bluuebunny/crossref_metadata_2025 huggingface dataset:
Analysis of wakefield electron orbits in plasma wiggler
Authors: Ta Phuoc Kim , Corde Sebastien , Fitour Romuald , Shah Rahul , Albert Felicie , Rousseau Jean-Philippe , Burgy Fréderic , Rousse Antoine , Seredov Vasily , Pukhov Alexander
Published: July 2008

In relativistic laser plasma interaction, electrons can be simultaneously accelerated and wiggled in an ion cavity created in the wake of an intense short pulse laser propagating in an underdense plasma. As a consequence of their motion, the accelerated electrons emit an intense x-ray beam called laser produced betatron radiation. Being an emission from charged particles, the features of the betatron source are directly linked to the electrons trajectories. In particular, the radiation is emitted in the direction of the electrons velocity. In this article we show how an image of electrons orbits in the wakefield cavity can be deduced from the structure of x-ray spatial profiles.
Strain sensing through the resonant properties of deformed metal nanowires
Authors: Park Harold S.
Published: July 2008

In this article, we study the potential of gold nanowires as resonant nanoscale strain sensors. The sensing ability of the nanowires is determined by calculating the variations in resonant frequency that occur due to applied uniaxial tensile and compressive strain. The resonant frequencies are obtained using the surface Cauchy–Born model, which captures surface stress effects on the nanowires through a nonlinear continuum mechanics framework; due to the continuum formulation, the strain-dependent nanowire resonant frequencies are calculated through the solution of a standard finite element eigenvalue problem, where the coupled effects of the applied uniaxial strain and surface stress are naturally included through the finite element stiffness matrix. The nanowires are found to be more sensitive to compressive than tensile strain, with resonant frequency shifts around 200–400 MHz with the application of 1% tensile and compressive strain. In general, the strain sensitivity of the nanowires is found to increase with decreasing cross-sectional size, with additional dependencies on their aspect ratio.
Electronic structure and effective masses of InN under pressure
Authors: Gorczyca I. , Plesiewicz J. , Dmowski L. , Suski T. , Christensen N. E. , Svane A. , Gallinat C. S. , Koblmueller G. , Speck J. S.
Published: July 2008

The pressure dependence of the electronic band structure of InN is investigated with emphasis on the conduction band effective mass and its dependence on free-electron concentration. Transport measurements are performed under hydrostatic pressure on three n-type samples of InN with different electron concentrations. The effective mass extracted from the electron mobility is found to increase with pressure, however with a pressure coefficient, which is lower for the samples with higher electron concentration. Calculations of the InN band structure are performed within the density functional theory by means of the linear muffin-tin-orbital method, including an empirical adjustment to reproduce known band edges at ambient pressure. The calculated variations of the highest occupied conduction band energy and the electron effective mass with free-electron concentration are compared to available experimental information. The results show a pronounced deviation from parabolic behavior of the lowest conduction band, and for k>0 this induces large differences between the values of the optical and curvature masses. Both the fundamental band gap and the electron effective mass increase with pressure, but due to the nonparabolic character of the conduction band, the pressure coefficient of the effective mass decreases with electron concentration, in agreement with the experimental observation.
Optical properties of helical and multiring Ag nanostructures: The effect of pitch height
Authors: Zhang Z.-Y. , Zhao Y.-P.
Published: July 2008

The pitch height–dependent optical extinction spectra and the electric field enhancement of helical and multiring nanostructures are studied by the discrete dipole approximation method. For light incident along the axis of the helix, with the increase of the pitch height, the plasmon peak wavelengths redshift monotonically and the electric coupling between two adjacent pitches weakens. The plasmon peak can also be tuned by changing the polarization of the incident light, particularly by circularly polarized light. In most cases, the maximum electric field is distributed near the surface of the helix. As a comparison, since multiring structures do not have helicity, the extinction spectra are polarization independent and the maximum electrical fields always distribute on the top ring. These results show that the optical properties of helical structures are different when irradiated by left or right circular polarized light. Understanding and manipulating pitch height allow one to tune the plasmon peak and rearrange the electric field enhancement distribution of helical nanostructures.
Characterization and modeling of fast traps in thermal agglomerating germanium nanocrystal metal-oxide-semiconductor capacitor
Authors: Chiang K. H. , Lu S. W. , Peng Y. H. , Kuan C. H. , Tsai C. S.
Published: July 2008

In this paper, the germanium (Ge) nanocrystals (NCs) are synthesized by using the rapid-thermal annealing and are embedded into a three-layer (SiO2∕NCs–Ge∕SiO2) capacitor structure. The samples with∕without the postmetallization annealing (PMA) treatment are investigated to compare and study the PMA affections. The charge storage characteristics of our samples are investigated with the capacitance-voltage (C-V) hystereses. The frequency independence of hysteresis windows is found and attributed to NCs as slow traps with a large characteristic time constant. The frequency-dependent C-V and conductance-voltage (G-V) experiments are further introduced to study the interface traps and the fast traps induced by the NC formation. In order to extract the related trap characteristics from the measured C-V and G-V, we propose to utilize the equivalent circuit and single-level trap model based on Shakley-Read-Hall theory. Three associated parameters including the areal trap density, trap conductance, and semiconductor capacitances are used to confirm that the single-level trap model is truly appropriate for our samples. It is then found from the model that the areal trap density is high and approaches almost uniform distribution along the valence band and bandgap but significantly reduced and then becomes decreased from valence band to the midgap after PMA treatment. In addition, after PMA treatment, the characteristic time constant becomes smaller for one order of magnitude at the same gate bias. It is attributed to the reduction of trap density and also agrees that the interface traps are dominant and has a small characteristic time constant.
Step-induced misorientation of GaN grown on r-plane sapphire
Authors: Smalc-Koziorowska J. , Dimitrakopulos G. P. , Sahonta S.-L. , Tsiakatouras G. , Georgakilas A. , Komninou Ph.
Published: July 2008

