bluuebunny/crossref_metadata_2025 huggingface dataset:
ATP‐binding to P‐type ATPases as revealed by biochemical, spectroscopic, and crystallographic experiments
Authors: Kubala Martin
Published: April 2006

P‐type ATPases form a large family of cation translocating ATPases. Recent progress in crystallography yielded several high‐resolution structures of Ca2+‐ATPase from sarco(endo)plasmic reticulum (SERCA) in various conformations. They could elucidate the conformational changes of the enzyme, which are necessary for the translocation of cations, or the mechanism that explains how the nucleotide binding is coupled to the cation transport. However, crystals of proteins are usually obtained only under conditions that significantly differ from the physiological ones and with ligands that are incompatible with the enzyme function, and both of these factors can inevitably influence the enzyme structure. Biochemical (such as mutagenesis, cleavage, and labeling) or spectroscopic experiments can yield only limited structural information, but this information could be considered relevant, because measurement can be performed under physiological conditions and with true ligands. However, interpretation of some biochemical or spectroscopic data could be difficult without precise knowledge of the structure. Thus, only a combination of both these approaches can extract the relevant information and identify artifacts. Briefly, there is good agreement between crystallographic and other experimental data concerning the overall shape of the molecule and the movement of cytoplasmic domains. On the contrary, the E1‐AMPPCP crystallographic structure is, in details, in severe conflict with numerous spectroscopic experiments and probably does not represent the physiological state. Notably, the E1‐ADP‐AlF4 structure is almost identical to the E1‐AMPPCP, again suggesting that the structure is primarily determined by the crystal‐growth conditions. The physiological relevance of the E2 and E2‐P structures is also questionable, because the crystals were prepared in the presence of thapsigargin, which is known to be a very efficient inhibitor of SERCA. Thus, probably only crystals of E1‐2Ca conformation could reflect some physiological state. Combination of biochemical, spectroscopic, and crystallographic data revealed amino acids that are responsible for the interaction with the nucleotide. High sequence homology of the P‐type ATPases in the cytoplasmic domains enables prediction of the ATP‐interacting amino acids also for other P‐type ATPases. Proteins 2006. © 2006 Wiley‐Liss, Inc.
Susceptibility of adult Coccinella septempunctata (Coleoptera: Coccinellidae) to insecticides with different modes of action
Authors: Bozsik András
Published: April 2006

Five insecticides (pyriproxifen, imidacloprid, deltamethrin + heptenophos, lambda‐cyhalothrin and Bacillus thuringiensis Berliner subsp. tenebrionis) were examined in the laboratory for their acute detrimental side‐effects at field rates on adult seven‐spot ladybird beetle, Coccinella septempunctata L. The toxicity of the preparations was determined by measuring the acute surface contact effects (dried spray on leaves of Philadelphus coronarius L.), except for B. thuringiensis where mixed pollen was treated. Four to six concentrations were tested (pyriproxifen 12.5, 25, 50, 100, 200, 400 mg AI litre−1; imidacloprid 62.4, 125, 250, 500 mg AI litre−1; deltamethrin + heptenophos 26.4, 53.1, 106.3, 212.5 mg AI litre−1; lambda‐cyhalothrin 1.1, 3.4, 10, 30 mg AI litre−1; B. thuringiensis 1.5, 3.0, 12.0, 48, 192, 768 mg AI litre−1), with 22 adults exposed per concentration. All tests were conducted in the laboratory of the Plant Protection Department (University of Debrecen, Hungary) at 22–25 °C, 40–60% RH, under a 16:8 h light:dark photoperiod in 1998–1999. Data were analyzed by probit analysis, probit transformation and analysis of variance. According to different categories of evaluation, pyriproxifen, imidacloprid and B. thuringiensis subsp. tenebrionis seem to be safe for C. septempunctata adults but the other two preparations were moderately harmful to them, which requires further semi‐field or field tests to measure their real effect under field conditions. Copyright © 2006 Society of Chemical Industry
XPS characterization of nitrogen‐doped carbon nanotubes
Authors: Morant C. , Andrey J. , Prieto P. , Mendiola D. , Sanz J. M. , Elizalde E.
Published: April 2006

In this work, CNTs have been bombarded with low energy N ions. X‐ray photoelectron spectroscopy have been used to determine the binding configuration of the N‐doped CNTs. AFM was also used to determine their morphology and mechanical properties. The same morphology is maintained after the N2+ bombardment. XPS analysis shows that the N 1s core level spectra for N‐doped CNTs can be deconvoluted in terms of two peaks related to sp2 (C–N=C) and sp3 hybridization (C–N configuration). This interpretation is in concordance with the increase of the hardness observed by AFM nanoindentations when the sp3 contributions increase. (© 2006 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
3rd order nonlinear optical properties of Au:SiO2 nanocomposite films with varying Au particle size
Authors: Jun H.‐S. , Lee K.‐S. , Yoon S.‐H. , Lee T. S. , Kim I. H. , Jeong J.‐H. , Cheong B. , Kim D. S. , Cho K. M. , Kim W. M.
Published: April 2006

Four Au:SiO2 composite films with varying Au particle size at fixed volume fraction were fabricated by alternate sputtering, and their 3rd order nonlinear optical properties were investigated by the z ‐scan technique using picosecond pulse laser. TEM analysis was used to estimate the particle size for samples with varying Au nominal thickness, and size dependent linear absorption spectra were examined. Particle size dependence on the imaginary part of 3rd order susceptibility at surface plasmon wavelength together with the dispersion of the real and the imaginary components around surface plasmon wavelength were resolved and compared with the theoretical values. (© 2006 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Towards the application of nanocrystalline metals in MEMS
Authors: Baghbanan Mohammadreza , Erb Uwe , Palumbo Gino
Published: April 2006

