bluuebunny/crossref_metadata_2025 huggingface dataset:
Basic helix–loop–helix protein E47-mediated p21Waf1/Cip1 gene expression regulates apoptosis of intestinal epithelial cells
Authors: Bhattacharya Sujoy , Guo Huazhang , Ray Ramesh M. , Johnson Leonard R.
Published: September 2007

Inhibition of ornithine decarboxylase by DFMO (α-difluromethylornithine) and subsequent polyamine depletion increases p21Cip1 protein, induces cell cycle arrest and confers resistance to apoptosis on intestinal epithelial cells. However, the mechanism by which polyamines regulate p21Cip1 expression and apoptosis is unknown. On the basis of the involvement of p21Cip1 as an anti-apoptotic protein, we tested the role of p21Cip1 in providing protection from apoptosis. Simultaneously, we investigated the role of E47, a basic helix–loop–helix protein, in the regulation of p21Cip1 gene transcription. Gene-specific siRNA (small interfering RNA) decreased E47 protein levels, increased p21Cip1 promoter activity and protein levels and protected cells from TNFα (tumour necrosis factor α)-induced apoptosis. Knockdown of p21Cip1 protein by siRNA resulted in cells becoming more susceptible to apoptosis. In contrast, incubation with EGF (epidermal growth factor) stimulated p21Cip1 mRNA and protein levels and rescued cells from apoptosis. During apoptosis, the level of E47 mRNA increased, causing a concomitant decrease in p21Cip1 mRNA and protein levels. Polyamine depletion decreased E47 mRNA levels and cell survival. Caspase 3-mediated cleavage of p130Cas has been implicated in p21Cip1 transcription. The progression of apoptosis led to a caspase 3-dependent cleavage of p130Cas and generated a 31 kDa fragment, which translocated to the nucleus, associated with nuclear E47 and inhibited p21Cip1 transcription. Polyamine depletion inhibited all these effects. Transient expression of the 31 kDa fragment prevented the expression of p21Cip1 protein and increased apoptosis. These results implicate p21Cip1 as an anti-apoptotic protein and suggest a role for polyamines in the regulation of p21Cip1 via the transcription repressor E47. Caspase-mediated cleavage of p130Cas generates a 31 kDa fragment, inhibits p21Cip1 transcription and acts as an amplifier of apoptotic signalling.
Domain mapping on the human metastasis regulator protein h-Prune reveals a C-terminal dimerization domain
Authors: Middelhaufe Sabine , Garzia Livia , Ohndorf Uta-Maria , Kachholz Barbara , Zollo Massimo , Steegborn Clemens
Published: September 2007

The human orthologue of the Drosophila prune protein (h-Prune) is an interaction partner and regulator of the metastasis suppressor protein NM23-H1 (non-metastatic protein 23). Studies on a cellular breast-cancer model showed that inhibition of the cAMP-specific PDE (phosphodiesterase) activity of h-Prune lowered the incidence of metastasis formation, suggesting that inhibition of h-Prune could be a therapeutic approach towards metastatic tumours. H-Prune shows no sequence similarity with known mammalian PDEs, but instead appears to belong to the DHH (Asp-His-His) superfamily of phosphoesterases. In order to investigate the structure and molecular function of h-Prune, we expressed recombinant h-Prune in a bacterial system. Through sequence analysis and limited proteolysis, we identified domain boundaries and a potential coiled-coil region in a C-terminal cortexillin homology domain. We found that this C-terminal domain mediated h-Prune homodimerization, as well as its interaction with NM23-H1. The PDE catalytic domain of h-Prune was mapped to the N-terminus and shown to be active, even when present in a monomeric form. Our findings indicate that h-Prune is composed of two independent active sites and two interaction sites for the assembly of oligomeric signalling complexes.
The control of phosphatidylinositol 3,4-bisphosphate concentrations by activation of the Src homology 2 domain containing inositol polyphosphate 5-phosphatase 2, SHIP2
Authors: Batty Ian H. , van der Kaay Jeroen , Gray Alex , Telfer Joan F. , Dixon Miles J. , Downes C. Peter
Published: September 2007

Activation of class Ia PI3K (phosphoinositide 3-kinase) produces PtdInsP3, a vital intracellular mediator whose degradation generates additional lipid signals. In the present study vanadate analogues that inhibit PTPs (protein tyrosine phosphatases) were used to probe the mechanisms which regulate the concentrations of these molecules allowing their independent or integrated function. In 1321N1 cells, which lack PtdInsP3 3-phosphatase activity, sodium vanadate or a cell permeable derivative, bpV(phen) [potassium bisperoxo(1,10-phenanthroline)oxovanadate (V)], increased the recruitment into anti-phosphotyrosine immunoprecipitates of PI3K activity and of the p85 and p110α subunits of class Ia PI3K and enhanced the recruitment of PI3K activity stimulated by PDGF (platelet-derived growth factor). However, neither inhibitor much increased cellular PtdInsP3 concentrations, but both diminished dramatically the accumulation of PtdInsP3 stimulated by PDGF or insulin and markedly increased the control and stimulated concentrations of PtdIns(3,4)P2. These actions were accounted for by the ability of PTP inhibitors to stimulate the activity of endogenous PtdInsP3 5-phosphatase(s), particularly SHIP2 (Src homology 2 domain containing inositol polyphosphate 5-phosphatase 2) and to inhibit types I and II PtdIns(3,4)P2 4-phosphatases. Thus bpV(phen) promoted the translocation of SHIP2 from the cytosol to a Triton X-100-insoluble fraction and induced a marked (5–10-fold) increase in SHIP2 specific activity mediated by enhanced tyrosine phosphorylation. The net effect of these inhibitors was, therefore, to switch the signal output of class I PI3K from PtdInsP3 to PtdIns(3,4)P2. A key component controlling this shift in the balance of lipid signals is the activation of SHIP2 by increased tyrosine phosphorylation, an effect observed in HeLa cells in response to both PTP inhibitors and epidermal growth factor.
Insights into polymer versus oligosaccharide synthesis: mutagenesis and mechanistic studies of a novel levansucrase from Bacillus megaterium
Authors: Homann Arne , Biedendieck Rebekka , Götze Sven , Jahn Dieter , Seibel Jürgen
Published: September 2007

