Sesbania Mosaic Virus (SeMV) Infectious Clone: Possible Mechanism of 3 ` and 5 ` End Repair and Role of Polyprotein Processing in Viral Replication

Sesbania mosaic virus (SeMV) is a positive stranded RNA virus belonging to the genus Sobemovirus. Construction of an infectious clone is an essential step for deciphering the virus gene functions in vivo. Using Agrobacterium based transient expression system we show that SeMV icDNA is infectious on Sesbania grandiflora and Cyamopsis tetragonoloba plants. The efficiency of icDNA infection was found to be significantly high on Cyamopsis plants when compared to that on Sesbania grandiflora. The coat protein could be detected within 6 days post infiltration in the infiltrated leaves. Different species of viral RNA (double stranded and single stranded genomic and subgenomic RNA) could be detected upon northern analysis, suggesting that complete replication had taken place. Based on the analysis of the sequences at the genomic termini of progeny RNA from SeMV icDNA infiltrated leaves and those of its 3' and 5' terminal deletion mutants, we propose a possible mechanism for 3' and 5' end repair in vivo. Mutation of the cleavage sites in the polyproteins encoded by ORF 2 resulted in complete loss of infection by the icDNA, suggesting the importance of correct polyprotein processing at all the four cleavage sites for viral replication. Complementation analysis suggested that ORF 2 gene products can act in trans. However, the trans acting ability of ORF 2 gene products was abolished upon deletion of the N-terminal hydrophobic domain of polyprotein 2a and 2ab, suggesting that these products necessarily function at the replication site, where they are anchored to membranes.

Effect of equal channel angular extrusion on wear and corrosion behavior of the orthopedic Ti-13Nb-13Zr alloy in simulated body fluid

We report investigations on the texture, corrosion and wear behavior of ultra-fine grained (UFG) Ti-13Nb-Zr alloy, processed by equal channel angular extrusion (ECAE) technique, for biomedical applications. The microstructure obtained was characterized by X-ray line profile analysis, scanning electron microscope (SEM) and electron back scattered diffraction (EBSD). We focus on the corrosion resistance and the fretting behavior, the main considerations for such biomaterials, in simulated body fluid. To this end. potentiodynamic polarization tests were carried out to evaluate the corrosion behavior of the UFG alloy in Hanks solution at 37 degrees C. The fretting wear behavior was carried out against bearing steel in the same conditions. The roughness of the samples was also measured to examine the effect of topography on the wear behavior of the samples. Our results showed that the ECAE process increases noticeably the performance of the alloy as orthopedic implant. Although no significant difference was observed in the fretting wear behavior, the corrosion resistance of the UFG alloy was found to be higher than the non-treated material. (c) 2012 Elsevier B.V. All rights reserved.

Crystal Structure of Escherichia coli Diaminopropionate Ammonia-lyase Reveals Mechanism of Enzyme Activation and Catalysis

Pyridoxal 5'-phosphate (PLP)-dependent enzymes utilize the unique chemistry of a pyridine ring to carry out diverse reactions involving amino acids. Diaminopropionate (DAP) ammonia-lyase (DAPAL) is a prokaryotic PLP-dependent enzyme that catalyzes the degradation of D-and L-forms of DAP to pyruvate and ammonia. Here, we report the first crystal structure of DAPAL from Escherichia coli (EcDAPAL) in tetragonal and monoclinic forms at 2.0 and 2.2 angstrom resolutions, respectively. Structures of EcDAPAL soaked with substrates were also determined. EcDAPAL has a typical fold type II PLP-dependent enzyme topology consisting of a large and a small domain with the active site at the interface of the two domains. The enzyme is a homodimer with a unique biological interface not observed earlier. Structure of the enzyme in the tetragonal form had PLP bound at the active site, whereas the monoclinic structure was in the apo-form. Analysis of the apo and holo structures revealed that the region around the active site undergoes transition from a disordered to ordered state and assumes a conformation suitable for catalysis only upon PLP binding. A novel disulfide was found to occur near a channel that is likely to regulate entry of ligands to the active site. EcDAPAL soaked with DL-DAP revealed density at the active site appropriate for the reaction intermediate aminoacrylate, which is consistent with the observation that EcDAPAL has low activity under crystallization conditions. Based on the analysis of the structure and results of site-directed mutagenesis, a two-base mechanism of catalysis involving Asp(120) and Lys(77) is suggested.

