Stripe domain structure in epitaxial (001) BiFeO3 thin films on orthorhombic TbScO3 substrate

We have analyzed the ferroelastic and ferroelectric domain structure of high crystalline quality (001) BiFeO3 films on orthorhombic (110) TbScO3 substrates. Two domains were present in stripes separated by (010) vertical boundaries, with spontaneous polarizations in adjacent domains rotated by 109 degrees. The striped morphology was caused by nucleation of only two ferroelastic domains on the low symmetry GdFeO3-type substrate. Domain engineering through substrate symmetry is an important finding for rhombohedral ferroelectric epitaxial thin films. The stripe pattern with vertical walls may be useful for extracting domain wall contributions to magnetism and electrical transport properties of BiFeO3 materials.

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.

Local conductance: A means to extract polarization and depolarizing fields near domain walls in ferroelectrics

Conducting atomic force microscopy images of bulk semiconducting BaTiO3 surfaces show clear stripe domain contrast. High local conductance correlates with strong out-of-plane polarization (mapped independently using piezoresponse force microscopy), and current- voltage characteristics are consistent with dipole-induced alterations in Schottky barriers at the metallic tip-ferroelectric interface. Indeed, analyzing current-voltage data in terms of established Schottky barrier models allows relative variations in the surface polarization, and hence the local domain structure, to be determined. Fitting also reveals the signature of surface-related depolarizing fields concentrated near domain walls. Domain information obtained from mapping local conductance appears to be more surface-sensitive than that from piezoresponse force microscopy. In the right materials systems, local current mapping could therefore represent a useful complementary technique for evaluating polarization and local electric fields with nanoscale resolution.

Rasch Analysis of the Daily Living Tasks Dependent on Vision (DLTV)

PURPOSE. To examine internal consistency, refine the response scale, and obtain a linear scoring system for the visual function instrument, the Daily Living Tasks Dependent on Vision (DLTV). METHODS. Data were available from 186 participants with a clinical diagnosis of AMD who completed the 22-item DLTV (DLTV-22) according to four-point ordinal response scale. An independent group of 386 participants with AMD were administered a reduced version of the DLTV with 11 items (DLTV-11), according to a five-point response scale. Rasch analysis was performed on both datasets and used to generate item statistics for measure order, response odds ratios per item and per person, and infit and outfit mean square statistics. The Rasch output from the DLTV-22 was examined to identify redundant items and for factorial validity and person item measure separation reliabilities. RESULTS. The average rating for the DLTV-22 changed monotonically with the magnitude of the latent person trait. The expected versus observed average measures were extremely close, with step calibrations evenly separated for the four-point ordinal scale. In the case of the DLTV-11, step calibrations were not as evenly separated, suggesting that the five-point scale should be reduced to either a four- or three-point scale. Five items in the DLTV-22 were removed, and all 17 remaining items had good infit and outfit mean squares. PCA with residuals from Rasch analysis identified two domains containing 7 and 10 items each. The domains had high person separation reliabilities (0.86 and 0.77 for domains 1 and 2, respectively) and item measure reliabilities (0.99 and 0.98 for domains 1 and 2, respectively). CONCLUSIONS. With the improved internal consistency, establishment of the accuracy and precision of the rating scale for the DLTV and the establishment of a valid domain structure we believe that it constitutes a useful instrument for assessing visual function in older adults with age-related macular degeneration.

RNAi Effector Diversity in Nematodes

While RNA interference (RNAi) has been deployed to facilitate gene function studies in diverse helminths, parasitic nematodes appear variably susceptible. To test if this is due to inter-species differences in RNAi effector complements, we performed a primary sequence similarity survey for orthologs of 77 Caenorhabditis elegans RNAi pathway proteins in 13 nematode species for which genomic or transcriptomic datasets were available, with all outputs subjected to domain-structure verification. Our dataset spanned transcriptomes of Ancylostoma caninum and Oesophagostomum dentatum, and genomes of Trichinella spiralis, Ascaris suum, Brugia malayi, Haemonchus contortus, Meloidogyne hapla, Meloidogyne incognita and Pristionchus pacificus, as well as the Caenorhabditis species C. brenneri, C. briggsae, C. japonica and C. remanei, and revealed that: (i) Most of the C. elegans proteins responsible for uptake and spread of exogenously applied double stranded (ds)RNA are absent from parasitic species, including RNAi-competent plant-nematodes; (ii) The Argonautes (AGOs) responsible for gene expression regulation in C. elegans are broadly conserved, unlike those recruited during the induction of RNAi by exogenous dsRNA; (iii) Secondary Argonautes (SAGOs) are poorly conserved, and the nuclear AGO NRDE-3 was not identified in any parasite; (iv) All five Caenorhabditis spp. possess an expanded RNAi effector repertoire relative to the parasitic nematodes, consistent with the propensity for gene loss in nematode parasites; (v) In spite of the quantitative differences in RNAi effector complements across nematode species, all displayed qualitatively similar coverage of functional protein groups. In summary, we could not identify RNAi effector deficiencies that associate with reduced susceptibility in parasitic nematodes. Indeed, similarities in the RNAi effector complements of RNAi refractory and competent nematode parasites support the broad applicability of this research genetic tool in nematodes.

