bluuebunny/crossref_metadata_2025 huggingface dataset:
Measurements of the internal magnetic field using the B-Stark motional Stark effect diagnostic on DIII-D (invited)
Authors: Pablant N. A. , Burrell K. H. , Groebner R. J. , Holcomb C. T. , Kaplan D. H.
Published: October 2010

Results are presented from the B-Stark diagnostic installed on the DIII-D tokamak. This diagnostic provides measurements of the magnitude and direction of the internal magnetic field. The B-Stark system is a version of a motional Stark effect (MSE) diagnostic based on the relative line intensities and spacing of the Stark split Dα emission from injected neutral beams. This technique may have advantages over MSE polarimetry based diagnostics in future devices, such as the ITER. The B-Stark diagnostic technique and calibration procedures are discussed. The system is shown to provide accurate measurements of Bθ/BT and |B| over a range of plasma conditions. Measurements have been made with toroidal fields in the range of 1.2–2.1 T, plasma currents in the range 0.5–2.0 MA, densities between 1.7 and 9.0×1019 m−3, and neutral beam voltages between 50 and 81 keV. The viewing direction and polarization dependent transmission properties of the collection optics are found using an in situ beam into gas calibration. These results are compared to values found from plasma equilibrium reconstructions and the MSE polarimetry system on DIII-D.
Development of electron cyclotron emission imaging system on Large Helical Device
Authors: Kuwahara D. , Tsuji-Iio S. , Nagayama Y. , Yoshinaga T. , Tsuchiya H. , Sugito S. , Yamaguchi S. , Kogi Y. , Akaki K. , Mase A.
Published: October 2010

A combined system of microwave imaging reflectometry and electron cyclotron emission (ECE) imaging has been developed for the Large Helical Device. This system includes a wide-band two-dimensional horn-antenna mixer array (HMA). The HMA consists of horn antennas, waveguides, mixers, and intermediate frequency circuits. The frequency response of the HMA is between 50 and 110 GHz. The ECE signal is selected using a 95 GHz local oscillator and a 93 GHz high-pass filter.
Multiscale characterization method for line edge roughness based on redundant second generation wavelet transform
Authors: Wang Fei , Li Ning , Zhao Xuezeng
Published: October 2010

We introduce a multiscale characterization method for line edge roughness (LER) based on redundant second generation wavelet transform. This method involves decomposing LER characteristics into independent bands with different spatial frequency components at different scales, and analyzing the reconstructed signals to work out the roughness exponent, the spatial frequency distribution characteristics, as well as the rms value. The effect of noise can be predicted using detailed signals in the minimum space of scale. This method was applied to numerical profiles for validation. Results show that according to the line edge profiles with similar amplitudes, the roughness exponent R can effectively reflect the degree of irregularity of LER and intuitively provide information on LER spatial frequency distribution.
Pressure-induced crystallization of amorphous Ge2Sb2Te5
Authors: Xu M. , Meng Y. , Cheng Y. Q. , Sheng H. W. , Han X. D. , Ma E.
Published: October 2010

Using in situ x-ray diffraction, we demonstrate a pressure-induced crystallization of as-deposited amorphous Ge2Sb2Te5 (a-GST) into a body-centered-cubic (bcc) solid solution at 28 GPa, and the back transformation from the bcc-GST to a-GST. A large hysteresis loop was observed, as the bcc-GST was retained until 15 GPa. Comparisons have been made, employing the x-ray data and the structural information obtained from ab initio molecular dynamics simulations, between the as-deposited a-GST and the a-GST obtained from the pressure-induced collapse of the rocksalt GST, both at a high hydrostatic pressure (20 GPa) prior to their crystallization to bcc. The results suggest that both routes have resulted in the same high-pressure amorphous state, which explains their crystallization into bcc-GST at similar pressures.
Path integral based calculations of symmetrized time correlation functions. I.
Authors: Bonella S. , Monteferrante M. , Pierleoni C. , Ciccotti G.
Published: October 2010

In this paper, we examine how and when quantum evolution can be approximated in terms of (generalized) classical dynamics in calculations of correlation functions, with a focus on the symmetrized time correlation function introduced by Schofield. To that end, this function is expressed as a path integral in complex time and written in terms of sum and difference path variables. Taylor series expansion of the path integral’s exponent to first and second order in the difference variables leads to two original developments. The first order expansion is used to obtain a simple, path integral based, derivation of the so-called Schofield’s quantum correction factor. The second order result is employed to show how quantum mechanical delocalization manifests itself in the approximation of the correlation function and hinders, even in the semiclassical limit, the interpretation of the propagators in terms of sets of guiding classical trajectories dressed with appropriate weights.
Theoretical study of photoinduced ring-opening in furan
Authors: Gromov E. V. , Trofimov A. B. , Gatti F. , Köppel H.
Published: October 2010

The potential energy surfaces (PESs) of the two lowest excited singlet states of furan [correlating with the Rydberg A12(3s) and valence B12(V) states at the C2v ground-state molecular configuration] have been studied in some detail with regard to the photoinduced ring-opening reaction. The surfaces have been characterized in terms of their stationary points and points of minimum energy conical intersections along the ring-opening pathway. The optimization of the geometrical parameters has been performed with the equation of motion coupled cluster singles and doubles method. The ab initio PESs have been modeled by energy grids and Taylor series. The resulting 11-dimensional PESs reproduce the ab initio results to a good accuracy and can be used in dynamical calculations.
Monochromatic x-ray radiography for areal-density measurement of inertial fusion energy fuel in fast ignition experiment
Authors: Fujioka Shinsuke , Fujiwara Takashi , Tanabe Minoru , Nishimura Hiroaki , Nagatomo Hideo , Ohira Shinji , Inubushi Yuichi , Shiraga Hiroyuki , Azechi Hiroshi
Published: October 2010

