bluuebunny/crossref_metadata_2025 huggingface dataset:
Nutrigenomics and nutrigenetics: the ‘omics’ revolution in nutritional science
Authors: Mariman Edwin C. M.
Published: May 2006

The execution of the Human Genome Project has brought forth a wealth of information about the structure of the genome, which can now be used to study how the interplay between our genes and factors from the environment such as nutrition relate to a state of health or disease. To enable such studies, novel technologies have been designed in particular to monitor the activity of multiple genes simultaneously at the level of the RNA by transcriptomics, or the level of the proteins by proteomics. In addition, genome information has boosted approaches to study the role of genetic variation to explain individual differences in responses to nutrition, underlying in part the susceptibility for nutrition‐related disorders. These new areas of science referred to as ‘nutrigenomics’ and ‘nutrigenetics’ respectively, will increase our fundamental knowledge of the interaction between life processes and our diet or specific components thereof, which may in time lead to the development of novel functional foods to improve the health status of the general population, and to the personalized diet to prevent the onset of nutrition‐related disorders in genetically predisposed individuals.
A simple non‐destructive method for the fixation and immunostaining of cultured cells encapsulated in alginate
Authors: Leal‐Egana Aldo , Heinrich J. Michael , Smith Mark D. , Nowicki Marcin , Bader Augustinus
Published: May 2006

In the present paper we report a simple non‐destructive method for the analysis of cells and their proteins encapsulated in alginate. Investigations with a co‐culture of the human hepatoma cell line HepG2 and primary human fibroblasts are reported. We studied the expression of three proteins, namely intracellular α‐foetoprotein and extracellular albumin, expressed by HepG2, and membrane‐bound CD90 (Thy‐1), expressed by the fibroblasts. Fluorimetric and colorimetric staining methods were evaluated and compared. We optimized the method by investigating a range of concentrations of the washing buffers. The technique protected the capsule and cell structures and enabled the investigated proteins to be clearly and reliably visualized within the encapsulated co‐culture in their respective intracellular, membrane‐bound and extracellular domains. These results demonstrate that this simple method is suitable for the non‐destructive analysis of protein expression by cells encapsulated in alginate.
Production of recombinant HIV‐1 Nef (negative factor) protein using Pichia pastoris and a low‐temperature fed‐batch strategy
Authors: Sirén Noora , Weegar Jan , Dahlbacka John , Kalkkinen Nisse , Fagervik Kaj , Leisola Matti , Von Weymarn Niklas
Published: May 2006

In the present paper we describe the cloning and extracellular expression of the HIV‐1 Nef (negative factor) protein utilizing the yeast Pichia pastoris, as well as the successful use of a low‐temperature fed‐batch strategy for decreasing end‐product degradation by proteases. The nef gene in a pPICZαA vector was integrated into the genome of three different P. pastoris strains, namely X‐33, GS115 and KM71H. On the basis of its efficient growth and production characteristics the wild‐type strain (X‐33) was found to be the best choice. The decreased end‐product degradation at low temperatures was not due to lower amounts of proteases but due to their diminished activity. The yield of biomass from methanol was improved 1.44‐fold utilizing the low‐temperature strategy compared with the standard fermentation. Purification of histidine‐tagged Nef was performed in one step using a Ni2+‐nitrilotriacetate–Sepharose column. The purified product was characterized by SDS/PAGE, Western blotting, matrix‐assisted laser‐desorption ionization–time‐of‐flight MS, reversed‐phase HPLC and N‐terminal‐sequence analysis.
Improved pharmacological properties for superoxide dismutase modified with mannan
Authors: Valdivia Aymara , Pérez Yunel , Dominguez Amalia , Caballero Julio , Hernández Yunior , Villalonga Reynaldo
Published: May 2006

