bluuebunny/crossref_metadata_2025 huggingface dataset:
Orthorhombic-to-tetragonal transition of SrRuO3 layers in Pr0.7Ca0.3MnO3/SrRuO3 superlattices
Authors: Ziese M , Vrejoiu I , Pippel E , Hähnel A , Nikulina E , Hesse D
Published: August 2011

High-quality Pr0.7Ca0.3MnO3/SrRuO3 superlattices with ultrathin layers were fabricated by pulsed-laser deposition on SrTiO3 substrates. The superlattices were studied by atomically resolved scanning transmission electron microscopy, high-resolution transmission electron microscopy, resistivity and magnetoresistance measurements. The superlattices grew coherently without growth defects. Viewed along the growth direction, SrRuO3 and Pr0.7Ca0.3MnO3 layers were terminated by RuO2 and MnO2, respectively, which imposes a unique structure to their interfaces. Superlattices with a constant thickness of the SrRuO3 layers, but varying thickness of the Pr0.7Ca0.3MnO3 layers showed a change of crystalline symmetry of the SrRuO3 layers. At a low Pr0.7Ca0.3MnO3 layer thickness of 1.5 nm transmission electron microscopy proved the SrRuO3 layers to be orthorhombic, whereas these were non-orthorhombic for a Pr0.7Ca0.3MnO3 layer thickness of 4.0 nm. Angular magnetoresistance measurements showed orthorhombic (with small monoclinic distortion) symmetry in the first case and tetragonal symmetry of the SrRuO3 layers in the second case. Mechanisms driving this orthorhombic to tetragonal transition are briefly discussed.
Crystallization process and magnetic properties of amorphous iron oxide nanoparticles
Authors: Phu N D , Ngo D T , Hoang L H , Luong N H , Chau N , Hai N H
Published: August 2011

This paper studied the crystallization process, phase transition and magnetic properties of amorphous iron oxide nanoparticles prepared by the microwave heating technique. Thermal analysis and magnetodynamics studies revealed many interesting aspects of the amorphous iron oxide nanoparticles. The as-prepared sample was amorphous. Crystallization of the maghemite γ-Fe2O3 (with an activation energy of 0.71 eV) and the hematite α-Fe2O3 (with an activation energy of 0.97 eV) phase occurred at around 300 °C and 350 °C, respectively. A transition from the maghemite to the hematite occurred at 500 °C with an activation energy of 1.32 eV. A study of the temperature dependence of magnetization supported the crystallization and the phase transformation. Raman shift at 660 cm−1 and absorption band in the infrared spectra at 690 cm−1 showed the presence of disorder in the hematite phase on the nanoscale which is supposed to be the origin of the ferromagnetic behaviour of that antiferromagnetic phase.
Effect of grain size on exchange-biased Heusler alloys
Authors: Endo H , Hirohata A , Sagar J , Fleet L R , Nakayama T , O'Grady K
Published: August 2011

We report on an investigation into the effects of grain size of both antiferromagnetic IrMn and ferromagnetic Heusler alloy layers on the magnetic properties of exchange-biased films. IrMn/Co2FeSi was grown by a HiTUS sputtering system which allows control of the grain size. We found that small IrMn grains (⩽7 nm) could not generate an exchange bias H
ex, while those above 8 nm in size showed H
ex between 100 and 200 Oe. H
ex showed a minor decrease with increasing Co2FeSi grain sizes (up to 15–20 nm) but M
s gradually increased. Our results show that sharp interfacial matching is required between 8 and 10 nm IrMn grains and 15 nm Co2FeSi grains to exhibit both large H
ex and M
s for device applications.
Comparison of as-grown and annealed GaN/InGaN : Mg samples
Authors: Deng Qingwen , Wang Xiaoliang , Xiao Hongling , Wang Cuimei , Yin Haibo , Chen Hong , Lin Defeng , Jiang Lijuan , Feng Chun , Li Jinmin , Wang Zhanguo , Hou Xun
Published: August 2011

Mg-doped InGaN was grown on unintentionally doped GaN layer, and Mg and defect behaviours in both GaN and InGaN : Mg were investigated through photoluminescence measurement at 7 K. Mg acceptor was found in unintentionally doped GaN after thermal annealing in N2 ambient, and Mg activation energy was estimated to be 200 meV and 110 meV for GaN and InGaN, respectively. Particularly, the ultraviolet band (3.0–3.2 eV) in the GaN layer was infrequently observed in the unannealed sample but quenched in the annealed sample; this band may be associated with oxygen-substituted nitrogen defects. Moreover, the measurement errors of photoluminescence and x-ray diffraction originated from strain were taken into account.
Dynamical behaviour of the resistive switching in ceramic YBCO/metal interfaces
Authors: Acha C
Published: August 2011

Studies related to the dynamics of resistive switching (RS) in ceramic YBCO/metal interfaces were performed. The change in interface resistance during the application of square pulses and its current–voltage (I–V) characteristics were measured. The obtained non-linear current dependence of the differential resistance can be very well reproduced by modelling the electrical behaviour of the interface with simple circuit elements. The RS produces defined changes in the parameters of the circuit model that reveal the particular dynamics of the mechanism beneath the resistance change in complex oxide/metal interfaces.
Highly doped p-type microcrystalline silicon thin films fabricated by a low-frequency inductively coupled plasma at a low temperature
Authors: Yan W S , Wei D Y , Xu S , Sern C C , Zhou H P
Published: August 2011