A novel levansucrase was identified in the supernatant of a cell culture of Bacillus megaterium DSM319. In order to test for the contribution of specific amino acid residues to levansucrase catalysis, the wild-type enzyme along with 16 variants based on sequence alignments and structural information were heterologously produced in Escherichia coli. The purified enzymes were characterized kinetically and the product spectrum of each variant was determined. Comparison of the X-ray structures of the levansucrases from Gram-positive Bacillus subtilis and Gram-negative Gluconacetobacter diazotrophicus in conjunction with the corresponding product spectra identified crucial amino acid residues responsible for product specificity and catalysis. Highly conserved regions such as the previously described RDP and DXXER motifs were identified as being important. Two crucial structural differences localized at amino acid residues Arg370 and Asn252 were of high relevance in polymer compared with oligosaccharide synthesis.
Ablation of a small transmembrane protein of Trypanosoma brucei (TbVTC1) involved in the synthesis of polyphosphate alters acidocalcisome biogenesis and function, and leads to a cytokinesis defect
Authors: Fang Jianmin , Rohloff Peter , Miranda Kildare , Docampo Roberto
Published: September 2007

Inorganic poly P (polyphosphate) is an abundant component of acidocalcisomes of Trypanosoma brucei. In the present study we report the presence of a protein homologous with the yeast Vtc1p (vacuolar transporter chaperone 1) in T. brucei that is essential for poly P synthesis, acidocalcisome biogenesis and cytokinesis. Localization studies in a cell line expressing a TbVTC1 fused to GFP (green fluorescent protein) revealed its co-localization with the V-H+-PPase (vacuolar H+-pyrophosphatase), a marker for acidocalcisomes. Western blot analysis of acidocalcisome fractions and immunogold electron microscopy using polyclonal antibodies against a fragment of TbVTC1 confirmed the acidocalcisome localization. Ablation of TbVTC1 expression by RNA interference caused an abnormal morphology of acidocalcisomes, indicating that their biogenesis was disturbed, with a decreased pyrophosphate-driven H+ uptake and Ca2+ content, a significant decrease in the amount of poly P and a deficient response to hyposmotic stress. Ablation of TbVTC1 expression for longer periods produced marked gross morphological alterations compatible with a defect in cytokinesis, followed by cell death. Overexpression of the TbVTC1 gene caused mild alterations in growth rate, but had no perceptible effect on acidocalcisome morphology. We propose that the PPi-driven H+ pumping deficiency induced by ablation of TbVTC1 leads to alterations in the protonmotive force of acidocalcisomes, which results in deficient fusion or budding of the organelles, decreased H+ and Ca2+ content, and decreased synthesis of poly P. A decrease in the poly P content would lead to osmotic sensitivity and defects in cytokinesis.
Urinary-type plasminogen activator (uPA) and its receptor (uPAR) in squamous cell carcinoma of the oral cavity
Authors: Shi Zonggao , Stack M. Sharon
Published: September 2007

OSCC (oral squamous cell carcinoma) is the most common oral malignancy and is estimated to affect approx. 350000 new patients worldwide this year. OSCC is characterized by a high degree of morbidity and mortality, as most patients exhibit local, regional and distant metastasis at the time of diagnosis. Recent genome-wide screening efforts have identified the serine proteinase uPA (urinary-type plasminogen activator, also known as urokinase) as a strong biomarker for prediction of poor disease outcome and a key candidate for molecular classification of oral neoplasms using a ‘gene signature’ approach. The proteinase uPA binds a surface-anchored receptor designated uPAR (uPA receptor), focalizing proteolytic activity to the pericellular milieu. Furthermore, uPA–uPAR can interact with transmembrane proteins to modify multiple signal transduction pathways and influence a wide variety of cellular behaviours. Correlative clinical data show elevated uPA–uPAR in oral tumour tissues, with tumours exhibiting high levels of both uPA and uPAR as the most invasive. Combined in vitro, pre-clinical and clinical data support the need for further analysis of uPA–uPAR as a prognostic indicator as well as a potential therapeutic target in OSCC.
Biorthogonal quantum systems
Authors: Curtright Thomas , Mezincescu Luca
Published: September 2007

Models of PT symmetric quantum mechanics provide examples of biorthogonal quantum systems. The latter incorporate all the structure of PT symmetric models, and allow for generalizations, especially in situations where the PT construction of the dual space fails. The formalism is illustrated by a few exact results for models of the form H=(p+ν)2+∑k>0μkexp(ikx). In some nontrivial cases, equivalent Hermitian theories are obtained and shown to be very simple: They are just free (chiral) particles. Field theory extensions are briefly considered.
Proton formation in 2+1 resonance enhanced multiphoton excitation of HCl and HBr via (Ω=) Rydberg and ion-pair states
Authors: Romanescu Constantin , Loock Hans-Peter
Published: September 2007

