Rv1027c-Rv1028c encode functional KdpDE two - Component system in Mycobacterium tuberculosis

In Mycobacterium tuberculosis Rv1027c-Rv1028c genes are predicted to encode KdpDE two component system, which is highly conserved across all bacterial species. Here, we show that the system is functionally active and KdpD sensor kinase undergoes autophosphorylation and transfers phosphoryl group to KdpE, response regulator protein. We identified His(642) and Asp(52) as conserved phosphorylation sites in KdpD and KdpE respectively and by SPR analysis confirmed the physical interaction between them. KdpD was purified with prebound divalent ions and their importance in phosphorylation was established using protein refolding and ion chelation approaches. Genetically a single transcript encoded both KdpD and KdpE proteins. Overall, we report that M. tuberculosis KdpDE system operates like a canonical two component system. (C) 2014 Elsevier Inc. All rights reserved.

Confining Dirac electrons on a topological insulator surface using potentials and a magnetic field

We study the effects of extended and localized potentials and a magnetic field on the Dirac electrons residing at the surface of a three-dimensional topological insulator like Bi2Se3. We use a lattice model to numerically study the various states; we show how the potentials can be chosen in a way which effectively avoids the problem of fermion doubling on a lattice. We show that extended potentials of different shapes can give rise to states which propagate freely along the potential but decay exponentially away from it. For an infinitely long potential barrier, the dispersion and spin structure of these states are unusual and these can be varied continuously by changing the barrier strength. In the presence of a magnetic field applied perpendicular to the surface, these states become separated from the gapless surface states by a gap, thereby giving rise to a quasi-one-dimensional system. Similarly, a magnetic field along with a localized potential can give rise to exponentially localized states which are separated from the surface states by a gap and thereby form a zero-dimensional system. Finally, we show that a long barrier and an impurity potential can produce bound states which are localized at the impurity, and an ``L''-shaped potential can have both bound states at the corner of the L and extended states which travel along the arms of the potential. Our work opens the way to constructing wave guides for Dirac electrons.

Angular momentum transport and evolution of lopsided galaxies

The surface brightness distribution in the majority of stellar galactic discs falls off exponentially. Often what lies beyond such a stellar disc is the neutral hydrogen gas whose distribution also follows a nearly exponential profile at least for a number of nearby disc galaxies. Both the stars and gas are commonly known to host lopsided asymmetry especially in the outer parts of a galaxy. The role of such asymmetry in the dynamical evolution of a galaxy has not been explored so far. Following Lindblad's original idea of kinematic density waves, we show that the outer part of an exponential disc is ideally suitable for hosting lopsided asymmetry. Further, we compute the transport of angular momentum in the combined stars and gas disc embedded in a dark matter halo. We show that in a pure star and gas disc, there is a transition point where the free precession frequency of a lopsided mode, Omega - kappa, changes from retrograde to prograde and this in turn reverses the direction of angular momentum flow in the disc leading to an unphysical behaviour. We show that this problem is overcome in the presence of a dark matter halo, which sets the angular momentum flow outwards as required for disc evolution, provided the lopsidedness is leading in nature. This, plus the well-known angular momentum transport in the inner parts due to spiral arms, can facilitate an inflow of gas from outside perhaps through the cosmic filaments.

Electron transfer statistics and thermal fluctuations in molecular junctions

We derive analytical expressions for probability distribution function (PDF) for electron transport in a simple model of quantum junction in presence of thermal fluctuations. Our approach is based on the large deviation theory combined with the generating function method. For large number of electrons transferred, the PDF is found to decay exponentially in the tails with different rates due to applied bias. This asymmetry in the PDF is related to the fluctuation theorem. Statistics of fluctuations are analyzed in terms of the Fano factor. Thermal fluctuations play a quantitative role in determining the statistics of electron transfer; they tend to suppress the average current while enhancing the fluctuations in particle transfer. This gives rise to both bunching and antibunching phenomena as determined by the Fano factor. The thermal fluctuations and shot noise compete with each other and determine the net (effective) statistics of particle transfer. Exact analytical expression is obtained for delay time distribution. The optimal values of the delay time between successive electron transfers can be lowered below the corresponding shot noise values by tuning the thermal effects. (C) 2015 AIP Publishing LLC.

