bluuebunny/crossref_metadata_2025 huggingface dataset:
The [1+1] two-photon dissociation spectra of CO2+ via ÃΠu,1∕22(υ1υ2)←X̃Πg,1∕22(000) transitions
Authors: Yang Maoping , Zhang Limin , Zhuang Xiujuan , Lai Likun , Yu Shuqin
Published: April 2008

In the wavelength range of 235–354nm, we have obtained the mass-resolved [1+1] two-photon dissociation spectra of CO2+ via ÃΠu,1∕22(υ1υ20)←X̃Πg,1∕22(000) transitions by preparing CO2+ ions in the X̃Πg,1∕22(000) state via [3+1] multiphoton ionization of CO2 molecules at 333.06nm. The vibronic bands of (υ120;υ1=0–11)μΠ1∕22 and (υ120;υ1=0–6)κΠ1∕22 involving the bending mode of CO2+(ÃΠu,1∕22) were assigned. The spectroscopic constants of Te=27908.9±1.1cm−1 [above CO2+(X̃Πg,1∕22)], ν1=1126.00±0.36cm−1, χ11=−1.602±0.005cm−1, ν2(μΠ1∕22)=402.5±13.3cm−1, and ν2(κΠ1∕22)=493.1±23.6cm−1 for CO2+(ÃΠu,1∕22) are deduced from the data of the ÃΠu,1∕22(υ1υ20)←X̃Πg,1∕22(000) transitions. The observed intensity reversal between (500)Π1∕22 and (420)μΠ1∕22 can be attributed to the conformational variation of CO2+(ÃΠu,1∕22) from linear to bent, then the conversion potential barrier is estimated to be 5209cm−1 above CO2+(ÃΠu,1∕22(000)). The wavelength and level dependence of the photofragment branching ratios have been measured and the dissociation dynamics of CO2+ via ÃΠu,1∕22 state is discussed.
Molecular dynamics simulation of nanocolloidal amorphous silica particles: Part II
Authors: Jenkins S. , Kirk S. R. , Persson M. , Carlen J. , Abbas Z.
Published: April 2008

Explicit molecular dynamics simulations were applied to a pair of amorphous silica nanoparticles with diameter of 3.2nm immersed in a background electrolyte. Mean forces acting between the pair of silica nanoparticles were extracted at four different background electrolyte concentrations. The dependence of the interparticle potential of mean force on the separation and the silicon to sodium ratio, as well as on the background electrolyte concentration, are demonstrated. The pH was indirectly accounted for via the ratio of silicon to sodium used in the simulations. The nature of the interaction of the counterions with charged silica surface sites (deprotonated silanols) was also investigated. The effect of the sodium double layer on the water ordering was investigated for three Si:Na+ ratios. The number of water molecules trapped inside the nanoparticles was investigated as the Si:Na+ ratio was varied. Differences in this number between the two nanoparticles in the simulations are attributed to differences in the calculated electric dipole moment. The implications of the form of the potentials for aggregation are also discussed.
Statistical properties of ideal three-dimensional Hall magnetohydrodynamics: The spectral structure of the equilibrium ensemble
Authors: Servidio Sergio , Matthaeus William H. , Carbone Vincenzo
Published: April 2008

The nonlinear dynamics of ideal, incompressible Hall magnetohydrodynamics (HMHD) is investigated through classical Gibbs ensemble methods applied to the finite Galerkin representation. The spectral structure of HMHD is derived in a three-dimensional periodic geometry and compared with the MHD case. This provides a general picture of spectral transfer and cascade by the assumption that ideal Galerkin HMHD follows equilibrium statistics as in the case of Euler [U. Frisch et al., J. Fluid Mech. 68, 769 (1975)] and MHD [T. Stribling and W. H. Matthaeus, Phys. Fluids B 2, 1979 (1990)] theories. In HMHD, the equilibrium ensemble is built on the conservation of three quadratic invariants: The total energy, the magnetic helicity, and the generalized helicity. The latter replaces the cross helicity in MHD. In HMHD equilibrium, several differences appear with respect to the MHD case: (i) The generalized helicity (and in a weaker way the energy and the magnetic helicity) tends to condense in the longest wavelength, as in MHD, but also admits the novel feature of spectral enhancement, not a true condensation, at the smallest scales; (ii) equipartition between kinetic and magnetic energy, typical of Alfvénic MHD turbulence, is broken; (iii) modal distributions of energy and helicities show minima due to the presence of the ion skin depth. Ensemble predictions are compared to numerical simulations with a low-order truncation Galerkin spectral code, and good agreement is seen. Implications for general turbulent states are discussed.
Thermal conductivity of nitrogenated ultrananocrystalline diamond films on silicon
Authors: Shamsa M. , Ghosh S. , Calizo I. , Ralchenko V. , Popovich A. , Balandin A. A.
Published: April 2008

The authors report on the experimental investigation of the thermal conductivity of nitrogenated ultrananocrystalline diamond (UNCD) films on silicon. For better accuracy, the thermal conductivity was measured by using two different approaches: the 3ω method and transient “hot disk” technique. The temperature dependence of the thermal conductivity of the nitrogenated UNCD films was compared to that of undoped UNCD films and microcrystalline diamond (MCD) films on silicon. It was shown that the temperature dependence of the thermal conductivity of UNCD films, which is substantially different from that for MCD films, can be adequately described by the phonon-hopping model. The room-temperature thermal conductivity of UNCD is 8.6–16.6 W/m K and decreases with the addition of nitrogen. The obtained results shed light on the nature of thermal conduction in partially disordered nanostructured materials and can be used for estimating the thermal resistance of doped UNCD films.
Influence of compositional ratio K/Na on physical properties in (KxNa1−x)NbO3 ceramics
Authors: Wu L. , Zhang J. L. , Wang C. L. , Li J. C.
Published: April 2008