Molecular beam cooled HCl was state selected by two-photon excitation of the V∑1(0+) [v=9,11–13,15], E∑1(0+) [v=0], and g∑−3(0+) [v=0] states through either the Q(0) or Q(1) lines of the respective ∑1,3(0+)←←X∑1(0+) transition. Similarly, HBr was excited to the V∑1(0+) [v=m+3, m+5−m+8], E∑1(0+) [v=0], and H∑1(0+) [v=0] states through the Q(0) or Q(1) lines. Following absorption of a third photon, protons were formed by three different mechanisms and detected using velocity map imaging. (1) H*(n=2) was formed in coincidence with Pi2 halogen atoms and subsequently ionized. For HCl, photodissociation into H*(n=2)+Cl(P1∕22) was dominant over the formation of Cl(P3∕22) and was attributed to parallel excitation of the repulsive [(2)Π2∙∙4lλ] superexcited (Ω=0) states. For HBr, the Br(P3∕22)∕Br(P1∕22) ratio decreases with increasing excitation energy. This indicates that both the [(3)Π1∕22∙∙5lλ] and the [B∑2∙∙5lλ] superexcited (Ω=0) states contribute to the formation of H*(n=2). (2) For selected intermediate states HCl was found to dissociate into the H++Cl− ion pair with over 20% relative yield. A mechanism is proposed by which a bound [A∑2∙∙nlσ]∑1(0+) superexcited state acts as a gateway state to dissociation into the ion pair. (3) For all intermediate states, protons were formed by dissociation of HX+[v+] following a parallel, ΔΩ=0, excitation. The quantum yield for the dissociation process was obtained using previously reported photoionization efficiency data and was found to peak at v+=6–7 for HCl and v+=12 for HBr. This is consistent with excitation of the repulsive A∑1∕22 and (2)Π2 states of HCl+, and the (3)Π2 state of HBr+. Rotational alignment of the Ω=0+ intermediate states is evident from the angular distribution of the excited H*(n=2) photofragments. This effect has been observed previously and was used here to verify the reliability of the measured spatial anisotropy parameters.
Electrostatic Landau pole for κ-velocity distributions
Authors: Valentini Francesco , D’Agosta Roberto
Published: September 2007

In this paper, the analytical solution of the linear electrostatic Vlasov dispersion relation is obtained for non-Maxwellian equilibrium distributions of particle velocities (κ distributions). The unphysical singularities for certain values of the parameter κ, recovered by several authors in solving the Landau integral, are discussed in detail, and a way to cancel these singularities and get the correct solution for Langmuir waves is proposed. The solution of the electrostatic dispersion relation presented in this paper provides a theoretical prediction for the oscillation frequency and the damping rate of Langmuir waves, for real values of κ>1∕2 and in particular in the range 1∕2<κ⩽3∕2, where previous analytical solutions fail. Velocity distributions with small values of κ have been frequently observed in solar wind plasmas; therefore, the results presented in this paper are relevant in the interpretation of the solar wind experimental data. Eulerian Vlasov numerical simulations have been performed to substantiate the analytical results; the numerical results are in very good agreement with the theoretical predictions.
Quantum dynamics in macrosystems with several coupled electronic states: Hierarchy of effective Hamiltonians
Authors: Gindensperger Etienne , Cederbaum Lorenz S.
Published: September 2007

We address the nonadiabatic quantum dynamics of macrosystems with several coupled electronic states, taking into account the possibility of multistate conical intersections. The general situation of an arbitrary number of states and arbitrary number of nuclear degrees of freedom (modes) is considered. The macrosystem is decomposed into a system part carrying a few, strongly coupled modes and an environment, comprising the vast number of remaining modes. By successively transforming the modes of the environment, a hierarchy of effective Hamiltonians for the environment is constructed. Each effective Hamiltonian depends on a reduced number of effective modes, which carry cumulative effects. By considering the system’s Hamiltonian along with a few members of the hierarchy, it is shown mathematically by a moment analysis that the quantum dynamics of the entire macrosystem can be numerically exactly computed on a given time scale. The time scale wanted defines the number of effective Hamiltonians to be included. The contribution of the environment to the quantum dynamics of the macrosystem translates into a sequential coupling of effective modes. The wave function of the macrosystem is known in the full space of modes, allowing for the evaluation of observables such as the time-dependent individual excitation along modes of interest as well as spectra and electronic-population dynamics.
Computer simulations of catanionic surfactants adsorbed at air/water interfaces. II. Full coverage
Authors: Clavero Esteban , Rodriguez Javier , Laria Daniel
Published: September 2007

We extend our previous molecular dynamics experiments [Rodriguez et al., J. Phys. Chem. B 109, 24427 (2005)] to the analysis of the adsorption of catanionic surfactants at water/air interfaces, at a surfactant coverage close to that of the saturated monolayer: 30.3Å2 per headgroup. The mixture of surfactants investigated corresponds to equal amounts of dodecytrimethylammonium (DTA) and dodecylsulfate (DS). The structure of the interface is analyzed in terms of the local densities and orientational correlations of all relevant interfacial species. In accordance with experimental evidence, the DTA headgroups penetrate deeper into the aqueous substrate than the DS ones, although the average positions of all headgroups, with respect to the interface, lie in positions somewhat more external than the ones observed at lower coverages. Average tail tilts are close to 45°. The characteristics of the headgroup-water substrate correlations are also analyzed using a tessellation procedure of the interface. The density and polarization responses of the interfacial domains closest to the DS headgroups are enhanced, compared to those adjacent to the DTA detergents. Dynamical aspects related to the diffusion and to the orientational correlations of different water layers in close contact with the surfactant are also investigated.
Secondary and primary relaxations in hyperbranched polyglycerol: A comparative study in the frequency and time domains
Authors: Garcia-Bernabé Abel , Dominguez-Espinosa Gustavo , Diaz-Calleja Ricardo , Riande Evaristo , Haag Rainer
Published: September 2007

