bluuebunny/crossref_metadata_2025 huggingface dataset:
Diamond micro-Raman thermometers for accurate gate temperature measurements
Authors: Simon Roland B. , Pomeroy James W. , Kuball Martin
Published: May 2014

Determining the peak channel temperature in AlGaN/GaN high electron mobility transistors and other devices with high accuracy is an important and challenging issue. A surface-sensitive thermometric technique is demonstrated, utilizing Raman thermography and diamond microparticles to measure the gate temperature. This technique enhances peak channel temperature estimation, especially when it is applied in combination with standard micro-Raman thermography. Its application to other metal-covered areas of devices, such as field plates is demonstrated. Furthermore, this technique can be readily applied to other material/device systems.
Room-temperature operation of a titanium supersaturated silicon-based infrared photodetector
Authors: García-Hemme E. , García-Hernansanz R. , Olea J. , Pastor D. , del Prado A. , Mártil I. , González-Díaz G.
Published: May 2014

We report room-temperature operation of 1 × 1 cm2 infrared photoconductive photodetectors based on silicon supersaturated with titanium. We have fabricated these Si-based infrared photodetectors devices by means of ion implantation followed by a pulsed laser melting process. A high sub-band gap responsivity of 34 mV W−1 has been obtained operating at the useful telecommunication applications wavelength of 1.55 μm (0.8 eV). The sub-band gap responsivity shows a cut-off frequency as high as 1.9 kHz. These Si-based devices exhibit a non-previous reported specific detectivity of 1.7 × 104 cm Hz1/2 W−1 at 660 Hz, under a 1.55 μm wavelength light. This work shows the potential of Ti supersaturated Si as a fully CMOS-compatible material for the infrared photodetection technology.
Latitudinal dependence of nonlinear interaction between electromagnetic ion cyclotron wave and terrestrial ring current ions
Authors: Su Zhenpeng , Zhu Hui , Xiao Fuliang , Zheng Huinan , Zhang Min , Liu Y. C.-M. , Shen Chao , Wang Yuming , Wang Shui
Published: May 2014

Electromagnetic ion cyclotron (EMIC) waves can lead to the rapid decay (on a timescale of hours) of the terrestrial ring current. Such decay process is usually investigated in the framework of quasi-linear theory. Here, both theoretical analysis and test-particle simulation are performed to understand the nonlinear interaction between ring current ions and EMIC waves. In particular, the dependence of the nonlinear wave-particle interaction processes on the ion initial latitude is investigated in detail. These nonlinear processes are classified into the phase trapping and phase bunching, and the phase bunching is further divided into the channel and cluster effects. Compared to the prediction of the quasi-linear theory, the ring current decay rate can be reduced by the phase trapping, increased by the channel effect phase bunching, but non-deterministically influenced by the cluster effect phase bunching. The ion initial latitude changes the occurrence of the phase trapping, modulates the transport direction and strength of the cluster effect phase bunching, and only slightly affects the channel effect phase bunching. The current results suggest that the latitudinal dependence of these nonlinear processes should be considered in the evaluation of the ring current decay induced by EMIC waves.
Initial phase zone for phase locking to the resonance, using “main condition” of phase stability in DC-biased single-sided multipactor
Authors: Mostajeran M.
Published: May 2014

In the present work, the concept of accurate phase stability is employed to study a DC-biased single-sided multipactor. A “main condition” of phase stability was introduced in our previous studies of two-sided multipactors [M. Mostajeran, J. Instrum. 8, P04024 (2013); M. Mostajeran and M. Lamehi Rachti, Nucl. Instrum. Methods Phys. Res. A 615, 1–5 (2010)]. Using the same condition and assuming zero initial velocity for the secondary electrons, a regime of multipactors outside the resonance zones is found. The theoretical results are then verified by numerical simulation.
Identification of oxygen defects in CdTe revisited: First-principles study
Authors: T-Thienprasert J. , Watcharatharapong T. , Fongkaew I. , Du M. H. , Singh D. J. , Limpijumnong S.
Published: May 2014

By using first-principles calculations, several SO2 complexes in CdTe were studied. Based on experimental observation, SO2 complexes have been recently proposed by Lavrov et al. [Phys. Rev. B. 84, 233201 (2011)] to be the cause of the observed IR absorption peaks at 1096.8 and 1108.4 cm−1 in O-doped CdTe. Chen et al. [Phys. Rev. Lett. 96, 035508 (2006)] were originally proposed that the peaks come from OTe-VCd complex. Our calculations indicate that the SO2 molecule on the Te site [(SO2)Te] has a low formation energy but its calculated vibration frequencies (∼900 cm−1) are lower than the observed IR modes. However, (SO2)Te can form a complex with VCd with two possible configurations that give the vibration frequencies in a good agreement with the two observed IR peaks. The binding energies of the complex in these two configurations are about 1 eV under p-type conditions; indicating that the complex is quite stable. The two configurations are related to each other by a rotation of the SO2 molecule with an energy barrier of ∼0.4 eV. Therefore, the two configurations can co-exist at a low temperature and the high energy one gradually transforms to the low energy one as temperature increases. This agrees with the experimental observation that, at a high temperature, the two IR modes merged into one.
Electrical and optical characteristics of diffuse nanosecond pulsed discharge plasma using a needle-array electrode in atmospheric air
Authors: Liu Zhi-jie , Wang Wen-chun , Zhang Li , Wang Sen , Yang De-zheng , Zhang Shuai , Tang Kai
Published: May 2014

