MS_RHII-RSD, a Dual-Function RNase HII-(p)ppGpp Synthetase from Mycobacterium smegmatis

In the noninfectious soil saprophyte Mycobacterium smegmatis, intracellular levels of the stress alarmones guanosine tetraphosphate and guanosine pentaphosphate, together termed (p)ppGpp, are regulated by the enzyme Rel(Msm). This enzyme consists of a single, bifunctional polypeptide chain that is capable of both synthesizing and hydrolyzing (p)ppGpp. The rel(Msm), knockout strain of M. smegmatis (Delta rel(Msm)) is expected to show a (p)ppGpp null (p)ppGpp(0)] phenotype. Contrary to this expectation, the strain is capable of synthesizing (p)ppGpp in vivo. In this study, we identify and functionally characterize the open reading frame (ORF), MSMEG_5849, that encodes a second functional (p)ppGpp synthetase in M. smegmatis. In addition to (p)ppGpp synthesis, the 567-amino-acid-long protein encoded by this gene is capable of hydrolyzing RNA(.)DNA hybrids and bears similarity to the conventional RNase HII enzymes. We have classified this protein as actRel(Msm) in accordance with the recent nomenclature proposed and have named it MS_RHII-RSD, indicating the two enzymatic activities present RHII, RNase HII domain, originally identified as (d) under bar omain of (u) under bar nknown (f) under bar unction 429 (DUF429), and RSD, RelA_SpoT nucleotidyl transferase domain, the SYNTH domain responsible for (p)ppGpp synthesis activity]. MS_RHII-RSD is expressed and is constitutively active in vivo and behaves like a monofunctional (p)ppGpp synthetase in vitro. The occurrence of the RNase HII and (p)ppGpp synthetase domains together on the same polypeptide chain is suggestive of an in vivo role for this novel protein as a link connecting the essential life processes of DNA replication, repair, and transcription to the highly conserved stress survival pathway, the stringent response.

Vaporization and collision modeling of liquid fuel sprays in a co-axial fuel and air pre-mixer

Droplet collision occurs frequently in regions where the droplet number density is high. Even for Lean Premixed and Pre-vaporized (LPP) liquid sprays, the collision effects can be very high on the droplet size distributions, which will in turn affect the droplet vaporization process. Hence, in conjunction with vaporization modeling, collision modeling for such spray systems is also essential. The standard O'Rourke's collision model, usually implemented in CFD codes, tends to generate unphysical numerical artifact when simulations are performed on Cartesian grid and the results are not grid independent. Thus, a new collision modeling approach based on no-time-counter method (NTC) proposed by Schmidt and Rutland is implemented to replace O'Rourke's collision algorithm to solve a spray injection problem in a cylindrical coflow premixer. The so called ``four-leaf clover'' numerical artifacts are eliminated by the new collision algorithm and results from a diesel spray show very good grid independence. Next, the dispersion and vaporization processes for liquid fuel sprays are simulated in a coflow premixer. Two liquid fuels under investigation are jet-A and Rapeseed Methyl Esters (RME). Results show very good grid independence in terms of SMD distribution, droplet number distribution and fuel vapor mass flow rate. A baseline test is first established with a spray cone angle of 90 degrees and injection velocity of 3 m/s and jet-A achieves much better vaporization performance than RME due to its higher vapor pressure. To improve the vaporization performance for both fuels, a series of simulations have been done at several different combinations of spray cone angle and injection velocity. At relatively low spray cone angle and injection velocity, the collision effect on the average droplet size and the vaporization performance are very high due to relatively high coalescence rate induced by droplet collisions. Thus, at higher spray cone angle and injection velocity, the results expectedly show improvement in fuel vaporization performance since smaller droplet has a higher vaporization rate. The vaporization performance and the level of homogeneity of fuel-air mixture can be significantly improved when the dispersion level is high, which can be achieved by increasing the spray cone angle and injection velocity. (C) 2012 Elsevier Ltd. All rights reserved.

