152 research outputs found
High Rate of Mobilization for blaCTX-Ms
The blaCTX-Ms have been mobilized to plasmids more frequently than other class A Ξ²-lactamases
Systematic Identification of Factors for Provirus Silencing in Embryonic Stem Cells
Embryonic stem cells (ESCs) repress the expression of exogenous proviruses and endogenous retroviruses (ERVs). Here, we systematically dissected the cellular factors involved in provirus repression in embryonic carcinomas (ECs) and ESCs by a genome-wide siRNA screen. Histone chaperones (Chaf1a/b), sumoylation factors (Sumo2/Ube2i/Sae1/Uba2/Senp6), and chromatin modifiers (Trim28/Eset/Atf7ip) are key determinants that establish provirus silencing. RNA-seq analysis uncovered the roles of Chaf1a/b and sumoylation modifiers in the repression of ERVs. ChIP-seq analysis demonstrates direct recruitment of Chaf1a and Sumo2 to ERVs. Chaf1a reinforces transcriptional repression via its interaction with members of the NuRD complex (Kdm1a, Hdac1/2) and Eset, while Sumo2 orchestrates the provirus repressive function of the canonical Zfp809/Trim28/Eset machinery by sumoylation of Trim28. Our study reports a genome-wide atlas of functional nodes that mediate proviral silencing in ESCs and illuminates the comprehensive, interconnected, and multi-layered genetic and epigenetic mechanisms by which ESCs repress retroviruses within the genome
Substrate age and tree islands influence carbon and nitrogen dynamics across a retrogressive semiarid chronosequence
The long-term dynamics of carbon (C) and nitrogen (N) in semiarid ecosystems remain poorly understood. We measured pools and fluxes of surface soil C and N, as well as other soil properties, under tree canopies and in intercanopy spaces at four sites that form a volcanic substrate age gradient in semiarid piΓ±on-juniper woodlands of northern Arizona, United States. Clay content and soil water-holding capacity increased consistently with substrate age, but both soil organic C and N increased only up to the 750,000 year site and then declined at the oldest (3,000,000 year) site. Measures of soil C and N flux displayed a similar pattern to total C and N pools. Pools and fluxes of C and N among the three canopy types became more homogeneous with substrate age up to the 750,000 year site, but disparity between tree and intercanopy microsites widened again at the oldest site. The Ξ΄15N of both tree leaves and surface soils became progressively more enriched across the substrate age gradient, consistent with a N cycle increasingly dominated by isotope fractionating losses. Our results point to consistencies in patterns of ecosystem development between semiarid and more humid ecosystems and suggest that pedogenic development may be an important factor controlling the spatial distribution of soil resources in semiarid ecosystems. These data should help both unify and broaden current theory of terrestrial ecosystem development
The Ninth Data Release of the Sloan Digital Sky Survey: First Spectroscopic Data from the SDSS-III Baryon Oscillation Spectroscopic Survey
The Sloan Digital Sky Survey III (SDSS-III) presents the first spectroscopic
data from the Baryon Oscillation Spectroscopic Survey (BOSS). This ninth data
release (DR9) of the SDSS project includes 535,995 new galaxy spectra (median
z=0.52), 102,100 new quasar spectra (median z=2.32), and 90,897 new stellar
spectra, along with the data presented in previous data releases. These spectra
were obtained with the new BOSS spectrograph and were taken between 2009
December and 2011 July. In addition, the stellar parameters pipeline, which
determines radial velocities, surface temperatures, surface gravities, and
metallicities of stars, has been updated and refined with improvements in
temperature estimates for stars with T_eff<5000 K and in metallicity estimates
for stars with [Fe/H]>-0.5. DR9 includes new stellar parameters for all stars
presented in DR8, including stars from SDSS-I and II, as well as those observed
as part of the SDSS-III Sloan Extension for Galactic Understanding and
Exploration-2 (SEGUE-2).