In this paper, a stable and diffuse dielectric barrier discharge plasma excited by bipolar nanosecond pulse is obtained under a needle-array electrode at atmospheric pressure in air. The images of the diffuse discharge, electric characteristics, and the optical emission spectra emitted from the diffuse discharge are investigated under mono and multi needle electrodes configuration. The peak value of discharge current, the average power, the power density, the emission intensity of N2 (C3Πu →B3Πg, 0-0), and the gas temperature of the diffuse dielectric barrier discharge plasmas are investigated under different needle electrode numbers based on the waveforms of pulse voltage-current and the optical emission spectra. Moreover, the plasma area is obviously enlarged in the transverse direction when the needle electrode number is increased from 1 to 13. An area approximately 65 × 45 mm2 diffuse discharge plasma region under 13 needle electrodes can be obtained and the discharge plasma still keeps good uniformity, which could be used for large-area surface processing in several fields spanning from biological sterilization and plasma medicine to surface modification of materials and synthesis of functional materials.
Precisely predicting and designing the elasticity of metallic glasses
Authors: Liu Z. Q. , Wang R. F. , Qu R. T. , Zhang Z. F.
Published: May 2014

We reveal that the elastic moduli of metallic glasses (MGs) invariably vary in a much steeper manner than that predicted by the conventional “rule of mixtures” in individual alloy systems. Such deviations are proved to originate fundamentally from their disordered atomic structures and intrinsic local heterogeneities. By treating the MGs as atomic-level dual phase hybrids, we further propose universal relations to be capable of precisely predicting and designing the elastic constants of MGs. This may contribute to the development of MGs with intended properties and behaviors, and allow new understandings on the structures and properties as well as their relationships in MGs.
Microwave losses in MgO, LaAlO3, and (La0.3Sr0.7)(Al0.65Ta0.35)O3 dielectrics at low power and in the millikelvin temperature range
Authors: Arzeo M. , Lombardi F. , Bauch T.
Published: May 2014

We have investigated both the temperature and the power dependence of microwave losses for various dielectrics commonly used as substrates for the growth of high critical temperature superconductor thin films. We present measurement of niobium superconducting λ∕2 coplanar waveguide resonators, fabricated on MgO, LaAlO3, and (La0.3Sr0.7)(Al0.65Ta0.35)O3 (LSAT), at the millikelvin temperature range and at low input power. By comparing our results with the two-level system model, we have discriminated among different dominant loss mechanisms. LSAT has shown the best results as regards the dielectric losses in the investigated regimes.
Negative and conventional magnetocaloric effects of a MnRhAs single crystal
Authors: Balli M. , Fruchart D. , Zach R.
Published: May 2014

We report on the magnetic and magnetocaloric properties of a MnRhAs single crystal. The ternary arsenide exhibits a rather complex magnetic behaviour. A first order metamagnetic type transition from antiferromagnetic (AFI) to ferromagnetic (“F”) states takes place at TT ∼ 158 K, and a second order transition from F to AFII states occurs at TC ∼ 196 K, the paramagnetic state occurring at T > TN = 238 K. Magnetic entropy changes were calculated using, Maxwell relation, and Clausius-Clapeyron equation. Both approaches are compared and discussed. The AFI-F transition in MnRhAs gives rise to an interestingly high level of negative magnetocaloric effect. Under a field change 0-1 T, the maximum magnetic entropy variation is about 3 J/kg K. For sufficiently high enough magnetic fields, the magnetocaloric working temperature range below 158 K can be covered. The F-AFII transition is accompanied by a relatively modest magnetocaloric effect (−2.3 J/kg K for 5 T at TC = 196 K), but it improves the working temperature span as well as the magnetocaloric properties. A minimum estimated refrigerant capacity of about 900 J/kg can be provided by a MnRhAs single crystal compound.
Investigations of stochastic resonance in two-terminal device with vanadium dioxide film
Authors: Aliev V. Sh. , Bortnikov S. G. , Badmaeva I. A.
Published: May 2014

The results of stochastic resonance investigation in a nonlinear system, consisting of a microstructure with a polycrystalline vanadium dioxide (VO2) film grown on sapphire and resistor in series are reported. Nonlinearity of the system was provided due to insulator-metal phase transition in VO2. In the stochastic resonance regime at 100 Hz signal frequency, the transition coefficient of signal-to-noise ratio reached 87 in contrast to 250 for microstructures with VO2 films grown on silica in our previous investigations. The measured characteristics of microstructures with VO2 films grown on silica and sapphire substrates were found to be qualitatively similar. For both substrates, a stochastic resonance was observed at threshold switching voltage from insulating to metallic state of VO2. For sapphire substrate the output signal-to-noise ratio rose at higher signal frequencies. The stochastic resonance phenomenon in VO2 films is explained in terms of the monostable damped oscillator model.
Quantitative non-contact voltage profiling of quasi one-dimensional nanoelectronic devices
Authors: Jeong Huiseong , Ahn Y. H. , Lee Soonil , Park Ji-Yong
Published: May 2014

