bluuebunny/crossref_metadata_2025 huggingface dataset:
Dynamics of free jets submitted to upstream acoustic modulations
Authors: Birbaud A. L. , Durox D. , Ducruix S. , Candel S.
Published: January 2007

The response of low Reynolds number air jets to acoustic modulations is investigated with systematic experiments. Flow transfer functions, power spectral densities of the perturbations plotted in the form of space-frequency maps, instantaneous jet images recorded using laser tomography, and phase-conditioned velocity fields serve to identify the different regimes of motion. Results indicate that five regions can be distinguished in a diagram where the jet Strouhal number StD serves as a horizontal coordinate while the shear layer Strouhal number Stθ constitutes the vertical coordinate. Boundaries of the different regions are defined by the characteristic values of these two dimensionless groups at preferred mode and neutral wave conditions, corresponding, respectively, to a maximum of amplification and a vanishing rate of growth. The forcing frequencies imparted to the flow can be ordered with respect to these characteristic parameters. The flow transfer functions at the excitation frequency indicate that perturbations have a different nature depending on the value of the jet Strouhal number based on the exhaust diameter StD. Convective, mixed type, and acoustic ranges are identified. Detailed measurements of the spatial evolution of the forced components and corresponding harmonics provide information on the nonlinear power transfer between the different modes for modulation amplitudes reaching 10% of the mean flow velocity. The StD−Stθ mapping is used to categorize the various modes of interaction observed in the experiments.
Acoustic Bragg mirrors and cavities made using piezoelectric oxides
Authors: Soukiassian A. , Tian W. , Tenne D. A. , Xi X. X. , Schlom D. G. , Lanzillotti-Kimura N. D. , Bruchhausen A. , Fainstein A. , Sun H. P. , Pan X. Q. , Cros A. , Cantarero A.
Published: January 2007

The concept and design of acoustic Bragg mirrors and cavities made of multilayers of piezoelectric oxides with superior acoustic performance and potential applications in electronic and optical terahertz modulators are described. With these applications in mind the authors have grown phonon mirrors consisting of BaTiO3∕SrTiO3 superlattices on SrTiO3 substrates by reactive molecular-beam epitaxy and investigated their properties. Characterization of the superlattices by x-ray diffraction and high-resolution transmission electron microscopy reveals high structural quality with nearly atomically abrupt interfaces. The authors have observed folded acoustic phonons at the expected frequencies using uv Raman spectroscopy.
Photoreflectance spectroscopy with a step-scan Fourier-transform infrared spectrometer: Technique and applications
Authors: Shao Jun , Lu Wei , Yue Fangyu , Lü Xiang , Huang Wei , Li Zhifeng , Guo Shaoling , Chu Junhao
Published: January 2007

We report on a new technique of realizing photoreflectance (PR) spectroscopy with a step-scan Fourier-transform infrared spectrometer. The experimental configuration is briefly described and a detailed theoretical analysis is conducted. The results reveal two distinct features of this PR technique that (i) the PR related signal is enhanced by a factor of at least 100 relative to those of the conventional PR techniques and (ii) the unwanted spurious signal introduced by either diffuse reflected pump beam or pump-beam induced material’s photoluminescence reaching the photodetector of the PR configuration is eliminated without any special consideration of normalization for deducing the final PR spectrum. Applications are given as examples in the study of GaNAs/GaAs single quantum wells and GaInP/AlGaInP multiple quantum wells, respectively, under different pump-beam excitation energy and/or power. The experimental results approve the theoretically predicted features and illustrate the possibility of investigating weak PR features by using high pump-beam power. A brief comparison of this technique with the conventional PR techniques is given, and the extendibility of this technique to long-wavelength spectral regions is pointed out.
High saturation solar light beam induced current scanning of solar cells
Authors: Vorster F. J. , van Dyk E. E.
Published: January 2007

The response of the electrical parameters of photovoltaic cells under concentrated solar irradiance has been the subject of many studies performed in recent times. The high saturation conditions typically found in solar cells that are subjected to highly concentrated solar radiation may cause electrically active cell features to behave differently than under monochromatic laser illumination, normally used in light beam induced current (LBIC) investigations. A high concentration solar LBIC (S-LBIC) measurement system has been developed to perform localized cell characterization. The responses of silicon solar cells that were measured qualitatively include externally biased induced cell current at specific cell voltages, IV, open circuit voltage, Voc, and the average rate of change of the cell bias with the induced current, ΔV∕ΔIV, close to the zero bias region. These images show the relative scale of the parameters of a cell up to the penetration depth of the solar beam and can be obtained with relative ease, qualifying important electrical response features of the solar cell. The S-LBIC maps were also compared with maps that were similarly obtained using a high intensity He–Ne laser beam probe. This article reports on the techniques employed and initial results obtained.
Induction and measurement of minute flow rates through nanopipes
Authors: Sinha Shashank , Pia Rossi Maria , Mattia D. , Gogotsi Yury , Bau Haim H.
Published: January 2007