Ultrafast, two-dimensional x-ray imaging is an important diagnostics for the inertial fusion energy research, especially in investigating implosion dynamics at the final stage of the fuel compression. Although x-ray radiography was applied to observing the implosion dynamics, intense x-rays emitted from the high temperature and dense fuel core itself are often superimposed on the radiograph. This problem can be solved by coupling the x-ray radiography with monochromatic x-ray imaging technique. In the experiment, 2.8 or 5.2 keV backlight x-rays emitted from laser-irradiated polyvinyl chloride or vanadium foils were selectively imaged by spherically bent quartz crystals with discriminating the out-of-band emission from the fuel core. This x-ray radiography system achieved 24 μm and 100 ps of spatial and temporal resolutions, respectively.
A coaxial thermocouple for shock tunnel applications
Authors: Menezes Viren , Bhat Sandeep
Published: October 2010

A chromel-constantan coaxial surface junction thermocouple has been designed, fabricated, calibrated, and tested to measure the temperature-time history on the surface of a body in a hypersonic freestream of Mach 8 in a shock tunnel. The coaxial thermocouple with a diameter of 3.25 mm was flush mounted in the surface of a hemisphere of 25 mm diameter. The hypersonic freestream was of a very low temperature and density, and had a flow time of about a millisecond. Preliminary test results indicate that the thermocouple is quite sensitive to low temperature-rarefied freestreams, and also has a response time of a few microseconds (≈5 μs) to meet the requirements of short duration transient measurements. The sensor developed is accurate, robust, reproducible, and is highly inexpensive.
A tangentially viewing fast ion D-alpha diagnostic for NSTX
Authors: Bortolon A. , Heidbrink W. W. , Podestà M.
Published: October 2010

A second fast ion D-alpha (FIDA) installation is planned at NSTX to complement the present perpendicular viewing FIDA diagnostics. Following the present diagnostic scheme, the new diagnostic will consist of two instruments: a spectroscopic diagnostic that measures fast ion spectra and profiles at 16 radial points with 5–10 ms resolution and a system that uses a band pass filter and photomultiplier to measure changes in FIDA light with 50 kHz sampling rate. The new pair of FIDA instruments will view the heating beams tangentially. The viewing geometry minimizes spectral contamination by beam emission or edge sources of background emission. The improved velocity-space resolution will provide detailed information about neutral-beam current drive and about fast ion acceleration and transport by injected radio frequency waves and plasma instabilities.
Hydration dependent studies of highly aligned multilayer lipid membranes by neutron scattering
Authors: Trapp Marcus , Gutberlet Thomas , Juranyi Fanni , Unruh Tobias , Demé Bruno , Tehei Moeava , Peters Judith
Published: October 2010

We investigated molecular motions on a picosecond timescale of 1,2-dimyristoyl-sn-glycero-3-phosphocholine (DMPC) model membranes as a function of hydration by using elastic and quasielastic neutron scattering. Two different hydrations corresponding to approximately nine and twelve water molecules per lipid were studied, the latter being the fully hydrated state. In our study, we focused on head group motions by using chain deuterated lipids. Information on in-plane and out-of-plane motions could be extracted by using solid supported DMPC multilayers. Our studies confirm and complete former investigations by König et al. [J. Phys. II (France) 2, 1589 (1992)] and Rheinstädter et al. [Phys. Rev. Lett. 101, 248106 (2008)] who described the dynamics of lipid membranes, but did not explore the influence of hydration on the head group dynamics as presented here. From the elastic data, a clear shift of the main phase transition from the Pβ ripple phase to the Lα liquid phase was observed. Decreasing water content moves the transition temperature to higher temperatures. The quasielastic data permit a closer investigation of the different types of head group motion of the two samples. Two different models are needed to fit the elastic incoherent structure factor and corresponding radii were calculated. The presented data show the strong influence hydration has on the head group mobility of DMPC.
Multidimensional partial differential equation systems: Generating new systems via conservation laws, potentials, gauges, subsystems
Authors: Cheviakov Alexei F. , Bluman George W.
Published: October 2010

For many systems of partial differential equations (PDEs), including nonlinear ones, one can construct nonlocally related PDE systems. In recent years, such nonlocally related systems have proven to be useful in applications. In particular, they have yielded systematically nonlocal symmetries, nonlocal conservation laws, noninvertible linearizations, and new exact solutions for many different PDE systems of interest. However, the overwhelming majority of new results and theoretical understanding pertain only to PDE systems with two independent variables. The situation for PDE systems with more than two independent variables turns out to be much more complicated due to gauge freedom relating potential variables. The current paper, together with the companion paper [A. F. Cheviakov and G. W. Bluman, J. Math. Phys. 51, 103522 (2010)], synthesizes and systematically extends known results for nonlocally related systems arising for multidimensional PDE systems, i.e., for PDE systems with three or more independent variables. The presented framework includes potential systems arising from lower-degree conservation laws of a given PDE system. Nonlocally related multidimensional PDE systems are discussed in terms of their construction, properties, and applications.
Communication: Relationships between Intermolecular potential, thermodynamics, and dynamic scaling in viscous systems
Authors: Grzybowski A. , Paluch M. , Grzybowska K. , Haracz S.
Published: October 2010

