bluuebunny/crossref_metadata_2025 huggingface dataset:
Synchronization and chaotic dynamics of coupled mechanical metronomes
Authors: Ulrichs Henning , Mann Andreas , Parlitz Ulrich
Published: December 2009

Synchronization scenarios of coupled mechanical metronomes are studied by means of numerical simulations showing the onset of synchronization for two, three, and 100 globally coupled metronomes in terms of Arnol’d tongues in parameter space and a Kuramoto transition as a function of coupling strength. Furthermore, we study the dynamics of metronomes where overturning is possible. In this case hyperchaotic dynamics associated with some diffusion process in configuration space is observed, indicating the potential complexity of metronome dynamics.
Longitudinal detection of ferromagnetic resonance using x-ray transmission measurements
Authors: Boero G. , Rusponi S. , Kavich J. , Rizzini A. Lodi , Piamonteze C. , Nolting F. , Tieg C. , Thiele J.-U. , Gambardella P.
Published: December 2009

We describe a setup for the x-ray detection of ferromagnetic resonance in the longitudinal geometry using element-specific transmission measurements. Thin magnetic film samples are placed in a static magnetic field collinear with the propagation direction of a polarized soft x-ray beam and driven to ferromagnetic resonance by a continuous wave microwave magnetic field perpendicular to it. The transmitted photon flux is measured both as a function of the x-ray photon energy and as a function of the applied static magnetic field. We report experiments performed on a 15 nm film of doped Permalloy (Ni73Fe18Gd7Co2) at the L3/L2-edges of Fe, Co, and Ni. The achieved ferromagnetic resonance sensitivity is about 0.1 monolayers/Hz. The obtained results are interpreted in the framework of a conductivity tensor based formalism. The factors limiting the sensitivity as well as different approaches for the x-ray detection of ferromagnetic resonance are discussed.
Radiation damage in biomimetic dye molecules for solar cells
Authors: Cook Peter L. , Johnson Phillip S. , Liu Xiaosong , Chin An-Li , Himpsel F. J.
Published: December 2009

A significant obstacle to organic photovoltaics is radiation damage, either directly by photochemical reactions or indirectly via hot electrons. Such effects are investigated for biomimetic dye molecules for solar cells (phthalocyanines) and for a biological analog (the charge transfer protein cytochrome c). Both feature a central transition metal atom (or H2) surrounded by nitrogen atoms. Soft x-ray absorption spectroscopy and photoelectron spectroscopy are used to identify three types of radiation-induced changes in the electronic structure of these molecules. (1) The peptide bonds along the backbone of the protein are readily broken, while the nitrogen cage remains rather stable in phthalocyanines. This finding suggests minimizing peptide attachments to biologically inspired molecules for photovoltaic applications. (2) The metal atom in the protein changes its 3d electron configuration under irradiation. (3) The Fermi level EF shifts relative to the band gap in phthalocyanine films due to radiation-induced gap states. This effect has little influence on the optical absorption, but it changes the lineup between the energy levels of the absorbing dye and the acceptor/donor electrodes that collect the charge carriers in a solar cell.
Flux growth at ambient pressure of millimeter-sized single crystals of LaFeAsO, LaFeAsO1−xFx, and LaFe1−xCoxAsO
Authors: Yan J.-Q. , Nandi S. , Zarestky J. L. , Tian W. , Kreyssig A. , Jensen B. , Kracher A. , Dennis K. W. , McQueeney R. J. , Goldman A. I. , McCallum R. W. , Lograsso T. A.
Published: December 2009

Millimeter-sized single crystals of LaFeAsO, LaFeAsO1−xFx, and LaFe1−xCoxAsO were grown in NaAs flux at ambient pressure. The detailed growth procedure and crystal characterizations are reported. The as-grown crystals have typical dimensions of 3×4×0.05–0.3 mm3 with the crystallographic c-axis perpendicular to the plane of the platelike single crystals. Various characterizations confirmed the high quality of our LaFeAsO crystals. Co and F were introduced into the lattice leading to superconducting LaFe1−xCoxAsO and LaFeAsO1−xFx single crystals, respectively. This growth protocol is expected to be broadly applicable to grow other RMAsO (R=rare earth, M=transition metal) compounds.
Electric field driven quantum phase transition between band insulator and topological insulator
Authors: Li Jun , Chang Kai
Published: December 2009

We demonstrate theoretically that electric field can drive a quantum phase transition between band insulator to topological insulator in CdTe/HgCdTe/CdTe quantum wells. The numerical results suggest that the electric field could be used as a switch to turn on or off the topological insulator phase, and temperature can affect significantly the phase diagram for different gate voltage and compositions. Our theoretical results provide us an efficient way to manipulate the quantum phase of HgTe quantum wells.
Influence of gases on Lamb waves propagations in resonator
Authors: Zhou Lianqun , Manceau Jean-François , Bastien François
Published: December 2009

We investigate gases effects on the Lamb wave resonant modes. Various frequency ranges are studied for the antisymmetric mode considering wave velocities either higher or lower than the gas sound velocity. We observe that the relative frequency shifts in the low frequency range of the antisymmetric mode is rather important; in the high frequency range of this mode, the quality factor decreases quickly when the Lamb wave phase velocity approaches the gas sound velocity. We find a good agreement between calculations and experiments in air and helium. The results suggest the possibility to get aerodynamics parameters of gas flow.
Enhanced giant magnetoresistance in Ni-doped antipervoskite compounds GaCMn3−xNix(x=0.05,0.10)
Authors: Wang B. S. , Tong P. , Sun Y. P. , Li L. J. , Tang W. , Lu W. J. , Zhu X. B. , Yang Z. R. , Song W. H.
Published: December 2009

