bluuebunny/crossref_metadata_2025 huggingface dataset:
MOM1 mediates DNA‐methylation‐independent silencing of repetitive sequences in Arabidopsis
Authors: Vaillant Isabelle , Schubert Ingo , Tourmente Sylvette , Mathieu Olivier
Published: November 2006

The heterochromatic regions around centromeres of animal and plant chromosomes are composed of tandem repetitive sequences, interspersed with transposons and transposon derivatives. These sequences are largely transcriptionally silent and highly methylated, and are associated with specifically modified histones. Although embedded in heterochromatin, Arabidopsis 5S ribosomal RNA genes are among the most highly transcribed genes. However, some 5S genes are silenced, and we show here that this silencing can be suppressed by a reduction in CG methylation. Importantly, we show that mutation of MORPHEUS’ MOLECULE 1 (MOM1) releases 5S repeat silencing independently of chromatin properties, as illustrated by the absence of detectable alteration of DNA and histone H3 methylation patterns. MOM1 also prevents transcription of 180‐bp satellite repeats and 106B dispersed repeats but not of transposons. Our results provide evidence that transcription of densely methylated and highly repetitive heterochromatic sequences is controlled by two distinct epigenetic silencing pathways, one dependent on and the other independent of DNA methylation.
Molecular mechanism of P pilus termination in uropathogenic Escherichia coli
Authors: Verger Denis , Miller Eric , Remaut Han , Waksman Gabriel , Hultgren Scott
Published: November 2006

P pili are important adhesive fibres that are assembled by the conserved chaperone–usher pathway. During pilus assembly, the subunits are incorporated into the growing fibre by the donor‐strand exchange mechanism, whereby the β‐strand of the chaperone, which complements the incomplete immunoglobulin fold of each subunit, is displaced by the amino‐terminal extension of an incoming subunit in a zip‐in‐zip‐out exchange process that is initiated at the P5 pocket, an exposed hydrophobic pocket in the groove of the subunit. In vivo, termination of P pilus growth requires a specialized subunit, PapH. Here, we show that PapH is incorporated at the base of the growing pilus, where it is unable to undergo donor‐strand exchange. This inability is not due to a stronger PapD–PapH interaction, but to a lack of a P5 initiator pocket in the PapH structure, suggesting that PapH terminates pilus growth because it is lacking the initiation point by which donor‐strand exchange proceeds.
Leucocyte expression of the chemokine scavenger D6
Authors: McKimmie C.S. , Graham G.J.
Published: November 2006

Selective sequestration of inflammatory chemokines is critical for the successful resolution of inflammatory responses in vivo. D6 is an atypical chemokine receptor that scavenges inflammatory chemokines and is pivotal in resolving models of chemokine-driven cutaneous inflammation. We provide evidence that expression of D6 is not limited to the lymphatic endothelium at sites of inflammation as previously believed. Instead we postulate that D6 expression in leucocytes may have a significant impact upon chemokine bioavailability during the resolution phase of inflammation. D6 expressed on the lymphatic endothelia may instead have complementary roles in preventing inappropriate leucocyte migration to the lymph node by keeping the endothelium free from inflammatory chemokines.
Dual-specificity phosphatase 1: a critical regulator of innate immune responses
Authors: Abraham S.M. , Clark A.R.
Published: November 2006

Innate immune responses are critically dependent on MAPK (mitogen-activated protein kinase) signalling pathways, in particular JNK (c-Jun N-terminal kinase) and p38 MAPK. Both of these kinases are negatively regulated via their dephosphorylation by DUSP1 (dual­-specificity phosphatase 1). Several pro- and anti-inflammatory stimuli converge to regulate the DUSP1 gene and to modulate the time course of its expression. In turn, the pattern of expression of DUSP1 dictates the kinetics of activation of JNK and p38 MAPK, and this influences the expression of several mediators of innate immunity. DUSP1 is therefore a central regulator of innate immunity, and its expression can profoundly affect the outcome of inflammatory challenges. We discuss possible implications for immune-mediated inflammatory diseases and their treatment.
Protein tyrosine phosphatases as negative regulators of the immune response
Authors: Dolton G.M. , Sathish J.G. , Matthews R.J.
Published: November 2006

In this mini-review, we provide an overview of those PTPs (protein tyrosine phosphatases) that are relevant to the immune response, highlighting the function of a number of intracellular and transmembrane PTPs that have been identified as having important negative regulatory roles on distinct aspects of host immunity.
The human androgen receptor AF1 transactivation domain: interactions with transcription factor IIF and molten-globule-like structural characteristics
Authors: Lavery D.N. , McEwan I.J.
Published: November 2006

The AR (androgen receptor) is a ligand-activated transcription factor and member of the steroid receptor superfamily. The AR responds to the ligands testosterone and dihydrotestosterone and activates multiple downstream genes required in development and reproduction. During the events of transactivation, the AR makes specific protein–protein interactions with several basal transcription factors such as TBP (TATA-box-binding protein) and TFIIF (transcription factor IIF). These interactions occur predominantly within a defined region termed AF1 (activation function-1) located within the highly disordered N-terminal domain of the receptor. Our focus is on the structural aspects of AF1 and how this flexible and disordered domain generates functional interactions with regulators of transcription. Our working hypothesis is that AR-AF1 domain exhibits induced folding when contacted by transcription regulators (such as TFIIF) into a more compact and ‘active’ conformation, enabling further co-regulator recruitment and ultimately transcription. Structural flexibility and intrinsic disorder of AR-AF1 were studied using predictive algorithms and fluorescence spectroscopy under different experimental conditions and the results revealed this domain retains characteristics indicative of molten-globule or pre-molten-globule-like structures. We hypothesize that this partially folded intermediate state is important for, and enables the AF1 domain to make, multiple protein–protein interactions. The structural aspects of AR-AF1 and interactions with TFIIF are discussed.
Transcription regulatory circuits in bacterial plasmids
Authors: Thomas C.M.
Published: November 2006