Flavored co-annihilations

Neutralino dark matter in supersymmetric models is revisited in the presence of flavor violation in the soft supersymmetry breaking sector. We focus on flavor violation the sleptonic sector and study the implications for the co-annihilation regions. Flavor is introduced by a single (mu) over tilde (R) - (T) over tilde (R) insertion in the slepton mass matrix. Limits on insertion from BR(tau -> mu + gamma) are weak in some regions of the parameter space where happen within the amplitudes. We look for overlaps in parameter space where the co-annihilation condition as well as the cancellations within the amplitudes occur. mSUGRA, such overlap regions are not existent, whereas they are present in models non-universal Higgs boundary conditions (NUHM). The effect of flavor violation is fold: (a) it shifts the co-annihilation regions towards lighter neutralino masses (b) co-annihilation cross sections would be modified with the inclusion of flavor violating which can contribute significantly. Even if flavor violation is within the presently limits, this is sufficient to modify the thermally averaged cross-sections by about 15)% in mSUGRA and (20{30)% in NUHM, depending on the parameter space. In overlap regions, the flavor violating cross sections become comparable and in some even dominant to the flavor conserving ones. A comparative study of the channels is for mSUGRA and NUHM cases.

Diffusion mechanism in the mu phase in Nb-X (X = Ni, Co, Fe) systems

Nb is one of the common refractory elements added in Ni, Co and Fe based superalloys. This lead to the formation of brittle topological close packed (tcp) mu phase, which is deleterious to the structure. It mainly grows by interdiffusion and in the present article, the interdiffusion process in different Nb-X (X=Ni, Co, Fe) systems is discussed. The activation energy for interdiffusion is lower in the Co-Nb system (173 kJ/mol) than Fe-Nb system (233 kJ/mol), which is again lower than the value found in the Ni-Nb system (319.7 kJ/mol). The mole fraction of Nb in this phase is less than Fe or Co at stoichiometric compositions in the Nb-Fe (that is Fe7Nb6) and Nb-Co (that is Co7Nb6) systems. On the other hand, the mole fraction of Nb is higher than Ni in the same phase (Ni6Nb2) in Ni-Nb system. However, in all the phases, Nb has lower diffusion rate. Possible diffusion mechanism in this phase is discussed with respect to the crystal structure.

An Exported Heat Shock Protein 40 Associates with Pathogenesis-Related Knobs in Plasmodium falciparum Infected Erythrocytes

Cell surface structures termed knobs are one of the most important pathogenesis related protein complexes deployed by the malaria parasite Plasmodium falciparum at the surface of the infected erythrocyte. Despite their relevance to the disease, their structure, mechanisms of traffic and their process of assembly remain poorly understood. In this study, we have explored the possible role of a parasite-encoded Hsp40 class of chaperone, namely PFB0090c/PF3D7_0201800 (KAHsp40) in protein trafficking in the infected erythrocyte. We found the gene coding for PF3D7_0201800 to be located in a chromosomal cluster together with knob components KAHRP and PfEMP3. Like the knob components, KAHsp40 too showed the presence of PEXEL motif required for transport to the erythrocyte compartment. Indeed, sub-cellular fractionation and immunofluorescence analysis (IFA) showed KAHsp40 to be exported in the erythrocyte cytoplasm in a stage dependent manner localizing as punctuate spots in the erythrocyte periphery, distinctly from Maurer's cleft, in structures which could be the reminiscent of knobs. Double IFA analysis revealed co-localization of PF3D7_0201800 with the markers of knobs (KAHRP, PfEMP1 and PfEMP3) and components of the PEXEL translocon (Hsp101, PTEX150). KAHsp40 was also found to be in a complex with KAHRP, PfEMP3 and Hsp101 as confirmed by co-immunoprecipitation assay. Our results suggest potential involvement of a parasite encoded Hsp40 in chaperoning knob assembly in the erythrocyte compartment.

How Do Glassy Domains Grow?

We construct equations for the growth kinetics of structural glass within mode-coupling theory, through a nonstationary variant of the three-density correlator defined by G. Biroli et al. Phys. Rev. Lett. 97, 195701 (2006)]. We solve a schematic form of the resulting equations to obtain the coarsening of the three-point correlator chi(3)(t, t(w)) as a function of waiting time tw. For a quench into the glass, we find that chi(3) attains a peak value similar to t(w)(0.5) at t - t(w) similar to t(w)(0.8), providing a theoretical basis for the numerical observations of Parisi J. Phys. Chem. B 103, 4128 (1999)] and Kob and Barrat Phys. Rev. Lett. 78, 4581 (1997)]. The aging is not ``simple'': the t(w) dependence cannot be attributed to an evolving effective temperature.