In this communication, we provide a recipe for a consistent relation between dynamic scaling and thermodynamic properties well-grounded by the same intermolecular generalized Lennard-Jones potential, which is derived by using an essentially modified Avramov model within the framework of the “thermodynamic scaling” idea. This relation is experimentally verified very well for supercooled van der Waals liquids, and consequently, it can be a good basis for a proper universal description of molecular dynamics and thermodynamics of viscous systems.
Effect of Li doping in NiO thin films on its transparent and conducting properties and its application in heteroepitaxial p-n junctions
Authors: Dutta Titas , Gupta P. , Gupta A. , Narayan J.
Published: October 2010

Li doped NiO (LixNi1−xO) thin films were epitaxially grown along [111] orientation on c-sapphire by pulsed laser deposition. The structural, electrical, and optical properties of the films were investigated using x-ray diffraction, four probe technique, and UV-visible spectra, respectively. The epitaxial growth of [111] Li doped NiO on [0001] sapphire was determined by using high resolution x-ray Φ scan. Effects of the deposition condition and Li doping concentration variations on the electrical and optical properties of Li doped NiO films were also investigated. The analysis of the resistivity data show that doped Li ions occupy the substitutional sites in the films, enhancing the p-type conductivity. The minimum resistivity of 0.15 Ω cm was obtained for Li0.07Ni0.93O film. The activation energy of Li doped NiO films were estimated to be in the range of 0.11–0.14 eV. Based upon these values, a possible electrical transport mechanism is discussed. A p-n heterojunction has also been fabricated for the optimized p-Li doped NiO with n-ZnO. The insertion of i-MgZnO between the p and n layer led to improved current-voltage characteristics due to reduced leakage current. In the diode architecture, a heteroepitaxial relationship of [111]NiO‖[0001]MgZnO‖[0001]ZnO‖[0001]GZO‖[0001]Al2O3 among the layers was obtained. The p-i-n heterojunction showed good rectification behavior with turn on voltage of 2.8 V and breakdown voltage of 8.0 V.
Electrical annealing for flexible organic light-emitting diodes having poly(3,4-ethylenedioxythiophene):poly(styrene sulfonate) anodes
Authors: Park Byoungchoo , Park Chan Hyuk , Yim Younchan , Park Jongwoon
Published: October 2010

We present a postproduction method of electrical annealing (E-annealing) to improve the performance of flexible organic light-emitting diodes (FOLEDs) having conductive polymer anodes on a polyethersulfone substrate. The polymer that was used for the anodes was dimethylsulfoxide-doped poly(3,4-ethylenedioxythiophene):poly(styrene sulfonate). It was found that E-annealing of the fabricated FOLEDs can reduce the turn-on voltage and enhance the brightness with reduced flowing current, thereby enhancing the device efficiency. With the E-annealing method, we have successfully demonstrated efficient solution-processed green FOLEDs, which show a peak luminescence of 6 100 cd/m2 and a maximum current efficiency of 16.4 cd/A. An ion migration model to explain the phenomena related to the improvement of FOLEDs is also proposed.
Thermodynamics of strained vanadium dioxide single crystals
Authors: Gu Yijia , Cao Jinbo , Wu Junqiao , Chen Long-Qing
Published: October 2010

Vanadium dioxide undergoes a metal–insulator transition, in which the strain condition plays an important role. To investigate the strain contribution, a phenomenological thermodynamic potential for the vanadium dioxide single crystal was constructed. The transformations under the uniaxial stress, wire, and thin film boundary conditions were analyzed, and the corresponding phase diagrams were constructed. The calculated phase diagrams agree well with existing experimental data, and show that the transformation temperature (and Curie temperature) strongly depends on the strain condition.
Piezoelectric fields of localized states in trapezoidal InGaN quantum wells
Authors: Lee Dong-Yul , Lee Jae-Hoon , Han Sang-Heon , Cheong Myung Goo , Kim Dong-Joon , Park June-Sik , Hong Sangsu , Leem Jae-Young
Published: October 2010

The piezoelectric fields of localized states in trapezoidal InGaN quantum wells (QWs) were investigated using electric field dependent electroreflectance (ER) spectroscopy. From the energy shift in ER peak in a bias range from 0 to −24 V, the piezoelectric field of the dominant QWs was estimated to be −1.22 MV/cm. In contrast, the localized states exhibited a piezoelectric field that was about 30%–60% weaker than for the dominant QW states. The reduced piezoelectric field in the localized states can be attributed to the partial release of compressive strain in the local InGaN regions, along with a relative reduction in the effective reverse-bias. The relative decrease in the reverse-bias can be explained by the voltage drop in the localized states that is caused by an increase in the leakage current under a reverse-bias.
Complete experimental rovibrational eigenenergies of HNC up to 3743cm−1 above the ground state
Authors: Mellau Georg Ch.
Published: October 2010