Highly doped p-type microcrystalline silicon thin films are fabricated by a low-frequency inductively coupled plasma at a low temperature of 150 °C. The effects of radio frequency power on the microstructures of thin films such as x-ray diffraction patterns, crystalline volume fraction, grain size and surface morphology are investigated. The deposition rate of the thin films increases from 22 to 35 nm min−1 when the power increases from 1200 to 2000 W. The optical properties of the thin films are studied using UV–VIS–near IR spectroscopy. The Hall effect measurements show that the fabricated thin films present a high doping concentration from 1.2 × 1019 to 1.3 × 1020 cm−3 with increasing power from 1200 to 2000 W. The effect of power on these properties of thin films, especially for high doping, is understood from the impact of power on the plasma properties of the species in the chamber such as the electron energy distribution function (EEDF), electron density and Debye length. The EEDF presents an evolution with increasing power accompanying an increase in electron density and a decrease in Debye length. It is found that the higher the electron density, the higher is the doping concentration. This shows that high electron density is favourable for heavy doping. In fact, the high electron density is determined by the electromagnetic (H) mode of the low-frequency inductively coupled plasma.
Colossal resistivity with diminished tangent loss in Zn–Ni ferrite nanoparticles
Authors: Younas M , Atif M , Nadeem M , Siddique M , Idrees M , Grossinger R
Published: August 2011

We have investigated the electrical and magnetic response of the sol–gel synthesized Zn
x
Ni1−x
Fe2O4 (x = 0.0, 0.5 and 1) nanoparticles. The ratio of A-site sextet intensity to that of B-site sextet is featured in terms of divergence in coordination of Fe3+ ions from four-fold (A-site) to six-fold (B-site). Canted spin structure and weakening of Fe3+(A)–Fe3+(B) interactions at the surface of the nanoparticles assign the reduced value of room temperature magnetization in these nanoparticles. Shift of the blocking temperature with Zn content is ascribed to the change in the magnetic anisotropy. Colossal resistivity and reduced dielectric constant are discussed on the basis of dangling bond, superparamagnetic character, canted spin structure and polarizability of the cations. Diminished tangent loss is stipulated in terms of decrease in magnetocrystalline anisotropy and collapse of long-range magnetic order. We report colossal resistivity (i.e. 3.15 × 109 Ω cm), reduced dielectric constant (3.97) and diminished tangent loss (0.07) for Ni0.5Zn0.5Fe2O4 nanoparticles.
The spectrum of Schrödinger operators and Hodge Laplacians on conformally cusp manifolds
Authors: Golénia Sylvain , Moroianu Sergiu
Published: August 2011

We describe the spectrum of the

k
k

-form Laplacian on conformally cusp Riemannian manifolds. The essential spectrum is shown to vanish precisely when the

k
k

and

k
−
1

k-1

de Rham cohomology groups of the boundary vanish. We give Weyl-type asymptotics for the eigenvalue-counting function in the purely discrete case. In the other case we analyze the essential spectrum via positive commutator methods and establish a limiting absorption principle. This implies the absence of the singular spectrum for a wide class of metrics. We also exhibit a class of potentials

V
V

such that the Schrödinger operator has compact resolvent, although in most directions the potential

V
V

tends to

−
∞

-\infty

. We correct a statement from the literature regarding the essential spectrum of the Laplacian on forms on hyperbolic manifolds of finite volume, and we propose a conjecture about the existence of such manifolds in dimension 4 whose cusps are rational homology spheres.
A novel function of Tis11b/BRF1 as a regulator ofDll4mRNA 3′-end processing
Authors: Desroches-Castan Agnès , Cherradi Nadia , Feige Jean-Jacques , Ciais Delphine
Published: August 2011

Tis11b/BRF1 belongs to the tristetraprolin family, the members of which are involved in AU-rich-dependent regulation of mRNA stability/degradation. Mouse inactivation of the Tis11b gene has revealed disorganization of the vascular network and up-regulation of the proangiogenic factor VEGF. However, the VEGF deregulation alone cannot explain the phenotype of Tis11b knockouts. Therefore we investigated the role of Tis11b in expression of Dll4, another angiogenic gene for which haploinsufficiency is lethal. In this paper, we show that Tis11b silencing in endothelial cells leads to up-regulation of Dll4 protein and mRNA expressions, indicating that Dll4 is a physiological target of Tis11b. Tis11b protein binds to endogenous Dll4 mRNA, and represses mRNA expression without affecting its stability. In the Dll4 mRNA 3′ untranslated region, we identified one particular AUUUA motif embedded in a weak noncanonical polyadenylation (poly(A)) signal as the major Tis11b-binding site. Moreover, we observed that inhibition of Tis11b expression changes the ratio between mRNAs that are cleaved or read through at the poly(A) signal position, suggesting that Tis11b can interfere with mRNA cleavage and poly(A) efficiency. Last, we report that this Tis11b-mediated mechanism is used by endothelial cells under hypoxia for controlling Dll4 mRNA levels. This work constitutes the first description of a new function for Tis11b in mammalian cell mRNA 3′-end maturation.
Kinesin-3 and dynein cooperate in long-range retrograde endosome motility along a nonuniform microtubule array
Authors: Schuster Martin , Kilaru Sreedhar , Fink Gero , Collemare Jérôme , Roger Yvonne , Steinberg Gero
Published: August 2011