Local electrical characterization tools, such as Electrostatic force microscopy (EFM), can provide local electrical information of nanoelectronic devices, albeit mostly qualitative. For example, EFM images are convolution of local surface potential, capacitance, and contact potential variations in the device. In this study, we demonstrate a calibration procedure to obtain quantitative local voltage distributions of quasi one-dimensional nanoelectronic devices based on carbon nanotubes and ZnO nanowires. By comparing the results with IV measurements of the same devices, we can obtain local electrical properties of devices such as contact resistance, intrinsic resistivity of the nanomaterial, and resistance of a defect.
Electrical efficiency study of alternating current and direct current power topologies in office building with integrated photovoltaics in Matlab-Simulink environment
Authors: Viitanen J. , Halonen L.
Published: May 2014

Electrical efficiency and the energy balance of an office building (Espoo, Finland: 60.11°N, 24.49°E) with an integrated photovoltaic system were studied using a Matlab-Simulink model. The model consisted of measured on-site photovoltaic data, measured luminaire data, and consumption data of computers and ventilation system that was obtained from online sources. Similar model was studied with four different voltages: 12 V DC, 24 V DC, 48 V DC, and 230 V AC, and the system components were selected accordingly. All components selected for the simulations were commercially available. Light-emitting diode (LED)- and fluorescent-lamp lighting were used in the simulation, and they were compared to each other. Based on the simulations, the annual energy balance of each simulated option was calculated, and the annual grid electricity costs were estimated. The results were calculated for similar systems with and without battery backup system. The energy balance of the building was studied in different months, as the seasonal differences in the available solar energy vary considerably in the location of the simulated building. The total energy consumption of the building was lowest when 230 V AC was used as the system voltage. This was mainly due to the fact that computer power supplies designed for smaller DC voltages were considerably less energy efficient, than those designed for 230 V AC. When only the energy efficiency of the lighting was considered, 48 V DC provided best results with LED lighting and 24 V DC with the fluorescent lamp lighting. The LED lighting was more energy efficient than the fluorescent lamp lighting in all studied voltages. 12 V DC system required thicker wires than the other options, and even then, the wire losses were more prominent. Battery backup system reduced the amount of bought and sold grid energy in all tested situations. Whether this is economically sensible depends on the price of the sold and bought grid energy. In this study, the initial assumption was that the price was the same regardless of the direction of energy flow, and in that case, the battery backup provided no savings, in terms of direct energy costs. The seasonal differences in the grid energy requirement were considerable. In July, the building was self sufficient in electricity production on a daily level, in April, about 80% of the electricity was produced locally, and in December, only 2%–5% of the needed electricity was produced locally.
Formation of an Unusual Bis(diguanidinate) Ligand via Nucleophilic Attack of a Guanidinate onto a Carbodiimide
Authors: Melen Rebecca L. , Simmonds Hayley R. , Wadepohl Hubert , Wood Paul T. , Gade Lutz H. , Wright Dominic S.
Published: May 2014

During an investigation of the synthesis of the new mono- and bis(guanidinate) complexes [{iPr2NC(···NiPr)2}GaCl2] (2) and [{iPr2NC(···NiPr)2}2GaCl] (3) from the in situ reactions of the lithium guanidinate [{iPr2NC(···NiPr)2}Li]n (1) with GaCl3, an unexpected new guanidinate expansion reaction was uncovered in which it is found that the nucleophilic addition of 2 to the carbodiimide, iPrN=C=NiPr, gives [iPrN{C(NiPr)=NiPr}{C(=NiPr)NiPr2}GaCl2] (4), containing an unusual bis(diguanidinate) ligand.
Real-time conformational changes in LacY
Authors: Smirnova Irina , Kasho Vladimir , Kaback H. Ronald
Published: May 2014

Significance

The lactose permease from
Escherichia coli
(LacY), a model for the major facilitator superfamily, catalyzes the symport of a galactopyranoside and an H
+
across the membrane by a mechanism in which the sugar-binding site in the middle of the protein becomes alternately accessible to either side of the membrane. The global conformational change is dissected into events that occur on the cytoplasmic and periplasmic aspects of LacY. Rates of individual steps are measured directly during opening or closing of periplasmic or cytoplasmic cavities by utilizing changes in Trp-bimane fluorescence with LacY in a phospholipid membrane. The findings provide a better understanding of the alternating access mechanism.
Multiple solvent, N-methyl-2-pyrrolidone, acts as a novel adjuvant for enhancing cutaneous immune responses
Authors: Tatsuno Tomoko , Miyazaki Kentaro , Yamashiro Hiromichi
Published: May 2014

N-methyl-2-pyrrolidone (NMP) is known for its multi-solvent properties. However, its biological, especially immunological significance still remains to be elucidated. In this study, we show for the first time that NMP stimulates the skin immune system by activating epidermal Langerhans cells (LCs). In contrast with the placebo tape, when the NMP-containing adhesive tape was applied on murine skin, LCs were stimulated immediately. Activated LCs not only exhibited enhanced expression of major histocompatibility complex class II and morphological changes, including the loss of dendrites, but also migrated effectively to draining lymph nodes. In addition, application of the tyrosine-related protein-2 peptide, which is the cytotoxic T lymphocyte (CTL) epitope against B16 melanoma, in combination with the NMP tape, resulted in explosive expansion of specific CTLs in mouse spleens. Taken together, these results demonstrate a novel role of NMP as an adjuvant in percutaneous peptide immunization.
Establishment of a new method to quantitatively evaluate hyphal fusion ability in Aspergillus oryzae
Authors: Tsukasaki Wakako , Maruyama Jun-ichi , Kitamoto Katsuhiko
Published: May 2014