The [H,C,N] system is one of the ideal candidate molecules to test new models aimed to calculate the manifold of the rotational, vibrational, and electronic states of a triatomic molecule. The isomerization reaction HCN⇌HNC is one of the most important model systems for the study of unimolecular reactions. This paper reports on the experimental characterization of all 1191 eigenenergies up to 3743cm−1 relative to the ground state in the HNC part of the potential surface using high temperature hot gas emission spectroscopy. The spectroscopic constants for the first 27 vibrational states including highly excited bending vibrations up to v2=7 are reported. The first 14 rotational perturbations have been identified and the perturbed eigenenergies were determined. The 3200 eigenenergies up to J=70 for the first 47 vibrational substates are included as supplement to this paper.
Copper-on-copper homoepitaxy studied by infrared spectroscopy of adsorbed CO
Authors: Hancock Michael , Fein Casey , Tobin R. G.
Published: October 2010

Infrared spectroscopy of adsorbed CO was used to characterize the dependence of surface structure on deposition temperature during homoepitaxial growth on Cu(100). Intensity borrowing due to dipole coupling greatly enhances the absorption signal due to defect-bonded CO, making it possible to detect and quantify defect concentrations at the level of a few percent. For deposition temperatures between 300 and 400 K, the defect density increases slightly with decreasing deposition temperature but remains below 2%. There is a sharp increase in defect density, up to 5%–6%, as the deposition temperature is decreased from 300 to 250 K. At lower deposition temperatures, there is some sign of a leveling off in defect density, but the IR absorption spectrum becomes so broad that meaningful analysis becomes impractical, while visible degradation of the low-energy electron diffraction pattern indicates worsening surface order. No indication of “re-entrant” ordering at low temperatures was observed for deposition temperatures down to 150 K.
Polarized Raman spectroscopic study of relaxed high density amorphous ices under pressure
Authors: Suzuki Yoshiharu , Tominaga Yasunori
Published: October 2010

We have made high density amorphous ice (HDA) by the pressure-induced amorphization of hexagonal ice at 77 K and measured the volume change on isobaric heating in a pressure range between 0.1 and 1.5 GPa. The volume of HDA on heating below ∼0.35 GPa increases, while the volume of HDA on heating above ∼0.35 GPa decreases. The polarized OH-stretching Raman spectra of the relaxed HDAs are compared with that of the unannealed HDA. The relaxed HDAs are prepared at 0.2 GPa at 130 K and 1.5 GPa at 160 K. It is found that the relatively strong totally symmetric OH-stretching vibration mode around 3100 cm−1 exists in the depolarized reduced Raman spectrum χVH″ of the unannealed HDA and that its intensity rapidly decreases by relaxation. The χVH″ profiles of the relaxed HDA are similar to those of liquid water. These results indicate that the HDA reaches a nearly equilibrium state by annealing and the intrinsic state of HDA relates to a liquid state. The pressure-volume curve of the relaxed HDA at 140 K seems to be smooth in the pressure range below 1.5 GPa.
Depth-cumulated epithelial redox ratio and stromal collagen quantity as quantitative intrinsic indicators for differentiating normal, inflammatory, and dysplastic epithelial tissues
Authors: Zhuo Shuangmu , Zheng Liqin , Chen Jianxin , Xie Shusen , Zhu Xiaoqin , Jiang Xingshan
Published: October 2010

Multiphoton microscopy was used to isolate the intrinsic emission contribution of epithelial cellular origins and stromal collagen in normal, inflammatory, and dysplastic epithelial tissues, and quantify the depth-cumulated epithelial redox ratio and stromal collagen quantity. It was found that both inflammatory and dysplastic epithelial tissues display a large decrease in stromal collagen quantity but have very different epithelial redox ratio. These results suggest that probing differences in epithelial redox ratio in addition to stromal collagen quantity can serve as quantitative intrinsic indicators for differentiating normal, inflammatory, and dysplastic epithelial tissues.
Ionic properties of liquid crystals dispersed with carbon nanotubes and montmorillonite nanoplatelets
Authors: Liu Hsuan-Hung , Lee Wei
Published: October 2010

The ionic properties of liquid crystals doped with one-dimensional carbon nanotubes, two-dimensional montmorillonite, and a mixture of both are investigated. The results indicate that the relaxation times of electrode polarization and ionic conductivity are time-dependent after the cell fabrication regardless of doping. While all of the dopants are effective in capturing impurity ions, the cells containing the hybrid dopant exhibit the feeblest ionic effect at room temperature.
Write strategies for multiterabit per square inch scanned-probe phase-change memories
Authors: Wright C. D. , Shah P. , Wang Lei , Aziz M. M. , Sebastian A. , Pozidis H.
Published: October 2010

A mark-length write strategy for multiterabit per square inch scanned-probe memories is described that promises to increase the achievable user density by at least 50%, and potentially up to 100% or more, over conventional approaches. The viability of the write strategy has been demonstrated by experimental scanning probe write/read measurements on phase-change (GeSbTe) media. The advantages offered by adopting mark-length recording are likely to be equally applicable to other forms of scanned probe storage.
Low-temperature conductance oscillations in junctionless nanowire transistors
Authors: Park Jong-Tae , Kim Jin Young , Lee Chi-Woo , Colinge Jean-Pierre
Published: October 2010

Junctionless nanowire transistors show more marked oscillations conductance oscillations than inversion-mode devices. These oscillations can be observed at higher temperature, drain voltage, and gate voltage than in surface-channel, inversion-mode multigate metal-oxide-semiconductor field-effect devices. Clear oscillations are observed at 77 K at a drain voltage of 100 mV in devices with a 10×10 nm2 cross section.
Effects of soil temperature regimes after fire on seed dormancy and germination in six Australian Fabaceae species
Authors: Santana Victor M. , Bradstock Ross A. , Ooi Mark K. J. , Denham Andrew J. , Auld Tony D. , Baeza M. Jaime
Published: October 2010