Distinct functional domains of the Salmonella enterica WbaP transferase that is involved in the initiation reaction for synthesis of the O antigen subunit

WbaP is a membrane enzyme that initiates O antigen synthesis in Salmonella enterica by catalysing the transfer of galactose 1-phosphate (Gal-1-P) onto undecaprenyl phosphate (Und-P). WbaP possesses at least three predicted structural domains: an N-terminal region containing four transmembrane helices, a large central periplasmic loop, and a C-terminal domain containing the last transmembrane helix and a large cytoplasmic tail. In this work, we investigated the contribution of each region to WbaP function by constructing a series of mutant WbaP proteins and using them to complement O antigen synthesis in DeltawbaP mutants of S. enterica serovars Typhi and Typhimurium. Truncated forms of WbaP lacking the periplasmic loop exhibited altered chain-length distributions in O antigen polymerization, suggesting that this central domain is involved in modulating the chain-length distribution of the O polysaccharide. The N-terminal and periplasmic domains were dispensable for complementation of O antigen synthesis in vivo, suggesting that the C-terminal domain carries the sugar-phosphate transferase activity. However, despite the fact that they complemented the synthesis of O antigen in the DeltawbaP mutant in vivo, membrane extracts containing WbaP derivatives without the N-terminal domain failed to transfer radioactive Gal from UDP-Gal into a lipid-rich fraction. These results suggest that the N-terminal region of WbaP, which contains four transmembrane domains, is essential for the insertion or stability of the protein in the bacterial membrane. We propose that the domain structure of WbaP enables this protein not only to function in the transfer of Gal-1-P to Und-P but also to establish critical interactions with additional proteins required for the correct assembly of O antigen in S. enterica.

MFM imaging of micron-sized permalloy ellipses

The magnetic domain structure of micron-sized elliptic permalloy elements has been studied by magnetic force microscope (MFM) measurements, and has been compared to results from micromagnetic simulations. The elements all have the same aspect ratio, whereas the inter-elemental distance has been varied. Both the zero-field states and in field domain configurations have been studied. In zero-applied field, two different stable flux-closure states were found in both the MFM measurements and in the simulations. The different stable domain states occur as a result of minute differences in the local magnetic environment occurring during the demagnetization process. (C) 2004 Elsevier B.V. All rights reserved.

First-Order Reversal Curve Probing of Spatially Resolved Polarization Switching Dynamics in Ferroelectric Nanocapacitors

Spatially resolved polarization switching In ferroelectric nanocapacitors was studied on the sub-25 nm scale using the first-order reversal curve (FORC) method. The chosen capacitor geometry allows both high-veracity observation of the domain structure and mapping of polarization switching in a uniform field, synergistically combining microstructural observations and probing of uniform-field polarization responses as relevant to device operation. A classical Kolmogorov-Avrami-Ishibashi model has been adapted to the voltage domain, and the individual switching dynamics of the FORC response curves are well approximated by the adapted model. The comparison with microstructures suggests a strong spatial variability of the switching dynamics inside the nanocapacitors.

Structure of the adenylation domain of an NAD+-dependent DNA ligase

Background: DNA ligases catalyse phosphodiester bond formation between adjacent bases in nicked DNA, thereby sealing the nick. A key step in the catalytic mechanism is the formation of an adenylated DNA intermediate. The adenyl group is derived from either ATP (in eucaryotes and archaea) or NAD+4 (in bacteria). This difference in cofactor specificity suggests that DNA ligase may be a useful antibiotic target.

Results: The crystal structure of the adenylation domain of the NAD+-dependent DNA ligase from Bacillus stearothermophilus has been determined at 2.8 Å resolution. Despite a complete lack of detectable sequence similarity, the fold of the central core of this domain shares homology with the equivalent region of ATP-dependent DNA ligases, providing strong evidence for the location of the NAD+-binding site.

Conclusions: Comparison of the structure of the NAD+4-dependent DNA ligase with that of ATP-dependent ligases and mRNA-capping enzymes demonstrates the manifold utilisation of a conserved nucleotidyltransferase domain within this family of enzymes. Whilst this conserved core domain retains a common mode of nucleotide binding and activation, it is the additional domains at the N terminus and/or the C terminus that provide the alternative specificities and functionalities in the different members of this enzyme superfamily.

A possible model of benzimidazole binding to beta-tubulin disclosed by invoking an inter-domain movement.

Although it is well established that benzimidazole (BZMs) compounds exert their therapeutic effects through binding to helminth beta-tubulin and thus disrupting microtubule-based processes in the parasites, the precise location of the benzimidazole-binding site on the beta-tubulin molecule has yet to be determined. In the present study, we have used previous experimental data as cues to help identify this site. Firstly, benzimidazole resistance has been correlated with a phenylalanine-to-tyrosine substitution at position 200 of Haemonchus contortus beta-tubulin isotype-I. Secondly, site-directed mutagenesis studies, using fungi, have shown that other residues in this region of the protein can influence the interaction of benzimidazoles with beta-tubulin. However, the atomic structure of the alphabeta-tubulin dimer shows that residue 200 and the other implicated residues are buried within the protein. This poses the question: how might benzimidazoles interact with these apparently inaccessible residues? In the present study, we present a mechanism by which those residues generally believed to interact with benzimidazoles may become accessible to the drugs. Furthermore, by docking albendazole-sulphoxide into a modelled H. contortus beta-tubulin molecule we offer a structural explanation for how the mutation conferring benzimidazole resistance in nematodes may act, as well as a possible explanation for the species-specificity of benzimidazole anthelmintics.

TDM modelling and evaluation of different domain transforms for LSI

Latent semantic indexing (LSI) is a popular technique used in information retrieval (IR) applications. This paper presents a novel evaluation strategy based on the use of image processing tools. The authors evaluate the use of the discrete cosine transform (DCT) and Cohen Daubechies Feauveau 9/7 (CDF 9/7) wavelet transform as a pre-processing step for the singular value decomposition (SVD) step of the LSI system. In addition, the effect of different threshold types on the search results is examined. The results show that accuracy can be increased by applying both transforms as a pre-processing step, with better performance for the hard-threshold function. The choice of the best threshold value is a key factor in the transform process. This paper also describes the most effective structure for the database to facilitate efficient searching in the LSI system.