Mannan from Sacharomyces cerevisiae was activated by oxidation with NaIO4 (sodium m‐periodate) and further linked to SOD (superoxide dismutase) via reductive alkylation with NaBH4 (sodium borohydride). The gly‐cosidated enzyme contained an average of 1.2 mol of polysaccharide per mol of protein and retained 52% of its initial activity. The modified enzyme was 560‐fold more resistant to inactivation with H2O2 and acquired a lectin‐recognition capacity in respect of concanavalin A. The anti‐inflammatory activity of SOD was increased 2‐fold and its plasma half‐life time was prolonged from 4.8 min to 1.7 h after glycosylation with the polymer.
Effect of Ku proteins on IRES‐mediated translation
Authors: Silvera Deborah , Koloteva‐Levine Nadejda , Burma Sandeep , Elroy‐Stein Orna
Published: May 2006

Background information. Ku is an abundant nuclear heterodimeric protein composed of 70 and 86 kDa subunits. As an activator of the catalytic subunit of DNA‐PK (DNA‐dependent protein kinase), Ku plays an important role in DNA repair and recombination. Ku is also involved in actions independent of DNA‐PK, such as transcription regulation and telomere maintenance. Although Ku is localized in the cytoplasm under specific cellular conditions, no functions for Ku outside of the nucleus have as yet been reported. In addition to DNA binding, Ku binds specific RNA sequences with high affinity. However, no specific cellular mRNA targets for Ku have been identified.

Results. In a yeast three‐hybrid system, Ku70 bound to an RNA bait that contained an IRES (internal ribosomal entry site) element. A single band with migration properties similar to those of Ku70 was immunoprecipitated with anti‐Ku antibody, using UV cross‐linked complexes formed by HeLa cell nuclear extracts and an IRES‐containing RNA probe. IRES activity was reduced in Ku80−/− cells. Overexpression of Ku proteins stimulated IRES‐dependent translation.

Conclusions. The present study suggests that Ku binds IRES elements within RNA molecules, and that Ku plays a role in the modulation of IRES‐mediated mRNA translation.
Regulation of the actin cytoskeleton by PIP2 in cytokinesis
Authors: Logan Michael R. , Mandato Craig A.
Published: May 2006

Cytokinesis is a sequential process that occurs in three phases: assembly of the cytokinetic apparatus, furrow progression and fission (abscission) of the newly formed daughter cells. The ingression of the cleavage furrow is dependent on the constriction of an equatorial actomyosin ring in many cell types. Recent studies have demonstrated that this structure is highly dynamic and undergoes active polymerization and depolymerization throughout the furrowing process. Despite much progress in the identification of contractile ring components, little is known regarding the mechanism of its assembly and structural rearrangements. PIP2 (phosphatidylinositol 4,5‐bisphosphate) is a critical regulator of actin dynamics and plays an essential role in cell motility and adhesion. Recent studies have indicated that an elevation of PIP2 at the cleavage furrow is a critical event for furrow stability. In this review we discuss the role of PIP2‐mediated signalling in the structural maintenance of the contractile ring and furrow progression. In addition, we address the role of other phosphoinositides, PI(4)P (phosphatidylinositol 4‐phosphate) and PIP3 (phosphatidylinositol 3,4,5‐triphosphate) in these processes.
Regulation of ecto-5′-nucleotidase activity via Ca2+-dependent, annexin 2-mediated membrane rearrangement?
Authors: Babiychuk E.B. , Draeger A.
Published: May 2006

The spatial segregation of the plasma membrane plays a prominent role in distinguishing and sorting a large number of signals a cell receives simultaneously. The plasma membrane comprises regions known as lipid rafts, which serve as signal-transduction hubs and platforms for sorting membrane-associated proteins. Ca2+-binding proteins of the annexin family have been ascribed a role in the regulation of raft dynamics. Glycosylphosphatidylinositol-anchored 5′-nucleotidase is an extracellular, raft-associated enzyme responsible for conversion of extracellular ATP into adenosine. Our results point to a regulation of ecto-5′-nucleotidase activity by Ca2+-dependent, annexin-mediated stabilization of membrane rafts.
Movement of calcium signals and calcium-binding proteins: firewalls, traps and tunnels
Authors: Barrow S.L. , Sherwood M.W. , Dolman N.J. , Gerasimenko O.V. , Voronina S.G. , Tepikin A.V.
Published: May 2006

