Draft Genome Sequence of Rhizobium rhizogenes Strain ATCC 15834.

Here, we present the draft genome of Rhizobium rhizogenes strain ATCC 15834. The genome contains 7,070,307 bp in 43 scaffolds. R. rhizogenes, also known as Agrobacterium rhizogenes, is a plant pathogen that causes hairy root disease. This hairy root induction has been used in biotechnology for the generation of transgenic root cultures

Tracing the Filamentary Structure of the Galaxy Distribution at z~0.8

We study filamentary structure in the galaxy distribution at z ~ 0.8 using data from the Deep Extragalactic Evolutionary Probe 2 (DEEP2) Redshift Survey and its evolution to z ~ 0.1 using data from the Sloan Digital Sky Survey (SDSS). We trace individual filaments for both surveys using the Smoothed Hessian Major Axis Filament Finder, an algorithm which employs the Hessian matrix of the galaxy density field to trace the filamentary structures in the distribution of galaxies. We extract 33 subsamples from the SDSS data with a geometry similar to that of DEEP2. We find that the filament length distribution has not significantly changed since z ~ 0.8, as predicted in a previous study using a \LamdaCDM cosmological N-body simulation. However, the filament width distribution, which is sensitive to the non-linear growth of structure, broadens and shifts to smaller widths for smoothing length scales of 5-10 Mpc/h from z ~ 0.8 to z ~ 0.1, in accord with N-body simulations.Comment: 10 pages, 8 figures, accepted for the publication in MNRA

Draft Genome Sequence of Kocuria sp. Strain UCD-OTCP (Phylum Actinobacteria).

Here, we present the draft genome of Kocuria sp. strain UCD-OTCP, a member of the phylum Actinobacteria, isolated from a restaurant chair cushion. The assembly contains 3,791,485 bp (G+C content of 73%) and is contained in 68 scaffolds

Phosphatidylserine treatment relieves the block to retrovirus infection of cells expressing glycosylated virus receptors

BACKGROUND: A major determinant of retrovirus host range is the presence or absence of appropriate cell-surface receptors required for virus entry. Often orthologs of functional receptors are present in a wide range of species, but amino acid differences can render these receptors non-functional. In some cases amino acid differences result in additional N-linked glycosylation that blocks virus infection. The latter block to retrovirus infection can be overcome by treatment of cells with compounds such as tunicamycin, which prevent the addition of N-linked oligosaccharides. RESULTS: We have discovered that treatment of cells with liposomes composed of phosphatidylserine (PS) can also overcome the block to infection mediated by N-linked glycosylation. Importantly, this effect occurs without apparent change in the glycosylation state of the receptors for these viruses. This effect occurs with delayed kinetics compared to previous results showing enhancement of virus infection by PS treatment of cells expressing functional virus receptors. CONCLUSION: We have demonstrated that PS treatment can relieve the block to retrovirus infection of cells expressing retroviral receptors that have been rendered non-functional by glycosylation. These findings have important implications for the current model describing inhibition of virus entry by receptor glycosylation

Draft Genome Sequence of Dietzia sp. Strain UCD-THP (Phylum Actinobacteria).

Here, we present the draft genome sequence of an actinobacterium, Dietzia sp. strain UCD-THP, isolated from a residential toilet handle. The assembly contains 3,915,613 bp. The genome sequences of only two other Dietzia species have been published, those of Dietzia alimentaria and Dietzia cinnamea

Draft Genome Sequence of Curtobacterium flaccumfaciens Strain UCD-AKU (Phylum Actinobacteria).

Here we present the draft genome of an actinobacterium, Curtobacterium flaccumfaciens strain UCD-AKU, isolated from a residential carpet. The genome assembly contains 3,692,614 bp in 130 contigs. This is the first member of the Curtobacterium genus to be sequenced

The DEEP2 Galaxy Redshift Survey: The Voronoi-Delaunay Method Catalog of Galaxy Groups

We present a public catalog of galaxy groups constructed from the spectroscopic sample of galaxies in the fourth data release from the Deep Extragalactic Evolutionary Probe 2 (DEEP2) Galaxy Redshift Survey, including the Extended Groth Strip (EGS). The catalog contains 1165 groups with two or more members in the EGS over the redshift range 0 0.6 in the rest of DEEP2. Twenty-five percent of EGS galaxies and fourteen percent of high-z DEEP2 galaxies are assigned to galaxy groups. The groups were detected using the Voronoi-Delaunay method (VDM) after it has been optimized on mock DEEP2 catalogs following similar methods to those employed in Gerke et al. In the optimization effort, we have taken particular care to ensure that the mock catalogs resemble the data as closely as possible, and we have fine-tuned our methods separately on mocks constructed for the EGS and the rest of DEEP2. We have also probed the effect of the assumed cosmology on our inferred group-finding efficiency by performing our optimization on three different mock catalogs with different background cosmologies, finding large differences in the group-finding success we can achieve for these different mocks. Using the mock catalog whose background cosmology is most consistent with current data, we estimate that the DEEP2 group catalog is 72% complete and 61% pure (74% and 67% for the EGS) and that the group finder correctly classifies 70% of galaxies that truly belong to groups, with an additional 46% of interloper galaxies contaminating the catalog (66% and 43% for the EGS). We also confirm that the VDM catalog reconstructs the abundance of galaxy groups with velocity dispersions above ~300 km s^(–1) to an accuracy better than the sample variance, and this successful reconstruction is not strongly dependent on cosmology. This makes the DEEP2 group catalog a promising probe of the growth of cosmic structure that can potentially be used for cosmological tests