Lead-free KxNa1−xNbO3 (KNN) ceramics with x=0.10–0.80 were prepared by a conventional solid-state reaction method to investigate the influence of the K/Na ratio on their physical properties. It has been found that the KNN ceramics with x=0.45–0.60 exhibit quite different microstructures from those with other alkali compositional ratios. The lattice parameter discontinuity previously reported at x=0.475 has not been confirmed. The existence of a change in the line slopes of lattice parameter variation with x is verified in the vicinity of x=0.35. The permittivity ε′, piezoelectric constant d33, and planar electromechanical coupling coefficient kp show broad peaks in the compositional range of x=0.40–0.60, where d33 and kp are nearly independent of the K/Na ratio and all the ceramics have the high piezoelectric values of d33∼125 pC/N and kp∼0.41, respectively. From the analyses, we suggest that the high piezoelectric properties for the KNN ceramics near x=0.50 are closely related to their microstructures of well-faceted and uniformly distributed large grains rather than the widely believed morphotropic phase boundary effect of lattice parameter discontinuity.
Open-loop control of fully nonlinear self-excited oscillations
Authors: Hallberg M. P. , Strykowski P. J.
Published: April 2008

Experiments conducted using a low-density axisymmetric jet reveal that the self-excited nature can be altered by modulating the external pressure field using an acoustic driver. A region exists in the forcing frequency-amplitude space where the self-sustaining frequency is entirely absent and solely replaced by the forcing frequency and harmonics thereof. Inside this region, the centerline streamwise velocity disturbance level can be significantly increased or decreased. Visual evidence suggests these alterations coincide with dramatic changes in jet spreading and demonstrates that forcing can provide an effective means of controlling mixing in self-excited jets. Results support theoretical predictions made by Pier [B. Pier, Proc. R. Soc. London, Ser. A 459, 1105 (2003)].
Invited Review Article: Microwave spectroscopy based on scanning thermal microscopy: Resolution in the nanometer range
Authors: Meckenstock Ralf
Published: April 2008

Scanning thermal microscope-detected ferromagnetic resonance (SThM-FMR) combines a thermal near-field microscope with a FMR spectrometer and detects the thermal response due to resonant microwave absorption by measuring the resistivity change in the thermal nanoprobe. The advantage of this technique is to provide imaging capabilities at fixed resonance conditions as well as local microwave spectroscopy at the nanoscale. A technique that uses the same setup but detects the thermoelastic response of the sample is the scanning thermoelastic microscope-detected FMR (SThEM-FMR). This latter technique is advantageous when FMR spectra of single nanostructures have to be recorded at a fixed position. The experimental setups and the signal generation processes of SThM/SThEM-FMR are described in detail. With the SThM-FMR setups a temperature resolution of 1mK and a local resolution of 30nm are actually achieved. With SThEM-FMR the obtained local resolution is 10nm. The detection limits of both techniques can be as low as 106 spins. To demonstrate the potential of these new techniques SThM/SThEM-FMR investigations of local magnetic anisotropies, magnetization dynamics of single nanodots and inhomogeneous FMR excitations due to finite size effects are presented. Simultaneously, information on the magnetic parameters, the topography, and the thermal properties is provided. To describe the further potential of this recently developed SThM-FMR technique, combined magnetoresistance and FMR investigations are presented and an outlook on possible future applications is given.
Extraction of Schottky diode parameters from current-voltage data for a chemical-vapor-deposited diamond/silicon structure over a wide temperature range
Authors: Rodrigues A. M.
Published: April 2008

Characteristic parameters of Schottky diodes formed from a chemical-vapor-deposited diamond/n+-Si junction were obtained experimentally from the I-V characteristics in the temperature range of 119–400K. Diode parameters, such as the barrier height φB0 and the ideality factor n, calculated using thermionic emission theory were found to be strongly temperature dependent. The temperature dependence of the parameters is attributed to surface states, series resistance, and inhomogeneities in the material. Diode parameters obtained using Cheung’s technique showed good agreement with the experimental results and are in accordance with the results expected for this structure.
Record flux pinning in melt-textured NEG-123 doped by Mo and Nb nanoparticles
Authors: Muralidhar M. , Sakai N. , Jirsa M. , Murakami M. , Hirabayashi I.
Published: April 2008

We report on a highly improved pinning performance in the melt-textured (Nd0.33Eu0.33Gd0.33)Ba2Cu3Oy+35mol% Gd2BaCuO5 (70nm in size) composite doped by tiny amounts of nanometer-sized MoO3 or NbO3 particles. The doping led to a spontaneous formation of clouds with extremely small (⩽10nm) (Nd,Eu,Gd)2BaCuXO5 particles, X=Mo,Nb. With an optimum content of MoO3 and NbO3, the self-field supercurrent at 77K was twofold and threefold higher than before, respectively. At 65K the supercurrent reached 700kA∕cm2 with Mo and 925kA∕cm2 with Nb at both 0 and 4.5T, and the self-field current at 90K was 100A∕cm2 in the Nb-doped sample, which is a value high enough for a safe levitation.
Modeling of high energy laser ignition of energetic materials
Authors: Lee Kyung-cheol , Kim Ki-hong , Yoh Jack J.
Published: April 2008

