bluuebunny/crossref_metadata_2025 huggingface dataset:
Physical and functional interactions between MutY glycosylase homologue (MYH) and checkpoint proteins Rad9–Rad1–Hus1
Authors: Shi Guoli , Chang Dau-Yin , Cheng Chih-Chien , Guan Xin , Venclovas Česlovas , Lu A-Lien
Published: October 2006

The MYH (MutY glycosylase homologue) increases replication fidelity by removing adenines or 2-hydroxyadenine misincorporated opposite GO (7,8-dihydro-8-oxo-guanine). The 9-1-1 complex (Rad9, Rad1 and Hus1 heterotrimer complex) has been suggested as a DNA damage sensor. Here, we report that hMYH (human MYH) interacts with hHus1 (human Hus1) and hRad1 (human Rad1), but not with hRad9. In addition, interactions between MYH and the 9-1-1 complex, from both the fission yeast Schizosaccharomyces pombe and human cells, are partially interchangeable. The major Hus1-binding site is localized to residues 295–350 of hMYH and to residues 245–293 of SpMYH (S. pombe MYH). Val315 of hMYH and Ile261 of SpMYH play important roles for their interactions with Hus1. hHus1 protein and the 9-1-1 complex of S. pombe can enhance the glycosylase activity of SpMYH. Moreover, the interaction of hMYH–hHus1 is enhanced following ionizing radiation. A significant fraction of the hMYH nuclear foci co-localizes with hRad9 foci in H2O2-treated cells. These results reveal that the 9-1-1 complex plays a direct role in base excision repair.
GTP in the mitochondrial matrix plays a crucial role in organellar iron homoeostasis
Authors: Gordon Donna M. , Lyver Elise R. , Lesuisse Emmanuel , Dancis Andrew , Pain Debkumar
Published: October 2006

Mitochondria are the major site of cellular iron utilization for the synthesis of essential cofactors such as iron–sulfur clusters and haem. In the present study, we provide evidence that GTP in the mitochondrial matrix is involved in organellar iron homoeostasis. A mutant of yeast Saccharomyces cerevisiae lacking the mitochondrial GTP/GDP carrier protein (Ggc1p) exhibits decreased levels of matrix GTP and increased levels of matrix GDP [Vozza, Blanco, Palmieri and Palmieri (2004) J. Biol. Chem. 279, 20850–20857]. This mutant (previously called yhm1) also manifests high cellular iron uptake and tremendous iron accumulation within mitochondria [Lesuisse, Lyver, Knight and Dancis (2004) Biochem. J. 378, 599–607]. The reason for these two very different phenotypic defects of the same yeast mutant has so far remained elusive. We show that in vivo targeting of a human nucleoside diphosphate kinase (Nm23-H4), which converts ATP into GTP, to the matrix of ggc1 mutants restores normal iron regulation. Thus the role of Ggc1p in iron metabolism is mediated by effects on GTP/GDP levels in the mitochondrial matrix.
Man2C1, an α-mannosidase, is involved in the trimming of free oligosaccharides in the cytosol
Authors: Suzuki Tadashi , Hara Izumi , Nakano Miyako , Shigeta Masaki , Nakagawa Takatoshi , Kondo Akihiro , Funakoshi Yoko , Taniguchi Naoyuki
Published: October 2006

The endoplasmic-reticulum-associated degradation of misfolded (glyco)proteins ensures that only functional, correctly folded proteins exit from the endoplasmic reticulum and that misfolded ones are degraded by the ubiquitin–proteasome system. During the degradation of misfolded glycoproteins, they are deglycosylated by the PNGase (peptide:N-glycanase). The free oligosaccharides released by PNGase are known to be further catabolized by a cytosolic α-mannosidase, although the gene encoding this enzyme has not been identified unequivocally. The findings in the present study demonstrate that an α-mannosidase, Man2C1, is involved in the processing of free oligosaccharides that are formed in the cytosol. When the human Man2C1 orthologue was expressed in HEK-293 cells, most of the enzyme was localized in the cytosol. Its activity was enhanced by Co2+, typical of other known cytosolic α-mannosidases so far characterized from animal cells. The down-regulation of Man2C1 activity by a small interfering RNA drastically changed the amount and structure of oligosaccharides accumulating in the cytosol, demonstrating that Man2C1 indeed is involved in free oligosaccharide processing in the cytosol. The oligosaccharide processing in the cytosol by PNGase, endo-β-N-acetylglucosaminidase and α-mannosidase may represent the common ‘non-lysosomal’ catabolic pathway for N-glycans in animal cells, although the molecular mechanism as well as the functional importance of such processes remains to be determined.
Driving frequency effect on electron heating mode transition in capacitive discharge
Authors: You S. J. , Ahn S. K. , Chang H. Y.
Published: October 2006

A study was conducted on the dependence of the electron heating mode transition upon driving frequency in capacitive discharge. The evolution of the electron energy distribution functions (EEDFs) over a wide range of gas pressures was investigated at different driving frequencies. Regardless of the driving frequency, the measured EEDFs exhibited a typical evolution of EEDF from bi-Maxwellian distribution to Druyvesteyn-like distribution with gas pressure, signifying the electron heating mode transition from collisionless to collisional heating. However, the gas pressure, which the heating mode transition takes place, significantly decreased as the driving frequency increased. This result is ascribed to the fact that the collisionless stochastic heating becomes inefficient at high frequency compared with collisional heating.
Magnetic properties of cobalt ferrite–silica nanocomposites prepared by a sol-gel autocombustion technique
Authors: Cannas C. , Musinu A. , Piccaluga G. , Fiorani D. , Peddis D. , Rasmussen H. K. , Mørup S.
Published: October 2006

