bluuebunny/crossref_metadata_2025 huggingface dataset:
Nanoparticles of K2Ca2(SO4)3:Eu as effective detectors for swift heavy ions
Authors: Salah Numan , Lochab S. P. , Kanjilal D. , Ranjan Ranju , Habib Sami S. , Rupasov A. A. , Aleynikov V. E.
Published: September 2007

The modification of thermoluminescence (TL) and photoluminescence (PL) properties of K2Ca2(SO4)3:Eu nanoparticles by swift heavy ions (SHI), irradiation is studied. Pellets form of the nanomaterials were irradiated by 48 MeV Li3+, 75 MeV C6+, and 90 MeV O7+ ion beams. The fluence range is 1×109−1×1013 ions/cm2. The modification in TL glow curves of the nanomaterials irradiated by Li3+, C6+, and O7+ ion beams are essentially similar to those induced by γ-ray irradiation. These glow curves have single peaks at around 427 K with a small variation in their positions by around ±3 K. The TL intensity of the ion beams irradiated nanomaterials is found to decease, while going from low to high atomic number (Z) ions (i.e., Li3+→O7+). The TL response curve of the pellets irradiated by Li3+ ions is linear in the whole range of studied fluences. The curves for C6+ and O7+ irradiated samples are linear at lower fluences (1×109–1×1012 ion/cm2) and then saturate at higher fluence. These results for the nanomaterials are much better than that of the corresponding microcrystalline samples irradiated with a Li3+ ion. The curves were linear up to the fluence 1×1011 ion/cm2 and then become sublinear at higher fluences. The TL efficiency values of K2Ca2(SO4)3:Eu nanoparticles irradiated by 48 MeV Li3+, 75 MeV C6+, and 90 MeV O7+ ion beams have been measured relative to γ rays of C60o and are found to be 0.515, 0.069, and 0.019, respectively. This value for the Li3+ ion (0.515) is much higher than that of the corresponding microcrystalline material (0.0014). These superiorities for the nanomaterials make K2Ca2(SO4)3:Eu nanophosphor a suitable candidate for detecting the doses of swift heavy ions. PL studies on the ion beams irradiated and unirradiated K2Ca2(SO4)3:Eu nanoparticles show a single band at 384 nm, which could be assigned to Eu2+ emission, while the microcrystalline form of this material shows emission at 436 nm. This wide blueshift in PL of the nanomaterial could be attributed to the extension of the band gap of Eu2+ due to the absence of crystal field effects.
Lattice thermal conductivity of group-IV and III–V semiconductor alloys
Authors: Adachi Sadao
Published: September 2007

The room-temperature thermal conductivity of semiconductor alloys is analyzed using a simplified model of the alloy-disorder scattering. Good agreement is achieved between the present model and published experimental data on various group-IV and III−V semiconductor alloys. A complete set of alloy-disorder parameters are estimated, which makes it possible to calculate the lattice thermal conductivity for optional composition of III−V semiconductor alloys, including III−N alloys. An ordering effect is also examined for the explanation of some intermetallic and semiconductor compounds like CuAu and SiC.
All-carbon nanoswitch based on C70 molecule: A first principles study
Authors: OuYang Fangping , Xu Hui , Fan Toujiao
Published: September 2007

We have demonstrated the electron transport properties of an all-carbon molecular junction based on the C70 molecule connecting with two armchair single-wall carbon nanotubes using first principles transport calculations. It is shown that the Landauer conductance of this carbon hybrid system can be tuned within several orders of magnitude not only by changing the orientation of the C70 molecule but also by rotating one of the tubes around the symmetry axis of the system at fixed distances. This fact could make this pure-carbon molecular system a possible candidate for a nanoelectronic switching device. Moreover, we have also studied the nitrogen doping effect of such a molecular device. The results reveal that molecular configuration selection and nitrogen doping would play important roles in such switching devices.
Electronic structure of pentacene/ultrathin gate dielectric interfaces for low-voltage organic thin film transistors
Authors: Cho S. W. , Park D. S. , Jang W. C. , Cho M.-H. , Yoo K.-H. , Jeong K. , Whang C.-N. , Yi Y. , Chung K. B.
Published: September 2007

This paper describes the fabrication of pentacene-based thin film transistors (TFTs) with ultrathin (4.5nm) SiO2 and SiON gate dielectric layers for low-voltage operations. The device with the SiON gate dielectric layer operated at gate voltages lower than −3.0V, showing a threshold voltage of −0.45V, which was lower than the threshold voltage of the SiO2 device (−2.5V). The electronic structures of the interface between the pentacene and dielectric layers were investigated by in situ ultraviolet photoelectron spectroscopy (UPS) and x-ray photoelectron spectroscopy (XPS) to determine the reason for the lower operating voltage. The UPS and XPS results demonstrated that the interface dipole modified the potential of the dielectric layer, explaining the lower operating voltage. The electronic structure allowed for band bending at the interface, resulting in complete energy level diagrams for pentacene on SiO2 and SiON. The shifts in the threshold and turn-on voltages were explained by the energy level diagrams.
Amplification of terahertz radiation in quantum cascade structures
Authors: Mauro Cosimo , Green Richard P. , Tredicucci Alessandro , Beltram Fabio , Beere Harvey E. , Ritchie David A.
Published: September 2007