We report an enhanced negative giant magnetoresistance (GMR) with larger temperature span in Ni-doped antipervoskite compounds GaCMn3−xNix. The observed GMR can peak at ∼75% (at 85 kOe) and exceed 60% (at 50 kOe) over a temperature span of approximate 110 and 50K for x=0.05 and 0.10, respectively. Compared with the parent GaCMn3, the well-enhanced GMR in Ni-doped samples is suggested to be associated with the partially suppressed antiferromagnetic (AFM) ground state, which favors the transition from the high-resistivity AFM state to the low-resistivity canted ferromagnetic state under an external magnetic field.
Transport signatures of percolation and electronic phase homogeneity in La1−xSrxCoO3 single crystals
Authors: He C. , El-Khatib S. , Eisenberg S. , Manno M. , Lynn J. W. , Zheng H. , Mitchell J. F. , Leighton C.
Published: December 2009

The influence of nanoscopic magnetoelectronic phase separation on electrical transport in La1−xSrxCoO3 crystals is reported. It is demonstrated; (i) that the T=0 metal-insulator transition can be quantitatively understood using double exchange-modified percolation theory, and, (ii) that the onset of a phase-pure low T ferromagnetic state at high x has a profound effect on the high T transport due to a crossover in the nature of the spin fluctuations. It is concluded that many features of the transport in La1−xSrxCoO3 can be thoroughly understood based on our current understanding of the phase-separated state.
Transparent photostable ZnO nonvolatile memory transistor with ferroelectric polymer and sputter-deposited oxide gate
Authors: Park C. H. , Im Seongil , Yun Jungheum , Lee Gun Hwan , Lee Byoung H. , Sung Myung M.
Published: December 2009

We report on the fabrication of transparent top-gate ZnO nonvolatile memory thin-film transistors (NVM-TFTs) with 200 nm thick poly(vinylidene fluoride/trifluoroethylene) ferroelectric layer; semitransparent 10 nm thin AgOx and transparent 130 nm thick indium-zinc oxide (IZO) were deposited on the ferroelectric polymer as gate electrode by rf sputtering. Our semitransparent NVM-TFT with AgOx gate operates under low voltage write-erase (WR-ER) pulse of ±20 V, but shows some degradation in retention property. In contrast, our transparent IZO-gated device displays very good retention properties but requires anomalously higher pulse of ±70 V for WR and ER states. Both devices stably operated under visible illuminations.
Stability regime of pulse frequency for single event electrospraying
Authors: Stachewicz Urszula , Yurteri Caner U. , Marijnissen Jan C. M. , Dijksman J. Frits
Published: December 2009

This study demonstrates that the hydrodynamic phenomena taking place inside the capillary limits the frequency range of voltage pulses for stable single event electrospraying (SEE), when the meniscus/cone size is defined by the inner diameter of the nozzle. For the analysis of SEE, we used a one-dimensional model describing the displacement and oscillations of the liquid inside the nozzle. The frequency range of voltage pulses for stable SEE is related to the natural oscillation frequency of the fluid column inside the capillary.
Bias stress and condensation of mobile trap agents in printed organic transistors
Authors: Hiraoka Maki , Yamada Toshikazu , Hasegawa Tatsuo
Published: December 2009

We report the relationship between the device instability and the presence of hydrophilic/hydrophobic boundary that is conventionally utilized to obtain well-defined film patterning in printed electronics devices. Pentacene thin-film transistors composed of inkjet-printed synthetic-metal electrodes exhibit notable bias stress effects whose appearance and disappearance depend critically on the positioning of the hydrophilic/hydrophobic boundary within the channel. The Kelvin probe force microscopy measurements revealed that the bias-stress effect is originated in the temporal evolution of trapped charge densities accumulated at the hydrophilic/hydrophobic boundary, in which the mobile nature of trap agents on the hydrophilic surface take crucial role.
Enhancement of electric oxygen-iodine laser performance using a rectangular discharge and longer gain length
Authors: Benavides G. F. , Zimmerman J. W. , Woodard B. S. , Carroll D. L. , Palla A. D. , Day M. T. , Verdeyen J. T. , Solomon W. C.
Published: December 2009

Herein the authors report on the demonstration of a 95% enhancement in continuous-wave laser power on the 1315 nm transition of atomic iodine via a 50% increase in gain length, flow rates, and discharge power. O2(a Δ1) is produced by a single radio-frequency-excited electric discharge sustained in an O2–He–NO gas mixture flowing through a rectangular geometry, and I(P21/2) is then pumped using energy transferred from O2(a Δ1). A gain of 0.26% cm−1 was obtained and the total laser output power was 54.8 W.
Rechargeable electronic textile battery
Authors: Bhattacharya R. , de Kok M. M. , Zhou J.
Published: December 2009

We present a simple fabrication process that produces polymeric charge storage devices directly onto a textile surface. By using a coating of poly-(3,4-ethylenedioxythiophene):poly(styrene sulphonic acid) (PEDOT) as a solid electrolytic layer deposited between two woven silver coated polyamide yarns, we have created a simple polymeric textile battery. By studying the device’s surface morphology and chemical composition, we determined that in the presence of an electric field, silver ions from the anode yarn migrate to the cathode yarn through the PEDOT. Despite this migration, the device could be charged and discharged five times without suffering degradation in electrical performance.
Tendency to promote ferroelectric distortion in Pr-modified PbTiO3
Authors: Kalyani Ajay Kumar , Garg Rohini , Ranjan Rajeev
Published: December 2009