Hyphal fusion is involved in the formation of an interconnected colony in filamentous fungi, and it is the first process in sexual/parasexual reproduction. However, it was difficult to evaluate hyphal fusion efficiency due to the low frequency in Aspergillus oryzae in spite of its industrial significance. Here, we established a method to quantitatively evaluate the hyphal fusion ability of A. oryzae with mixed culture of two different auxotrophic strains, where the ratio of heterokaryotic conidia growing without the auxotrophic requirements reflects the hyphal fusion efficiency. By employing this method, it was demonstrated that AoSO and AoFus3 are required for hyphal fusion, and that hyphal fusion efficiency of A. oryzae was increased by depleting nitrogen source, including large amounts of carbon source, and adjusting pH to 7.0.
Genome-wide analysis ofSaccharomyces cerevisiaeidentifies cellular processes affecting intracellular aggregation of Alzheimer's amyloid-β42: importance of lipid homeostasis
Authors: Nair S. , Traini M. , Dawes I. W. , Perrone G. G.
Published: May 2014

Amyloid-β (Aβ)–containing plaques are a major neuropathological feature of Alzheimer's disease (AD). The two major isoforms of Aβ peptide associated with AD are Aβ40 and Aβ42, of which the latter is highly prone to aggregation. Increased presence and aggregation of intracellular Aβ42 peptides is an early event in AD progression. Improved understanding of cellular processes affecting Aβ42 aggregation may have implications for development of therapeutic strategies. Aβ42 fused to green fluorescent protein (Aβ42-GFP) was expressed in ∼4600 mutants of a Saccharomyces cerevisiae genome-wide deletion library to identify proteins and cellular processes affecting intracellular Aβ42 aggregation by assessing the fluorescence of Aβ42-GFP. This screening identified 110 mutants exhibiting intense Aβ42-GFP–associated fluorescence. Four major cellular processes were overrepresented in the data set, including phospholipid homeostasis. Disruption of phosphatidylcholine, phosphatidylserine, and/or phosphatidylethanolamine metabolism had a major effect on intracellular Aβ42 aggregation and localization. Confocal microscopy indicated that Aβ42-GFP localization in the phospholipid mutants was juxtaposed to the nucleus, most likely associated with the endoplasmic reticulum (ER)/ER membrane. These data provide a genome-wide indication of cellular processes that affect intracellular Aβ42-GFP aggregation and may have important implications for understanding cellular mechanisms affecting intracellular Aβ42 aggregation and AD disease progression.
Role of TGF-β receptor III localization in polarity and breast cancer progression
Authors: Meyer Alison E. , Gatza Catherine E. , How Tam , Starr Mark , Nixon Andrew B. , Blobe Gerard C.
Published: May 2014

The majority of breast cancers originate from the highly polarized luminal epithelial cells lining the breast ducts. However, cell polarity is often lost during breast cancer progression. The type III transforming growth factor-β cell surface receptor (TβRIII) functions as a suppressor of breast cancer progression and also regulates the process of epithelial-to-mesenchymal transition (EMT), a consequence of which is the loss of cell polarity. Many cell surface proteins exhibit polarized expression, being targeted specifically to the apical or basolateral domains. Here we demonstrate that TβRIII is basolaterally localized in polarized breast epithelial cells and that disruption of the basolateral targeting of TβRIII through a single amino acid mutation of proline 826 in the cytosolic domain results in global loss of cell polarity through enhanced EMT. In addition, the mistargeting of TβRIII results in enhanced proliferation, migration, and invasion in vitro and enhanced tumor formation and invasion in an in vivo mouse model of breast carcinoma. These results suggest that proper localization of TβRIII is critical for maintenance of epithelial cell polarity and phenotype and expand the mechanisms by which TβRIII prevents breast cancer initiation and progression.
DualAligner
: a dual alignment-based strategy to align protein interaction networks
Authors: Seah Boon-Siew , Bhowmick Sourav S. , Dewey C. Forbes
Published: May 2014

Motivation: Given the growth of large-scale protein–protein interaction (PPI) networks obtained across multiple species and conditions, network alignment is now an important research problem. Network alignment performs comparative analysis across multiple PPI networks to understand their connections and relationships. However, PPI data in high-throughput experiments still suffer from significant false-positive and false-negatives rates. Consequently, high-confidence network alignment across entire PPI networks is not possible. At best, local network alignment attempts to alleviate this problem by completely ignoring low-confidence mappings; global network alignment, on the other hand, pairs all proteins regardless. To this end, we propose an alternative strategy: instead of full alignment across the entire network or completely ignoring low-confidence regions, we aim to perform highly specific protein-to-protein alignments where data confidence is high, and fall back on broader functional region-to-region alignment where detailed protein–protein alignment cannot be ascertained. The basic idea is to provide an alignment of multiple granularities to allow biological predictions at varying specificity.

