Identification of key amino acid residues in the catalytic mechanism of diaminopropionate ammonialyase from Salmonella typhimurium

Diaminopropionate ammonialyase (DAPAL), a fold-typeII pyridoxal 5-phosphate-dependent enzyme, catalyzes the ,-elimination of diaminopropionate (DAP) to pyruvate and ammonia. DAPAL was able to utilize both d- and l-DAP as substrates with almost equal efficiency. Mutational analysis of functionally important residues such as Thr385, Asp125 and Asp194 was carried out to understand the mechanism by which the isomers are hydrolyzed. Further, the putative residues involved in the formation of disulfide bond Cys271 and Cys299 were also mutated. T385S, T385D sDAPAL were as active with dl-DAP as substrate as sDAPAL, whereas the later exhibited a threefold increase in catalytic efficiency with d-Ser as substrate. Further analysis of these mutants suggested that DAPAL might follow an anti-E-2 mechanism of catalysis that does not involve the formation of a quinonoid intermediate. Of the two mutants of Asp125, D125E showed complete loss of activity with d-DAP as substrate, whereas the reaction with l-DAP was not affected significantly, demonstrating that Asp125 was essential for abstraction of protons from the d-isomer. By contrast, mutational analysis of Asp194 showed that the residue may not be directly involved in proton abstraction from l-DAP. sDAPAL does not form a disulfide bond in solution, although the position of Cys299 and Cys271 in the modeled structure of sDAPAL favored the formation of a disulfide bond. Further, unlike eDAPAL, sDAPAL could be activated by monovalent cations. Mutation of the cysteine residues showed that Cys271 may be involved in coordinating the monovalent cation, as observed in the case of other fold-typeII enzymes.

Generating Efficient Data Movement Code for Heterogeneous Architectures with Distributed-Memory

Programming for parallel architectures that do not have a shared address space is extremely difficult due to the need for explicit communication between memories of different compute devices. A heterogeneous system with CPUs and multiple GPUs, or a distributed-memory cluster are examples of such systems. Past works that try to automate data movement for distributed-memory architectures can lead to excessive redundant communication. In this paper, we propose an automatic data movement scheme that minimizes the volume of communication between compute devices in heterogeneous and distributed-memory systems. We show that by partitioning data dependences in a particular non-trivial way, one can generate data movement code that results in the minimum volume for a vast majority of cases. The techniques are applicable to any sequence of affine loop nests and works on top of any choice of loop transformations, parallelization, and computation placement. The data movement code generated minimizes the volume of communication for a particular configuration of these. We use a combination of powerful static analyses relying on the polyhedral compiler framework and lightweight runtime routines they generate, to build a source-to-source transformation tool that automatically generates communication code. We demonstrate that the tool is scalable and leads to substantial gains in efficiency. On a heterogeneous system, the communication volume is reduced by a factor of 11X to 83X over state-of-the-art, translating into a mean execution time speedup of 1.53X. On a distributed-memory cluster, our scheme reduces the communication volume by a factor of 1.4X to 63.5X over state-of-the-art, resulting in a mean speedup of 1.55X. In addition, our scheme yields a mean speedup of 2.19X over hand-optimized UPC codes.

Parallel Flow-Sensitive Pointer Analysis by Graph-Rewriting

Precise pointer analysis is a problem of interest to both the compiler and the program verification community. Flow-sensitivity is an important dimension of pointer analysis that affects the precision of the final result computed. Scaling flow-sensitive pointer analysis to millions of lines of code is a major challenge. Recently, staged flow-sensitive pointer analysis has been proposed, which exploits a sparse representation of program code created by staged analysis. In this paper we formulate the staged flow-sensitive pointer analysis as a graph-rewriting problem. Graph-rewriting has already been used for flow-insensitive analysis. However, formulating flow-sensitive pointer analysis as a graph-rewriting problem adds additional challenges due to the nature of flow-sensitivity. We implement our parallel algorithm using Intel Threading Building Blocks and demonstrate considerable scaling (upto 2.6x) for 8 threads on a set of 10 benchmarks. Compared to the sequential implementation of staged flow-sensitive analysis, a single threaded execution of our implementation performs better in 8 of the benchmarks.