Fine-Structure FeII* Emission and Resonant MgII Emission in z = 1 Star-Forming Galaxies

We present a study of the prevalence, strength, and kinematics of ultraviolet FeII and MgII emission lines in 212 star-forming galaxies at z = 1 selected from the DEEP2 survey. We find FeII* emission in composite spectra assembled on the basis of different galaxy properties, indicating that FeII* emission is prevalent at z = 1. In these composites, FeII* emission is observed at roughly the systemic velocity. At z = 1, we find that the strength of FeII* emission is most strongly modulated by dust attenuation, and is additionally correlated with redshift, star-formation rate, and [OII] equivalent width, such that systems at higher redshifts with lower dust levels, lower star-formation rates, and larger [OII] equivalent widths show stronger FeII* emission. We detect MgII emission in at least 15% of the individual spectra and we find that objects showing stronger MgII emission have higher specific star-formation rates, smaller [OII] linewidths, larger [OII] equivalent widths, lower dust attenuations, and lower stellar masses than the sample as a whole. MgII emission strength exhibits the strongest correlation with specific star-formation rate, although we find evidence that dust attenuation and stellar mass also play roles in the regulation of MgII emission. Future integral field unit observations of the spatial extent of FeII* and MgII emission in galaxies with high specific star-formation rates, low dust attenuations, and low stellar masses will be important for probing the morphology of circumgalactic gas.Comment: 29 pages, 22 figures, 2 tables; accepted to Ap

X-rays across the galaxy population - II. The distribution of AGN accretion rates as a function of stellar mass and redshift

We use deep Chandra X-ray imaging to measure the distribution of specific black hole accretion rates ($L_X$ relative to the stellar mass of the galaxy) and thus trace AGN activity within star-forming and quiescent galaxies, as a function of stellar mass (from $10^{8.5}-10^{11.5} M_\odot$) and redshift (to $z \sim 4$). We adopt near-infrared selected samples of galaxies from the CANDELS and UltraVISTA surveys, extract X-ray data for every galaxy, and use a flexible Bayesian method to combine these data and to measure the probability distribution function of specific black hole accretion rates, $\lambda_{sBHAR}$. We identify a broad distribution of $\lambda_{sBHAR}$ in both star-forming and quiescent galaxies---likely reflecting the stochastic nature of AGN fuelling---with a roughly power-law shape that rises toward lower $\lambda_{sBHAR}$, a steep cutoff at $\lambda_{sBHAR} \gtrsim 0.1-1$ (in Eddington equivalent units), and a turnover or flattening at $\lambda_{sBHAR} \lesssim 10^{-3}-10^{-2}$. We find that the probability of a star-forming galaxy hosting a moderate $\lambda_{sBHAR}$ AGN depends on stellar mass and evolves with redshift, shifting toward higher $\lambda_{sBHAR}$ at higher redshifts. This evolution is truncated at a point corresponding to the Eddington limit, indicating black holes may self-regulate their growth at high redshifts when copious gas is available. The probability of a quiescent galaxy hosting an AGN is generally lower than that of a star-forming galaxy, shows signs of suppression at the highest stellar masses, and evolves strongly with redshift. The AGN duty cycle in high-redshift ($z\gtrsim2$) quiescent galaxies thus reaches $\sim$20 per cent, comparable to the duty cycle in star-forming galaxies of equivalent stellar mass and redshift

2019 Novel Coronavirus (COVID-19) Pandemic: Built Environment Considerations To Reduce Transmission.

With the rapid spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) that results in coronavirus disease 2019 (COVID-19), corporate entities, federal, state, county, and city governments, universities, school districts, places of worship, prisons, health care facilities, assisted living organizations, daycares, homeowners, and other building owners and occupants have an opportunity to reduce the potential for transmission through built environment (BE)-mediated pathways. Over the last decade, substantial research into the presence, abundance, diversity, function, and transmission of microbes in the BE has taken place and revealed common pathogen exchange pathways and mechanisms. In this paper, we synthesize this microbiology of the BE research and the known information about SARS-CoV-2 to provide actionable and achievable guidance to BE decision makers, building operators, and all indoor occupants attempting to minimize infectious disease transmission through environmentally mediated pathways. We believe this information is useful to corporate and public administrators and individuals responsible for building operations and environmental services in their decision-making process about the degree and duration of social-distancing measures during viral epidemics and pandemics