Characterization of bacterial community structure in a hydrocarbon-contaminated tropical African soil

The bacterial community structure in a hydrocarbon-contaminated Mechanical Engineering Workshop (MWO) soil was deciphered using 16S rRNA gene clone library analysis. Four hundred and thirty-seven clones cutting across 13 bacterial phyla were recovered from the soil. The representative bacterial phyla identified from MWO soil are Proteobacteria, Bacteroidetes, Chloroflexi, Acidobacteria, Firmicutes, Actinobacteria, Verrucomicrobia, Planctomycetes, Ignavibacteriae, Spirochaetes, Chlamydiae, Candidatus Saccharibacteria and Parcubacteria. Proteobacteria is preponderant in the contaminated soil (51.2%) with all classes except Epsilonproteobacteria duly represented. Rarefaction analysis indicates 42%, 52% and 77% of the clone library is covered at the species, genus and family/class delineations with Shannon diversity (H′) and Chao1 richness indices of 5.59 and 1126, respectively. A sizeable number of bacterial phylotypes in the clone library shared high similarities with strains previously described to be involved in hydrocarbon biodegradation. Novel uncultured genera were identified that have not been previously reported from tropical African soil to be associated with natural attenuation of hydrocarbon pollutants. This study establishes the involvement of a wide array of physiologically diverse bacterial groups in natural attenuation of hydrocarbon pollutants in soil

Formation of Pillars at the Boundaries between H II Regions and Molecular Clouds

We investigate numerically the hydrodynamic instability of an ionization front (IF) accelerating into a molecular cloud, with imposed initial perturbations of different amplitudes. When the initial amplitude is small, the imposed perturbation is completely stabilized and does not grow. When the initial perturbation amplitude is large enough, roughly the ratio of the initial amplitude to wavelength is greater than 0.02, portions of the IF temporarily separate from the molecular cloud surface, locally decreasing the ablation pressure. This causes the appearance of a large, warm HI region and triggers nonlinear dynamics of the IF. The local difference of the ablation pressure and acceleration enhances the appearance and growth of a multimode perturbation. The stabilization usually seen at the IF in the linear regimes does not work due to the mismatch of the modes of the perturbations at the cloud surface and in density in HII region above the cloud surface. Molecular pillars are observed in the late stages of the large amplitude perturbation case. The velocity gradient in the pillars is in reasonably good agreement with that observed in the Eagle Nebula. The initial perturbation is imposed in three different ways: in density, in incident photon number flux, and in the surface shape. All cases show both stabilization for a small initial perturbation and large growth of the second harmonic by increasing amplitude of the initial perturbation above a critical value.Comment: 21 pages, 8 figures, accepted for publication in ApJ. high resolution figures available upon reques

Evolution of the Kdo2-lipid A biosynthesis in bacteria

<p>Abstract</p> <p>Background</p> <p>Lipid A is the highly immunoreactive endotoxic center of lipopolysaccharide (LPS). It anchors the LPS into the outer membrane of most Gram-negative bacteria. Lipid A can be recognized by animal cells, triggers defense-related responses, and causes Gram-negative sepsis. The biosynthesis of Kdo₂-lipid A, the LPS substructure, involves with nine enzymatic steps.</p> <p>Results</p> <p>In order to elucidate the evolutionary pathway of Kdo₂-lipid A biosynthesis, we examined the distribution of genes encoding the nine enzymes across bacteria. We found that not all Gram-negative bacteria have all nine enzymes. Some Gram-negative bacteria have no genes encoding these enzymes and others have genes only for the first four enzymes (LpxA, LpxC, LpxD, and LpxB). Among the nine enzymes, five appeared to have arisen from three independent gene duplication events. Two of such events happened within the Proteobacteria lineage, followed by functional specialization of the duplicated genes and pathway optimization in these bacteria.</p> <p>Conclusions</p> <p>The nine-enzyme pathway, which was established based on the studies mainly in <it>Escherichia coli </it>K12, appears to be the most derived and optimized form. It is found only in <it>E. coli </it>and related Proteobacteria. Simpler and probably less efficient pathways are found in other bacterial groups, with Kdo₂-lipid A variants as the likely end products. The Kdo₂-lipid A biosynthetic pathway exemplifies extremely plastic evolution of bacterial genomes, especially those of Proteobacteria, and how these mainly pathogenic bacteria have adapted to their environment.</p

Perilipin regulates the thermogenic actions of norepinephrine in brown adipose tissue

In response to cold, norepinephrine (NE)-induced triacylglycerol hydrolysis (lipolysis) in adipocytes of brown adipose tissue (BAT) provides fatty acid substrates to mitochondria for heat generation (adaptive thermogenesis). NE-induced lipolysis is mediated by protein kinase A (PKA)-dependent phosphorylation of perilipin, a lipid droplet-associated protein that is the major regulator of lipolysis. We investigated the role of perilipin PKA phosphorylation in BAT NE-stimulated thermogenesis using a novel mouse model in which a mutant form of perilipin, lacking all six PKA phosphorylation sites, is expressed in adipocytes of perilipin knockout (Peri KO) mice. Here, we show that despite a normal mitochondrial respiratory capacity, NE-induced lipolysis is abrogated in the interscapular brown adipose tissue (IBAT) of these mice. This lipolytic constraint is accompanied by a dramatic blunting (∼70%) of the in vivo thermal response to NE. Thus, in the presence of perilipin, PKA-mediated perilipin phosphorylation is essential for NE-dependent lipolysis and full adaptive thermogenesis in BAT. In IBAT of Peri KO mice, increased basal lipolysis attributable to the absence of perilipin is sufficient to support a rapid NE-stimulated temperature increase (∼3.0°C) comparable to that in wild-type mice. This observation suggests that one or more NE-dependent mechanism downstream of perilipin phosphorylation is required to initiate and/or sustain the IBAT thermal response