The magnetic properties of cobalt ferrite–silica nanocomposites with different concentrations (15, 30, and 50wt%) and sizes (7, 16, and 28nm) of ferrite particles have been studied by static magnetization measurements and Mössbauer spectroscopy. The results indicate a superparamagnetic behavior of the nanoparticles, with weak interactions slightly increasing with the cobalt ferrite content and with the particle size. From high-field Mössbauer spectra at low temperatures, the cationic distribution and the degree of spin canting have been estimated and both parameters are only slightly dependent on the particle size. The magnetic anisotropy constant increases with decreasing particle size, but in contrast to many other systems, the cobalt ferrite nanoparticles are found to have an anisotropy constant that is smaller than the bulk value. This can be explained by the distribution of the cations. The weak dependence of spin canting degree on particle size indicates that the spin canting is not simply a surface phenomenon but also occurs in the interiors of the particles.
Surface reconstructions of cubic gallium nitride (001) grown by radio frequency nitrogen plasma molecular beam epitaxy under gallium-rich conditions
Authors: Haider Muhammad B. , Yang Rong , Constantin Costel , Lu Erdong , Smith Arthur R. , Al-Brithen Hamad A. H.
Published: October 2006

Cubic GaN has been grown under gallium (Ga)-rich growth conditions using radio frequency nitrogen plasma molecular beam epitaxy on MgO(001) substrates. Reflection high energy electron diffraction patterns indicate the smoothness of the c-GaN surface and show 2× and even 8× periodicities after the growth at sample temperature Ts<200°C and 1×1 at higher temperatures. Scanning tunneling microscopy images reveal a sequence of variant surface reconstructions including c(4×12), 4×7, c(4×16), 4×9, c(4×20), and 4×11. These variant reconstructions correspond to slightly different Ga adatom coverages all less than 1∕4 ML, with 4×11 having the highest, and c(4×12) the lowest Ga coverage. The electronic properties of these six variant reconstructions are investigated, and they are found to have a metallic nature.
Spectroscopy of isolated, mass-selected tryptophan-Ag3 complexes: A model for photoabsorption enhancement in nanoparticle-biomolecule hybrid systems
Authors: Compagnon Isabelle , Tabarin Thibault , Antoine Rodolphe , Broyer Michel , Dugourd Philippe , Mitrić Roland , Petersen Jens , Bonačić-Koutecký Vlasta
Published: October 2006

We wish to show that gas-phase studies of small metal cluster-biomolecule complexes provide fundamental insights into the mechanism leading to enhanced optical absorption in nanoparticle-biomolecular hybrid systems. Here we present, for the first time, a joint experimental and theoretical study of photoabsorption and photofragmentation of the silver trimer-tryptophan cation complex ([Trp∙Ag3]+). We demonstrate that binding the metal cluster to a biomolecule leads to a remarkably high optical absorption as compared to the bare tryptophan or the [Trp∙Ag]+ complex. As calculations show this arises due to coupling between the excitations in the metallic subunit with a charge transfer excitation to the tryptophan molecule.
Influence of atomistic physics on electro-osmotic flow: An analysis based on density functional theory
Authors: Nilson Robert H. , Griffiths Stewart K.
Published: October 2006

Molecular density profiles and charge distributions determined by density functional theory (DFT) are used in conjunction with the continuum Navier-Stokes equations to compute electro-osmotic flows in nanoscale channels. The ion species of the electrolyte are represented as centrally charged hard spheres, and the solvent is treated as a dense fluid of neutral hard spheres having a uniform dielectric constant. The model explicitly accounts for Lennard-Jones interactions among fluid and wall molecules, hard sphere repulsions, and short range electrical interactions, as well as long range Coulombic interactions. Only the last of these interactions is included in classical Poisson-Boltzmann (PB) modeling of the electric field. Although the proposed DFT approach is quite general, the sample calculations presented here are limited to symmetric monovalent electrolytes. For a prescribed surface charge, this DFT model predicts larger counterion concentrations near charged channel walls, relative to classical PB modeling, and hence smaller concentrations in the channel center. This shifting of counterions toward the walls reduces the effective thickness of the Debye layer and reduces electro-osmotic velocities as compared to classical PB modeling. Zeta potentials and fluid speeds computed by the DFT model are as much as two or three times smaller than corresponding PB results. This disparity generally increases with increasing electrolyte concentration, increasing surface charge density and decreasing channel width. The DFT results are found to be comparable to those obtained by molecular dynamics simulation, but require considerably less computing time.
Fiber-top atomic force microscope
Authors: Iannuzzi D. , Deladi S. , Berenschot J. W. , de Man S. , Heeck K. , Elwenspoek M. C.
Published: October 2006

We present the implementation of an atomic force microscope (AFM) based on fiber-top design. Our results demonstrate that the performances of fiber-top AFMs in contact mode are comparable to those of similar commercially available instruments. Our device thus represents an interesting alternative to existing AFMs, particularly for applications outside specialized research laboratories, where a compact, user-friendly, and versatile tool might often be preferred.
Elastomeric carbon nanotube circuits for local strain sensing
Authors: Maune Hareem , Bockrath Marc
Published: October 2006