Photoluminescence, thermoluminescence and EPR studies of solvothermally derived Ni2+ doped Y(OH)(3) and Y2O3 multi-particle-chain microrods

Rod like structures of hexagonal Y(OH)(3):Ni2+ and cubic Y2O3:Ni2+ phosphors have been successfully synthesized by solvothermal method. X-ray diffraction studies of as-formed product shows hexagonal phase, whereas the product heat treated at 700 degrees C shows pure cubic phase. Scanning electron micrographs (SEM) of Y(OH)(3):Ni2+ show hexagonal rods while Y2O3:Ni2+ rods were found to consist of many nanoparticles stacked together forming multi-particle-chains. EPR studies suggest that the site symmetry around Ni2+ ions is predominantly octahedral. PL spectra show emission in blue, green and red regions due to the T-3(1)(P-3)->(3)A(2)(F-3), T-1(2)(D-1)->(3)A(2)(F-3) and T-1(2)(D-1)-> T-3(2)(F-3) transitions of Ni2+ ions, respectively. TL studies were carried out for Y(OH)(3):Ni2+ and Y2O3:Ni2+ phosphor upon gamma-dose for 1-6 kGy. A single well resolved glow peaks at 195 and 230 degrees C were recorded for Y(OH)(3):Ni2+ and Y2O3:Ni2+, respectively. The glow peak intensity increases linearly up to 4 kGy and 5 kGy for Y(OH)(3):Ni2+ and Y2O3:Ni2+, respectively. The kinetic parameters such as activation energy (E), frequency factor (s) and order of kinetics (b) were estimated by different methods. The phosphor follows simple glow peak structure, linear response with gamma dose, low fading and simple trap distribution, suggesting that it is quite suitable for radiation dosimetry. (C) 2014 Elsevier B.V. All rights reserved.

Synthesis and photoluminescence properties of a novel Sr2CeO4:Dy3+ nanophosphor with enhanced brightness by Li+ co-doping

A series of Dy3+ (0.5-9 mol%) and Li+ (0.5-3 mol%) co-doped strontium cerate (Sr2CeO4) nanopowders are synthesized by low temperature solution combustion synthesis. The effects of Li+ doping on the crystal structure, chemical composition, surface morphology and photoluminescence properties are investigated. The X-ray diffraction results confirm that all the samples calcined at 900 degrees C show the pure orthorhombic (Pbam) phase. Scanning electron microscopy analysis reveals that the particles adopt irregular morphology and the porous nature of the product. Room temperature photoluminescence results indicate that the phosphor can be effectively excited by near UV radiation (290 to 390 nm) which results in the blue (484 nm) and yellow (575 nm) emission. Furthermore, PL emission intensity and wavelength are highly dependent on the concentration of Li+ doping. The emission intensity is enhanced by similar to 3 fold with Li+ doping. White light is achieved by merely varying dopant concentration. The colour purity of the phosphor is confirmed by CIE co-ordinates (x = 0.298, y = 0.360). The study demonstrates a simple and efficient method for the synthesis of novel nanophosphors with enhanced white emission.

Salts of hexamethylenetetramine with organic acids: Enhanced anomeric interactions with a lowering of molecular symmetry revealed by crystal structures

The hexamethylenetetramine (HMT) framework displays interesting stereoelectronic interactions of the anomeric type. In the highly symmetrical parent system, the nitrogen centres act as both donors and acceptors. Protonation lowers symmetry and also leads to an enhancement of the anomeric interaction around the protonated centre. X-ray diffraction crystal structures of four derivatives of HMT - with succinic, (DL)-malic, phthalic and 4-hydroxybenzoic acids - reveal significant trends. (The first three form well-defined salts, 4-hydroxybenzoic acid forming a co-crystalline compound.) Each molecular structure is essentially characterised by a major anomeric interaction involving the protonated centre as acceptor. In two cases (succinic and 4-hydroxybenzoic), secondary protonation leads to a weaker anomeric interaction site that apparently competes with the dominant one. Bond length changes indicate that the anomeric interaction decreases as malic > phthalic > succinic > 4-hydroxybenzoic, which correlates with the degree of proton transfer to the nitrogen centre. Along with other bond length and angle changes, the results offer insight into the applicability of the antiperiplanar lone pair hypothesis (ALPH) in a rigid system. (C) 2014 Elsevier B.V. All rights reserved.