A simple technique to simultaneously induce fluid flow through an individual nanopipe and measure the flow rate and the pressure difference across the pipe is described. Two liquid drops of different sizes are positioned at the two ends of the nanopipe. Due to the higher capillary pressure of the smaller drop, flow is driven from the smaller drop to the bigger drop. The instantaneous pressures of the two drops are estimated from the drops’ shapes and sizes. The flow rate is estimated by monitoring the sizes of the drops as functions of time with a microscope and a video camera. A theory that correlates the drops’ sizes and the flow rate is derived. Measurements are carried out with an ionic salt and glycerin to estimate the effective tube radius of the nanopipes with diameters ranging from 200 to 300nm. The tubes’ diameters are independently measured with a scanning electron microscope. The method is also verified by tracking the motion of fluorescent particles through the nanopipe. The paper provides a simple technique for studying extremely low flow rates in nanofluidic systems. When working with low-evaporation fluids such as ionic salts, the measurements can be carried out with an electron microscope.
Rotating multipoles on the f- and γ-planes
Authors: Kizner Z. , Khvoles R. , McWilliams J. C.
Published: January 2007

A family of semianalytical solutions is presented describing multipolar vortical structures with zero total circulation in a variety of two-dimensional models. Analytics are used to determine the form of a multipole edge, or separatrix, and the solution outside this separatrix. The interior is solved using a Newton-Kantorovich (successive linearization) procedure combined with a collocation method. The models considered are the quasigeostrophic f- and γ-planes, with either the rigid-lid or free-surface conditions. A multipole, termed also an (m+1)-pole, is a vortical system that possesses an m-fold symmetry (m≥2) and is comprised of a central core vortex and m satellite vortices surrounding the core. Fluid parcels in the core and the satellites revolve oppositely, and the multipole as a whole rotates steadily. The characteristics of the multipoles are examined as functions of m and a parameter that incorporates the Rossby deformation radius, γ-effect, and the vortex’s angular velocity. The analogy between the β-plane modons and γ-plane multipoles is tracked.
Ultrafast magnetization dynamics probed by anisotropic magnetoresistance
Authors: Schumacher H. W. , Serrano-Guisan S. , Rott K. , Reiss G.
Published: January 2007

The authors use time resolved measurements of the anisotropic magnetoresistance (AMR) to study ultrafast magnetization dynamics of microstructured disks of Permalloy. The devices show an AMR of the order of 0.25% revealing the characteristic cos2 angular dependence. From the time resolved AMR the authors derive the in plane angular excursion of the magnetization with angular resolution down to 1°. From the decay of the homogeneous precession the authors derive a Gilbert damping parameter of 0.008±0.001. This technique can be applied to study magnetization precession and damping in individual micropatterned devices of a wide variety of magnetic thin film and multilayer materials.
Steepness effect on modulation instability of the nonlinear wave train
Authors: Chiang Wen-Son , Hwung Hwung-Hweng
Published: January 2007

The long-term evolution of a nonlinear wave train in deep water with varied initial wave steepness between 0.1 and 0.3 was experimentally investigated in a super wave flume (300m long, 5m wide, and 5.2m deep). The initial wave train was the combination of one carrier wave and a pair of imposed sideband components which is the most unstable mode, referred to as sideband instability theory. Sixty-six wave gauges were installed downstream along the wave flume to simultaneously measure the evolution of a wave train. Increasing modulation of the wave train was observed due to sideband instability until a critical value which either wave breaking is initiated or maximum modulation is reached. The near recurrence of the initial state of the wave train is exhibited for the nonbreaking case. An effective frequency downshift of the wave spectrum accompanied with wave breaking is observed as the initial wave steepness is larger than 0.11. At postbreaking, the wave train reveals periodic modulation and demodulation, meanwhile, the related wave spectrum shows a down and upshift, respectively. Present results support the hypothesis that the frequency downshift induced by wave breaking is not permanent.
Preparation of ZnO substrates for epitaxy: Structural, surface, and electrical properties
Authors: Graubner S. , Neumann C. , Volbers N. , Meyer B. K. , Bläsing J. , Krost A.
Published: January 2007

The authors investigate the influence of a high temperature annealing in O2 atmosphere on the structural properties of ZnO substrates. Only at temperatures above 1100°C are atomic step heights and terraces seen by atomic force microscopy. The structural properties of the substrates were determined from the full width at half maximum (FWHM) of the rocking curve of the (0002) reflection. The FWHM is between 28 and 33arcsec for different substrates cut from one ingot but does not change with the annealing. The electrical properties, however, change from highly resistive to n-type conductive, which makes the substrates suitable for top-to-bottom contacting.
Accurate measurement of extremely low surface recombination velocities on charged, oxidized silicon surfaces using a simple metal-oxide-semiconductor structure
Authors: Jellett W. E. , Weber K. J.
Published: January 2007

The authors report a simple technique to determine the surface recombination velocity of silicon and other semiconductor surfaces which have been passivated with a dielectric layer, as a function of charge density. A metal-oxide-semiconductor structure, employing large area, partially transparent metal contacts, is used to enable the charging of the surfaces. Simultaneous measurement of the emitter saturation current density Joe and the effective instantaneous lifetime τinst allows accurate extraction of the effective surface recombination velocity Seff at any given injection level. Extremely low Joe values of 1.8fAcm−2 are measured on the silicon-silicon oxide (Si–SiO2) interface of a thermally oxidized, charged wafer.
Solvent-vapor treatment induced performance enhancement of poly(3-hexylthiophene):methanofullerene bulk-heterojunction photovoltaic cells
Authors: Zhao Yun , Xie Zhiyuan , Qu Yao , Geng Yanhou , Wang Lixiang
Published: January 2007