The authors use elastomeric polydimethylsiloxane substrates to strain single-walled carbon nanotubes and modulate their electronic properties, with the aim of developing flexible materials that can sense their local strain. They demonstrate micron-scale nanotube devices that can be cycled repeatedly through strains as high as 20% while providing reproducible local strain transduction via the device resistance. They also compress individual nanotubes and find that they undergo an undulatory distortion with a characteristic spatial period of 100–200nm, in agreement with continuum elasticity theory. These could potentially be used to create quantum-well superlattices within individual nanotubes, enabling novel devices and applications.
Min-map bias Monte Carlo for chain molecules: Biased Monte Carlo sampling based on bijective minimum-to-minimum mapping
Authors: Laso Manuel , Karayiannis Nikos Ch. , Müller Matthias
Published: October 2006

A novel Monte Carlo (MC) simulation scheme based on Theodorou’s bijective mapping strategy [D. N. Theodorou, J. Chem. Phys. 124, 034109 (2006)] is introduced. This min-map bias Monte Carlo acts in combination with any other proper, bare MC. It carries over the bare MC move from the original configuration space Ω(0), where trial move acceptance may be low, to a different configuration space, Ω(1), where acceptance is higher. The bare MC move is then performed in Ω(1) and the resulting configuration is finally mapped back to Ω(0). Mappings between Ω(0) and Ω(1) entail weighted selection of trial configurations, the bias of which is subsequently removed in the overall acceptance criterion. The new method is applied, in conjunction with continuum configurational bias as bare MC scheme, to the simulation of explicit hydrogen linear alkanes in the canonical ensemble. Min-map bias MC is found to alleviate the pervasive problem of very low acceptance rates encountered when using an explicit molecular description.
Core level and valence band photoemission spectra of Au clusters embedded in carbon
Authors: Takahiro K. , Oizumi S. , Terai A. , Kawatsura K. , Tsuchiya B. , Nagata S. , Yamamoto S. , Naramoto H. , Narumi K. , Sasase M.
Published: October 2006

X-ray photoelectron spectroscopy (XPS) has been applied for size estimation of Au clusters formed by ion implantation into glassy carbon. The 4f and 5d XPS spectra reveal the presence of the cluster 0.7–2.5nm in diameter, depending on the Au concentration. The relationship between XPS 4f-binding energy shift and 5d splitting is determined for the Au clusters embedded in the carbon and found to be significantly different from the previous data for the ones supported on a carbon substrate. We suppose that this difference results from the effect of the environment around a cluster on Coulomb charging during photoemission at the final state.
Femtosecond pump-probe spectroscopy of intersubband relaxation dynamics in narrow InGaAs∕AlAsSb quantum well structures
Authors: Tribuzy C. V.-B. , Ohser S. , Winnerl S. , Grenzer J. , Schneider H. , Helm M. , Neuhaus J. , Dekorsy T. , Biermann K. , Künzel H.
Published: October 2006

Intersubband relaxation dynamics in InGaAs∕AlAsSb multiquantum wells (QWs) is studied by single-color femtosecond pump-probe measurements. At early delay times, all samples show an exponential decay of the transient transmission occurring with time constants of the order of a picosecond. The relaxation dynamics at later delay times strongly depend on both QW thickness and doping location. A non-single-exponential decay behavior indicates extra competing relaxation channels, as further confirmed by solving three-level rate equations. It is shown that slowly decaying components are due to electron transfer to states related to indirect valleys in the wells or in the barriers.
The melting temperature of the six site potential model of water
Authors: Abascal José L. F. , Fernández Ramón García , Vega Carlos , Carignano Marcelo A.
Published: October 2006

The melting temperature of the six site potential of water is calculated using two different methods. The first one combines free energy calculations with Hamiltonian Gibbs-Duhem integration. The second method is based on the evolution (melting or freezing) of an explicit liquid-ice interface. Both methods yield very similar results, so we propose 289K as the melting temperature of the model.
Self-consistent theory of unipolar charge-carrier injection in metal∕insulator∕metal systems
Authors: Neumann F. , Genenko Y. A. , Melzer C. , von Seggern H.
Published: October 2006

A consistent device model to describe current-voltage characteristics of metal∕insulator∕metal systems is developed. In this model the insulator and the metal electrodes are described within the same theoretical framework using density of states distributions. This approach leads to differential equations for the electric field which have to be solved in a self-consistent manner by considering the continuity of the electric displacement and the electrochemical potential in the complete system. The model is capable of describing the current-voltage characteristics of the metal∕insulator∕metal system in forward and reverse biases for arbitrary values of the metal∕insulator injection barriers. In the case of high injection barriers, approximations are provided offering a tool for comparison with experiments. Numerical calculations are performed exemplarily using a simplified model of an organic semiconductor.
Interaction between amorphous silicon nanoclusters and neodymium ions
Authors: MacDonald A. N. , Hryciw A. , Lenz F. , Meldrum A.
Published: October 2006

The luminescent infrared transitions in Nd3+ can be activated via a transfer mechanism from amorphous silicon nanoclusters. The Nd photoluminescence (PL) has some unusual characteristics, including a weak temperature dependence of the PL intensity. The data are explained using a simple rate equation model which enables an effective nanocluster-to-neodymium transfer time of ∼0.15μs to be extracted. This is short enough to dominate the intrinsic nanocluster decay rates at low temperatures but long enough to imply that the coupling between the nanoclusters and the Nd ions is, in fact, weaker than for Nd-doped bulk silicon or other semiconductors.
On the thermodynamic modeling of the isosteric heat of adsorption and comparison with experiments
Authors: Chakraborty A. , Saha B. B. , Koyama S. , Ng K. C.
Published: October 2006