In the growth of nonpolar (1¯1¯20) a-plane GaN on r-plane (11¯02) sapphire by plasma-assisted molecular beam epitaxy, misoriented crystallites are observed close to the substrate. They have average diameter ∼10nm and are oriented with the (0001)GaN plane approximately parallel to the (21¯1¯3)sapph. plane and [011¯0]GaN∥[1¯101]sapph.. This semipolar orientation is promoted by a low misfit (2.4%) between (101¯1¯)GaN and (1¯21¯0)sapph. planes. Its introduction, after nitridation treatment, is due to GaN nucleation on {21¯1¯3}sapph. step facets inclined at 26° relative to the r-plane. Two variants are observed, leading to twinning when they abut inside the epilayer.
Measurement of the critical curve of a synthetic antiferromagnet
Authors: Radu Cosmin , Cimpoesu Dorin , Stancu Alexandru , Spinu Leonard
Published: July 2008

In this paper, we propose a method for a synthetic antiferromagnet structure’s critical curve determination. The method is based on reversible susceptibility’s singularities detection, as the magnetic field is swept along easy axis, in both positive and negative direction, while a hard axis bias field is also applied. By performing susceptibility measurements with different values of the bias field, the critical curve can be determined. Knowing the critical curve of a synthetic antiferromagnetic structure is essential for devices such as magnetic random access memories.
Highly sensitive coherent detection of terahertz waves at room temperature using a parametric process
Authors: Guo Ruixiang , Ohno Seigo , Minamide Hiroaki , Ikari Tomofumi , Ito Hiromasa
Published: July 2008

We report the experimental results of coherent detection of narrow-linewidth nanosecond terahertz radiation at room temperature using frequency conversion in a nonlinear MgO:LiNbO3 crystal. Mixing the terahertz radiation with a near-infrared intense pump pulse results in the excitation and amplification of the difference-frequency component, which is detected with an InGaAs-based photodiode. We demonstrate this method in a fast and very sensitive terahertz wave detector. The detector is capable of capturing the temporal profile of terahertz pulses with nanosecond resolution, and is at least one order more sensitive than a typical liquid-He-cooled Si bolometer for detecting nanosecond pulsed terahertz wave beams.
Interfacial destabilization and atomization driven by surface acoustic waves
Authors: Qi Aisha , Yeo Leslie Y. , Friend James R.
Published: July 2008

Surface acoustic wave atomization is a rapid means for generating micron and submicron aerosol droplets. Little, however, is understood about the mechanisms by which these droplets form due to the complex hydrodynamic processes that occur across widely varying length and time scales. Through experiments, scaling theory, and simple numerical modeling, we elucidate the interfacial destabilization mechanisms that lead to droplet formation. Using a millimeter-order fluid drop exposed to surface acoustic waves as it sits atop a single-crystal lithium niobate piezoelectric substrate, large aerosol droplets on the length scale of the parent drop dimension are ejected through a whipping and pinch-off phenomenon, which occurs at the asymmetrically formed crest of the drop due to leakage of acoustic radiation at the Rayleigh angle. Smaller micron order droplets, on the other hand, are formed due to the axisymmetric breakup of cylindrical liquid jets that are ejected as a consequence of interfacial destabilization. The 10μm droplet dimension correlates with the jet radius and the instability wavelength, both determined from a simple scaling argument involving a viscous-capillary dominant force balance. The results are further supported by numerical solution of the evolution equation governing the interfacial profile of a sessile drop along which an acoustic pressure wave is imposed. Viscous and capillary forces dominate in the bulk of the parent drop, but inertia is dominant in the ejected jets and within a thin boundary layer adjacent to the substrate where surface and interfacial accelerations are large. With the specific exception of parent drops that spread into thin films with thicknesses on the order of the boundary layer dimension prior to atomization, the free surface of the drop is always observed to vibrate at the capillary-viscous resonance frequency—even if the exciting frequency of the surface acoustic wave is several orders of magnitude larger—contrary to common assumptions used in deriving subharmonic models resulting in a Mathieu equation for the capillary wave motion, which has commonly led to erroneous predictions of the droplet size.
Electronic structure of Se, Se–Te, and Se–Te–Sb systems: Some observations from the x-ray spectroscopy and ab initio calculations
Authors: Yiu Yun Mui , Sham Tsun Kong , Kaur Gurinder
Published: July 2008