Gene regulation circuits control all aspects of the life of plasmids. This review gives an overview of the current orchestration of the circuits that control plasmid replication, plasmid transfer, plasmid segregation and plasmid maintenance.
A new paradigm for the regulation of the mammalian ribosomal RNA genes
Authors: Moss T. , Stefanovsky V. , Langlois F. , Gagnon-Kugler T.
Published: November 2006

Ribosome assembly occurs co-transcriptionally on the rRNA genes. This process requires the co-ordinated expression and assembly of many hundreds of proteins and is finely tuned to cell and organism growth. Co-ordinate regulation of the rRNA genes and the ribosomal protein genes is therefore essential for high-fidelity ribosome assembly. Recent work shows that rRNA gene transcription is regulated at the level of elongation via the mitogen-activated protein kinase pathway. We argue that this may provide an explanation for the high fidelity of ribosome assembly.
Structural dynamics of the human androgen receptor: implications for prostate cancer and neurodegenerative disease
Authors: Duff J. , Davies P. , Watt K. , McEwan I.J.
Published: November 2006

The AR (androgen receptor) is a ligand-activated transcription factor that mediates the action of the steroids testosterone and dihydrotestosterone. Alterations in the AR gene result in a number of clinical disorders, including: androgen-insensitivity, which leads to disruption of male development; prostate cancer; and a neuromuscular degenerative condition termed spinal bulbar muscular atrophy or Kennedy's disease. The AR gene is X-linked and the protein is coded for by eight exons, giving rise to a C-terminal LBD (ligand-binding domain; exons 4–8), linked by a hinge region (exon 4) to a Zn-finger DBD (DNA-binding domain; exons 2 and 3) and a large structurally distinct NTD (N-terminal domain; exon 1). Identification and characterization of mutations found in prostate cancer and Kennedy's disease patients have revealed the importance of structural dynamics in the mechanisms of action of receptors. Recent results from our laboratory studying genetic changes in the LBD and the structurally flexible NTD will be discussed.
Mechanisms of androgen receptor repression in prostate cancer
Authors: Powell S.M. , Brooke G.N. , Whitaker H.C. , Reebye V. , Gamble S.C. , Chotai D. , Dart D.A. , Belandia B. , Bevan C.L.
Published: November 2006

Anti-androgens used in prostate cancer therapy inhibit AR (androgen receptor) activity via largely unknown mechanisms. Although initially successful in most cases, they eventually fail and the disease progresses. We need to elucidate how anti-androgens work to understand why they fail, and prolong their effects or design further therapies. Using a cellular model, we found different anti-androgens have diverse effects on subcellular localization of AR, revealing that they work via different mechanisms and suggesting that an informed sequential treatment regime may benefit patients. In the presence of the anti-androgens bicalutamide and hydroxyflutamide, a significant proportion of the AR is translocated to the nucleus but remains inactive. Receptor inhibition under these conditions is likely to involve recruitment of co-repressor proteins, which interact with antagonist-occupied receptor but inhibit receptor-dependent transcription. Which co-repressors are required in vivo for AR repression by anti-androgens is not clear, but one candidate is the Notch effector Hey1. This inhibits ligand-dependent activity of the AR but not other steroid receptors. Further, it is excluded from the nucleus in most human prostate cancers, suggesting that abnormal subcellular distribution of co-repressors may contribute to the aberrant hormonal responses observed in prostate cancer. A decrease in co-repressor function is one possible explanation for the development of anti-androgen-resistant prostate cancer, and this suggests that it may not occur at the gross level of protein expression.
Transcriptional regulation of macrophage cholesterol trafficking by PPARα and LXR
Authors: Chinetti G. , Fruchart J.C. , Staels B.
Published: November 2006

PPARs (peroxisome-proliferator-activated receptors) and LXRs (liver X receptors) are ligand-activated transcription factors that control lipid and glucose metabolism, as well as the inflammatory response. Since the macrophage plays an important role in host defence and immuno-inflammatory pathologies, particular attention has been paid to the role of PPARs and LXRs in the control of macrophage gene expression and function. Altered macrophage functions contribute to the pathogenesis of many infectious, immunological and inflammatory disease processes, including atherosclerosis. Research over the last few years has revealed important roles for PPARs and LXRs in macrophage inflammation and cholesterol homoeostasis with consequences in atherosclerosis development. This review will discuss the role of these transcription factors in the control of cholesterol trafficking in macrophages.
Transforming growth factor-β-regulated expression of genes in macrophages implicated in the control of cholesterol homoeostasis
Authors: Ramji D.P. , Singh N.N. , Foka P. , Irvine S.A. , Arnaoutakis K.
Published: November 2006

The regulation of macrophage cholesterol homoeostasis is of crucial importance in the pathogenesis of atherosclerosis, an underlying cause of heart attack and stroke. Several recent studies have revealed a critical role for the cytokine TGF-β (transforming growth factor-β), a key regulator of the immune and inflammatory responses, in atherogenesis. We discuss here the TGF-β signalling pathway and its role in this disease along with the outcome of our recent studies on the action of the cytokine on the expression of key genes implicated in the uptake or efflux of cholesterol by macrophages and the molecular mechanisms underlying such regulation.
Does everything now make (anti)sense?
Authors: Timmons J.A. , Good L.
Published: November 2006