The non-Debye relaxation behavior of hyperbranched polyglycerol was investigated by broadband dielectric spectroscopy. A thorough study of the relaxations was carried out paying special attention to truncation effects on deconvolutions of overlapping processes. Hyperbranched polyglycerol exhibits two relaxations in the glassy state named in increasing order of frequency β and γ processes. The study of the evolution of these two fast processes with temperature in the time retardation spectra shows that the β absorption is swallowed by the α in the glass-liquid transition, the γ absorption being the only relaxation that remains operative in the liquid state. In heating, a temperature is reached at which the α absorption vanishes appearing the αγ relaxation. Two characteristics of α absorptions, decrease of the dielectric strength with increasing temperature and rather high activation energy, are displayed by the αγ process. Williams’ ansatz seems to hold for these topologically complex macromolecules.
Controlling the dissociative ionization of ethanol with 800 and 400nm two-color femtosecond laser pulses
Authors: Yazawa H. , Shioyama T. , Suda Y. , Yamanaka M. , Kannari F. , Itakura R. , Yamanouchi K.
Published: September 2007

Ethanol molecules were irradiated with a pair of temporally overlapping ultrashort intense laser pulses (1013–1014W∕cm2) with different colors of 400 and 800nm, and the dissociative ionization processes have been investigated. The yield ratio of the C–O bond breaking with respect to the C–C bond breaking was varied in the range of 0.17–0.53 sensitively depending on the delay time between the two laser pulses, and the absolute value of the yield of the C–O bond breaking was found to be increased largely when the Fourier-transform limited 800nm laser pulse overlaps the stretched 400nm laser pulse, demonstrating an advantage of the two-color intense laser fields in controlling chemical bond breaking processes.
Surface channel current in InAs∕GaSb type-II superlattice photodiodes
Authors: Mou Shin , Li Jian V. , Chuang Shun Lien
Published: September 2007

We observed experimental evidences of surface channel current on the sidewall of InAs∕GaSb superlattice photodiodes. We investigated the surface channel current by measuring the current-voltage (I-V) characteristics of the diodes. The experimental data compare very well with our theoretical model before and after ammonium sulfide passivation. By using the passivation, we reduced the surface channel current by five times, which supports that the surface channel current is induced by surface carriers. We believe that the surface channel current results from the inversion layer of a p-type superlattice with surface Fermi levels pinned above the conduction-band minimum in InAs∕GaSb superlattices.
In-plane substitution effect on the local structure of La1.88Sr0.12CuO4
Authors: Zhang Y. Q. , Qu J. F. , Wang B. M. , Xiang X. Q. , Li X. G.
Published: September 2007

The effect of in-plane substitution on the local structure has been studied by ultrasonic method in a series sample of La1.88Sr0.12Cu1−yZnyO4 (y=0.00,0.01,0.02,0.03). It is found that a small amount of Zn doping greatly promotes the formation of the local low-temperature tetragonal phase, whereas further doping is harmful to it, the tendency of which is to show a marked resemblance to the Zn-concentration dependence of the magnetic transition temperature TN reported by muon-spin-relaxation (μSR) study. Our results also provide additional evidence that the slight in-plane nonmagnetic doping introduces local pinning centers to stabilize the charge stripes in La1.88Sr0.12CuO4.
Relative humidity effects on the surface electrical properties of resistive plate chamber melaminic laminates uncoated and coated with polymerized linseed oil film
Authors: Bearzotti Andrea , Palummo Lucrezia
Published: September 2007

Relative humidity is an important quantity to control in many manufacturing environments such as semiconductor industry. Humidity and moisture can affect many electronic devices, generally rendering their operation worse. In this study we present results showing that in some specific applications, humidity can improve the performance of an electronic device. Resistive plate chambers are used as trigger detectors of the muon system in LHC (large hadron collider) experiments ATLAS (a toroidal LHC apparatus), CMS (compact muon solenoid) and ALICE (a large ion collider experiment) and as detector in cosmic rays experiment ARGO (astrophysical radiation with ground-based observatory). These detectors are made of phenolic-melaminic laminate electrodes, coated with a polymerized linseed oil film delimiting the gaseous sensitive volume. The loss of some of the detector capability can be progressive in time and due to the intrinsic limits of the detector materials. One of these effects is due to an increase of the total plate resistance, that is correlated to ion migration and relativity humidity phenomena. Our purpose is to understand the relative humidity (RH) influence on the conduction mechanisms on the electrodes surface. Results of amperometric measurements on laminate samples kept at a fixed temperature of 22°C, cycling RH between 10% and 90% are here presented.
A model for Si, SiCH, SiO2, SiOCH, and porous SiOCH etch rate calculation in inductively coupled fluorocarbon plasma with a pulsed bias: Importance of the fluorocarbon layer
Authors: Raballand V. , Cartry G. , Cardinaud C.
Published: September 2007