Results:  DualAligner performs dual network alignment , in which both region-to-region alignment, where whole subgraph of one network is aligned to subgraph of another, and protein-to-protein alignment, where individual proteins in networks are aligned to one another, are performed to achieve higher accuracy network alignments. Dual network alignment is achieved in DualAligner via background information provided by a combination of Gene Ontology annotation information and protein interaction network data. We tested DualAligner on the global networks from IntAct and demonstrated the superiority of our approach compared with state-of-the-art network alignment methods. We studied the effects of parameters in DualAligner in controlling the quality of the alignment. We also performed a case study that illustrates the utility of our approach.

Availability and implementation:  http://www.cais.ntu.edu.sg/∼assourav/DualAligner/

Contact:  seah0097@ntu.edu.sg or assourav@ntu.edu.sg

Supplementary information:  Supplementary data are available at Bioinformatics online.
New aspects of IgA synthesis in the gut
Authors: Suzuki Keiichiro , Nakajima Akira
Published: May 2014

In mammals, the gastrointestinal tract is colonized by extremely dense and diverse bacterial communities that are beneficial for health. Maintenance of the complexity and the proper localization and distribution of gut bacteria is of prime importance because when disrupted, the microbial community attacks the host’s tissues and causes inflammatory reactions. Our immune system provides the necessary mechanisms to maintain the homeostatic balance between microbial communities and the host. IgA plays crucial roles in regulation of host–bacteria interactions in the gut. IgA is the most abundant immunoglobulin isotype in our body, mostly produced by the IgA plasma cells residing in the lamina propria of the small and large intestine. Although it was well known that IgA provides protection against pathogens, only recently has it become clear that IgA plays critical roles in regulation of bacterial communities in the gut in steady-state conditions. Here, we summarize recent progress in our understanding of the various mechanisms of IgA synthesis in multiple anatomical sites and discuss how IgA limits bacterial access to the internal milieu of the host.
Extracting Wisdom from Experts and Small Crowds: Strategies for Improving Informant-based Measures of Political Concepts
Authors: Maestas Cherie D. , Buttice Matthew K. , Stone Walter J.
Published: May 2014

Social scientists have increasingly turned to expert judgments to generate data for difficult-to-measure concepts, but getting access to and response from highly expert informants can be costly and challenging. We examine how informant selection and post-survey response aggregation influence the validity and reliability of measures built from informant observations. We draw upon three surveys with parallel survey questions of candidate characteristics to examine the trade-off between expanding the size of the local informant pool and the pool's level of expertise. We find that a “wisdom-of-crowds” effect trumps the benefits associated with the expertise of individual informants when the size of the rater pool is modestly increased. We demonstrate that the benefits of expertise are best realized by prescreening potential informants for expertise rather than post-survey weighting by expertise.
Mining Novel Effector Proteins from the Esophageal Gland Cells ofMeloidogyne incognita
Authors: Rutter William B. , Hewezi Tarek , Abubucker Sahar , Maier Tom R. , Huang Guozhong , Mitreva Makedonka , Hussey Richard S. , Baum Thomas J.
Published: May 2014

Meloidogyne incognita is one of the most economically damaging plant pathogens in agriculture and horticulture. Identifying and characterizing the effector proteins which M. incognita secretes into its host plants during infection is an important step toward finding new ways to manage this pest. In this study, we have identified the cDNAs for 18 putative effectors (i.e., proteins that have the potential to facilitate M. incognita parasitism of host plants). These putative effectors are secretory proteins that do not contain transmembrane domains and whose genes are specifically expressed in the secretory gland cells of the nematode, indicating that they are likely secreted from the nematode through its stylet. We have determined that, in the plant cells, these putative effectors are likely to localize to the cytoplasm. Furthermore, the transcripts of many of these novel effectors are specifically upregulated during different stages of the nematode's life cycle, indicating that they function at specific stages during M. incognita parasitism. The predicted proteins showed little to no homology to known proteins from free-living nematode species, suggesting that they evolved recently to support the parasitic lifestyle. On the other hand, several of the effectors are part of gene families within the M. incognita genome as well as that of M. hapla, which points to an important role that these putative effectors are playing in both parasites. With the discovery of these putative effectors, we have increased our knowledge of the effector repertoire utilized by root-knot nematodes to infect, feed on, and reproduce on their host plants. Future studies investigating the roles that these proteins play in planta will help mitigate the effects of this damaging pest.
A Zoospore Inoculation Method with Phytophthora sojae to Assess the Prophylactic Role of Silicon on Soybean Cultivars
Authors: Guérin Valérie , Lebreton Amandine , Cogliati Erik E. , Hartley Sue E. , Belzile François , Menzies James G. , Bélanger Richard R.
Published: May 2014