The data generated by the FANTOM (Functional Annotation of Mouse) consortium, Compugen and Affymetrix have collectively provided evidence that most of the mammalian genomes are actively transcribed. The emergence of an antisense RNA world brings new practical complexities to the study and detection of gene expression. However, we also need to address the fundamental questions regarding the functional importance of these molecules. In this brief paper, we focus on non-coding natural antisense transcription, as it appears to be a potentially powerful mechanism for extending the complexity of the protein coding genome, which is currently unable to explain inter-species diversification.
Cytochrome P450 biodiversity and biotechnology
Authors: Kelly S.L. , Lamb D.C. , Kelly D.E.
Published: November 2006

CYP (cytochrome P450) biodiversity and biotechnology is of importance given the industrial applications and potential for the huge array of genes and proteins that can constitute up to 1% of a coding genome. Historical biotechnological roles for CYPs in mutant fungi diverting the flux of metabolites towards penicillin production, in biotransformations allowing the production of corticosteroids and CYPs as drug targets contribute to interest in the roles of orphan CYPs in the emerging genomes. This area includes studies related to biotransformations and bioremediation, natural product synthesis and its manipulation, tools for exploiting CYPs and using CYPs as biomarkers and drug targets. Fundamental studies on diverse structure and function, on the ecological and evolution of CYPs through geological time and in drug/pesticide resistance also contribute distinctively to this field of CYP research.
The role of cytochrome P450 enzymes in the biosynthesis of camalexin
Authors: Glawischnig E.
Published: November 2006

The biosynthesis of camalexin, the main phytoalexin of the model plant Arabidopsis thaliana, involves at least two CYP (cytochrome P450) steps. It is synthesized from tryptophan via indole-3-acetaldoxime in a reaction catalysed by CYP79B2 and CYP79B3. Based on the pad3 mutant phenotype, CYP71B15 (PAD3) had also been suggested as a camalexin biosynthetic gene. CYP71B15 catalyses the final step in camalexin biosynthesis, as recombinant CYP71B15 and microsomes from Arabidopsis leaves expressing functional PAD3 converted dihydrocamalexic acid into camalexin. The biosynthetic pathway is co-ordinately induced, strictly localized to the site of pathogen infection. This provides a model system to study the regulation of CYP enzymes involved in phytoalexin biosynthesis.
Function and engineering of the 15β-hydroxylase CYP106A2
Authors: Virus C. , Lisurek M. , Simgen B. , Hannemann F. , Bernhardt R.
Published: November 2006

CYP106A2 from Bacillus megaterium ATCC 13368 is a bacterial cytochrome P450 that is capable of transforming steroid hormones. It can be easily expressed in Escherichia coli with a high yield. Its activity in vitro can be achieved by using the adrenal redox proteins adrenodoxin and adrenodoxin reductase. So far, it was not possible to crystallize CYP106A2 because of degradation during the crystallization process. Nevertheless, CYP106A2 is an interesting enzyme for biotechnological use. It hydroxylates pharmaceutically important steroids such as progesterone and 11-deoxycortisol. However, it will be necessary for efficient application of CYP106A2 in biotechnology to improve the hydroxylation activity and manipulate the regiospecificity. The present paper gives an overview of recent developments in protein engineering of CYP106A2.
Towards engineered topogenesis of cytochrome b5 and P450 for in vivo transformation of xenobiotics
Authors: Kaderbhai M.A. , Kelly S.L. , Kaderbhai N.N.
Published: November 2006

Nature is endowed with catalysts capable of an unprecedented diversity of biotransformations, beyond the capabilities of synthetic chemistries. In a biotechnological context, there is a growing and emerging need to tap this catalytic potential. CYP (cytochrome P450) represents a superfamily of enzymes capable of a diverse array of catalytic activities. Distinct members are engaged in biosynthetic reactions within many organisms, while others have a role in the detoxification of foreign compounds. The latter substrates include medicines, pollutants, pesticides, carcinogens, perfumes and herbicides, representing considerable applied importance for pharmacology and toxicology. CYPs show a high degree of stereo- and regio-specificity for their reactions, which have wide industrial applications. Recombinant CYPs are commonly expressed as active recombinant cytosolic forms in Escherichia coli. However, selective permeability of E. coli to many substrates and products can cause problems with product recovery when using whole-cell systems. To overcome these problems, we have been developing approaches to facilitate export of functional recombinant haemoproteins to the inner membrane, periplasm and the outer membrane of E. coli. Here, we describe the progress in relation to cytochrome b5 and CYPs.
Proteomic analysis of cytochromes P450: a mass spectrometry approach
Authors: Wang Y. , Al-Gazzar A. , Seibert C. , Sharif A. , Lane C. , Griffiths W.J.
Published: November 2006

In human, the CYP (cytochrome P450) superfamily comprises 57 genes arranged in 18 families and 42 subfamiles. These genes encode for enzymes involved in the metabolism of drugs, foreign chemicals, fatty acids, eicosanoids and cholesterol. Additionally, they play roles in bile acid biosynthesis, steroid synthesis and metabolism, and vitamin D3 synthesis and metabolism. Mutations in many CYP genes cause inborn errors of metabolism and contribute to increased risk of cancer. MS provides a convenient method for the identification and quantification of CYP enzymes, and in the present paper we will review the current state of the technology for such an analysis.
Vascular matrix adhesion and the blood–brain barrier
Authors: del Zoppo G.J. , Milner R. , Mabuchi T. , Hung S. , Wang X. , Koziol J.A.
Published: November 2006