The polarity of microtubules (MTs) determines the motors for intracellular motility, with kinesins moving to plus ends and dynein to minus ends. In elongated cells of Ustilago maydis, dynein is thought to move early endosomes (EEs) toward the septum (retrograde), whereas kinesin-3 transports them to the growing cell tip (anterograde). Occasionally, EEs run up to 90 μm in one direction. The underlying MT array consists of unipolar MTs at both cell ends and antipolar bundles in the middle region of the cell. Cytoplasmic MT-organizing centers, labeled with a γ-tubulin ring complex protein, are distributed along the antipolar MTs but are absent from the unipolar regions. Dynein colocalizes with EEs for 10–20 μm after they have left the cell tip. Inactivation of temperature-sensitive dynein abolishes EE motility within the unipolar MT array, whereas long-range motility is not impaired. In contrast, kinesin-3 is continuously present, and its inactivation stops long-range EE motility. This indicates that both motors participate in EE motility, with dynein transporting the organelles through the unipolar MT array near the cell ends, and kinesin-3 taking over at the beginning of the medial antipolar MT array. The cooperation of both motors mediates EE movements over the length of the entire cell.
Endocytosis is essential for dynamic translocation of a syntaxin 1 orthologue during fission yeast meiosis
Authors: Kashiwazaki Jun , Yamasaki Yuriko , Itadani Akiko , Teraguchi Erika , Maeda Yukari , Shimoda Chikashi , Nakamura Taro
Published: August 2011

Syntaxin is a component of the target soluble N-ethylmaleimide–sensitive factor attachment protein receptor complex, which is responsible for fusion of membrane vesicles at the target membrane. The fission yeast syntaxin 1 orthologue Psy1 is essential for both vegetative growth and spore formation. During meiosis, Psy1 disappears from the plasma membrane (PM) and dramatically relocalizes on the nascent forespore membrane, which becomes the PM of the spore. Here we report the molecular details and biological significance of Psy1 relocalization. We find that, immediately after meiosis I, Psy1 is selectively internalized by endocytosis. In addition, a meiosis-specific signal induced by the transcription factor Mei4 seems to trigger this internalization. The internalization of many PM proteins is facilitated coincident with the initiation of meiosis, whereas Pma1, a P-type ATPase, persists on the PM even during the progression of meiosis II. Ergosterol on the PM is also important for the internalization of PM proteins in general during meiosis. We consider that during meiosis in Schizosaccharomyces pombe cells, the characteristics of endocytosis change, thereby facilitating internalization of Psy1 and accomplishing sporulation.
Angiomotin family proteins are novel activators of the LATS2 kinase tumor suppressor
Authors: Paramasivam Murugan , Sarkeshik Ali , Yates John R. , Fernandes Maria J. G. , McCollum Dannel
Published: August 2011

LATS2 kinase functions as part of the Hippo pathway to promote contact inhibition of growth and tumor suppression by phosphorylating and inhibiting the transcriptional coactivator YAP. LATS2 is activated by the MST2 kinase. How LATS2 is activated by MST2 in response to changes in cell density is unknown. Here we identify the angiomotin-family tight junction protein AMOTL2 as a novel activator of LATS2. Like AMOTL2, the other angiomotin-family proteins AMOT and AMOTL1 also activate LATS2 through a novel conserved domain that binds and activates LATS2. AMOTL2 binds MST2, LATS2, and YAP, suggesting that AMOTL2 might serve as a scaffold protein. We show that LATS2, AMOTL2, and YAP all localize to tight junctions, raising the possibility that clustering of Hippo pathway components at tight junctions might function to trigger LATS2 activation and growth inhibition in response to increased cell density.
Glucose regulates clathrin adaptors at thetrans-Golgi network and endosomes
Authors: Aoh Quyen L. , Graves Lee M. , Duncan Mara C.
Published: August 2011

Glucose is a rich source of energy and the raw material for biomass increase. Many eukaryotic cells remodel their physiology in the presence and absence of glucose. The yeast Saccharomyces cerevisiae undergoes changes in transcription, translation, metabolism, and cell polarity in response to glucose availability. Upon glucose starvation, translation initiation and cell polarity are immediately inhibited, and then gradually recover. In this paper, we provide evidence that, as in cell polarity and translation, traffic at the trans-Golgi network (TGN) and endosomes is regulated by glucose via an unknown mechanism that depends on protein kinase A (PKA). Upon glucose withdrawal, clathrin adaptors exhibit a biphasic change in localization: they initially delocalize from the membrane within minutes and later partially recover onto membranes. Additionally, the removal of glucose induces changes in posttranslational modifications of adaptors. Ras and Gpr1 signaling pathways, which converge on PKA, are required for changes in adaptor localization and changes in posttranslational modifications. Acute inhibition of PKA demonstrates that inhibition of PKA prior to glucose withdrawal prevents several adaptor responses to starvation. This study demonstrates that PKA activity prior to glucose starvation primes membrane traffic at the TGN and endosomes in response to glucose starvation.
Contextual analysis of RNAi-based functional screens using interaction networks
Authors: Gonzalez Orland , Zimmer Ralf
Published: August 2011

Motivation: Considerable attention has been directed in recent years toward the development of methods for the contextual analysis of expression data using interaction networks. Of particular interest has been the identification of active subnetworks by detecting regions enriched with differential expression. In contrast, however, very little effort has been made toward the application of comparable methods to other types of high-throughput data.