A comparison is presented of the cross‐sectional mechanical properties (i.e. hardness and Young's modulus) for electrodeposited microsystem components with conventional polycrystalline and nanocrystalline structures. It is shown that nanocrystalline electrodeposits exhibit considerabily improved cross‐sectional properties both in terms of uniformity (hardness and Young's modulus) and overall hardness level. (© 2006 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Carbon nanotubes and nucleic acids: tools and targets
Authors: Onoa Bibiana , Zheng Ming , Dresselhaus Mildred S. , Diner Bruce A.
Published: April 2006

Nucleic acids, with their intrinsic structural properties as well as their high specificity, are playing an important role in the rapid development of nano‐technologies. In turn, these new technologies and their efficient performance enable fast and precise methods for detection of nucleic acids, improving the diagnosis of diseases and identification of pathogens. We discuss the use of nucleic acids to disperse and sort single walled carbon nanotubes (SWNTs), and carbon nanotube‐based field effect transistors (CNT‐FETs) to electrically detect specific nucleic acid sequences. Both DNA and RNA are efficient agents for dispersion and separation of SWNTs by diameter and chirality. Fractions enriched in a narrow band gap distribution of DNA:SWNT hybrids do not alter the electronic performance of field effect transistors. A CNT‐FET fulfills the requirements for a nanosensing device that can greatly exceed the existing technologies. Electrical detection of specific nucleic acid sequence could potentially overcome the current limitations of optical detection, by increasing sensitivity and speed, while reducing sample manipulation, size, and cost. (© 2006 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Coupling carbon nanotubes through DNA linker using a biological recognition complex
Authors: Goux‐Capes L. , Filoramo A. , Cote D. , Bourgoin J.‐Ph. , Patillon J.‐N.
Published: April 2006

We present a simple and versatile method for linking single wall carbon nanotubes (SWNT) together through DNA by non‐covalent chemistry using streptavidin‐biotin recognition complex. Streptavidin coated SWNTs are reacted with biotin or bis‐biotin ended DNA double strands leading to SWNT‐DNA and SWNT‐DNA‐SWNT adducts in high yield. This method avoids strong acidic treatment of SWNTs prior to functionalization as usually required in covalent routes. Complementary characterizations by gel electrophoresis and AFM demonstrated the efficiency of the present binding method. In addition, SWNTs bound to DNA can be aligned on a substrate using the combing properties of DNA strands, bringing a new tool into the toolkit for self‐assembling SWNTs onto surfaces. (© 2006 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
The Central Role of Wear Debris in Periprosthetic Osteolysis
Authors: Purdue P. Edward , Koulouvaris Panagiotis , Nestor Bryan J. , Sculco Thomas P.
Published: April 2006

Periprosthetic osteolysis remains the leading complication of total hip arthroplasty, often resulting in aseptic loosening of the implant, and a requirement for revision surgery. Wear-generated particular debris is the main cause of initiating this destructive process. The purpose of this article is to review recent advances in our understanding of how wear debris causes osteolysis, and emergent strategies for the avoidance and treatment of this disease. The most important cellular target for wear debris is the macrophage, which responds to particle challenge in two distinct ways, both of which contribute to increased bone resorption. First, it is well known that wear debris activates proinflammatory signaling, which leads to increased osteoclast recruitment and activation. More recently, it has been established that wear also inhibits the protective actions of antiosteoclastogenic cytokines such as interferon gamma, thus promoting differentiation of macrophages to bone-resorbing osteoclasts. Osteoblasts, fibroblasts, and possibly lymphocytes may also be involved in responses to wear. At a molecular level, wear particles activate MAP kinase cascades, NFκB and other transcription factors, and induce expression of suppressors of cytokine signaling. Strategies to reduce osteolysis by choosing bearing surface materials with reduced wear properties (such as metal-on-metal) should be balanced by awareness that reducing particle size may increase biological activity. Finally, although therapeutic agents against proinflammatory mediators [such as tumor necrosis factor (TNF)] and osteoclasts (bisphosphonates and molecules blocking RANKL signaling) have shown promise in animal models, no approved treatments are yet available to osteolysis patients. Considerable efforts are underway to develop such therapies, and to identify novel targets for therapeutic intervention.
Flow in a tube with non-uniform, time-dependent curvature: governing equations and simple examples
Authors: Lynch D. G. , Waters S. L. , Pedley T. J.
Published: April 2006

