PhyloFacts: an online structural phylogenomic encyclopedia for protein functional and structural classification

The Berkeley Phylogenomics Group presents PhyloFacts, a structural phylogenomic encyclopedia containing almost 10,000 'books' for protein families and domains, with pre-calculated structural, functional and evolutionary analyses. PhyloFacts enables biologists to avoid the systematic errors associated with function prediction by homology through the integration of a variety of experimental data and bioinformatics methods in an evolutionary framework. Users can submit sequences for classification to families and functional subfamilies. PhyloFacts is available as a worldwide web resource from

Berkeley Phylogenomics Group web servers: resources for structural phylogenomic analysis

Phylogenomic analysis addresses the limitations of function prediction based on annotation transfer, and has been shown to enable the highest accuracy in prediction of protein molecular function. The Berkeley Phylogenomics Group provides a series of web servers for phylogenomic analysis: classification of sequences to pre-computed families and subfamilies using the PhyloFacts Phylogenomic Encyclopedia, FlowerPower clustering of proteins sharing the same domain architecture, MUSCLE multiple sequence alignment, SATCHMO simultaneous alignment and tree construction and SCI-PHY subfamily identification. The PhyloBuilder web server provides an integrated phylogenomic pipeline starting with a user-supplied protein sequence, proceeding to homolog identification, multiple alignment, phylogenetic tree construction, subfamily identification and structure prediction. The Berkeley Phylogenomics Group resources are available at http://phylogenomics.berkeley.edu

The Evolution of Late-Time Optical Emission from Sn 1979c

Optical spectra of the bright Type II-L supernova SN 1979C obtained in April 2008 with the 6.5 m Multiple Mirror Telescope are compared with archival late-time spectra to follow the evolution of its optical emission over the age range of 11-29 years. We estimate an Hα flux decrease of around 35% from 1993 to 2008 but noticeable increases in the strength of blueshifted emission of forbidden oxygen lines. While the maximum expansion of the broad ~6700 km s–1 Hα emission appears largely unchanged from 1993, we find a significant narrowing of the double-peaked emission profiles in the [O I] λλ6300, 6364 and [O II] λλ7319, 7330 lines. A comparison of late-time optical spectra of a few other Type II SNe which, like SN 1979C, exhibit bright late-time X-ray, optical, and radio emissions, suggests that blueshifted double-peaked oxygen emission profiles may be a common phenomenon. Finally, detection of a faint, broad emission bump centered around 5800 Å suggests the presence of WC-type Wolf-Rayet stars in the SN\u27s host star cluster

Late-Time Optical Emission from Core-Collapse Supernovae

Ground-based optical spectra and Hubble Space Telescope images of 10 core-collapse supernovae (CCSNe) obtained several years to decades after outburst are analyzed with the aim of understanding the general properties of their late-time emissions. New observations of SN 1957D, 1970G, 1980K, and 1993J are included as part of the study. Blueshifted line emissions in oxygen and/or hydrogen with conspicuous line substructure are a common and long-lasting phenomenon in the late-time spectra. Followed through multiple epochs, changes in the relative strengths and velocity widths of the emission lines are consistent with expectations for emissions produced by interaction between SN ejecta and the progenitor star\u27s circumstellar material. The most distinct trend is an increase in the strength of [O III]/([O I]+[O II]) with age, and a decline in Hα/([O I]+[O II]) which is broadly consistent with the view that the reverse shock has passed through the H envelope of the ejecta in many of these objects. We also present a spatially integrated spectrum of the young Galactic supernova remnant Cassiopeia A (Cas A). Similarities observed between the emission line profiles of the ≈330 yr old Cas A remnant and decades old CCSNe suggest that observed emission line asymmetry in evolved CCSN spectra may be associated with dust in the ejecta, and that minor peak substructure typically interpreted as clumps or blobs of ejecta may instead be linked with large-scale rings of SN debris

High Density Circumstellar Interaction in the Luminous Type IIn SN 2010jl: The first 1100 days

HST and ground based observations of the Type IIn SN 2010jl are analyzed, including photometry, spectroscopy in the ultraviolet, optical and NIR bands, 26-1128 days after first detection. At maximum the bolometric luminosity was $\sim 3\times10^{43}$ erg/s and even at 850 days exceeds $10^{42}$ erg/s. A NIR excess, dominating after 400 days, probably originates in dust in the circumstellar medium (CSM). The total radiated energy is $> 6.5\times10^{50}$ ergs, excluding the dust component. The spectral lines can be separated into one broad component due to electron scattering, and one narrow with expansion velocity $\sim 100$ km/s from the CSM. The broad component is initially symmetric around zero velocity but becomes blueshifted after $\sim 50$ days, while remaining symmetric about a shifted centroid velocity. Dust absorption in the ejecta is unlikely to explain the line shifts, and we attribute the shift instead to acceleration by the SN radiation. From the optical lines and the X-ray and dust properties, there is strong evidence for large scale asymmetries in the CSM. The ultraviolet lines indicate CNO processing in the progenitor, while the optical shows a number of narrow coronal lines excited by the X-rays. The bolometric light curve is consistent with a radiative shock in an $r^{-2}$ CSM with a mass loss rate of $\sim 0.1$ M_sun/yr. The total mass lost is $> 3$ M_sun. These properties are consistent with the SN expanding into a CSM characteristic of an LBV progenitor with a bipolar geometry. The apparent absence of nuclear processing is attributed to a CSM still opaque to electron scattering.Comment: ApJ in press. Updated and changed after referees comment