In addition to direct fire cues such as heat, smoke and charred wood, the passage of fire leads indirectly to changes in environmental conditions which may be able to break physical dormancy in hard-coated seeds. After a fire, the open canopy and the burnt material lying on the surface alter the thermal properties of the soil, resulting in elevated soil temperatures for long periods of time. We simulated daily temperature regimes experienced at different depths of soil profile after a summer fire. Our aim was to determine whether these temperature regimes and the duration of exposure (5, 15 and 30 days) play an important role breaking physical seed dormancy in six legumes from south-eastern Australia. Our results showed that simulated temperature regimes break seed dormancy. This effect is specially pronounced at temperatures that are expected to occur near the soil surface (0–2 cm depth). The duration of exposure interacts with temperature to break dormancy, with the highest germination rates reached after the longest duration and highest temperatures. However, the germination response varied among species. Therefore, this indirect post-fire cue could play a role in the regeneration of plant communities, and could stimulate seedling emergence independent of direct fire cues as well as in interaction with direct cues.
Dynamic and specific interaction between synaptic NR2-NMDA receptor and PDZ proteins
Authors: Bard Lucie , Sainlos Matthieu , Bouchet Delphine , Cousins Sarah , Mikasova Lenka , Breillat Christelle , Stephenson F. Anne , Imperiali Barbara , Choquet Daniel , Groc Laurent
Published: October 2010

The relative content of NR2 subunits in the NMDA receptor confers specific signaling properties and plasticity to synapses. However, the mechanisms that dynamically govern the retention of synaptic NMDARs, in particular 2A-NMDARs, remain poorly understood. Here, we investigate the dynamic interaction between NR2 C termini and proteins containing PSD-95/Discs-large/ZO-1 homology (PDZ) scaffold proteins at the single molecule level by using high-resolution imaging. We report that a biomimetic divalent competing ligand, mimicking the last 15 amino acids of NR2A C terminus, specifically and efficiently disrupts the interaction between 2A-NMDARs, but not 2B-NMDARs, and PDZ proteins on the time scale of minutes. Furthermore, displacing 2A-NMDARs out of synapses lead to a compensatory increase in synaptic NR2B-NMDARs, providing functional evidence that the anchoring mechanism of 2A- or 2B-NMDARs is different. These data reveal an unexpected role of the NR2 subunit divalent arrangement in providing specific anchoring within synapses, highlighting the need to study such dynamic interactions in native conditions.
Universal robotic gripper based on the jamming of granular material
Authors: Brown Eric , Rodenberg Nicholas , Amend John , Mozeika Annan , Steltz Erik , Zakin Mitchell R. , Lipson Hod , Jaeger Heinrich M.
Published: October 2010

Gripping and holding of objects are key tasks for robotic manipulators. The development of universal grippers able to pick up unfamiliar objects of widely varying shape and surface properties remains, however, challenging. Most current designs are based on the multifingered hand, but this approach introduces hardware and software complexities. These include large numbers of controllable joints, the need for force sensing if objects are to be handled securely without crushing them, and the computational overhead to decide how much stress each finger should apply and where. Here we demonstrate a completely different approach to a universal gripper. Individual fingers are replaced by a single mass of granular material that, when pressed onto a target object, flows around it and conforms to its shape. Upon application of a vacuum the granular material contracts and hardens quickly to pinch and hold the object without requiring sensory feedback. We find that volume changes of less than 0.5% suffice to grip objects reliably and hold them with forces exceeding many times their weight. We show that the operating principle is the ability of granular materials to transition between an unjammed, deformable state and a jammed state with solid-like rigidity. We delineate three separate mechanisms, friction, suction, and interlocking, that contribute to the gripping force. Using a simple model we relate each of them to the mechanical strength of the jammed state. This advance opens up new possibilities for the design of simple, yet highly adaptive systems that excel at fast gripping of complex objects.
Human ISWI chromatin-remodeling complexes sample nucleosomes via transient binding reactions and become immobilized at active sites
Authors: Erdel Fabian , Schubert Thomas , Marth Caroline , Längst Gernot , Rippe Karsten
Published: October 2010

Chromatin remodeling complexes can translocate nucleosomes along the DNA in an ATP-dependent manner. Here, we studied autofluorescent protein constructs of the human ISWI family members Snf2H, Snf2L, the catalytically inactive Snf2L+13 splice variant, and the accessory Acf1 subunit in living human and mouse cells by fluorescence microscopy/spectroscopy. Except for Snf2L, which was not detected in the U2OS cell line, the endogenous ISWI proteins were abundant at nuclear concentrations between 0.14 and 0.83 μM. A protein interaction analysis showed the association of multimeric Snf2H and Acf1 into a heterotetramer or higher-order ACF complex. During the G1/2 cell cycle phase, Snf2H and Snf2L displayed average residence times <150 ms in the chromatin-bound state. The comparison of active and inactive Snf2H/Snf2L indicated that an immobilized fraction potentially involved in active chromatin remodeling comprised only 1–3%. This fraction was largely increased at replication foci in S phase or at DNA repair sites. To rationalize these findings we propose that ISWI remodelers operate via a “continuous sampling” mechanism: The propensity of nucleosomes to be translocated is continuously tested in transient binding reactions. Most of these encounters are unproductive and efficient remodeling requires an increased binding affinity to chromatin. Due to the relatively high intranuclear remodeler concentrations cellular response times for repositioning a given nucleosome were calculated to be in the range of tens of seconds to minutes.
Fluid dynamical niches of phytoplankton types
Authors: d’Ovidio Francesco , De Monte Silvia , Alvain Séverine , Dandonneau Yves , Lévy Marina
Published: October 2010

