Functional analysis of the large periplasmic loop of the Escherichia coli K-12 WaaL O-antigen ligase

WaaL is a membrane enzyme implicated in ligating undecaprenyl-diphosphate (Und-PP)-linked O antigen to lipid A-core oligosaccharide. We determined the periplasmic location of a large (EL5) and small (EL4) adjacent loops in the Escherichia coli K-12 WaaL. Structural models of the EL5 from the K-12, R1 and R4 E. coli ligases were generated by molecular dynamics. Despite the poor amino acid sequence conservation among these proteins, the models afforded similar folds consisting of two pairs of almost perpendicular alpha-helices. One alpha-helix in each pair contributes a histidine and an arginine facing each other, which are highly conserved in WaaL homologues. Mutations in either residue rendered WaaL non-functional, since mutant proteins were unable to restore O antigen surface expression. Replacements of residues located away from the putative catalytic centre and non-conserved residues within the centre itself did not affect ligation. Furthermore, replacing a highly conserved arginine in EL4 with various amino acids inactivates WaaL function, but functionality reappears when the positive charge is restored by a replacement with lysine. These results lead us to propose that the conserved amino acids in the two adjacent periplasmic loops could interact with Und-PP, which is the common component in all WaaL substrates.

Functional characterization and membrane topology of Escherichia coli WecA, a sugar-phosphate transferase initiating the biosynthesis of enterobacterial common antigen and O-antigen lipopolysaccharide

WecA is an integral membrane protein that initiates the biosynthesis of enterobacterial common antigen and O-antigen lipopolysaccharide (LPS) by catalyzing the transfer of N-acetylglucosamine (GlcNAc)-1-phosphate onto undecaprenyl phosphate (Und-P) to form Und-P-P-GlcNAc. WecA belongs to a large family of eukaryotic and prokaryotic prenyl sugar transferases. Conserved aspartic acids in putative cytoplasmic loops 2 (Asp90 and Asp91) and 3 (Asp156 and Asp159) were targeted for replacement mutagenesis with either glutamic acid or asparagine. We examined the ability of each mutant protein to complement O-antigen LPS synthesis in a wecA-deficient strain and also determined the steady-state kinetic parameters of the mutant proteins in an in vitro transfer assay. Apparent K(m) and V(max) values for UDP-GlcNAc, Mg(2+), and Mn(2+) suggest that Asp156 is required for catalysis, while Asp91 appears to interact preferentially with Mg(2+), possibly playing a role in orienting the substrates. Topological analysis using the substituted cysteine accessibility method demonstrated the cytosolic location of Asp90, Asp91, and Asp156 and provided a more refined overall topological map of WecA. Also, we show that cells expressing a WecA derivative C terminally fused with the green fluorescent protein exhibited a punctate distribution of fluorescence on the bacterial surface, suggesting that WecA localizes to discrete regions in the bacterial plasma membrane.

Conserved aspartic acids are essential for the enzymic activity of the WecA protein initiating the biosynthesis of O-specific lipopolysaccharide and enterobacterial common antigen in Escherichia coli

The integral membrane protein WecA mediates the transfer of N-acetylglucosamine (GlcNAc) 1-phosphate to undecaprenyl phosphate (Und-P) with the formation of a phosphodiester bond. Bacteria employ this reaction during the biosynthesis of enterobacterial common antigen as well as of many O-specific lipopolysaccharides (LPSs). Alignment of a number of prokaryotic and eukaryotic WecA-homologous sequences identified a number of conserved aspartic acid (D) residues in putative cytoplasmic loops II and III of the inner-membrane protein. Site-directed mutagenesis was used to study the role of the conserved residues D90, D91 (loop II), D156 and D159 (loop III). As controls, D35, D94 and D276 were also mutagenized. The resulting WecA derivatives were assessed for function by complementation analysis of O-antigen biosynthesis, by the ability to incorporate radiolabelled precursor to a biosynthetic intermediate, by detection of the terminal GlcNAc residue in LPS and by a tunicamycin competition assay. It was concluded from these analyses that the conserved aspartic acid residues are functionally important, but also that they participate differently in the transfer reaction. Based on these results it is proposed that D90 and D91 are important in forwarding the reaction product to the next biosynthetic step, while D156 and D159 are a part of the catalytic site of the enzyme.