A theoretical framework for the estimation of the isosteric heat of adsorption between an adsorbate (vapor) and an adsorbent (solid) is proposed based on the thermodynamic requirements of chemical equilibrium, Maxwell relations, and the entropy of the adsorbed phase. The derived equation for the isosteric heat of adsorption is verified against three sets of judiciously selected adsorbent+adsorbate data that are found in the literature and the predictions are found to agree within the experimental uncertainties of the reported data.
Silicate layer formation at HfO2/SiO2/Si interface determined by x-ray photoelectron spectroscopy and infrared spectroscopy
Authors: He G. , Zhang L. D. , Fang Q.
Published: October 2006

A high-k Hf-silicate interfacial layer grown by the solid phase reaction between sputtered metallic Hf films and an underlying SiO2/Si substrate through in situ vacuum annealing and subsequent thermal oxidation has been investigated. By means of the chemical shifts of Si 2p, Hf 4f, and O 1s core-level spectra determined by x-ray photoelectron spectroscopy (XPS), the formation of an interfacial Si-O-Si bond as the dominant reaction during in situ thermal oxidation of the Hf/SiO2/Si gate stack has been confirmed. In situ vacuum anneals without air exposure at 700 °C accelerates the interface reaction and results in the formation of Si-rich Hf-silicate interfacial layer. Analysis by Fourier transform infrared spectroscopy (FTIR) has indicated that vacuum annealed samples containing the silicate interface layer effectively suppresses the growth of the interfacial SiOx layer compared to unannealed samples during postdeposition annealing.
Probing the population inversion in intersubband laser by magnetic field spectroscopy
Authors: Semtsiv M. P. , Dressler S. , Masselink W. T. , Fedorov G. , Smirnov D.
Published: October 2006

The magnetic field dependence of the midinfrared quantum-cascade laser emission spectra is used to identify the particular Wannier-Stark states responsible for the laser action in two different laser designs. The active regions in both quantum-cascade lasers are based on a modified bound-to-continuum design, but have differing degrees of coupling between the injector miniband and the bound state. The effects of the magnetic field and the injection-barrier width on the emission wavelength indicate that the laser emission in the quantum-cascade laser with less coupling between the injector and the bound state originates from a transition between the injector and extractor minibands. The transition from injector miniband to extractor miniband has both a lower energy and a lower oscillator strength than the transition originating from the bound state, but dominates because of the low population of the upper bound state. This result has important implications for further miniband engineering of quantum-cascade-laser active regions for laser action at the shortest possible wavelengths.
Titanium nanostructural surface processing for improved biocompatibility
Authors: Cheng Hsin-Chung , Lee Sheng-Yang , Chen Chang-Chih , Shyng Yih-Chuen , Ou Keng-Liang
Published: October 2006

X-ray photoelectron spectroscopy, grazing incident x-ray diffraction, transmission electron microscopy, and scanning electron microscopy were conducted to evaluate the effect of titanium hydride on the formation of nanoporous TiO2 on Ti during anodization. Nano-titanium-hydride was formed cathodically before anodizing and served as a sacrificial nanoprecipitate during anodization. Surface oxidation occurred and a multinanoporous structure formed after cathodic pretreatments followed by anodization treatment. The sacrificial nanoprecipitate is directly dissolved and the Ti transformed to nanoporous TiO2 by anodization. The formation of sacrificial nanoprecipitates by cathodic pretreatment and of the multinanostructure by anodization is believed to improve biocompatibility, thereby promoting osseointegration.
Electro-optic interband excitonic absorption of nanoring double quantum wells
Authors: Guo X. G. , Cao J. C.
Published: October 2006

The excitonic absorption spectra of nanoring double quantum wells (NDQWs) subjected to radial and lateral electric fields are theoretically investigated. The electro-optic excitonic absorption spectra show very different behaviors for different electric-field configurations. The evolution of the main excitonic peaks of the NDQW with the radial electric fields is similar with that of square double quantum wells. Since the circular symmetry of the NDQW is not destroyed, the absorption peaks associated with ring structure are insensitive to the radial electric fields. However, because of the loss of such symmetry, these absorption peaks are broadened into continuum even at low lateral electric fields. Meanwhile, due to the exciton ionization and the inhomogeneous electric-field effect, the main excitonic peaks are intensively broadened and reduced by the lateral electric fields.
Elastic, piezoelectric, and dielectric properties of tetragonal Pb(Mg1∕3Nb2∕3)O3–PbTiO3 single crystals
Authors: He Chongjun , Zhou Dan , Wang Feifei , Xu Haiqing , Lin Di , Luo Haosu
Published: October 2006

The elastic, piezoelectric, and dielectric properties of tetragonal 0.65Pb(Mg1∕3Nb2∕3)O3–0.35PbTiO3 (PMN-35%PT) single crystals were determined. The piezoelectric constant d33 is ∼1250pC∕N; the electromechanical coefficients k15, k31, k33, and kt are 0.70, 0.48, 0.91, and 0.61, respectively. The dielectric properties were measured as a function of temperature for (001)-oriented crystals. Compared with the crystals with compositions in the morphotropic phase boundary, PMN-35%PT crystals have much more stable phase structure from room temperature to Curie temperature, which makes them promising materials for high power applications in fabricating transducers, actuators, and generators.
Formation and growth mechanism of B10N nanotubes via a carbon nanotube–substitution reaction
Authors: Han Wei-Qiang , Todd Peter J. , Strongin Myron
Published: October 2006