We explore the use of quantum cascade structures as amplifiers for terahertz radiation. For this purpose, two section devices were fabricated, in which the output from a ν∼2.3 THz laser section is amplified in a subsequent stage. For relatively short devices we obtain an amplification of 1.5×, in good agreement with the calculated level. Based on these results we predict that amplifications of up to 13 dB could be obtained for such structures using increased amplifier lengths of a few millimeters.
Band offsets and transport mechanisms of hydrogenated nanocrystalline silicon/crystalline silicon heterojunction diode: Key properties for device applications
Authors: Lu J. J. , Chen J. , He Y. L. , Shen W. Z.
Published: September 2007

We have studied the electrical properties of hydrogenated nanocrystalline silicon/crystalline silicon heterojunction diode, focusing on the band offsets and electron transport mechanisms. Capacitance-voltage (C-V) analysis reveals that the band discontinuity mainly exists on the valence-band side, and an interface charge density on the order of 1011cm−2 is estimated via the numerical C-V matching technique. Temperature- and bias-dependent transport mechanisms have been clarified by dark current-voltage-temperature measurements, and the extracted parameters indicate a transition from nontunneling to tunneling dominant transport from 350to20K.
Antenna impedance measurements in a magnetized plasma. II. Dipole antenna
Authors: Blackwell David D. , Walker David N. , Messer Sarah J. , Amatucci William E.
Published: September 2007

This paper presents experimental impedance measurements of a dipole antenna immersed in a magnetized plasma. The impedance was derived from the magnitude and phase of the reflected power using a network analyzer over a frequency range of 1MHz–1GHz. The plasma density was varied between 107and1010cm−3 in weakly (ωce<ωpe) and strongly (ωce>ωpe) magnetized plasmas in the Space Physics Simulation Chamber at the Naval Research Laboratory. Over this range of plasma conditions the wavelength in the plasma varies from the short dipole limit (λ≫L) to the long dipole limit (λ∼L). As with previous impedance measurements, there are two resonant frequencies observed as frequencies where the impedance of the antenna is real. Measurements have indicated that in the short dipole limit the majority of the power deposition takes place at the lower resonance frequency which lies between the cyclotron frequency and the upper hybrid frequency. These measured curves agree very well with the analytic theory for a short dipole in a magnetoplasma. In the long dipole regime, in addition to the short dipole effects still being present, there is resonant energy deposition which peaks at much higher frequencies and correlates to 1∕2 and 3∕2 wavelength dipole resonances. The wavelengths in the plasma predicted by these resonances are consistent with the antenna radiating R and L-waves.
Thermal conductance across grain boundaries in diamond from molecular dynamics simulation
Authors: Watanabe Taku , Ni Boris , Phillpot Simon R. , Schelling Patrick K. , Keblinski Pawel
Published: September 2007

We determine the dependence of the interfacial conductance on twist angle for (001) symmetric twist grain boundaries (GBs) in diamond. We find that the conductances are extremely large, ranging from 7.7to17.6GW∕m2K. Nevertheless, when normalized to the single-crystal conductivity, the resulting Kapitza lengths are actually longer in diamond than in Si, indicating that the diamond GBs are relatively worse conductors of heat. This result is consistent with the poorer bonding across the diamond grain boundaries. We find that the interfacial conductance and Kapitza length can be well fitted by an extended Read-Shockley model.
Simplified mathematical model for the formation of null singularities inside black holes. II. Proof for a particular case
Authors: Gorbonos Dan , Wolansky Gershon
Published: September 2007

We study a simple system of two hyperbolic semilinear equations inspired by the Einstein equations. The system, which was introduced by Ori and Gorbonos [J. Math. Phys., 48, 092502 (2007)], is a model for singularity formation inside black holes. We show for a particular case of the equations that the system demonstrates a finite time blowup. The singularity that is formed is a null singularity. Then we show that in this particular case the singularity has features that are analogous to known features of models of black-hole interiors—which describe the inner-horizon instability. Our simple system may provide insight into the formation of null singularities inside spinning or charged black holes.
Dynamics of elastic waves in two-dimensional phononic crystals with chaotic defect
Authors: Chen Jie , Cheng Jian-Chun , Li Baowen
Published: September 2007

The authors study dynamics of wave function in two-dimensional phononic crystals with different billiard defects. It is found that the elastic wave is localized in the defect region with soft material. The spatial statistical properties of wave function are studied. More strikingly, they find that given the same area, the chaotic billiard contains more energy than the integrable billiards such as rectangular and circular billiards. The dependence of this “chaotic effect” on wave number k is also studied.
The effect of band offset on the retention properties of metal-ferroelectric (PbZr0.53Ti0.47O3)-insulator (Dy2O3,Y2O3)-semiconductor capacitors and field effect transistors
Authors: Su Yu-Di , Shih Wen-Chieh , Lee Joseph Ya-min
Published: September 2007

Metal-ferroelectric-insulator-semiconductor field effect transistors (MFISFETs) and capacitors with the structures of Al∕Pb (Zr0.53,Ti0.47) O3 (PZT)∕Dy2O3∕Si and Al∕PZT∕Y2O3∕Si were fabricated. The variation of the memory window as a function of annealing temperature was studied. The maximum capacitor-voltage (C-V) memory window of Al∕PZT∕Dy2O3∕Si capacitors was 2.95V. The retention times of Al∕PZT∕Y2O3∕Si and Al∕PZT∕Dy2O3∕Si MFISFETs were 11.5days and 11.1h, respectively. The longer retention time of Al∕PZT∕Y2O3∕Si MFISFETs is attributed to the larger conduction band offset at the Y2O3∕Si interface (2.3eV) compared to that of Dy2O3∕Si (0.79eV).
Crystalline structure’s influence on the near-field optical properties of single plasmonic nanowires
Authors: Laroche Thierry , Vial Alexandre , Roussey Matthieu
Published: September 2007