In the board game ‘Snakes and Ladders’, placed on the image of a pancreatic acinar cell, calcium ions have to move from release sites in the secretory region to the nucleus. There is another important contraflow – from calcium entry channels in the basal part of the cell to ER (endoplasmic reticulum) terminals in the secretory granule region. Both transport routes are perilous as the messenger can disappear in any place on the game board. It can be grabbed by calcium ATPases of the ER (masquerading as a snake but functioning like a ladder) and tunnelled through its low buffering environment, it can be lured into the whirlpools of mitochondria uniporters and forced to regulate the tricarboxylic acid cycle, and it can be permanently placed inside the matrix of secretory granules and released only outside the cell. The organelles could trade calcium (e.g. from the ER to mitochondria and vice versa) almost depriving this ion the light of the cytosol and noble company of cytosolic calcium buffers. Altogether it is a rich and colourful story.
Self-organized Te redistribution during driven reconnection processes in high-temperature plasmas
Authors: Park H. K. , Mazzucato E. , Luhmann N. C. , Domier C. W. , Xia Z. , Munsat T. , Donné A. J. H. , Classen I. G. J. , van de Pol M. J. ,   TEXTOR team
Published: May 2006

Two-dimensional (2D) images of electron temperature fluctuations with high temporal and spatial resolution were employed to study the sawtooth oscillation in Toroidal EXperiment for Technology Oriented Research [S. S. Abdallaev et al., Nucl. Fusion 43, 299 (2003)] tokamak plasmas. The new findings are: (1) 2D images revealed that the reconnection is localized and permitted the determination of the physical dimensions of the reconnection zone in the poloidal and toroidal planes. (2) The combination of a pressure bulge due to finite pressure effects or a kink instability accompanied with a sharp pressure point leads to an “X-point” reconnection process. (3) Reconnection can take place anywhere along the q∼1 rational magnetic surface (both high- and low-field sides). (4) Heat flow from the core to the outside of the inversion radius during the reconnection time is through the finite opening on the poloidal and toroidal planes and the flow is highly collective. These new findings are compared with the characteristics of various theoretical models and experimental results for the study of the sawtooth oscillation in tokamak plasmas.
Infrared absorptions of NH3(H2) complexes trapped in solid neon
Authors: Jacox Marilyn E. , Thompson Warren E.
Published: May 2006

When a very small concentration of H2 is added to a Ne:NH3=800:1 sample and the resulting mixture is deposited at 4.3K, a new absorption appears at 4151.1cm−1 which can be assigned to the H2 stretching fundamental of H2 (j=1) complexed with NH3. Other new absorptions which appear near the vibrational fundamentals of NH3 are assigned to the NH3 moiety in this complex and in the complex of NH3 with H2 (j=0). The results of experiments in which HD or D2 is added to the Ne:NH3 mixture support these assignments. Ab initio and density functional calculations predict the observed infrared activation of the H2-stretching vibration for a structure in which the axis of the H2 molecule is collinear with the threefold axis of the NH3. The dependence of the observed absorption patterns on the concentration of H2 in the sample indicates that complexes of NH3 with two or more H2 molecules also form readily.
Boundary slip and wetting properties of interfaces: Correlation of the contact angle with the slip length
Authors: Voronov Roman S. , Papavassiliou Dimitrios V. , Lee Lloyd L.
Published: May 2006