Rrp1B gene polymorphism (1307T > C) in metastatic progression of breast cancer

Rrp1B (ribosomal RNA processing1 homolog B) is a novel candidate metastasis modifier gene in breast cancer. Functional gene assays demonstrated that a physical and functional interaction existing between Rrp1b and metastasis modifier gene SIPA1 causes reduction in the tumor growth and metastatic potential. Ectopic expression of Rrp1B modulates various metastasis predictive extra cellular matrix (ECM) genes associated with tumor suppression. The aim of this study is to determine the functional significance of single nucleotide polymorphism (SNP) in human Rrp1B gene (1307 T > C; rs9306160) with breast cancer development and progression. The study consists of 493 breast cancer cases recruited from Nizam's Institute of Medical Sciences, Hyderabad, and 558 age-matched healthy female controls from rural and urban areas. Genomic DNA was isolated by non-enzymatic method. Genotyping was done by amplification refractory mutation system (ARMS-PCR) method. Genotypes were reconfirmed by sequencing and results were analyzed statistically. We have performed Insilco analysis to know the RNA secondary structure by using online tool m fold. The TT genotype and T allele frequencies of Rrp1B1307 T > C polymorphism were significantly elevated in breast cancer (chi (2); p = < 0.008) cases compared to controls under different genetic models. The presence of T allele had conferred 1.75-fold risk for breast cancer development (OR = 1.75; 95 % CI = 1.15-2.67). The frequency of TT genotype of Rrp1b 1307T > C polymorphism was significantly elevated in obese patients (chi (2); p = 0.008) and patients with advanced disease (chi (2); p = 0.01) and with increased tumor size (chi (2); p = 0.01). Moreover, elevated frequency of T allele was also associated with positive lymph node status (chi (2); p = 0.04) and Her2 negative receptor status (chi (2); p = 0.006). Presence of Rrp1b1307TT genotype and T allele confer strong risk for breast cancer development and progression.

Characterization of rice small heat shock proteins targeted to different cellular organelles

Small heat shock proteins (sHSPs) are a family of ATP-independent molecular chaperones which prevent cellular protein aggregation by binding to misfolded proteins. sHSPs form large oligomers that undergo drastic rearrangement/dissociation in order to execute their chaperone activity in protecting substrates from stress. Substrate-binding sites on sHSPs have been predominantly mapped on their intrinsically disordered N-terminal arms. This region is highly variable in sequence and length across species, and has been implicated in both oligomer formation and in mediating chaperone activity. Here, we present our results on the functional and structural characterization of five sHSPs in rice, each differing in their subcellular localisation, viz., cytoplasm, nucleus, chloroplast, mitochondria and peroxisome. We performed activity assays and dynamic light scattering studies to highlight differences in the chaperone activity and quaternary assembly of sHSPs targeted to various organelles. By cloning constructs that differ in the length and sequence of the tag in the N-terminal region, we have probed the sensitivity of sHSP oligomer assembly and chaperone activity to the length and amino acid composition of the N-terminus. In particular, we have shown that the incorporation of an N-terminal tag has significant consequences on sHSP quaternary structure.

Structures of substrate- and nucleotide-bound propionate kinase from Salmonella typhimurium: substrate specificity and phosphate-transfer mechanism