The finite difference time domain method is employed to study the crystalline structure’s influence on the propagation of a local excitation along metallic nanowires of subwavelength cross section. The metallic nanowires are elongated cylinders deposited on a transparent substrate. A tightly focused gaussian beam illuminates one end of the nanowires. According to recent experimental studies, the authors show that the propagation length of the localized surface plasmon excitations depends on the crystalline structure of the nanowire. Thus, they are able to determine the effective permittivity of metals in such a nanostructure versus its crystalline properties. The authors also demonstrate that the field of optical information transport could greatly benefit from the care of the subwavelength optical waveguide’s crystallinity.
Nanoscale ablation on patterned diamondlike carbon film with femtosecond laser pulses
Authors: Miyaji Godai , Miyazaki Kenzo
Published: September 2007

The authors have studied the origin of nanostructure formation on diamondlike carbon film in femtosecond laser ablation at low fluence. Using the thin film target patterned with submicrometer-size stripes, they have observed that the nanostructure starts to be formed on the crest of stripes along the direction perpendicular to the laser polarization. The experimental results have shown that nanoscale ablation for the nanostructuring would preferentially be initiated by the enhancement of localized electric field on the stripe surface with high curvature.
Confinement of enhanced field investigated by tip-sample gap regulation in tapping-mode tip-enhanced Raman microscopy
Authors: Yano Taka-aki , Ichimura Taro , Taguchi Atsushi , Hayazawa Norihiko , Verma Prabhat , Inouye Yasushi , Kawata Satoshi
Published: September 2007

The authors developed a tip-enhanced near field Raman microscope that can precisely regulate longitudinal distance between a metallic tip and sample molecules. This was done by employing a time-gated photoncounting scheme that enabled us to observe exponentially decaying near field Raman intensity with the tip-sample distance. The exponential decay shows a characteristic of the enhanced field generated by the localization of the surface plasmon polaritons near the tip apex. This microscope was applied to evaluate metal-coated tips and also to investigate confinement of the field generated at a gap between two metal nanostructures from the decay curves.
Conductive atomic force microscopy investigation of transverse current across metallic and semiconducting single-walled carbon nanotubes
Authors: Baldacchini Chiara , Cannistraro Salvatore
Published: September 2007

The comprehension of conduction mechanisms in single-walled carbon nanotubes is a crucial task for developing efficient nanodevices. Appealing hybrid architectures could exploit charge transport perpendicular to the main nanotube axis in order to minimize carrier path and phonon scattering effects. Such transverse transport is investigated in metallic and semiconducting nanotubes by means of conductive atomic force microscopy. The transverse current response is interpreted in the framework of a tunneling transport model, and reveals that conduction across metallic nanotubes is either tunneling- or bandlike, depending on the force applied by the tip, while charge carriers always tunnel through the semiconducting nanotubes.
Microfluidic photonic crystal double heterostructures
Authors: Smith Cameron L. C. , Wu Darran K. C. , Lee Michael W. , Monat Christelle , Tomljenovic-Hanic Snjezana , Grillet Christian , Eggleton Benjamin J. , Freeman Darren , Ruan Yinlan , Madden Steve , Luther-Davies Barry , Giessen Harald , Lee Yong-Hee
Published: September 2007

We demonstrate postprocessed and reconfigurable photonic crystal double-heterostructure cavities via selective fluid infiltration. We experimentally investigate the microfluidic cavities via evanescent probing from a tapered fiber at telecommunication wavelengths. Fabry-Pérot fringes associated with modes of the induced cavity are in good agreement with the theory. We also demonstrate a cavity with quality factor Q=4300. Our defect-writing technique does not require nanometer-scale alterations in lattice geometry and may be undertaken at any time after photonic crystal waveguide fabrication.
The effect of magnesium vacancies on the π intraband scattering in MgxB2 as determined by point contact Andreev reflection
Authors: Yates K. A. , Miyoshi Y. , Grunwell J. , Riggall K. , Cohen L. F. , Chen S. K. , MacManus Driscoll J. L. , Serquis A.
Published: September 2007

In order to introduce structural defects into the π band with minimal distortions in the σ band, bulk samples of varying magnesium content were prepared. Point contact Andreev reflection measurements reveal that the density of states of the π band and the behavior of the energy gaps in field imply a relative increase of π band to σ band scattering with increasing magnesium deficiency. The results are consistent with the observed increase of the low temperature Hc2 value in magnesium deficient MgB2.
Tunable terahertz quantum cascade lasers with an external cavity
Authors: Xu Jihua , Hensley Joel M. , Fenner D. B. , Green Richard P. , Mahler Lukas , Tredicucci Alessandro , Allen Mark G. , Beltram Fabio , Beere Harvey E. , Ritchie David A.
Published: September 2007

Tunable quantum cascade lasers operating in the terahertz frequency range are demonstrated. By using an external cavity based on the reflection from a movable mirror, both broad and fine tuning of the frequency are achieved by varying the cavity length. Coarse tuning up to 3cm−1 is obtained near the center frequency of 4.8THz (∼160cm−1), and continuous mode-hop-free tuning is observed over ∼ 0.4cm−1, nearly corresponding to the cavity free spectral range.
Extraction and Characterization of Lipids from the Kernels, Leaves, and Stalks of Nine Grain Sorghum Parent Lines
Authors: Christiansen K. L. , Weller C. L. , Schlegel V. L. , Cuppett S. L. , Carr T. P.
Published: September 2007