The integrity of the cerebral microvasculature depends on the interaction between its component cells and the extracellular matrix, as well as reorganized cell–cell interactions. In the central nervous system, matrix adhesion receptors are expressed in the microvasculature and by neurons and their supporting glial cells. Cells within cerebral microvessels express both the integrin and dystroglycan families of matrix adhesion receptors. However, the functional significance of these receptors is only now being explored. Endothelial cells and astrocytes within cerebral capillaries co-operate to generate and maintain the basal lamina and the unique barrier functions of the endothelium. Integrins and the dystroglycan complex are found on the matrix-proximate faces of both endothelial cells and astrocyte end-feet. Pericytes rest against the basal lamina. In the extravascular compartment, select integrins are expressed on neurons, microglial cells and oligodendroglia. Significant alterations in both cellular adhesion receptors and their matrix ligands occur during focal cerebral ischaemia, which support their functional significance in the normal state. We propose that matrix adhesion receptors are essential for the maintenance of the integrity of the blood–brain permeability barrier and that modulation of these receptors contributes to alterations in the barrier during brain injury.
Insights into cytoprotection from ground squirrel hibernation, a natural model of tolerance to profound brain oligaemia
Authors: Lee Y.-J. , Hallenbeck J.M.
Published: November 2006

Progression of acute ischaemic brain damage is complex and multifactorial. Also, evidence suggests that participating molecules and signal transduction pathways can function differently in different cellular contexts. Hibernation torpor, a model of natural tolerance to profoundly reduced blood flow and oxygen delivery to brain, along with models of induced ischaemic tolerance can guide efforts to identify cytoprotective mechanisms that are multifactorial and that target multiple mechanisms in multiple cellular contexts. Post-translational modification of proteins by conjugation with the SUMO (small ubiquitin-related modifier) is massively increased in hibernation and may be such a mechanism.
Blood genomic profiling: novel diagnostic and therapeutic strategies for stroke?
Authors: Baird A.E.
Published: November 2006

Findings from gene expression profiling studies are leading to new diagnostic and therapeutic strategies that can be applied in medical practice, especially in the field of oncology. Promising results of gene expression profiling of the peripheral blood in patients with ischaemic stroke have been obtained in recent pilot studies, demonstrating a partially reproducible gene signature of acute cerebral ischaemia. However, questions remain. Given that blood is at least in part a surrogate tissue for ischaemic stroke, the specificity of these signatures needs to be evaluated. Furthermore, it needs to be determined whether standardization of this methodology is required and whether clinical signatures can be identified that are improvements over the tools currently used in clinical practice. Clinically useful signatures would include those of haemorrhagic as well as ischaemic stroke, reclassification of stroke type and prognosis, and vascular disease risk. If these conditions are met, then it should be possible to develop cost-effective and rapid assays.
Mitochondrial pathways of neuronal necrosis
Authors: Niquet J. , Seo D.-W. , Wasterlain C.G.
Published: November 2006

We examined the mechanism of neuronal necrosis induced by hypoxia, excitotoxicity or non-excitotoxic hypoxia. Our observations showed that neuronal necrosis can be an active process starting with early mitochondrial swelling, followed by cytochrome c release and caspase cascade. Energy failure and/or calcium overloading of mitochondria may trigger this sequence of events. We called this form of necrosis ‘programmed necrosis’. We discuss in this paper the contribution of another mitochondrial death factor, apoptosis-inducing factor.
Valence and conduction intersubband transitions in SiGe, Ge-rich, quantum wells on [001] Si0.5Ge0.5 substrates: A tight-binding approach
Authors: Virgilio Michele , Grosso Giuseppe
Published: November 2006

Electronic and optical properties of germanium-rich Si∕SiGe quantum wells grown on Si0.5Ge0.5 substrates are investigated by a nearest neighbor tight-binding Hamiltonian. The basis set includes spds* orbitals with both spin states. Appropriate scaling laws account for strain effects. We present full electronic band structure calculations both for valence and conduction bands. Confinement effects on the electronic states are considered in detail. Optical spectra related to hole and electron intersubband transitions are derived. Our results for optical absorption due to valence intersubband transitions show excellent agreement with experimental spectra and previous k∙p calculations. For the same quantum well samples, spectra due to conduction intersubband absorption are provided here.
Direct detection of 0.1–20keV electrons with delta doped, fully depleted, high purity silicon p-i-n diode arrays
Authors: Nikzad Shouleh , Cunningham T. J. , Hoenk Michael E. , Ruiz R. P. , Soules D. M. , Holland Stephen E.
Published: November 2006

Direct detection of 0.1–20keV electrons is demonstrated using a boron delta doped high purity Si p-i-n diode array. Molecular beam epitaxy is used to grow a delta layer on the back surface of these fully depletable p-i-n diode arrays to form an electrode for detecting shallow-penetrating ionizing radiation. Device structure, processing, and characterization methods used for device testing and measurement of its response to electrons are discussed. Use of this detector for measuring the Si quantum yield over this wide energy range is also discussed.
Optical modeling of liquid crystal biosensors
Authors: Hwang Dae Kun , Rey Alejandro D.
Published: November 2006