Motivated by the study of blood flow in the major coronary arteries, which are situated on the outer surface of the pumping heart, we analyse flow of an incompressible Newtonian fluid in a tube whose curvature varies both along the tube and with time. Attention is restricted to the case in which the tube radius is fixed and its centreline moves in a plane. Nevertheless, the governing equations are very complicated, because the natural coordinate system involves acceleration, rotation and deformation of the frame of reference, and their derivation forms a major part of the paper. Then they are applied to two particular, relatively simple examples: a tube of uniform but time-dependent curvature; and a sinuous tube, representing a small-amplitude oscillation about a straight pipe. In the former case the curvature is taken to be small and to vary by a small amount, and the solution is developed as a triple power series in mean curvature ratio δ0, curvature variation ε and Dean numberD. In the latter case the Reynolds number is taken to be large and a linearized solution for the perturbation to the flow in the boundary layer at the tube wall is obtained, following Smith (1976a). In each case the solution is taken far enough that the first non-trivial effects of the variable curvature can be determined. Results are presented in terms of the oscillatory wall shear stress distribution and, in the uniform curvature case, the contribution of steady streaming to the mean wall shear stress is calculated. Estimation of the parameters for the human heart indicates that the present results are not directly applicable, but point the way for future work.
Inviscid Batchelor-model flow past an airfoil with a vortex trapped in a cavity
Authors: Bunyakin A. V. , Chernyshenko S. I. , Stepanov G. Yu.
Published: April 2006

An efficient method of constructing inviscid Batchelor-model flows is developed. The method is based on an analytic continuation of the potential part of the flow into the closed-streamline vortex region. Numerical solutions are presented for Batchelor-model flows past airfoils with cavities. With the airfoil and dividing streamline shape, the eddy vorticity, and the jump in the Bernoulli constant across the eddy boundary given, the program calculates the corresponding cavity shape and the entire flow.
Hydraulic jumps at boundaries in rotating fluids
Authors: Fedorov Alexey V. , Melville W. Kendall
Published: April 2006

We consider three-dimensional hydraulic jumps (shocks) propagating along boundaries in rotating fluids. This study is motivated by earlier work (Fedorov & Melville 1995), which dealt with the evolution to breaking of nonlinear Kelvin waves. We obtain the jump relations and derive an evolution equation for the jump as it propagates along the boundary. It is shown that after some initial adjustment the Kelvin-type jump assumes a permanent form and propagates with a constant velocity along the boundary or the coast. At some distance offshore the jump becomes oblique to the coastline, and the final shape of the jump and its speed depend only on the jump strength. The jump gives rise to a moderate mass transport offshore. The potential vorticity remains almost constant across the jump. The energy loss in the jump is proportional to the third power of the jump amplitude, which is similar to classical two-dimensional hydraulic jumps in non-rotating fluids. Jump properties are discussed for both weak and strong nonlinearity, and the role of a boundary layer region behind the leading edge of the jump is considered.
Non-isothermal spreading of a thin liquid film on an inclined plane
Authors: López P. Gilberto , Bankoff S. George , Miksis Michael J.
Published: April 2006

A thin layer of liquid advancing over a dry, heated, inclined plate is studied. A lubrication model with contact line motion is derived. The plate is at constant temperature, and the surface Biot number is specified. The steady-state solution is obtained numerically. In addition, the steady-state solution is studied analytically in the neighbourhood of the contact line. A linear stability analysis about the steady state is then performed. The effects of gravity, thermocapillarity and contact line motion are discussed. In particular, we determine a band of unstable wavenumbers, and the maximum growth rate as a function of these parameters.
Planar flows past thin multi-blade configurations
Authors: Smith F. T. , Timoshin S. N.
Published: April 2006

Two-dimensional steady laminar flows past multiple thin blades positioned in near or exact sequence are examined for large Reynolds numbers. Symmetric configurations require solution of the boundary-layer equations alone, in parabolic fashion, over the successive blades. Non-symmetric configurations in contrast yield a new global inner–outer interaction in which the boundary layers, the wakes and the potential flow outside have to be determined together, to satisfy pressure-continuity conditions along each successive gap or wake. A robust computational scheme is used to obtain numerical solutions in direct or design mode, followed by analysis. Among other extremes, many-blade analysis shows a double viscous structure downstream with two streamwise length scales operating there. Lift and drag are also considered. Another new global interaction is found further downstream. All the interactions involved seem peculiar to multi-blade flows.
The growth of periodic waves in gas-fluidized beds
Authors: Harris S. E.
Published: April 2006

In this paper, we analyse the development of initially small, periodic, voidage disturbances in gas-fluidized beds. The one-dimensional model was proposed by Needham & Merkin (1983), and Crighton (1991) showed that weakly nonlinear waves satisfied a perturbed Korteweg–de Vries or KdV equation. Here, we take periodic cnoidal wave solutions of the KdV equation and follow their evolution when the perturbation terms are amplifying. Initially, all such waves grow, but at a later stage a rescaling shows that shorter wavelengths are stabilized in a weakly nonlinear state. Longer wavelengths continue to develop and eventually strongly nonlinear solutions are required. Necessary conditions for periodic waves are found and matching back onto the growing cnoidal waves is possible. It is shown further that these fully nonlinear waves also reach an equilibrium state. A comparison with numerical results from Needham & Merkin (1986) and Anderson, Sundaresan & Jackson (1995) is then carried out.
Miscible displacements in capillary tubes. Part 1. Experiments
Authors: Petitjeans P. , Maxworthy T.
Published: April 2006