Structural, microstructural, and dielectric studies have been carried out on Pr-modified PbTiO3. A comparative analysis with La-modified PbTiO3 suggests that for chemical modification by same amount, the Pr-modified system has larger tetragonal strain and Curie point. No clear feature of relaxor ferroelectric state is observed for Pr concentration as high as x=0.35, suggesting that Pr modification is less effective, as compared to La-modification, in inducing a relaxor ferroelectric state. Results suggest that inspite of increased chemical disorder, Pr modification partly tends to restore the ferroelectric distortion of the lattice through partial occupancy of the Pr4+ ions on the Ti4+ sites.
Mixed-mode oscillations and chaos in a prey-predator system with dormancy of predators
Authors: Kuwamura Masataka , Chiba Hayato
Published: December 2009

It is shown that the dormancy of predators induces mixed-mode oscillations and chaos in the population dynamics of a prey-predator system under certain conditions. The mixed-mode oscillations and chaos are shown to bifurcate from a coexisting equilibrium by means of the theory of fast-slow systems. These results may help to find experimental conditions under which one can demonstrate chaotic population dynamics in a simple phytoplankton-zooplankton (-resting eggs) community in a microcosm with a short duration.
Coupling of light from an optical fiber taper into silver nanowires
Authors: Dong Chun-Hua , Ren Xi-Feng , Yang Rui , Duan Jun-Yuan , Guan Jian-Guo , Guo Guang-Can , Guo Guo-Ping
Published: December 2009

We report the coupling of photons from an optical fiber taper to surface plasmon modes of silver nanowires. The coupling efficiency can be modulated by adjusting the cross angle and the polarization of the input light. The launch of propagating plasmons can be realized not only at ends of the nanowires but also at the midsection. In addition, we present the coupling of light into multiple nanowires from a single optical fiber taper simultaneously. Our demonstration offers an efficient method for optimizing plasmon coupling into nanoscale metallic waveguides and promotes the realization of highly integrated plasmonic devices.
Impact of two-floor air prism arrays as an embedded reflector for enhancing the output power of InGaN/GaN light emitting diodes
Authors: Kim Hyung Gu , Kim Hyun Kyu , Kim Hee Yun , Ryu Jae Hyoung , Kang Ji Hye , Han Nam , Uthirakumar Periyayya , Hong Chang-Hee
Published: December 2009

This paper reports on the impact of two-floor air prism (TFAP) arrays InGaN/GaN light emitting diodes (LEDs) as an embedded reflector with low refractive indices. The reflectance spectra, measured over the entire visible spectral region, shows strong reflectance modulations due to the TFAP arrays in GaN. The light output powers of TFAP LEDs is seen to be 2.62 times higher than that of conventional LEDs, and 1.55 times higher than that of LEDs with one floor air prism arrays, respectively, at injection currents of 100 mA. This significant enhancement is attributable to a combined effect of effective shaping with 62° angled sidewalls and high refractive index difference between the embedded air prism and the GaN.
Revealing the reversible rotation of magnetization in exchange-coupled composite media switching
Authors: Hauet T. , Florez S. , Margulies D. , Ikeda Y. , Lengsfield B. , Supper N. , Takano K. , Hellwig O. , Terris B. D.
Published: December 2009

We present a study of the magnetic reversal mechanism for exchange coupled composite perpendicular media, i.e., hard granular layer/exchange-coupling layer (ECL)/soft layer (SL) systems, without soft underlayer. Using a vibrating sample magnetometer, the out-of-plane and in-plane components of the magnetization are monitored simultaneously, while sweeping an external out-of-plane magnetic field. The in-plane signal reveals the reversible rotation of the magnetization during the switching process. The amplitude of this rotation is correlated with the variations in coercivity and angular dependence of the remanent coercivity for different ECL and SL thicknesses.
Well-width dependence of valley splitting in Si/SiGe quantum wells
Authors: Sasaki Kohei , Masutomi Ryuichi , Toyama Kiyohiko , Sawano Kentarou , Shiraki Yasuhiro , Okamoto Tohru
Published: December 2009

The valley splitting in Si two-dimensional electron systems is studied using Si/SiGe single quantum wells (QWs) with different well widths. The energy gaps for 4 and 5.3 nm QWs, obtained from the temperature dependence of the longitudinal resistivity at the Landau level filling factor ν=1, are much larger than those for 10 and 20 nm QWs. This is consistent with the well-width dependence of the bare valley splitting estimated from the comparison with the Zeeman splitting in the Shubnikov–de Haas oscillations.
Enhanced thermal conductivity of polymer composites filled with three-dimensional brushlike AlN nanowhiskers
Authors: Shi Zhongqi , Radwan Mohamed , Kirihara Soshu , Miyamoto Yoshinari , Jin Zhihao
Published: December 2009

The thermal conductivity of polymer composites was improved by loading three-dimensional (3D) brushlike AlN nanowhiskers fillers synthesized by simple combustion method. Through filling 47 vol % of the synthesized AlN nanowhiskers, the thermal conductivity of the composite was significantly increased to 4.2 W m−1 K−1, which was 2.3 times higher than that of the composite filled with the same content of commercial AlN equiaxed particles. According to Agari model analysis and microstructure observation, the thermal conductivity enhancement can be ascribed to the 3D brushlike AlN nanowhiskers promoted the formation of a more effect percolating network in the matrix with lower thermal resistance.
Numerical investigation of rising bubble wake and shape variations
Authors: Gaudlitz Daniel , Adams Nikolaus A.
Published: December 2009