The objectives of this study were to identify and quantify lipid classes extracted from the stalk, leaves, and the whole kernels of nine different sorghum parent lines. All extractions were performed with a Soxtec using n‐hexane as the extraction solvent. Analytical methods including high‐performance liquid chromatography (HPLC), gas chromatography (GC), and thin‐layer chromatography (TLC) were used to identify and quantify the extracted lipid classes: triacylglycerides (TAG), diglycerides (DG), policosanols (PA), free sterols (FS), phytosterols (PS), free fatty acids (FFA), tocopherols (T), and fatty aldehydes. Overall, extracts from the leaves had higher amounts of soluble matter. Extracts from leaves contained more alcohols and sterols, whereas extracts from the stalks and the whole kernels contained the greatest amount of free fatty acids and fatty aldehydes, respectively. Trace amounts of tocopherol were detected by HPLC in all 27 samples. The lipid profiles of extracts from the whole kernels, leaves, and stalks from the same plant differed. The lipid profiles of extracts from each anatomical part of the sorghum plant differed between the nine parent lines.
Molecular Weight Distribution of (1→3)(1→4)‐β‐Glucan Affects Pasting Properties of Flour from Oat Lines with High and Typical Amounts of β‐Glucan
Authors: Yao Ni , Jannink Jean‐Luc , White Pamela J.
Published: September 2007

Experimental (N979‐5‐2‐4 and IA95111) and traditional oat lines (Jim and Paul) with average %β‐glucan of 7.5, 7.8, 4.9, and 4.4%, respectively, were grown in 2002, 2003, and 2004. Molecular weight (MW) distributions of the β‐glucans were examined for potential variations among growing years and for relationships with pasting properties measured by Rapid ViscoAnalyser under three separate conditions: 1) in silver nitrate (SN) solution to inactivate enzymes; 2) hydrolyzed by α‐amylase to eliminate the effect of starch; and 3) treated with lichenase to remove β‐glucan. The β‐glucan was extracted by a process involving multiple precipitation and dialysis steps, and the MW distributions were determined by HPLC. %β‐Glucan in N979‐5‐2‐4 and IA95111 lines were consistently and significantly greater (P < 0.05) than in Jim and Paul lines during three growing years. The contribution of β‐glucan to peak viscosity on the RVA was substantially greater than that of the starch for all three years. The molecular number average and peak MW of β‐glucan from N979‐5‐2‐4 and IA95111 were greater than these values for Jim and Paul, and values were consistent among years. The MW of extracted β‐glucan was associated with pasting properties after amylase hydrolysis, but not after treatment with lichenase or in SN solution.
Experimental Determination of Longitudinal Expansion During Extrusion of Starches
Authors: Kumar A. , Ganjyal G. M. , Jones D. D. , Hanna M. A.
Published: September 2007

Expansion during extrusion of starches is a unique phenomenon used extensively in the food industry. Sectional expansion index is usually determined as the ratio of the square of the diameter of the final extrudate to the square of diameter of the die through which the product is expelled. Longitudinal expansion index is calculated indirectly by doing a mass balance across the extruder and making an assumption for density of the dough melt in the die. The objective of this research was to determine the longitudinal expansion index experimentally using a die designed to measure the velocity of the melt dough inside the die. A tracer was induced to change the conductivity of the melt dough. The velocity inside the die was then determined by measuring the time of travel of a tracer with the help of electrical probes. Corn starch (25% amylose and 30% moisture content) was extruded in a twin‐screw extruder at a barrel temperature of 140°C, screw speeds of 80, 120, and 160 rpm, and feed rates corresponding to the screw speeds varying from 7.35 to 13. 35 kg/hr. An inverse relationship was observed between the longitudinal expansion and the sectional expansion indices.
Structural Implications of Mutations in the Pea SYM8 Symbiosis Gene, the DMI1 Ortholog, Encoding a Predicted Ion Channel
Authors: Edwards Anne , Heckmann Anne B. , Yousafzai Faridoon , Duc Gerard , Downie J. Allan
Published: September 2007

The Pisum sativum SYM8 gene plays an essential part in both rhizobial and mycorrhizal symbioses. Mutation of sym8 in the original type line R25 blocks nodulation, mycorrhization, and Nod-factor-induced calcium spiking, an early component of the nodulation signaling pathway. We describe four new sym8 alleles of pea, which fall into the same complementation group as R25. The sym8 mutants are phenotypically similar to Medicago truncatula dmi1 mutants and map to a syntenic location. We used sequence homology to isolate the pea ortholog of M. truncatula DMI1 and have shown that the cloned pea ortholog can complement a M. truncatula dmi1 mutant for nodulation. Each of the five pea sym8 mutants carries a mutation in the DMI1 ortholog, confirming that the pea SYM8 is the DMI1 ortholog. Based on predicted structural similarities with an archaebacterial ion channel, we propose that SYM8 forms a tetrameric calcium-gated channel of a predicted structure similar to the archaebacterial potassium channel but containing a filter region that is different. The predicted structure identifies four aspartate residues (one from each subunit) forming the channel opening. We made a mutation changing the aspartate to valine and identified a missense mutation (changing alanine to valine adjacent to the aspartate residues) in this predicted filter region; both mutations caused a loss of function. We also identified a loss-of-function missense mutation (changing arginine to isoleucine) in a domain proposed to link the predicted channel and the gating ring domains, indicating that this mutation may block function by preventing a protein conformational change being transmitted from the gating-ring domain to the pore domain.
A Key Role for the Arabidopsis WIN3 Protein in Disease Resistance Triggered by Pseudomonas syringae That Secrete AvrRpt2
Authors: Lee Min Woo , Lu Hua , Jung Ho Won , Greenberg Jean T.
Published: September 2007