Conformational Dynamics of the Human Propeller Telomeric DNA Quadruplex on a Microsecond Time Scale

The human telomeric DNA sequence with four repeats can fold into a parallel-stranded propeller-type topology. NMR structures solved under molecular crowding experiments correlate with the crystal structures found with crystal-packing interactions that are effectively equivalent to molecular crowding. This topology has been used for rationalization of ligand design and occurs experimentally in a number of complexes with a diversity of ligands, at least in the crystalline state. While G-quartet stems have been well characterised, the interactions of the TTA loop with the G-quartets are much less defined. To better understand the conformational variability and structural dynamics of the propeller-type topology, we performed molecular dynamics simulations in explicit solvent up to 1.5 µs. The analysis provides a detailed atomistic account of the dynamic nature of the TTA loops highlighting their interactions with the G-quartets including formation of an A:A base pair, triad, pentad and hexad. The results present a threshold in quadruplex simulations, with regards to understanding the flexible nature of the sugar-phosphate backbone in formation of unusual architecture within the topology. Furthermore, this study stresses the importance of simulation time in sampling conformational space for this topology.

Pipelined two-port adaptor for wave digital filtering

The application of fine-grain pipelining techniques in the design of high-performance wave digital filters (WDFs) is described. The problems of latency in feedback loops can be significantly reduced if computations are organized most significant, as opposed to least significant, bit first and if the results are fed back as soon as they are formed. The result is that chips can be designed which offer significantly higher sampling rates than otherwise can be obtained using conventional methods. How these concepts can be extended to the more challenging problem of WDFs is discussed. It is shown that significant increases in the sampling rate of bit-parallel circuits can be achieved using most significant bit first arithmetic.

Ionically-Mediated Electromechanical Hysteresis in Transition Metal Oxides

Nanoscale electromechanical activity, remanent polarization states, and hysteresis loops in paraelectric TiO2 and SrTiO3 thin films are observed using scanning probe microscopy. The coupling between the ionic dynamics and incipient ferroelectricity in these materials is analyzed using extended Landau-Ginzburg-Devonshire (LGD) theory. The possible origins of electromechanical coupling including ionic dynamics, surface-charge induced electrostriction, and ionically induced ferroelectricity are identified. For the latter, the ionic contribution can change the sign of first order LGD expansion coefficient, rendering material effectively ferroelectric. The lifetime of these ionically induced ferroelectric states is then controlled by the transport time of the mobile ionic species and well above that of polarization switching. These studies provide possible explanation for ferroelectric-like behavior in centrosymmetric transition metal oxides.

Variable temperature electrochemical strain microscopy of Sm-doped ceria

Variable temperature electrochemical strain microscopy has been used to study the electrochemical activity of Sm-doped ceria as a function of temperature and bias. The electrochemical strain microscopy hysteresis loops have been collected across the surface at different temperatures and the relative activity at different temperatures has been compared. The relaxation behavior of the signal at different temperatures has been also evaluated to relate kinetic process during bias induced electrochemical reactions with temperature and two different kinetic regimes have been identified. The strongly non-monotonic dependence of relaxation behavior on temperature is interpreted as evidence for water-mediated mechanisms.

Probing Ferroelectrics Using Optical Second Harmonic Generation

Nonlinear optics is an essential component of modern laser systems and optoelectronic devices. It has also emerged as an important tool in probing the electronic, vibrational, magnetic, and crystallographic structure of materials ranging from oxides and metals, to polymers and biological samples. This review focuses on the specific technique of optical second harmonic generation (SHG), and its application in probing ferroelectric complex oxide crystals and thin films. As the dominant SHG interaction mechanism exists only in materials that lack inversion symmetry, SHG is a sensitive probe of broken inversion symmetry, and thus also of bulk polar phenomena in materials. By performing in-situ SHG polarimetry experiments in different experimental conditions such as sample orientation, applied electric field, and temperature, one can probe ferroelectric hysteresis loops and phase transitions. Careful modeling of the polarimetry data allows for the determination of the point group symmetry of the crystal. In epitaxial thin films with a two-dimensional arrangement of well-defined domain orientations, one can extract information about intrinsic material properties such as nonlinear coefficients, as well as microstructural information such as the local statistics of the different domain variants being probed. This review presents several detailed examples of ferroelectric systems where such measurements and modeling are performed. The use of SHG microscopic imaging is discussed, and its ability to reveal domain structures and phases not normally visible with linear optics is illustrated.