The unsteady and open wake and unsteady shape changes in a bubble rising on a zigzag path are investigated by performing direct numerical simulations. For the description of phase interfaces the hybrid particle-level-set method is employed. An air bubble with a volume-equivalent diameter of dB=5.2 mm rising in water is considered. The bubble Reynolds number is set as ReB=598. We observe a zigzagging bubble ascent path, which is caused by periodic shedding of hairpin vortices from the bubble surface to the bubble wake. Chains of up to four hairpin vortices can be observed. A twisting of the vortex chains indicates the transition from a zigzag to a spiralling ascent path. The bubble exhibits a time-averaged ellipsoidal shape and 2,2-mode shape oscillations. The shedding of hairpin vortices is accompanied by bubble-shape deformations which can be represented by traveling surface waves. This phenomenon results in a periodic asymmetric bubble deformation and is in agreement with experimental observations.
X-ray excited luminescence of cuprous iodide single crystals: On the nature of red luminescence
Authors: Gao Pan , Gu Mu , Liu Xiao-Lin , Liu Bo , Huang Shi-Ming
Published: December 2009

The x-ray excited luminescence spectra of different quality CuI crystals were measured. The prevailing blue luminescence and the unusual red luminescence were found at the same time. The relative intensity of these two luminescence peaks was different because of the change of defect concentration in crystals. By comparing the spectra of CuI crystals before and after annealing in vacuum, air or iodine vapors, the origin of the red luminescence in the as-grown crystals was ascribed to the presence of iodine vacancy, as confirmed by the energy dispersive x-ray analysis.
Degradation in InAlN/GaN-based heterostructure field effect transistors: Role of hot phonons
Authors: Leach J. H. , Zhu C. Y. , Wu M. , Ni X. , Li X. , Xie J. , Özgür Ü. , Morkoç H. , Liberis J. , Šermukšnis E. , Matulionis A. , Cheng H. , Kurdak Ç.
Published: December 2009

We report on high electric field stress measurements at room temperature on InAlN/AlN/GaN heterostructure field effect transistor structures. The degradation rate as a function of the average electron density in the GaN channel (as determined by gated Hall bar measurements for the particular gate biases used), has a minimum for electron densities around 1×1013 cm−2, and tends to follow the hot phonon lifetime dependence on electron density. The observations are consistent with the buildup of hot longitudinal optical phonons and their ultrafast decay at about the same electron density in the GaN channel. In part because they have negligible group velocity, the build up of these hot phonons causes local heating, unless they decay rapidly to longitudinal acoustic phonons, and this is likely to cause defect generation which is expected to be aggravated by existing defects. These findings call for modified approaches in modeling device degradation.
Spatial Distortions Induced by Dotted Patterns
Authors: Gamberini Luciano , Roncato Sergio
Published: December 2009

Prolonged steady fixation of parallel, radial, or concentric lines positioned close to each other generates phenomena of illusory oscillation, waving, and shimmering. Purkinje reported a first observation of these phenomena almost two centuries ago (review by Wade, 1977 Perception6 407–433). Here we show that illusory waving and oscillation phenomena arise at first glance when dotted lines are either interposed between continuous lines, or positioned very close to straight edges. Phenomenological and individual observations indicate that dotted and linear patterns are independent sources of different illusory effects: the former of waving, the latter of shimmering/scintillating. The two effects enhance each other when dotted and continuous lines are alternated. Possible accounts of the phenomena are discussed. Waving is likely to originate from the perceived alteration of dot spacing, which in turn gives rise to depth cues and the consequent illusory deviation in depth. Shimmering and scintillating are attributed to imperfect binocular fusion, which can cause phenomena of brightness induction. A theory of the combination of the two illusory effects is put forward.
Vitamin B12 deficiency reduces proliferation and promotes differentiation of neuroblastoma cells and up-regulates PP2A, proNGF, and TACE
Authors: Battaglia-Hsu Shyue-fang , Akchiche Nassila , Noel Nicole , Alberto Jean-Marc , Jeannesson Elise , Orozco-Barrios Carlos Enrique , Martinez-Fong Daniel , Daval Jean-Luc , Guéant Jean-Louis
Published: December 2009

Vitamin B12 (cobalamin, Cbl) is indispensable for proper brain development and functioning, suggesting that it has neurotrophic effects beside its well-known importance in metabolism. The molecular basis of these effects remains hypothetical, one of the reasons being that no efficient cell model has been made available for investigating the consequences of B12 cellular deficiency in neuronal cells. Here, we designed an approach by stable transfection of NIE115 neuroblastoma cells to impose the anchorage of a chimeric B12-binding protein, transcobalamin-oleosin (TO) to the intracellular membrane. This model produced an intracellular sequestration of B12 evidenced by decreased methyl-Cbl and
S
-adenosylmethionine and increased homocysteine and methylmalonic acid concentrations. B12 deficiency affected the proliferation of NIE115 cells through an overall increase in catalytic protein phosphatase 2A (PP2A), despite its demethylation. It promoted cellular differentiation by improving initial outgrowth of neurites and, at the molecular level, by augmenting the levels of proNGF and p75
NTR
. The up-regulation of PP2A and pro-nerve growth factor (NGF) triggered changes in ERK1/2 and Akt, two signaling pathways that influence the balance between proliferation and neurite outgrowth. Compared with control cells, a 2-fold increase of p75
NTR
-regulated intramembraneous proteolysis (RIP) was observed in proliferating TO cells (
P
< 0.0001) that was associated with an increased expression of two tumor necrosis factor (TNF)-α converting enzyme (TACE) secretase enzymes, Adam 10 and Adam 17. In conclusion, our data show that B12 cellular deficiency produces a slower proliferation and a speedier differentiation of neuroblastoma cells through interacting signaling pathways that are related with increased expression of PP2A, proNGF, and TACE.
Nanoridges that characterize the surface morphology of flowers require the synthesis of cutin polyester
Authors: Li-Beisson Yonghua , Pollard Mike , Sauveplane Vincent , Pinot Franck , Ohlrogge John , Beisson Fred
Published: December 2009