The authors report enhanced poly(3-hexylthiophene) (P3HT):methanofullerene (PCBM) bulk-heterojunction photovoltaic cells via 1,2-dichlorobenzene (DCB) vapor treatment and thermal annealing. DCB vapor treatment can induce P3HT self-organizing into ordered structure leading to enhanced absorption and high hole mobility. Further annealing the device at a high temperature, PCBM molecules begin to diffuse into aggregates and together with the ordered P3HT phase form bicontinuous pathways in the entire layer for efficient charge separation and transport. Compared to the control device that is merely annealed, optical absorption, short-circuit current, and power conversion efficiency are increased for the DCB vapor-treated cell.
Room temperature multiferroic properties of single-phase (Bi0.9La0.1)FeO3–Ba(Fe0.5Nb0.5)O3 solid solution ceramics
Authors: Paik Hanjong , Hwang Hosung , No Kwangsoo , Kwon Seunghwa , Cann David P.
Published: January 2007

The crystal structure and multiferroic properties of single-phase (Bi0.9La0.1)FeO3–Ba(Fe0.5Nb0.5)O3 ceramics were investigated. The rhombohedral-type structure of 1.0(Bi0.9La0.1)FeO3) was transformed to a monoclinic-type structure for the 0.5(Bi0.9La0.1)FeO3–0.5Ba(Fe0.5Nb0.5)O3) composition. It shows the coexistence of ferroelectricity and magnetism at room temperature, represented by a high dielectric constant with ferroelectric hysteresis and clear magnetic hysteresis behavior. The authors propose that the solid solution of A and B site cations according to their ionic radii and valence state stabilized the spontaneous polarization and magnetization at room temperature.
Electronic structure and magnetism in compressed 3d transition metals
Authors: Iota Valentin , Klepeis Jae-Hyun Park , Yoo Choong-Shik , Lang Jonathan , Haskel Daniel , Srajer George
Published: January 2007

The authors present a systematic study of high-pressure effects on electronic structure and magnetism in 3d transition metals (Fe, Co, and Ni) based on x-ray magnetic circular dichroism measurements. The data show that the net magnetic moment in Fe vanishes above 18GPa upon the transition to hcp Fe, while both cobalt and nickel remain ferromagnetic to well over 100GPa. The authors estimate the total disappearance of moment in hcp Co at around 150GPa and predict a nonmagnetic Ni phase above 250GPa. The present data suggest that the suppression of ferromagnetism in Fe, Co, and Ni is due to pressure-induced broadening of the 3d valence bands.
Photogalvanic effects for interband absorption in AlGaN∕GaN superlattices
Authors: Cho K. S. , Chen Y. F. , Tang Y. Q. , Shen B.
Published: January 2007

The linear and circular photogalvanic effects (CPGEs), induced by ultraviolet (325nm) radiation, have been observed in the (0001)-oriented Al0.15Ga0.85N∕GaN superlattices. The CPGE current changes sign upon reversing the radiation helicity, and it is up to two orders of magnitude larger than that obtained by far-infrared radiation. This result suggests the existence of a sizeable Rashba spin splitting in AlGaN∕GaN superlattices. It also provides a possibility for the generation of spin orientation-induced current at room temperature.
Magnetostatic interactions in patterned CoPt films embedded in a permalloy matrix
Authors: Schnittger S. , Dreyer S. , Jooss Ch. , Sievers S. , Siegner U.
Published: January 2007

In order to study magnetostatic interactions in magnetic arrays, a two-dimensional pattern of hard magnetic (001) L10 CoPt squares embedded into a permalloy matrix was fabricated. The structural and magnetic properties of these arrays were characterized by magneto-optical measurements, atomic force and magnetic force microscopies. The hard magnetic squares are not exchange coupled to the soft magnet, yet a magnetostatic coupling was observed. This coupling modifies the domain structure of the permalloy matrix. In periodic arrays of embedded CoPt squares, the stray field interaction induces a long-range ordered domain pattern in the soft magnetic matrix and short-range correlations of edge domains in adjacent CoPt squares.
Charging phenomena in pentacene-gold nanoparticle memory device
Authors: Leong W. L. , Lee P. S. , Mhaisalkar S. G. , Chen T. P. , Dodabalapur A.
Published: January 2007

The authors demonstrate a new organic memory system, using pentacene as the active semiconductor layer and citrate-stabilized gold (Au) nanoparticles as charge storage elements. A pronounced clockwise capacitance-voltage (C-V) hysteresis is observed with a memory window of 1.25–2.05V achievable under 5–10V programing range. Similar clockwise C-V hysteresis window and an almost constant full width at half maximum of the conductance peaks in conductance-voltage (G-V) characteristics, obtained in the frequency range of 50kHz–1MHz, indicated that positive charge trapping/detrapping originated mainly from the Au nanoparticles.
Low temperature growth of crystalline magnesium oxide on hexagonal silicon carbide (0001) by molecular beam epitaxy
Authors: Goodrich T. L. , Parisi J. , Cai Z. , Ziemer K. S.
Published: January 2007

Magnesium oxide (111) was grown epitaxially on hexagonal silicon carbide (6H-SiC) (0001) substrates at low temperatures by molecular beam epitaxy and a remote oxygen plasma source. The films were characterized by reflection high-energy electron diffraction, Auger electron spectroscopy, x-ray photoelectron spectroscopy, and atomic force microscopy. Crystal structure, morphology, and growth rate of the magnesium oxide (MgO) films were found to be dependent on the magnesium flux, indicating a magnesium adsorption controlled growth mechanism. The single crystalline MgO thin films had an epitaxial relationship where MgO (111)‖6H-SiC (0001) and were stable in both air and 10−9Torr up to 1023K.
Phase transitional behavior and electrical properties of lead-free (K0.44Na0.52Li0.04)(Nb0.96−xTaxSb0.04)O3 piezoelectric ceramics
Authors: Yang Zupei , Chang Yunfei , Wei Lingling
Published: January 2007