Optical simulations of a liquid crystal biosensor device are performed using an integrated optical/textural model based on the equations of nematodynamics and two optical methods: the Berreman optical matrix method [J. Opt. Soc. Am. 62, 502 (1972)] and the discretization of the Maxwell equations based on the finite difference time domain (FDTD) method. Testing the two optical methods with liquid crystal films of different degrees of orientational heterogeneities demonstrates that only the FDTD method is suitable to model this device. Basic substrate-induced texturing process due to protein adsorption gives rise to an orientation correlation function that is nearly linear with the transmitted light intensity, providing a basis to calibrate the device. The sensitivity of transmitted light to film thickness, protein surface coverage, and wavelength is established. A crossover incident light wavelength close to λco≈500nm is found, such that when λ>λco thinner films are more sensitive to the amount of protein surface coverage, while for λ<λco the reverse holds. In addition it is found that for all wavelengths the sensitivity increases with the amount of protein coverage. The integrated device model based on FDTD optical simulations in conjunction with the Landau-de Gennes nematodynamics model provides a rational basis for further progress in liquid crystal biosensor devices.
On the Weyl algebras for systems with semibounded and bounded configuration space
Authors: Bracci L. , Picasso L. E.
Published: November 2006

We define the Weyl algebra suitable to represent the quantization postulate for one-dimensional systems whose configuration space is semibounded. It consists of a group {V(β)=exp(−iβq),β∊R} of unitary operators and a semigroup {U(α),α⩾0} of nonunitary isometries. We show that the spectrum σ(q) is a half-line [x0,∞), with an arbitrary x0>−∞, and that the irreducible representations of the Weyl algebra with the same x0 are equivalent. We also consider the case when the semigroup of translations is substituted with a semigroup of partial isometries of index 1 (particle confined to a segment of unit length). The uniqueness of the irreducible representations of the related Weyl algebra is proved also for this case by exploiting the result for the half-line.
Effects of a fluctuating sheared flow on cross phase in passive-scalar turbulent diffusion
Authors: Leconte M. , Beyer P. , Benkadda S. , Garbet X.
Published: November 2006

Transport barriers are key elements concerning energy and particle confinement in fusion devices. They play a fundamental role in the L→H transition observed in most tokamaks' edges. It has been shown that a shear in the E×B velocity could trigger and sustain such a barrier. The E×B velocity shear model has proven to be of great interest in the study of the formation and characteristics of transport barriers. Here we address a particular case of flow shear stabilization, namely the effect of a shear flow on the diffusion of a passive scalar. A shear flow reduces the radial flux (radial transport) Γ of a passive scalar field (we consider the pressure field) via the reduction of the turbulence energy ⟨p2⟩ and/or via the reduction of the cross phase cosδ between the fluctuations of the pressure and velocity fields. We compare our results with those of different analytical models for passive-scalar advection or diffusion [Terry et al., Phys. Rev. Lett. 87, 185001 (2001); Kim and Diamond, Phys. Rev. Lett. 91, 075001 (2003)]. However, these studies yielded contradictory results. The purpose of this study is to shed light on this particular issue using numerical simulations to clarify the role of the reduction of the amplitude of turbulence and cross phase in regulating the radial transport.
Experimental evidence of fragile-to-strong dynamic crossover in DNA hydration water
Authors: Chen S.-H. , Liu L. , Chu X. , Zhang Y. , Fratini E. , Baglioni P. , Faraone A. , Mamontov E.
Published: November 2006

We used high-resolution quasielastic neutron scattering spectroscopy to study the single-particle dynamics of water molecules on the surface of hydrated DNA samples. Both H2O and D2O hydrated samples were measured. The contribution of scattering from DNA is subtracted out by taking the difference of the signals between the two samples. The measurement was made at a series of temperatures from 270 down to 185K. The relaxing-cage model was used to analyze the quasielastic spectra. This allowed us to extract a Q-independent average translational relaxation time ⟨τT⟩ of water molecules as a function of temperature. We observe clear evidence of a fragile-to-strong dynamic crossover (FSC) at TL=222±2K by plotting log⟨τT⟩ versus T. The coincidence of the dynamic transition temperature Tc of DNA, signaling the onset of anharmonic molecular motion, and the FSC temperature TL of the hydration water suggests that the change of mobility of the hydration water molecules across TL drives the dynamic transition in DNA.
Spectral function of InAs∕InGaAs quantum dots in a well detector using Green’s function
Authors: Naser M. A. , Deen M. J. , Thompson D. A.
Published: November 2006

Theoretical modeling of an InAs∕InGaAs quantum dot-in-a well (DWELL) detector is reported. The DWELL structure consists of pyramidal-shaped InAs quantum dots with dimensions of 11nm (base) and 6.5nm (height) placed on the top half of an InGaAs quantum well of 11nm width, which is buried in a GaAs matrix. The Green’s function method is used to calculate the spectral function and the density of states of the DWELL. The kinetic equation that governs Green’s functions is solved numerically using the method of finite differences. From the information obtained from the density of states, the responsivity of the DWELL can be estimated. The calculated energy eigenvalues are compared with the experimentally measured responsivity of a DWELL detector.
Electrical spin injection in forward biased Schottky diodes based on InGaAs–GaAs quantum well heterostructures
Authors: Baidus N. V. , Vasilevskiy M. I. , Gomes M. J. M. , Dorokhin M. V. , Demina P. B. , Uskova E. A. , Zvonkov B. N. , Kulakovskii V. D. , Brichkin A. S. , Chernenko A. V. , Zaitsev S. V.
Published: November 2006