Effector proteins injected by the pathogenic bacteria Pseudomonas syringae into plants can have profound effects on the pathogen–host interaction due to their efficient recognition by plants and the subsequent triggering of defenses. The AvrRpt2 effector triggers strong local and systemic defense (called systemic acquired resistance [SAR]) responses in Arabidopsis thaliana plants that harbor a functional RPS2 gene that encodes an R protein in the coiled-coil, nucleotide-binding domain, leucine-rich repeat class. The newly identified win3-T mutant shows greatly reduced resistance to P. syringae carrying avrRpt2. In win3-T plants, RIN4 cleavage, an early AvrRpt2-induced event, is normal. However, salicylic acid accumulation is compromised, as is SAR induction and the local hypersensitive cell death response after infection by P. syringae carrying avrRpt2. WIN3 encodes a member of the firefly luciferase protein superfamily. Expression of WIN3 at an infection site partially requires PAD4, a protein known to play a quantitative role in RPS2-mediated signaling. WIN3 expression in tissue distal to an infection site requires multiple salicylic acid regulatory genes. Finally, win3-T plants show modestly increased susceptibility to virulent P. syringae and modestly reduced SAR in response to P. syringae carrying avrRpm1. Thus, WIN3 is a key element of the RPS2 defense response pathway and a basal and systemic defense component.
Biofilm Formation, Epiphytic Fitness, and Canker Development in Xanthomonas axonopodis pv. citri
Authors: Rigano Luciano A. , Siciliano Florencia , Enrique Ramón , Sendín Lorena , Filippone Paula , Torres Pablo S. , Qüesta Julia , Dow J. Maxwell , Castagnaro Atilio P. , Vojnov Adrián A. , Marano María Rosa
Published: September 2007

The phytopathogenic bacterium Xanthomonas axonopodis pv. citri is responsible for the canker disease affecting citrus plants throughout the world. Here, we have evaluated the role of bacterial attachment and biofilm formation in leaf colonization during canker development on lemon leaves. Crystal violet staining and confocal laser scanning microscopy analysis of X. axonopodis pv. citri strains expressing the green fluorescent protein were used to evaluate attachment and biofilm formation on abiotic and biotic (leaf) surfaces. Wild-type X. axonopodis pv. citri attached to and formed a complex, structured biofilm on glass in minimal medium containing glucose. Similar attachment and structured biofilm formation also were seen on lemon leaves. An X. axonopodis pv. citri gumB mutant strain, defective in production of the extracellular polysaccharide xanthan, did not form a structured biofilm on either abiotic or biotic surfaces. In addition, the X. axonopodis pv. citri gumB showed reduced growth and survival on leaf surfaces and reduced disease symptoms. These findings suggest an important role for formation of biofilms in the epiphytic survival of X. axonopodis pv. citri prior to development of canker disease.
New Type III Effectors from Xanthomonas campestris pv. vesicatoria Trigger Plant Reactions Dependent on a Conserved N-Myristoylation Motif
Authors: Thieme Frank , Szczesny Robert , Urban Alexander , Kirchner Oliver , Hause Gerd , Bonas Ulla
Published: September 2007

Pathogenicity of the gram-negative plant pathogen Xanthomonas campestris pv. vesicatoria depends on a type III secretion system, which translocates bacterial effector proteins into the plant cell. In this study, we identified two novel type III effectors, XopE1 and XopE2 (Xanthomonas outer proteins), using the AvrBs3 effector domain as reporter. XopE1 and XopE2 belong to the HopX family and possess a conserved putative N-myristoylation motif that is also present in the effector XopJ from X. campestris pv. vesicatoria 85-10. XopJ is a member of the YopJ/AvrRxv family of acetyltransferases. Confocal laser scanning microscopy and immunocytochemistry revealed that green fluorescent protein fusions of XopE1, XopE2, and XopJ localized to the plant cell plasma membrane. Targeting to the membrane is probably due to N-myristoylation, because a point mutation in the putative myristoylated glycine residue G2 in XopE1, XopE2, and XopJ resulted in cytoplasmic localization of the mutant proteins. Results of hydroxylamine treatments of XopE2 protein extracts suggest that the proteins are additionally anchored in the host cell plasma membrane by palmitoylation. The membrane localization of the effectors strongly influences the phenotypes they trigger in the plant. Agrobacterium-mediated expression of xopE1 and xopJ in Nicotiana benthamiana led to cell-death reactions that, for xopJ, were dependent on the N-myristoylation motif. In the case of xopE1(G2A), cell death was more pronounced with the mutant than with the wild-type protein. In addition, XopE2 has an avirulence activity in Solanum pseudocapsicum.
Allelic Variation in the Effector Genes of the Tomato Pathogen Cladosporium fulvum Reveals Different Modes of Adaptive Evolution
Authors: Stergiopoulos Ioannis , De Kock Maarten J. D. , Lindhout Pim , De Wit Pierre J. G. M.
Published: September 2007