We present a model for simulating high energy laser heating and ignition of confined energetic materials. The model considers the effect of irradiating a steel plate with long laser pulses and continuous lasers of several kilowatts and the thermal response of well-characterized high explosives for ignition. Since there is enough time for the thermal wave to propagate into the target and to create a region of hot spot in the high explosives, electron thermal diffusion of ultrashort (femto- and picosecond) lasing is ignored; instead, heat diffusion of absorbed laser energy in the solid target is modeled with thermal decomposition kinetic models of high explosives. Numerically simulated pulsed-laser heating of solid target and thermal explosion of cyclotrimethylenetrinitramine, triaminotrinitrobenzene, and octahydrotetranitrotetrazine are compared to experimental results. The experimental and numerical results are in good agreement.
Dye-sensitized solar cells using ZnO tetrapods
Authors: Hsu Y. F. , Xi Y. Y. , Yip C. T. , Djurišić A. B. , Chan W. K.
Published: April 2008

One dimensional (1D) ZnO nanostructures are of interest for applications in dye-sensitized solar cells (DSSCs) since they exhibit significantly improved electron transport compared to that in porous films. However, 1D nanostructures also have a significantly lower surface area than the porous films. Thus, the achieved solar cell efficiencies are typically much lower in spite of the improved charge transport. In this work, we investigated DSSCs based on ZnO tetrapods to achieve an increased surface area compared to that of 1D nanostructures. The cell performance as a function of the tetrapod film thickness and the dye used was studied. To further increase the surface area, mixed morphologies (tetrapods with nanoparticles) were also investigated. Under optimal conditions, an AM 1.5 power conversion efficiency of ∼1.2% was achieved.
Transition edge sensors for bolometric applications: responsivity and saturation
Authors: Goldie D. J. , Audley M. D. , Glowacka D. M. , Tsaneva V. N. , Withington S.
Published: April 2008

Microstrip-coupled transition edge sensors (TESs) combined with waveguide-horn technology produce sensitive bolometric detectors with well-defined, single-mode beam patterns and excellent polarization characteristics. These devices are now being deployed for astronomical observations. In bolometric applications, where power levels are monitored, the critical parameter that characterizes the detection is the power-to-current responsivity sI(ω), where ω is the postdetection angular frequency. In real applications, such as on a ground-based telescope, the signal of interest is superimposed on a background such as the thermal emission from the atmosphere. The power emitted by the atmosphere changes slowly in time and these changes may change the responsivity of the detector. A detailed understanding of how sI(ω) changes as a function of applied power levels and how the TES response saturates is vital for accurate calibration of astronomical data. In this paper we describe measurements of the changes in the current flowing through a TES as a function of the circuit bias and the applied power. From these measurements we calculate the efficiency of the coupling of power into the TES from a closely thermally coupled microstrip termination resistor and we determine the zero frequency responsivity sI(0) as a function of both the circuit bias and power. The variation of the responsivity is compared with predictions of a small-signal model: for the case when the loop gain LI is high, when simplifying approximations to the full solution to the electrothermal equations apply; and using the electrothermal parameters of the TES, determined by impedance measurements, as inputs to the full model solution. We find good agreement between theory and measurement in both cases in the relevant regimes.
Surface scaling of magnetism in Cr:ZnO dilute magnetic dielectric thin films
Authors: Roberts Bradley K. , Pakhomov Alexandre B. , Voll Patricia , Krishnan Kannan M.
Published: April 2008

Measurements of the spontaneous magnetic moment and conductance of oxygen-saturated ZnO:Cr thin films and tunnel junctions show an exponential drop with increasing thickness. All films are in the insulating state. The type and concentration of dominant point defects in the bulk do not provide conditions for magnetic ordering, while surfaces play an important role in magnetism. We suggest that in film thicknesses below a characteristic length (∼30nm), surface states or enhanced concentration of point defects near the surface (oxygen vacancies or incorporated hydrogen) lead to surface magnetism. Ballistic tunneling is observed in junctions <100nm, with penetration depth of ∼10nm.
New Coordination Polymers of Lanthanide(III) with Tetrazole-1-acetic Acid: Synthesis, Crystal Structures, and Magnetic Properties
Authors: Zhang Xiu-Qing , Yu Qing , Bian He-Dong , Yan Shi-Ping , Liao Dai-Zheng , Gu Wen , Liang Hong
Published: April 2008

New coordination polymers {[Ln(tza)3(H2O)2]·mH2O}n (Ln = LaIII 1 and PrIII 2, m = 2; Ln = NdIII 3, m = 1.5) and {[Sm2(tza)6(H2O)5]·H2O}n 4 (Htza = tetrazole-1-acetic acid) have been synthesized and characterized by IR spectroscopy, elemental analysis, X-ray crystallography, and magnetic measurements. The Htza ligand coordinates to the lanthanide cations through the carboxylate group in a monodentate, bridging bidentate coordination mode or bridging tridentate to two metal centres. Complexes 1 and 2 are isostructural. Complex 3 has a similar structure to 1 and 2, but the arrangement of ligands has changed. Complex 4 consists of two types of metallic molecules. Magnetic measurements show weak antiferromagnetic coupling between the metal centres in complexes 2 and 3.
Synthesis and Chiral Recognition Properties of a Novel Colorimetric Chiral Sensor for Carboxylic Anions
Authors: Chen Zhi-Hong , He Yong-Bing , Hu Chen-Guang , Huang Xiao-Huan , Hu Ling
Published: April 2008