Results: Here, we propose a new method based on co-clustering that is specifically designed for the exploratory analysis of large-scale, RNAi-based functional screens. We demonstrate our approach by applying it to a genome-scale dataset aimed at identifying host factors of the human pathogen, hepatitis C virus (HCV). In addition to recovering known cellular modules relevant to HCV infection, the results enabled us to identify new candidates and formulate biological hypotheses regarding possible roles and mechanisms for a number of them. For example, our analysis indicated that HCV, similar to other enveloped viruses, exploits elements within the endosomal pathway in order to acquire a membrane and facilitate assembly and release. This echoed a number of recent studies which showed that the ESCRT-III complex is essential to productive infection.

Contact:  gonzalez@bio.ifi.lmu.de

Supplementary Information:  Supplementary data are available at Bioinformatics online.
Seasonal Progress of Charcoal Rot and Its Impact on Soybean Productivity
Authors: Mengistu Alemu , Smith J. R. , Ray J. D. , Bellaloui N.
Published: August 2011

The seasonal progress of charcoal rot (caused by Macrophomina phaseolina) was measured over two growing seasons in four separate experiments: irrigated infested, irrigated non-infested, non-irrigated infested, and non-irrigated noninfested. Disease was assessed at V5, R1, R3, R5, R6, and R7 growth stages based on colony forming units (CFU) of M. phaseolina recovered from the lower stem and root tissues and the area under the disease progress curve (AUDPC). The population density of M. phaseolina increased slowly from the V5 to R6 growth stages and then rapidly from the R6 to R7 growth stages for all genotypes in all four experiments. Yield loss due to charcoal rot ranged from 6 to 33% in irrigated environments. The extent of yield loss was affected by severity of charcoal rot, which in turn was affected by year. Yield loss due to charcoal rot was consistently measured in all paired comparisons in irrigated environments, suggesting that charcoal rot can be an important disease in irrigated environments. Disease severity based on CFU accounted for more yield loss variation (42%) than did the AUDPC (36%) when used to assess disease. Growth stage R7 was found to be the optimum stage for assessing disease using CFU. In addition, screening soybean genotypes under irrigation environment may have utility in breeding programs where there is a need for evaluating soybean genotypes for both disease resistance and yield.
A Test of Taxonomic and Biogeographic Predictivity: Resistance to Potato virus Y in Wild Relatives of the Cultivated Potato
Authors: Cai X. K. , Spooner D. M. , Jansky S. H.
Published: August 2011

A major justification for taxonomic research is its assumed ability to predict the presence of traits in a group for which the trait has been observed in a representative subset of the group. Similarly, populations in similar environments are expected to be more alike than populations in divergent environments. Consequently, it is logical to assume that taxonomic relationships and biogeographical data have the power to predict the distribution of disease resistance phenotypes among plant species. The objective of this study was to test predictivity in a group of widely distributed wild potato species, based on hypotheses that closely related organisms (taxonomy) or organisms from similar environments (biogeography) share resistance to a simply inherited trait (Potato virus Y [PVY]). We found that wild potato species with an endosperm balance number (EBN) of 1 (a measure of cross compatibility) shared resistances to PVY more than species with different EBN values. However, a large amount of variation was found for resistance to PVY among and within species. We also found that populations from low elevations were more resistant than those from high elevations. Because PVY is vectored by aphids, we speculate that the distribution of aphids may determine the level of selection pressure for PVY resistance.
Identification of the Molecular Make-Up of the Potato virus Y Strain PVYZ: Genetic Typing of PVYZ-NTN
Authors: Kerlan Camille , Nikolaeva Olga V. , Hu Xiaojun , Meacham Teresa , Gray Stewart M. , Karasev Alexander V.
Published: August 2011

Potato virus Y (PVY) strains were originally defined by interactions with different resistance genes in standard potato cultivars. Five distinct strain groups are defined that cause local or systemic hypersensitive responses (HRs) in genetic background with a corresponding N gene: PVYO, PVYN, PVYC, PVYZ, and PVYE. The nucleotide sequences of multiple isolates of PVYO and PVYN differ from each other by ≈8% along their genomes. Additionally, complete genome sequences of multiple recombinant isolates are composed of segments of parental PVYO and PVYN sequences. Here, we report that recombinant isolate PVY-L26 induces an HR in potato ‘Maris Bard’ carrying the putative Nz gene, and is not recognized by two other resistance genes, Nc and Nytbr. These genetic responses in potato, combined with the inability of PVY-L26 to induce vein necrosis in tobacco, clearly define it as an isolate from the PVYZ strain group and provide the first information on genome structure and sequence of PVYZ. The genome of PVY-L26 displays typical features of European NTN-type isolates with three recombinant junctions (PVYEU-NTN), and the PVY-L26 is named PVYZ-NTN. Three typical PVYNTN isolates and two PVYN isolates, all inducing vein necrosis in tobacco, were compared with PVY-L26. One PVYNTN isolate elicited HR reactions in Maris Bard, similar to PVY-L26, while two induced a severe systemic HR-like reaction quite different from the quasi-symptomless reaction induced by two PVYN isolates. ‘Yukon Gold’ potato from North America produced HR against several PVYNTN isolates, including PVY-L26, but only late and limited systemic necrosis against one PVYN isolate. Consequently, according to symptoms in potato indicators, both PVYZ and PVYNTN isolates appeared biologically very close and clearly distinct from PVYO and PVYN strain groups.
Genetic divergence and classification of non-structural protein 1 among porcine rotaviruses of species B
Authors: Suzuki Tohru , Kuga Kazufumi , Miyazaki Ayako , Tsunemitsu Hiroshi
Published: August 2011