In a previous paper we showed that selective etching of porous SiOCH with respect to SiO2 and SiCH is clearly enhanced when using a pulsed bias in inductively coupled fluorocarbon plasma. To understand this pulsed process, a model for etch rate calculation is developed in the present paper. This model explains the etching/deposition threshold shift toward higher bias voltage in pulsed conditions. Rather good confidence is obtained with experimental SiO2, Si, SiOCH and SiCH etch rates. Porous SiOCH etching is found to behave slightly differently compared to SiO2 or SiCH; its chemical etching is assumed to occur even during the beginning of off period. This point could explain why good selectivities between porous SiOCH and SiO2 and SiCH are obtained.
Impact of the top silicon thickness on phonon-limited electron mobility in (110)-oriented ultrathin-body silicon-on-insulator n-metal-oxide-semiconductor field-effect transistors
Authors: Moon Hui-Chang , Kim Seong-Je , Shim Tae-Hun , Park Jea-Gun
Published: September 2007

We investigated through a theoretical simulation how the phonon-limited electron mobility in both (110)- and (100)-oriented ultrathin-body (UTB) silicon-on-insulator (SOI) n-metal-oxide-semiconductor field-effect transistors (MOSFETs) depends on the top silicon thickness within a range from 20to2nm. No electron mobility enhancement was observed in (110) UTB SOI n-MOSFETs when the top silicon thickness was around 5nm, unlike in (100) UTB n-MOSFETs. Thus, electron mobility in (110) UTB SOI n-MOSFETs decreased with top silicon thickness, particularly in the range below 10nm. We attributed the electron mobility degradation in (110) UTB SOI n-MOSFETs within the top silicon thickness range below 10nm to a decrease in the effective width of the inversion layer and an increase in intravalley acoustic phonon scattering, rather than to less carrier repopulation due to less band splitting between two- and fourfold valleys.
Single-mode laser action in quantum cascade lasers with spiral-shaped chaotic resonators
Authors: Audet Ross , Belkin Mikhail A. , Fan Jonathan A. , Lee Benjamin G. , Lin Kai , Capasso Federico , Narimanov Evgenii E. , Bour David , Corzine Scott , Zhu Jintian , Höfler Gloria
Published: September 2007

The authors have fabricated and characterized quantum cascade lasers with spiral-shaped microresonators. The lasers operate in pulsed mode at room temperature with peak optical power greater than 20mW and in continuous wave at temperatures up to 125K. They exhibit single-mode emission in both pulsed mode and continuous wave operation, with a 30dB side-mode suppression ratio at injection currents well above threshold. Subthreshold spectral measurements indicate that the spiral cavities support whispering-gallery-like modes. Single-mode lasing occurs on one of these modes. Far-field profiles reveal enhanced directionality compared to microdisk lasers.
Suppression of oxygen vacancy formation in Hf-based high-k dielectrics by lanthanum incorporation
Authors: Umezawa N. , Shiraishi K. , Sugino S. , Tachibana A. , Ohmori K. , Kakushima K. , Iwai H. , Chikyow T. , Ohno T. , Nara Y. , Yamada K.
Published: September 2007

The effects of lanthanum incorporation into HfO2 dielectrics were studied using first-principles total energy calculations. The author’s computational result clearly showed that the formation energy of a neutral oxygen vacancy (VO0) in the vicinity of substitutional La atoms at Hf sites is 0.7eV larger than that in pure HfO2, indicating that the concentration of VO0’s is drastically reduced by La incorporation. This effect is understood to be caused by the decrease in the local dielectric constant κL around La atoms due to the strong ionic character of the La–O bond compared to the Hf–O bond.
Observation of inhomogeneous domain nucleation in epitaxial Pb(Zr,Ti)O3 capacitors
Authors: Kim D. J. , Jo J. Y. , Kim T. H. , Yang S. M. , Chen B. , Kim Y. S. , Noh T. W.
Published: September 2007

We investigated domain nucleation process in epitaxial Pb(Zr,Ti)O3 capacitors under a modified piezoresponse force microscope. We obtained domain evolution images during polarization switching process and observed that domain nucleation occurs at particular sites. This inhomogeneous nucleation process should play an important role in an early stage of switching and under a high electric field. We found that the number of nuclei is linearly proportional to log(switching time), suggesting a broad distribution of activation energies for nucleation. The nucleation sites for a positive bias differ from those for a negative bias, indicating that most nucleation sites are located at the ferroelectric/electrode interfaces.
Nanostructure of chemically phase separated La–Ce–Mn–O thin films
Authors: Stingl C. , Moshnyaga V. , Luo Y. , Damaschke B. , Samwer K. , Seibt M.
Published: September 2007

The perovskite compound La0.67Ce0.33MnO3 (LCeMO) is a candidate for electron doping rather than the hole doping common in manganites. However, it is not clear whether Ce, which has a smaller ionic radius than other dopants, can be incorporated into the crystal lattice. Thin LCeMO films were prepared by two different deposition techniques. In both cases, a chemical phase separation is observed, which in one case leads to a self-organized columnar nanostructure with no indication for n-type doping. In the other case, we find hole doping induced by La vacancies.
Synthesis of high purity Au nanobelts via the one-dimensional self-assembly of triangular Au nanoplates
Authors: Zhang Jianhui , Liu Huaiyong , Wang Zhenlin , Ming Naiben
Published: September 2007