Lead-free (K0.44Na0.52Li0.04)(Nb0.96−xTaxSb0.04)O3 piezoelectric ceramics have been synthesized by conventional solid state sintering process. Two morphotropic phase boundaries (MPBs) respectively corresponding to the orthorhombic to tetragonal and tetragonal to pseudocubic phases are observed with increasing x. The ceramics with x=0.20 between the two MPBs show significantly enhanced electrical properties, which are as follows: piezoelectric constant d33=252pC∕N, planar coupling coefficient kp=0.42, dielectric constant εr=1503, and dielectric loss tanδ=0.025, and they show good stability. Lead-free superthin buzzer disks have been prepared by using piezoceramic membrane with x=0.20. (K0.44Na0.52Li0.04)(Nb0.96−xTaxSb0.04)O3 ceramics are very promising as lead-free replacements for lead zirconate titanate.
Conductive atomic force microscopy study of silica nanotrench structure
Authors: Sun Z. G. , Kuramochi H. , Akinaga H. , Yu H. H. , Gu E. D.
Published: January 2007

Conductive atomic force microscope had been applied to study the electrical transportation mechanism together with topographic information on a periodical silica nanotrench structure. The bottom of the trench is covered by a 4nm silica thin film, while the ridges between the trenches are made up of 90nm thick silica film. On the same bias, the current transport through the bottom is larger than the current transport through the ridges. In the bottom, rectifying characteristics are observed; the conduction mechanism can be ascribed as a Schottky emission. Strong inhomogeneous electrical properties are also observed. A high resolution with a lateral resolution below 6nm is demonstrated in the conductive atomic force microscope study.
Visualizing Arp2/3 complex activation mediated by binding of ATP and WASp using structural mass spectrometry
Authors: Kiselar Janna G. , Mahaffy Rachel , Pollard Thomas D. , Almo Steven C. , Chance Mark R.
Published: January 2007

Actin-related protein (Arp) 2/3 complex nucleates new branches in actin filaments playing a key role in controlling eukaryotic cell motility. This process is tightly regulated by activating factors: ATP and WASp-family proteins. However, the mechanism of activation remains largely hypothetical. We used radiolytic protein footprinting with mass spectrometry in solution to probe the effects of nucleotide- and WASp-binding on Arp2/3. These results represent two significant advances in such footprinting approaches. First, Arp2/3 is the most complex macromolecular assembly yet examined; second, only a few picomoles of Arp2/3 was required for individual experiments. In terms of structural biology of Arp 2/3, we find that ATP binding induces conformational changes within Arp2/3 complex in Arp3 (localized in peptide segments 5–18, 212–225, and 318–327) and Arp2 (within peptide segment 300–316). These data are consistent with nucleotide docking within the nucleotide clefts of the actin-related proteins promoting closure of the cleft of the Arp3 subunit. However, ATP binding does not induce conformational changes in the other Arp subunits. Arp2/3 complex binds to WASp within the C subdomain at residue Met 474 and within the A subdomain to Trp 500. Our data suggest a bivalent attachment of WASp to Arp3 (within peptides 162–191 and 318–329) and Arp2 (within peptides 66–80 and 87–97). WASp-dependent protections from oxidation within peptides 54–65 and 80–91 of Arp3 and in peptides 300–316 of Arp2 suggest domain rearrangements of Arp2 and Arp3 resulting in a closed conformational state consistent with an “actin-dimer” model for the active state.
Biosynthesis of gossypol in cotton.
Authors: Mao YingBo , Lu Shan , Wang LingJian , Chen XiaoYa
Published: January 2007

Cotton plants accumulate gossypol and related sesquiterpenoids in pigment glands as their defensive machinery against pathogens and herbivores. However, the accumulation of gossypol, which is toxic and antispermatogenic, also makes it hard to use cottonseeds for human and animal consumption. Detailed understanding of gossypol biosynthesis and its regulation should provide better strategies for resolving this problem. Recent progresses have been made to dissect gossypol pathway at molecular level. Genes encoding farnesyl diphosphate synthase (geranyltranstransferase), (+)-δ-cadinene synthase (CDN1 or CAD1), (+)-δ-cadinene-8-hydroxylase (CYP706B1), and
S
-adenosyl-L-Met: desoxyhemigossypol-6-O-methyltransferase, have been isolated, and their expression patterns analysed. A WRKY transcription factor from
Gossypium arboreum
, GaWRKY1, was found to activate CDN1-A gene expression through binding to W-box palindrome on the CDN1-A promoter. A laccase, GaLAC1, which might be involved in the later steps of gossypol biosynthesis, was also identified. In addition, a necrosis- and ethylene-inducing protein from
Verticillium dahliae
, VdNEP, was found to be involved in the interaction between cotton plants and the fungal pathogen. The expression of these genes has been studied under different developmental stages, and under treatment of fungal elicitor preparation. Antisense inhibition of CDN1 gene expression has reported to result in reduced gossypol accumulation in cottonseed to a varied degree. (+)-δ-Cadinene-8-hydroxylase, encoded by a single copy gene in the cotton genome, might be a better alternative for genetic engineering to specifically deplete gossypol biosynthesis/accumulation from cottonseeds.
Current status, likely migration and strategies to mitigate the threat to wheat production from rzace Ug99 (TTKS) of stem rust pathogen.
Authors: Singh R. P. , Hodson D. P. , Jin Yue , Huerta-Espino J. , Kinyua M. G. , Wanyera R. , Njau P. , Ward R. W.
Published: January 2007

