Draft genome sequence of Kocuria sp. strain UCD-OTCP (phylum Actinobacteria)

© 2013 Coil et al. 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

Draft genome sequence of an actinobacterium, Brachybacterium muris strain UCD-AY4

© 2013 Lo et al. Here we present the draft genome of an actinobacterium, Brachybacterium muris UCD-AY4. The assembly contains 3,257,338 bp and has a GC content of 70%. This strain was isolated from a residential bath towel and has a 16S rRNA gene 99.7% identical to that of the original B. muris strain, C3H-21

Draft genome sequence of Curtobacterium flaccumfaciens strain UCD-AKU (phylum Actinobacteria)

© 2013 Flanagan et al. 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

Draft genome sequence of Microbacterium sp. strain UCD-TDU (phylum Actinobacteria)

© 2013 Bendiks et al. Here, we present the draft genome sequence of Microbacterium sp. strain UCD-TDU, a member of the phylum Actinobacteria. The assembly contains 3,746,321 bp (in 8 scaffolds). This strain was isolated from a residential toilet as part of an undergraduate student research project to sequence reference genomes of microbes from the built environment

Draft genome sequence of Dietzia sp. strain UCD-THP (phylum Actinobacteria)

© 2013 Diep et al. 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

Swabs to genomes: A comprehensive workflow

© 2015 Dunitz et al. The sequencing, assembly, and basic analysis of microbial genomes, once a painstaking and expensive undertaking, has become much easier for research labs with access to standard molecular biology and computational tools. However, there are a confusing variety of options available for DNA library preparation and sequencing, and inexperience with bioinformatics can pose a significant barrier to entry for many who may be interested in microbial genomics. The objective of the present study was to design, test, troubleshoot, and publish a simple, comprehensive workflow from the collection of an environmental sample (a swab) to a published microbial genome; empowering even a lab or classroom with limited resources and bioinformatics experience to performit

X-ray selected AGN in groups at redshifts z~1

We explore the role of the group environment in the evolution of AGN at the redshift interval 0.7<z<1.4, by combining deep Chandra observations with extensive optical spectroscopy from the All-wavelength Extended Groth strip International Survey (AEGIS). The sample consists of 3902 optical sources and 71 X-ray AGN. Compared to the overall optically selected galaxy population, X-ray AGN are more frequently found in groups at the 99% confidence level. This is partly because AGN are hosted by red luminous galaxies, which are known to reside, on average, in dense environments. Relative to these sources, the excess of X-ray AGN in groups is significant at the 91% level only. Restricting the sample to 0.7<z<0.9 and M_B<-20mag in order to control systematics we find that X-ray AGN represent (4.7\pm1.6) and (4.5\pm1.0)% of the optical galaxy population in groups and in the field respectively. These numbers are consistent with the AGN fraction in low redshift clusters, groups and the field. The results above, although affected by small number statistics, suggest that X-ray AGN are spread over a range of environments, from groups to the field, once the properties of their hosts (e.g. colour, luminosity) are accounted for. There is also tentative evidence, significant at the 98% level, that the field produces more X-ray luminous AGN compared to groups, extending similar results at low redshift to z~1. This trend may be because of either cold gas availability or the nature of the interactions occurring in the denser group environment (i.e. prolonged tidal encounters).Comment: To appear in MNRA

The clustering of X-ray selected AGN at z=0.1

The clustering properties of moderate luminosity ($L_X = \rm 10^{41} - 10^{44} \, erg \,s^{-1}$) X-ray selected AGN at $z\approx0.1$ are explored. X-ray sources in the redshift interval $0.03<z<0.2$ are selected from a serendipitous XMM survey of the SDSS footprint (XMM/SDSS) and are cross-correlated with the SDSS Main galaxy sample. The inferred X-ray AGN auto-correlation function is described by a power law with amplitude $r_0\approx5\,$h$^{-1}$Mpc and slope $\gamma\approx2.0$. The corresponding mass of the dark matter haloes that host X-ray AGN at $z\approx0.1$ is \approx 10^{13} \,h ^{-1} \, M_{\sun}. Comparison with studies at higher redshift shows that this mass scale is characteristic of moderate luminosity X-ray AGN out to $z\approx 1$. Splitting the AGN sample by rest-frame color shows that X-ray sources in red hosts are more clustered than those associated with blue galaxies, in agreement with results at $z\approx1$. We also find that the host galaxies of X-ray AGN have lower stellar masses compared to the typical central galaxy of a \approx 10^{13} \,h ^{-1} \, M_{\sun} dark matter halo. AGN hosts either have experienced less stellar mass growth compared to the average central galaxy of a \approx 10^{13} \,h ^{-1} \, M_{\sun} halo or a fraction of them are associated with satellite galaxies.Comment: MNRAS accepted 14 pages, 8 figures, 5 table

Draft genome sequences of 26 Porphyromonas strains isolated from the canine oral microbiome

� 2015 Coil et al. We present the draft genome sequences for 26 strains of Porphyromonas (P. canoris, P. gulae, P. cangingavalis, P. macacae, and 7 unidentified) and an unidentified member of the Porphyromonadaceae family. All of these strains were isolated from the canine oral cavity, from dogs with and without early periodontal disease

Large Scale Structure of the Universe

Galaxies are not uniformly distributed in space. On large scales the Universe displays coherent structure, with galaxies residing in groups and clusters on scales of ~1-3 Mpc/h, which lie at the intersections of long filaments of galaxies that are >10 Mpc/h in length. Vast regions of relatively empty space, known as voids, contain very few galaxies and span the volume in between these structures. This observed large scale structure depends both on cosmological parameters and on the formation and evolution of galaxies. Using the two-point correlation function, one can trace the dependence of large scale structure on galaxy properties such as luminosity, color, stellar mass, and track its evolution with redshift. Comparison of the observed galaxy clustering signatures with dark matter simulations allows one to model and understand the clustering of galaxies and their formation and evolution within their parent dark matter halos. Clustering measurements can determine the parent dark matter halo mass of a given galaxy population, connect observed galaxy populations at different epochs, and constrain cosmological parameters and galaxy evolution models. This chapter describes the methods used to measure the two-point correlation function in both redshift and real space, presents the current results of how the clustering amplitude depends on various galaxy properties, and discusses quantitative measurements of the structures of voids and filaments. The interpretation of these results with current theoretical models is also presented.Comment: Invited contribution to be published in Vol. 8 of book "Planets, Stars, and Stellar Systems", Springer, series editor T. D. Oswalt, volume editor W. C. Keel, v2 includes additional references, updated to match published versio