Experiments have been performed, in capillary tubes, on the displacement of a viscous fluid (glycerine) by a less viscous one (a glycerine–water mixture) with which it is miscible in all proportions. A diagnostic measure of the amount of viscous fluid left behind on the tube wall has been found, for both vertical and horizontal tubes, as a function of the Péclet (Pe) and Atwood (At) numbers, as well as a parameter that is a measure of the relative importance of viscous and gravitational effects. The asymptotic value of this diagnostic quantity, for largePeand anAtof unity, has been found to agree with that found in immiscible displacements, while the agreement with the numerical results of Part 2 (Chen & Meiburg 1966), over the whole range ofAt, is very good. At values of the averagePegreater than 1000 a sharp interface existed so that it was possible to make direct comparisons between the present results and a prior experiment with immiscible fluids, in particular an effective surface tension at the diffusing interface could be evaluated. The effect of gravity on the amount of viscous fluid left on the tube wall has been investigated also, and compared with the results of Part 2. A subsidiary experiment has been performed to measure both the average value of the diffusion coefficient between pure glycerine and several glycerine–water mixtures, in order to be able to calculate a representative Péclet number for each experiment, and the local value as a function of the local concentration of glycerine, in the dilute limit.
Concentration waves and the instability of bubbly flows
Authors: Lammers J. H. , Biesheuvel A.
Published: April 2006

This paper examines whether G. K. Batchelor's (1988) theory of the propagation of planar concentration disturbances and the occurrence of instabilities in uniform fluidized beds can be applied to bubbly flows. According to this theory the propagation of long weakly nonlinear gas volume concentration waves is governed by the Burgers equation. Experiments on the propagation of weak concentration shock waves and small, but finite, amplitude periodic waves are presented; good agreement is found with classic solutions of Burgers’ equation. For example, the phenomenon of amplitude saturation, familiar from nonlinear acoustics, is established here for concentration waves. Batchelor's instability conditions are given for bubbly flows, and his model for the bulk modulus of elasticity of the dispersed phase is used to obtain estimates of the critical volume concentration at which a uniform bubbly flow becomes unstable to planar disturbances. Observations of the onset of instabilities of bubbly flow in a pipe are described, and compared with what would be expected from Batchelor's theory.
Diffusion in stably stratified turbulence
Authors: Kimura Y. , Herring J. R.
Published: April 2006

We examine results of direct numerical simulations (DNS) of homogeneous turbulence in the presence of stable stratification. We focus on the effects of stratification on eddy diffusion, and the distribution of pairs of particles released in the flow. DNS results are presented over a range of stratification, and at Reynolds numbers compatible with aliased free spectral results for a resolution of 128 mesh points. We compare results for particle dispersion to simple analytic theories such as that proposed by Csanady (1964) and Pearson et al. (1983) by adapting the basic Langevin model to decaying turbulence at low Reynolds numbers. Stable stratification is found to arrest both single particle displacements and pair separation in the direction of stratification, but it leaves these quantities nearly unaltered in the transverse direction. With respect to the dynamics of stratified flows, we find that regions of strong viscous dissipation are intermittently spaced, and are associated with large horizontal vorticity, consistent with recent experimental results by Fincham et al. (1994).
Spatio—temporal behaviour in a rotating annulus with a source—sink flow
Authors: Arco E. Crespo Del , Maubert P. , Randriamampianina A. , Bontoux P.
Published: April 2006

The axisymmetric flows arising in a rotating annulus with a superimposed forced flow are investigated with a pseudo-spectral numerical method. The flow enters the annulus at the inner radius with a radial velocity, then develops into a geostrophic flow azimuthally directed and flanked by two Ekman (nonlinear) boundary layers, and finally exits the outer radius, with a radially directed velocity. In this study the rotation rate of the cavity is fixed and very high. When the forced flow is weak, the flow is steady. On increasing the mass flow rate, the flow evolves to a chaotic temporal behaviour through several bifurcations, which perturbs the basic spatial configuration of the flow. The first bifurcation drives the steady state into an oscillatory regime, associated with a break of symmetry with respect to the midheight of the annulus. The entry flow travels radially through the cavity as in the steady flow, but it wavers and then is alternately sucked towards each Ekman layer. The frequency of this oscillation is close to the rotation rate frequency of the cavity, which is characteristic of inertial waves in rotating flows. A second transition to a quasi-periodic regime is characterized by the appearance of a second frequency. Further increases in the flow rate lead to a period-five state, via a locking of both frequencies, and then to a chaotic motion. This second frequency is of the order of the inverse of the Ekman spin-up characteristic time, suggesting that this instability is originated by the relaxation of the perturbations in the flow field. These perturbations of the unsteady flow field are corotating vortices along the rigid boundary walls. They are excited by the entry flow and their strength diminishes with increasing radius due to the low value of the Reynolds number. The parameters characterizing the unstable flows are also consistent with this explanation. The conclusion is that in this configuration, the origin of the described dynamical behaviour is not the instability of the Ekman boundary layers, as could be expected, but the instability of the entry flow. The reason is the importance of the nonlinear inertial terms in cavities with small radius of curvature.
Layer formation in monodispersive suspensions and colloids
Authors: Hosoi A. E. , Dupont Todd F.
Published: April 2006

We present theoretical results on spontaneous stratification of sedimenting suspensions and colloids caused by a lateral temperature gradient. Fluid motion is treated in the Stokes approximation, and motion of suspended particles is described by Burgers equation with convection. The internal structure and interaction of shocks at convection roll boundaries is studied numerically using a reduced one-dimensional model based on a Galerkin approach. Qualitative comparison is made to experimental data.
Development of structure within the turbulent wake of a porous body. Part 1. The initial formation region
Authors: Huang Z. , Keffer J. F.
Published: April 2006