The allelic variation in four avirulence (Avr) and four extracellular protein (Ecp)–encoding genes of the tomato pathogen Cladosporium fulvum was analyzed for a worldwide collection of strains. The majority of polymorphisms observed in the Avr genes are deletions, point mutations, or insertions of transposon-like elements that are associated with transitions from avirulence to virulence, indicating adaptive evolution of the Avr genes to the cognate C. fulvum resistance genes that are deployed in commercial tomato lines. Large differences in types of polymorphisms between the Avr genes were observed, especially between Avr2 (indels) and Avr4 (amino-acid substitutions), indicating that selection pressure favors different types of adaptation. In contrast, only a limited number of polymorphisms were observed in the Ecp genes, which mostly involved synonymous modifications. A haplotype network based on the polymorphisms observed in the effector genes revealed a complex pattern of evolution marked by reticulations that suggests the occurrence of genetic recombination in this presumed asexual fungus. This, as well as the identification of strains with identical polymorphisms in Avr and Ecp genes but with opposite mating-type genes, suggests that development of complex races can be the combined result of positive selection and genetic recombination.
The Role of luxS in the Fire Blight Pathogen Erwinia amylovora Is Limited to Metabolism and Does Not Involve Quorum Sensing
Authors: Rezzonico Fabio , Duffy Brion
Published: September 2007

Erwinia amylovora is a gram-negative phytopathogen that causes fire blight of pome fruit and related members of the family Rosaceae. We sequenced the putative autoinducer-2 (AI-2) synthase gene luxS from E. amylovora. Diversity analysis indicated that this gene is extremely conserved among E. amylovora strains. Quorum sensing mediated by LuxS has been implicated in coordinated gene expression, growth, and virulence in other enterobacteria; however, our evidence suggests this is not the function in E. amylovora. Mutational analysis pointed to a role in colonization of apple blossoms, the primary infection court for fire blight, although little if any role in virulence on apple shoots and pear fruit was observed. Expression of key virulence genes hrpL and dspA/E was reduced in mutants of two E. amylovora strains. Stronger effects on gene expression were observed for metabolic genes involved in the activated methyl cycle with mutants having greater levels of expression. No quorum-sensing effect was observed in co-culture experiments with wild-type and mutant strains either in vitro or in apple blossoms. Known receptors essential for AI-2 quorum sensing, the LuxPQ sensor kinase or the Lsr ABC-transporter, are absent in E. amylovora, further suggesting a primarily metabolic role for luxS in this bacterium.
An Oligonucleotide Microarray Resource for Transcriptional Profiling of Bradyrhizobium japonicum
Authors: Chang Woo-Suk , Franck William L. , Cytryn Eddie , Jeong Sooyoung , Joshi Trupti , Emerich David W. , Sadowsky Michael J. , Xu Dong , Stacey Gary
Published: September 2007

A DNA microarray, comprising 70-mer oligonucleotides, representing 8,453 open reading frames (ORFs), was constructed based on the Bradyrhizobium japonicum strain USDA110 genomic sequence. New annotation predicted 199 additional genes, which were added to the microarray and were shown to be transcribed. These arrays were used to profile transcription in cells under a variety of conditions, including growth in minimal versus rich medium, osmotic stress, and free-living cells versus bacteroids. Increased expression was seen for genes involved in translation, motility, and cell envelope synthesis in rich medium whereas expression increased in minimal medium for genes involved in vitamin biosynthesis and stress responses. Treatment with 50 mM NaCl activated stress-inducible genes but repressed genes involved in chemotaxis and motility. Strikingly, no known transport systems for accumulation of compatible solutes or osmoprotectants were induced in response to osmotic stress. A number of nif, fix, and hup genes, but not all, were upregulated in bacteroids. The B. japonicum type III secretion system, known to be important in early nodulation, was downregulated in bacteroids. The availability of a reliable, low-cost B. japonicum microarray provides a useful tool for functional genomic studies of one of the most agriculturally important bacteria.
Detached and AttachedArabidopsisLeaf Assays Reveal Distinctive Defense Responses Against HemibiotrophicColletotrichumspp.
Authors: Liu Guosheng , Kennedy Regan , Greenshields David L. , Peng Gary , Forseille Lily , Selvaraj Gopalan , Wei Yangdou
Published: September 2007

The agriculturally important genus Colletotrichum is an emerging model pathogen for studying defense in Arabidopsis. During the process of screening for novel pathogenic Colletotrichum isolates on Arabidopsis, we found significant differences in defense responses between detached and attached leaf assays. A near-adapted isolate Colletotrichum linicola A1 could launch a typical infection only on detached, but not attached, Arabidopsis leaves. Remarkably, resistance gene-like locus RCH1-mediated resistance in intact plants also was compromised in detached leaves during the attacks with the virulent reference isolate C. higginsianum. The differences in symptom development between the detached leaf and intact plant assays were further confirmed on defense-defective mutants following inoculation with C. higginsianum, where the greatest inconsistency occurred on ethylene-insensitive mutants. In intact Arabidopsis plants, both the salicylic acid- and ethylene-dependent pathways were required for resistance to C. higginsianum and were associated with induced expression of pathogenesis-related genes PR1 and PDF1.2. In contrast, disease symptom development in detached leaves appeared to be uncoupled from these defense pathways and more closely associated with senescence: an observation substantiated by coordinated gene expression analysis and disease symptom development, and chemically and genetically mimicking senescence.
Analysis of the Spatial Distribution of Identical and Two Distinct Virus Populations Differently Labeled with Cyan and Yellow Fluorescent Proteins in Coinfected Plants
Authors: Takahashi Tsubasa , Sugawara Tomohiko , Yamatsuta Tsubasa , Isogai Masamichi , Natsuaki Tomohide , Yoshikawa Nobuyuki
Published: September 2007