Chiral colorimetric sensor 4 has been synthesized, and the structure characterized by IR and 1H NMR spectroscopy, mass spectrometry, and elemental analysis. The chiral recognition of the receptor was studied by 1H NMR and UV-vis spectroscopy. The results of non-linear curve fitting indicate that the receptor 4 and l- or d-mandelate and alanine anions form a 1:1 stoichiometric complex. The obvious colour change of receptor 4 can be observed by the naked eye when the enantiomers of mandelate and alanine anions are added, which demonstrates that receptor 4 may be used as the colorimetric sensor for the two carboxylic anions.
Synthesis and Spectroscopic Properties of Low-Symmetry Tribenzoporphyrazines with Annulated 6H-1,4-Diazepine Ring
Authors: Donzello Maria Pia , Ercolani Claudio , Mannina Luisa , Viola Elisa , Bubnova Alëna , Khelevina Ol'ga G. , Stuzhin Pavel A.
Published: April 2008

Template co-condensation of 2,3-dicyano-5,7-diphenyl-6H-1,4-diazepine 1 with 10-fold molar excess of phthalodinitrile 2 in the presence of MgII propoxide or butoxide in the corresponding alcohol leads to a mixture of MgII-diazepinoporphyrazines 3–6 from which the low symmetry 3:1 species 3, which contains three annulated benzene and one 1,4-diazepine rings, is separated by column chromatography as the aquo complex, [2,4-diphenyltribenzo[b,g,l][1,4]diazepino[2,3-q]porphyrazinato(aquo)magnesium(ii)], [Bz3DzPzMg(H2O)]. The complex 3 can be demetalated in acetic or trifluoroacetic acids under mild conditions with formation of the corresponding free-base [Bz3DzPzH2] 3a. This latter is also formed by co-cyclotetramerization of the same precursors 1 and 2 in the presence of sodium ethoxide in ethanol or lithium butoxide in butanol followed by demetalation of the intermediate disodium or dilithium salts in acid medium. The constitution and structure of the obtained compounds were established on the basis of elemental analysis, mass spectrometry, and 1H NMR spectra. The variable temperature 1H NMR measurements provide evidence that in porphyrazines 3 and 3a the 1,4-diazepine ring exists predominantly in the 6H-form over a wide temperature range. The free energy of activation for the inversion of the 1,4-diazepine ring determined for 3 is 45.6 ± 1.7 kJ mol–1. Solution UV-visible spectra measurements in acidic media (CH2Cl2/CF3COOH) provide evidence that the MgII complex 3 is easily protonated on the meso-N atom of the porphyrazine macrocycle followed by slow demetallation with formation of the free base 3a in its neutral form or as a species protonated on the diazepine ring.
Cell–cell contact interactions conditionally determine suppression and selection of the neoplastic phenotype
Authors: Rubin Harry
Published: April 2008

Separation of chemical and physical carcinogenesis into the stages of initiation (mutation) and promotion (selection) established that incipient neoplastic cells could persist in the organism indefinitely without expression. Spontaneous mutations associated with cancer also lie dormant in untreated normal tissue. Without selection, there is no tumor development. Experiments in cell culture showed that confluent normal fibroblasts suppress growth of contacting transformed fibroblasts, and that normal keratinocytes similarly suppress tumor formation by adjacent papilloma cells. With cells that are generally more susceptible to transformation, however, prolonged contact inhibition progressively selects mutants that favor neoplastic growth. Selection of individual mutant cells allows them to become a significant fraction of the population and creates an enlarged target for additional genetic hits. Crucially, this enrichment step, not the initial mutation step, is the numerically limiting factor in tumor development. Unexpectedly, variants that are resistant to spontaneous transformation are selectedin vitroby growing cells for many low density passages at maximal exponential rate. Confluent cultures of resistant variants suppress the growth and normalize the morphology of contacting transformed cells. Varying the conditions for selection shows that tumorigenic transformation is preceded by intermediate steps of progressively higher saturation density that are increasingly permissive for the expression of the more neoplastic cells in the population. There is also evidence of increasing permissiveness with age of normal tissuesin vivofor solitary cancer cells transplanted in their midst. Spontaneous transformation in culture can be used to identify dietary components that are required for promotion and may therefore be applicable in prevention of human cancer.
Ephaptic conduction in a cardiac strand model with 3D electrodiffusion
Authors: Mori Yoichiro , Fishman Glenn I. , Peskin Charles S.
Published: April 2008

We study cardiac action potential propagation under severe reduction in gap junction conductance. We use a mathematical model of cellular electrical activity that takes into account both three-dimensional geometry and ionic concentration effects. Certain anatomical and biophysical parameters are varied to see their impact on cardiac action potential conduction velocity. This study uncovers quantitative features of ephaptic propagation that differ from previous studies based on one-dimensional models. We also identify a mode of cardiac action potential propagation in which the ephaptic and gap-junction-mediated mechanisms alternate. Our study demonstrates the usefulness of this modeling approach for electrophysiological systems especially when detailed membrane geometry plays an important role.
Molecular architecture of Gα
o
and the structural basis for RGS16-mediated deactivation
Authors: Slep Kevin C. , Kercher Michele A. , Wieland Thomas , Chen Ching-Kang , Simon Melvin I. , Sigler Paul B.
Published: April 2008