Porcine rotavirus B (RVB) has frequently been detected in diarrhoea of suckling and weaned pigs. Moreover, epidemiological studies using ELISA have demonstrated high antibody prevalence in sera from sows, indicating that RVB infections are widespread. Because it is difficult to propagate RVBs serially in cell culture, genetic analysis of RNA segments of porcine RVBs other than those encoding VP7 and NSP2 has been scarcely performed. We conducted sequence and phylogenetic analyses focusing on non-structural protein 1 (NSP1), using 15 porcine RVB strains isolated from diarrhoeic faeces collected around Japan. Sequence analysis showed that the porcine NSP1 gene contains two overlapping ORFs. Especially, peptide 2 of NSP1 retains highly conserved cysteine and histidine residues among RVBs. Comparison of NSP1 nucleotide and deduced amino acid sequences from porcine RVB strains demonstrated low identities to those from other RVB strains. Phylogenetic analysis of RVB NSP1 revealed the presence of murine, human, ovine, bovine and porcine clusters. Furthermore, the NSP1 genes of porcine RVBs were divided into three genotypes, suggesting the possibility that porcine species might be an original host of RVB infection. Of nine strains common to those used in our previous study, only one strain was classified into a different genotype from the others in the analysis of VP7, in contrast to the analysis of NSP1, where all belonged to the same cluster. This fact suggests the occurrence of gene reassortment among porcine RVBs. These findings should provide more beneficent information to understand the evolution and functions of RVBs.
An AP2 Domain-Containing Gene, ESE1, Targeted by the Ethylene Signaling Component EIN3 Is Important for the Salt Response in Arabidopsis
Authors: Zhang Lixia , Li Zhuofu , Quan Ruidang , Li Guojing , Wang Ruigang , Huang Rongfeng
Published: August 2011

Accumulating investigations reveal that ethylene signaling is involved in the salt response in Arabidopsis (Arabidopsis thaliana), and it has been reported that overexpression of a number of ethylene response factor (ERF) genes enhances salt tolerance; however, transcriptional regulation of the ethylene signal component ETHYLENE INSENSITIVE3 (EIN3) in the salt response has not been clearly defined. Consulting microarray data and transcriptional confirmations showed that three of the ERF genes were ethylene and salt inducible, named ESE1 to ESE3. Additionally, the expression of one of the ESE genes (ESE1) was suppressed in ein2, ein3-1, eil1-3, and ein3 eil1 but enhanced in EIN3-overexpressing (EIN3ox) lines. Inhibitors of ethylene biosynthesis, aminoethoxyvinylglycine, and ethylene action, AgNO3, reduced the expression of ESE1, while ethylene overproduction eto mutants enhanced the expression of ESE1, indicating that ESE1 is an ethylene-modulated gene downstream of EIN3/EIL1. Further analyses with biochemical and molecular approaches revealed that EIN3 physically binds to the ESE1 promoter, demonstrating that ESE1 was one target of EIN3. ESE1 in turn binds to promoters of salt-related genes, such as RD29A and COR15A. Moreover, either EIN3ox or ESE1ox was sufficient to enhance transcript levels of salt-related genes and salt tolerance. In addition, ESE1ox in ein3 enhanced the salt response during seed germination and seedling development, demonstrating that ESE1 is genetically downstream of EIN3. Thus, the evidence in this report reveals that the transcriptional complex of EIN3-ESE1 is a crucial event in the salt response, thereby connecting the transcriptional regulation of EIN3 and the downstream ERF protein ESE1 in the salt response.
Genome-Wide Characterization of the HD-ZIP IV Transcription Factor Family in Maize: Preferential Expression in the Epidermis
Authors: Javelle Marie , Klein-Cosson Catherine , Vernoud Vanessa , Boltz Véronique , Maher Chris , Timmermans Marja , Depège-Fargeix Nathalie , Rogowsky Peter M.
Published: August 2011

Transcription factors of the plant-specific homeodomain leucine zipper IV (HD-ZIP IV) family have been found from moss to higher plants, and several family members have been associated with epidermis-related expression and/or function. In maize (Zea mays), four of the five characterized HD-ZIP IV family members are expressed specifically in the epidermis, one contributes to trichome development, and target genes of another one are involved in cuticle biosynthesis. Assessing the phylogeny, synteny, gene structure, expression, and regulation of the entire family in maize, 12 novel ZmHDZIV genes were identified in the recently sequenced maize genome. Among the 17 genes, eight form homeologous pairs duplicated after the split of maize and sorghum (Sorghum bicolor), whereas a fifth duplication is shared with sorghum. All 17 ZmHDZIV genes appear to be derived from a basic module containing seven introns in the coding region. With one possible exception, all 17 ZmHDZIV genes are expressed and show preferential expression in immature reproductive organs. Fourteen of 15 ZmHDZIV genes with detectable expression in laser-dissected tissues exhibit a moderate to very strong expression preference for the epidermis, suggesting that at least in maize, the majority of HD-ZIP IV family members may have epidermis-related functions. Thirteen ZmHDZIV genes carry conserved motifs of 19 and 21 nucleotides in their 3′ untranslated region. The strong evolutionary conservation and the size of the conserved motifs in the 3′ untranslated region suggest that the expression of HD-ZIP IV genes may be regulated by small RNAs.
Importance of fish behaviour in modelling conservation problems: food limitation as an example
Authors: Railsback S. F. , Harvey B. C.
Published: August 2011

