Draft Genome Sequence for Desulfovibrio africanus Strain PCS.

Desulfovibrio africanus strain PCS is an anaerobic sulfate-reducing bacterium (SRB) isolated from sediment from Paleta Creek, San Diego, CA. Strain PCS is capable of reducing metals such as Fe(III) and Cr(VI), has a cell cycle, and is predicted to produce methylmercury. We present the D. africanus PCS genome sequence

Evaporite karst geohazards in the Delaware Basin, Texas: review of traditional karst studies coupled with geophysical and remote sensing characterization

Evaporite karst throughout the Gypsum Plain of west Texas is complex and extensive, including manifestations ranging from intrastratal brecciation and hypogene caves to epigene features and suffosion caves. Recent advances in hydrocarbon exploration and extraction has resulted in increased infrastructure development and utilization in the area; as a result, delineation and characterization of potential karst geohazards throughout the region have become a greater concern. While traditional karst surveys are essential for delineating the subsurface extent and morphology of individual caves for speleogenetic interpretation, these methods tend to underestimate the total extent of karst development and require surficial manifestation of karst phenomena. Therefore, this study utilizes a composite suite of remote sensing and traditional field studies for improved karst delineation and detection of potential karst geohazards within gypsum karst. Color InfraRed (CIR) imagery were utilized for delineation of lineaments associated with fractures, while Normalized Density Vegetation Index (NDVI) analyses were used to delineate regions of increased moisture flux and probable zones of shallow karst development. Digital Elevation Models (DEM) constructed from high-resolution LiDAR (Light Detection and Ranging) data were used to spatially interpret sinkholes, while analyses of LiDAR intensity data were used in a novel way to categorize local variations in surface geology. Resistivity data, including both direct current (DC) and capacitively coupled (CC) resistivity analyses, were acquired and interpreted throughout the study area to delineate potential shallow karst geohazards specifically associated with roadways of geohazard concern; however, detailed knowledge of the surrounding geology and local karst development proved essential for proper interpretation of resistivity inversions. The composite suite of traditional field investigations and remotely sensed karst delineations used in this study illustrate how complex gypsum karst terrains can be characterized with greater detail through the utilization of rapidly advancing technologies, especially in arid environments with low vegetation densities

Thermal derivation of the Coleman-De Luccia tunneling prescription

We derive the rate for transitions between de Sitter vacua by treating the field theory on the static patch as a thermal system. This reproduces the Coleman-De Luccia formalism for calculating the rate, but leads to a modified interpretation of the bounce solution and a different prediction for the evolution of the system after tunneling. The bounce is seen to correspond to a sequence of configurations interpolating between initial and final configurations on either side of the tunneling barrier, all of which are restricted to the static patch. The final configuration, which gives the initial data on the static patch for evolution after tunneling, is obtained from one half of a slice through the center of the bounce, while the other half gives the configuration before tunneling. The formalism makes no statement about the fields beyond the horizon. This approach resolves several puzzling aspects and interpretational issues concerning the Coleman-De Luccia and Hawking-Moss bounces. We work in the limit where the back reaction of matter on metric can be ignored, but argue that the qualitative aspects remain in the more general case. The extension to tunneling between anti-de Sitter vacua is discussed.Comment: 28 pages, 5 figures; minor rephrasing, typos correcte

Spectrophotometric analysis of ternary uranyl systems to replace tri-N-butyl phosphate (TBP) in used fuel reprocessing

In this report, the interaction of monoamide/diamide and monoamide/diglycolamide mixtures with UO2+2 are investigated in pH = 1 methanolic nitric acid media. These monoamides include N,N-dimethylacetamide (DMAA), N,N-diethylacetamide (DEAA), N,N-dibutylacetamide (DBAA) and N,N-dibutylbutanamide (DBBA). N,N,N′N′-tetraethylmalonamide (TEMA) and N,N,N′,N′-tetraethyldiglycolamide (TEDGA), which were chosen as model diamides and diglycolamides, respectively. Complex stability constants for each ligand were modelled using the Stability Quotients Using Absorbance Data program using UV–visible data. Complex stoichiometry of ligand mixtures was determined using Job plots and UV–Vis spectrometry. Monoamides were confirmed to produce only disolvate complexes with UO2+2 in solution. The log10(K) values for monoamides were found to be independent of amine-side chain length, but were slightly dependent on the carbonyl-side chain length. TEDGA was found to produce multiple uranyl complexes in solution. Job plot data indicated that the uranyl cation strongly prefers to bond either only with the monoamide or diamide in ternary monoamide–diamide–UO2 systems. Monoamide–diglycolamide–UO2 systems were more complicated, with Job plot data indicating the potential for multiple ternary species being present is dependent on the monoamide structure

Complete Genome Sequence of Pelosinus fermentans JBW45, a Member of a Remarkably Competitive Group of Negativicutes in the Firmicutes Phylum.