The authors demonstrate efficient hole spin injection from a ferromagnetic metal (Ni) contact in a forward biased light emitting Schottky diode (LESD) fabricated on a GaAs based heterostructure with a quantum well (QW). The spin polarization of the injected holes was detected by measuring the circular polarization of the electroluminescence (EL) from the near surface InGaAs∕GaAs QW. An intermediate gold layer has been used in order to improve the spin injection efficiency. Over 40% degree of circular polarization of the EL has been observed at T=2K for the LESD structure with Au–Ni–Au Schottky contact.
Ultrafast time-resolved electron diffraction with megavolt electron beams
Authors: Hastings J. B. , Rudakov F. M. , Dowell D. H. , Schmerge J. F. , Cardoza J. D. , Castro J. M. , Gierman S. M. , Loos H. , Weber P. M.
Published: November 2006

A rf photocathode electron gun is used as an electron source for ultrafast time-resolved pump-probe electron diffraction. The authors observed single-shot diffraction patterns from a 160nm Al foil using the 5.4MeV electron beam from the Gun Test Facility at the Stanford Linear Accelerator. Excellent agreement with simulations suggests that single-shot diffraction experiments with a time resolution approaching 100fs are possible.
Current-induced curing of defective carbon nanotubes
Authors: Suekane Osamu , Nagataki Atsuko , Nakayama Yoshikazu
Published: November 2006

Defective carbon nanotubes (CNTs) were cured using current-induced thermal excitation. The original straight position of a CNT with an artificially induced plastic bend was restored using an applied current of 2.4μA∕nm. That current is nearly equivalent to the current causing sublimation of CNTs. Thermal excitation cures CNTs with defects of pentagons and heptagons. Such cured CNTs have high crystallinity, as confirmed by applying the second process to them to induce an artificial plastic bend and to recover their straight position. That curing phenomenon was also confirmed using a sample of a one-turn coiled CNT with pentagons and heptagons.
Optical gain of InGaAsN∕InP quantum wells for laser applications
Authors: Carrère H. , Marie X. , Lombez L. , Amand T.
Published: November 2006

Dilute nitride structures offer the possibility of growing tensile-strained quantum well lasers on InP substrate emitting in the telecommunication L band. The authors have calculated the characteristics of InGaAs(N)∕InAsP∕InP quantum well structures and compared to the ones of N-free quantum well structures. It appears that the introduction of a fraction of nitrogen as small as 0.3% is enough to pass over the emission wavelength of 1.57μm and induces an increase of the material gain by a factor 3.
Electronic density tailing outside π-conjugated polymer surface
Authors: Hao X. T. , Hosokai T. , Mitsuo N. , Kera S. , Mase K. , Okudaira K. K. , Ueno N.
Published: November 2006

Penning ionization electron spectroscopy (PIES) was adopted to examine surface electronic property of conjugated poly(3-hexylthiophene) (P3HT) aiming to detect the electronic density tailing outside a polymer surface. The electronic wave function of the highest occupied molecular orbital (HOMO) state is shielded by side hexyl chain for a P3HT film with edge-on conformation and was not detected by PIES, while it is tailing outside the polymer surface for face-on conformation and was observed clearly by PIES. The presence of HOMO electronic wave function outside the polymer surface makes it possible to form HOMO-HOMO overlapping with overlayer materials, and therefore more efficient charge transfer is expected in a heterojunction structure for device application.
Temperature dependent metal-induced lateral crystallization of amorphous SiGe on insulating substrate
Authors: Kanno Hiroshi , Toko Kaoru , Sadoh Taizoh , Miyao Masanobu
Published: November 2006

Metal-induced lateral crystallization (MILC) of amorphous SiGe films on SiO2 has been investigated as a function of Ge fraction (0%–100%) and annealing temperature (320–550°C). High temperature annealing (>500°C) caused spontaneous nucleation in amorphous SiGe with a high Ge fraction (>70%). This suppressed the progress of MILC. Spontaneous nucleation was significantly suppressed by lowering the annealing temperature (<400°C). As a result, large poly-SiGe regions (>20μm) were observed around Ni patterns even for high Ge fractions (>70%). In this way, MILC of amorphous SiGe was achieved for samples with whole Ge fractions (0%–100%).
Thermoluminescence properties of ZnO and ZnO:Yb nanophosphors
Authors: Pal U. , Meléndrez R. , Chernov V. , Barboza-Flores M.
Published: November 2006

ZnO and ZnO:Yb thermoluminescence nanophosphors have been developed and tested under beta radiation. Spherical nanoparticles of sizes ranging from 130to1200nm were prepared through a glycol mediated chemical synthesis. The Yb doping had a thermoluminescence quenching effect compared to undoped ZnO. The 5% Yb concentration produced a low fading, a single thermoluminescence glow peak structure, and a dose linearity behavior adequate for thermoluminescence dosimetry applications. The ZnO:Yb nanophosphor has a great potential as a dosimeter for monitoring in ionizing radiation fields.
Observation of large magnetoresistance of magnetic Heusler alloy Ni50Mn36Sn14 in high magnetic fields
Authors: Koyama Keiichi , Okada Hironari , Watanabe Kazuo , Kanomata Takeshi , Kainuma Ryosuke , Ito Wataru , Oikawa Katsunari , Ishida Kiyohito
Published: November 2006

The magnetic and electrical properties on magnetic Heusler alloy Ni50Mn36Sn14 were studied in magnetic fields up to 18T in 4.2–270K temperature range. It was found that at the vicinity of 160K the resistivity jump of 46% is accompanied by the magnetic phase transition. Furthermore, the large magnetoresistance effect of 50% by the magnetic field induced magnetic phase transition was observed.
Transparent cobalt doped MgO–Ga2O3–SiO2 nano-glass-ceramic composites
Authors: Duan X. L. , Yuan D. R. , Yu F. P. , Wang L. H.
Published: November 2006