Simulation experiments using the inSTREAM individual‐based brown trout Salmo trutta population model explored the role of individual adaptive behaviour in food limitation, as an example of how behaviour can affect managers' understanding of conservation problems. The model includes many natural complexities in habitat (spatial and temporal variation in characteristics such as depth and velocity, temperature, hiding and feeding cover, drift‐food supply and predation risk), fish physiology (especially, how food intake and growth vary with hydrodynamics, cover, fish size and temperature) and behaviour. When drift‐food concentration was increased over a wide range in 7 year simulations, the simulated population was always food limited. In fact, as food supply increased, the population increased at an increasing rate and consumed a higher percentage of the food supply, apparently because higher food concentrations make more stream area energetically profitable for drift feeders. The behaviour most responsible for this response was activity selection: when food was abundant, fish chose to feed less frequently and more nocturnally, thereby reducing predation mortality so more fish survived longer. These results indicate that the traditional concept of food limitation, that food availability stops limiting population size when it exceeds some threshold level, may not be useful and can be misleading. Results also strongly contradict the concept that a salmonid population is not food limited if the total food supply is greater than the population's consumption. Explicit consideration of adaptive behaviour produced a novel but believable understanding of food effects on salmonid populations. Published 2011. This article is a U.S. Government work and is in the public domain in the USA.
Genetic characterization of the HrpL regulon of the fire blight pathogenErwinia amylovorareveals novel virulence factors
Authors: MCNALLY R. RYAN , TOTH IAN K. , COCK PETER J. A. , PRITCHARD LEIGHTON , HEDLEY PETE E. , MORRIS JENNY A. , ZHAO YOUFU , SUNDIN GEORGE W.
Published: August 2011

The bacterial pathogenErwinia amylovorais the causal agent of fire blight, an economically significant disease of apple and pear. Disease initiation byE. amylovorarequires the translocation of effector proteins into host cells via the hypersensitive response and pathogenicity (hrp) type III secretion system (T3SS). The alternative sigma factor HrpL positively regulates the transcription of structural and translocated components of the T3SS viahrppromoter elements. To characterize genome‐wide HrpL‐dependent gene expression inE. amylovoraEa1189, wild‐type and Ea1189ΔhrpLstrains were cultured inhrp‐inducing minimal medium, and total RNA was compared using a custom microarray designed to represent the annotated genes ofE. amylovoraATCC 49946. The results revealed 24 genes differentially regulated in Ea1189ΔhrpLrelative to Ea1189 with fold‐change expression ratios greater than 1.5; of these, 19 genes exhibited decreased transcript abundance and five genes showed increased transcript abundance relative to Ea1189. To expand our understanding of the HrpL regulon and to elucidate direct versus indirect HrpL‐mediated effects on gene expression, the genome ofE. amylovoraATCC 49946 was examinedin silicousing a hidden Markov model assembled from knownErwiniaspp.hrppromoters. This technique identified 15 putative type III novelhrppromoters, seven of which were validated with quantitative polymerase chain reaction based on expression analyses. It was found that HrpL‐regulated genes encode all known components of thehrpT3SS, as well as five putative type III effectors. Eight genes displayed apparent indirect HrpL regulation, suggesting that the HrpL regulon is connected to downstream signalling networks. The construction of deletion mutants of three novel HrpL‐regulated genes resulted in the identification of additional virulence factors as well as mutants displaying abnormal motility and biofilm phenotypes.
Attachment and emotional understanding: a study on late‐adopted pre‐schoolers and their parents
Authors: Barone L. , Lionetti F.
Published: August 2011

Objective The aim of this study was to characterize the role of attachment in adoption, first by assessing the influence of adoptive parents on their late‐adopted children and second by investigating the role of children's attachment on an emotional understanding task.

Design On children's arrival into adoptive families, parents' attachment was evaluated. After 12–18 months, children's attachment towards mothers and fathers was assessed. Twelve months later, children participated in an emotional understanding task.

Method Parents' attachment was assessed using the Adult Attachment Interview. Children's attachment and emotional understanding were evaluated respectively using the Manchester Child Attachment Story Task and the Test of Emotion Comprehension.

Results A correspondence of 80% (security vs. insecurity) and 60% (security vs. avoidant or ambivalent insecurityK= 0.40) between mothers' and children's pattern of attachment was found. A secure state of mind in both adoptive parents was a protective factor towards children's attachment disorganization. Finally, there was a significant association between children's security of attachment and their performance on the emotional understanding task.

Conclusion Adoption appears to be an intervention that assures the adoptive child an opportunity to catch up on emotional development and to partially resolve prior traumatic attachment experiences; adoptive parents play a central role in the emotional adjustment of their children.
Effects of Helicobacter pylori, geohelminth infection and selected commensal bacteria on the risk of allergic disease and sensitization in 3‐year‐old Ethiopian children
Authors: Amberbir A. , Medhin G. , Erku W. , Alem A. , Simms R. , Robinson K. , Fogarty A. , Britton J. , Venn A. , Davey G.
Published: August 2011

Background Epidemiological studies have suggested that gastro‐intestinal infections including Helicobacter pylori, intestinal microflora (commensal bacteria) and geohelminths may influence the risk of asthma and allergy but data from early life are lacking.

Objective We aimed to determine the independent effects of these infections on allergic disease symptoms and sensitization in an Ethiopian birth cohort.

Methods In 2008/09, 878 children (87% of the 1006 original singletons in a population‐based birth cohort) were followed up at age 3 and interview data obtained on allergic symptoms and potential confounders. Allergen skin tests to Dermatophagoides pteronyssinus and cockroach were performed, levels of Der p 1 and Bla g 1 in the child's bedding measured and stool samples analysed for geohelminths and, in a random subsample, enterococci, lactobacilli, bifidobacteria and H. pylori antigen. The independent effects of each exposure on wheeze, eczema, hayfever and sensitization were determined using multiple logistic regression.