The genome of Pelosinus fermentans JBW45, isolated from a chromium-contaminated site in Hanford, Washington, USA, has been completed with PacBio sequencing. Nine copies of the rRNA gene operon and multiple transposase genes with identical sequences resulted in breaks in the original draft genome and may suggest genomic instability of JBW45

Mouse WRN Helicase Domain Is Not Required for Spontaneous Homologous Recombination-Mediated DNA Deletion

Werner syndrome is a rare disorder that manifests as premature aging and age-related diseases. WRN is the gene mutated in WS, and is one of five human RecQ helicase family members. WS cells exhibit genomic instability and altered proliferation, and in vitro studies suggest that WRN has a role in suppressing homologous recombination. However, more recent studies propose that other RecQ helicases (including WRN) promote early events of homologous recombination. To study the role of WRN helicase on spontaneous homologous recombination, we obtained a mouse with a deleted WRN helicase domain and combined it with the in vivo pink-eyed unstable homologous recombination system. In this paper, we demonstrate that WRN helicase is not necessary for suppressing homologous recombination in vivo contrary to previous reports using a similar mouse model

A Phosphatidylinositol-3-Kinase-Dependent Signal Transition Regulates ARF1 and ARF6 during Fcγ Receptor-Mediated Phagocytosis

Fcγ receptor (FcγR)–mediated phagocytosis of IgG-coated particles is regulated by 3′-phosphoinositides (3′PIs) and several classes of small GTPases, including ARF6 from the ADP Ribosylation Factor subfamily. The insensitivity of phagocytosis to brefeldin A (BFA), an inhibitor of certain ARF guanine nucleotide exchange factors (GEFs), previously indicated that ARF1 did not participate in phagocytosis. In this study, we show that ARF1 was activated during FcγR-mediated phagocytosis and that blocking normal ARF1 cycling inhibited phagosome closure. We examined the distributions and activation patterns of ARF6 and ARF1 during FcγR-mediated phagocytosis using fluorescence resonance energy transfer (FRET) stoichiometric microscopy of macrophages expressing CFP- or YFP-chimeras of ARF1, ARF6, and a GTP-ARF-binding protein domain. Both GTPases were activated by BFA-insensitive factors at sites of phagocytosis. ARF6 activation was restricted to the leading edge of the phagocytic cup, while ARF1 activation was delayed and delocalized over the phagosome. Phagocytic cups formed after inhibition of PI 3-kinase (PI-3K) contained persistently activated ARF6 and minimally activated ARF1. This indicates that a PI-3K-dependent signal transition defines the sequence of ARF GTPase activation during phagocytosis and that ARF6 and ARF1 coordinate different functions at the forming phagosome

Mutant Alcohol Dehydrogenase Leads to Improved Ethanol Tolerance in Clostridium Thermocellum

Clostridium thermocellum is a thermophilic, obligately anaerobic, Gram-positive bacterium that is a candidate microorganism for converting cellulosic biomass into ethanol through consolidated bioprocessing. Ethanol intolerance is an important metric in terms of process economics, and tolerance has often been described as a complex and likely multigenic trait for which complex gene interactions come into play. Here, we resequence the genome of an ethanol-tolerant mutant, show that the tolerant phenotype is primarily due to a mutated bifunctional acetaldehyde-CoA/alcohol dehydrogenase gene (adhE), hypothesize based on structural analysis that cofactor specificity may be affected, and confirm this hypothesis using enzyme assays. Biochemical assays confirm a complete loss of NADH-dependent activity with concomitant acquisition of NADPH-dependent activity, which likely affects electron flow in the mutant. The simplicity of the genetic basis for the ethanol-tolerant phenotype observed here informs rational engineering of mutant microbial strains for cellulosic ethanol production

Hubble Space Telescope NICMOS Observations of T Dwarfs: Brown Dwarf Multiplicity and New Probes of the L/T Transition

We present the results of a Hubble Space Telescope NICMOS imaging survey of 22 T-type field brown dwarfs. Five are resolved as binary systems with angular separations of 0"05-0"35, and companionship is established on the basis of component F110W-F170M colors (indicative of CH4 absorption) and low probabilities of background contamination. Prior ground-based observations show 2MASS 1553+1532AB to be a common proper motion binary. The properties of these systems - low multiplicity fraction (11[+7][-3]% resolved, as corrected for sample selection baises), close projected separations (a = 1.8-5.0 AU) and near-unity mass ratios - are consistent with previous results for field brown dwarf binaries. Three of the binaries have components that span the poorly-understood transition between L dwarfs and T dwarfs. Spectral decomposition analysis of one of these, SDSS 1021-0304AB, reveals a peculiar flux reversal between its components, as its T5 secondary is ~30% brighter at 1.05 and 1.27 micron than its T1 primary. This system, 2MASS 0518-2828AB and SDSS 1534+1615AB all demonstrate that the J-band brightening observed between late-type L to mid-type T dwarfs is an intrinsic feature of this spectral transition, albeit less pronounced than previously surmised. We also find that the resolved binary fraction of L7 to T3.5 dwarfs is twice that of other L and T dwarfs, an anomaly that can be explained by a relatively rapid evolution of brown dwarfs through the L/T transition, perhaps driven by dynamic (nonequilibrium) depletion of photospheric condensates.Comment: ~40 pages, 17 figures, accepted for publication to ApJ. Note that emulateapj style file cuts off part of Table