Electronic structures of Se, Se80Te20, and Se80−xSbxTe20(0≤x≤9) systems have been investigated using x-ray photoelectron spectroscopy and x-ray absorption near edge spectroscopy (XANES). The experimental results show strong Se–Se and Se–Te interaction as well as antimony dilution effects in the ternary alloy. The interpretation of the results is assisted by theoretical calculations. The densities of states for the energy bands have been evaluated with the full potential augmented plane wave method based on the density functional theory (DFT) and the real-space multiple scattering (RSMS) approach using small clusters of model crystal structures. The ab initio calculation methods for the XANES spectra of Se, Se80Te20, and Se80−xSbxTe20(0≤x≤9) systems are compared with the experimental data. It is found that the DFT calculation provides better agreement with the pre-edge resonance, while RSMS yields good agreement with the postedge region. The interplay of x-ray spectroscopy results and theory is discussed.
On the reliability of scrape-off layer ion temperature measurements by retarding field analyzers
Authors: Kočan M. , Gunn J. P. , Komm M. , Pascal J.-Y. , Gauthier E. , Bonhomme G.
Published: July 2008

The retarding field analyzer (RFA) is one of the only widely accepted diagnostics for measurements of ion temperature Ti in the tokamak scrape-off layer. In this paper we analyze some instrumental effects of the RFA and their influence on Ti measurements. It is shown that selective ion transmission through the RFA slit is responsible for an overestimation of Ti by less than 14%, even for a relatively thick slit plate. Therefore, thicker slit plates are preferable, since they reduce, e.g., the risk of melting during off-normal events, and the effect of positive space charge inside the cavity. The influence of the electron repelling grid, as well as misalignment of the slit with respect to the magnetic field on Ti measurements are negligible.
Observation of spectral drift in engineered quadratic nonlinear media
Authors: Marangoni M. , Sanna G. , Brida D. , Conforti M. , Cirmi G. , Manzoni C. , Baronio F. , Bassi P. , De Angelis C. , Cerullo G.
Published: July 2008

Spectral blueshifts of femtosecond pulses induced by quadratic cascaded nonlinearities are experimentally studied in an engineered aperiodically poled stoichiometric lithium tantalate crystal with optimized nonlinear pattern and chirp of the input pump pulses. Starting from nearly Gaussian input pulses centered at 1420nm with 70nm spectral width, spectral shifts as high as 40nm were obtained in combination with an almost unaltered spectral shape and a transform-limited pulse duration.
Plasma shaping effects on the geodesic acoustic mode in toroidally axisymmetric plasmas
Authors: Gao Zhe , Wang Ping , Sanuki H.
Published: July 2008

The geodesic acoustic mode (GAM) is studied in noncircular, finite aspect ratio, toroidal plasmas with a gyrokinetic theory and a local magnetohydrodynamics equilibrium model. Dependencies of the GAM frequency on finite aspect ratio and elongation are investigated when trapped particle effects are neglected in the large aspect ratio limit. It is found that the GAM frequency sharply decreases with an increasing elongation by dependence of [2∕(κ2+1)]1∕2 and slightly decreases with an increasing inverse aspect ratio by dependence of about 1−3ε2∕4, where κ and ε are the plasma elongation and inverse aspect ratio. The elongation dependence comes from the modification of classical ion polarization balanced by that of curvature drift polarization while the aspect ratio dependence is due to the former in the leading order.
Effective well of a static Kingdon trap
Authors: Ordonez C. A.
Published: July 2008

A theory is developed that describes ion confinement within a centrifugal-electrostatic effective potential energy well, which is produced by a static Kingdon trap. Both a cylindrical configuration and a spherical configuration are treated. The conditions required for forming the deepest effective potential energy well are determined. Criteria for confining particles that have a drifting Maxwellian velocity distribution are established.
Full-field particle velocimetry with a photorefractive optical novelty filter
Authors: Woerdemann Mike , Holtmann Frank , Denz Cornelia
Published: July 2008

We utilize the finite time constant of a photorefractive optical novelty filter microscope to access full-field velocity information of fluid flows on microscopic scales. In contrast to conventional methods such as particle image velocimetry and particle tracking velocimetry, not only image acquisition of the tracer particle field but also evaluation of tracer particle velocities is done all-optically by the novelty filter. We investigate the velocity dependent parameters of two-beam coupling based optical novelty filters and demonstrate calibration and application of a photorefractive velocimetry system. Theoretical and practical limits to the range of accessible velocities are discussed.
Rendering a color palette by light-emitting diodes
Authors: Žukauskas A. , Vaicekauskas R. , Ivanauskas F. , Vaitkevičius H. , Shur M. S.
Published: July 2008

We present a new approach to the optimization of sources of white light based on colored light-emitting diodes (LEDs) and show that a pentachromatic source composed of LEDs with the equidistant peak wavelengths at about 450, 500, 550, 600, and 650nm renders all 1269 colors of the Munsell palette almost indistinguishably from daylight.
Detection of Si nanoclusters by x-ray scattering during silicon film deposition by mesoplasma chemical vapor deposition
Authors: Diaz Jose Mario A. , Kambara Makoto , Yoshida Toyonobu
Published: July 2008

A laboratory-scale small angle x-ray scattering (SAXS) system was designed to detect free silicon nanoclusters generated in the gas phase during silicon film deposition by an inductively coupled mesoplasma chemical vapor deposition system at different SiH4 partial pressures and rf powers. Analysis of the SAXS profiles collected from the vicinity of the plasma-substrate boundary layer has revealed the presence of a polydisperse system of spherical scatterers having a loosely bound structure with around 2–3nm in size. A small amount of larger-sized nanoclusters was found to form as the rf power decreased, and emergence of such large nanoclusters was seen to be associated with the transition from an epitaxial to agglomerated microstructure of the films so deposited.
Magnetic shape memory effect in thin foils
Authors: Heczko Oleg , Soroka Aleksandr , Hannula Simo-Pekka
Published: July 2008