The objective of this study was to evaluate whether silicon (Si) amendments, known to have a prophylactic role against biotrophic and hemibiotrophic pathogens, could protect soybean against Phytophthora sojae. To fulfill this objective, the initial challenge was to develop a method of inoculation that reproduced the natural infection process while allowing regular Si feeding to the plants. In a first set of experiments, inoculation of P. sojae zoospores directly into hydroponic solutions led to reproducible infections and expected phenotypes when using ‘Williams’ (rps), ‘L75-6141’ (Rps1a), ‘haro15’ (Rps1k), and ‘L77-1863’ (Rps1b) soybean challenged to races 3 and 7 of P. sojae. This approach offers the advantage of testing simultaneously many soybean cultivars against different races of P. sojae in a controlled environment, and the expression of partial and root resistance. In a second set of experiments aimed at testing the effect of Si, our results clearly showed that Si amendments had a significant effect on disease reduction and plant yield. The effect was particularly noticeable when combined with a cultivar displaying a certain level of resistance to the disease. These results demonstrate a useful method of direct inoculation of soybean plants with P. sojae zoospores through a hydroponic system and show that Si amendments can represent an alternative method of control of P. sojae against soybean.
Fungicide Resistance of Two Species of Alternaria from Potato in the Columbia Basin of Washington
Authors: Tymon Lydia , Johnson Dennis A.
Published: May 2014

Fungicides are extensively used in the Columbia Basin of Washington in an effort to manage early blight and brown spot on potato caused by Alternaria solani and A. alternata, respectively. Azoxystrobin and boscalid interfere with cellular respiration, and fungicide resistance is expected to occur in fungal populations due to the narrow modes of action dictated by each fungicide. The objective of this research was to assess A. solani and A. alternata populations in the Columbia Basin of Washington for azoxystrobin and boscalid resistance by initially screening isolates at a threshold concentration using mycelial growth and spore germination. Fifty isolates of A. solani and 58 of A. alternata were randomly selected for screening from 671 isolates collected from potato in the Columbia Basin from 2009 to 2011. Screening at a threshold concentration was done to estimate the range of fungicide resistance within the populations of A. solani and A. alternata in the region. Resistance of five isolates that differed in sensitivity to azoxystrobin and boscalid were then assessed for mycelial growth and spore germination at three fungicide concentrations in order to determine where rates were no longer effective. A. solani mycelial growth ratios and percent spore germination on azoxystrobin-amended media did not change from 2010 to 2011. A slight decrease in resistance of mycelial growth to azoxystrobin was exhibited among A. alternata isolates collected between 2010 and 2011. No change in sensitivity to azoxystrobin was observed in mycelial growth ratios among A. alternata isolates collected between 2010 and 2011. Resistance to boscalid by A. solani increased as indicated by a significant increase in mean mycelial growth ratio from 2010 to 2011, whereas A. alternata showed no change. Spore germination of A. solani was less at 100 μg/ml than at 1 or 10 μg/ml azoxystrobin. Spore germination of A. alternata did not differ among 1, 10, or 100 μg/ml azoxystrobin. Spore germination of A. solani and A. alternata did not differ among 0.5, 5, or 50 μg/ml boscalid. Resistance to azoxystrobin and boscalid in A. solani and A. alternata populations was shown to be present in the Columbia Basin and will likely become widespread with continued used of site-specific fungicides.
Postinfection Activity of Synthetic Antimicrobial Peptides Against Stemphylium vesicarium in Pear
Authors: Puig M. , Moragrega C. , Ruz L. , Montesinos E. , Llorente I.
Published: May 2014

Brown spot of pear is a fungal disease of economic importance caused by Stemphylium vesicarium that affects the pear crops in Europe. Due to the characteristics of this disease and the moderate efficacy of available fungicides, the effectiveness of control measures is very limited; however, synthetic antimicrobial peptides (AMPs) may be a complement to these fungicides. In the present study, 12 AMPs of the CECMEL11 library were screened for fungicidal activity against S. vesicarium. In vitro experiments showed that eight AMPs significantly reduced the germination of conidia. The most effective peptides, BP15, BP22, and BP25, reduced fungal growth and sporulation at concentrations below 50 μM. Leaf assays showed that preventive application of BP15 and BP22 did not reduce infection; however, when the peptides were applied curatively, infection was significantly reduced. The use of a BP15 fluorescein 5-isothiocyanate conjugate revealed that the peptide binds to hyphae and germ tubes and produces malformations that irreversibly stop their development.
A Recombinant of Bean common mosaic virus Induces Temperature-Insensitive Necrosis in an I Gene-Bearing Line of Common Bean
Authors: Feng Xue , Poplawsky Alan R. , Karasev Alexander V.
Published: May 2014