Transparent cobalt doped MgO–Ga2O3–SiO2 nano-glass-ceramic composites were prepared from Si, Ga, Mg, and Co molecular precursors by a sol-gel method. X-ray diffraction patterns and transmission electron microscopy showed that the resulting material is composed of an amorphous silicate network that encloses nanocrystalline MgGa2O4 particles. Analysis of the absorption and luminescence properties indicates that Co ions are, at least partially, trapped in the crystalline phase and located in tetrahedral sites in MgGa2O4 nanocrystals. The absorption section was calculated to be 1.15×10−19cm2.
Silver-nanoparticle-decorated carbon nanoscaffolds: Application as a sensing platform
Authors: Henley S. J. , Carey J. D. , Silva S. R. P.
Published: November 2006

Cluster-assembled nanostructured carbon with a fractal morphology is employed as a large-area surface scaffold for metal decoration. By depositing silver by pulsed laser ablation densely packed, distributions of metal nanoparticles are produced. The authors show, using the surface-enhanced Raman effect and the modification of fluorescence quantum yields near metallic surfaces, that silver-coated nanostructured carbon can be used to sense low concentrations of biomolecules.
Shot noise thermometry down to 10mK
Authors: Spietz Lafe , Schoelkopf R. J. , Pari Patrick
Published: November 2006

The authors report measurements of the shot noise thermometer (SNT), a primary thermometer based on the electronic noise from a tunnel junction, in the range from 10to200mK. They demonstrate operation of the SNT down to 10mK with 10% accuracy at the lowest measured temperature. At 10mK, where for a measurement frequency of f=450MHz, hf=2.5kBT, the authors demonstrate that provided that quantum corrections are taken into account, the SNT continues to be a practical thermometer. They also show that self-heating is not a measurable problem and demonstrate a simplified readout of the SNT.
Magnetoresistance oscillations in two-dimensional electron systems under monochromatic and bichromatic radiations
Authors: Lei X. L. , Liu S. Y.
Published: November 2006

The magnetoresistance oscillations in high-mobility two-dimensional electron systems induced by two radiation fields of frequencies 31 and 47GHz are analyzed in a wide magnetic-field range down to 100G, using the balance-equation approach to magnetotransport for high-carrier-density systems. The frequency mixing processes are shown to be important. The predicted peak positions, relative heights, radiation-intensity dependence and their relation with monochromatic resistivities are in good agreement with recent experimental finding [M. A. Zudov et al., Phys. Rev. Lett. 96, 236804 (2006)].
Voltage-controlled multicolor emitting devices
Authors: Wang Fuzhi , Wang Ping , Fan Xing , Dang Xiangnan , Zhen Changgua , Zou Dechun , Kim Eun Hwa , Lee Do Nam , Kim Byeong Hyo
Published: November 2006

Voltage-controlled multicolor emitting devices were fabricated by combining an organic light-emitting diode and a solid-state electrochemiluminescent device. Though the device has a simple-stacking structure with Ru(II) complex, tris(8-hydroxyquinolinato) aluminum, 4,4′-bis(2,2′-diphenylvinyl)-1,1′-biphenyl, and N,N′-bis(naphthalen-1-yl)-N,N′-bis(phenyl)-benzidine as basic materials, it is able to stably emit different colors, from pure green to pure red or from pure blue to pure red, under different driving biases. Its luminance can reach up to 1836cd∕m2 with current efficiency reaching 1.84cd∕A. The Ru(II) complex is considered to play a dominant role in this kind of device due to its unique reversible redox property.
Cotunneling current in Si single-electron transistor based on multiple islands
Authors: Ohkura Kensaku , Kitade Tetsuya , Nakajima Anri
Published: November 2006

The authors fabricated highly doped Si single-electron transistors (SETs) with three islands. The valley current of the obtained Coulomb oscillation was systematically investigated in comparison with the cotunneling theory. The temperature dependence of the valley current was well described by the inelastic cotunneling theory above 40K in the low drain voltage region. Since the inelastic cotunneling current was confirmed to be dominant in the high temperature region and is exponentially suppressed by multiplexing islands, SETs with multiple islands are promising for the practical application such as reliable circuit operations.
Optical properties of CdTe∕ZnTe quantum dots sandwiched between two quantum wells with ZnTe separation barriers
Authors: Lee H. S. , Park H. L. , Kim T. W.
Published: November 2006

Temperature-dependent photoluminescence (PL) measurements were performed to investigate the optical properties of CdTe∕ZnTe nanostructures. The activation energy of the CdTe∕ZnTe quantum dots (QDs) sandwiched between two quantum wells (QWs) with ZnTe separation barriers, as obtained from the temperature-dependent PL spectra, was much larger than the activation energies of the QDs alone and of the QDs combined with a single QW. This behavior can be attributed to a transfer of carriers from the QWs to the QDs through a separation layer due to a nonresonant multiphonon-assisted tunneling process resulting from carrier thermal emission.
High density InAs∕GaAs quantum dots with enhanced photoluminescence intensity using antimony surfactant-mediated metal organic chemical vapor deposition
Authors: Guimard Denis , Nishioka Masao , Tsukamoto Shiro , Arakawa Yasuhiko
Published: November 2006