High purity (∼88%) gold nanobelts have been synthesized in the water/polyvinylpyrrolidone (PVP)/n-pentanol system created to realize the selective-adsorption of PVP on Au which directs Au to grow in belt form via the one-dimensional (1D) self-assembly of triangular Au nanoplates. These nanobelts present uniform thickness and lateral dimension, large aspect ratio up to 160, unique 60° angle end structure, and double-peak plasmon resonance property. The PVP directed 1D self-assembly method demonstrated here may provide a general route for the shape-selective synthesis of the other 1D functional nanostructures.
Temperature and pressure dependence of the recombination processes in 1.5μm InAs∕InP (311)B quantum dot lasers
Authors: Massé N. F. , Homeyer E. , Marko I. P. , Adams A. R. , Sweeney S. J. , Dehaese O. , Piron R. , Grillot F. , Loualiche S.
Published: September 2007

The threshold current and its radiative component in 1.5μm InAs∕InP (311)B quantum dot lasers are measured as a function of the temperature. Despite an almost temperature insensitive radiative current, the threshold current increases steeply with temperature leading to a characteristic temperature T0≈55K around 290K. Direct observation of spontaneous emission from the wetting layer shows that some leakage from the dots to the wetting layer occurs in these devices. However, a decrease in the threshold current as a function of pressure is also measured suggesting that Auger recombination dominates the nonradiative current and temperature sensitivity of these devices.
Characteristic trapping lifetime and capacitance-voltage measurements of GaAs metal-oxide-semiconductor structures
Authors: Brammertz Guy , Martens Koen , Sioncke Sonja , Delabie Annelies , Caymax Matty , Meuris Marc , Heyns Marc
Published: September 2007

The authors show the implications that the free carrier trapping lifetime has on the capacitance-voltage (CV) characterization method applied to metal-oxide-semiconductor (MOS) structures. It is shown that, whereas the CV characterization method for deducing interface state densities works well for Si, the generally used frequency range of 100Hz–1MHz is much less adapted to GaAs MOS structures. Only interface trapping states in very small portions of the GaAs bandgap are measured with this frequency range, and mainly the very important midgap region is not properly probed. Performing an additional measurement at 150°C on GaAs MOS structures eliminates this problem.
Effect of length and size of heterojunction on the transport properties of carbon-nanotube devices
Authors: Li Xiao-Fei , Chen Ke-Qiu , Wang Lingling , Long Meng-Qiu , Zou B. S. , Shuai Z.
Published: September 2007

By applying nonequilibrium Green’s functions in combination with the density-functional theory, we investigate the electronic transport properties of molecular junctions constructed by the mirror symmetrical straight carbon-nanotube heterojunctions. The results show that the length and size of heterojunction play an important role in the electronic transport properties of these systems. The negative differential resistance behavior can be observed in such devices with certain length and size of heterojunction. A mechanism is suggested for the negative differential resistance behavior.
Gap solitons in optically induced two-dimensional square photonic lattices in LiNbO3:Fe crystals
Authors: Qi Xinyuan , Liu Simin , Zhang Guoquan , Guo Ru , Liu Zhaohong , Zhou Lipeng , Li Yuan
Published: September 2007

We fabricated two-dimensional square photonic lattices with a backbone structure in self-defocusing LiNbO3:Fe crystals through optical induction. We systematically observed four kinds of gap solitons and their power spectra in the nonlinear photonic lattices. Our results show that the lightwave is confined more tightly when it is launched into a low-index region at the input face of the crystal than when it is launched into a backbone ridge waveguide.
QTL analysis of malting quality traits in two barley populations
Authors: Panozzo J. F. , Eckermann P. J. , Mather D. E. , Moody D. B. , Black C. K. , Collins H. M. , Barr A. R. , Lim P. , Cullis B. R.
Published: September 2007

Selection for malting quality traits is a major breeding objective for barley breeding programs. With molecular markers linked to loci affecting these traits, this selection can be undertaken at an earlier stage of the breeding program than is possible using conventional tests. Quantitative trait loci (QTLs) associated with malting quality traits were mapped in 2 populations derived from parents with elite malting quality. Progeny from an Arapiles/Franklin population grown in 4 environments and an Alexis/Sloop population grown in 5 environments were tested for grain protein percentage, α-amylase activity, diastatic power, hot water extract, wort viscosity, wort β-glucan, β-glucanase, and free α-amino acids. QTL analysis was performed using a one-stage approach, which allowed for modelling of spatial variation in the field, and in each phase of the malting quality analysis in the laboratory. QTLs for malting quality traits were detected on all chromosomes and for both populations. Few of these QTLs were significant in all of the environments, indicating that QTL × environment interactions were important. There were many coincident QTLs for traits that are expected to be related such as diastatic power and α-amylase activity, wort β-glucan and wort viscosity and for some traits that are not expected to be related such as hot water extract and malt viscosity.
Leaf rust of spring wheat in Northern Kazakhstan and Siberia: incidence, virulence, and breeding for resistance
Authors: Morgounov A. , Rosseeva L. , Koyshibayev M.
Published: September 2007

Northern Kazakhstan and Western Siberia of Russia represent a relatively uniform continuous area of spring wheat cultivation of ~20 million ha. Despite the dry climate, cultivation of susceptible varieties resulted in epidemics of leaf rust on average in 1 year out of 4, affecting up to 5 million ha with yield losses of up to 25–30%. The leaf rust population showed absence of virulence for genes Lr9 and Lr24 and low frequency of isolates with virulence to Lr11, Lr16, Lr18, and Lr28. The field observations indicated that genes Lr28 and Lr36 provide resistance. All the wheat cultivars are susceptible to leaf rust and only recently have several resistant lines and new varieties have been tested in trials. The current resistance breeding efforts are based on incorporation of the resistance from local and foreign sources. The breeding strategy is not based on detailed knowledge of the leaf rust population and its interaction with the host because of limited pathology and genetics research capacity. However, practical breeding efforts in combining proven resistance with adaptation traits resulted in the development of new competitive resistant germplasm. Shuttle breeding between the region and CIMMYT-Mexico to enhance resistance contributes to regional efforts.
Floral ontogeny of Swainsona formosa (Fabaceae: Faboideae: Galegeae)
Authors: Tapingkae T. , Taji A. , Kristiansen P.
Published: September 2007