The magnetic shape memory (MSM) effect was observed in Ni–Mn–Ga freestanding thin foils down to 90μm in thickness using top-down approach. The foils were prepared by thinning the bulk crystals exhibiting MSM effect. The effect was evaluated from the magnetization curves. The significant decrease in magnetic field needed to initiate the MSM effect (magnetic field induced strain or martensite structure reorientation) was observed for the studied foils down to μ0H=0.088T or H=70kA∕m. Observation suggests that the pinning of twin boundaries on the internal obstacles rather than pinning on surface lowers twin boundaries’ mobility.
Ultraviolet electroluminescence from controlled arsenic-doped ZnO nanowire homojunctions
Authors: Zhang Jun-Yan , Li Ping-Jian , Sun Hui , Shen Xin , Deng Tian-Song , Zhu Kong-Tao , Zhang Qi-Feng , Wu Jin-Lei
Published: July 2008

ZnO nanowire arrays were grown on semi-insulating intrinsic GaAs substrates, and controlled arsenic-doping process was carried out to realize the n-ZnO∕p-ZnO nanowire array/GaAs structures. The constructed ZnO nanowire homojunctions demonstrated a clear rectifying behavior and the turn-on voltage was above 4.0V. The corresponding ultraviolet electroluminescence spectra were obtained for the applied forward voltage above 30V (20mA). The distinct ultraviolet electroluminescence peak, centered at 382nm, is nonlinearly enhanced with an increase in the applied forward voltage. The origin of the strong ultraviolet electroluminescence was discussed in terms of the controlled arsenic-doping process.
Non-magnetic simplified cylindrical cloak with suppressed zeroth order scattering
Authors: Yan Wei , Yan Min , Qiu Min
Published: July 2008

A type of simplified cloaks with matched exterior boundaries is proposed. The cloak uses nonmagnetic material for the TM polarization and can function with a relatively thin thickness. It is shown that the zeroth order scattering of such cloak is dominant among all cylindrical scattering terms. A gap is added at the cloak’s inner surface to eliminate the zeroth order scattering through the mechanism of scattering resonance. The reduction in scattering is relatively smooth, indicating that the proposed scattering reduction method has good tolerance to perturbations. Numerical simulations also confirm that the proposed structure has very low scattering.
Detection of charge transfer processes in Cr-doped SrTiO3 single crystals
Authors: La Mattina F. , Bednorz J. G. , Alvarado S. F. , Shengelaya A. , Keller H.
Published: July 2008

An insulator-to-metal transition is observed in Cr-doped SrTiO3 single crystals upon extended exposure to a high electric field, namely, electroconditioning (EC). Electron paramagnetic resonance (EPR) and transport measurements under laser irradiation show anticorrelation between the Cr3+ EPR signal and the electrical current. This proves that the Cr3+ ions are responsible for the photocurrent that initiates the EC process. We observe the presence of Cr3+∕Cr4+ mixed valencies in the bulk in the conducting state. The EPR characterization of the spectra in the conducting state excludes the possibility of a Cr3+-oxygen vacancy complex in the bulk as a result of the EC.
Uncooled infrared detectors for 3–5μm and beyond
Authors: Jayaweera P. V. V. , Matsik S. G. , Perera A. G. U. , Liu H. C. , Buchanan M. , Wasilewski Z. R.
Published: July 2008

Avoiding cryogenic cooling not only reduces the cost and weight but also simplifies the infrared detector system allowing widespread usage. Here an uncooled infrared detection using intravalence bands is reported. A set of three p-GaAs∕AlxGa1−xAs multiple heterojunction detector structures were used to demonstrate the concept experimentally. A preliminary detector showed peak responsivity of 0.29mA∕W at 2.5μm at 300K. The intravalence band approach can be used to cover various wavelength ranges by using different material systems giving rise to the possibilities of a dual band detector operating in atmospheric windows.
High temperature stability of postgrowth annealed transparent and conductive ZnO:Al films
Authors: Bayraktaroglu Burhan , Leedy Kevin , Bedford Robert
Published: July 2008

High temperature stability of Al-doped ZnO transparent thin films in air has been improved by a combination of optimized growth parameters and postgrowth treatment. Optical transparency was better than 90% for wavelengths ranging from 380 to at least 2500nm with films that also had resistivities of 2×10−4Ωcm. Depending on the growth conditions, film resistivities showed different degrees of increase in resistivity after storing in air at elevated temperatures. Films grown at lower pressures were stable up to 400°C for short exposure times (2h) and exhibited virtually no change in resistivity at 260°C for over 2500h.
Exchange bias in nanoscale antidot arrays
Authors: Tripathy D. , Adeyeye A. O. , Singh N.
Published: July 2008

Exchange bias effects have been systematically investigated in nanoscale Cu (10 nm)/Ni80Fe20 (30 nm)/Ir75Mn25 (30 nm)/Cu (2 nm) multilayer antidot arrays. The antidot arrays exhibit asymmetric and shifted hysteresis loops along the induced exchange bias direction, with higher coercivity and exchange bias field values as compared to a continuous film deposited under identical conditions. The evolution in exchange bias field with increasing antidot diameter is ascribed to the constraints imposed on the domain size in the Ir75Mn25 layer and reduced ferromagnetic-ferromagnetic interactions in the Ni80Fe20 layer.
How vision begins: An odyssey
Authors: Luo Dong-Gen , Xue Tian , Yau King-Wai
Published: July 2008