Correlations between contact angle, a measure of the wetting of surfaces, and slip length are developed using nonequilibrium molecular dynamics for a Lennard-Jones fluid in Couette flow between graphitelike hexagonal-lattice walls. The fluid-wall interaction is varied by modulating the interfacial energy parameter εr=εsf∕εff and the size parameter σr=σsf∕σff, (s=solid, f=fluid) to achieve hydrophobicity (solvophobicity) or hydrophilicity (solvophilicity). The effects of surface chemistry, as well as the effects of temperature and shear rate on the slip length are determined. The contact angle increases from 25° to 147° on highly hydrophobic surfaces (as εr decreases from 0.5 to 0.1), as expected. The slip length is functionally dependent on the affinity strength parameters εr and σr: increasing logarithmically with decreasing surface energy εr (i.e., more hydrophobic), while decreasing with power law with decreasing size σr. The mechanism for the latter is different from the energetic case. While weak wall forces (small εr) produce hydrophobicity, larger σr smoothes out the surface roughness. Both tend to increase the slip. The slip length grows rapidly with a high shear rate, as wall velocity increases three decades from 100to105m∕s. We demonstrate that fluid-solid interfaces with low εr and high σr should be chosen to increase slip and are prime candidates for drag reduction.
From local hybrid functionals to “localized local hybrid” potentials: Formalism and thermochemical tests
Authors: Arbuznikov Alexei V. , Kaupp Martin , Bahmann Hilke
Published: May 2006

Hybrid exchange-correlation functionals with position-dependent exact-exchange admixture (local hybrid functionals) have been implemented self-consistently for the first time. Functional derivatives with respect to the occupied orbitals have been derived and were subsequently transformed into local and multiplicative potentials within the framework of the optimized effective potential. The resulting local and multiplicative Kohn-Sham potentials are termed “localized local hybrid” (LLH) potentials. They have been evaluated in calculations of atomization energies for a series of main-group molecules. It is shown that LLH potentials yield somewhat better thermochemical results than non-self-consistent post-GGA calculations with the same local hybrid energy functionals for orbitals obtained with a different potential. The choice of the “local mixing function” (LMF) is discussed. This is the key quantity for the performance of local hybrid functionals that determines the amount of exact-exchange admixture at a given point in space. Careful analyses of average exact-exchange admixtures and of the spatial variation of two different LMFs for various molecules provide insight into the shortcomings of the currently used local hybrid functionals. Beyond a too large average exact-exchange admixture, both LMFs used appear to provide an unbalanced description of exact-exchange admixture across bonds to hydrogen. LLH potentials open the way for property calculations with local hybrid functionals.
Photodissociation dynamics of the HCNN radical
Authors: Faulhaber Ann Elise , Gascooke Jason R. , Hoops Alexandra A. , Neumark Daniel M.
Published: May 2006

The photodissociation dynamics of the diazomethyl (HCNN) radical have been studied using fast radical beam photofragment translational spectroscopy. A photofragment yield spectrum was obtained for the range of 25510–40820cm−1, and photodissociation was shown to occur for energies above 25600cm−1. The only product channel observed was the formation of CH and N2. Fragment translational energy and angular distributions were obtained at several energies in the range covered by the photofragment yield spectrum. The fragment translational energy distributions showed at least two distinct features at energies up to 4.59eV, and were not well fit by phase space theory at any of the excitation energies studied. A revised C–N bond dissociation energy and heat of formation for HCNN, D0(HC–NN)=1.139±0.019eV and ΔfH0(HCNN)=5.010±0.023eV, were determined.
Molecular dynamics of polystyrene solutions in microwave fields
Authors: Purdue Mark J. , MacElroy J. M. D. , O’Shea D. F. , Okuom Macduff O. , Blum Frank D.
Published: May 2006

Equilibrium and nonequilibrium molecular dynamics simulation techniques were used to assess the influence of an applied microwave field on the dynamics of methylamine-methanol and methylamine-dimethylformamide (DMF) solutions bound within atactic polystyrene over a range of polymer densities from 35to96wt% polymer. Atomistically detailed systems were studied, ranging from 3000 to 10 644 particles, using previously established potential models. Structural and dynamical properties were determined in the canonical (NVT) ensemble at 298K. The simulated DMF self-diffusion coefficients in polystyrene solutions were compared with the zero-field experimental results established with pulsed-gradient spin-echo NMR spectrometry. A simulated external microwave field, with a rms electric field intensity of 0.1V∕Å, was applied to these systems and the simulated dynamical results over field frequencies up to 104GHz were compared with the zero-field values. Simulated evidence of athermal effects on the diffusive characteristics of these mixtures is reported.
Plasma accelerators race to 10GeV and beyond
Authors: Katsouleas T.
Published: May 2006

