Ligand Similarity Complements Sequence, Physical Interaction, and Co-Expression for Gene Function Prediction

The expansion of protein-ligand annotation databases has enabled large-scale networking of proteins by ligand similarity. These ligand-based protein networks, which implicitly predict the ability of neighboring proteins to bind related ligands, may complement biologically-oriented gene networks, which are used to predict functional or disease relevance. To quantify the degree to which such ligand-based protein associations might complement functional genomic associations, including sequence similarity, physical protein-protein interactions, co-expression, and disease gene annotations, we calculated a network based on the Similarity Ensemble Approach (SEA: sea.docking.org), where protein neighbors reflect the similarity of their ligands. We also measured the similarity with functional genomic networks over a common set of 1,131 genes, and found that the networks had only small overlaps, which were significant only due to the large scale of the data. Consistent with the view that the networks contain different information, combining them substantially improved Molecular Function prediction within GO (from AUROC~0.63-0.75 for the individual data modalities to AUROC~0.8 in the aggregate). We investigated the boost in guilt-by-association gene function prediction when the networks are combined and describe underlying properties that can be further exploited

The First Data Release of the KODIAQ Survey

We present and make publicly available the first data release (DR1) of the Keck Observatory Database of Ionized Absorption toward Quasars (KODIAQ) survey. The KODIAQ survey is aimed at studying galactic and circumgalactic gas in absorption at high-redshift, with a focus on highly-ionized gas traced by OVI, using the HIRES spectrograph on the Keck-I telescope. KODIAQ DR1 consists of a fully-reduced sample of 170 quasars at 0.29 < z_em < 5.29 observed with HIRES at high resolution (36,000 <= R <= 103,000) between 2004 and 2012. DR1 contains 247 spectra available in continuum normalized form, representing a sum total exposure time of ~1.6 megaseconds. These co-added spectra arise from a total of 567 individual exposures of quasars taken from the Keck Observatory Archive (KOA) in raw form and uniformly processed using a HIRES data reduction package made available through the XIDL distribution. DR1 is publicly available to the community, housed as a higher level science product at the KOA. We will provide future data releases that make further QSOs, including those with pre-2004 observations taken with the previous-generation HIRES detectors.Comment: 14 pages, 9 figures, Submitted to AJ. All data products available at the Keck Observatory Archive beginning May 15, 2015. URL: https://koa.ipac.caltech.edu/applications/KODIA

The Large, Oxygen-Rich Halos of Star-Forming Galaxies Are A Major Reservoir of Galactic Metals

The circumgalactic medium (CGM) is fed by galaxy outflows and accretion of intergalactic gas, but its mass, heavy element enrichment, and relation to galaxy properties are poorly constrained by observations. In a survey of the outskirts of 42 galaxies with the Cosmic Origins Spectrograph onboard the Hubble Space Telescope, we detected ubiquitous, large (150 kiloparsec) halos of ionized oxygen surrounding star-forming galaxies, but we find much less ionized oxygen around galaxies with little or no star formation. This ionized CGM contains a substantial mass of heavy elements and gas, perhaps far exceeding the reservoirs of gas in the galaxies themselves. It is a basic component of nearly all star-forming galaxies that is removed or transformed during the quenching of star formation and the transition to passive evolution.Comment: This paper is part of a set of three papers on circumgalactic gas observed with the Cosmic Origins Spectrograph on HST, to be published in Science, together with related papers by Tripp et al. and Lehner & Howk, in the November 18, 2011 edition. This version has not undergone final copyediting. Please see Science online for the final printed versio

Improvement of stabilizer based entanglement distillation protocols by encoding operators

This paper presents a method for enumerating all encoding operators in the Clifford group for a given stabilizer. Furthermore, we classify encoding operators into the equivalence classes such that EDPs (Entanglement Distillation Protocol) constructed from encoding operators in the same equivalence class have the same performance. By this classification, for a given parameter, the number of candidates for good EDPs is significantly reduced. As a result, we find the best EDP among EDPs constructed from [[4,2]] stabilizer codes. This EDP has a better performance than previously known EDPs over wide range of fidelity.Comment: 22 pages, 2 figures, In version 2, we enumerate all encoding operators in the Clifford group, and fix the wrong classification of encoding operators in version

Interaction of Cryptococcus neoformans Rim101 and Protein Kinase A Regulates Capsule