Distinctive nanoridges on the surface of flowers have puzzled plant biologists ever since their discovery over 75 years ago. Although postulated to help attract insect pollinators, the function, chemical nature, and ontogeny of these surface nanostructures remain uncertain. Studies have been hampered by the fact that no ridgeless mutants have been identified. Here, we describe two mutants lacking nanoridges and define the biosynthetic pathway for 10,16-dihydroxypalmitate, a major cutin monomer in nature. Using gene expression profiling, two candidates for the formation of floral cutin were identified in the model plant
Arabidopsis thaliana
: the glycerol-3-phosphate acyltransferase 6 (GPAT6) and a member of a cytochrome P450 family with unknown biological function (CYP77A6). Plants carrying null mutations in either gene produced petals with no nanoridges and no cuticle could be observed by either scanning or transmission electron microscopy. A strong reduction in cutin content was found in flowers of both mutants. In planta overexpression suggested GPAT6 preferentially uses palmitate derivatives in cutin synthesis. Comparison of cutin monomer profiles in knockouts for CYP77A6 and the fatty acid ω-hydroxylase CYP86A4 provided genetic evidence that CYP77A6 is an in-chain hydroxylase acting subsequently to CYP86A4 in the synthesis of 10,16-dihydroxypalmitate. Biochemical activity of CYP77A6 was demonstrated by production of dihydroxypalmitates from 16-hydroxypalmitate, using
CYP77A6
-expressing yeast microsomes. These results define the biosynthetic pathway for an abundant and widespread monomer of the cutin polyester, show that the morphology of floral surfaces depends on the synthesis of cutin, and identify target genes to investigate the function of nanoridges in flower biology.
Adventitious changes in long-range gene expression caused by polymorphic structural variation and promoter competition
Authors: Lower Karen M. , Hughes Jim R. , De Gobbi Marco , Henderson Shirley , Viprakasit Vip , Fisher Chris , Goriely Anne , Ayyub Helena , Sloane-Stanley Jackie , Vernimmen Douglas , Langford Cordelia , Garrick David , Gibbons Richard J. , Higgs Douglas R.
Published: December 2009

It is well established that all of the
cis
-acting sequences required for fully regulated human α-globin expression are contained within a region of ≈120 kb of conserved synteny. Here, we show that activation of this cluster in erythroid cells dramatically affects expression of apparently unrelated and noncontiguous genes in the 500 kb surrounding this domain, including a gene (
NME4
) located 300 kb from the α-globin cluster. Changes in
NME4
expression are mediated by physical
cis
-interactions between this gene and the α-globin regulatory elements. Polymorphic structural variation within the globin cluster, altering the number of α-globin genes, affects the pattern of
NME4
expression by altering the competition for the shared α-globin regulatory elements. These findings challenge the concept that the genome is organized into discrete, insulated regulatory domains. In addition, this work has important implications for our understanding of genome evolution, the interpretation of genome-wide expression, expression-quantitative trait loci, and copy number variant analyses.
Forced G1-phase reduction alters mode of division, neuron number, and laminar phenotype in the cerebral cortex
Authors: Pilaz Louis-Jan , Patti Dorothée , Marcy Guillaume , Ollier Edouard , Pfister Sabina , Douglas Rodney J. , Betizeau Marion , Gautier Elodie , Cortay Veronique , Doerflinger Nathalie , Kennedy Henry , Dehay Colette
Published: December 2009

The link between cortical precursors G1 duration (TG1) and their mode of division remains a major unresolved issue of potential importance for regulating corticogenesis. Here, we induced a 25% reduction in TG1 in mouse cortical precursors via forced expression of cyclin D1 and cyclin E1. We found that in utero electroporation-mediated gene transfer transfects a cohort of synchronously cycling precursors, necessitating alternative methods of measuring cell-cycle phases to those classical used. TG1 reduction promotes cell-cycle reentry at the expense of differentiation and increases the self-renewal capacities of Pax6 precursors as well as of Tbr2 basal precursors (BPs). A population level analysis reveals sequential and lineage-specific effects, showing that TG1 reduction: (
i
) promotes Pax6 self-renewing proliferative divisions before promoting divisions wherein Pax6 precursors generate Tbr2 BPs and (
ii
) promotes self-renewing proliferative divisions of Tbr2 precursors at the expense of neurogenesis, thus leading to an amplification of the BPs pool in the subventricular zone and the dispersed mitotic compartment of the intermediate zone. These results point to the G1 mode of division relationship as an essential control mechanism of corticogenesis. This is further supported by long-term studies showing that TG1 reduction results in cytoarchitectural modifications including supernumerary supragranular neuron production. Modeling confirms that the TG1-induced changes in neuron production and laminar fate are mediated via the changes in the mode of division. These findings also have implications for understanding the mechanisms that have contributed to brain enlargement and complexity during evolution.
Antagonistic action of Bicoid and the repressor Capicua determines the spatial limits of Drosophila head gene expression domains
Authors: Löhr Ulrike , Chung Ho-Ryun , Beller Mathias , Jäckle Herbert
Published: December 2009