Heterotrimeric G proteins relay extracellular cues from heptahelical transmembrane receptors to downstream effector molecules. Composed of an α subunit with intrinsic GTPase activity and a βγ heterodimer, the trimeric complex dissociates upon receptor-mediated nucleotide exchange on the α subunit, enabling each component to engage downstream effector targets for either activation or inhibition as dictated in a particular pathway. To mitigate excessive effector engagement and concomitant signal transmission, the Gα subunit's intrinsic activation timer (the rate of GTP hydrolysis) is regulated spatially and temporally by a class of GTPase accelerating proteins (GAPs) known as the regulator of G protein signaling (RGS) family. The array of G protein-coupled receptors, Gα subunits, RGS proteins and downstream effectors in mammalian systems is vast. Understanding the molecular determinants of specificity is critical for a comprehensive mapping of the G protein system. Here, we present the 2.9 Å crystal structure of the enigmatic, neuronal G protein Gα
o
in the GTP hydrolytic transition state, complexed with RGS16. Comparison with the 1.89 Å structure of apo-RGS16, also presented here, reveals plasticity upon Gα
o
binding, the determinants for GAP activity, and the structurally unique features of Gα
o
that likely distinguish it physiologically from other members of the larger Gα
i
family, affording insight to receptor, GAP and effector specificity.
A yeast TDP-43 proteinopathy model: Exploring the molecular determinants of TDP-43 aggregation and cellular toxicity
Authors: Johnson Brian S. , McCaffery J. Michael , Lindquist Susan , Gitler Aaron D.
Published: April 2008

Protein misfolding is intimately associated with devastating human neurodegenerative diseases, including Alzheimer's, Huntington's, and Parkinson's. Although disparate in their pathophysiology, many of these disorders share a common theme, manifested in the accumulation of insoluble protein aggregates in the brain. Recently, the major disease protein found in the pathological inclusions of two of these diseases, amyotrophic lateral sclerosis (ALS) and frontal temporal lobar degeneration with ubiquitin-positive inclusions (FTLD-U), was identified as the 43-kDa TAR–DNA-binding protein (TDP-43), providing a molecular link between them. TDP-43 is a ubiquitously expressed nuclear protein that undergoes a pathological conversion to an aggregated cytoplasmic localization in affected regions of the nervous system. Whether TDP-43 itself can convey toxicity and whether its abnormal aggregation is a cause or consequence of pathogenesis remain unknown. We report a yeast model to define mechanisms governing TDP-43 subcellular localization and aggregation. Remarkably, this simple model recapitulates several salient features of human TDP-43 proteinopathies, including conversion from nuclear localization to cytoplasmic aggregation. We establish a connection between this aggregation and toxicity. The pathological features of TDP-43 are distinct from those of yeast models of other protein-misfolding diseases, such as polyglutamine. This suggests that the yeast model reveals specific aspects of the underlying biology of the disease protein rather than general cellular stresses associated with accumulating misfolded proteins. This work provides a mechanistic framework for investigating the toxicity of TDP-43 aggregation relevant to human disease and establishes a manipulable, high-throughput model for discovering potential therapeutic strategies.
Different Ubiquitin Signals Act at the Golgi and Plasma Membrane to Direct GAP1 Trafficking
Authors: Risinger April L. , Kaiser Chris A.
Published: April 2008

The high capacity general amino acid permease, Gap1p, in Saccharomyces cerevisiae is distributed between the plasma membrane and internal compartments according to availability of amino acids. When internal amino acid levels are low, Gap1p is localized to the plasma membrane where it imports available amino acids from the medium. When sufficient amino acids are imported, Gap1p at the plasma membrane is endocytosed and newly synthesized Gap1p is delivered to the vacuole; both sorting steps require Gap1p ubiquitination. Although it has been suggested that identical trans-acting factors and Gap1p ubiquitin acceptor sites are involved in both processes, we define unique requirements for each of the ubiquitin-mediated sorting steps involved in delivery of Gap1p to the vacuole upon amino acid addition. Our finding that distinct ubiquitin-mediated sorting steps employ unique trans-acting factors, ubiquitination sites on Gap1p, and types of ubiquitination demonstrates a previously unrecognized level of specificity in ubiquitin-mediated protein sorting.
UNC-108/Rab2 Regulates Postendocytic Trafficking inCaenorhabditis elegans
Authors: Chun Denise K. , McEwen Jason M. , Burbea Michelle , Kaplan Joshua M.
Published: April 2008

After endocytosis, membrane proteins are often sorted between two alternative pathways: a recycling pathway and a degradation pathway. Relatively little is known about how trafficking through these alternative pathways is differentially regulated. Here, we identify UNC-108/Rab2 as a regulator of postendocytic trafficking in both neurons and coelomocytes. Mutations in the Caenorhabditis elegans Rab2 gene unc-108, caused the green fluorescent protein (GFP)-tagged glutamate receptor GLR-1 (GLR-1::GFP) to accumulate in the ventral cord and in neuronal cell bodies. In neuronal cell bodies of unc-108/Rab2 mutants, GLR-1::GFP was found in tubulovesicular structures that colocalized with markers for early and recycling endosomes, including Syntaxin-13 and Rab8. GFP-tagged Syntaxin-13 also accumulated in the ventral cord of unc-108/Rab2 mutants. UNC-108/Rab2 was not required for ubiquitin-mediated sorting of GLR-1::GFP into the multivesicular body (MVB) degradation pathway. Mutations disrupting the MVB pathway and unc-108/Rab2 mutations had additive effects on GLR-1::GFP levels in the ventral cord. In coelomocytes, postendocytic trafficking of the marker Texas Red-bovine serum albumin was delayed. These results demonstrate that UNC-108/Rab2 regulates postendocytic trafficking, most likely at the level of early or recycling endosomes, and that UNC-108/Rab2 and the MVB pathway define alternative postendocytic trafficking mechanisms that operate in parallel. These results define a new function for Rab2 in protein trafficking.
Global Regulation of the Interphase Microtubule System by Abundantly Expressed Op18/Stathmin
Authors: Sellin Mikael E. , Holmfeldt Per , Stenmark Sonja , Gullberg Martin
Published: April 2008