A substitution-reaction route has been demonstrated as an efficient synthesis route for producing single-walled and multiwalled B10N nanotubes (BNNTs). The nanotubes have diameters smaller than those of the starting carbon nanotubes and also have similar lengths to the starting carbon nanotubes. The isotopic ratio of B10 in BNNTs depends on the isotopic ratio of the starting B2O3. A detailed growth model is also given for the carbon nanotube–substitution reaction.
Double-interface growth mode of fractal silver trees within replacement reaction
Authors: Fang Jixiang , Ma Xiaoni , Cai Hanhui , Song Xiaoping , Ding Bingjun , Guo Yong
Published: October 2006

Crystals are generally considered to grow by attachment of atoms to the surface of growing grains. In this letter the authors present experimental results which demonstrate that silver amorphous phase deposits continuously and rapidly on the surface of formed nanocrystals in a replacement reaction on zinc plate. The amorphous phase interrupts the growth of nanocrystals by atom-by-atom attachment, instead, a fractal or dendritic growth still goes on by the deposition and crystallization of amorphous phase, and self-assembling of the crystallized nanograins. A double-interface mode is proposed to interpret the growth of fractal silver trees in AgNO3 solution.
Evaluation of radiative efficiency in InGaN blue-violet laser-diode structures using electroluminescence characteristics
Authors: Ryu H. Y. , Ha K. H. , Chae J. H. , Kim K. S. , Son J. K. , Nam O. H. , Park Y. J. , Shim J. I.
Published: October 2006

The authors analyzed radiative efficiency of InGaN laser diodes (LDs) emitting at 405nm. Based on semiconductor rate equations, the radiative efficiency is unambiguously determined by the analysis of electroluminescence characteristics. The radiative efficiency exceeds 70% even far below threshold of ∼3mA at a high temperature of 80°C. This highly radiative characteristic is attributed to reduced contribution of nonradiative recombination in LDs with low-dislocation-density active material. It is also found that the radiative efficiency is almost independent of threshold current, indicating that nonradiative recombination is not a major factor which determines lasing threshold in 405nm emitting InGaN LDs having low dislocation density.
Second-harmonic generation in periodically poled lithium niobate waveguides fabricated by femtosecond laser pulses
Authors: Lee Y. L. , Yu N. E. , Jung C. , Yu B.-A. , Sohn I.-B. , Choi S.-C. , Noh Y.-C. , Ko D.-K. , Yang W.-S. , Lee H.-M. , Kim W.-K. , Lee H.-Y.
Published: October 2006

The authors have demonstrated the second-harmonic generation (SHG) in optical channel waveguides which were fabricated in periodically poled lithium niobate (PPLN) by tightly focused femtosecond laser (781nm) pulses. The measured quasi-phase-matched wavelength and 3dB bandwidth for SHG in a 44.8-mm-long PPLN waveguide which has a domain period of 16.6μm were about 1563 and 0.25nm, respectively. The value of the index difference between the fundamental and harmonic wavelengths in laser written waveguide was inferred to be 0.047.
Effects of vacancy-carboxyl pair functionalization on electronic properties of carbon nanotubes
Authors: Wang Chenchen , Zhou Gang , Wu Jian , Gu Bing-Lin , Duan Wenhui
Published: October 2006

Density functional calculations are performed to investigate the functionalization of carbon nanotubes with the vacancy and carboxyl group that always appear in pairs after chemical oxidation (such as oxidative acid treatment). It is found that the geometrical structures and electronic properties of the nanotubes are changed significantly, with the formation of a strong covalent bond between the carboxyl and the defected tube. The electrical conductivity of the system could be considerably enhanced, which sensitively depends upon the axial density of vacancy-carboxyl pairs. A promising approach, controllable oxidative acid treatment, is designed to make carbon nanotube-based chemical and nanoelectronic devices.
Electronic states of oxidized GaN(0001) surfaces
Authors: Dong Y. , Feenstra R. M. , Northrup J. E.
Published: October 2006

The structure and electronic properties of oxidized (0001) surfaces of GaN grown by plasma-assisted molecular beam epitaxy are investigated by scanning tunneling microscopy/spectroscopy, Auger electron spectroscopy, and first-principles theory. For oxygen exposure at room temperature an amorphous gallium oxide layer is found to form, resulting in a distribution of midgap electronic states extending out from the GaN valence band edge. The influence of these states on the electron concentration in buried AlGaN∕GaN heterojunctions is discussed.
Structural and optical properties of InGaN∕GaN multiple quantum wells grown on nano-air-bridged GaN template
Authors: Zang K. Y. , Wang Y. D. , Liu H. F. , Chua S. J.
Published: October 2006