Sequence and structural basis for chromosomal fragility during translocations in cancer

Chromosomal aberration is considered to be one of the major characteristic features in many cancers. Chromosomal translocation, one type of genomic abnormality, can lead to deregulation of critical genes involved in regulating important physiological functions such as cell proliferation and DNA repair. Although chromosomal translocations were thought to be random events, recent findings suggest that certain regions in the human genome are more susceptible to breakage than others. The possibility of deviation from the usual B-DNA conformation in such fragile regions has been an active area of investigation. This review summarizes the factors that contribute towards the fragility of these regions in the chromosomes, such as DNA sequences and the role of different forms of DNA structures. Proteins responsible for chromosomal fragility, and their mechanism of action are also discussed. The effect of positioning of chromosomes within the nucleus favoring chromosomal translocations and the role of repair mechanisms are also addressed.

A new diketopyrrolopyrrole-based co-polymer for ambipolar field-effect transistors and solar cells

A new thieno3,2-b]thiophenediketopyrrolopyrrole-benzo1,2-b:4,5-b']dithio phene based narrow optical gap co-polymer (PTTDPP-BDT) has been synthesized and characterized for field-effect transistors and solar cells. In field-effect transistors the polymer exhibited ambipolar charge transport behaviour with maximum hole and electron mobilities of 10(-3) cm(2) V-1 s(-1) and 10(-5) cm(2)V(-1) s(-1), respectively. The respectable charge transporting properties of the polymer were consistent with X-ray diffraction measurements that showed close molecular packing in the solid state. The difference in hole and electron mobilities was explained by density functional theory calculations, which showed that the highest occupied molecular orbital was delocalized along the polymer backbone with the lowest unoccupied molecular orbital localized on the bis(thieno3,2-b]thiophene)diketopyrrolopyrrole units. Bulk heterojunction photovoltaic devices with the fullerene acceptor PC70BM were fabricated and delivered a maximum conversion efficiency of 3.3% under AM1.5G illumination. (C) 2012 Elsevier B.V. All rights reserved.

Co-evolution of content popularity and delivery in mobile P2P networks

Mobile P2P technology provides a scalable approach for content delivery to a large number of users on their mobile devices. In this work, we study the dissemination of a single item of content (e. g., an item of news, a song or a video clip) among a population of mobile nodes. Each node in the population is either a destination (interested in the content) or a potential relay (not yet interested in the content). There is an interest evolution process by which nodes not yet interested in the content (i.e., relays) can become interested (i.e., become destinations) on learning about the popularity of the content (i.e., the number of already interested nodes). In our work, the interest in the content evolves under the linear threshold model. The content is copied between nodes when they make random contact. For this we employ a controlled epidemic spread model. We model the joint evolution of the copying process and the interest evolution process, and derive joint fluid limit ordinary differential equations. We then study the selection of parameters under the content provider's control, for the optimization of various objective functions that aim at maximizing content popularity and efficient content delivery.

Magneto-Transport Study of Pure and Co Doped ZnO Thin Films

A detailed low temperature magneto-transport study is carried out to understand the transport mechanism in pure and Co doped ZnO thin films grown by pulsed laser deposition (PLD) technique. A negative transverse magneto-resistance (MR) (with a value similar to 4% at 4.5 K) which decreases monotonically with the increase in temperature, is observed for the undoped ZnO film. A competition between positive and negative MR is observed for the Co doped ZnO samples. In this case at higher field values negative MR contribution dominates over the positive MR, which gives rise to a slope change in the MR data. Our data for MR shows excellent agreement with the semi-empirical formula given by Khosla et al., which is originally proposed for the degenerate semiconductors. This formula incorporates the third order perturbation expansion of the s-d exchange scattering of the conduction electrons from the localised spins. We have also obtained the Hall mobility, carrier conc. and mean free path as function of temperature for the pure ZnO film.

Flavoured co-annihilation

In minimal supergravity (mSUGRA) or CMSSM, one of the main co-annihilating partners of the neutralino is the lightest stau, (tau) over tilde (1). In the presence of flavour violation in the right-handed sector, the co-annihilating partner would be a flavour mixed state. The flavour effect is two-fold: (a) It changes the mass of (tau) over tilde (1) thus modifying the parameter space of the co-annihilation and (b) flavour violating scatterings could now contribute to the cross-sections in the early Universe. In fact, it is shown that for large enough delta similar to 0.2, these processes would constitute the dominant channels in co-annihilation regions. The amount of flavour mixing permissible is constrained by flavour violating tau -> mu or tau -> e processes. For Delta(RR) mass insertions, the constraints from flavour violation are not strong enough in some regions of the parameter space due to partial cancellations in the amplitudes. In mSUGRA, the regions with cancelations within LFV amplitudes do not overlap with the regions of co-annihilations. In non-universal Higgs model (NUHM), however, these regions do overlap leading to significant flavoured co-annihilations. At the LHC and other colliders, these regions can constitute for interesting signals.