This paper reviews the concepts, recent history, and current challenges for realizing ultracompact particle accelerators based on surfing on plasma waves. Ideas that seemed fanciful when first proposed by John Dawson in the late 1970s have now come to fruition as a result of the development of ultrashort high-power laser and particle beam drivers, tunnel-ionized plasma sources, and one-to-one particle simulation capability. Breakthroughs in the past 2 years have dramatically advanced the field. Laser-driven gas jets now produce 100MeV beams of electrons that are monoenergetic and that have transverse beam quality and brightness exceeding that in conventional accelerators. Electron-beam driven plasma waves driven by the 28GeV electron beam of the Stanford Linear Accelerator Center have been used to accelerate electrons in the tail of the beam by more than 10GeV in less than 30cm. The prospects for extending both of these schemes to the energy frontier (currently 50GeV) and beyond are discussed.
Effective molecular diffusion coefficient in a two-phase gel medium
Authors: Hickey Owen A. , Mercier Jean-François , Gauthier Michel G. , Tessier Frédéric , Bekhechi Smaine , Slater Gary W.
Published: May 2006

We derive a mean-field expression for the effective diffusion coefficient of a probe molecule in a two-phase medium consisting of a hydrogel with large gel-free solvent inclusions, in terms of the homogeneous diffusion coefficients in the gel and in the solvent. Upon comparing with exact numerical lattice calculations, we find that our expression provides a remarkably accurate prediction for the effective diffusion coefficient, over a wide range of gel concentration and relative volume fraction of the two phases. Moreover, we extend our model to handle spatial variations of viscosity, thereby allowing us to treat cases where the solvent viscosity itself is inhomogeneous. This work provides robust grounds for the modeling and design of multiphase systems for specific applications, e.g., hydrogels as novel food agents or efficient drug-delivery platforms.
Two-photon absorption strength: A new tool for the quantification of two-photon absorption
Authors: Fortrie Rémy , Chermette Henry
Published: May 2006

In this paper, we define the two-photon absorption strength, a new characterization tool, similar to the oscillator strength, but for two-photon absorption. It allows the quantification of the two-photon absorption properties of molecular systems which are one-photon transparent. Its definition is such that the corresponding numerical values are around 100 for small molecules. We also show that this new theoretical tool allows the direct comparison of experimental and theoretical data without requiring the introduction of any arbitrary band width. As an example, the experimental and theoretical (AM1+CNDO∕S and HF+CIS∕3-21G) two-photon absorption properties of the 2,2′-bi(9,9-dihexylfluorene) molecule are compared.
Dielectric properties of pyrochlore (Bi1.5Zn0.5)(Nb0.5M1.5)O7 (M=Ti, Sn, Zr, and Ce) dielectrics
Authors: Du Huiling , Yao Xi , Wang Hong
Published: May 2006

Pyrochlore type systems with generic formula (Bi1.5Zn0.5)(Nb0.5M1.5)O7 (M=Ti, Sn, Zr, and Ce) have been synthesized to investigate the influence of M on the dielectric properties. It was found that the incorporation of Sn or Ce resulted in a reasonably reduced dielectric constant. The incorporation of Zr and Ce has led to an appreciable increase in dc conductivity in high temperature. The dc conductivity diminishes as the size of M grows. Dielectric constants, temperature coefficient, and dc conductivity of series ceramics were studied and the relationships among composition, crystal structure, and properties were discussed.
Wideband measurement of shear induced birefringence by quadrupole method
Authors: Hosoda M. , Horii K. , Nomura H. , Sakai K.
Published: May 2006