Accelerating code on multi-cores with FastFlow

FastFlow is a programming framework specifically targeting cache-coherent shared-memory multi-cores. It is implemented as a stack of C++ template libraries built on top of lock-free (and memory fence free) synchronization mechanisms. Its philosophy is to combine programmability with performance. In this paper a new FastFlow programming methodology aimed at supporting parallelization of existing sequential code via offloading onto a dynamically created software accelerator is presented. The new methodology has been validated using a set of simple micro-benchmarks and some real applications. © 2011 Springer-Verlag.

Self-Similar Nested Flux Closure Structures in a Tetragonal Ferroelectric

In specific solid-state materials, under the right conditions, collections of magnetic dipoles are known to spontaneously form into a variety of rather complex geometrical patterns, exemplified by vortex and skyrmion structures. While theoretically, similar patterns should be expected to form from electrical dipoles, they have not been clearly observed to date: the need for continued experimental exploration is therefore clear. In this Letter we report the discovery of a rather complex domain arrangement that has spontaneously formed along the edges of a thin single crystal ferroelectric sheet, due to surface-related depolarizing fields. Polarization patterns are such that nanoscale “flux-closure” loops are nested within a larger mesoscale flux closure object. Despite the orders of magnitude differences in size, the geometric forms of the dual-scale flux closure entities are rather similar.

Influence of a Single Grain Boundary on Domain Wall Motion in Ferroelectrics

Epitaxial tetragonal 425 and 611 nm thick Pb(ZrTi)O (PZT) films are deposited by pulsed laser deposition on SrRuO-coated (100) SrTiO 24° tilt angle bicrystal substrates to create a single PZT grain boundary with a well-defined orientation. On either side of the bicrystal boundary, the films show square hysteresis loops and have dielectric permittivities of 456 and 576, with loss tangents of 0.010 and 0.015, respectively. Using piezoresponse force microscopy (PFM), a decrease in the nonlinear piezoelectric response is observed in the vicinity (720-820 nm) of the grain boundary. This region represents the width over which the extrinsic contributions to the piezoelectric response (e.g., those associated with the domain density/configuration and/or the domain wall mobility) are influenced by the presence of the grain boundary. Transmission electron microscope (TEM) images collected near and far from the grain boundary indicate a strong preference for (101)/(1-01) type domain walls at the grain boundary, whereas (011)/(01-1) and (101)/(1-01) are observed away from this region. It is proposed that the elastic strain field at the grain boundary interacts with the ferro-electric/elastic domain structure, stabilizing (101)/(1-01) rather than (011)/(01-1) type domain walls, which inhibits domain wall motion under applied field and decreases non-linearity. © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Twinning anisotropy of tantalum during nanoindentation

Unlike other BCC metals, the plastic deformation of nanocrystalline Tantalum during compression is regulated by deformation twinning. Whether or not this twinning exhibits anisotropy was investigated through simulation of displacement-controlled nanoindentation test using molecular dynamics simulation. MD data was found to correlate well with the experimental data in terms of surface topography and hardness measurements. The mechanism of the transport of material was identified due to the formation and motion of prismatic dislocations loops (edge dislocations) belonging to the 1/2<111> type and <100> type Burgers vector family. Further analysis of crystal defects using a fully automated dislocation extraction algorithm (DXA) illuminated formation and migration of twin boundaries on the (110) and (111) orientation but not on the (010) orientation and most importantly after retraction all the dislocations disappeared on the (110) orientation suggesting twinning to dominate dislocation nucleation in driving plasticity in tantalum. A significant finding was that the maximum shear stress (critical Tresca stress) in the deformation zone exceeded the theoretical shear strength of tantalum (Shear modulus/ 2π~10.03 GPa) on the (010) orientation but was lower than it on the (110) and the (111) orientations. In light to this, the conventional lore of assuming the maximum shear stress being 0.465 times the mean contact pressure was found to break down at atomic scale.