Stem or black rust, caused by
Puccinia graminis tritici
, has historically caused severe losses to wheat (
Triticum aestivum
) production worldwide. Successful control of the disease for over three decades through the use of genetic resistance has resulted in a sharp decline in research activity in recent years. Detection and spread in East Africa of race TTKS, commonly known as Ug99, is of high significance as most wheat cultivars currently grown in its likely migration path, i.e. to North Africa through Arabian Peninsula and then to Middle East and Asia, are highly susceptible to this race and the environment is conducive to disease epidemics. Identifying/developing adapted resistant cultivars in a relatively short time and replacing the susceptible cultivars before rust migrates out of East Africa is the strategy to mitigate potential losses. Although several alien genes will provide resistance to this race, the long-term strategy should focus on rebuilding the 'Sr2-complex' (combination of slow rusting gene Sr2 with other unknown additive genes of similar nature) to achieve long-term durability. A Global Rust Initiative has been launched to monitor the further migration of this race, facilitate field testing in Kenya or Ethiopia of wheat cultivars and germplasm developed by wheat breeding programmes worldwide, understand the genetic basis of resistance especially the durable type, carry out targeted breeding to incorporate diverse resistance genes into key cultivars and germplasm, and enhance the capacity of national programmes. A few wheat genotypes that combine stem rust resistance with high yield potential and other necessary traits have been identified but need rigorous field testing to determine their adaptation in target areas.
TILLInG and its potential for plant agriculture.
Authors: Ritchie R. D. , Nielsen N. C.
Published: January 2007

Targeting Induced Local Lesions In Genomes (TILLInG) is a reverse genetic strategy, which combines traditional mutagenesis with high-throughput molecular biology protocols. TILLInG was first established in
Arabidopsis thaliana
when other reverse genetic strategies did not produce acceptable results. TILLInG libraries have been established in several species and more are in progress. Time must be invested in creating a good TILLInG population, such that the mutation frequency is balanced with lethality. In addition, the DNA must be stable. The number of examples of the usefulness of TILLInG libraries is continually growing. While there are some disadvantages, most can be overcome. The flexibility of TILLInG has established it as a useful strategy with great potential to advance agriculture.
Crop research to benefit poor farmers in marginal areas of the developing world: a review of technical challenges and tools.
Authors: Bellon M. R.
Published: January 2007

Despite great successes in crop research for the developing world, many poor farmers in marginal areas have not benefited. There is increasing recognition that crop research can and should benefit these farmers. This paper reviews some of the key technical issues related to the challenge of formulating and carrying out crop research that is targeted, relevant and appropriate to these farmers, with a particular emphasis on crop improvement. It examines the reasons that underpin the lack of research impacts, and some of the key challenges and tools available to make this happen. The challenges include breeding for marginal environments, incorporating risk and vulnerability as important dimensions of crop research, recognizing the demand for multiple traits and diverse varieties, as well as addressing neglected and underutilized species important to the poor. The tools are comprised of a combination of crop environmental classification systems with poverty mapping to target and prioritize research at the global and national levels, the use of participatory research approaches, particularly in plant breeding, as well as non-market valuation methodologies to make research products relevant and appropriate to the poor at the local level. The paper briefly examines the promise of modern biotechnology.
The Cyclin-dependent Kinase Cdc28p Regulates Multiple Aspects of Kar9p Function in Yeast
Authors: Moore Jeffrey K. , Miller Rita K.
Published: January 2007

During mitosis in the yeast Saccharomyces cerevisiae, Kar9p directs one spindle pole body (SPB) toward the incipient daughter cell by linking the associated set of cytoplasmic microtubules (cMTs) to the polarized actin network on the bud cortex. The asymmetric localization of Kar9p to one SPB and attached cMTs is dependent on its interactions with microtubule-associated proteins and is regulated by the yeast Cdk1 Cdc28p. Two phosphorylation sites in Kar9p were previously identified. Here, we propose that the two sites are likely to govern Kar9p function through separate mechanisms, each involving a distinct cyclin. In the first mechanism, phosphorylation at serine 496 recruits Kar9p to one SPB. A phosphomimetic mutation at serine 496 bypasses the requirement of BIK1 and CLB5 in generating Kar9p asymmetry. In the second mechanism, Clb4p may target serine 197 of Kar9p for phosphorylation. This modification is required for Kar9p to direct cMTs to the bud. Two-hybrid analysis suggests that this phosphorylation may attenuate the interaction between Kar9p and the XMAP215-homologue Stu2p. We propose that phosphorylation at serine 197 regulates the release of Kar9p from Stu2p at the SPB, either to clear it from the mother-SPB or to allow it to travel to the plus end.
Retinoblastoma Protein Regulation by the COP9 Signalosome
Authors: Ullah Zakir , Buckley Martin S. , Arnosti David N. , Henry R. William
Published: January 2007