We developed a new method for the measurement of the dynamic birefringence induced by the alternating shear deformation in fluid samples. A quadrupole piezoactuator generates the pure shear deformation in the frequency range from 1Hzto5kHz and causes the molecular orientation, or the anisotropic conformation of polymers and molecular associations, which is observed by the optical ellipsometry technique. The spectrum of the shear-induced birefringence observed for the isotropic phase of the liquid crystal p-n-hexyl p′-cyanobiphenyl (6CB) shows linear dependence on the frequency up to 5kHz, corroborating the effective band of the experimental system. The sensitivity of the system was demonstrated by the quantitative measurement of the birefringence for the isotropic phase of p-n-pentyl p′-cyanobiphenyl (5CB). The system was also applied to the aqueous solution of the worm such as micelles and the result shows the relaxation of shear induced birefringence at around 10Hz, which agrees well with the previous reports.
Larmor radius size density holes discovered in the solar wind upstream of Earth’s bow shock
Authors: Parks G. K. , Lee E. , Mozer F. , Wilber M. , Lucek E. , Dandouras I. , Rème H. , Mazelle C. , Cao J. B. , Meziane K. , Goldstein M. L. , Escoubet P.
Published: May 2006

The Cluster and Double Star satellites recently observed plasma density holes upstream of Earth’s collisionless bow shock to apogee distances of ∼19 and 13 earth radii, respectively. A survey of 147 isolated density holes using 4s time resolution data shows they have a mean duration of ∼17.9±10.4s, but holes as short as 4s are observed. The average fractional density depletion (δn∕n) inside the holes is ∼0.68±0.14. The upstream edge of density holes can have enhanced densities that are five or more times the solar wind density. Particle distributions show the steepened edge can behave like a shock. Multispacecraft analyses show the density holes move with the solar wind, can have an ion gyroradius scale, and could be expanding. A small normal electric field points outward. Similarly shaped magnetic holes accompany the density holes indicating strong coupling between fields and particles. The density holes are only observed with upstream particles, suggesting that backstreaming particles interacting with the solar wind are important.
Charging properties of a dust grain in collisional plasmas
Authors: Khrapak S. A. , Morfill G. E. , Khrapak A. G. , D’yachkov L. G.
Published: May 2006

Charging related properties of a small spherical grain immersed in a collisional plasma are investigated. Asymptotic expressions for charging fluxes, grain surface potential, long range electrostatic potential, and the properties of grain charge fluctuations due to the discrete nature of the charging process are obtained. These analytical results are in reasonable agreement with the available results of numerical modeling.
Addressing the problem of plasma shell formation around an exploding wire in water
Authors: Grinenko A. , Efimov S. , Fedotov A. , Krasik Ya. E. , Schnitzer I.
Published: May 2006

Analysis of time- and space-resolved spectrum of radiation emitted from the discharge channel generated by an underwater electrical wire explosion is reported. The purpose of this investigation was to detect a possible shunting corona discharge. During careful analysis of the emitted radiation no evidence for such discharge was found. Discharge temperature of 7eV was estimated by quantitative analysis of the emitted spectra.
Generation of zonal flows by ion-temperature-gradient and related modes in the presence of neoclassical viscosity
Authors: Mikhailovskii A. B. , Smolyakov A. I. , Kovalishen E. A. , Shirokov M. S. , Tsypin V. S. , Galvão R. M. O.
Published: May 2006

Generation of zonal flows by primary waves that are more complex than those considered in the standard drift-wave model is studied. The effects of parallel ion velocity and ion perturbed temperature and the part of the nonlinear mode interaction proportional to the ion pressure are taken into account. This generalization of the standard model allows the analysis of generation of zonal flows by a rather wide variety of primary modes, including ion temperature gradients, ion sound, electron drift, and drift-sound modes. All the listed effects, which are present in the slab geometry model, are complemented by effects of neoclassical viscosity inherent to toroidal geometry. We show that the electrostatic potential of secondary small-scale modes is expressed in terms of a nonlinear shift of the mode frequency and interpret this shift in terms of the perpendicular and parallel Doppler, nonlinear Kelvin-Helmholtz (KH), and nonlinear ion-pressure-gradient effects. A basic assumption of our model is that the primary modes form a nondispersive monochromatic wave packet. The analysis of zonal-flow generation is performed following an approach similar to that of convective-cell theory. Neoclassical zonal-flow instabilities are separated into fast and slow ones, and these are divided into two varieties. The first of them is independent of the nonlinear KH effect, while the second one is sensitive to it.
Electron parallel-flow shear driven low-frequency electromagnetic modes in collisionless magnetoplasma
Authors: Shukla P. K. , Eliasson B. , Koepke M.
Published: May 2006