The astrometry error introduced in the DR8 imaging catalogs has been
corrected in the DR9 data products. The next data release for SDSS-III will be
in Summer 2013, which will present the first data from the Apache Point
Observatory Galactic Evolution Experiment (APOGEE) along with another year of
data from BOSS, followed by the final SDSS-III data release in December 2014.Comment: 9 figures; 2 tables. Submitted to ApJS. DR9 is available at
http://www.sdss3.org/dr
Hypolithic Microbial Community of Quartz Pavement in the High-Altitude Tundra of Central Tibet
The hypolithic microbial community associated with quartz pavement at a high-altitude tundra location in central Tibet is described. A small-scale ecological survey indicated that 36% of quartz rocks were colonized. Community profiling using terminal restriction fragment length polymorphism revealed no significant difference in community structure among a number of colonized rocks. Real-time quantitative PCR and phylogenetic analysis of environmental phylotypes obtained from clone libraries were used to elucidate community structure across all domains. The hypolithon was dominated by cyanobacterial phylotypes (73%) with relatively low frequencies of other bacterial phylotypes, largely represented by the chloroflexi, actinobacteria, and bacteriodetes. Unidentified crenarchaeal phylotypes accounted for 4% of recoverable phylotypes, while algae, fungi, and mosses were indicated by a small fraction of recoverable phylotypes
Restriction of HIV-1-based lentiviral vectors in adult primary marrow-derived and peripheral mobilized human CD34+ hematopoietic stem and progenitor cells occurs prior to viral DNA integration
Genetic variation of St. Louis encephalitis virus
St. Louis encephalitis virus (SLEV) has been regularly isolated throughout the Americas since 1933. Previous phylogenetic studies involving 62 isolates have defined seven major lineages (IβVII), further divided into 14 clades. In this study, 28 strains isolated in Texas in 1991 and 2001β2003, and three older, previously unsequenced strains from Jamaica and California were sequenced over the envelope protein gene. The inclusion of these new sequences, and others published since 2001, has allowed better delineation of the previously published SLEV lineages, in particular the clades of lineage II. Phylogenetic analysis of 106 isolates identified 13 clades. All 1991 and 2001β2003 isolates from Nueces, Jefferson and Harris Counties (Texas Gulf Coast) group in clade IIB with other isolates from these counties isolated during the 1980s and 1990s. This lack of evidence for introduction of novel strains into the Texas Gulf Coast over a long period of time is consistent with overwintering of SLEV in this region. Two El Paso isolates, both from 2002, group in clade VA with recent Californian isolates from 1998β2001 and some South American strains with a broad temporal range. Overall, these data are consistent with multiple introductions of SLEV from South America into North America, and provide support for the hypothesis that in most situations, SLEV circulates within a locality, with occasional incursions from other areas. Finally, SLEV has much lower nucleotide (10.1β%) and amino acid variation (2.8β%) than other members of the Japanese encephalitis virus complex (maximum variation 24.6β% nucleotide and 11.8β% amino acid)
Stream denitrification across biomes and its response to anthropogenic nitrate loading
Author Posting. Β© The Author(s), 2008. This is the author's version of the work. It is posted here by permission of Nature Publishing Group for personal use, not for redistribution. The definitive version was published in Nature 452 (2008): 202-205, doi:10.1038/nature06686.Worldwide, anthropogenic addition of bioavailable nitrogen (N) to the
biosphere is increasing and terrestrial ecosystems are becoming increasingly N
saturated, causing more bioavailable N to enter groundwater and surface waters.
Large-scale N budgets show that an average of about 20-25% of the N added to the
biosphere is exported from rivers to the ocean or inland basins, indicating
substantial sinks for N must exist in the landscape. Streams and rivers may be
important sinks for bioavailable N owing to their hydrologic connections with
terrestrial systems, high rates of biological activity, and streambed sediment
environments that favor microbial denitrification. Here, using data from 15N
tracer experiments replicated across 72 streams and 8 regions representing several
biomes, we show that total biotic uptake and denitrification of nitrate increase with
stream nitrate concentration, but that the efficiency of biotic uptake and
denitrification declines as concentration increases, reducing the proportion of instream
nitrate that is removed from transport. Total uptake of nitrate was related
to ecosystem photosynthesis and denitrification was related to ecosystem
respiration. Additionally, we use a stream network model to demonstrate that
excess nitrate in streams elicits a disproportionate increase in the fraction of nitrate
that is exported to receiving waters and reduces the relative role of small versus
large streams as nitrate sinks.Funding for this research was provided by the National Science
Foundation
Stability of Yellow Fever Virus under Recombinatory Pressure as Compared with Chikungunya Virus
Recombination is a mechanism whereby positive sense single stranded RNA viruses exchange segments of genetic information. Recent phylogenetic analyses of naturally occurring recombinant flaviviruses have raised concerns regarding the potential for the emergence of virulent recombinants either post-vaccination or following co-infection with two distinct wild-type viruses. To characterize the conditions and sequences that favor RNA arthropod-borne virus recombination we constructed yellow fever virus (YFV) 17D recombinant crosses containing complementary deletions in the envelope protein coding sequence. These constructs were designed to strongly favor recombination, and the detection conditions were optimized to achieve high sensitivity recovery of putative recombinants. Full length recombinant YFV 17D virus was never detected under any of the experimental conditions examined, despite achieving estimated YFV replicon co-infection levels of βΌ2.4Γ106 in BHK-21 (vertebrate) cells and βΌ1.05Γ105 in C710 (arthropod) cells. Additionally YFV 17D superinfection resistance was observed in vertebrate and arthropod cells harboring a primary infection with wild-type YFV Asibi strain. Furthermore recombination potential was also evaluated using similarly designed chikungunya virus (CHIKV) replicons towards validation of this strategy for recombination detection. Non-homologus recombination was observed for CHIKV within the structural gene coding sequence resulting in an in-frame duplication of capsid and E3 gene. Based on these data, it is concluded that even in the unlikely event of a high level acute co-infection of two distinct YFV genomes in an arthropod or vertebrate host, the generation of viable flavivirus recombinants is extremely unlikely
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