Op18/stathmin (Op18), a conserved microtubule-depolymerizing and tubulin heterodimer-binding protein, is a major interphase regulator of tubulin monomer–polymer partitioning in diverse cell types in which Op18 is abundant. Here, we addressed the question of whether the microtubule regulatory function of Op18 includes regulation of tubulin heterodimer synthesis. We used two human cell model systems, K562 and Jurkat, combined with strategies for regulatable overexpression or depletion of Op18. Although Op18 depletion caused extensive overpolymerization and increased microtubule content in both cell types, we did not detect any alteration in polymer stability. Interestingly, however, we found that Op18 mediates positive regulation of tubulin heterodimer content in Jurkat cells, which was not observed in K562 cells. By analysis of cells treated with microtubule-poisoning drugs, we found that Jurkat cells regulate tubulin mRNA levels by a posttranscriptional mechanism similarly to normal primary cells, whereas this mechanism is nonfunctional in K562 cells. We present evidence that Op18 mediates posttranscriptional regulation of tubulin mRNA in Jurkat cells through the same basic autoregulatory mechanism as microtubule-poisoning drugs. This, combined with potent regulation of tubulin monomer–polymer partitioning, enables Op18 to exert global regulation of the microtubule system.
Aurora A Phosphorylates MCAK to Control Ran-dependent Spindle Bipolarity
Authors: Zhang Xin , Ems-McClung Stephanie C. , Walczak Claire E.
Published: April 2008

During mitosis, mitotic centromere-associated kinesin (MCAK) localizes to chromatin/kinetochores, a cytoplasmic pool, and spindle poles. Its localization and activity in the chromatin region are regulated by Aurora B kinase; however, how the cytoplasmic- and pole-localized MCAK are regulated is currently not clear. In this study, we used Xenopus egg extracts to form spindles in the absence of chromatin and centrosomes and found that MCAK localization and activity are tightly regulated by Aurora A. This regulation is important to focus microtubules at aster centers and to facilitate the transition from asters to bipolar spindles. In particular, we found that MCAK colocalized with NuMA and XMAP215 at the center of Ran asters where its activity is regulated by Aurora A-dependent phosphorylation of S196, which contributes to proper pole focusing. In addition, we found that MCAK localization at spindle poles was regulated through another Aurora A phosphorylation site (S719), which positively enhances bipolar spindle formation. This is the first study that clearly defines a role for MCAK at the spindle poles as well as identifies another key Aurora A substrate that contributes to spindle bipolarity.
RNAplex: a fast tool for RNA–RNA interaction search
Authors: Tafer Hakim , Hofacker Ivo L.
Published: April 2008

Motivation: Regulatory RNAs often unfold their action via RNA-RNA interaction. Transcriptional gene silencing by means of siRNAs and miRNA as well as snoRNA directed RNA editing rely on this mechanism. Additionally ncRNA regulation in bacteria is mainly based upon RNA duplex formation. Finding putative target sites for newly discovered ncRNAs is a lengthy task as tools for cofolding RNA molecules like RNAcofold and RNAup are too slow for genome-wide search. Tools like RNAhybrid that neglects intramolecular interactions have runtimes proportional to 𝒪(m · n), albeit with a large prefactor. Still in many cases the need for even faster methods exists.

Results: We present a new program, RNAplex, especially designed to quickly find possible hybridization sites for a query RNA in large RNA databases. RNAplex uses a slightly different energy model which reduces the computational time by a factor 10–27 compared to RNAhybrid. In addition a length penalty allows to focus the target search on short highly stable interactions.

Availability: RNAplex can be downloaded at http://www.tbi.univie.ac.at/~htafer/

Contact:  ivo@tbi.univie.ac.at

Supplementary information:  Supplementary data are available at Bioinformatics online.
William Maxwell Cowan. 27 September 1931 — 30 June 2002
Authors: Raisman Geoffrey
Published: April 2008

William Maxwell Cowan (‘Max’) was born in 1931 in Johannesburg. His father was a former Glasgow shipyard engineer driven by the imminent closure of the Clyde shipyards to seek employment in the mining industry in South Africa. Max's parents had intended him to be a real–estate lawyer. However, after taking the initial courses in languages, economics and history at Witwatersrand University, a short vacation work period as a trainee nurse in a psychiatric hospital had aroused what was to be his lifelong interest in the workings of the brain. Max decided he wanted to transfer to medical school.
Studying the effect of cell division on expression patterns of the segment polarity genes
Authors: Chaves Madalena , Albert Réka
Published: April 2008