This paper deals with the initial region (x/d = 1 to 20) of a turbulent wake generated by a mesh strip. The purpose of the study is to identify the formation mechanism of the large-scale vortices which have developed by the end of this zone. The region is characterized by the evolution and interaction of two parallel shear layers generated at the edges of the mesh. Multi-point hot-wire velocity measurements establish that the merging and interaction of the small-scale eddies account for the formation of the large-scale vortices. A numerical simulation based on a discrete vortex method was carried out to gain further insight into the interaction between the two shear layers. Both the experimental and numerical results suggest that low-frequency perturbation plays an important role in the communication between the two shear layers.
Conservation and biomonitoring in the Vikramshila Gangetic Dolphin Sanctuary, Bihar, India
Authors: Choudhary Sunil K. , Smith Brian D. , Dey Subhasis , Dey Sushant , Prakash Satya
Published: April 2006

From March 2001 to December 2003 eight direct count surveys in an upstream direction were conducted for Ganges river dolphins Platanista gangetica gangetica in the Vikramshila Gangetic Dolphin Sanctuary, a c. 60 km long segment of the middle Ganges River in Bihar, India. The mean number of dolphins recorded during upstream surveys was 119.4±SD 31.8 (range 88–174), with an encounter rate of 1.8 dolphins km−1 (range 1.4–2.8). During these surveys a rich diversity of other threatened aquatic wildlife was also documented, including the Indian smooth-coated otter Lutrogale perspicillata, gharial Gavialis gangeticus, a variety of freshwater turtles, and 135 water bird species. An assessment of fisheries documented 76 fish species of which 43% were caught exclusively in monofilament gill nets, a gear known to kill dolphins by entanglement. Eight new records of fishes preyed upon by Ganges river dolphins were identified from the stomach contents of two dolphin carcasses (Setipinna brevifilis, Osteobrama cotio cotio, Puntius sophore, Crosochelius latius, Mystus cavasius, Heteropneustus fossilis, Macrognathus pancalus, Sperata seenghala). These fishes and other species previously recorded in the diet of the dolphins composed 33.3% of the total catch sampled in 2001–2003. Interviews of 108 fishing households revealed that literacy rates were low (29.9%) and almost 50% earned less than USD 411 per year. The most important conservation actions that could be taken are for national and state governments to establish civil control and promote the development of community-based fishing cooperatives. These cooperatives could enjoy ownership rights to certain river segments in exchange for employing sustainable fishing techniques that are less injurious to dolphins.
A diode laser system for heating minerals for (U‐Th)/He chronometry
Authors: Foeken Jurgen P. T. , Stuart Finlay M. , Dobson Katherine J. , Persano Cristina , Vilbert David
Published: April 2006

We have developed a diode laser (25 W, 808 nm) system for He extraction from minerals for (U‐Th)/He chronometry. The laser beam is delivered via a 600 μm fiber cable and focused using a binocular microscope. Temperatures necessary for He release from apatite (500–600°C) and zircon (1100–1300°C) encapsulated in Pt‐foil tubes are attained by heating to 0.5 W for 30 s and 1.25–2.5 W for 20 min, respectively, using a defocused beam. Heating at these powers does not result in measurable U and/or Th loss from apatite, as noted by the preservation of the distinct Th/U in multiple splits of two different Durango apatite crystals. Analyses of Durango and the California Institute of Technology internal standard apatite 97MR22 yield (U‐Th)/He ages of 32.8 ± 1.8 Ma (1σ, n = 11) and 4.6 ± 0.5 (1σ, n = 5), respectively, well within accepted ages. The (U‐Th)/He age and Th/U of five Fish Canyon Tuff zircon aliquots yield 29.3 ± 2.2 Ma (1σ) and 0.6 ± 0.03, respectively, and are indistinguishable from ages produced by resistance furnace He extraction. Heating of unencapsulated minerals shows that the diode laser couples well with optically opaque minerals (e.g., hornblende, biotite, muscovite, garnet) and basalt groundmass, suggesting that diode lasers offer a cheap, small, low‐maintenance alternative to Nd:YAG and Ar ion lasers for 40Ar/39Ar, cosmogenic noble gas, and stable isotope studies.
Rocket and incoherent scatter radar common‐volume electron measurements of the equatorial lower ionosphere
Authors: Friedrich M. , Torkar K. M. , Lehmacher G. A. , Croskey C. L. , Mitchell J. D. , Kudeki E. , Milla M.
Published: April 2006

A coordinated rocket and radar investigation has enabled the comparison of electron density measurements in essentially a common volume of the equatorial lower ionosphere. The rocket instrumentation included a Faraday rotation experiment, uniquely adapted for measuring electrons at low latitude, and fixed‐bias Langmuir probes. The ALTAIR tracking radar was configured in an incoherent scatter mode. For the 75–92 km region, we note very good agreement between Faraday rotation and radar electron density measurements. Langmuir probe current measurements, calibrated to the Faraday rotation data, provided information about fine‐scale electron density vertical structure and extended the rocket‐radar comparisons of electron density to 130 km. Good overall agreement was also observed at higher altitudes, with evidence of electron density layering ‐ including sporadic E ‐ detected by both measurement techniques. The outcomes from our study support this unique Faraday rotation approach and the IS radar for measuring electron density in the equatorial lower ionosphere.
Radial diffusion of relativistic electrons into the radiation belt slot region during the 2003 Halloween geomagnetic storms
Authors: Loto'aniu T. M. , Mann I. R. , Ozeke L. G. , Chan A. A. , Dent Z. C. , Milling D. K.
Published: April 2006