A Rare Phenoxido/Acetato/Azido Bridged Trinuclear and an Unprecedented Phenoxido/Azido Bridged One-Dimensional Polynuclear Nickel(II) Complexes: Synthesis, Crystal Structure, and Magnetic Properties with Theoretical Investigations on the Exchange Mechanism

The reaction of a tridentate Schiff base ligand HL (2-(3-dimethylaminopropylimino)-methyl]-phenol) with Ni(II) acetate or perchlorate salts in the presence of azide as coligand has led to two new Ni(II) complexes of formulas Ni3L2(OAc)(2)(mu(1,1)-N-3)(2)(H2O)(2)]center dot 2H(2)O (1) and Ni2L2(mu(1,1)-N-3) (mu(1,3)-N-3)](n)(2). Single crystal X-ray structures show that complex 1 is a linear trinuclear Ni(II) compound containing a mu(2)-phenwddo, an end-on (EO) azido and a syn-syn acetato bridge between the terminal and the central Ni(II) ions. Complex 2 can be viewed as a one-dimensional (1D) chain in which the triply bridged (di-mu(2)-phenoxido and EO azido) dimeric Ni-2 units are linked to each other in a zigzag pattern by a single end-to-end (EE) azido bridge. Variable-temperature magnetic susceptibility studies indicate the presence of moderate ferromagnetic exchange coupling in complex 1 with J value of 16.51(6) cm(-1). The magnetic behavior of 2 can be fitted in an alternating ferro- and antiferromagnetic model J(FM) = +34.2(2.8) cm(-1) and J(AF) = -21.6(1.1) cm(-1)] corresponding to the triple bridged dinuclear core and EE azido bridge respectively. Density functional theory (DFT) calculations were performed to corroborate the magnetic results of 1 and 2. The contributions of the different bridges toward magnetic interactions in both compounds have also been calculated.

Diffusion mechanism in XSi2 and X5Si3 (X= Nb, Mo, V) phases

In view of the importance of the suicides in the high temperature applications, the diffusion behaviour is compared in different systems for two types of silicides, XSi2 and X5Si3 (X=Nb, Mo, V). Atomic mechanism of diffusion and defects present in the structure are discussed. In both the phases, Si has faster diffusion rate than the metal species. This is expected from the nearest neighbour (NN) bonds present in the XSi2 phase but rather unusual in the X5Si3 phase. Relative mobilities of the species calculated indicate the presence of high concentration of Si antisites. Moreover, the concentration of the defects is different in different systems to find different diffusion rates.

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.

Diffusion mechanism in the gold-copper system

Interdiffusion study is conducted in the Au-Cu system, which has complete solid solution in the higher temperature range and ordered phases in the lower temperature range. First experiments are conducted at higher temperatures, where atoms can diffuse randomly. Higher values of interdiffusion coefficients are found in the range of 40-50 at.% Cu. This trend is explained with the help of thermodynamic factor and possible concentration of vacancies. Following an experiment is conducted at 623 K (350 degrees C), where the ordered phases are grown. The interdiffusion coefficients at this temperature are compared after extrapolating the data calculated at higher temperatures.

Diffusion and growth mechanism of phases in the Pd-Sn system

Growth mechanism of phases and atomic mechanism of diffusion are discussed in the Pd-Sn system. The Kirkendall marker plane location indicates that the PdSn4 phase grows because of diffusion of Sn. Atomic arrangement in the crystal indicates that Sn can diffuse through its own sublattice but Pd cannot diffuse unless antisites are present. The negligible diffusion of Pd indicates the absence of Pd antisites. The activation energy value indicates that the contribution from grain boundary diffusion cannot be neglected although experiments were conducted in the homologous temperature range of 0.7-0.79.

Ex Situ X-ray Diffraction, X-ray Absorption Near Edge Structure, Electron Spin Resonance, and Transmission Electron Microscopy Study of the Hydrothermal Crystallization of Vanadium Oxide Nanotubes: An Insight into the Mechanism of Formation

The nucleation and growth of vanadium oxide nanotubes (VOx-NT) have been followed by a combination of numerous ex situ techniques. long the hydrothermal process. Intermediate solid phases extracted at different reaction times have been characterized by powder X-ray diffraction, scanning and transmission electron microscopy, electron spin resonance, and V-K edge :X-ray absorption near-edge structure spectroscopy. The supernatant vanadate solutions extracted during the hydrothermal treatment have been studied by liquid V-51 NMR and flame. spectroscopy. For short durations of the hydrothermal synthesis, the initial V2O5-surfactant intercalate. is progressively transformed into VOx-NT whose crystallization starts to be detected after a hydrothermal treatment of 24 h. Upon heating from 24 h to 7 days, VOx-NT are obtained in larger amount and with an improved crystallinity. The detection of soluble amines and cyclic metavanadate V4O12](4-) in the supernatant solution along the hydrothermal process suggests that VOx-NT result from a dissolution precipitation mechanism. Metavanadate species V4O12](4-) could behave as molecular precursors in the polymerization reactions leading to VOx-NT.

