Unusual Metabolism and Hypervariation in the Genome of a Gracilibacterium (BD1-5) from an Oil-Degrading Community.

The candidate phyla radiation (CPR) comprises a large monophyletic group of bacterial lineages known almost exclusively based on genomes obtained using cultivation-independent methods. Within the CPR, Gracilibacteria (BD1-5) are particularly poorly understood due to undersampling and the inherent fragmented nature of available genomes. Here, we report the first closed, curated genome of a gracilibacterium from an enrichment experiment inoculated from the Gulf of Mexico and designed to investigate hydrocarbon degradation. The gracilibacterium rose in abundance after the community switched to dominance by Colwellia Notably, we predict that this gracilibacterium completely lacks glycolysis, the pentose phosphate and Entner-Doudoroff pathways. It appears to acquire pyruvate, acetyl coenzyme A (acetyl-CoA), and oxaloacetate via degradation of externally derived citrate, malate, and amino acids and may use compound interconversion and oxidoreductases to generate and recycle reductive power. The initial genome assembly was fragmented in an unusual gene that is hypervariable within a repeat region. Such extreme local variation is rare but characteristic of genes that confer traits under pressure to diversify within a population. Notably, the four major repeated 9-mer nucleotide sequences all generate a proline-threonine-aspartic acid (PTD) repeat. The genome of an abundant Colwellia psychrerythraea population has a large extracellular protein that also contains the repeated PTD motif. Although we do not know the host for the BD1-5 cell, the high relative abundance of the C. psychrerythraea population and the shared surface protein repeat may indicate an association between these bacteria.IMPORTANCE CPR bacteria are generally predicted to be symbionts due to their extensive biosynthetic deficits. Although monophyletic, they are not monolithic in terms of their lifestyles. The organism described here appears to have evolved an unusual metabolic platform not reliant on glucose or pentose sugars. Its biology appears to be centered around bacterial host-derived compounds and/or cell detritus. Amino acids likely provide building blocks for nucleic acids, peptidoglycan, and protein synthesis. We resolved an unusual repeat region that would be invisible without genome curation. The nucleotide sequence is apparently under strong diversifying selection, but the amino acid sequence is under stabilizing selection. The amino acid repeat also occurs in a surface protein of a coexisting bacterium, suggesting colocation and possibly interdependence

Identification of genes differentially expressed as result of adenovirus type 5- and adenovirus type 12-transformation

Background: Cells transformed by human adenoviruses (Ad) exhibit differential capacities to induce tumours in immunocompetent rodents; for example, Ad12-transformed rodent cells are oncogenic whereas Ad5-transformed cells are not. The E1A gene determines oncogenic phenotype, is a transcriptional regulator and dysregulates host cell gene expression, a key factor in both cellular transformation and oncogenesis. To reveal differences in gene expression between cells transformed with oncogenic and non-oncogenic adenoviruses we have performed comparative analysis of transcript profiles with the aim of identifying candidate genes involved in the process of neoplastic transformation. Results: Analysis of microarray data revealed that a total of 232 genes were differentially expressed in Ad12 E1- or Ad5 E1-transformed BRK cells compared to untransformed baby rat kidney (BRK) cells. Gene information was available for 193 transcripts and using gene ontology (GO) classifications and literature searches it was possible to assign known or suggested functions to 166 of these identified genes. A subset of differentially-expressed genes from the microarray was further examined by real-time PCR and Western blotting using BRK cells immortalised by Ad12 E1A or Ad5 E1A in addition to Ad12 E1- or Ad5 E1-transformed BRK cells. Up-regulation of RelA and significant dysregulation of collagen type I mRNA transcripts and proteins were found in Ad-transformed cells. Conclusion: These results suggest that a complex web of cellular pathways become altered in Ad-transformed cells and that Ad E1A is sufficient for the observed dysregulation. Further work will focus on investigating which splice variant of Ad E1A is responsible for the observed dysregulation at the pathway level, and the mechanisms of E1A-mediated transcriptional regulation