The I gene is a single, dominant gene conferring temperature-sensitive resistance to all known strains of Bean common mosaic virus (BCMV) in common bean (Phaseolus vulgaris). However, the closely related Bean common mosaic necrosis virus (BCMNV) induces whole plant necrosis in I-bearing genotypes of common bean, and the presence of additional, recessive genes is required to prevent this severe whole plant necrotic reaction caused by BCMNV. Almost all known BCMNV isolates have so far been classified as having pathotype VI based on their interactions with the five BCMV resistance genes, and all have a distinct serotype A. Here, we describe a new isolate of BCMV, RU1M, capable of inducing whole plant necrosis in the presence of the I gene, that appears to belong to pathotype VII and exhibits B-serotype. Unlike other isolates of BCMV, RU1M was able to induce severe whole plant necrosis below 30°C in bean cultivar Jubila that carries the I gene and a protective recessive gene bc-1. The whole genome of RU1M was cloned and sequenced and determined to be 9,953 nucleotides long excluding poly(A), coding for a single polyprotein of 3,186 amino acids. Most of the genome was found almost identical (>98%) to the BCMV isolate RU1-OR (also pathotype VII) that did not induce necrotic symptoms in ‘Jubila’. Inspection of the nucleotide sequences for BCMV isolates RU1-OR, RU1M, and US10 (all pathotype VII) and three closely related sequences of BCMV isolates RU1P, RU1D, and RU1W (all pathotype VI) revealed that RU1M is a product of recombination between RU1-OR and a yet unknown potyvirus. A 0.8-kb fragment of an unknown origin in the RU1M genome may have led to its ability to induce necrosis regardless of temperature in beans carrying the I gene. This is the first report of a BCMV isolate inducing temperature-insensitive necrosis in an I gene containing bean genotype.
Definition of Plant-Pathogenic Pseudomonas Genomospecies of the Pseudomonas syringae Complex Through Multiple Comparative Approaches
Authors: Marcelletti Simone , Scortichini Marco
Published: May 2014

A total of 34 phytopathogenic strain genomes belonging to the Pseudomonas syringae species complex and related species, including many pathotype strains, were assessed using average nucleotide identity (ANI) analysis. Their taxonomic relationships were consistently confirmed by the tetranucleotide frequency correlation coefficient (TETRA) values, multilocus sequence typing analysis (MLSA) performed with seven housekeeping genes, using both maximum likelihood and Bayesian methods, and split consensus network analyses. The ANI, MLSA, and split consensus analyses provided consistent and identical results. We confirmed the occurrence of the well-demarcated genomospecies inferred sensu Gardan et al. using DNA-DNA hybridization and ribotyping analyses. However, some P. syringae strains of the pathovars morsprunorum and lachrymans were placed in different genomospecies in our analyses. Genomospecies 1, 2, 4, 6, and 9 resulted well demarcated, whereas strains of genomospecies 3 and 8 had ANI values between 95 and 96% in some cases, confirming that this threshold reveals very closely related species that might represent cases of splitting entities or the convergence of different species to the same ecological niche. This study confirms the robustness of the combination of genomic and phylogenetic approaches in revealing taxonomic relationships among closely related bacterial strains and provides the basis for a further reliable demarcation of the phytopathogenic Pseudomonas species. Within each species, the pathovars might represent distinct ecological units. The possibility of performing extensive and standardized host range and phenotypic tests with many strains of different pathovars can assist phytobacteriologists for better determining the boundaries of these ecological units.
Establishing homology between mitochondrial calcium uniporters, prokaryotic magnesium channels and chlamydial IncA proteins
Authors: Lee Andre , Vastermark Ake , Saier Milton H.
Published: May 2014

Mitochondrial calcium uniporters (MCUs) (TC no. 1.A.77) are oligomeric channel proteins found in the mitochondrial inner membrane. MCUs have two well-conserved transmembrane segments (TMSs), connected by a linker, similar to bacterial MCU homologues. These proteins and chlamydial IncA proteins (of unknown function; TC no. 9.B.159) are homologous to prokaryotic Mg2+transporters, AtpI and AtpZ, based on comparison scores of up to 14.5sds. A phylogenetic tree containing all of these proteins showed that the AtpZ proteins cluster coherently as a subset within the large and diverse AtpI cluster, which branches separately from the MCUs and IncAs, both of which cluster coherently. The MCUs and AtpZs share the same two TMS topology, but the AtpIs have four TMSs, and IncAs can have either two (most frequent) or four (less frequent) TMSs. Binary alignments, comparison scores and motif analyses showed that TMSs 1 and 2 align with TMSs 3 and 4 of the AtpIs, suggesting that the four TMS AtpI proteins arose via an intragenic duplication event. These findings establish an evolutionary link interconnecting eukaryotic and prokaryotic Ca2+and Mg2+transporters with chlamydial IncAs, and lead us to suggest that all members of the MCU superfamily, including IncAs, function as divalent cation channels.
Structure of the LCMV nucleoprotein provides a template for understanding arenavirus replication and immunosuppression
Authors: West Brandyn R. , Hastie Kathryn M. , Saphire Erica Ollmann
Published: May 2014

The X-ray crystal structure of theLymphocytic choriomeningitis virusnucleoprotein C-terminal immunosuppressive domain (LCMV NPΔ340) was determined to 2.0 Å resolution. The structure indicates that LCMV NPΔ340, like the other structurally characterized arenaviral nucleoproteins, adopts the fold of an exonuclease. This structure provides a crucial three-dimensional template for functional exploration of the replication and immunosuppression of this prototypic arenavirus.
Structural and bioinformatic characterization of anAcinetobacter baumanniitype II carrier protein
Authors: Allen C. Leigh , Gulick Andrew M.
Published: May 2014