Results Children were commonly infected with H. pylori (41%; 253/616), enterococci (38.1%; 207/544), lactobacilli (31.1%; 169/544) and bifidobacteria (18.9%; 103/544) whereas geohelminths were only found in 8.5% (75/866). H. pylori infection was associated with a borderline significant reduced risk of eczema (adjusted OR 0.49, 95% CI 0.24–1.01, P=0.05) and D. pteronyssinus sensitization (adjusted OR 0.42, 95% CI 0.17–1.08, P=0.07). Geohelminths and intestinal microflora were not significantly associated with any of the outcomes measured.

Conclusion and Clinical Relevance Among young children in a developing country, we found evidence to support the hypothesis of a protective effect of H. pylori infection on the risk of allergic disease. Further investigation of the mechanism of this effect is therefore of potential therapeutic and preventive value.

Cite this as: A. Amberbir, G. Medhin, W. Erku, A. Alem, R. Simms, K. Robinson, A. Fogarty, J. Britton, A. Venn, and G. Davey, Clinical & Experimental Allergy, 2011 (41) 1422–1430.
Age‐ and gender‐specific prevalence of carotid atherosclerosis and its association with metabolic syndrome in Hangzhou, China
Authors: Yin Jun‐Hua , Song Zhen‐Ya , Shan Peng‐Fei , Xu Jun , Ye Zhi‐Min , Xu Xiao‐Hong , Zhang Song‐Zhao , Liang Qin , Zhao Yi , Ren Zhen , Yu Yi‐Ping
Published: August 2011

Objective  Because of rapid alterations in lifestyle and the incidence of metabolic syndrome (MetS), the prevalence of carotid atherosclerosis (CA) and carotid plaque (CP) may increase in China. We aimed to evaluate the prevalence of CA and CP as well as its relation to MetS in an East Chinese population.

Methods  The study included 6142 subjects who underwent general health screening including carotid ultrasonography in 2009. Diagnoses of MetS were made according to the revised Adult Treatment Panel III criteria.

Results  The prevalence of CA and CP increased gradually with age. These conditions were more prevalent in men than in women (CA: 22·1%vs 12·0%, P < 0·001; CP: 12·6%vs 7·2%, P < 0·001). Multivariate logistic regression analysis showed that male gender, age, blood pressure, fasting blood glucose (FBG) and low‐density lipoprotein cholesterol were risk factors for CA and CP, while high‐density lipoprotein cholesterol was protective for CA. Age ≥50 years has the largest impact on CA and CP, followed by elevated blood pressure and elevated blood glucose. Individuals with MetS had a higher prevalence of CA (27·7%vs 20·0% in men, 24·0%vs 10·3% in women; P < 0·001 in both) and CP (16·6%vs 11·2% in men, P < 0·001; 11·8%vs 6·5% in women, P < 0·005) than those without MetS. The prevalence and odds ratios of CA and CP aggregated with an increasing number of MetS components, even in individuals exhibiting only one component.

Conclusions  These results indicate that CA and CP have become a major public health problem in China. MetS and its components were associated with an increased prevalence of CA and CP.
Topo IIα gene alterations correlated with survival in patients with diffuse large B‐cell lymphoma
Authors: Chen Zhenwen , Wang Jinfen , Zhang Hongwei , Liu Dongmei , Li Yi , Xu Yirong , Tan Dongfeng , Chen Dong , Zhao Xia , Wang Guoping
Published: August 2011

Eur J Clin Invest 2012; 42 (3): 310–320

Background  Topoisomerase IIα (topo IIα) protein expression has prognostic significance in many cancers. However, it is still unclear whether topo IIα protein expression and gene alterations play roles as prognostic factors in diffuse large B‐cell lymphoma (DLBCL).

Materials and methods  We selected 102 patients with DLBCL who were homogeneously treated with CHOP chemotherapy and followed up. Using tissue microarray technology, all of the cases, consisting of 25 germinal centre B‐cell‐like (GCB) and 77 nongerminal centre B‐cell‐like (non‐GCB) types, were studied. Topo IIα protein expression was detected by immunohistochemistry. Gene copy number of topo IIα was analysed by chromogenic in situ hybridization. Cox regression, chi‐square test and Kaplan–Meier statistics were performed using SPSS 15·0.

Results  Topo IIα protein overexpression was found in 91 (91/102, 89·2%) cases, while topo IIα gene amplification was absent in all cases. Chromosome 17 deletion was identified in 3 (3/102, 2·9%) cases, diploid in 66 (66/102, 64·7%) cases and aneuploidy in 33 (33/102, 32·4%) cases. By multivariate analysis, no significant differences in progression‐free survival (PFS) and overall survival (OS) were observed in patients with topo IIα protein overexpression (P > 0·05), while chromosome 17 aneuploidy predicted worse PFS and OS (P < 0·001).

Conclusions  These results suggested that chromosome 17 aneuploidy, but not topo IIα protein expression, could predict worse survival in patients with DLBCL.
Global patterns of specialization and coexistence in bird assemblages
Authors: Belmaker Jonathan , Sekercioglu Cagan H. , Jetz Walter
Published: August 2011

Aim  Increased specialization has been hypothesized to facilitate local coexistence and thus high species richness, but empirical evaluations of the richness–specialization relationships have been relatively scant. Here, we provide a first assessment of this relationship for terrestrial bird assemblages at global extent and from fine to coarse grains.