The free energy associated with shear in the equilibrium parallel electron velocity is shown to be responsible for the excitation of low-frequency electromagnetic waves in collisionless magnetoplasma. New dispersion relations are derived by using the hydrodynamic equations for the electron fluid, the magnetic-field-aligned (parallel) drift of which varies in one of the perpendicular directions, and by using a kinetic ion model, together with Ampère’s law and Poisson’s equation. The dispersion relations are analyzed both analytically and numerically for a set of parameters representative of a laboratory experiment. New filamentary instabilities are predicted.
Temperature dependence of BaTiO3 infrared dielectric properties
Authors: Huang Zhiming , Xue Jianqiang , Ge Yujian , Qin Jianhuan , Hou Yun , Chu Junhao , Zhang Daohua
Published: May 2006

The infrared dielectric constants of the perovskite BaTiO3 are obtained by infrared spectroscopic ellipsometry in the temperature range of 20–150°C. Apparent temperature-dependent distribution of the spectral weight variation is observed for complex dielectric function. Both high frequency dielectric function and bound electrical charge show the temperature dependence from the tetragonal to the cubic phase transition. The bound electrical charge appears to be composed of a hopping component and a temperature-dependent one for BaTiO3 with first-order transitions.
Efficient CuInS2 solar cells by reactive magnetron sputtering
Authors: Unold T. , Sieber I. , Ellmer K.
Published: May 2006

We demonstrate CuInS2 thin film solar cell device efficiencies larger than 10% by preparing the absorber layers by reactive magnetron sputtering from metallic targets in an argon-hydrogen sulfide atmosphere. At deposition temperatures below 500°C the polycrystalline films show a compact morphology with grain sizes of several micrometers. Solar cell devices show optical and electrical properties that are comparable to coevaporated or sequentially processed cells, in particular, diffusion lengths larger than 2μm and fill factors larger than 70%. We conclude that ion bombardment during the sputtering process does not lead to a significant increase of electronically active defects in these devices.
Laser characteristics with ultimate-small modal volume in photonic crystal slab point-shift nanolasers
Authors: Nozaki Kengo , Baba Toshihiko
Published: May 2006

We recently reported the laser operation of a nanocavity consisting only of a shift in two of the lattice points in a GaInAsP photonic crystal slab. In this study, we investigated the laser characteristics in detail. For lithographic tuning, three different modes were observed, and good agreement between the experimental results and theoretical calculations performed using the finite-difference time-domain method was obtained. These results suggest that the fundamental mode has a modal volume of 0.02μm3∼2.1(λ∕2n)3, which is the smallest in any kind of laser. Such an ultrasmall modal volume will ensure efficient electron-photon coupling.
Quasistatic transduction of the fundamental symmetric Lamb mode in longitudinal wave transducers
Authors: Yantchev Ventsislav , Katardjiev Ilia
Published: May 2006

The Green’s function formalism has been applied to the analysis of the fundamental symmetric Lamb mode excited by means of longitudinal wave (LW) transducers. The Lamb wave Green’s function has been related to the properties of the effective permittivity defined as a function of the wave slowness and the relative plate thickness. An electrostatic analysis that neglects the piezoelectric coupling is employed to relate the charge density to the applied voltage. This analysis is subsequently used to calculate the radiation conductance of a LW transducer. The results obtained are consistent with the equivalent circuit approach and define the device coupling as a function of the plate thickness and the intrinsic Lamb wave coupling.
Broadening and tuning of spontaneous Raman emission in porous silicon at 1.5μm
Authors: Sirleto L. , Ferrara M. A. , Rendina I. , Jalali B.
Published: May 2006