Retinal rods and cones, which are the front-end light detectors in the eye, achieve wonders together by being able to signal single-photon absorption and yet also able to adjust their function to brightness changes spanning 109-fold. How these cells detect light is now quite well understood. Not surprising for almost any biological process, the intial step of seeing reveals a rich complexity as the probing goes deeper. The odyssey continues, but the knowledge gained so far is already nothing short of remarkable in qualitative and quantitative detail. It has also indirectly opened up the mystery of odorant sensing. Basic science aside, clinical ophthalmology has benefited tremendously from this endeavor as well. This article begins by recapitulating the key developments in this understanding from the mid-1960s to the late 1980s, during which period the advances were particularly rapid and fit for an intricate detective story. It then highlights some details discovered more recently, followed by a comparison between rods and cones.
Interneuron activity controls endocannabinoid-mediated presynaptic plasticity through calcineurin
Authors: Heifets Boris D. , Chevaleyre Vivien , Castillo Pablo E.
Published: July 2008

Retrograde signaling by endocannabinoids (eCBs) mediates a widely expressed form of long-term depression at excitatory and inhibitory synapses (eCB-LTD), involving a reduction in neurotransmitter release. In the hippocampus, eCB-LTD occurs at interneuron (IN)-pyramidal cell (PC) synapses (I-LTD), and its induction requires a presynaptic reduction of cAMP/PKA signaling resulting from minutes of type 1 cannabinoid receptor (CB1R) activation. Although repetitive activity of glutamatergic synapses initiates the eCB mobilization required for I-LTD, it is unclear whether CB1R-containing GABAergic terminals are passive targets of eCBs or whether they actively contribute to induction. Here, we show that the minutes-long induction period for I-LTD may serve as a window to integrate associated spontaneous activity in the same IN receiving the retrograde eCB signal. Indeed, reducing spontaneous IN firing blocked I-LTD, which could be rescued with extra stimulation of inhibitory afferents. Moreover, cell pair recordings showed that a single IN expressed LTD onto a PC only if it was active during eCB signaling. Several methods of disrupting presynaptic Ca
2+
dynamics all blocked I-LTD, strongly suggesting that IN spikes regulate I-LTD by raising Ca
2+
at the nerve terminal. Finally, inhibiting the Ca
2+
-activated phosphatase, calcineurin, fully blocked I-LTD, but blocking another phosphatase did not. Our findings support a model where both CB1R signaling and IN activity shift the balance of kinase and phosphatase activity in the presynaptic terminal to induce I-LTD.
A germ-line-selective advantage rather than an increased mutation rate can explain some unexpectedly common human disease mutations
Authors: Choi Soo-Kyung , Yoon Song-Ro , Calabrese Peter , Arnheim Norman
Published: July 2008

Two nucleotide substitutions in the human FGFR2 gene (C755G or C758G) are responsible for virtually all sporadic cases of Apert syndrome. This condition is 100–1,000 times more common than genomic mutation frequency data predict. Here, we report on the C758G
de novo
Apert syndrome mutation. Using data on older donors, we show that spontaneous mutations are not uniformly distributed throughout normal testes. Instead, we find foci where C758G mutation frequencies are 3–4 orders of magnitude greater than the remaining tissue. We conclude this nucleotide site is not a mutation hot spot even after accounting for possible Luria–Delbruck “mutation jackpots.” An alternative explanation for such foci involving positive selection acting on adult self-renewing Ap spermatogonia experiencing the rare mutation could not be rejected. Further, the two youngest individuals studied (19 and 23 years old) had lower mutation frequencies and smaller foci at both mutation sites compared with the older individuals. This implies that the mutation frequency of foci increases as adults age, and thus selection could explain the paternal age effect for Apert syndrome and other genetic conditions. Our results, now including the analysis of two mutations in the same set of testes, suggest that positive selection can increase the relative frequency of premeiotic germ cells carrying such mutations, although individuals who inherit them have reduced fitness. In addition, we compared the anatomical distribution of C758G mutation foci with both new and old data on the C755G mutation in the same testis and found their positions were not correlated with one another.
Single treatment with RNAi against prion protein rescues early neuronal dysfunction and prolongs survival in mice with prion disease
Authors: White Melanie D. , Farmer Michael , Mirabile Ilaria , Brandner Sebastian , Collinge John , Mallucci Giovanna R.
Published: July 2008

Prion diseases are fatal neurodegenerative conditions for which there is no effective treatment. Prion propagation involves the conversion of cellular prion protein, PrP
C
, to its conformational isomer, PrP
Sc
, which accumulates in disease. Here, we show effective therapeutic knockdown of PrP
C
expression using RNAi in mice with established prion disease. A single administration of lentivirus expressing a shRNA targeting PrP into each hippocampus of mice with established prion disease significantly prolonged survival time. Treated animals lived 19% and 24% longer than mice given an “empty” lentivirus, or not treated, respectively. Lentivirally mediated RNAi of PrP also prevented the onset of behavioral deficits associated with early prion disease, reduced spongiform degeneration, and protected against neuronal loss. In contrast, mice receiving empty virus or no treatment developed early cognitive impairment and showed severe spongiosis and neuronal loss. The focal use of RNAi therapeutically in prion disease further supports strategies depleting PrP
C
, which we previously established to be a valid target for prion-based treatments. This approach can now be used to define the temporal, quantitative, and regional requirements for PrP knockdown for effective treatment of prion disease and to explore mechanisms involved in predegenerative neuronal dysfunction and its rescue.
The ancestral symbiont sensor kinase CSK links photosynthesis with gene expression in chloroplasts
Authors: Puthiyaveetil Sujith , Kavanagh T. Anthony , Cain Peter , Sullivan James A. , Newell Christine A. , Gray John C. , Robinson Colin , van der Giezen Mark , Rogers Matthew B. , Allen John F.
Published: July 2008