The biogeochemical role of phytoplanktonic organisms strongly varies from one plankton type to another, and their relative abundance and distribution have fundamental consequences at the global and climatological scales. In situ observations find dominant types often associated to specific physical and chemical water properties. However, the mechanisms and spatiotemporal scales by which marine ecosystems are organized are largely not known. Here we investigate the spatiotemporal organization of phytoplankton communities by combining multisatellite data, notably high-resolution ocean-color maps of dominant types and altimetry-derived Lagrangian diagnostics of the surface transport. We find that the phytoplanktonic landscape is organized in (sub-)mesoscale patches (10–100 km) of dominant types separated by physical fronts induced by horizontal stirring. These physical fronts delimit niches supported by water masses of similar history and whose lifetimes are comparable with the timescale of the bloom onset (few weeks). The resonance between biological activity and physical processes suggest that the spatiotemporal (sub-)mesoscales associated to stirring are determinant in the observation and modeling of marine ecosystems.
IL-27 structural analysis demonstrates similarities with ciliary neurotrophic factor (CNTF) and leads to the identification of antagonistic variants
Authors: Rousseau Francois , Basset Laetitia , Froger Josy , Dinguirard Nathalie , Chevalier Sylvie , Gascan Hugues
Published: October 2010

IL-27, consisting of the subunits IL-27p28 and Epstein–Barr virus-induced gene 3 (EBI3), is a heterodimeric cytokine belonging to the IL-6/IL-12 family of cytokines. IL-27p28 is a four-helical cytokine requiring association with the soluble receptor EBI3 to be efficiently secreted and functionally active. Computational and biological analyses of the IL-27 binding site 1 to its receptor revealed important structural proximities with the ciliary neurotrophic factor group of cytokines and highlighted the contribution of p28 Trp
97
, as well as of EBI3 Phe
97
, Asp
210
, and Glu
159
, as key residues in the interactions between both cytokine subunits. WSX-1 (IL-27R) and gp130 compose the IL-27 receptor-signaling complex, recruiting the STAT-1 and STAT-3 pathways. A study of IL-27 binding site 3 showed that Trp
197
was crucial for the cytokine's interaction with gp130, but that the mutated cytokine still recognized IL-27R on the cell surface. IL-27 exerts both pro- and anti-inflammatory functions, promoting proliferation and differentiation of Th1 and inhibiting Th17 differentiation. Our results led us to develop mutated forms of human and mouse IL-27 with antagonistic activities. Using an in vivo mouse model of concanavalin A-induced Th1-cell–mediated hepatitis, we showed that the murine IL-27 antagonist W195A decreased liver inflammation by downregulating the synthesis of CXCR3 ligands and several acute phase proteins. Together, these data suggest that IL-27 antagonism could be of interest in down-modulating acute IL-27–driven Th1-cell–mediated immune response.
Transcriptional silencing functions of the yeast protein Orc1/Sir3 subfunctionalized after gene duplication
Authors: Hickman Meleah A. , Rusche Laura N.
Published: October 2010

The origin recognition complex (ORC) defines origins of replication and also interacts with heterochromatin proteins in a variety of species, but how ORC functions in heterochromatin assembly remains unclear. The largest subunit of ORC, Orc1, is particularly interesting because it contains a nucleosome-binding BAH domain and because it gave rise to Sir3, a key silencing protein in
Saccharomyces cerevisiae
, through gene duplication. We examined whether Orc1 possessed a Sir3-like silencing function before duplication and found that Orc1 from the yeast
Kluyveromyces lactis,
which diverged from
S. cerevisiae
before the duplication, acts in conjunction with the deacetylase Sir2 and the histone-binding protein Sir4 to generate heterochromatin at telomeres and a mating-type locus. Moreover, the ability of KlOrc1 to spread across a silenced locus depends on its nucleosome-binding BAH domain and the deacetylase Sir2. Interestingly, KlOrc1 appears to act independently of the entire ORC, as other subunits of the complex, Orc4 and Orc5, are not strongly associated with silenced domains. These findings demonstrate that Orc1 functioned in silencing before duplication and suggest that Orc1 and Sir2, both of which are broadly conserved among eukaryotes, may have an ancient history of cooperating to generate chromatin structures, with Sir2 deacetylating histones and Orc1 binding to these deacetylated nucleosomes through its BAH domain.
Definition of a high-affinity Gag recognition structure mediating packaging of a retroviral RNA genome
Authors: Gherghe Cristina , Lombo Tania , Leonard Christopher W. , Datta Siddhartha A. K. , Bess Julian W. , Gorelick Robert J. , Rein Alan , Weeks Kevin M.
Published: October 2010