The segment polarity gene family, and its gene regulatory network, is at the basis ofDrosophilaembryonic development. The network's capacity for generating and robustly maintaining a specific gene expression pattern has been investigated through mathematical modelling. The models have provided several useful insights by suggesting essential network links, or uncovering the importance of the relative time scales of different biological processes in the formation of the segment polarity genes' expression patterns. But the developmental pattern formation process raises many other questions. Two of these questions are analysed here: the dependence of the signalling protein sloppy paired on the segment polarity genes and the effect of cell division on the segment polarity genes' expression patterns. This study suggests that cell division increases the robustness of the segment polarity network with respect to perturbations in biological processes.
Mutagenesis in eukaryotes dependent on DNA polymerase zeta and Rev1p
Authors: Lawrence Christopher W. , Maher Veronica M.
Published: April 2008

DNA polymerase zeta (Pol ζ) and Rev1p carry out translesion replication in budding yeast,Saccharomyces cerevisiae, and are jointly responsible for almost all base pair substitution and frameshift mutations induced by DNA damage in this organism. In addition, Pol ζ is responsible for the majority of spontaneous mutations in yeast and has been proposed as the enzyme responsible for somatic hypermutability. Pol ζ, a non–processive enzyme that lacks a 3' to 5' exonuclease proofreading activity, is composed of Rev3p, the catalytic subunit, and a second subunit encoded byREV7. In keeping with its role, extension by Pol ζ is relatively tolerant of abnormal DNA structure at the primer terminus and is much more capable of extension from terminal mismatches than yeast DNA polymerase alpha (Pol α). Rev1p is a bifunctional enzyme that possesses a deoxycytidyl transferase activity that incorporates deoxycytidyl opposite abasic sites in the template and a second, at present poorly defined, activity that is required for the bypass of a variety of lesions as well as abasic sites. Human homologues of the yeastREV1andREV3have been identified and, based on the phenotype of cells producing antisense RNA to one or other of these genes, their products appear also to be employed in translation replication and spontaneous mutagenesis. We suggest that Pol ζ is best regarded as a replication enzyme, albeit one that is used only intermittently, that promotes extension at forks the progress of which is blocked for any reason, whether the presence of an unedited terminal mismatch or unrepaired DNA lesion.
Simian homologues of Epstein–Barr virus
Authors: Wang Fred , Rivailler Pierre , Rao Pasupuleti , Cho Young-gyu
Published: April 2008

γ–Herpesviruses closely related to the Epstein–Barr virus (EBV) are known to naturally infect Old World non–human primates and are classified in the same lymphocryptovirus (LCV) genera. LCV infecting humans and Old World primates share similar biology, and recent studies have demonstrated that these viruses share a similar repertoire of viral genes. Surprisingly, the latent infection genes associated with cell growth transformation demonstrate the most striking sequence divergence, but the functional mechanisms for these genes are generally well conserved. The recent discovery of LCVs naturally infecting New World primates has rewritten the old paradigm of LCV host range restriction to humans and Old World non–human primates, so that these viruses are more widespread than previously believed. However, the New World LCV genome has significant and interesting differences from EBV and other Old World LCVs despite similar biological properties. Thus, the simian homologues of EBV can provide an important animal model for studying LCV pathogenesis, and the similarities and differences that have evolved among these related viruses can provide a unique perspective towards a better understanding of EBV.
Quantitative genetic studies of antisocial behaviour
Authors: Viding Essi , Larsson Henrik , Jones Alice P
Published: April 2008

This paper will broadly review the currently available twin and adoption data on antisocial behaviour (AB). It is argued that quantitative genetic research can make a significant contribution to further the understanding of how AB develops. Genetically informative study designs are particularly useful for investigating several important questions such as whether: the heritability estimates vary as a function of assessment method or gender; the relative importance of genetic and environmental influences varies for different types of AB; the environmental risk factors are truly environmental; and genetic vulnerability influences susceptibility to environmental risk. While the current data are not yet directly translatable for prevention and treatment programmes, quantitative genetic research has concrete translational potential. Quantitative genetic research can supplement neuroscience research in informing about different subtypes of AB, such as AB coupled with callous–unemotional traits. Quantitative genetic research is also important in advancing the understanding of the mechanisms by which environmental risk operates.
Mycobacterium tuberculosis co-existence with humans: making an imprint on the macrophage P2X7 receptor gene?
Authors: Mokrousov Igor , Sapozhnikova Nadezhda , Narvskaya Olga
Published: April 2008

The development of tuberculosis (TB) infection in humans depends on the mycobacterial strain and the human host, and is multigenically controlled in both. ATP ligation of P2X7receptors expressed on human macrophages infected with mycobacteria induces cell death and subsequent loss of intracellular bacterial viability. This study analysed the allelic distribution of two single-nucleotide polymorphisms (SNPs) in theP2RX7gene in the Slavic population of the St Petersburg area of Russia. Analysis of the −762 C/TP2RX7promoter SNP revealed no significant association between pulmonary TB patients and control subjects (3×2χ2=3.2, 1 d.f.,P=0.2). The −762C allele was highly and almost equally represented in both groups in this study (68.2 % in patients and 69.3 % in controls). This result differs strikingly from a Gambian study where this allele was found in only 7 and 12 % of pulmonary TB patients and controls, respectively [Li, C. M., Campbell, S. J., Kumararatne, D. S., Bellamy, R., Ruwende, C., McAdam, K. P. W. J., Hill, A. V. S. & Lammas, D. A. (2002).J Infect Dis186, 1458–1462]. In contrast, the frequency of the C allele at position 1513 in exon 13, resulting in a loss of P2X7function, was significantly higher among pulmonary TB patients in this study (P=0.02). Thus, analysis of the P2X7receptor gene in the Russian Slavic population showed that the 1513C allele, acting dominantly, is a possible risk factor for clinical TB, whereas the −762P2RX7polymorphism did not appear to be associated with human susceptibility to TB.
Selective antimicrobial activity of maggots against pathogenic bacteria
Authors: Jaklič Domen , Lapanje Aleš , Zupančič Klemen , Smrke Dragica , Gunde-Cimerman Nina
Published: April 2008