Microorganisms produce a variety of natural productsviasecondary metabolic biosynthetic pathways. Two of these types of synthetic systems, the nonribosomal peptide synthetases (NRPSs) and polyketide synthases (PKSs), use large modular enzymes containing multiple catalytic domains in a single protein. These multidomain enzymes use an integrated carrier protein domain to transport the growing, covalently bound natural product to the neighboring catalytic domains for each step in the synthesis. Interestingly, some PKS and NRPS clusters contain free-standing domains that interact intermolecularly with other proteins. Being expressed outside the architecture of a multi-domain protein, these so-called type II proteins present challenges to understand the precise role they play. Additional structures of individual and multi-domain components of the NRPS enzymes will therefore provide a better understanding of the features that govern the domain interactions in these interesting enzyme systems. The high-resolution crystal structure of a free-standing carrier protein fromAcinetobacter baumanniithat belongs to a larger NRPS-containing operon, encoded by the ABBFA_003406–ABBFA_003399 genes ofA. baumanniistrain AB307-0294, that has been implicated inA. baumanniimotility, quorum sensing and biofilm formation, is presented here. Comparison with the closest structural homologs of other carrier proteins identifies the requirements for a conserved glycine residue and additional important sequence and structural requirements within the regions that interact with partner proteins.
Tannic acid-modified fatty amide anticorrosive coatings from Pongamia glabra oil
Authors: Alam Manawwer , M. Alandis Naser
Published: May 2014

Purpose

– The purpose of this investigation was to develop sustainable resource-based anticorrosive coating material using Pongamia glabra seed oil and tannic acid (TA), as well as to improve the coating properties.

Design/methodology/approach

– TA-modified fatty amide diol was synthesized by condensation polymerization. First, Pongamia glabra seed oil was converted to fatty amide diol (Pongamia oil fatty amide, PFA) that was further modified by TA with different parts per hundred of resin (10, 15 and 20) to develop a polyether fatty amide (PFA-TA). The confirmation of reaction between TA and PFA was carried out using Fourier transform infrared spectroscopy. The thermal behavior of PFA-TA was studied by thermogravimetric analyses. Coatings of several PFA-TA resins were applied to steel (i.e. plain carbon steel) coupons to investigate their physico-mechanical and anticorrosive performance. The corrosion protection performance was observed using AC impedance and polarization tests.

Findings

– TA-modified fatty amide coatings showed the highest scratch hardness of 2.5 kg, flexibility (1/8 inch) and gloss at 45° was 60-62. Among all compositions, PFA-TA15 showed the best physico-mechanical and anticorrosion performance. Corrosion tests of coated panels were examined in different corrosive media (3.5 wt per cent HCl, 3.5 wt per cent NaOH and 5.0 wt per cent NaCl) using potentiodynamic polarization and AC impedance measurements. PFA-TA may find application as an eco-friendly protective coating, and thermal analyses revealed that it can be safely used up to 300°C.

Originality/value

– This paper provides the development of protective coatings for steel from non-edible seed oil and TA to utilize sustainable resources.
Corrosion control in CO2/H2S-produced water of offshore oil fields
Authors: Lu Yuan , Zhang Ying , Liu Zhenguo , Zhang Yong , Wang Chaoming , Guo Haijun
Published: May 2014

Purpose

– In order to solve the corrosion problems in the South China Sea, the purpose of this paper was to study the main influences of corrosion including temperature, H2S content and corrosion inhibitor content in CO2/H2S oil field-produced water.

Design/methodology/approach

– The corrosion products formed on the steel surface were observed and analyzed using scanning electron microscope (SEM) and X-ray diffraction (XRD).

Findings

– The results indicate that temperature significantly influences the corrosion rate, which is a maximum at 70°C. The corrosion rate decreases as H2S content increases which is less than 10 mg/L, but then it increases rapidly. The FeCO3/Fe
x
S
y
protective film and a corrosion inhibition also were considered.

Research limitations/implications

– A mixture containing an imidazoline derivate and an organic amine can enhance the corrosion resistance of the corrosion product film.

Practical implications

– A mixture containing an imidazoline derivate and an organic amine can enhance the corrosion product film corrosion resistance.

Social implications

– Imidazoline is one kind of environmentally safe agent which can be used in the ocean.

Originality/value

– The corrosion can be controlled to a satisfactory extent in the presence of a mixture containing an imidazoline derivate and an organic amine.
The durability of sulfate resisting mortar with partial replacement by cement kiln dust
Authors: M. Kassim Moayad
Published: May 2014

Purpose

– The purpose of this study was to reuse cement kiln dust (CKD) in cement products and report the results of determining the long-term compression and flexural tensile strengths of mortars containing CKD as a partial replacement of sulfate-resistant cement (SRC). During the manufacturing of Portland cement, voluminous quantities of the byproduct dust are produced, which is commonly known as CKD. In the past decade, according to environmental requirements, many researchers have attempted to reuse CKD in cement products.

Design/methodology/approach

– The long-term compression and flexural tensile strengths of mortars containing CKD as a partial replacement of SRC were tested. The replacement ratios in this study were 0, 5, 10, 15 and 20 per cent. The specimens were exposed to a highly saline environment after normal curing in water for a 28-day period.

Findings

– The results indicated a slight increase in the strength of CKD–SRC mortar containing 10 per cent CKD and moderate sulfate resistance when the CKD ratio reached 20 per cent, as compared to the reference mortar. In addition, CKD did not adversely affect the properties of SRC mortar subjected to sulfate exposure, even after one year.

Originality/value

– The tests were inducted for the first time on SRC, and the new results can be used to produce an environmental-friendly concrete.