Model Pseudoconvex Domains and Bumping

The Levi geometry at weakly pseudoconvex boundary points of domains in C-n, n >= 3, is sufficiently complicated that there are no universal model domains with which to compare a general domain. Good models may be constructed by bumping outward a pseudoconvex, finite- type Omega subset of C-3 in such a way that: (i) pseudoconvexity is preserved, (ii) the (locally) larger domain has a simpler defining function, and (iii) the lowest possible orders of contact of the bumped domain with partial derivative Omega, at the site of the bumping, are realized. When Omega subset of C-n, n >= 3, it is, in general, hard to meet the last two requirements. Such well-controlled bumping is possible when Omega is h-extendible/semiregular. We examine a family of domains in C-3 that is strictly larger than the family of h-extendible/semiregular domains and construct explicit models for these domains by bumping.

Preferential oxidation of CO on Ni/CeO2 catalysts in the presence of excess H-2 and CO2

Preferential oxidation of CO (CO-PROX) was carried out over Ni supported on CeO2 prepared by the co-precipitation method. The influence of metal loadings (2.5, 5 and 10 wt.% Ni) and the reaction conditions such as reaction temperature and feed composition on CO oxidation and oxidation selectivity were evaluated by using dry reformate gas. No other reactions like CO or CO2 methanation, coking, reverse water gas shift (RWGS) reaction is observed in the temperature range of 100-200 A degrees C on these catalysts. Hydrogen oxidation dominates over CO oxidation above the temperature of 200 A degrees C. An increase in oxygen leads to an increase in CO conversion but a simultaneous decrease in the O-2 selectivity. It has been noticed that 5 and 10 % Ni/CeO2 show better catalytic activity towards CO-PROX reaction. These catalysts were characterized by S-BET, XRD, TEM, XPS and H-2-TPR.

Activation of Lattice Oxygen of TiO2 by Pd2+ Ion: Correlation of Low-Temperature CO and Hydrocarbon Oxidation with Structure of Ti1-xPdxO2-x (x=0.01-0.03)

Lattice oxygen of TiO2 is activated by the substitution of Pd ion in its lattice. Ti1-xPdxO2-x (x = 0.01-0.03) have been synthesized by solution combustion method crystallizing in anatase TiO2 structure. Pd is in +2 oxidation state and Ti is in +4 oxidation state in the catalyst. Pd is more ionic in TiO2 lattice compared to Pd in PdO. Oxygen storage capacity defined by ``amount of oxygen that is used reversibly to oxidize CO'' is as high as 5100 mu mol/g of Ti0.97Pd0.03O1.97. Oxygen is extracted by CO to CO2 in absence of feed oxygen even at room temperature which is more than 20 times compared to pure TiO2. Rate of CO oxidation is 2.75 mu mol g(-1) s(-1) at 60 degrees C over Ti0.97Pd0.03O1.97 and C2H2 gets oxidized to CO2 and H2O at room temperature. Catalyst is not poisoned on long time operation of the reactor. Such high catalytic activity is due to activated lattice oxygen created by the substitution of Pd ion as seen from first-principles density functional theory (DFT) calculations with 96 atom supercells of Ti32O64, Ti31Pd1O63, Ti30Pd2O62, and Ti29Pd3O61. The compounds crystallize in anatase TiO2 structure with Pd2+ ion in nearly square planar geometry and TiO6 octahedra are distorted by the creation of weakly bound oxygens. Structural analysis of Ti31Pd1O63 which is close to 3% Pd ion substituted TiO2 shows that oxygens associated with both Ti and Pd ions in the lattice show bond valence sum of 1.87, a low value characteristic of weak oxygen in the lattice compared to oxygens with valence 2 and above in the same lattice. Exact positions of activated oxygens have been identified in the lattice from DFT calculations.

Analysis of an Interior Penalty Method for Fourth Order Problems on Polygonal Domains

Error analysis for a stable C (0) interior penalty method is derived for general fourth order problems on polygonal domains under minimal regularity assumptions on the exact solution. We prove that this method exhibits quasi-optimal order of convergence in the discrete H (2), H (1) and L (2) norms. L (a) norm error estimates are also discussed. Theoretical results are demonstrated by numerical experiments.