Swainsona formosa (G.Don) J.Thompson (Sturt’s desert pea) is used in commercial floriculture for cut flowers and ornamental pot plants; however, accurate identification of the growth stages is critically important in making management decisions in floricultural crops. This plant was investigated by stereomicroscopy and scanning electron microscopy (SEM) to identify flowering time and stages of floral development. This is the first work to describe the complete floral ontogeny in a member of tribe Galegeae. Conversion from vegetative to reproductive stages began within 40–46 days after seed germination for axillary branches and within 46–52 days for central stems. Plants required 807.5 days °C growing degree-days for axillary branches and 921.5 days °C for central stems to reach 50% flowering. The central stem grew more nodes (11.1 ± 0.97 nodes) before the initiation of the first flower than did the axillary branches (7.2 ± 0.93 nodes). The order of floral organ initiation within each whorl is unidirectional, except for the petal whorl, which is simultaneous; the flower is organised into five whorls and shows a pentamerous arrangement of sepals and petals, 10 stamens in two whorls and a central carpel.
Flowering phenology, nectary structure and breeding system in Corymborkis flava (Spiranthoideae:Tropidieae), a terrestrial orchid from a Neotropical forest
Authors: Vieira Milene Faria , Andrade Maria Regina S. , Bittencourt Nelson S. , de Carvalho-Okano Rita M.
Published: September 2007

Flowering phenology, breeding system and nectary structure of Corymborkis flava (Sw.) Kuntze were studied in a fragment of the Atlantic Forest in south-eastern Brazil. The flowering period extended from March (end of rainy season) to early June and seed dispersal occurred from June to September (dry season). Flowering peak occurred mainly in April, with up to 34 open flowers per plant being observed. The yellow, odourless and tubular flowers lasted ~7.8 days. The flowers present a perigonal nectary located in the basal lateral parts of the labellum; this is the first report on the nectary location and characterisation in the Tropidieae tribe. At the pre-anthesis stage, cells of both secretory parenchyma and epidermis of the nectary are filled with compound amyloplasts. However, starch grains were not observed in these tissues in senescent flowers, indicating that these starch grains are hydrolysed and used as source of sugars for nectar production. The nectar accumulates between the cuticle and the outer periclinal wall of the epidermal cells before flowing out into the nectar chamber. C. flava is a self-compatible species and spontaneous self-pollination does not occur because of hercogamy. The high pollinia removal (0.80) and insertion (0.82) per flower, as well as the high natural fruit-set indicate an efficient natural pollination system. The present study contributes for the knowledge of the diversity of reproductive strategies and nectary structures in Orchidaceae.
Generalised pollination of Diuris alba (Orchidaceae) by small bees and wasps
Authors: Indsto James O. , Weston Peter H. , Clements Mark A. , Dyer Adrian G. , Batley Michael , Whelan Robert J.
Published: September 2007

Most Diuris species possess flowers of pea-like form and colour, and occur in association with flowering peas of the tribe Mirbeliae. Previous studies of the pollination of Diuris maculata sensu lato have found evidence for guild mimicry of pea flowers. The flowers of Diuris alba are also pea-like in form but not in colour, and this species is frequently found in habitats where peas are uncommon or absent. We investigated the pollination of Diuris alba, which we expected may have a distinct pollination system at Lake Munmorah, New South Wales. Many Diuris species lack floral rewards, but D. alba produced a small amount of nectar. Flower visitors, and hence putative pollinators, were mainly female Exoneura bees, but also the wasps Eurys pulcher and a Paralastor species. Reproductive success of D. alba, both in woodland containing abundant Dillwynia retorta and in heathland where this pea was absent, was higher than in the previously studied D. maculata s.l. We suggest that the pollination of D. alba is more generalised than that found in the legume guild mimic D. maculata s.l. Although its flowers may display structural similarity to pea flowers, other characteristics suggest that its pollination system has diverged from a presumed pea-mimicry ancestral condition.
Musicians have enhanced subcortical auditory and audiovisual processing of speech and music
Authors: Musacchia Gabriella , Sams Mikko , Skoe Erika , Kraus Nina
Published: September 2007

Musical training is known to modify cortical organization. Here, we show that such modifications extend to subcortical sensory structures and generalize to processing of speech. Musicians had earlier and larger brainstem responses than nonmusician controls to both speech and music stimuli presented in auditory and audiovisual conditions, evident as early as 10 ms after acoustic onset. Phase-locking to stimulus periodicity, which likely underlies perception of pitch, was enhanced in musicians and strongly correlated with length of musical practice. In addition, viewing videos of speech (lip-reading) and music (instrument being played) enhanced temporal and frequency encoding in the auditory brainstem, particularly in musicians. These findings demonstrate practice-related changes in the early sensory encoding of auditory and audiovisual information.
Circadian regulation of insect olfactory learning
Authors: Decker Susan , McConnaughey Shannon , Page Terry L.
Published: September 2007