Salts of hexamethylenetetramine with organic acids: Enhanced anomeric interactions with a lowering of molecular symmetry revealed by crystal structures

The hexamethylenetetramine (HMT) framework displays interesting stereoelectronic interactions of the anomeric type. In the highly symmetrical parent system, the nitrogen centres act as both donors and acceptors. Protonation lowers symmetry and also leads to an enhancement of the anomeric interaction around the protonated centre. X-ray diffraction crystal structures of four derivatives of HMT - with succinic, (DL)-malic, phthalic and 4-hydroxybenzoic acids - reveal significant trends. (The first three form well-defined salts, 4-hydroxybenzoic acid forming a co-crystalline compound.) Each molecular structure is essentially characterised by a major anomeric interaction involving the protonated centre as acceptor. In two cases (succinic and 4-hydroxybenzoic), secondary protonation leads to a weaker anomeric interaction site that apparently competes with the dominant one. Bond length changes indicate that the anomeric interaction decreases as malic > phthalic > succinic > 4-hydroxybenzoic, which correlates with the degree of proton transfer to the nitrogen centre. Along with other bond length and angle changes, the results offer insight into the applicability of the antiperiplanar lone pair hypothesis (ALPH) in a rigid system. (C) 2014 Elsevier B.V. All rights reserved.

Hydrodynamic instability and shear layer effect on the response of an acoustically excited laminar premixed flame

Combustion instabilities can cause serious problems which limit the operating envelope of low-emission lean premixed combustion systems. Predicting the onset of combustion instability requires a description of the unsteady heat release driving the instability, i.e., the heat release response transfer function of the system. This study focuses on the analysis of fully coupled two-way interactions between a disturbance field and a laminar premixed flame that incorporates gas expansion effects by solving the conservation equations of a compressible fluid. Results of the minimum and maximum flame front deflections are presented to underline the impact of the hydrodynamic instability on the flame and the shear layer effect on the initial flame front wrinkling which is increased at decreasing gas expansion. These phenomena influence the magnitude of the burning area and burning area rate response of the flame at lower frequency excitation more drastically than reduced-order model (ROM) predictions even for low temperature ratios. It is shown that the general trend of the flame response magnitudes can be well captured at higher frequency excitation, where stretch effects are dominant. The phase response is influenced by the DL mechanism, which cannot be captured by the ROM, and by the resulting discrepancy in the flame pocket formation and annihilation process at the flame tip. (C) 2014 The Combustion Institute. Published by Elsevier Inc. All rights reserved,

Low frequency modulation of jets in quasigeostrophic turbulence

Quasigeostrophic turbulence on a beta-plane with a finite deformation radius is studied numerically, with particular emphasis on frequency and combined wavenumber-frequency domain analyses. Under suitable conditions, simulations with small-scale random forcing and large-scale drag exhibit a spontaneous formation of multiple zonal jets. The first hint of wave-like features is seen in the distribution of kinetic energy as a function of frequency; specifically, for progressively larger deformation scales, there are systematic departures in the form of isolated peaks (at progressively higher frequencies) from a power-law scaling. Concomitantly, there is an inverse flux of kinetic energy in frequency space which extends to lower frequencies for smaller deformation scales. The identification of these peaks as Rossby waves is made possible by examining the energy spectrum in frequency-zonal wavenumber and frequency-meridional wavenumber diagrams. In fact, the modified Rhines scale turns out to be a useful measure of the dominant meridional wavenumber of the modulating Rossby waves; once this is fixed, apart from a spectral peak at the origin (the steady jet), almost all the energy is contained in westward propagating disturbances that follow the theoretical Rossby dispersion relation. Quite consistently, noting that the zonal scale of the modulating waves is restricted to the first few wavenumbers, the energy spectrum is almost entirely contained within the corresponding Rossby dispersion curves on a frequency-meridional wavenumber diagram. Cases when jets do not form are also considered; once again, there is a hint of Rossby wave activity, though the spectral peaks are quite muted. Further, the kinetic energy scaling in frequency domain follows a -5/3 power-law and is distributed much more broadly in frequency-wavenumber diagrams. (C) 2015 AIP Publishing LLC.