Bicoid (Bcd) is the anterior determinant in
Drosophila
. Accordingly, loss of Bcd causes loss of head and thorax and their replacement with posterior structures.
bcd
mRNA is maternally deposited at the anterior pole and Bcd forms an anterior-to-posterior (AP) concentration gradient. The expression of a series of zygotic head genes is thought to be differentially regulated by distinct threshold concentrations of the Bcd gradient. Thereby Bcd functions as a morphogen, instructing fields of cells to take on specific fates. Here, we show that spatial limits of anterior genes are also set in the absence of a Bcd gradient and depend on factors of the maternal terminal system. The receptor tyrosine kinase Torso (Tor), a key component of this system, is active in the pole regions of the embryo. Its activity downregulates the maternally deposited repressor Capicua (Cic), leaving high Cic activity in the central regions and decreasingly lower Cic activities toward the poles. We show that the positions of posterior boundaries of Bcd target genes are dependent not only on Bcd, but also on Tor-mediated Cic activity. The results indicate that Cic can mediate repression through distinct binding sites within a Bcd responsive enhancer and that gene activation by Bcd is antagonized by Cic. The activating and repressive effects of Bcd and Cic, respectively, are integrated by the Bcd target gene enhancer. We conclude that the spatial domains of head gene expression are determined by Bcd in concert with Tor-dependent repressors.
Probing of the rates of alternating access in LacY with Trp fluorescence
Authors: Smirnova Irina , Kasho Vladimir , Sugihara Junichi , Kaback H. Ronald
Published: December 2009

Sugar/H
+
symport by lactose permease (LacY) utilizes an alternating access mechanism in which sugar and H
+
binding sites in the middle of the molecule are alternatively exposed to either side of the membrane by sequential opening and closing of inward- and outward-facing hydrophilic cavities. Here, we introduce Trp residues on either side of LacY where they are predicted to be in close proximity to side chains of natural Trp quenchers in either the inward- or outward-facing conformers. In the inward-facing conformer, LacY is tightly packed on the periplasmic side, and Trp residues placed at positions 245 (helix VII) or 378 (helix XII) are in close contact with His-35 (helix I) or Lys-42 (helix II), respectively. Sugar binding leads to unquenching of Trp fluorescence in both mutants, a finding clearly consistent with opening of the periplasmic cavity. The pH dependence of Trp-245 unquenching exhibits a pK
a
of 8, typical for a His side chain interacting with an aromatic group. As estimated from stopped-flow studies, the rate of sugar-induced opening is ≈100 s
−1
. On the cytoplasmic side, Phe-140 (helix V) and Phe-334 (helix X) are located on opposite sides of a wide-open hydrophilic cavity. In precisely the opposite fashion from the periplasmic side, mutant Phe-140→Trp/Phe-334→His exhibits sugar-induced Trp quenching. Again, quenching is pH dependent (pK
a
= 8), but remarkably, the rate of sugar-induced quenching is only ≈0.4 s
−1
. The results provide yet another strong, independent line of evidence for the alternating access mechanism and demonstrate that the methodology described provides a sensitive probe to measure rates of conformational change in membrane transport proteins.
Ceres: software for the integrated analysis of transcription factor binding sites and nucleosome positions in Saccharomyces cerevisiae
Authors: Morris Robert T. , O'Connor Timothy R. , Wyrick John J.
Published: December 2009

Motivation: There is accumulating evidence that the chromatin environment of transcription factor (TF) binding sites in promoter regions has a critical influence on their regulatory potential. Recent studies have mapped TF binding sites and nucleosome positions throughout the yeast genome; however, there is a lack of computation tools to integrate these data types.

Results: We have developed the Ceres software to facilitate the integrated analysis of TF binding sites and nucleosome positions in the model eukaryote S.cerevisiae. Ceres enables users to dynamically display the spatial organization of TF binding sites and nucleosome positions of individual genes, or the average profiles for large gene sets. Ceres provides novel statistical tools to test for the enrichment of TF binding sites and chromatin environments for user-selected gene sets. Ceres also enables users to search the genome for combinations of TF binding sites that are associated with specific chromatin environments. Preliminary analysis using the Ceres software indicates that functional and conserved TF binding sites are often associated with specific chromatin environments.

Availability:  http://bioinformatics1.smb.wsu.edu/Ceres

Contact:  jwyrick@wsu.edu

Supplementary information:  Supplementary data are available at Bioinformatics online.
Effect of Temperature on Severity of Fusarium Wilt of Lettuce Caused by Fusarium oxysporum f. sp. lactucae
Authors: Scott J. C. , Gordon T. R. , Shaw D. V. , Koike S. T.
Published: December 2009

The effect of temperature on Fusarium wilt of lettuce (Lactuca sativa), caused by Fusarium oxysporum f. sp. lactucae, was examined in a controlled environment. Nine lettuce cultivars planted in infested potting mix (500 or 5,000 CFU/g) were maintained under high/low diurnal temperature regimes of 26/18°C, 28/20°C, or 33/26°C. Three cultivars were resistant to Fusarium wilt under all test conditions, and thus were little affected by differences in inoculum level or temperature. The remaining cultivars were more susceptible and manifested more severe symptoms at the higher inoculum level and when maintained at higher temperatures. The tendency for the disease to be more severe under warmer conditions may be due, in part, to an effect of temperature on growth of the pathogen. Radial growth rates calculated for six isolates of F. oxysporum f. sp. lactucae were observed to increase from 10°C up to an apparent maximum near 25°C. The results of this study suggest that growers can reduce the risk of damage from Fusarium wilt by avoiding susceptible cultivars during the warmest planting periods. Further, isolates of F. oxysporum f. sp. lactucae were shown to have a distinctive colony morphology in culture, which made it possible to distinguish them from nonpathogenic strains.
Fusarium oxysporum f. sp. palmarum, a Novel Forma Specialis Causing a Lethal Disease of Syagrus romanzoffiana and Washingtonia robusta in Florida
Authors: Elliott M. L. , Des Jardin E. A. , O'Donnell K. , Geiser D. M. , Harrison N. A. , Broschat T. K.
Published: December 2009