Apple latent spherical virus (ALSV) expressing yellow and cyan fluorescent proteins (ALSV-YFP and ALSV-CFP) was used to investigate the distribution of identical virus populations in coinfected plants. In Chenopodium quinoa plants inoculated with a mixture of ALSV-YFP and ALSV-CFP, fluorescence from YFP and CFP was always distributed separately in both inoculated and upper uninoculated leaves. Inoculation of each ALSV-YFP and ALSV-CFP to different leaves of a C. quinoa plant resulted in the separate distribution of each virus population among different upper leaves. When C. quinoa leaves were first inoculated with ALSV-CFP and then ALSV-YFP was reinoculated into the same leaves at various times after the first inoculation, ALSV-YFP infected only tissues where ALSV-CFP infection had not been established. The spatial separation was also found in Nicotiana benthamiana leaves coinoculated with Bean yellow mosaic virus (BYMV)-YFP and BYMV-CFP. In contrast, both YFP and CFP fluorescence signals were observed in the same tissues of N. benthamiana leaves mixed infected with ALSV-YFP and BYMV-CFP. YFP fluorescence from ALSV-YFP in mixed-infected leaves was brighter and longer than in leaves infected with ALSV-YFP singly.
Sensitivity to a Phytotoxin from Rhizoctonia solani Correlates with Sheath Blight Susceptibility in Rice
Authors: Brooks Steven A.
Published: September 2007

Sheath blight is one of the most important and intractable diseases of rice (Oryza sativa) where limited control has been achieved using traditional approaches. Quantitative inheritance, extraneous traits, and environmental factors confound genetic analysis of host resistance. A method was developed to isolate and utilize a phytotoxin from Rhizoctonia solani to investigate the genetics of sheath blight susceptibility. Infiltration of the toxin preparation into plant leaves induced necrosis in rice, maize, and tomato. Using 17 rice cultivars known to vary in sheath blight resistance, genotypes were identified that were sensitive (tox-S) and insensitive (tox-I) to the toxin, and a correlation (r = 0.66) between toxin sensitivity and disease susceptibility was observed. Given the broad host range of R. solani, genotypes of host species may be both tox-S and tox-I. A total of 154 F2 progeny from a cross between Cypress (tox-S) and Jasmine 85 (tox-I) segregated in a 9:7 ratio for tox-S/tox-I, indicating an epistatic interaction between two genes controls sensitivity to the toxin in rice. This work provides the means to genetically map toxin sensitivity genes and eliminate susceptible genotypes when developing sheath blight-resistant rice cultivars.
Wheat streak mosaic virus Lacking Helper Component-Proteinase Is Competent to Produce Disease Synergism in Double Infections with Maize chlorotic mottle virus
Authors: Stenger Drake C. , Young Brock A. , Qu Feng , Morris T. Jack , French Roy
Published: September 2007

The tritimovirus Wheat streak mosaic virus (WSMV) and the machlomovirus Maize chlorotic mottle virus (MCMV) each cause systemic chlorosis in infected maize plants. Infection of maize with both viruses produces corn lethal necrosis disease (CLND). Here, we report that complete deletion of the WSMV helper component-proteinase (HC-Pro) coding region had no effect on induction of CLND symptoms following coinoculation of maize with WSMV and MCMV. We further demonstrated that elevation of virus titers in double infections, relative to single infections, also was independent of WSMV HC-Pro. Thus, unlike potyvirus HC-Pro, WSMV HC-Pro was dispensable for disease synergism. Because disease synergism involving potyviruses requires HC-Pro-mediated suppression of posttranscriptional gene silencing (PTGS), we hypothesized that WSMV HC-Pro may not be a suppressor of PTGS. Indeed, WSMV HC-Pro did not suppress PTGS of a green fluorescent protein (GFP) transgene in an Agrobacterium-mediated coinfiltration assay in which potyvirus HC-Pro acted as a strong suppressor. Furthermore, coinfiltration with potyvirus HC-Pro, but not WSMV HC-Pro, resulted in elevated levels of the GFP target mRNA under conditions which trigger PTGS. Collectively, these results revealed significant differences in HC-Pro function among divergent genera of the family Potyviridae and suggest that the tritimovirus WSMV utilizes a gene other than HC-Pro to suppress PTGS and mediate synergistic interactions with unrelated viruses.
Characterization of a U.S. Isolate ofBeet black scorch virus
Authors: Weiland John J. , Van Winkle David , Edwards Michael C. , Larson Rebecca L. , Shelver Weilin L. , Freeman Thomas P. , Liu Hsing-Yeh
Published: September 2007