Olfactory learning in insects has been used extensively for studies on the neurobiology, genetics, and molecular biology of learning and memory. We show here that the ability of the cockroach
Leucophaea maderae
to acquire olfactory memories is regulated by the circadian system. We investigated the effect of training and testing at different circadian phases on performance in an odor-discrimination test administered 30 min after training (short-term memory) or 48 h after training (long-term memory). When odor preference was tested by allowing animals to choose between two odors (peppermint and vanilla), untrained cockroaches showed a clear preference for vanilla at all circadian phases, indicating that there was no circadian modulation of initial odor preference or ability to discriminate between odors. After differential conditioning, in which peppermint odor was associated with a positive unconditioned stimulus of sucrose solution and vanilla odor was associated with a negative unconditioned stimulus of saline solution, cockroaches conditioned in the early subjective night showed a strong preference for peppermint and retained the memory for at least 2 days. Animals trained and tested at other circadian phases showed significant deficits in performance for both short- and long-term memory. Performance depended on the circadian time (CT) of training, not the CT of testing, and results indicate that memory acquisition rather than retention or recall is modulated by the circadian system. The data suggest that the circadian system can have profound effects on olfactory learning in insects.
What a difference a decade makes: Insights into translesion DNA synthesis
Authors: Yang Wei , Woodgate Roger
Published: September 2007

Living organisms are continually under attack from a vast array of DNA-damaging agents that imperils their genomic integrity. As a consequence, cells posses an army of enzymes to repair their damaged chromosomes. However, DNA lesions often persist and pose a considerable threat to survival, because they can block the cell's replicase and its ability to complete genome duplication. It has been clear for many years that cells must possess a mechanism whereby the DNA lesion could be tolerated and physically bypassed. Yet it was only within the past decade that specialized DNA polymerases for “translesion DNA synthesis” or “TLS” were identified and characterized. Many of the TLS enzymes belong to the recently described “Y-family” of DNA polymerases. By possessing a spacious preformed active site, these enzymes can physically accommodate a variety of DNA lesions and facilitate their bypass. Flexible DNA-binding domains and a variable binding pocket for the replicating base pair further allow these TLS polymerases to select specific lesions to bypass and favor distinct non-Watson–Crick base pairs. Consequently, TLS polymerases tend to exhibit much lower fidelity than the cell's replicase when copying normal DNA, which results in a dramatic increase in mutagenesis. Occasionally this can be beneficial, but it often speeds the onset of cancer in humans. Cells use both transcriptional and posttranslational regulation to keep these low-fidelity polymerases under strict control and limit their access to a replication fork. Our perspective focuses on the mechanistic insights into TLS by the Y-family polymerases, how they are regulated, and their effects on genomic (in)stability that have been described in the past decade.
A study of communication pathways in methionyl- tRNA synthetase by molecular dynamics simulations and structure network analysis
Authors: Ghosh Amit , Vishveshwara Saraswathi
Published: September 2007

The enzymes of the family of tRNA synthetases perform their functions with high precision by synchronously recognizing the anticodon region and the aminoacylation region, which are separated by ≈70 Å in space. This precision in function is brought about by establishing good communication paths between the two regions. We have modeled the structure of the complex consisting of
Escherichia coli
methionyl-tRNA synthetase (MetRS), tRNA, and the activated methionine. Molecular dynamics simulations have been performed on the modeled structure to obtain the equilibrated structure of the complex and the cross-correlations between the residues in MetRS have been evaluated. Furthermore, the network analysis on these simulated structures has been carried out to elucidate the paths of communication between the activation site and the anticodon recognition site. This study has provided the detailed paths of communication, which are consistent with experimental results. Similar studies also have been carried out on the complexes (MetRS + activated methonine) and (MetRS + tRNA) along with ligand-free native enzyme. A comparison of the paths derived from the four simulations clearly has shown that the communication path is strongly correlated and unique to the enzyme complex, which is bound to both the tRNA and the activated methionine. The details of the method of our investigation and the biological implications of the results are presented in this article. The method developed here also could be used to investigate any protein system where the function takes place through long-distance communication.
Circadian control by the reduction/oxidation pathway: Catalase represses light-dependent clock gene expression in the zebrafish
Authors: Hirayama Jun , Cho Sehyung , Sassone-Corsi Paolo
Published: September 2007

Light is the key entraining stimulus for the circadian clock, but several features of the signaling pathways that convert the photic signal to clock entrainment remain to be deciphered. Here, we show that light induces the production of hydrogen peroxide (H
2
O
2
) that acts as the second messenger coupling photoreception to the zebrafish circadian clock. Treatment of light-responsive Z3 cells with H
2
O
2
triggers the induction of
zCry1a
and
zPer2
genes and the subsequent circadian oscillation of
zPer1
. Remarkably, the induction kinetics and oscillation profile in response to H
2
O
2
are identical to those initiated by light. Catalase (
Cat
), an antioxidant enzyme degrading H
2
O
2
, shows an oscillating pattern of expression and activity, antiphasic to
zCry1a
and
zPer2
. Interestingly, overexpression of zCAT results in a reduced light-dependent
zCry1a
and
zPer2
gene induction. In contrast, inhibition of zCAT function enhances light-mediated inducibility of these clock genes. These findings implicate the enzymatic function of zCAT enzyme in the negative regulation of light-dependent clock gene transcriptional activation. Our findings provide an attractive link between the regulation of the cellular reduction/oxidation (redox) state and the photic signaling pathways implicated in circadian control.