Location  World‐wide.

Methods  We use two indices of specialization that describe species‐level resource use: diet and habitat specialization. The relationship between richness and mean assemblage‐level specialization was independently assessed at realm, biome‐realm, 12,100 km2 equal‐area grid cells and fine‐grained scales. To identify assemblages that are diverse relative to environmental conditions we: (1) applied quantile regressions, (2) statistically accounted for other environmental variables which may constrain richness, and (3) parsed the data according to the residuals of a model relating species richness to the environmental variables.

Results  Assemblage species richness increases with both measures of specialization at all scales. Statistically, richness appears constrained by levels of specialization, with the highest richness values only found in specialized assemblages. Richness is positively associated with specialization even after accounting for gradients in resource availability. Net primary productivity and assemblage specialization have complementary statistical effects on assemblage species richness. Contrary to expectations based on niche partitioning of local resources, the relationship between specialization and richness is steep even at coarse scales.

Main conclusions  The results demonstrate that for an entire clade, totalling > 9000 species, specialization and species richness are related, at least for diverse assemblages. The strong patterns observed across scales suggest that this relationship does not solely originate from (1) limits on coexistence in present‐day assemblages, or (2) increased specialization in richer assemblages imposed by species’ abilities to partition ecological space. Instead, regional‐scale influences on the species pool may determine much of the observed relationship between richness and specialization. Although causal attribution is not straightforward, these findings support the idea that, for the scale of our analysis, specialization may be related to the past origination of high‐diversity assemblages, rather than their contemporary assembly.
Are physical intervention techniques likely to cause pain or injury when applied to manage the severely aggressive older adult? A survey of physiotherapist’s expert views in the UK
Authors: Stubbs Brendon , Hollins Lee
Published: August 2011

Aim.  To establish whether a professional consensus can be established amongst musculoskeletal physiotherapists or whether they believe certain physical intervention techniques would cause pain or injury if applied to an older adult.

Background.  Physiotherapist involvement in the context of a multidisciplinary team framework to develop adaptive techniques as required for complex physical presentations has resulted in lower injury rates than in working‐age adults. Physiotherapists are experts in anatomy and human movement and are ideally placed to contribute to the safe application of physical intervention in older adults.

Design.  A survey design was used.

Method.  A questionnaire was developed and tested to ascertain the physiotherapist’s opinions of the likelihood of each technique causing the patient pain and/or injury. The lead author distributed 41 questionnaires to physiotherapists in two busy hospitals in the UK.

Results.  Thirty‐four (83%) of physiotherapists returned the completed questionnaires. The physiotherapists had particular concerns about the use of wrist flexion and kneeling on the older adult in prone causing pain and/or injury. Some other techniques that we have advocated in our earlier research were approved by many of the respondents, e.g. supporting the forearm with both hands proximal to the wrist joint. None of the physiotherapists had attended a physical intervention course or applied it in the clinical setting, thus enabling them to analyse the techniques purely from a biomechanical movement perspective. Implications for nursing practice are discussed.

Conclusions.  It is anticipated that this research will stimulate nurses and course providers to develop patient group‐specific physical intervention techniques and thus reduce the risk of causing them pain and/or injury.

Relevance to clinical practice.  This study reaffirms the heightened risks associated with applying restraint techniques to older adults. An issue that needs to be addressed is whether the duty of care which is explicit and implicit within the relationship between nurse and patient is to be fully discharged. It also reinforces prior research that has called for patient‐specific physical intervention techniques and highlights some commonly used techniques that may have a deleterious effect on aggressive older adults. It also identifies the professional support that physiotherapists can offer to teams implementing physical intervention techniques within the context of clinical practice.
Flying Start NHS™: easing the transition from student to registered health professional
Authors: Banks Pauline , Roxburgh Michelle , Kane Helen , Lauder William , Jones Martyn , Kydd Angela , Atkinson John
Published: August 2011

Aims and objectives.  To evaluate the impact and effectiveness of Flying Start NHS™ on the confidence, competence and career development of newly qualified practitioners.

Background.  The first year of practice as a registered nurse, midwife, or allied health professional is recognised as challenging. This paper presents the findings of a two‐year evaluation of Flying Start NHS™, a web‐based programme developed by NHS Education Scotland to support newly qualified health professionals during the transition from student to qualified practitioner.

Design.  Descriptive design with one to one and focus group interviews, plus a survey.

Methods.  The evaluation employed a multi‐method approach including telephone interviews with Flying Start NHS™ leads/coordinators (n = 21) and mentors (n = 22) and focus groups with newly qualified practitioners (n = 95). An online survey was completed by 547 newly qualified practitioners.

Results.  A majority of newly qualified practitioners reported that Flying Start NHS™ had been useful in terms of clinical skills development and confidence. Those who were able to take protected time were more likely to complete the learning units and report that the support they received was good. Both newly qualified practitioners and mentors reported a lack of time. Newly qualified practitioners who took up posts in the community expressed greater satisfaction with the support received.

Conclusions.  NHS Boards should ensure that there is an ethos of support at all levels, as well as an understanding of the purpose of Flying Start NHS™ and what newly qualified practitioners require to do to complete it. The expectation that newly qualified practitioners will enrol on Flying Start NHS™ should be accompanied by an expectation that they will complete the programme in their first year, coupled with support to enable them to do so.

Relevance to clinical practice.  Undertaking Flying Start NHS™ in the first year of employment increases clinical skills development and confidence. Mentors require training and time to enable them to provide support.