Kinases are ubiquitous enzymes that are pivotal to many biochemical processes. There are contrasting views on the phosphoryl-transfer mechanism in propionate kinase, an enzyme that reversibly transfers a phosphoryl group from propionyl phosphate to ADP in the final step of non-oxidative catabolism of L-threonine to propionate. Here, X-ray crystal structures of propionate- and nucleotide-bound Salmonella typhimurium propionate kinase are reported at 1.8-2.0 angstrom resolution. Although the mode of nucleotide binding is comparable to those of other members of the ASKHA superfamily, propionate is bound at a distinct site deeper in the hydrophobic pocket defining the active site. The propionate carboxyl is at a distance of approximate to 5 angstrom from the -phosphate of the nucleotide, supporting a direct in-line transfer mechanism. The phosphoryl-transfer reaction is likely to occur via an associative S(N)2-like transition state that involves a pentagonal bipyramidal structure with the axial positions occupied by the nucleophile of the substrate and the O atom between the - and the -phosphates, respectively. The proximity of the strictly conserved His175 and Arg236 to the carboxyl group of the propionate and the -phosphate of ATP suggests their involvement in catalysis. Moreover, ligand binding does not induce global domain movement as reported in some other members of the ASKHA superfamily. Instead, residues Arg86, Asp143 and Pro116-Leu117-His118 that define the active-site pocket move towards the substrate and expel water molecules from the active site. The role of Ala88, previously proposed to be the residue determining substrate specificity, was examined by determining the crystal structures of the propionate-bound Ala88 mutants A88V and A88G. Kinetic analysis and structural data are consistent with a significant role of Ala88 in substrate-specificity determination. The active-site pocket-defining residues Arg86, Asp143 and the Pro116-Leu117-His118 segment are also likely to contribute to substrate specificity.

Structural studies on tobacco streak virus coat protein: Insights into the pleomorphic nature of ilarviruses

Tobacco streak virus (TSV), the type member of Ilarvirus genus, is a major plant pathogen. TSV purified from infected plants consists of a ss-RNA genome encapsidated in spheroidal particles with diameters of 27, 30 and 33 nm constructed from multiple copies of a single species of coat protein (CP) subunits. Apart from protecting the viral genome, CPs of ilarviruses play several key roles in the life cycle of these viruses. Unlike the related bromo and cucumoviruses, ilarvirus particles are labile and pleomorphic, which has posed difficulties in their crystallization and structure determination. In the current study, a truncated TSV-CP was crystallized in two distinct forms and their structures were determined at resolutions of 2.4 angstrom and 2.1 angstrom, respectively. The core of TSV CP was found to possess the canonical beta-barrel jelly roll tertiary structure observed in several other viruses. Dimers of CP with swapped C-terminal arms (C-arm) were observed in both the crystal forms. The C-arm was found to be flexible and is likely to be responsible for the polymorphic and pleomorphic nature of TSV capsids. Consistent with this observation, mutations in the hinge region of the C-arm that reduce the flexibility resulted in the formation of more uniform particles. TSV CP was found to be structurally similar to that of Alfalfa mosaic virus (AMV) accounting for similar mechanism of genome activation in alfamo and ilar viruses. This communication represents the first report on the structure of the CP from an ilarvirus. (C) 2015 Elsevier Inc. All rights reserved.

Efficient density matrix renormalization group algorithm to study Y junctions with integer and half-integer spin

An efficient density matrix renormalization group (DMRG) algorithm is presented and applied to Y junctions, systems with three arms of n sites that meet at a central site. The accuracy is comparable to DMRG of chains. As in chains, new sites are always bonded to the most recently added sites and the superblock Hamiltonian contains only new or once renormalized operators. Junctions of up to N = 3n + 1 approximate to 500 sites are studied with antiferromagnetic (AF) Heisenberg exchange J between nearest-neighbor spins S or electron transfer t between nearest neighbors in half-filled Hubbard models. Exchange or electron transfer is exclusively between sites in two sublattices with N-A not equal N-B. The ground state (GS) and spin densities rho(r) = < S-r(z)> at site r are quite different for junctions with S = 1/2, 1, 3/2, and 2. The GS has finite total spin S-G = 2S(S) for even (odd) N and for M-G = S-G in the S-G spin manifold, rho(r) > 0(< 0) at sites of the larger (smaller) sublattice. S = 1/2 junctions have delocalized states and decreasing spin densities with increasing N. S = 1 junctions have four localized S-z = 1/2 states at the end of each arm and centered on the junction, consistent with localized states in S = 1 chains with finite Haldane gap. The GS of S = 3/2 or 2 junctions of up to 500 spins is a spin density wave with increased amplitude at the ends of arms or near the junction. Quantum fluctuations completely suppress AF order in S = 1/2 or 1 junctions, as well as in half-filled Hubbard junctions, but reduce rather than suppress AF order in S = 3/2 or 2 junctions.