All retroviral genomic RNAs contain a cis-acting packaging signal by which dimeric genomes are selectively packaged into nascent virions. However, it is not understood how Gag (the viral structural protein) interacts with these signals to package the genome with high selectivity. We probed the structure of murine leukemia virus RNA inside virus particles using SHAPE, a high-throughput RNA structure analysis technology. These experiments showed that NC (the nucleic acid binding domain derived from Gag) binds within the virus to the sequence UCUG-UR-UCUG. Recombinant Gag and NC proteins bound to this same RNA sequence in dimeric RNA in vitro; in all cases, interactions were strongest with the first U and final G in each UCUG element. The RNA structural context is critical: High-affinity binding requires base-paired regions flanking this motif, and two UCUG-UR-UCUG motifs are specifically exposed in the viral RNA dimer. Mutating the guanosine residues in these two motifs—only four nucleotides per genomic RNA—reduced packaging 100-fold, comparable to the level of nonspecific packaging. These results thus explain the selective packaging of dimeric RNA. This paradigm has implications for RNA recognition in general, illustrating how local context and RNA structure can create information-rich recognition signals from simple single-stranded sequence elements in large RNAs.
IFN-γ abrogates endotoxin tolerance by facilitating Toll-like receptor-induced chromatin remodeling
Authors: Chen Janice , Ivashkiv Lionel B.
Published: October 2010

An important mechanism by which IFN-γ primes macrophages for enhanced innate immune responses is abrogation of feedback inhibitory pathways. Accordingly, IFN-γ abrogates endotoxin tolerance, a major negative feedback loop that silences expression of inflammatory cytokine genes in macrophages previously exposed to endotoxin/Toll-like receptor (TLR) ligands. Mechanisms by which IFN-γ inhibits endotoxin tolerance have not been elucidated. Here, we show that pretreatment with IFN-γ prevented tolerization of primary human monocytes and restored TLR4-mediated induction of various proinflammatory cytokines, including IL-6 and TNFα. Surprisingly, IFN-γ did not alter proximal TLR4 signaling defects in tolerized monocytes. Instead, IFN-γ blocked tolerance-associated down-regulation ofIL6andTNFtranscription, RNA polymerase II recruitment, and NF-κB and CCAAT/enhancer-binding protein β transcription factor binding to theIL6andTNFpromoters in tolerized monocytes. The mechanism by which IFN-γ restoredIL6expression was by facilitating TLR4-induced recruitment of chromatin remodeling machinery to theIL6promoter and promotingIL6locus accessibility in tolerized monocytes. Our results suggest that IFN-γ overcomes endotoxin tolerance by facilitating TLR-induced chromatin remodeling to allow expression of proinflammatory genes. These results identify a mechanism by which IFN-γ promotes activation of macrophages and highlight the importance of chromatin remodeling and transcriptional control in the regulation of inflammatory cytokine production in tolerant and activated macrophages.
Boron-containing organic pigments from a Jurassic red alga
Authors: Wolkenstein Klaus , Gross Jürgen H. , Falk Heinz
Published: October 2010

Organic biomolecules that have retained their basic chemical structures over geological periods (molecular fossils) occur in a wide range of geological samples and provide valuable paleobiological, paleoenvironmental, and geochemical information not attainable from other sources. In rare cases, such compounds are even preserved with their specific functional groups and still occur within the organisms that produced them, providing direct information on the biochemical inventory of extinct organisms and their possible evolutionary relationships. Here we report the discovery of an exceptional group of boron-containing compounds, the borolithochromes, causing the distinct pink coloration of well-preserved specimens of the Jurassic red alga
Solenopora jurassica
. The borolithochromes are characterized as complicated spiroborates (boric acid esters) with two phenolic moieties as boron ligands, representing a unique class of fossil organic pigments. The chiroptical properties of the pigments unequivocally demonstrate a biogenic origin, at least of their ligands. However, although the borolithochromes originated from a fossil red alga, no analogy with hitherto known present-day red algal pigments was found. The occurrence of the borolithochromes or their possible diagenetic products in the fossil record may provide additional information on the classification and phylogeny of fossil calcareous algae.
Hypoxia abrogates antichlamydial properties of IFN-γ in human fallopian tube cells in vitro and ex vivo
Authors: Roth Anna , König Peter , van Zandbergen Ger , Klinger Matthias , Hellwig-Bürgel Thomas , Däubener Walter , Bohlmann Michael K. , Rupp Jan
Published: October 2010

IFN-γ has an important role in the adaptive immune response against intracellular pathogens. In urogenital tract (UGT) infections with the obligate intracellular pathogenChlamydia trachomatis, IFN-γ–mediated control of chlamydial growth implies the JAK-STAT signaling cascades and subsequent induction of the indoleamine 2,3-dioxygenase (IDO). As oxygen concentrations in the UGT are low under physiological conditions (O2< 5%) and further decrease during an inflammatory process, we wondered whether antibacterial properties of IFN-γ are maintained under hypoxic conditions. Using primary cells that were isolated from human fallopian tubes and an ex vivo human fallopian tube model (HFTM), we found that even high IFN-γ concentrations (200 units/mL) were not sufficient to limit growth ofC. trachomatisunder hypoxia. Reduced antibacterial activity of IFN-γ under hypoxia was restricted to the urogenital serovars D and L2, but was not observed with the ocular serovar A. Impaired effectiveness of IFN-γ on chlamydial growth under hypoxia was accompanied by reduced phosphorylation of Stat-1 on Tyr701 and diminished IDO activity. This study shows that IFN-γ effector functions on intracellularC. trachomatisdepend on the environmental oxygen supply, which could explain inadequate bacterial clearance and subsequent chronic infections eventually occurring in the UGT of women.
Coordination of Fc receptor signaling regulates cellular commitment to phagocytosis
Authors: Zhang Youxin , Hoppe Adam D. , Swanson Joel A.
Published: October 2010