Lobe-specific Expression of Phosphodiesterase 5 in Rat Prostate

OBJECTIVE To investigate the level and location of phosphodiesterase 5 (PDE5) expression in rat prostate. METHODS The ventral, dorsal, and lateral lobes of rat prostate were examined for PDE5 expression by Western blotting. Intact rat urogenital complex, including the urinary bladder and accessory reproductive glands, was examined for PDE5 expression by immunohistochemistry. Individual prostatic lobes were further examined by immunofluorescence for expression of PDE5, alpha-smooth muscle actin, and rat endothelial cell antigen. RESULTS Western blot analysis showed that PDE5 was expressed at a significantly lower level in dorsal lobe (DL) than in ventral lobe (VL) or lateral lobe (LL). Immunohistochemistry and immunofluorescence analyses showed that PDE5 was expressed in both acinar epithelium and periacinar smooth muscle. However, although similar levels of smooth muscle PDE5 expression were observed in all 3 prostatic lobes, significantly lower level of epithelial PDE5 expression was found in DL compared with VL or LL. In prostatic blood vessels, PDE5 expression was clearly visible in the endothelium but not as easily detectable in the smooth muscle. CONCLUSION PDE5 was expressed in the acinar epithelium and periacinar smooth muscle of rat prostate. However, the epithelial PDE5 expression was significantly less in DL than in VL or LL. Regardless, the acinar wall, not the blood vessel wall, is the predominant PDE5 expression site in rat prostate. (C) 2015 Elsevier Inc.

Interferon-Gamma and Nitric Oxide Synthase 2 Mediate the Aggregation of Resident Adherent Peritoneal Exudate Cells: Implications for the Host Response to Pathogens

Interferon-gamma (Ifn gamma), a key macrophage activating cytokine, plays pleiotropic roles in host immunity. In this study, the ability of Ifn gamma to induce the aggregation of resident mouse adherent peritoneal exudate cells (APECs), consisting primarily of macrophages, was investigated. Cell-cell interactions involve adhesion molecules and, upon addition of Ifn gamma, CD11b re-localizes preferentially to the sites of interaction on APECs. A functional role of CD11b in enhancing aggregation is demonstrated using Reopro, a blocking reagent, and siRNA to Cd11b. Studies with NG-methyl-L-arginine (LNMA), an inhibitor of Nitric oxide synthase (Nos), NO donors, e.g., S-nitroso-N-acetyl-DL-penicillamine (SNAP) or Diethylenetriamine/ nitric oxide adduct (DETA/NO), and Nos2(-/-) mice identified Nitric oxide (NO) induced by Ifn gamma as a key regulator of aggregation of APECs. Further studies with Nos2(-/-) APECs revealed that some Ifn. responses are independent of NO: induction of MHC class II and CD80. On the other hand, Nos2 derived NO is important for other functions: motility, phagocytosis, morphology and aggregation. Studies with cytoskeleton depolymerizing agents revealed that Ifn gamma and NO mediate the cortical stabilization of Actin and Tubulin which contribute to aggregation of APECs. The biological relevance of aggregation of APECs was delineated using infection experiments with Salmonella Typhimurium (S. Typhimurium). APECs from orally infected, but not uninfected, mice produce high amounts of NO and aggregate upon ex vivo culture in a Nos2-dependent manner. Importantly, aggregated APECs induced by Ifn gamma contain fewer intracellular S. Typhimurium compared to their single counterparts post infection. Further experiments with LNMA or Reopro revealed that both NO and CD11b are important for aggregation; in addition, NO is bactericidal. Overall, this study elucidates novel roles for Ifn gamma and Nos2 in regulating Actin, Tubulin, CD11b, motility and morphology during the aggregation response of APECs. The implications of aggregation or ``group behavior'' of APECs are discussed in the context of host resistance to infectious organisms.

