a modified Thouless functional, which is based upon an asymmetric Rayleigh quotient, in an orthogonalized atomic orbital representation. In this way, the computational bottleneck of calculating molecular orbitals is avoided. The variational space is reduced to the physically-relevant transitions by projections. The feasibility of an RPA implementation scaling linearly with system size, N, is investigated by monitoring convergence behavior with respect to the quality of initial guess and sensitivity to noise under thresholding, both for well- and ill-conditioned problems. The molecular- orbital-free algorithm is found to be robust and computationally efficient providing a first step toward a large-scale, reduced complexity calculation of time-dependent optical properties and linear response. The algorithm is extensible to other forms of time-dependent perturbation theory including, but not limited to, time-dependent Density Functional theory.Comment: 9 pages, 7 figure

SN2012ab: A Peculiar Type IIn Supernova with Aspherical Circumstellar Material

We present photometry, spectra, and spectropolarimetry of supernova (SN) 2012ab, mostly obtained over the course of $\sim 300$ days after discovery. SN 2012ab was a Type IIn (SN IIn) event discovered near the nucleus of spiral galaxy 2MASXJ12224762+0536247. While its light curve resembles that of SN 1998S, its spectral evolution does not. We see indications of CSM interaction in the strong intermediate-width emission features, the high luminosity (peak at absolute magnitude $M=-19.5$), and the lack of broad absorption features in the spectrum. The H$\alpha$ emission undergoes a peculiar transition. At early times it shows a broad blue emission wing out to $-14{,}000$ km $\mathrm{s^{-1}}$ and a truncated red wing. Then at late times ($>$ 100$\,$days) it shows a truncated blue wing and a very broad red emission wing out to roughly $+20{,}000$ km $\mathrm{s^{-1}}$. This late-time broad red wing probably arises in the reverse shock. Spectra also show an asymmetric intermediate-width H$\alpha$ component with stronger emission on the red side at late times. The evolution of the asymmetric profiles requires a density structure in the distant CSM that is highly aspherical. Our spectropolarimetric data also suggest asphericity with a strong continuum polarization of $\sim 1-3$% and depolarization in the H$\alpha$ line, indicating asphericity in the CSM at a level comparable to that in other SNe IIn. We estimate a mass-loss rate of $\dot{M} = 0.050\, {\rm M}_{\odot}\,\mathrm{yr^{-1}}$ for $v_{\rm pre} = 100$$\,$km$\,$$\mathrm{s^{-1}}$ extending back at least 75$\,$yr prior to the SN. The strong departure from axisymmetry in the CSM of SN 2012ab may suggest that the progenitor was an eccentric binary system undergoing eruptive mass loss.Comment: 18 pages, 12 figure