Similar to their human counterparts, the Drosophila Rbf1 and Rbf2 Retinoblastoma family members control cell cycle and developmentally regulated gene expression. Increasing evidence suggests that Rbf proteins rely on multiprotein complexes to control target gene transcription. We show here that the developmentally regulated COP9 signalosome (CSN) physically interacts with Rbf2 during embryogenesis. Furthermore, the CSN4 subunit of the COP9 signalosome co-occupies Rbf target gene promoters with Rbf1 and Rbf2, suggesting an active role for the COP9 signalosome in transcriptional regulation. The targeted knockdown of individual CSN subunits leads to diminished Rbf1 and Rbf2 levels and to altered cell cycle progression. The proteasome-mediated destruction of Rbf1 and Rbf2 is increased in cells and embryos with diminished COP9 activity, suggesting that the COP9 signalosome protects Rbf proteins during embryogenesis. Previous evidence has linked gene activation to protein turnover via the promoter-associated proteasome. Our findings suggest that Rbf repression may similarly involve the proteasome and the promoter-associated COP9 signalosome, serving to extend Rbf protein lifespan and enable appropriate programs of retinoblastoma gene control during development.
Advanced survival models for risk-factor analysis in scrapie
Authors: Corbière Fabien , Barillet Francis , Andréoletti Olivier , Fidelle Francis , Laphitz-Bordet Nathalie , Schelcher François , Joly Pierre
Published: January 2007

Because of the confounding effects of long incubation duration and flock management, accurate epidemiological studies of scrapie outbreaks are difficult to carry out. In this study, 641 Manech red-faced sheep from six scrapie-affected field flocks in Pyrénées Atlantiques, France, were monitored for clinical scrapie over a 6–9 year period. Over this period, 170 scrapie clinical cases were recorded and half of the culled animals were submitted for post-mortem transmissible spongiform encephalopathy diagnosis to assess their infectious status. Collected data were analysed using a ‘mixture cure model’ approach, which allowed for the discriminating effect of PrP genotype and flock origin on incidence and incubation period. Simulations were performed to evaluate the applicability of such a statistical model to the collected data. As expected, ARR heterozygote sheep were less at risk of becoming infected than ARQ/ARQ individuals and had a greater age at clinical onset. Conversely, when compared with ARQ/ARQ, the VRQ haplotype was associated with an increased infection risk, but not a shorter incubation period. Considering the flock effect, we observed that a high incidence rate was not associated with shorter incubation periods and that the incubation period could be significantly different in flocks harbouring similar infection risks. These results strongly support the conclusion that other parameters, such as the nature of the agent or flock management, could interfere with epidemiological dynamics of the infection in scrapie-affected flocks.
Assessment of the extent of variation in influenza A virus cytotoxic T-lymphocyte epitopes by using virus-specific CD8+ T-cell clones
Authors: Berkhoff E. G. M. , Geelhoed-Mieras M. M. , Fouchier R. A. M. , Osterhaus A. D. M. E. , Rimmelzwaan G. F.
Published: January 2007

The influenza A virus nucleoprotein (NP) and matrix protein are major targets for human virus-specific cytotoxic T-lymphocyte (CTL) responses. Most of the CTL epitopes that have been identified so far are conserved. However, sequence variation in CTL epitopes of the NP has recently been demonstrated to be associated with escape from virus-specific CTLs. To assess the extent of variation in CTL epitopes during influenza A virus evolution, 304 CTL clones derived from six study subjects were obtained with specificity for an influenza A/H3N2 virus isolated in 1981. Subsequently, the frequency of the CTL clones that failed to recognize a more recent influenza virus strain isolated in 2003 was determined. In four of six study subjects, CTLs were found to be specific for variable epitopes, accounting for 2.6 % of all CTL clones. For some of these CTL clones, the minimal epitope and the residues responsible for abrogation of T-cell recognition were identified.
Molecular analysis of highly pathogenic avian influenza virus of subtype H5N1 isolated from wild birds and mammals in northern Germany
Authors: Weber Siegfried , Harder Timm , Starick Elke , Beer Martin , Werner Ortrud , Hoffmann Bernd , Mettenleiter Thomas C. , Mundt Egbert
Published: January 2007

Analysis of the full-length sequences of all eight segments of the German wild-bird H5N1 highly pathogenic avian influenza virus index isolate, A/Cygnus cygnus/Germany/R65/2006, and an H5N1 isolate from a cat (A/cat/Germany/R606/2006) obtained during an outbreak in February 2006 revealed a very high similarity between these two sequences. One amino acid substitution in the PA gene, encoding a protein involved in virus RNA replication, and one amino acid substitution in the haemagglutinin (HA) protein were observed. Phylogenetic analyses of the HA and neuraminidase nucleotide sequences showed that avian influenza H5N1 isolates from the Astrakhan region located in southern Russia were the closest relatives. Reassortment events could be excluded in comparison with other ‘Qinghai-like’ H5N1 viruses. In addition, an H5N1 isolate originating from a single outbreak in poultry in Germany was found to be related closely to the H5N1 viruses circulating at that time in the wild-bird population.
African swine fever virus A238L inhibitor of NF-κB and of calcineurin phosphatase is imported actively into the nucleus and exported by a CRM1-mediated pathway
Authors: Silk Rhiannon N. , Bowick Gavin C. , Abrams Charles C. , Dixon Linda K.
Published: January 2007

This study examined nuclear and cytoplasmic shuttling of the African swine fever virus (ASFV) A238L protein, which is an inhibitor of NF-κB and of calcineurin phosphatase. The results showed that the protein was present in both the nucleus and the cytoplasm in ASFV-infected cells and that the higher molecular mass 32 kDa form of the A238L protein was the predominant nuclear form, which accumulated later in infection. In contrast, both the 28 and 32 kDa forms of the A238L protein were present in the cytoplasm. The A238L protein was actively imported into the nucleus and exported by a CRM1-mediated pathway, although a pool of the protein remained in the cytoplasm and did not enter the nucleus. By using a recombinant ASFV from which the A238L gene had been deleted, it was shown that expression of A238L did not inhibit nuclear import of the NF-κB p50 or p65 subunit and did not inhibit nuclear export of p65 by a CRM1-mediated pathway. The results were consistent with a model in which A238L functions within both the nucleus and the cytoplasm.
Prevalence of PB1-F2 of influenza A viruses
Authors: Zell Roland , Krumbholz Andi , Eitner Annett , Krieg Reimar , Halbhuber Karl-Jürgen , Wutzler Peter
Published: January 2007