The first reported U.S. isolate of Beet black scorch necrovirus (BBSV) was obtained and characterized. Host range of the virus for localized and occasionally systemic infection included the Chenopodiaceae and Tetragonia expansa; Nicotiana benthamiana supported symptomless systemic infection by the virus. The complete nucleotide sequence of the genomic RNA of the virus, designated BBSV-Co, exhibits 93% similarity to the genome of the ‘Ningxia’ isolate of BBSV from China. Amino acid sequence similarity in predicted genes ranged from 95% in the p4 gene to 97% in the p82 and coat protein genes. A potential additional gene exists within the U.S. isolate of BBSV that is absent from Chinese isolates of BBSV due to nucleotide differences between these isolates within the coat protein gene. Coat protein analysis by isoelectric focusing and by mass spectroscopy indicated the presence of phosphorylated residues. Using primer extension analysis of the 5′ end of the genome and site-directed mutants of genomic clones of BBSV-Co from which infectious RNA was produced, the native 5′ end of the BBSV-Co genome was determined to be 5′-GAAACCTAACC…3′, lacking the two terminal adenosine nucleotides in the published sequences of BBSV from China.
Evaluation of Likelihood of Co-Occurrence ofErwinia amylovorawith Mature Fruit of Winter Pear
Authors: Temple Todd N. , Stockwell Virginia O. , Pusey P. Lawrence , Johnson Kenneth B.
Published: September 2007

Phytosanitary concerns about fire blight prohibit export of U.S.-grown pears to some countries without this disease. To examine these concerns, we evaluated the potential for co-occurrence of Erwinia amylovora with mature, symptomless winter pear fruit by inoculation experiments and by survey of commercial orchards. Immature pear and apple fruit were inoculated in orchards with E. amylovora strain 153N as resuspended lyophilized cells or as ooze from diseased tissues. Regardless of inoculum source, population size of Ea153N on fruit declined by an order of magnitude every 3 to 4 days during the first 2 weeks after inoculation; at 56 days after inoculation, Ea153N was not detected, except on 1 of 450 fruit with 4 colony forming units (CFU). After inoculation of flowers, calyx-end survival of Ea153N on pear and apple fruit declined from high populations at petal fall to a few cells at harvest, with no detection of the pathogen after a 7-week cold storage. Migration of Ea153N into symptomless pear fruit from diseased branches was evaluated by enrichment assay and nested polymerase chain reaction of internal fruit core tissues; these assays failed to detect the pathogen in healthy fruit from diseased trees. At harvest, E. amylovora could not be detected on 5,599 of 5,600 fruit of d'Anjou pear sampled from commercial orchards in major production areas of the Pacific Northwest; one fruit yielded 32 CFU of the pathogen. Postharvest, mature pear fruit contaminated with Ea153N and subsequently wounded required a dose of >10,000 cells at the wound site to allow for persistence of the pathogen through a 7-week-cold storage. We conclude that epiphytic E. amylovora shows similar survival characteristics on both pear and apple fruit, this pathogen is not an endophyte within mature symptomless pear fruit, its presence is exceptionally rare on commercially produced fruit, and that epiphytic survival of E. amylovora through a postharvest chilling period is unlikely given the unrealistically high population size required for persistence.
The Influence of Climate on Foliar Symptoms of Eutypa Dieback in Grapevines
Authors: Sosnowski M. R. , Shtienberg D. , Creaser M. L. , Wicks T. J. , Lardner R. , Scott E. S.
Published: September 2007

Foliar symptoms of Eutypa dieback, caused by Eutypa lata, in grapevines, cv. Shiraz, varied from year to year in a 6-year study conducted in South Australia and, although trends were similar for vineyards within geographical regions, differences were observed between regions. We attempted to elucidate the causes underlying this variation and hypothesized that it was influenced by climatic factors. A number of possible relationships were identified between climate and symptom expression: (i) increased symptom expression was related to increased winter rainfall 18 months earlier, (ii) decreased disease incidence and prevalence were related to increased temperature in spring, and (iii) a reduction in disease incidence was related to both very high and very low rainfall in October. Theories for these relationships are proposed and require further investigation. A conceptual model was developed which requires validation and has the potential to predict the incidence of foliar symptoms of Eutypa dieback. Information from this study could lead to an improved integrated pest management system to suppress foliar symptoms and sustain productivity of vines infected with E. lata.
Detection of Erysiphe necator in Air Samples Using the Polymerase Chain Reaction and Species-Specific Primers
Authors: Falacy Jennifer S. , Grove Gary G. , Mahaffee Walter F. , Galloway Heather , Glawe Dean A. , Larsen Richard C. , Vandemark George J.
Published: September 2007

A polymerase chain reaction (PCR) assay employing species-specific primers was developed to differentiate Erysiphe necator from other powdery mildews common in the northwest United States. DNA was extracted from mycelia, conidia, and/or chasmothecia that were collected from grape leaves with a Burkard cyclonic surface sampler. To differentiate E. necator from other erysiphaeceous fungi, primer pairs Uncin144 and Uncin511 were developed to select unique sequences of the internal transcribed spacer regions of E. necator. Using these primers in PCR amplifications, a 367-bp amplicon specific to E. necator was generated, but no amplicons were generated from other erysiphaceous species collected from 48 disparate hosts representing 26 vascular plant families. The PCR limit of detection was one to five conidia of E. necator placed directly into reaction mixtures or 100 to 250 conidia placed on glass rods coated with silicon grease. During field studies, this PCR assay facilitated the detection of E. necator inoculum in air samples within hours of sample rod collection and prior to disease onset. Amplification of E. necator DNA did not occur when the PCR assay was conducted on vineyard air samples collected while grapes were dormant or during periods when vine growth occurred but E. necator remained dormant. The initial PCR detection of E. necator of the season occurred during seasonal ascospore releases caused by precipitation events between bud burst and the prebloom period during the 3 years of the study. Detection ceased for 7 to 11 days following ascospore release and then resumed several days prior to the observance of microscopic symptoms and signs of powdery mildew in the field. Results of this study represent the initial step toward the goal of incorporating an inoculum availability component into current and future grapevine powdery mildew risk assessment models.