A new disease of Syagrus romanzoffiana (queen palm) and Washingtonia robusta (Mexican fan palm) has spread across the southern half of Florida during the past 5 years. The initial foliar symptom is a one-sided chlorosis or necrosis of older leaf blades, with a distinct reddish-brown stripe along the petiole and rachis and an associated discoloration of internal tissue. Within 2 to 3 months after onset of symptoms, the entire canopy becomes desiccated and necrotic but the leaves do not droop or hang down around the trunk. Based on pathogenicity and morphological and molecular characterization, the etiological agent has been identified as a new forma specialis of Fusarium oxysporum, designated f. sp. palmarum. Sequence analysis of a portion of the translation elongation factor 1-α gene (EF-1α) separated 27 representative isolates into two EF-1α groups, which differed by two transition mutations. Members of both EF-1α groups are pathogenic on both species of palm. A phylogenetic analysis inferred from partial EF-1α sequences from a genetically diverse set of F. oxysporum isolates, including three other formae speciales pathogenic on palm (i.e., f. sp. albedinis, f. sp. canariensis, and f. sp. elaeidis), suggested that f. sp. palmarum and f. sp. albedinis may be more closely related to one another than either is to the two other palm pathogens.
Mefenoxam Sensitivity in Phytophthora cinnamomi Isolates
Authors: Hu Jiahuai , Hong Chuanxue , Stromberg Erik L. , Moorman Gary W.
Published: December 2009

Phytophthora cinnamomi is a destructive root pathogen of numerous woody plant species in the ornamental plant nursery. Sixty-five isolates of P. cinnamomi were evaluated for mefenoxam sensitivity on 20% clarified V8 agar amended with mefenoxam at 0 or 100 μg/ml. In the presence of mefenoxam at 100 μg/ml, eight isolates were intermediately sensitive, with mycelium growth ranging between 11 and 18% of the nonamended control, and 57 isolates were highly sensitive, with little or no mycelium growth. Five intermediately sensitive and five sensitive isolates were chosen to characterize their responses to mefenoxam at 0, 0.1, 1, 10, and 100 μg/ml. For intermediately sensitive isolates, the mefenoxam concentration causing 50% inhibition of mycelium growth (EC50 values) ranged between 0.03 and 0.08 μg/ml; EC50 values for sensitive isolates varied from 0.01 to 0.02 μg/ml. Five intermediately sensitive and seven sensitive isolates were selected further to assess in vivo sensitivity to mefenoxam using Lupinus angustifolius ‘Russell Hybrids’. Lupine seedlings were treated with distilled water or mefenoxam at label rate (Subdue MAXX, 1 fl. oz. of product per 100 gal.) and then, 2 days later, inoculated with a 5-mm-diameter mycelial plug of P. cinnamomi on each cotyledon. Mefenoxam-treated plants averaged more than 96% less disease than water-treated plants. Mefenoxam provided adequate protection of lupines from infection by all 12 isolates regardless of their in vitro levels of sensitivity to mefenoxam. The ability to develop mefenoxam resistance was assessed in P. cinnamomi isolates with different mefenoxam sensitivity by UV mutagenesis and adapting mycelium to increasing concentrations of mefenoxam. Both UV mutagenesis and mycelium adaptation generated isolates with reduced sensitivity to mefenoxam. These isolates, however, did not grow as quickly as their corresponding parent. This study suggests that P. cinnamomi populations from ornamental nurseries in Virginia are sensitive to mefenoxam.
Soilborne Pathogens of Cereals in an Irrigated Cropping System: Effects of Tillage, Residue Management, and Crop Rotation
Authors: Paulitz T. C. , Schroeder K. L. , Schillinger W. F.
Published: December 2009

An irrigated cropping systems experiment was conducted for 6 years in east-central Washington State to examine agronomic and economic alternatives to continuous annual winter wheat (Triticum aestivum) with burning and plowing, and to determine how root diseases of cereals are influenced by management practices. The continuous winter wheat treatment with burning and plowing was compared with a 3-year no-till rotation of winter wheat–spring barley (Hordeum vulgare)–winter canola (Brassica napus) and three straw management treatments: burning, straw removal, and leaving the straw stubble standing after harvest. Take-all disease and inoculum increased from years 1 to 4 in the continuous winter wheat treatment with burning and plowing, reducing plant growth compared to the no-till treatments with crop rotations. Inoculum of Rhizoctonia solani AG-8 was significantly lower in the tilled treatment compared to the no-till treatments. Inoculum concentration of Fusarium pseudograminearum was higher than that of F. culmorum, and in one of three years, the former was higher in treatments with standing stubble and mechanical straw removal compared to burned treatments. Residue management method had no effect on Rhizoctonia inoculum, but spring barley had more crown roots and tillers and greater height with stubble burning. This 6-year study showed that irrigated winter wheat can be produced in a no-till rotation without major disease losses and demonstrated how cropping practices influence the dynamics of soilborne cereal diseases and inoculum over time.
Citrus Stubborn Severity Is Associated with Spiroplasma citri Titer But Not with Bacterial Genotype
Authors: Mello Alexandre F. S. , Yokomi Raymond K. , Melcher Ulrich , Chen Jianchi C. , Fletcher Jacqueline
Published: December 2009