Breeding CWG-R crested wheatgrass for reduced-maintenance turf

Using reduced-maintenance turfgrass as an alternative to current high-maintenance turfgrass species would conserve resources, labor, and potentially reduce pollutants in the environment. CWG-R is an experimental population of crested wheatgrass [Agropyron cristatum (L.) Gaertn.] from Iran that has shown potential as a low-maintenance turf. The objective of this research was to estimate the genetic variation for turf traits within the CWG-R population when evaluated under a reduced-maintenance regimen. Ninety CWG-R clonal lines were established in 1998 near Logan, UT, as spaced-plant plots in a RCB design with four replicates. Maintenance of 50% ET0 replacement, 97.74 kg of nitrogen ha1yr1, and mowing at 7.62 cm was approximately 40% lower than typical for high-input Kentucky bluegrass (Poa pratensis L.) turf. Critical turf traits, including spring regrowth, season-long (March–October) and mid-summer (June–July) turf quality, color, and rhizomatous spread were evaluated in 1999 and 2000. Significant genetic variation among clonal lines was evident with broad-sense heritabilities of 0.65, 0.76, 0.45, and 0.76 for spring regrowth, season-long turf quality, color, and rhizomatous spread, respectively. Several clonal lines remained green throughout the summer months and maintained acceptable turf quality and color ratings during the critical mid-summer period. The high broad-sense heritability estimates within this population indicate potential for successful improvement of critical turf traits by phenotypic selection. These results indicate that that CWG-R could be an important low-maintenance turf-type crested wheatgrass germplasm

A Deep XMM-Newton Survey of M33: Point Source Catalog, Source Detection and Characterization of Overlapping Fields

We have obtained a deep 8-field XMM-Newton mosaic of M33 covering the galaxy out to the D$_{25}$ isophote and beyond to a limiting 0.2--4.5 keV unabsorbed flux of 5$\times$10$^{-16}$ erg cm$^{-2}$ s$^{-1}$ (L${>}$4$\times$10$^{34}$ erg s$^{-1}$ at the distance of M33). These data allow complete coverage of the galaxy with high sensitivity to soft sources such as diffuse hot gas and supernova remnants. Here we describe the methods we used to identify and characterize 1296 point sources in the 8 fields. We compare our resulting source catalog to the literature, note variable sources, construct hardness ratios, classify soft sources, analyze the source density profile, and measure the X-ray luminosity function. As a result of the large effective area of XMM-Newton below 1 keV, the survey contains many new soft X-ray sources. The radial source density profile and X-ray luminosity function for the sources suggests that only $\sim$15% of the 391 bright sources with L${>}$3.6$\times$10$^{35}$ erg s$^{-1}$ are likely to be associated with M33, and more than a third of these are known supernova remnants. The log(N)--log(S) distribution, when corrected for background contamination, is a relatively flat power-law with a differential index of 1.5, which suggests many of the other M33 sources may be high-mass X-ray binaries. Finally, we note the discovery of an interesting new transient X-ray source, which we are unable to classify.Comment: 26 pages, 6 tables, 13 figures, accepted for publication in ApJ

Cross-sectional study examining the epidemiology of chronic pain in Nepal

Abstract. Introduction:. The World Health Organization recognizes chronic pain as a global public health concern; however, there is a bias towards research conducted in relatively affluent nations. There is a dearth of large-scale epidemiological studies in Nepal using rigorously validated, cross-culturally adapted instruments. Objectives:. The aim of this study was to examine the prevalence of both chronic pain and chronic pain of predominantly neuropathic origin and their associations with a range of sociodemographic and psychosocial characteristics. Methods:. We conducted a cross-sectional study of adults (≥18 years) in all households in Ranipani, Baluwa Village Development Committee, Nepal. All adults (n = 887) were approached, and those consenting, who met the inclusion criteria (n = 520, 58.6%), participated. Questionnaires validated in Nepali were used to examine several constructs: demographics; chronic pain; neuropathic pain; pain catastrophizing; resilience, pain intensity; pain interference; sleep disturbance; and depression. Results:. The point prevalence of chronic pain was 53.3% (n = 277). The point prevalence of chronic pain of predominantly neuropathic origin was 12.7% (n = 66). Chronic pain was associated with female gender, older age, and manual labour occupations. Using standardized scoring techniques, compared with available population estimates from other countries, those with chronic pain were associated with lower pain intensity and resilience scores and higher pain catastrophizing, pain interference, and depression scores. Conclusion:. These findings are broadly comparable to epidemiological studies from other countries, and these indicate areas for targeting interventions (eg, occupational and mental health). For comparison, more data are needed, from larger population samples in this region