PB1-F2 is a pro-apoptotic polypeptide of many influenza A virus (FLUAV) isolates encoded by an alternative ORF of segment 2. A comprehensive GenBank search was conducted to analyse its prevalence. This search yielded 2226 entries of 80 FLUAV subtypes. Of these sequences, 87 % encode a PB1-F2 polypeptide greater than 78 aa. However, classic swine influenza viruses and human H1N1 isolates collected since 1950 harbour a truncated PB1-F2 sequence. While PB1-F2 of human H1N1 viruses terminates after 57 aa, classic swine H1N1 sequences have in-frame stop codons after 11, 25 and 34 codons. Of the avian sequences, 96 % encode a full-length PB1-F2. One genetic lineage of segment 2 sequences which is avian-like and different from the classic swine FLUAV comprises PB1-F2 sequences of porcine FLUAVs isolated in Europe (H1N1, H1N2, H3N2). Of these PB1-F2 sequences, 42 % also exhibit stop codons after 11, 25 and 34 codons. These amino acid positions are highly conserved among all FLUAV isolates irrespective of their origin. Molecular genetic analyses reveal that PB1-F2 is under constraint of the PB1 gene. The PB1-F2 polypeptide of FLUAVs isolated from European pigs is expressed in host cells as demonstrated by immunohistochemistry. Using different PB1-F2 versions fused to an enhanced GFP, mitochondrial localization is demonstrated for those PB1-F2 polypeptides which are greater than 78 aa while a truncated version (57 aa) shows a diffuse cytoplasmic distribution. This indicates similar properties and function of porcine and human FLUAV PB1-F2.
The ribonucleotide reductase domain of the R1 subunit of herpes simplex virus type 2 ribonucleotide reductase is essential for R1 antiapoptotic function
Authors: Chabaud Stéphane , Sasseville A. Marie-Josée , Elahi Seyyed Mehdy , Caron Antoine , Dufour Florent , Massie Bernard , Langelier Yves
Published: January 2007

The R1 subunit (ICP10) of herpes simplex virus type 2 (HSV-2) ribonucleotide reductase (RR), which in addition to its C-terminal reductase domain possesses a unique N-terminal domain of about 400 aa, protects cells against apoptosis. As the NH2domain on its own is not antiapoptotic, it has been postulated that both domains of R1 or part(s) of them could be necessary for this function. Here, N- and C-terminal deletions were introduced in HSV-2 R1 to map the domain(s) involved in its antiapoptotic potential. The results showed that, whereas most of the NH2domain including part of the recently described putativeα-crystallin domain is dispensable for antiapoptotic activity, it is the integrity of the structured RR domain that is required for protection. As theα-crystallin domain appears to play an important role in protein folding and oligomerization, the N-terminal boundary of the antiapoptotic domain could not be defined precisely. In addition, this study provided evidence that overexpression of HSV-2 R2 at levels up to 30-fold more than HSV-2 R1 did not decrease protection from tumour necrosis factor alpha, indicating that the R1 surface where R2 binds is not involved in antiapoptotic activity. Importantly, this result suggests that the co-expression of both RR subunits during the lytic cycle should not affect protection from this cytokine.
Contributions of the lymphocytic choriomeningitis virus glycoprotein and polymerase to strain-specific differences in murine liver pathogenicity
Authors: Bergthaler Andreas , Merkler Doron , Horvath Edit , Bestmann Lukas , Pinschewer Daniel D.
Published: January 2007

Hepatic involvement is commonly observed in arenavirus infections, but the viral determinants of liver disease are only partially understood. Here we exploited newly developed reverse-genetic techniques withLymphocytic choriomeningitis virus(LCMV), the prototype arenavirus, to address specifically the contribution of the viral glycoprotein (GP) to liver pathogenicity. It is well established that strain WE, but not ARM, causes hepatitis in mice. We found that this property correlated with the superior capacity of WE to propagate in cultured macrophages and hepatocyte-derived cells. In mice, the ability to establish prolonged viraemia allowed the virus to propagate from initially infected Kupffer cells in the liver to neighbouring hepatocytes that underwent apoptosis. Reverse-genetic replacement of the GP in strain ARM with WE-GP resulted in only a very modest increase in liver pathogenicity, if any. Yet, an ARM-derived variant virus with a mutated polymerase gene caused severe liver disease when engineered to display WE-GP but considerably less when expressing ARM-GP. This reverse-genetic approach to an animal model of arenaviral hepatitis reveals a previously underestimated contributory role of the GP that alone is, however, insufficient to cause disease.
Analysis and phylogenetic comparisons of full-length VP2 genes of the 24 bluetongue virus serotypes
Authors: Maan S. , Maan N. S. , Samuel A. R. , Rao S. , Attoui H. , Mertens P. P. C.
Published: January 2007