MACHINING OF MMCs: A REVIEW

Over the last few decades, Metal Matrix Composites (MMCs) have emerged as a material system offering tremendous potential for future applications. The primary advantages offered by these materials are their improved mechanical properties, particularly in the areas of wear, strength and stiffness. Of the MMCs, Aluminum matrix composites have grown in prominence due to their low density, low melting point and low cost. However, machining these materials remains a challenging task mainly due to the high abrasiveness of the reinforcing phases. Conventional machining processes such as turning, milling or drilling are adopted for machining MMCs. In this article, the existing and ongoing developments in machining MMCs vis-a-vis tool life, tool wear, machinability and understanding chip formation mechanism have been highlighted. Most of the studies discussed in this review will focus on Aluminum matrix composites. Certain areas of machining studies which have hitherto not been investigated have also been detailed.

Dynamic mechanism design for markets with strategic resources

The assignment of tasks to multiple resources becomes an interesting game theoretic problem, when both the task owner and the resources are strategic. In the classical, nonstrategic setting, where the states of the tasks and resources are observable by the controller, this problem is that of finding an optimal policy for a Markov decision process (MDP). When the states are held by strategic agents, the problem of an efficient task allocation extends beyond that of solving an MDP and becomes that of designing a mechanism. Motivated by this fact, we propose a general mechanism which decides on an allocation rule for the tasks and resources and a payment rule to incentivize agents' participation and truthful reports. In contrast to related dynamic strategic control problems studied in recent literature, the problem studied here has interdependent values: the benefit of an allocation to the task owner is not simply a function of the characteristics of the task itself and the allocation, but also of the state of the resources. We introduce a dynamic extension of Mezzetti's two phase mechanism for interdependent valuations. In this changed setting, the proposed dynamic mechanism is efficient, within period ex-post incentive compatible, and within period ex-post individually rational.

SuSeFLAV 1.2: Program for supersymmetric mass spectra with seesaw mechanism and rare lepton flavor violating decays

Accurate supersymmetric spectra are required to confront data from direct and indirect searches of supersymmetry. SuSeFLAV is a numerical tool capable of computing supersymmetric spectra precisely for various supersymmetric breaking scenarios applicable even in the presence of flavor violation. The program solves MSSM RGEs with complete 3 x 3 flavor mixing at 2-loop level and one loop finite threshold corrections to all MSSM parameters by incorporating radiative electroweak symmetry breaking conditions. The program also incorporates the Type-I seesaw mechanism with three massive right handed neutrinos at user defined mass scales and mixing. It also computes branching ratios of flavor violating processes such as l(j) -> l(i)gamma, l(j) -> 3 l(i), b -> s gamma and supersymmetric contributions to flavor conserving quantities such as (g(mu) - 2). A large choice of executables suitable for various operations of the program are provided. Program summary Program title: SuSeFLAV Catalogue identifier: AEOD_v1_0 Program summary URL: http://cpc.cs.qub.ac.uk/summaries/AEOD_v1_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: GNU General Public License No. of lines in distributed program, including test data, etc.: 76552 No. of bytes in distributed program, including test data, etc.: 582787 Distribution format: tar.gz Programming language: Fortran 95. Computer: Personal Computer, Work-Station. Operating system: Linux, Unix. Classification: 11.6. Nature of problem: Determination of masses and mixing of supersymmetric particles within the context of MSSM with conserved R-parity with and without the presence of Type-I seesaw. Inter-generational mixing is considered while calculating the mass spectrum. Supersymmetry breaking parameters are taken as inputs at a high scale specified by the mechanism of supersymmetry breaking. RG equations including full inter-generational mixing are then used to evolve these parameters up to the electroweak breaking scale. The low energy supersymmetric spectrum is calculated at the scale where successful radiative electroweak symmetry breaking occurs. At weak scale standard model fermion masses, gauge couplings are determined including the supersymmetric radiative corrections. Once the spectrum is computed, the program proceeds to various lepton flavor violating observables (e.g., BR(mu -> e gamma), BR(tau -> mu gamma) etc.) at the weak scale. Solution method: Two loop RGEs with full 3 x 3 flavor mixing for all supersymmetry breaking parameters are used to compute the low energy supersymmetric mass spectrum. An adaptive step size Runge-Kutta method is used to solve the RGEs numerically between the high scale and the electroweak breaking scale. Iterative procedure is employed to get the consistent radiative electroweak symmetry breaking condition. The masses of the supersymmetric particles are computed at 1-loop order. The third generation SM particles and the gauge couplings are evaluated at the 1-loop order including supersymmetric corrections. A further iteration of the full program is employed such that the SM masses and couplings are consistent with the supersymmetric particle spectrum. Additional comments: Several executables are presented for the user. Running time: 0.2 s on a Intel(R) Core(TM) i5 CPU 650 with 3.20 GHz. (c) 2012 Elsevier B.V. All rights reserved.