Laboratory Study on Sediment Diffusion and Deposition into Blind Channels

Any waterway with one end closed and the other open is generally called a blind channel. The main flow tends to expand, separate, and cause circulation at the mouth of blind channels. The main flow continuously transfers momentum and sediment into the circulation region through the turbulent mixing region (TMR) between them, thus leading to a large amount of sediment deposition in the blind channels. This paper experimentally investigated the properties of the water flow and sediment diffusion in TMR, demonstrating that both water flow and sediment motion in TMR approximately coincide with a similar structure as in the free mixing layer induced by a jet. The similarity functions of flow velocity and sediment concentration are then assumed, based on observation, and the resulting calculation of these functions is substantially facilitated. For the kind of low velocity flow system of blind channels with a finite width, a simple formula for the sediment deposition rate in blind channels is established by analyzing the gradient of crosswise velocity and sediment concentration in TMR.

Influence of the Processing Conditions on the Characteristics of the Clad Layers Produced with Laminar Plasma Technology

Laminar plasma technology was used to produce ceramic hardened layers of Al2O3-40% mass Ni composite powders on stainless steel substrates. In order to investigate the influences of processing conditions on the morphologies of the surface modified layers, two different powder-feeding methods were tested, one with carrier gas called the powder injection method, and the other without carrier gas called powder transfers method. The microscopic investigations demonstrate that the cross-section of the clad layers consists of two distinct microstructural regions, in which the Al2O3 phases exhibit different growth mechanisms. When the powder transfers method is adopted, the number density and volume fraction of the Al2O3 particles increase considerably and their distributions exhibit zonal periodical characteristics. When the powder-feeding rate increases, the microstructure of the Al2O3 phases changes from a small globular to a long needle shape. Finite element simulations show that the transient thermo-physical features of the pool substances, such as solidification rate and cooling rate, influence strongly the mechanisms of the nucleation and the directional growth of the Al2O3 phases in the thermal processing.

Numerical Analysis of LEC Growth of GaAs with an Axial Magnetic Field

A set of numerical analyses for momentum and heat transfer For a 3 in. (0.075 m) diameter Liquid Encapsulant Czochralski (LEC) growth of single-crystal GaAs with or without all axial magnetic field was carried Out using the finite-element method. The analyses assume a pseudosteady axisymmetric state with laminar floats. Convective and conductive heat transfers. radiative heat transfer between diffuse surfaces and the Navier-Stokes equations for both melt and encapsulant and electric current stream function equations Cor melt and crystal Lire considered together and solved simultaneously. The effect of the thickness of encapsulant. the imposed magnetic field strength as well as the rotation rate of crystal and crucible on the flow and heat transfer were investigated. (C) 2002 Published by Elsevier Science Ltd.