The antimony surfactant-mediated growth of InAs∕GaAs quantum dots (QDs) by metal organic chemical vapor deposition was investigated. The authors show that the growth of InAs QDs on Sb:GaAs(100) can result in both a strong increase of the dot density, up to 1011cm−2, and the suppression of coalescence. They achieved InAs∕Sb:GaAs QDs with density above 4×1010cm−2, ground-state emission above 1.30μm, and enhanced photoluminescence intensity at room temperature compared to that of InAs∕GaAs QDs. Remarkably, InAs∕Sb:GaAs QDs do not exhibit an emission blueshift under annealing at temperatures as high as 630°C, contrary to InAs∕GaAs QDs.
Multiple pathways of selected gene amplification during adaptive mutation
Authors: Kugelberg Elisabeth , Kofoid Eric , Reams Andrew B. , Andersson Dan I. , Roth John R.
Published: November 2006

In a phenomenon referred to as “adaptive mutation,” a population of bacterial cells with a mutation in the
lac
operon (
lac
−
) accumulates Lac
+
revertants during prolonged exposure to selective growth conditions (lactose). Evidence was provided that selective conditions do not increase the mutation rate but instead favor the growth of rare cells with a duplication of the leaky
lac
allele. A further increase in copy number (amplification) improves growth and increases the likelihood of a sequence change by adding more mutational targets to the clone (cells and
lac
copies per cell). These duplications and amplifications are described here. Before selection, cells with large (134-kb)
lac
duplications and long junction sequences (>1 kb) were common (0.2%). The same large repeats were found after selection in cells with a low-copy-number
lac
amplification. Surprisingly, smaller repeats (average, 34 kb) were found in high-copy-number amplifications. The small-repeat duplications form when deletions modify a preexisting large-repeat duplication. The shorter repeat size allowed higher
lac
amplification and better growth on lactose. Thus, selection favors a succession of gene-amplification types that make sequence changes more probable by adding targets. These findings are relevant to genetic adaptation in any biological systems in which fitness can be increased by adding gene copies (e.g., cancer and bacterial drug resistance).
The Role of K+Channels in Determining Pulmonary Vascular Tone, Oxygen Sensing, Cell Proliferation, and Apoptosis: Implications in Hypoxic Pulmonary Vasoconstriction and Pulmonary Arterial Hypertension
Authors: MOUDGIL ROHIT , MICHELAKIS EVANGELOS D. , ARCHER STEPHEN L.
Published: November 2006

Potassium channels are tetrameric, membrane‐spanning proteins that selectively conduct K+at near diffusion‐limited rates. Their remarkable ionic selectivity results from a highly‐conserved K+recognition sequence in the pore. The classical function of K+channels is regulation of membrane potential (EM) and thence vascular tone. In pulmonary artery smooth muscle cells (PASMC), tonic K+egress, driven by a 145/5 mM intracellular/extracellular concentration gradient, contributes to aEMof about −60 mV. It has been recently discovered that K+channels also participate in vascular remodeling by regulating cell proliferation and apoptosis. PASMC express voltage‐gated (Kv), inward rectifier (Kir), calcium‐sensitive (KCa), and two‐pore (K2P) channels. Certain K+channels are subject to rapid redox regulation by reactive oxygen species (ROS) derived from the PASMC's oxygen‐sensor (mitochondria and/or NADPH oxidase). Acute hypoxic inhibition of ROS production inhibits Kv1.5, which depolarizesEM, opens voltage‐sensitive, L‐type calcium channels, elevates cytosolic calcium, and initiates hypoxic pulmonary vasoconstriction (HPV). Hypoxia‐inhibited K+currents are not seen in systemic arterial SMCs. Kvexpression is also transcriptionally regulated by HIF‐1α and NFAT. Loss of PASMC Kv1.5 and Kv2.1 contributes to the pathogenesis of pulmonary arterial hypertension (PAH) by causing a sustained depolarization, which increases intracellular calcium and K+, thereby stimulating cell proliferation and inhibiting apoptosis, respectively. Restoring Kvexpression (via Kv1.5 gene therapy, dichloroacetate, or anti‐survivin therapy) reduces experimental PAH. Electrophysiological diversity exists within the pulmonary circulation. Resistance PASMC have a homogeneous Kvcurrent (including an oxygen‐sensitive component), whereas conduit PASMC current is a Kv/KCamosaic. This reflects regional differences in expression of channel isoforms, heterotetramers, splice variants, and regulatory subunits as well as mitochondrial diversity. In conclusion, K+channels regulate pulmonary vascular tone and remodeling and constitute potential therapeutic targets in the regression of PAH.
Male swordtails court with an audience in mind
Authors: Fisher Heidi S , Rosenthal Gil G
Published: November 2006

Females are usually considered to be the target of male courtship behaviour. In nature, however, social interactions rarely occur without other observers; thus, it is conceivable that some male courtship behaviours are directed not towards females, but rather towards male rivals. The northern swordtail,
Xiphophorus birchmanni
, is a freshwater fish found in high densities in natural streams. Males court by swimming close to and in parallel with the female, raising their large sail-like dorsal fin, and quivering briefly. Here, we show that females prefer males that display small dorsal fins to those with large ones, and that males are less aggressive to other males with large dorsal fins. Male swordtails also raise their dorsal fins more frequently when courting in the presence of other males. These results suggest that, despite female avoidance of large dorsal fins, males that raise their fin during courtship benefit by intimidating potential competitors; the intended receivers of this signal are thus males, not females. Intrasexual selection can therefore offset the forces of intersexual selection, even in a courtship display.