A study was undertaken to estimate the radial diffusion timescale, τLL, for relativistic electrons (2–6 MeV) to diffuse into the slot region due to drift‐resonance with Pc5 ULF waves (2–10 mHz) on 29 October 2003. Large amplitude ULF waves were observed by ground‐based magnetometer arrays to penetrate deep into the slot region (L ≃ 2–3) starting at 0600 UT and maximising (∼200 nT p‐p) between 0930–1630 UT. Around the same time, the SAMPEX PET instrument measured an over two orders of magnitude increase in relativistic (2–6 MeV) electron flux levels in ∼24 hours within the slot region. The ground‐based D‐component magnetic power spectral densities (PSDδB) for 29 October were estimated for six latitudinally spaced ground stations covering L ∼ 2.3–4.3 for an observed ULF wave with central frequency ∼4 mHz. The PSDδB values were used to calculate the in situ equatorial poloidal wave electric field power spectral densities (PSDδEm) using a standing Alfvén wave model. The radial diffusion coefficients, DLL, were estimated using the PSDδEm values. The fastest τLL were 3–5 hours at L > 4, while τLL initially increased with decreasing L‐value below L ≃ 4; peaking at L ≃ 3 with τLL ∼ 12–24 hours with PSDδEm estimated using a wave frequency bandwidth between Δf = 1 mHz and Δf = 2.5 mHz. The τLL over the L‐range L ∼ 2.3–3.3 were consistent with the timescales observed by SAMPEX for the increase in relativistic fluxes in the slot region on 29 October. The authors believe that this is the first example of the ULF wave drift‐resonance with relativistic electrons explaining a radiation belt slot region filling event.
Surficial properties of landslides and surrounding units in Ophir Chasma, Mars
Authors: Chojnacki Matthew , Jakosky Bruce M. , Hynek Brian M.
Published: April 2006

We mapped the surface layers of the Ophir Chasma region using observations made by the Mars Global Surveyor's Thermal Emission Spectrometer (TES) and the Mars Odyssey's Thermal Emission Imaging System (THEMIS). Our goal is to understand the surface physical characteristics and how they relate to the local geology. TES observations indicate that Ophir Chasma possesses some of the most diverse thermal properties on Mars where the approximate global maximum and minimum values of the derived thermal inertia have been detected within ∼100 km of each other. The thermal maps, used in conjunction with elevation data, meteorological modeling and high‐resolution images, have led to many insights on how the thermal inertia relates to the local morphology and mineralogy. The landslide units on the northern margin of Ophir Chasma have a diverse range of characteristics. A fairly linear relation between elevation and thermal inertia was found that is consistent with the global trend. Recent and/or ongoing aeolian processes are likely closely linked to the current thermal properties of the canyon. These aeolian processes, in turn, are affected by the topography of not only Ophir, but Hebes and Candor Chasmata and neighboring regions. This study has confirmed previous geological interpretations as well as allowed new insights of how the thermal properties of a surface relates to its geology.
Solar proton events in cosmogenic isotope data
Authors: Usoskin Ilya G. , Solanki Sami K. , Kovaltsov Gennady A. , Beer Jürg , Kromer Bernd
Published: April 2006

A possible contribution of solar energetic particle events to the production of cosmogenic 10Be and 14C in the atmosphere is studied. The solar particle effect is negligible in the 14C data, but extreme events may be detectable in high‐resolution 14C data. Although the overall effect is small in the 10Be data, strong events may contribute notably on the inter‐annual time scale. In combination with the 11‐year solar modulation of galactic cosmic rays, it may lead to an intermittent 5.5‐year periodicity, which is seen in high resolution 10Be data. We have identified ten episodes during 1750–1950 when 10Be may hold signatures of strong solar proton events. This opens a new possibility to study extreme solar particle events in the past using high resolution cosmogenic isotope data.
Notch targets the Cdk inhibitor Xic1 to regulate differentiation but not the cell cycle in neurons
Authors: Vernon Ann E , Movassagh Mehregan , Horan Ian , Wise Helen , Ohnuma Shinichi , Philpott Anna
Published: April 2006

The proneural protein neurogenin (XNGNR1) drives differentiation of primary neurons in combination with the cyclin‐dependent kinase (Cdk) inhibitor Xic1. Differentiation is inhibited by Notch signalling, resulting in a scattered neuronal distribution. Here we show that Notch signalling regulates the level of Xic1 transcription, yet this does not correlate with Notch's ability to perturb the cell cycle. Instead, Notch may regulate Xic1 levels to control its differentiation function directly, which is required in parallel with XNGNR1 to promote primary neurogenesis. Indeed, Notch‐mediated repression of both XNGNR1 and Xic1 must be relieved for neuronal differentiation to occur. Interestingly, although Xic1 is required for XNGNR1‐mediated neurogenesis, it is not required for XNGNR1‐mediated upregulation of Delta, allowing establishment of the negative feedback loop involved in lateral inhibition. Therefore, Notch targets Cdk inhibitor expression to regulate differentiation of primary neurons, and its effects on the cell cycle may be of secondary importance.
c‐Abl acetylation by histone acetyltransferases regulates its nuclear–cytoplasmic localization
Authors: di Bari Maria Giovanna , Ciuffini Laura , Mingardi Michele , Testi Roberto , Soddu Silvia , Barilà Daniela
Published: April 2006