The outer capsid protein VP2 of Bluetongue virus (BTV) is a target for the protective immune response generated by the mammalian host. VP2 contains the majority of epitopes that are recognized by neutralizing antibodies and is therefore also the primary determinant of BTV serotype. Full-length cDNA copies of genome segment 2 (Seg-2, which encodes VP2) from the reference strains of each of the 24 BTV serotypes were synthesized, cloned and sequenced. This represents the first complete set of full-length BTV VP2 genes (from the 24 serotypes) that has been analysed. Each Seg-2 has a single open reading frame, with short inverted repeats adjacent to conserved terminal hexanucleotide sequences. These data demonstrated overall inter-serotype variations in Seg-2 of 29 % (BTV-8 and BTV-18) to 59 % (BTV-16 and BTV-22), while the deduced amino acid sequence of VP2 varied from 22.4 % (BTV-4 and BTV-20) to 73 % (BTV-6 and BTV-22). Ten distinct Seg-2 lineages (nucleotypes) were detected, with greatest sequence similarities between those serotypes that had previously been reported as serologically ‘related’. Fewer similarities were observed between different serotypes in regions of VP2 that have been reported as antigenically important, suggesting that they may play a role in the neutralizing antibody response. The data presented form an initial basis for BTV serotype identification by sequence analyses and comparison of Seg-2, and for development of molecular diagnostic assays for individual BTV serotypes (by RT-PCR).
Identification and genetic diversity of two human parvovirus B19 genotype 3 subtypes
Authors: Parsyan Armen , Szmaragd Camille , Allain Jean-Pierre , Candotti Daniel
Published: January 2007

Three genotypes (1–3) of human parvovirus B19 have been identified. Analysis of 13 nearly full-length genotype 3 sequences from Ghana, Europe and Brazil identified two genetically distinct clusters. The classification of genotype 3 strains into two subtypes (B19/3a and B19/3b) is proposed. The rate of evolutionary change of B19 genotype 3 strains (2×10−4 nucleotide substitutions per site per year) was similar to those of B19 genotype 1 and carnivore parvoviruses, supporting the hypothesis that high mutation rates are characteristic of members of the family Parvoviridae. The estimated divergence time between B19/3a and B19/3b is 525 years. In Ghana, subtype B19/3a is predominant.
Host-dependent effects of the 3′ untranslated region of turnip crinkle virus RNA on accumulation in Hibiscus and Arabidopsis
Authors: Li Weimin , Wong Sek-Man
Published: January 2007

The 3′ untranslated region (UTR) of turnip crinkle virus (TCV) RNA is 253 nt long (nt 3798–4050) with a 27 nt hairpin structure near its 3′ terminus. In this study, the roles of the 3′ UTR in virus accumulation were investigated in protoplasts ofHibiscus cannabinusL. andArabidopsis thaliana(L.) Heynh. Our results showed that, inHibiscusprotoplasts, the minimal 3′ UTR essential for TCV accumulation extends from nt 3922 to 4050, but that maintenance of virus accumulation at wild-type (wt) levels requires the full-length 3′ UTR. However, inArabidopsisprotoplasts, only 33 nt (nt 4018–4050) at the 3′ extremity of the UTR is required for wt levels of accumulation, whereas other parts of the 3′ UTR are dispensable. The 27 nt hairpin within the 33 nt region is essential for virus accumulation in bothHibiscusandArabidopsisprotoplasts. However, transposition of nucleotides in base pairs within the upper or lower stems has no effect on virus accumulation in eitherHibiscusorArabidopsisprotoplasts, and alterations of the loop sequence also fail to affect replication. Disruption of the upper or lower stems and deletion of the loop sequence reduce viral accumulation inArabidopsisprotoplasts, but abolish virus accumulation inHibiscusprotoplasts completely. These results indicate that strict conservation of the hairpin structure is more important for replication inHibiscusthan inArabidopsisprotoplasts. In conclusion, both the 3′ UTR primary sequence and the 3′-terminal hairpin structure influence TCV accumulation in a host-dependent manner.
Dengue virus (DENV) antibody-dependent enhancement of infection upregulates the production of anti-inflammatory cytokines, but suppresses anti-DENV free radical and pro-inflammatory cytokine production, in THP-1 cells
Authors: Chareonsirisuthigul Takol , Kalayanarooj Siripen , Ubol Sukathida
Published: January 2007

The immunopathogenesis of dengue haemorrhagic fever and dengue shock syndrome is thought to be mediated by a variety of host factors. Enhancing antibodies are one of the key regulating molecules. These antibodies, via antibody-dependent enhancement (ADE) of infection, are able to facilitate dengue virus (DENV) growth in Fc-bearing host cells. The mechanism of ADE-enhanced DENV production is believed to be mediated through increasing the infected-cell mass. In the present work, the effect of ADE infection was explored further, focusing on the post-entry events of ADE infection. It was hypothesized that the higher virus production in ADE infection compared with DENV infection may be due to the ability of this infection pathway to suppress key antiviral molecules. Therefore, the influence of ADE infection on pro- and anti-inflammatory cytokines, including interleukin-12 (IL-12), gamma interferon (IFN-γ), tumour necrosis factor alpha (TNF-α), IL-6 and IL-10, was investigated and it was found that DENV infection via the Fc receptor-mediated pathway was able to suppress the transcription and translation of IL-12, IFN-γand TNF-α. In contrast, infection via this route facilitated expression and synthesis of the anti-inflammatory cytokines IL-6 and IL-10. Moreover, this study demonstrates that the ADE infection pathway also suppresses an innate anti-DENV mediator, nitric oxide radicals, by disrupting the transcription of the iNOS gene transcription factor, IRF-1, and blocking the activation of STAT-1. In conclusion, ADE infection not only facilitates the entry process, but also modifies innate and adaptive intracellular antiviral mechanisms, resulting in unrestricted DENV replication in THP-1 cells.