The Evolution of Late-Time Optical Emission From SN 1979C

Optical spectra of the bright Type II-L supernova SN 1979C obtained in April 2008 with the 6.5 m MMT telescope are compared with archival late-time spectra to follow the evolution of its optical emission over the age range of 11 to 29 years. We estimate an Halpha flux decrease of around 35% from 1993 to 2008 but noticeable increases in the strength of blueshifted emission of forbidden oxygen lines. While the maximum expansion of the broad ~6700 km/s Halpha emission appears largely unchanged from 1993, we find a significant narrowing of the double-peaked emission profiles in the [O I] 6300, 6364 and [O II] 7319, 7330 lines. A comparison of late-time optical spectra of a few other Type II supernovae which, like SN 1979C, exhibit bright late-time X-ray, optical, and radio emissions, suggests that blueshifted double-peaked oxygen emission profiles may be a common phenomenon. Finally, detection of a faint, broad emission bump centered around 5800 Angstroms suggests the presence of WC type Wolf-Rayet stars in the supernova's host star cluster.Comment: 6 pages, 4 figures, 1 table. Matches version accepted by Ap

CfAIR2: Near Infrared Light Curves of 94 Type Ia Supernovae

CfAIR2 is a large homogeneously reduced set of near-infrared (NIR) light curves for Type Ia supernovae (SN Ia) obtained with the 1.3m Peters Automated InfraRed Imaging TELescope (PAIRITEL). This data set includes 4607 measurements of 94 SN Ia and 4 additional SN Iax observed from 2005-2011 at the Fred Lawrence Whipple Observatory on Mount Hopkins, Arizona. CfAIR2 includes JHKs photometric measurements for 88 normal and 6 spectroscopically peculiar SN Ia in the nearby universe, with a median redshift of z~0.021 for the normal SN Ia. CfAIR2 data span the range from -13 days to +127 days from B-band maximum. More than half of the light curves begin before the time of maximum and the coverage typically contains ~13-18 epochs of observation, depending on the filter. We present extensive tests that verify the fidelity of the CfAIR2 data pipeline, including comparison to the excellent data of the Carnegie Supernova Project. CfAIR2 contributes to a firm local anchor for supernova cosmology studies in the NIR. Because SN Ia are more nearly standard candles in the NIR and are less vulnerable to the vexing problems of extinction by dust, CfAIR2 will help the supernova cosmology community develop more precise and accurate extragalactic distance probes to improve our knowledge of cosmological parameters, including dark energy and its potential time variation.Comment: 31 pages, 15 figures, 10 tables. Accepted to ApJS. v2 modified to more closely match journal versio

Type Ia Supernova Distances at z > 1.5 from the Hubble Space Telescope Multi-Cycle Treasury Programs: The Early Expansion Rate

We present an analysis of 15 Type Ia supernovae (SNe Ia) at redshift z > 1 (9 at 1.5 < z < 2.3) recently discovered in the CANDELS and CLASH Multi-Cycle Treasury programs using WFC3 on the Hubble Space Telescope. We combine these SNe Ia with a new compilation of 1050 SNe Ia, jointly calibrated and corrected for simulated survey biases to produce accurate distance measurements. We present unbiased constraints on the expansion rate at six redshifts in the range 0.07 < z < 1.5 based only on this combined SN Ia sample. The added leverage of our new sample at z > 1.5 leads to a factor of ~3 improvement in the determination of the expansion rate at z = 1.5, reducing its uncertainty to ~20%, a measurement of H(z=1.5)/H0=2.67 (+0.83,-0.52). We then demonstrate that these six measurements alone provide a nearly identical characterization of dark energy as the full SN sample, making them an efficient compression of the SN Ia data. The new sample of SNe Ia at z > 1 usefully distinguishes between alternative cosmological models and unmodeled evolution of the SN Ia distance indicators, placing empirical limits on the latter. Finally, employing a realistic simulation of a potential WFIRST SN survey observing strategy, we forecast optimistic future constraints on the expansion rate from SNe Ia.Comment: 14 pages, 5 figures, 7 tables; submitted to Ap