We describe a novel, typically prokaryotic, sensor kinase in chloroplasts of green plants. The gene for this chloroplast sensor kinase (CSK) is found in cyanobacteria, prokaryotes from which chloroplasts evolved. The CSK gene has moved, during evolution, from the ancestral chloroplast to the nuclear genomes of eukaryotic algae and green plants. The CSK protein is now synthesised in the cytosol of photosynthetic eukaryotes and imported into their chloroplasts as a protein precursor. In the model higher plant
Arabidopsis thaliana
, CSK is autophosphorylated and required for control of transcription of chloroplast genes by the redox state of an electron carrier connecting photosystems I and II. CSK therefore provides a redox regulatory mechanism that couples photosynthesis to gene expression. This mechanism is inherited directly from the cyanobacterial ancestor of chloroplasts, is intrinsic to chloroplasts, and is targeted to chloroplast genes.
A modified cysteinyl-labeling assay reveals reversible oxidation of protein tyrosine phosphatases in angiomyolipoma cells
Authors: Boivin Benoit , Zhang Sheng , Arbiser Jack L. , Zhang Zhong-Yin , Tonks Nicholas K.
Published: July 2008

The production of reactive oxygen species (ROS) exerts an additional tier of control over tyrosine phosphorylation-dependent signal transduction by transiently inhibiting the catalytic activity of specific protein tyrosine phosphatases (PTPs). Hence, the ability to detect reversible oxidation of PTPs
in vivo
is critical to understanding the complex biological role of ROS in the control of cellular signaling. Here, we describe an assay for identifying those PTPs that are reversibly oxidized
in vivo
, which utilizes the unique chemistry of the invariant catalytic Cys residue in labeling the active site with biotinylated small molecules under mildly acidic conditions. We have applied this cysteinyl-labeling assay to the study of platelet-derived growth factor (PDGF) receptor signaling in an angiomyolipoma cell model. Doing so has allowed us to detect reversible oxidation of several proteins in response to sustained PDGF stimulation. As in other cell systems, we have observed the reversible oxidation of the classical PTP SHP2 and the tumor suppressor phosphatase PTEN in response to PDGF stimulation. Furthermore, we detected reversible oxidation of members of two other subclasses of PTPs, the receptor PTP LAR and the dual-specificity phosphatase MKP1. These data demonstrate the broad selectivity of the assay, allowing us to detect representatives of all of the major subgroups of the PTP superfamily. We anticipate that this cysteinyl-labeling enrichment strategy can be applied broadly to study reversible oxidation as a mechanism of harnessing PTP catalytic activity in a variety of signaling pathways.
Exoplanet properties from Lick, Keck and AAT
Authors: Marcy G W , Butler R P , Vogt S S , Fischer D A , Wright J T , Johnson J A , Tinney C G , Jones H R A , Carter B D , Bailey J , O'Toole S J , Upadhyay S
Published: July 2008

Doppler-shift measurements with a remarkable precision of Δλ/λ=3×10−9, corresponding to velocities of 1 m s−1, have been made repeatedly of 2500 stars located within 300 light years. The observed gravitational perturbations of the stars have revealed 250 orbiting planets, with 27 that cross in front of the host star, blocking a fraction of the starlight to allow measurement of the planet's mass, radius and density. Two new discoveries are the first good analog of Jupiter (HD 154345b) and the first system of five planets (55 Cancri). The predominantly eccentric orbits of exoplanets probably result from planet–planet gravitational interactions or angular momentum exchange by mean-motion resonances. The planet mass distribution ranges from ∼15 M
JUP to as low as ∼5 M
Earth and rises toward lower masses as dN/dM∝M
−1.1. The distribution with orbital distance, a, rises (in logarithmic intervals) as dN/d log a∝a
+0.4. Extrapolation and integration suggests that 19% of all Sun-like stars harbor a gas-giant planet within 20 AU, but there remains considerable incompleteness for large orbits. Beyond 20 AU, the occurrence of gas-giant planets may be less than a few per cent as protoplanetary disk material there has lower densities and is vulnerable to destruction. Jupiter-mass planets occur more commonly around more massive stars than low mass stars. The transit of the Neptune-mass planet, Gliese 436b, yields a density of 1.55 g cm−3 suggesting that its interior has an iron–silicate core surrounded by an envelope of water–ice and an outer H–He shell. Planets with masses as low as five Earth-masses may be commonly composed of iron–nickel, rock and water along with significant amounts of H and He, making the term ‘super-Earth’ misleading. The transiting planet HD147506b has high orbital eccentricity but no significant orbital inclination to the line of sight, presenting a puzzle about its history. Its orbit together with the mean motion resonances of 4 of the 22 multi-planet systems provides further evidence for the role of planet–planet interactions in shaping planetary architectures.
YY1 Protects Cardiac Myocytes from Pathologic Hypertrophy by Interacting with HDAC5
Authors: Sucharov Carmen C. , Dockstader Karen , McKinsey Timothy A.
Published: July 2008