The impact of citrus stubborn disease, caused by Spiroplasma citri, on citrus production is associated with the symptom severity of infected trees but its association with bacterial levels and virulence are unknown. Fifty-eight S. citri isolates were cultivated from severely and mildly symptomatic trees and randomly amplified polymorphic DNA and short-sequence repeat fingerprinting differentiated four major S. citri genotypes among these isolates. Each genotype was present in both mildly and severely symptomatic trees, suggesting that readily detectable genetic differences in the S. citri populations did not account for differences in disease severity. No variation in the size of amplicons of the pathogenicity-related fructose operon was observed in isolates from trees having varying degrees of symptom expression. Quantitative polymerase chain reaction demonstrated that spiroplasma titer is over 6,000 times higher in fruit from severely symptomatic than from mildly symptomatic trees. The genotypic similarities among S. citri isolates from severely and mildly symptomatic trees, and the consistently higher bacterial titer in the former than in the latter, suggests that titer but not genotype is, at least in part, responsible for the greater symptom severity in some of the S. citri-affected trees in the orchard evaluated.
Effect of Foliar Fungicides on Corn with Simulated Hail Damage
Authors: Bradley C. A. , Ames K. A.
Published: December 2009

Quinone outside inhibitor (QoI) foliar fungicides can be effective at reducing foliar diseases in corn (Zea mays), and they have been shown to provide physiological benefits experimentally in other crops in the absence of disease. A new supplemental label for pyraclostrobin that was approved in January 2009 by the United States Environmental Protection Agency (EPA) states that corn plants applied with pyraclostrobin may have better tolerance to damage caused by hail. To determine the effects of QoI foliar fungicides on hail-damaged corn, field research trials were conducted near Champaign, IL in 2007 and 2008. Hail damage was simulated with a gasoline-powered string-mower at the V12 growth stage, which caused injury to leaves and defoliation. At VT, the foliar fungicides azoxystrobin and pyraclostrobin were applied to corn. Control treatments included a nontreated control and a nondamaged control. The simulated hail damage significantly (P ≤ 0.05) increased gray leaf spot severity (caused by Cercospora zeae-maydis) in 2007 but not in 2008. Simulated hail damage also significantly reduced yield compared with the nondamaged control in both 2007 and 2008. Foliar fungicides significantly reduced disease severity compared with the nontreated control in 2007 but not in 2008; however, foliar fungicides did not significantly improve yield in either the damaged or nondamaged plots compared with the nontreated controls. Results from our research trials indicated that foliar fungicides provided very little benefit to corn injured by simulated hail; thus, growers should consider factors other than hail damage when making fungicide application decisions for corn.
Races of Phytophthora sojae and Their Virulences on Soybean Cultivars in Heilongjiang, China
Authors: Zhang Shuzhen , Xu Pengfei , Wu Junjiang , Xue Allen G. , Zhang Jinxiu , Li Wenbin , Chen Chen , Chen Weiyuan , Lv Huiying
Published: December 2009

Phytophthora root and stem rot, caused by Phytophthora sojae, is an economically important disease of soybean (Glycine max) in Heilongjiang Province, China. The objectives of this research were to determine the race profile of P. sojae in Heilongjiang and evaluate soybean cultivars for reactions to the pathogen races. A total of 96 single-zoospore P. sojae isolates were obtained from soil samples collected from 35 soybean fields in 18 counties in Heilongjiang from 2005 to 2007. Eight races of P. sojae, including races 1, 3, 4, 5, 9, 13, 44, and 54, were identified on a set of eight differentials, each containing a single resistance Rps gene, from 80 of the 96 isolates. Races 1 and 3 were predominant races, comprising 58 and 14 isolates, and representing 60 and 7% of the pathogen population, respectively. Races 4, 5, 44, and 54 were identified for the first time in Heilongjiang, and each was represented by two to three isolates only. Sixty-two soybean cultivars commonly grown in Heilongjiang Province were evaluated for their resistance to the eight P. sojae races identified using the hypocotyl inoculation technique. Based on the percentage of plant mortality rated 5 days after inoculation, 44 cultivars were resistant (<30% mortality) to at least one race. These cultivars may be used as sources of resistance in soybean breeding programs.
Race 3, a New and Highly Virulent Race ofFusarium oxysporumf. sp.niveumCausing Fusarium Wilt in Watermelon
Authors: Zhou X. G. , Everts K. L. , Bruton B. D.
Published: December 2009

Three races (0, 1, and 2) of Fusarium oxysporum f. sp. niveum have been previously described in watermelon (Citrullus lanatus) based on their ability to cause disease on differential watermelon genotypes. Four isolates of F. oxysporum f. sp. niveum collected from wilted watermelon plants or infested soil in Maryland, along with reference isolates of races 0, 1, and 2, were compared for virulence, host range, and vegetative compatibility. Race identification was made on the watermelon differentials Sugar Baby, Charleston Gray, Dixielee, Calhoun Gray, and PI-296341-FR using a root-dip, tray-dip, or pipette inoculation method. All four Maryland isolates were highly virulent, causing 78 to 100% wilt on all differentials, one of which was PI-296341-FR, considered highly resistant to race 2. The isolates also produced significantly greater colonization in the lower stems of PI-296341-FR than a standard race 2 reference isolate. In field microplots, two of the isolates caused over 90% wilt on PI-296341-FR, whereas no disease was caused by a race 2 isolate. All four isolates were nonpathogenic on muskmelon, cucumber, pumpkin, and squash, confirming their host specific pathogenicity to watermelon. The Maryland isolates were vegetatively compatible to each other but not compatible with the race 2 isolates evaluated, indicating their genetic difference from race 2. This study proposes that the Maryland isolates belong to a new race, race 3, the most virulent race of F. oxysporum f. sp. niveum described to date.