Structural and optical properties of InGaN∕GaN multiple quantum wells (MQWs) grown on nano-air-bridged GaN template by metal organic chemical vapor deposition were investigated. The InGaN∕GaN MQWs on nano-air-bridged GaN demonstrate much better surface morphology, revealing low defect density ∼4×108cm−2 with step flow features measured by atomic force microscopy. The photoluminescence measurement shows one magnitude higher in intensity from less defective InGaN MQWs compared to that of the control InGaN MQWs. The improvement in photoluminescence of the InGaN MQWs is benefited from the reduction of threading dislocation density in the InGaN∕GaN active layers and GaN template, revealed from cross-sectional transmission electron microscopy. High resolution x-ray diffraction analysis results show higher indium mole fraction in the MQWs when grown on nano-air-bridged GaN template, due to the strain relaxation in the nano-air-bridged GaN template. This higher indium incorporation is consistent with the redshift of the photoluminescence peak.
AFLP analysis of genetic diversity within Saccharum officinarum and comparison with sugarcane cultivars
Authors: Aitken K. S. , Li J.-C. , Jackson P. , Piperidis G. , McIntyre C. L.
Published: October 2006

Molecular diversity among 421 clones of cultivated sugarcane and wild relatives was analysed using AFLP markers. Of these clones, 270 were Saccharum officinarum and 151 were either cultivars produced by the Australian breeding program or important parents used in the breeding program. The S. officinarum clones were obtained from a collection that contained clones from all the major regions where S. officinarum is grown. Five AFLP primer combinations generated 657 markers of which 614 were polymorphic. All clones contained a large number of markers; a result of the polyploid nature and heterozygosity of the genome. S. officinarum clones from New Guinea displayed greater diversity than S. officinarum clones from other regions. This is in agreement with the hypothesis that New Guinea is the centre of origin of this species. The S. officinarum clones from Hawaii and Fiji formed a separate group and may correspond to clones that have been introgressed with other members of the ‘Saccharum complex’. Greater diversity was found in the cultivars than in the S. officinarum clones due to the introgression of S. spontaneum chromatin. These cultivars clustered as expected based on pedigree. The major contribution of clones QN66-2008 and Nco310 to Australian sugarcane cultivars divided the cultivars into 2 main groups. Although only a few S. officinarum clones are known to have been used in the breeding of current cultivars, about 90% of markers present in the S. officinarum clone collection (2n = 80) were also present in the cultivar collection. This suggests that most of the observed genetic diversity in S. officinarum has been captured in Australian sugarcane germplasm.
Analysis of a three-way interaction including multi-attributes
Authors: Varela Mario , Crossa Jose , Rane Jagdish , Joshi Arun Kumar , Trethowan Richard
Published: October 2006

The additive main effect and multiplicative interaction (AMMI) has been widely used for studying and interpreting genotype × environment interaction (GEI) in agricultural experiments using multi-environment trials (METs). When METs are performed across several years the interaction is referred to as a 3-mode (3-way) data array, in which the modes are genotypes, environments, and years. The 3-way array can be applied to other conditions or factors artificially created by the researcher, such as different sowing dates or plant densities, etc. Three-way interaction data can be studied using the AMMI analysis. The objective of this study is to apply the 3-mode AMMI to 2 datasets. Dataset 1 comprises genotype (25) × location (4) × sowing time (4) interaction; 8 traits were measured. The structure of dataset 2 is genotype (20) × irrigation regimes (4) × year (3) on grain yield. Results of the 3-way AMMI on dataset 1 show that several important 3-way interactions were not detected when condensing location (4) × sowing time (4) into environments (16). An alternative 3-way array, genotype × attribute × locations for the early sowing date in Year 1, is considered. Results of the 3-way AMMI on dataset 2 show that different patterns of response of genotypes can be found at different irrigation methods and years.
Growth regulators restore germination of Orobanche seeds that are conditioned under water stress and suboptimal temperature
Authors: Song W. J. , Zhou W. J. , Jin Z. L. , Zhang D. , Yoneyama K. , Takeuchi Y. , Joel D. M.
Published: October 2006

Broomrapes (Orobanche spp.) are serious root parasitic weeds that cause great damage to crop production in many parts of the world. The study focussed on the influence of plant growth regulators on germination of Orobanche seeds conditioned under suboptimal temperature (at 13°C) and under water stress (at –1 and –2 MPa). Three widely distributed species of broomrapes (O. aegyptiaca, O. ramosa, and O. minor) were used in the experiments. Exogenous GA3 (10 mg/L), brassinolide (1 mg/L), and fluridone (10 mg/L) significantly increased the broomrape seed response to the germination stimulant GR24 (10–6 m) even when seeds were first conditioned at a suboptimal temperature and under water stress. The highest germination was obtained when the combined treatments with fluridone and brassinolide, or with GA3 and brassinolide were applied together with the germination stimulant. This indicates that there were additive effects among various plant growth regulators in the regulation of germination response in Orobanche seeds. With the prolongation of conditioning periods under low temperature stress, the restoration capacities of seed germination by a single growth regulator decreased, but the combined treatments of growth regulators retained their positive effects in restoring seed germination.
Legionella pneumophila
glucosyltransferase inhibits host elongation factor 1A
Authors: Belyi Yury , Niggeweg Ricarda , Opitz Bastian , Vogelsgesang Martin , Hippenstiel Stefan , Wilm Matthias , Aktories Klaus
Published: October 2006