YY1 is a transcription factor that can repress or activate the transcription of a variety of genes. Here, we show that the function of YY1 as a repressor in cardiac myocytes is tightly dependent on its ability to interact with histone deacetylase 5 (HDAC5). YY1 interacts with HDAC5, and overexpression of YY1 prevents HDAC5 nuclear export in response to hypertrophic stimuli and the increase in cell size and re-expression of fetal genes that accompany pathological cardiac hypertrophy. Knockdown of YY1 results in up-regulation of all genes present during fetal development and increases the cell size of neonatal cardiac myocytes. Moreover, overexpression of a YY1 deletion construct that does not interact with HDAC5 results in transcription activation, suggesting that HDAC5 is necessary for YY1 function as a transcription repressor. In support of this relationship, we show that knockdown of HDAC5 results in transcription activation by YY1. Finally, we show that YY1 interaction with HDAC5 is dependent on the HDAC5 phosphorylation domain and that overexpression of YY1 reduces HDAC5 phosphorylation in response to hypertrophic stimuli. Our results strongly suggest that YY1 functions as an antihypertrophic factor by preventing HDAC5 nuclear export and that up-regulation of YY1 in human heart failure may be a protective mechanism against pathological hypertrophy.
Interaction between Tumor Suppressor Adenomatous Polyposis Coli and Topoisomerase IIα: Implication for the G2/M Transition
Authors: Wang Yang , Azuma Yoshiaki , Moore David , Osheroff Neil , Neufeld Kristi L.
Published: July 2008

The tumor suppressor adenomatous polyposis coli (APC) is implicated in regulating multiple stages of the cell cycle. APC participation in G1/S is attributed to its recognized role in Wnt signaling. APC function in the G2/M transition is less well established. To identify novel protein partners of APC that regulate the G2/M transition, APC was immunoprecipitated from colon cell lysates and associated proteins were analyzed by matrix-assisted laser desorption ionization/time of flight (MALDI-TOF). Topoisomerase IIα (topo IIα) was identified as a potential binding partner of APC. Topo IIα is a critical regulator of G2/M transition. Evidence supporting an interaction between endogenous APC and topo IIα was obtained by coimmunoprecipitation, colocalization, and Förster resonance energy transfer (FRET). The 15-amino acid repeat region of APC (M2-APC) interacted with topo IIα when expressed as a green fluorescent protein (GFP)-fusion protein in vivo. Although lacking defined nuclear localization signals (NLS) M2-APC predominantly localized to the nucleus. Furthermore, cells expressing M2-APC displayed condensed or fragmented nuclei, and they were arrested in the G2 phase of the cell cycle. Although M2-APC contains a β-catenin binding domain, biochemical studies failed to implicate β-catenin in the observed phenotype. Finally, purified recombinant M2-APC enhanced topo IIα activity in vitro. Together, these data support a novel role for APC in the G2/M transition, potentially through association with topo IIα.
HDAC4 Promotes Growth of Colon Cancer Cells via Repression of p21
Authors: Wilson Andrew J. , Byun Do-Sun , Nasser Shannon , Murray Lucas B. , Ayyanar Kanyalakshmi , Arango Diego , Figueroa Maria , Melnick Ari , Kao Gary D. , Augenlicht Leonard H. , Mariadason John M.
Published: July 2008

The class II Histone deacetylase (HDAC), HDAC4, is expressed in a tissue-specific manner, and it represses differentiation of specific cell types. We demonstrate here that HDAC4 is expressed in the proliferative zone in small intestine and colon and that its expression is down-regulated during intestinal differentiation in vivo and in vitro. Subcellular localization studies demonstrated HDAC4 expression was predominantly nuclear in proliferating HCT116 cells and relocalized to the cytoplasm after cell cycle arrest. Down-regulating HDAC4 expression by small interfering RNA (siRNA) in HCT116 cells induced growth inhibition and apoptosis in vitro, reduced xenograft tumor growth, and increased p21 transcription. Conversely, overexpression of HDAC4 repressed p21 promoter activity. p21 was likely a direct target of HDAC4, because HDAC4 down-regulation increased p21 mRNA when protein synthesis was inhibited by cycloheximide. The importance of p21 repression in HDAC4-mediated growth promotion was demonstrated by the failure of HDAC4 down-regulation to induce growth arrest in HCT116 p21-null cells. HDAC4 down-regulation failed to induce p21 when Sp1 was functionally inhibited by mithramycin or siRNA-mediated down-regulation. HDAC4 expression overlapped with that of Sp1, and a physical interaction was demonstrated by coimmunoprecipitation. Chromatin immunoprecipitation (ChIP) and sequential ChIP analyses demonstrated Sp1-dependent binding of HDAC4 to the proximal p21 promoter, likely directed through the HDAC4–HDAC3–N-CoR/SMRT corepressor complex. Consistent with increased transcription, HDAC4 or SMRT down-regulation resulted in increased histone H3 acetylation at the proximal p21 promoter locus. These studies identify HDAC4 as a novel regulator of colon cell proliferation through repression of p21.
Epidermal Growth Factor–induced Enhancement of Glioblastoma Cell Migration in 3D Arises from an Intrinsic Increase in Speed But an Extrinsic Matrix- and Proteolysis-dependent Increase in Persistence
Authors: Kim Hyung-Do , Guo Tiffany W. , Wu Angela P. , Wells Alan , Gertler Frank B. , Lauffenburger Douglas A.
Published: July 2008