Identification of key amino acid residues in the catalytic mechanism of diaminopropionate ammonialyase from Salmonella typhimurium

Diaminopropionate ammonialyase (DAPAL), a fold-typeII pyridoxal 5-phosphate-dependent enzyme, catalyzes the ,-elimination of diaminopropionate (DAP) to pyruvate and ammonia. DAPAL was able to utilize both d- and l-DAP as substrates with almost equal efficiency. Mutational analysis of functionally important residues such as Thr385, Asp125 and Asp194 was carried out to understand the mechanism by which the isomers are hydrolyzed. Further, the putative residues involved in the formation of disulfide bond Cys271 and Cys299 were also mutated. T385S, T385D sDAPAL were as active with dl-DAP as substrate as sDAPAL, whereas the later exhibited a threefold increase in catalytic efficiency with d-Ser as substrate. Further analysis of these mutants suggested that DAPAL might follow an anti-E-2 mechanism of catalysis that does not involve the formation of a quinonoid intermediate. Of the two mutants of Asp125, D125E showed complete loss of activity with d-DAP as substrate, whereas the reaction with l-DAP was not affected significantly, demonstrating that Asp125 was essential for abstraction of protons from the d-isomer. By contrast, mutational analysis of Asp194 showed that the residue may not be directly involved in proton abstraction from l-DAP. sDAPAL does not form a disulfide bond in solution, although the position of Cys299 and Cys271 in the modeled structure of sDAPAL favored the formation of a disulfide bond. Further, unlike eDAPAL, sDAPAL could be activated by monovalent cations. Mutation of the cysteine residues showed that Cys271 may be involved in coordinating the monovalent cation, as observed in the case of other fold-typeII enzymes.

One pot auto-ignition based synthesis of novel Sr2CeO4: Ho3+ nanophosphor for photoluminescent applications

Ho3+ (0.25-7 mol%) doped Sr2CeO4 nanophosphors were synthesized by solution combustion method using urea as fuel. The structural properties of the nanophosphors were investigated by powder X-ray diffraction studies (PXRD), scanning electron microscopy (SEM) and transmission electron microscopy (TEM) techniques. UV-Visible and photoluminescence (PL) spectroscopic techniques were used for analysing the optical properties of the nanoparticles. PXRD and TEM results revealed the formation of Sr2CeO4: Ho3+ nanocrystalline particles with orthorhombic crystal structure. From the UV-Vis studies the optical band gap energy found to decrease from 5.9 to 5.74 eV with increase in dopant concentration. The PL spectra exhibit the broad excitation band from 200 to 400 nm which concurs well with the commercial near UV LED. The PL spectra vary with the dopant content due to energy transfer from the host to the activator. In this present work we demonstrate that color tuning of phosphor can be achieved by merely varying the Ho3+ ions concentration. The CIE and CCT chromaticity coordinates suggests Sr2CeO4: Ho3+ nanophosphors may be potentially applicable as promising single - phased phosphors for lighting applications. (C) 2015 Elsevier B.V. All rights reserved.

基于PROFIBUS-DP的激光加工系统数字化控制

提出采用PROFIBUS-DP现场总线技术实现对激光柔性加工系统的数字化控制，给出了控制实现过程中的DL动态链接库方案，详述了控制中的同步问题，并将其应用于汽车覆盖件模具激光表面硬化，编程采用VC++面向对象工具加以实现。