Bronze and iron weapons from Luristan

The 30,000 km2 province of Luristan is situated in western Iran and encompasses the upper valleys of the Zagros Mountains. Even today, local tribesmen inhabit Luristan with their settlement patterns similar to ancient times. Several scientific excavations in the Luristan region have uncovered evidence that this particular region was a major attraction for human settlements from the Paleolithic era onwards. In Ancient Iran, the existence of rich mines together with discoveries made by innovative and inventive artisans spurred the growth of the metalworking culture as an art and a skill among early human communities in Ancient Iran. The art of Luristan can be described as the art of nomadic herdsmen and horsemen with an emphasis on the crafting of small, easily portable objects, among these a number of bronze daggers, swords and other weapons. Throughout its history, Luristan was never an ethnic or political entity because Luristan has been occupied by various tribes and races, throughout its history. Next to Elamites, other tribes who inhabited Luristan were the Hurrians, Lullubians, Kutians, and Kassites. As local tribesmen of Luristan were illiterate, information about their history can only be partially reconstructed from the literature of their southern neighbors: the Elamites and Babylonians. Luristan smiths made weapons for both civilizations. The region was later invaded by Assyrians and finally the Iranians settled the area and absorbed the local tribes. Following an accidental find by the local inhabitants in Luristan in 1928 CE, a number of unlawful diggings reveal a number of metal objects made of bronze and iron that showed a high level of craftsmanship. These objects were offered for sale on the art market with fancy names to hide their origin. The subsequent scientific excavations several decades after the initial discovery provided fascinating information about the culture of Luristan. The metalworking art of Luristan spans a time period from the third millennium BC to the Iron Age. The artifacts from Luristan seem to possess many unique and distinctive qualities, and are especially noteworthy for the apparently endless, intricate diversity and detail that they characteristically depict. The bronze artifacts found in or attributed to Luristan can be each be classed under five separate heads: a) arms and armor, including swords, dirks, daggers, axes, mace heads, spearheads, shields, quiver plaques, protective bronze girdles, helmets; b) implements related to horsemanship, including decorative or ornamental objects for horses as well as bits and snaffles; c) items for personal adornment and hygiene, including anklets, bangles, bracelets, finger rings, earrings and tweezers; d) ceremonial and ritual objects, including talismans, idols, pins, anthropomorphic and zoomorphic figurines; and e) utilitarian objects comprising various vessels and tools, including beakers, bowls and jugs. The scope of this article is limited to a discussion of the bronze and iron weapons made in Luristan. The techniques used for making bronze weapons in Luristan included: casting with open molds, casting with close molds, and casting with lost wax process. For metal sheets used for quiver plaques and bronze protective belts, the hammering technique was used. Edged weapons made in Luristan can be classified into: a) daggers, dirks, and swords with tangs; b) daggers, dirks, and swords with flanges; and c) daggers, dirks, and swords with cast-on hilts. Next to bronze, iron was also used for making weapons such as the characteristic weapon from this area, the iron mask sword.

La heráldica, el retrato y el fin de la Edad Media : un acercamiento antropológico a la iconografía

Resumen: Durante la Edad Media hizo su aparición la heráldica como forma de identificar ciertos aspectos de las personas, ya sea por su condición social o por su actividad específica. El uso de blasones y escudos de armas desde el siglo XI generó una importante cantidad de signos, colores y símbolos que edificaron todo un “patrón de lectura” del “rostro social” de la persona que portaba tal insignia, sin importar o no la veracidad de su rostro al confeccionarse un retrato pintado o esculpido. Paralelo a esto, la retratística que hubo durante todo el período medieval de personas reales, sagradas o ideales avanzó hacia un progresivo naturalismo que finalizó en el siglo XV con la reproducción del retratado tal cual era su fisonomía y abandonando el canon estereotipado que durante los siglos precedentes habían proliferado. Finalmente, con el creciente Humanismo, la aparición de la perspectiva y el progresivo abandono de la identificación de determinado personaje con sólo su escudo de armas, sirvió para que el retratado mirase a los ojos del observador y “dialogase”, develando aspectos espirituales antes ocultos. El objetivo de este trabajo es acercarse con una visión antropológica a la cuestión del retrato tardomedieval y renacentista en conjunción con los cambios operados en la heráldica y la iconografía, comprobando que la mirada tiene marcada intencionalidad, los rostros se frontalizan progresivamente y la heráldica pierde el espesor que tuvo en siglos precedentes

Comparative Study Of The Influence Of Natural Convection On Directional Solidification Of Al-3.5 Wt% Ni And Al-7 Wt% Si Alloys

We present numerical simulations of thermosolutal convection for directional solidification of Al-3.5 wt% Ni and Al-7 wt% Si. Numerical results predict that fragmentation of dendrite arms resulting from dissolution could be favored in Al-7 wt% Si, but not in Al-3.5 wt% Ni. Corresponding experiments are in qualitative agreement with the numerical predictions. Distinguishing the two fragmentation mechanisms, namely dissolution and remelting, is critical during experiments on earth, when fluid flow is dominant. (C) 2007 COSPAR. Published by Elsevier Ltd. All rights reserved.