c‐Abl function is strictly dependent on its subcellular localization. Using an in vitro approach, we identify c‐Abl as a new substrate for p300, CBP (CREB‐binding protein) and PCAF (p300/CBP‐associated factor) histone acetyltransferases. Remarkably, acetylation markedly alters its subcellular localization. Point mutagenesis indicated that Lys 730, located in the second nuclear localization signal, is the main target of p300 activity. It has previously been reported that c‐Abl accumulates in the cytoplasm during myogenic differentiation. Here, we show that c‐Abl protein is acetylated at early stages of myogenic differentiation. Indeed, acetylation on Lys 730 drives c‐Abl accumulation in the cytoplasm and promotes differentiation. Thus, Lys 730 acetylation is a novel post‐translational modification of c‐Abl and a novel mechanism for modulating its subcellular localization that contributes to myogenic differentiation.
The allosteric enhancer PD81,723 increases chimaeric A1/A2A adenosine receptor coupling with Gs
Authors: Bhattacharya Samita , Youkey Rebecca L. , Ghartey Kobina , Leonard Matthew , Linden Joel , Tucker Amy L.
Published: April 2006

PD81,723 {(2-amino-4,5-dimethyl-3-thienyl)-[3-(trifluromethyl)-phenyl]methanone} is a selective allosteric enhancer of the Gi-coupled A1 AR (adenosine receptor) that is without effect on Gs-coupled A2A ARs. PD81,723 elicits a decrease in the dissociation kinetics of A1 AR agonist radioligands and an increase in functional agonist potency. In the present study, we sought to determine whether enhancer sensitivity is dependent on coupling domains or G-protein specificity of the A1 AR. Using six chimaeric A1/A2A ARs, we show that the allosteric effect of PD81,723 is maintained in a chimaera in which the predominant G-protein-coupling domain of the A1 receptor, the 3ICL (third intracellular loop), is replaced with A2A sequence. These chimaeric receptors are dually coupled with Gs and Gi, and PD81,723 increases the potency of N6-cyclopentyladenosine to augment cAMP accumulation with or without pretreatment of cells with pertussis toxin. Thus PD81,723 has similar functional effects on chimaeric receptors with A1 transmembrane sequences that couple with Gi or Gs. This is the first demonstration that an allosteric regulator can function in the context of a switch in G-protein-coupling specificity. There is no enhancement by PD81,723 of Gi-coupled A2A chimaeric receptors with A1 sequence replacing A2A sequence in the 3ICL. The results suggest that the recognition site for PD81,723 is on the A1 receptor and that the enhancer acts to directly stabilize the receptor to a conformational state capable of coupling with Gi or Gs.
Analysis of the cross-reactivity and of the 1.5 Å crystal structure of the Malassezia sympodialis Mala s 6 allergen, a member of the cyclophilin pan-allergen family
Authors: Glaser Andreas G. , Limacher Andreas , Flückiger Sabine , Scheynius Annika , Scapozza Leonardo , Crameri Reto
Published: April 2006

Cyclophilins constitute a family of proteins involved in many essential cellular functions. They have also been identified as a panallergen family able to elicit IgE-mediated hypersensitivity reactions. Moreover, it has been shown that human cyclophilins are recognized by serum IgE from patients sensitized to environmental cyclophilins. IgE-mediated autoreactivity to self-antigens that have similarity to environmental allergens is often observed in atopic disorders. Therefore comparison of the crystal structure of human proteins with similarity to allergens should allow the identification of structural similarities to rationally explain autoreactivity. A new cyclophilin from Aspergillus fumigatus (Asp f 27) has been cloned, expressed and showed to exhibit cross-reactivity in vitro and in vivo. The three-dimensional structure of cyclophilin from the yeast Malassezia sympodialis (Mala s 6) has been determined at 1.5 Å (1 Å=0.1 nm) by X-ray diffraction. Crystals belong to space group P41212 with unit cell dimensions of a=b=71.99 Å and c=106.18 Å. The structure was solved by molecular replacement using the structure of human cyclophilin A as the search model. The refined structure includes all 162 amino acids of Mala s 6, an active-site-bound Ala-Pro dipeptide and 173 water molecules, with a crystallographic R- and free R-factor of 14.3% and 14.9% respectively. The overall structure consists of an eight-stranded antiparallel β-barrel and two α-helices covering the top and bottom of the barrel, typical for cyclophilins. We identified conserved solvent-exposed residues in the fungal and human structures that are potentially involved in the IgE-mediated cross-reactivity.
Ser-2030, but not Ser-2808, is the major phosphorylation site in cardiac ryanodine receptors responding to protein kinase A activation upon β-adrenergic stimulation in normal and failing hearts
Authors: Xiao Bailong , Zhong Guofeng , Obayashi Masakazu , Yang Dongmei , Chen Keyun , Walsh Michael P. , Shimoni Yakhin , Cheng Heping , ter Keurs Henk , Chen S. R. Wayne
Published: April 2006