Vortex tubes in velocity fields of laboratory isotropic turbulence: dependence on the Reynolds number

The streamwise and transverse velocities are measured simultaneously in isotropic grid turbulence at relatively high Reynolds numbers, Re(lambda) = 110-330. Using a conditional averaging technique, we extract typical intermittency patterns, which are consistent with velocity profiles of a model for a vortex tube, i.e., Burgers vortex. The radii of the vortex tubes are several of the Kolmogorov length regardless of the Reynolds number. Using the distribution of an interval between successive enhancements of a small-scale velocity increment, we study the spatial distribution of vortex tubes. The vortex tubes tend to cluster together. This tendency is increasingly significant with the Reynolds number. Using statistics of velocity increments, we also study the energetical importance of vortex tubes as a function of the scale. The vortex tubes are important over the background flow at small scales especially below the Taylor microscale. At a fixed scale, the importance is increasingly significant with the Reynolds number.Comment: 8 pages, 3 PS files for 8 figures, to appear in Physical Review

dtorsin, the Drosophila Ortholog of the Early-Onset Dystonia TOR1A (DYT1), Plays a Novel Role in Dopamine Metabolism

Dystonia represents the third most common movement disorder in humans. At least 15 genetic loci (DYT1-15) have been identified and some of these genes have been cloned. TOR1A (formally DYT1), the gene responsible for the most common primary hereditary dystonia, encodes torsinA, an AAA ATPase family protein. However, the function of torsinA has yet to be fully understood. Here, we have generated and characterized a complete loss-of-function mutant for dtorsin, the only Drosophila ortholog of TOR1A. Null mutation of the X-linked dtorsin was semi-lethal with most male flies dying by the pre-pupal stage and the few surviving adults being sterile and slow moving, with reduced cuticle pigmentation and thin, short bristles. Third instar male larvae exhibited locomotion defects that were rescued by feeding dopamine. Moreover, biochemical analysis revealed that the brains of third instar larvae and adults heterozygous for the loss-of-function dtorsin mutation had significantly reduced dopamine levels. The dtorsin mutant showed a very strong genetic interaction with Pu (Punch: GTP cyclohydrolase), the ortholog of the human gene underlying DYT14 dystonia. Biochemical analyses revealed a severe reduction of GTP cyclohydrolase protein and activity, suggesting that dtorsin plays a novel role in dopamine metabolism as a positive-regulator of GTP cyclohydrolase protein. This dtorsin mutant line will be valuable for understanding this relationship and potentially other novel torsin functions that could play a role in human dystonia

On non-uniform smeared black branes

We investigate charged dilatonic black $p$-branes smeared on a transverse circle. The system can be reduced to neutral vacuum black branes, and we perform static perturbations for the reduced system to construct non-uniform solutions. At each order a single master equation is derived, and the Gregory-Laflamme critical wavelength is determined. Based on the non-uniform solutions, we discuss thermodynamic properties of this system and argue that in a microcanonical ensemble the non-uniform smeared branes are entropically disfavored even near the extremality, if the spacetime dimension is $D \le 13 +p$, which is the critical dimension for the vacuum case. However, the critical dimension is not universal. In a canonical ensemble the vacuum non-uniform black branes are thermodynamically favorable at $D > 12+p$, whereas the non-uniform smeared branes are favorable at $D > 14+p$ near the extremality.Comment: 24 pages, 2 figures; v2: typos corrected, submitted to Class.Quant.Gra

Estimates of electronic interaction parameters for LaMMO3_3 compounds (MM=Ti-Ni) from ab-initio approaches

We have analyzed the ab-initio local density approximation band structure calculations for the family of perovskite oxides, La$M$O$_3$ with $M$=Ti-Ni within a parametrized nearest neighbor tight-binding model and extracted various interaction strengths. We study the systematics in these interaction parameters across the transition metal series and discuss the relevance of these in a many-body description of these oxides. The results obtained here compare well with estimates of these parameters obtained via analysis of electron spectroscopic results in conjunction with the Anderson impurity model. The dependence of the hopping interaction strength, t, is found to be approximately $r^{-3}$.Comment: 18 pages; 1 tex file+9 postscript files (appeared in Phys Rev B Oct 15,1996

SO(4) Symmetry of the Transfer Matrix for the One-Dimensional Hubbard Model

The SO(4) invariance of the transfer matrix for the one-dimensional Hubbard model is clarified from the QISM (quantum inverse scattering method) point of view. We demonstrate the SO(4) symmetry by means of the fermionic R-matrix, which satisfy the graded Yang-Baxter relation. The transformation law of the fermionic L-operator under the SO(4) rotation is identified with a kind of gauge transformation, which determines the corresponding transformation of the fermionic creation and annihilation operators under the SO(4) rotation. The transfer matrix is confirmed to be invariant under the SO(4) rotation, which ensures the SO(4) invariance of the conserved currents including the Hamiltonian. Furthermore, we show that the representation of the higher conserved currents in terms of the Clifford algebra gives manifestly SO(4) invariant forms.Comment: 20 pages, LaTeX file using citesort.st