Legionella pneumophila
, the causal agent of Legionnaires' disease, is an intracellular parasite and invades and proliferates within different eukaryotic cells, including human alveolar macrophages. After several 100-fold multiplication within host cells, the pathogens are released for new invasion by induction of apoptosis or necrosis. Here we report that
L. pneumophila
produces a glucosyltransferase, which selectively modifies an ≈50-kDa mammalian protein by using UDP-glucose as a cosubstrate. MS analysis identified the protein substrate as the mammalian elongation factor (EF)1A.
Legionella
glucosyltransferase modifies its eukaryotic protein substrate at serine-53, which is located in the GTPase domain of the EF. Glucosylation of EF1A results in inhibition of eukaryotic protein synthesis and death of target cells. Our findings show a mode of inhibition of protein synthesis by microbial pathogens and offer a perspective for understanding of the host-pathogen interaction of
L. pneumophila
.
Nonlinear auditory mechanism enhances female sounds for male mosquitoes
Authors: Jackson Joseph C. , Robert Daniel
Published: October 2006

Sound plays an important role in the life history of mosquitoes. Male mosquitoes detect females by the sound generated by their wingbeat. Because female wings are weak acoustic radiators, males have been driven by sexual selection to evolve sensitive acoustic sensors. Mosquito antennae are very sensitive acoustic receivers, featuring up to 16,000 sensory cells, a number comparable with that contained in the human cochlea. The antennal sound receiver exhibits frequency selectivity, input amplification, and self-generated oscillations, features that parallel the functional sophistication of the cochlear amplifier. Although arguably the male antenna is well suited to receiving weak female sounds, the role of active mechanisms in mosquito hearing is far from understood. Previous mechanical studies on mosquito hearing largely focused on the steady-state antennal response to harmonic sounds, mostly evaluating the data through conventional Fourier transforms. Here, we report on the time-resolved mechanical behavior of the male antenna in response to female sounds. Crucially, stimuli were designed to reflect the temporal acoustic profile of a female flying by. With these stimuli, several previously unreported nonlinear features were unveiled, involving amplification, compression, and hysteresis. The time-resolved analysis reveals that, through the active participation of the sensory neurons, the antenna mechanically responds to enlarge its own range of detection. This behavior augments the capacity of the antennal receiver to detect female sounds, enhancing the male's chance to successfully pursue a passing female.
Veela
defines a molecular link between Cryptochrome and Timeless in the light-input pathway to
Drosophila
's circadian clock
Authors: Peschel Nicolai , Veleri Shobi , Stanewsky Ralf
Published: October 2006

Organisms use the daily cycles of light and darkness to synchronize their internal circadian clocks with the environment. Because they optimize physiological processes and behavior, properly synchronized circadian clocks are thought to be important for the overall fitness. In
Drosophila melanogaster
, the circadian clock is synchronized with the natural environment by light-dependent degradation of the clock protein Timeless, mediated by the blue-light photoreceptor Cryptochrome (Cry). Here we report identification of a genetic variant,
Veela
, which severely disrupts this process, because these genetically altered flies maintain behavioral and molecular rhythmicity under constant-light conditions that usually stop the clock. We show that the
Veela
strain carries a natural
timeless
allele (
ls-tim
), which encodes a less-light-sensitive form of Timeless in combination with a mutant variant of the F-box protein Jetlag. However, neither the
ls-tim
nor the
jetlag
genetic variant alone is sufficient to disrupt light input into the central pacemaker. We show a strong interaction between
Veela
and
cryptochrome
genetic variants, demonstrating that the Jetlag, Timeless, and Cry proteins function in the same pathway.
Veela
also reveals a function for the two natural variants of
timeless
, which differ in their sensitivity to light. In combination with the complex array of retinal and extraretinal photoreceptors known to signal light to the pacemaker, this previously undescribed molecular component of photic sensitivity mediated by the two Timeless proteins reveals that an unexpectedly rich complexity underlies modulation of this process.
Simulated maximum likelihood method for estimating kinetic rates in gene expression
Authors: Tian Tianhai , Xu Songlin , Gao Junbin , Burrage Kevin
Published: October 2006

Motivation: Kinetic rate in gene expression is a key measurement of the stability of gene products and gives important information for the reconstruction of genetic regulatory networks. Recent developments in experimental technologies have made it possible to measure the numbers of transcripts and protein molecules in single cells. Although estimation methods based on deterministic models have been proposed aimed at evaluating kinetic rates from experimental observations, these methods cannot tackle noise in gene expression that may arise from discrete processes of gene expression, small numbers of mRNA transcript, fluctuations in the activity of transcriptional factors and variability in the experimental environment.

Results: In this paper, we develop effective methods for estimating kinetic rates in genetic regulatory networks. The simulated maximum likelihood method is used to evaluate parameters in stochastic models described by either stochastic differential equations or discrete biochemical reactions. Different types of non-parametric density functions are used to measure the transitional probability of experimental observations. For stochastic models described by biochemical reactions, we propose to use the simulated frequency distribution to evaluate the transitional density based on the discrete nature of stochastic simulations. The genetic optimization algorithm is used as an efficient tool to search for optimal reaction rates. Numerical results indicate that the proposed methods can give robust estimations of kinetic rates with good accuracy.

Contact:  tian@maths.uq.edu.au
Recovering metabolic pathways via optimization
Authors: Beasley John E. , Planes Francisco J.
Published: October 2006

Motivation: A metabolic pathway is a coherent set of enzyme catalysed biochemical reactions by which a living organism transforms an initial (source) compound into a final (target) compound. Some of the different metabolic pathways adopted within organisms have been experimentally determined. In this paper, we show that a number of experimentally determined metabolic pathways can be recovered by a mathematical optimization model.