Epidermal growth factor (EGF) receptor-mediated cell migration plays a vital role in invasion of many tumor types. EGF receptor ligands increase invasiveness in vivo, but it remains unclear how consequent effects on intrinsic cell motility behavior versus effects on extrinsic matrix properties integrate to result in net increase of translational speed and/or directional persistence of migration in a 3D environment. Understanding this convolution is important for therapeutic targeting of tumor invasion, as key regulatory pathways for intrinsic versus extrinsic effects may not be coincident. Accordingly, we have undertaken a quantitative single-cell imaging study of glioblastoma cell movement in 3D matrices and on 2D substrata across a range of collagen densities with systematic variation of protease-mediated matrix degradation. In 3D, EGF induced a mild increase in cell speed and a strong increase in directional persistence, the latter depending heavily on matrix density and EGF-stimulated protease activity. In contrast, in 2D, EGF induced a similarly mild increase in speed but conversely a decrease in directional persistence (both independent of protease activity). Thus, the EGF-enhanced 3D tumor cell migration results only partially from cell-intrinsic effects, with override of cell-intrinsic persistence decrease by protease-mediated cell-extrinsic reduction of matrix steric hindrance.
Apparently low reproducibility of true differential expression discoveries in microarray studies
Authors: Zhang Min , Yao Chen , Guo Zheng , Zou Jinfeng , Zhang Lin , Xiao Hui , Wang Dong , Yang Da , Gong Xue , Zhu Jing , Li Yanhui , Li Xia
Published: July 2008

Motivation: Differentially expressed gene (DEG) lists detected from different microarray studies for a same disease are often highly inconsistent. Even in technical replicate tests using identical samples, DEG detection still shows very low reproducibility. It is often believed that current small microarray studies will largely introduce false discoveries.

Results: Based on a statistical model, we show that even in technical replicate tests using identical samples, it is highly likely that the selected DEG lists will be very inconsistent in the presence of small measurement variations. Therefore, the apparently low reproducibility of DEG detection from current technical replicate tests does not indicate low quality of microarray technology. We also demonstrate that heterogeneous biological variations existing in real cancer data will further reduce the overall reproducibility of DEG detection. Nevertheless, in small subsamples from both simulated and real data, the actual false discovery rate (FDR) for each DEG list tends to be low, suggesting that each separately determined list may comprise mostly true DEGs. Rather than simply counting the overlaps of the discovery lists from different studies for a complex disease, novel metrics are needed for evaluating the reproducibility of discoveries characterized with correlated molecular changes.

Contact:  guoz@ems.hrbmu.edu.cn; lixia@ems.hrbmu.edu.cn

Supplementaty information:  Supplementary data are available at Bioinformatics online.
Intronically encoded siRNAs improve dynamic range of mammalian gene regulation systems and toggle switch
Authors: Greber David , El-Baba Marie Daoud , Fussenegger Martin
Published: July 2008

Applications of conditional gene expression, whether for therapeutic or basic research purposes, are increasingly requiring mammalian gene control systems that exhibit far tighter control properties. While numerous approaches have been used to improve the widely used Tet-regulatory system, many applications, particularly with respect to the engineering of synthetic gene networks, will require a broader range of tightly performing gene control systems. Here, a generically applicable approach is described that utilizes intronically encoded siRNA on the relevant transregulator construct, and siRNA sequence-specific tags on the reporter construct, to minimize basal gene activity in the off-state of a range of common gene control systems. To demonstrate tight control of residual expression the approach was successfully used to conditionally express the toxic proteins RipDD and Linamarase. The intronic siRNA concept was also extended to create a new generation of compact, single-vector, autoinducible siRNA vectors. Finally, using improved regulation systems a mammalian epigenetic toggle switch was engineered that exhibited superior in vitro and in vivo induction characteristics in mice compared to the equivalent non-intronic system.
Monitoring of chloride and activity of glycine receptor channels using genetically encoded fluorescent sensors
Authors: Mukhtarov Marat , Markova Olga , Real Eleonore , Jacob Yves , Buldakova Svetlana , Bregestovski Piotr
Published: July 2008

Genetically encoded probes have become powerful tools for non-invasive monitoring of ions, distributions of proteins and the migration and formation of cellular components. We describe the functional expression of two molecular probes for non-invasive fluorescent monitoring of intracellular Cl ([Cl]
i
) and the functioning of glycine receptor (GlyR) channels. The first probe is a recently developed cyan fluorescent protein–yellow fluorescent protein-based construct, termed Cl-Sensor, with relatively high sensitivity to Cl (
K
app
∼30 mM). In this study, we describe its expression in retina cells using
in vivo
electroporation and analyse changes in [Cl]
i
at depolarization and during the first three weeks of post-natal development. An application of 40 mM K
+
causes an elevation in [Cl]
i
of approximately 40 mM. In photoreceptors from retina slices of a 6-day-old rat (P6 rat), the mean [Cl]
i
is approximately 50 mM, and for P16 and P21 rats it is approximately 30–35 mM. The second construct, termed BioSensor-GlyR, is a GlyR channel with Cl-Sensor incorporated into the cytoplasmic domain. This is the first molecular probe for spectroscopic monitoring of the functioning of receptor-operated channels. These types of probes offer a means of screening pharmacological agents and monitoring Cl under different physiological and pathological conditions and permit spectroscopic monitoring of the activity of GlyRs expressed in heterologous systems and neurons.