During Fcγ receptor (FcR)-mediated phagocytosis by macrophages, cytoplasm advances over IgG-coated particles by the sequential ligation of FcR in plasma membranes. If FcR signaling was strictly autonomous, then the signals generated during phagocytosis should be proportional to the number of ligated receptors. By measuring FcR-dependent responses to beads coated with various densities of IgG, this study identified nonlinear signaling that organizes an all or none response during particle ingestion. Phagocytosis of beads with IgG at low density either stalled after making small, actin-rich cups or proceeded to completion at the same rate as phagocytosis of high-density IgG beads. Signals were measured by quantifying the recruitment of YFP-labeled probes to phagocytic cup membranes. Although the magnitude of early signals correlated with IgG density, later signals showed an all or none response, which was regulated by the concentrations of 3′ phosphoinositides in phagocytic cup membranes. Thus, 3′ phosphoinositides, shown previously to be required for phagocytosis, function in a feedback regulatory mechanism affecting late but not early signals. This indicates a mechanism for the coordination of cell movements initiated by receptor signaling.
Thymic stromal lymphopoietin-mediated STAT5 phosphorylation via kinases JAK1 and JAK2 reveals a key difference from IL-7–induced signaling
Authors: Rochman Yrina , Kashyap Mohit , Robinson Gertraud W. , Sakamoto Kazuhito , Gomez-Rodriguez Julio , Wagner Kay-Uwe , Leonard Warren J.
Published: October 2010

Thymic stromal lymphopoietin (TSLP) is a type I cytokine that plays essential roles in allergic/inflammatory skin and airway disorders, in helminth infections, and in regulating intestinal immunity. TSLP signals via IL-7Rα and a specific TSLPR subunit that is highly related to the common cytokine receptor γ chain, γc. Although TSLP has effects on a broad range of hematopoetic cells and can induce STAT5 phosphorylation, TSLP was reported to not signal via JAK kinases, and the mechanism by which TSLP regulates STAT5 phosphorylation has been unclear. We now demonstrate the role of JAK1 and JAK2 in TSLP-mediated STAT5 phosphorylation in mouse and human primary CD4+T cells, in contrast to the known activation of JAK1 and JAK3 by the related cytokine, IL-7. We also show that just as JAK1 interacts with IL-7Rα, JAK2 is associated with TSLPR protein. Moreover, we demonstrate the importance of STAT5 activation for TSLP-mediated survival and proliferation of CD4+T cells. These findings clarify the basis for TSLP-mediated signaling and provide an example wherein a cytokine uses JAK1 and JAK2 to mediate the activation of STAT5.
Tree decline and the future of Australian farmland biodiversity
Authors: Fischer Joern , Zerger Andre , Gibbons Phil , Stott Jenny , Law Bradley S.
Published: October 2010

Farmland biodiversity is greatly enhanced by the presence of trees. However, farmland trees are declining worldwide, including in North America, Central America, and parts of southern Europe. We show that tree decline and its likely consequences are particularly severe in Australia's temperate agricultural zone, which is a threatened ecoregion. Using field data on trees, remotely sensed imagery, and a demographic model for trees, we predict that by 2100, the number of trees on an average farm will contract to two-thirds of its present level. Statistical habitat models suggest that this tree decline will negatively affect many currently common animal species, with predicted declines in birds and bats of up to 50% by 2100. Declines were predicted for 24 of 32 bird species modeled and for all of six bat species modeled. Widespread declines in trees, birds, and bats may lead to a reduction in economically important ecosystem services such as shade provision for livestock and pest control. Moreover, many other species for which we have no empirical data also depend on trees, suggesting that fundamental changes in ecosystem functioning are likely. We conclude that Australia's temperate agricultural zone has crossed a threshold and no longer functions as a self-sustaining woodland ecosystem. A regime shift is occurring, with a woodland system deteriorating into a treeless pasture system. Management options exist to reverse tree decline, but new policy settings are required to encourage their widespread adoption.
Omnipotent role of archaeal elongation factor 1 alpha (EF1α) in translational elongation and termination, and quality control of protein synthesis
Authors: Saito Kazuki , Kobayashi Kan , Wada Miki , Kikuno Izumi , Takusagawa Akira , Mochizuki Masahiro , Uchiumi Toshio , Ishitani Ryuichiro , Nureki Osamu , Ito Koichi
Published: October 2010

The molecular mechanisms of translation termination and mRNA surveillance in archaea remain unclear. In eukaryotes, eRF3 and HBS1, which are homologous to the tRNA carrier GTPase EF1α, respectively bind eRF1 and Pelota to decipher stop codons or to facilitate mRNA surveillance. However, genome-wide searches of archaea have failed to detect any orthologs to both GTPases. Here, we report the crystal structure of aRF1 from an archaeon,
Aeropyrum pernix
, and present strong evidence that the authentic archaeal EF1α acts as a carrier GTPase for aRF1 and for aPelota. The binding interface residues between aRF1 and aEF1α predicted from aRF1·aEF1α·GTP ternary structure model were confirmed by in vivo functional assays. The aRF1/eRF1 structural domain with GGQ motif, which corresponds to the CCA arm of tRNA, contacts with all three structural domains of aEF1α showing striking tRNA mimicry of aRF1/eRF1 and its GTPase-mediated catalysis for stop codon decoding. The multiple binding capacity of archaeal EF1α explains the absence of GTPase orthologs for eRF3 and HBS1 in archaea species and suggests that universal molecular mechanisms underlie translational elongation and termination, and mRNA surveillance pathways.