We have recently shown that RyR2 (cardiac ryanodine receptor) is phosphorylated by PKA (protein kinase A/cAMP-dependent protein kinase) at two major sites, Ser-2030 and Ser-2808. In the present study, we examined the properties and physiological relevance of phosphorylation of these two sites. Using site- and phospho-specific antibodies, we demonstrated that Ser-2030 of both recombinant and native RyR2 from a number of species was phosphorylated by PKA, indicating that Ser-2030 is a highly conserved PKA site. Furthermore, we found that the phosphorylation of Ser-2030 responded to isoproterenol (isoprenaline) stimulation in rat cardiac myocytes in a concentration- and time-dependent manner, whereas Ser-2808 was already substantially phosphorylated before β-adrenergic stimulation, and the extent of the increase in Ser-2808 phosphorylation after β-adrenergic stimulation was much less than that for Ser-2030. Interestingly, the isoproterenol-induced phosphorylation of Ser-2030, but not of Ser-2808, was markedly inhibited by PKI, a specific inhibitor of PKA. The basal phosphorylation of Ser-2808 was also insensitive to PKA inhibition. Moreover, Ser-2808, but not Ser-2030, was stoichiometrically phosphorylated by PKG (protein kinase G). In addition, we found no significant phosphorylation of RyR2 at the Ser-2030 PKA site in failing rat hearts. Importantly, isoproterenol stimulation markedly increased the phosphorylation of Ser-2030, but not of Ser-2808, in failing rat hearts. Taken together, these observations indicate that Ser-2030, but not Ser-2808, is the major PKA phosphorylation site in RyR2 responding to PKA activation upon β-adrenergic stimulation in both normal and failing hearts, and that RyR2 is not hyperphosphorylated by PKA in heart failure. Our results also suggest that phosphorylation of RyR2 at Ser-2030 may be an important event associated with altered Ca2+ handling and cardiac arrhythmia that is commonly observed in heart failure upon β-adrenergic stimulation.
Cardiac ryanodine receptor phosphorylation: target sites and functional consequences
Authors: Bers Donald M.
Published: April 2006

A study by Xiao and co-workers in this issue of the Biochemical Journal demonstrates PKA (protein kinase A)-dependent phosphorylation of Ser-2030 on the cardiac ryanodine receptor (RyR2) that is activated by β-adrenergic agonists. They show that RyR2 phosphorylation at this site is not appreciably altered in heart failure samples, but retains PKA-dependence of phosphorylation. They contrast this with RyR2 phosphorylation at Ser-2808, a site previously reported to be the key and only PKA target site on RyR2. Here Ser-2808 phosphorylation was found to be relatively insensitive to either PKA activation or inhibition. These results add important new information to a highly controversial field. This issue is important because it is increasingly clear that altered regulation of the gating of the RyR2 sarcoplasmic reticulum Ca2+-release channel (e.g. by phosphorylation) is critically important in mediating altered diastolic sarcoplasmic reticulum Ca2+ release. This may contribute to both reduced cardiac function and arrhythmogenesis in humans carrying mutations in the RyR2 gene and with acquired heart failure of varied aetiology. This study brings some new answers, but also raises additional new questions that will require further investigation.
Quantum real wave-packet dynamics of the N(S4)+NO(X̃Π2)→N2(X̃Σg+1)+O(P3) reaction on the ground and first excited triplet potential energy surfaces: Rate constants, cross sections, and product distributions
Authors: Gamallo Pablo , Sayós R. , González Miguel , Petrongolo Carlo , Defazio Paolo
Published: April 2006

The reaction N+NO→N2+O was studied by means of the time-dependent real wave-packet (WP) method and the J-shifting approximation. We consider the ground 1A″3 and first excited 1A′3 triplet states, which correlate with both reactants and products, using analytical potential energy surfaces (PESs) recently developed in our group. This work extends our previous quantum dynamics study, and probabilities, cross sections, and rate constants were calculated and interpreted on the basis of the different shapes of the PESs (barrierless 1A″3 and with barrier 1A′3 surfaces, respectively). The WP rate constant (k1) shows a weak dependence on T(200–2500K), as the dominant contribution to reactivity is provided by the barrierless ground PES. There is a good agreement of WP k1 with the measurements and variational transition state theory (VTST) data, and also between the WP and VTST k1(1A″3) results. Nevertheless, there is a large discrepancy between the WP and VTST k1(1A′3) results. Product state distributions were also calculated for the much more reactive 1A″3 PES. There is an excellent agreement with the experimental average fraction of vibrational energy in N2(25±3%), the only measured dynamics property of this reaction.
Recognition of complex patterned substrates by heteropolymer chains consisting of multiple monomer types
Authors: Kriksin Yuri A. , Khalatur Pavel G. , Khokhlov Alexei R.
Published: April 2006

We propose a statistical mechanical model of surface pattern recognition by heteropolymers with quenched monomer sequence distribution. The chemically heterogeneous pattern consists of different adsorption sites specifically distributed on a surface. The heteropolymer sequence is complementary with respect to the pattern. The concepts of recognition probability and recognition temperature are introduced. The algorithm for calculating the recognition probability is based on efficient recurrence procedures for evaluating the single-chain partition function of a chain macromolecule consisting of multiple monomer types, which interact with multiple types of adsorption sites. The temperature dependencies of the recognition probability are discussed. We address the critical role of the commensurability between the heteropolymer sequence and the distribution of the surface adsorbing sites on the polymer adsorption. Also, we address the question of how many types of monomer units in the heteropolymer are required for unambiguous recognition of compact target patterns. It is shown that perfect pattern recognition can be achieved for the strong-adsorption regime in the case of specifically structured compact patterns with multifunctional adsorption sites and heteropolymers with multiple monomer types when the degeneracy of the ground state is suppressed. The pattern recognition ability increases with the number of different types of monomer units and complementary adsorption sites. For random heteropolymers and patterns, the free energy change associated with the recognition process decreases linearly with increasing this number. Correlated random heteropolymers are capable of recognizing related patterns on a random background.