Contact:  john.beasley@brunel.ac.uk
Similar compositional biases are caused by very different mutational effects
Authors: Rocha Eduardo P.C. , Touchon Marie , Feil Edward J.
Published: October 2006

Compositional replication strand bias, commonly referred to as GC skew, is present in many genomes of prokaryotes, eukaryotes, and viruses. Although cytosine deamination in ssDNA (resulting in C→T changes on the leading strand) is often invoked as its major cause, the precise contributions of this and other substitution types are currently unknown. It is also unclear if the underlying mutational asymmetries are the same among taxa, are stable over time, or how closely the observed biases are to mutational equilibrium. We analyzed nearly neutral sites of seven taxa each with between three and six complete bacterial genomes, and inferred the substitution spectra of fourfold degenerate positions in nonhighly expressed genes. Using a bootstrap procedure, we extracted compositional biases associated with replication and identified the significant asymmetries. Although all taxa showed an overrepresentation of G relative to C on the leading strand (and imbalances between A and T), widely variable substitution asymmetries are noted. Surprisingly, all substitution types show significant asymmetry in at least one taxon, but none were universally biased in all taxa. Notably, in the two most biased genomes, A→G, rather than C→T, shapes the compositional bias. Given the variability in these biases, we propose that the process is multifactorial. Finally, we also find that most genomes are not at compositional equilibrium, and suggest that mutational-based heterotachy is deeply imprinted in the history of biological macromolecules. This shows that similar compositional biases associated with the same essential well-conserved process, replication, do not reflect similar mutational processes in different genomes, and that caution is required in inferring the roles of specific mutational biases on the basis of contemporary patterns of sequence composition.
Psychological status of patients with chronic urticaria
Authors: PASAOGLU Gülden , BAVBEK Sevim , TUGCU Handan , ABADOGLU Oznur , MISIRLIGIL Zeynep
Published: October 2006

Although chronic urticaria is the most common cutaneous disorder seen in our outpatient allergy clinics, to our knowledge, no study of psychiatric morbidity in allergy departments has been carried out in our country. For the present study, we used the Minnesota Multiphasic Personality Inventory (MMPI) to evaluate the personality traits and psychological status of patients with chronic idiopathic urticaria (CIU). Fifty‐nine outpatients with CIU and 59 healthy control subjects were enrolled in the study. Patients were included if no specific cause for their urticaria could be identified by detailed history and appropriate investigations. Psychiatric evaluation for all patients and controls was conducted at the Department of Psychiatry by using MMPI. Analysis of the MMPI profile showed that the scores for hypochondriasis, depression, hysteria, psychopathic deviance, paranoia, psychasthenia, schizophrenia, and social introversion were higher in patients with CIU compared to the control group (P < 0.05). The mean score of hysteria was significantly higher in women. There were no significant correlations between the scores of MMPI and duration of the disease. These data indicate that our patients with CIU seem to have more depressive, hysteric, touchy and suspicious personality traits with hypochondriac tendencies and in more conflict with their social environment. Attitudes such as perfectionism, need for approval, external control and need to be loved were also characteristics of the patient group. We believe that psychological status should be considered for effective management of patients with CIU.
Recessive dystrophic epidermolysis bullosa: Case of non‐Hallopeau–Siemens variant with premature termination codons in both alleles
Authors: YONEI Nozomi , OHTANI Toshio , FURUKAWA Fukumi
Published: October 2006

Dystrophic epidermolysis bullosa (DEB) is caused by mutations in the COL7A1 gene encoding collagen, the major component of anchoring fibrils. Premature termination codon (PTC) mutations in both alleles usually lead to the Hallopeau–Siemens variant that shows the most severe phenotype. We experienced a case of the non‐Hallopeau–Siemens variant (nHS‐RDEB), which had a mild clinical severity although it has PTC mutations in both alleles. Our patient was a compound heterozygote for a nonsense mutation (R669X) in exon 15 and a nonsense mutation (E2857X) in exon 116. But we confirmed the existence of some anchoring fibrils on electron micrograph. This suggested that a PTC close to the 3′ end of COL7A1 does not completely abolish the collagen VII mRNA. We hypothesized that the truncated procollagen VII from the mutant allele with a nonsense mutation (E2857X) in exon 116 included two out of eight cysteines needed for disulfide bond formation, and hence a few functional anchoring fibrils could be formed.
Case of childhood granulomatous periorificial dermatitis in a Korean boy treated by oral erythromycin
Authors: CHOI Yun‐Lim , LEE Kwang‐Jun , CHO Hye‐Jin , KIM Won‐Serk , LEE Joo‐Heung , YANG Jun‐Mo , LEE Eil‐Soo , LEE Dong‐Youn
Published: October 2006

ABSTRACTS

Childhood granulomatous periorificial dermatitis (CGPD) is a disease presenting most commonly in prepubertal children as yellow‐brown papules limited to the perioral, perinasal and periocular regions. The condition is benign, self‐limiting and is not associated with systemic involvement. We herein report a case of an 11‐year‐old Korean boy with multiple, asymptomatic, monomorphic, red‐to‐yellow‐colored papular eruptions on the perioral areas of 7‐month duration. Histopathological examination revealed upper dermal and perifollicular granulomatous infiltrate. After using oral erythromycin 500 mg daily for 1 year, the condition resolved completely without leaving a scar.