Maggot therapy, also known as biosurgery, is an ancient method for the healing of chronic infected wounds. Although clinicians have reported on the beneficial activities of the Lucilia sericata larvae that have been used for healing chronic wounds, the selectivity of this therapy against the different pathogenic micro-organisms that are found in chronic wounds has never been analysed. In the present study, we have investigated the in vitro activities of larval excreta/secreta both against selected bacterial strains that frequently occur in chronically infected wounds, and against bacteria isolated directly from the larvae and their excreta/secreta. Additionally, the antibacterial activities were investigated in in vivo studies, by comparing bacterial diversity in wounds before and after the application of L. sericata larvae. In conclusion, larval therapy is highly recommended, particularly for the treatment of wounds infected with Gram-positive bacteria, like Staphylococcus aureus, but less so for wounds infected with Gram-negative bacteria, especially Proteus spp. and Pseudomonas spp. strains. Bacteria from the genus Vagococcus were resistant to the maggot excreta/secreta.
Mycobacterium chelonae empyema in an immunocompetent patient
Authors: Hsieh Hsiao-Cheng , Lu Po-Liang , Chen Tun-Chieh , Chang Ko , Chen Yen-Hsu
Published: April 2008

Thoracic empyema caused by rapidly growing mycobacteria (RGM) and complicated with bronchopleural fistula is rarely reported, especially in immunocompetent patients. A 53-year-old healthy woman presented initially with a productive cough and intermittent fever. The patient received a complete treatment course following an initial diagnosis of pulmonary tuberculosis. After the anti-tuberculosis agents were discontinued, a right thoracic empyema with bronchopleural fistula occurred, and the pathogens from both pus and sputum were identified as Mycobacterium chelonae. Thoracotomy with decortication and wedge resection of the right middle lung was performed, followed by clarithromycin plus ciprofloxacin therapy for 36 months. This patient has not suffered a relapse in the last 3 years. In addition to the experience of successful treatment, this case indicates that RGM such as M. chelonae can emerge as causative pathogens of thoracic empyema, even in healthy persons.
Molecular diagnosis of sepsis in neutropenic patients with haematological malignancies
Authors: Mancini Nicasio , Clerici Daniela , Diotti Roberta , Perotti Mario , Ghidoli Nadia , De Marco Donata , Pizzorno Beatrice , Emrich Thomas , Burioni Roberto , Ciceri Fabio , Clementi Massimo
Published: April 2008

The rapid diagnosis of an infectious cause in the course of fever of unknown origin plays a pivotal role in the correct management of neutropenic patients. In this study, blood samples from febrile oncohaematological patients were tested using a novel commercial real-time PCR assay (LightCycler SeptiFast; Roche Molecular Systems) and blood culture (BacT/Alert 3D; bioMérieux). Twenty-one (20.4 %) and 34 (33 %) of the 103 samples under study tested positive by blood culture and PCR, respectively. The analysis of concordance evidenced a low correlation between the two approaches (83 %), mainly due to samples that tested negative by culture but positive using the molecular approach. Among 14 discordant cases negative by culture but positive by PCR, 12 were observed in sequential samples of patients with initial concordant results on samples drawn before the administration of a specific antimicrobial therapy. Moreover, DNA of a fastidious organism, Aspergillus fumigatus, not easily detectable by the cultural approach was rapidly detected in the two remaining discordant cases. Overall, the characteristics featured by the molecular method could be of interest in the development of new algorithms for the diagnosis of sepsis in critical patients.
Distribution of spa types among meticillin-resistant Staphylococcus aureus isolates during a 6 year period at a low-prevalence university hospital
Authors: Fenner Lukas , Widmer Andreas F. , Dangel Marc , Frei Reno
Published: April 2008

This study describes the distribution and frequencies of strain types by protein A-encoding gene (spa) typing among a total of 200 meticillin-resistant Staphylococcus aureus (MRSA) single-patient isolates collected between 2000 and 2005 at the University Hospital Basel, Switzerland. Nine frequent spa types accounted for 49.5 % of MRSA isolates, whereas spa type t041 (15 % of all isolates) belonged to a local epidemic strain that is also a common strain type in southern Germany. Successful control of the outbreak strain was documented by epidemiological data and confirmed by spa typing results. The spa type t044 (3.5 %), corresponding to a widely disseminated European community-acquired MRSA (CA-MRSA), was first observed in 2002. The well-known CA-MRSA USA300 clone was detected in four patients (2 %). Sporadic strains occurring less than four times (32 different spa types) accounted for 23 % of isolates. No predominant spa type was seen, indicating a great genetic diversity. Only 34.5 % of patient isolates were acquired nosocomially. The presence of one or more of ten common virulence genes was shown in 79 % of strains. It was demonstrated that the sequence-based spa typing method allows analysis of local MRSA epidemiology in relation to other regions and countries over time.