Chandra ACIS Survey of M33 (ChASeM33): X-ray Imaging Spectroscopy of M33SNR21, the Brightest X-ray Supernova Remnant in M33

We present and interpret new X-ray data for M33SNR21, the brightest X-ray supernova remnant (SNR) in M33. The SNR is in seen projection against (and appears to be interacting with) the bright HII region NGC592. Data for this source were obtained as part of the Chandra ACIS Survey of M33 (ChASeM33) Very Large Project. The nearly on-axis Chandra data resolve the SNR into a ~5" diameter (20 pc at our assumed M33 distance of 817+/-58 kpc) slightly elliptical shell. The shell is brighter in the east, which suggests that it is encountering higher density material in that direction. The optical emission is coextensive with the X-ray shell in the north, but extends well beyond the X-ray rim in the southwest. Modeling the X-ray spectrum with an absorbed sedov model yields a shock temperature of 0.46(+0.01,-0.02) keV, an ionization timescale of n_e t = $2.1 (+0.2,-0.3) \times 10^{12}$ cm$^{-3}$ s, and half-solar abundances (0.45 (+0.12, -0.09)). Assuming Sedov dynamics gives an average preshock H density of 1.7 +/- 0.3 cm$^{-3}$. The dynamical age estimate is 6500 +/- 600 yr, while the best fit $n_e t$ value and derived $n_e$ gives 8200 +/- 1700 yr; the weighted mean of the age estimates is 7600 +/- 600 yr. We estimate an X-ray luminosity (0.25-4.5 keV) of (1.2 +/- 0.2) times $10^{37}$ ergs s$^{-1}$ (absorbed), and (1.7 +/- 0.3) times $10^{37}$ ergs s$^{-1}$ (unabsorbed), in good agreement with the recent XMM-Newton determination. No significant excess hard emission was detected; the luminosity $\le 1.2\times 10^{35}$ ergs s$^{-1}$ (2-8 keV) for any hard point source.Comment: 27 pages, 6 figures (3 color). ApJ (in press

A survey of apomixis and ploidy levels among Poa L. (Poaceae) using flow cytometry

Poa is a complex genus taxonomically and genetically. As a result, relatively little information exists for this economically important genus with regards to reproductive mode and variability in chromosome number. We examined apomixis frequency and ploidy levels in 83 Poa accessions representing 33 species from the National Plant Germplasm System using flow cytometric techniques. In reproductive mode analysis, we analyzed at least three preparations of 50 seeds each from the accessions. In ploidy level analysis, at least three plants of each accession were analyzed. Sixty percent of the species had at least one apomictic or facultative apomictic accession; 40% were sexual. Thirty-three percent of the species had no sexual accessions. Autonomous apomixis was newly identified in P. bactriana and P. bulbosa in addition to it being previously reported in P. nervosa. Poa annua and P. trivialis were identified as obligate sexual, and P. nervosa as obligate apomictic. Two of four P. palustris accessions exhibited facultative apomixis. Ploidy levels among sexually reproducing Poa accessions ranged from 2n = 2x = 14 to 2n = 12x = 84, with most accessions between 2n = 3x = 21 to 2n = 8x = 56. Among apomictic accessions, ploidy levels ranged from 2n = 3x = 21 to 2n = 10x = 70, with most between 2n = 4x = 28 and 2n = 10x = 70. These results emphasize the wide variability in Poa, both among and within species