Mechanism for the Compressive Strain Induced Oscillations in the Conductance of Carbon Nanotubes

We report on the monotonic increase and the oscillation of electrical conductance in multiwalled carbon nanotubes with compressive strain. Combined experimental and theoretical analyses confirm that the conductance variation with strain is because of the transition from sp(2) to configurations that are promoted by the interaction of walls in the nanotubes. The intrawall interaction is the reason for the monotonic increase in the conduction, while the oscillations are attributable to interwall interactions. This explains the observed electromechanical oscillation in multiwalled nanotubes and its absence in single-walled nanotubes, thereby resolving a long-standing debate on the interpretation of these results. Moreover, the current carrying capability of nanotubes can be enhanced significantly by controlling applied strains. DOI: 10.1103/PhysRevLett.110.095504

On the mechanism and the length scales involved in the ductile fracture of a bulk metallic glass

Some bulk metallic glasses (BMGs) exhibit high crack initiation toughness due to shear band mediated plastic flow at the crack tip and yet do not display additional resistance to crack growth due to the lack of a microstructure. Thus, at crack initiation, the fracture behavior of BMGs transits from that of ductile alloys to that of brittle ceramics. In this paper, we attempt to understand the physics behind the characteristic length from the notch root at which this transition occurs, through testing of four-point bend specimens made of a nominally ductile Zr-based BMG in three different structural states. In the as-cast state, both symmetric (mode I) and asymmetric (mixed mode) bend specimens are tested. The process of shear band mediated plastic flow followed by crack initiation at the notch root was monitored through in situ imaging. Results show that stable crack growth occurs inside a dominant shear band through a distance of, similar to 60 mu m, irrespective of the structural state and mode mixity, before attaining criticality. Detailed finite element simulations show that this length corresponds to the distance from the notch root over which a positive hydrostatic stress gradient prevails. The mean ridge heights on fractured surfaces are found to correlate with the toughness of the BMG. The Argon and Salama model, which is based on the meniscus instability phenomenon at the notch root, is modified to explain the experimentally observed physics of fracture in ductile BMGs. (C) 2012 Acta Materialia Inc. Published by Elsevier Ltd. All rights reserved.

Mycobacterium tuberculosis mutT1 (Rv2985) and ADPRase (Rv1700) proteins constitute a two-stage mechanism of 8-Oxo-dGTP and 8-Oxo-GTP detoxification and adenosine to cytidine mutation avoidance

Approximately one third of the world population is infected with Mycobacterium tuberculosis, the causative agent of tuberculosis. A better understanding of the pathogen biology is crucial to develop new tools/strategies to tackle its spread and treatment. In the host macrophages, the pathogen is exposed to reactive oxygen species, known to damage dGTP and GTP to 8-oxo-dGTP and 8-oxo-GTP, respectively. Incorporation of the damaged nucleotides in nucleic acids is detrimental to organisms. MutT proteins, belonging to a class of Nudix hydrolases, hydrolyze 8-oxo-G nucleoside triphosphates/diphosphates to the corresponding nucleoside monophosphates and sanitize the nucleotide pool. Mycobacteria possess several MutT proteins. However, a functional homolog of Escherichia coli MutT has not been identified. Here, we characterized MtuMutT1 and Rv1700 proteins of M. tuberculosis. Unlike other MutT proteins, MtuMutT1 converts 8-oxo-dGTP to 8-oxo-dGDP, and 8-oxo-GTP to 8-oxo-GDP. Rv1700 then converts them to the corresponding nucleoside monophosphates. This observation suggests the presence of a two-stage mechanism of 8-oxo-dGTP/8-oxo-GTP detoxification in mycobacteria. MtuMutT1 converts 8-oxo-dGTP to 8-oxo-dGDP with a K-m of similar to 50 mu M and V-max of similar to 0.9 pmol/min per ng of protein, and Rv1700 converts 8-oxo-dGDP to 8-oxo-dGMP with a K-m of similar to 9.5 mu M and V-max of similar to 0.04 pmol/min per ng of protein. Together, MtuMutT1 and Rv1700 offer maximal rescue to E. coli for its MutT deficiency by decreasing A to C mutations (a hallmark of MutT deficiency). We suggest that the concerted action of MtuMutT1 and Rv1700 plays a crucial role in survival of bacteria against oxidative stress.