TRACE observations of driven loop oscillations

Aims: On 13 June 1998, the TRACE satellite was fortuitously well placed to observe the effects of a flare-induced EIT wave in the corona, and its subsequent interaction with coronal magnetic loops. In this study, we use these TRACE observations to corroborate previous theoretical work, which determined the response of a coronal loop to a harmonic driver in the context of ideal magnetohydrodynamics, as well as estimate the magnetic field strength and the degree of longitudinal inhomogeneity. Methods: Loop edges are tracked, both spatially and temporally, using wavelet modulus maxima algorithms, with corresponding loop displacements from its quiescent state analysed by fitting scaled sinusoidal functions. The physical parameters of the coronal loop are subsequently determined using seismological techniques. Results: The studied coronal loop is found to oscillate with two distinct periods, 501 ± 5 s and 274 ± 7 s, which could be interpreted as belonging to the fundamental kink mode and first harmonic, or could reflect the stage of an overdriven loop. Additional scenarios for explaining the two periods are listed, each resulting in a different value of the magnetic field and the intrinsic and sub-resolution properties of the coronal loop. When assuming the periods belong to the fundamental kink mode and its first harmonic, we obtain a magnetic field strength inside the oscillating coronal loop of 2.0 ± 0.7 G. In contrast, interpreting the oscillations as a combination of the loop's natural kink frequency and a harmonic EIT wave provides a magnetic field strength of 5.8 ± 1.5 G. Using the ratio of the two periods, we find that the gravitational scale height in the loop is 73 ± 3 Mm. Conclusions: We show that the observation of two distinct periods in a coronal loop does not necessarily lead to a unique conclusion. Multiple plausible scenarios exist, suggesting that both the derived strength of the magnetic field and the sub-resolution properties of the coronal loop depend entirely on which interpretation is chosen. The interpretation of the observations in terms of a combination of the natural kink mode of the coronal loop, driven by a harmonic EIT wave seems to result in values of the magnetic field consistent with previous findings. Other interpretations, which are realistic, such as kink fundamental mode/first harmonic and the oscillations of two sub-resolution threads result in magnetic field strengths that are below the average values found before.

Realizing Accelerated Cost-Effective Distributed RAID

The exponential growth in user and application data entails new means for providing fault tolerance and protection against data loss. High Performance Com- puting (HPC) storage systems, which are at the forefront of handling the data del- uge, typically employ hardware RAID at the backend. However, such solutions are costly, do not ensure end-to-end data integrity, and can become a bottleneck during data reconstruction. In this paper, we design an innovative solution to achieve a flex- ible, fault-tolerant, and high-performance RAID-6 solution for a parallel file system (PFS). Our system utilizes low-cost, strategically placed GPUs — both on the client and server sides — to accelerate parity computation. In contrast to hardware-based approaches, we provide full control over the size, length and location of a RAID array on a per file basis, end-to-end data integrity checking, and parallelization of RAID array reconstruction. We have deployed our system in conjunction with the widely-used Lustre PFS, and show that our approach is feasible and imposes ac- ceptable overhead.

Analysis of VSC-based HVDC System under DC Faults

This paper analyzes the behavior of a Voltage Source Converter Based HVDC system under DC cable fault conditions. The behavior of the HVDC system during a permanent line-to-earth fault is analyzed, outlining the systems configuration and behavior at each stage of the fault timeline. Operation of the proposed system under a single earthing configurations i.e. Converter (solid) earthed/AC transformer unearthed, was analyzed and simulated, with particular attention paid to the converters operation. It was observed that the development of potential earth loops within the system as a result of DC line- toearth faults leads to substantial overcurrent and results in system configuration oscillation.