Cryptococcus neoformans is a prevalent human fungal pathogen that must survive within various tissues in order to establish a human infection. We have identified the C. neoformans Rim101 transcription factor, a highly conserved pH-response regulator in many fungal species. The rim101Δ mutant strain displays growth defects similar to other fungal species in the presence of alkaline pH, increased salt concentrations, and iron limitation. However, the rim101Δ strain is also characterized by a striking defect in capsule, an important virulence-associated phenotype. This capsular defect is likely due to alterations in polysaccharide attachment to the cell surface, not in polysaccharide biosynthesis. In contrast to many other C. neoformans capsule-defective strains, the rim101Δ mutant is hypervirulent in animal models of cryptococcosis. Whereas Rim101 activation in other fungal species occurs through the conserved Rim pathway, we demonstrate that C. neoformans Rim101 is also activated by the cAMP/PKA pathway. We report here that C. neoformans uses PKA and the Rim pathway to regulate the localization, activation, and processing of the Rim101 transcription factor. We also demonstrate specific host-relevant activating conditions for Rim101 cleavage, showing that C. neoformans has co-opted conserved signaling pathways to respond to the specific niche within the infected host. These results establish a novel mechanism for Rim101 activation and the integration of two conserved signaling cascades in response to host environmental conditions

The COS Absorption Survey of Baryon Harbors (CASBaH): Warm-hot Circumgalactic Gas Reservoirs Traced by Ne VIII Absorption

We survey the highly ionized circumgalactic media (CGM) of 29 blindly selected galaxies at 0.49 < z_(gal) < 1.44 based on high-S/N ultraviolet spectra of z > 1 QSOs and the galaxy database from the COS Absorption Survey of Baryon Harbors (CASBaH). We detect the Ne VIII doublet in nine of the galaxies, and for gas with N(Ne VIII) > 10^13.3 cm^-2 (> 10^13.5 cm^-2), we derive a Ne VIII covering fraction f_c = 75 +15/-25% (44 +22/-20%) within impact parameter (rho) < 200 kpc of M_* = 10^(9.5-11.5) Msol galaxies and f_c = 70 +16/-22% (f_c = 42 +20/-17%) within rho < 1.5 virial radii. We estimate the mass in Ne VIII-traced gas to be M_gas(Ne VIII) > 10^9.5 Msol (Z/Zsol)^-1, or 6-20% of the expected baryonic mass if the Ne VIII absorbers have solar metallicity. Ionizing Ne VII to Ne VIII requires 207 eV, and photons with this energy are scarce in the CGM. However, for the median halo mass and redshift of our sample, the virial temperature is close to the peak temperature for the Ne VIII ion, and the Ne VIII-bearing gas is plausibly collisionally ionized near this temperature. Moreover, we find that photoionized Ne VIII requires cool and low-density clouds that would be highly underpressured (by approximately two orders of magnitude) relative to the putative, ambient virialized medium, complicating scenarios where such clouds could survive. Thus, more complex (e.g., non-equilibrium) models may be required; this first statistical sample of Ne VIII absorber/galaxy systems will provide stringent constraints for future CGM studies.Comment: Published in ApJL, Volume 877, Issue 2, Article L2

The Giant Gemini GMOS survey of zem > 4.4 quasars – I. Measuring the mean free path across cosmic time

We have obtained spectra of 163 quasars at zem > 4.4 with the Gemini Multi Object Spectrometers, the largest publicly available sample of high-quality, low-resolution spectra at these redshifts. From this data set, we generated stacked quasar spectra in three redshift intervals at z ∼ 5 to model the average rest-frame Lyman continuum flux and to assess the mean free path λ912mfp of the intergalactic medium to H I-ionizing radiation. At mean redshifts zq = (4.56, 4.86, 5.16), we measure λ912mfp=(22.2±2.3,15.1±1.8,10.3±1.6)h−170 proper Mpc with uncertainties dominated by sample variance. Combining our results with measurements from lower redshifts, the data are well modelled by a power law λ912mfp=A[(1+z)/5]η with A=(37±2)h−170 Mpc and η = −5.4 ± 0.4 at 2.3 < z < 5.5. This rapid evolution requires a physical mechanism – beyond cosmological expansion – which reduces the effective Lyman limit opacity. We speculate that the majority of H I Lyman limit opacity manifests in gas outside galactic dark matter haloes, tracing large-scale structures (e.g. filaments) whose average density and neutral fraction decreases with cosmic time. Our measurements of the mean free path shortly after H I reionization serve as a valuable boundary condition for numerical models thereof. Our measured λ912mfp≈10 Mpc at z = 5.2 confirms that the intergalactic medium is highly ionized without evidence for a break that would indicate a recent end to H I reionization