In the last three years, the possibility of light generation and/or amplification in silicon, based on Raman emission, has achieved significant results. However, limitations inherent to the physics of silicon have been pointed out, too. In this letter, an approach based on Raman scattering in porous silicon is investigated. Two significant advantages with respect to silicon are proved: the broadening of spontaneous Raman emission and the tuning of the Stokes shift. Finally, we discuss about the prospect of Raman amplifier in porous silicon.
Modified electrochromism of tungsten oxide via platinum nanophases
Authors: Park Kyung-Won , Shim Hee-Sang , Seong Tae-Yeon , Sung Yung-Eun
Published: May 2006

We report electrochromic properties of WO3 modified by platinum nanophases. The WO3 incorporated by Pt metallic nanophases (Pt–WO3) showed exactly reverse electrochromic phenomenon compared with that of both pure WO3 and WO3 intercepted and coated by metallic Pt thin-film layer. In addition, to investigate the origin of modified electrochromic properties, electrodes consisting of WO3 and/or Pt layers were designed and observed in optical properties during electrochemical reaction. The change of electrochromic properties in the Pt–WO3 is caused by modified structural and electrochemical properties of the WO3 by Pt metallic nanophases dispersed in the oxide matrix.
Backward diodelike behavior in La0.67Ca0.33MnO3−δ∕SrTiO3∕Nb–SrTiO3 p-i-n junction
Authors: Xiao Y. S. , Zhang X. P. , Zhao Y. G.
Published: May 2006

We report the fabrication of La0.67Ca0.33MnO3−δ∕SrTiO3∕Nb–SrTiO3 p-i-n junction by pulsed laser deposition. This p-i-n junction shows good rectifying property. The most interesting phenomena observed in this p-i-n junction are the backward diodelike behavior above 210K and the transition to the normal diodelike behavior at low temperatures. The backward diodelike behavior, which has not been reported for the manganite based p-n or p-i-n junctions, can be understood by the nearly degenerate model. The coexistence of the ferromagnetic phase and charge ordering phase in the ultrathin La0.67Ca0.33MnO3−δ thin film can account for the behavior of this p-i-n junction at low temperatures. It is also shown that the electric current in this p-i-n junction is dominated by tunneling process at small bias voltages and diffusion process at high bias voltages. This work implies that manganite based diodes can show various properties displayed by the conventional semiconductor diodes.
The nonredundant roles of two 4′-phosphopantetheinyl transferases in vital processes of
Mycobacteria
Authors: Chalut Christian , Botella Laure , de Sousa-D’Auria Célia , Houssin Christine , Guilhot Christophe
Published: May 2006

Mycobacterium tuberculosis
contains >20 enzymes that require activation by transfer of the 4′-phosphopantetheine moiety of CoA onto a conserved serine residue, a posttranslational modification catalyzed by 4′-phosphopantetheinyl transferases (PPTases). The modified proteins are involved in key metabolic processes such as cell envelope biogenesis and the production of virulence factors. We show that two PPTases conserved in all
Mycobacterium
spp. and in related genera activate two different subsets of proteins and are not functionally redundant. One enzyme, AcpS, activates the two fatty acid synthase systems of mycobacteria, whereas the other PPTase, PptT, acts on type-I polyketide synthases and nonribosomal peptide synthases, both of which are involved in the biosynthesis of virulence factors. We demonstrate that both PPTases are essential for
Mycobacterium smegmatis
viability and that PptT is required for the survival of
Mycobacterium bovis
bacillus Calmette–Guérin. These enzymes are thus central to the biology of mycobacteria and for mycobacterial pathogenesis and represent promising targets for new antituberculosis drugs.
Postsynaptic inositol 1,4,5-trisphosphate signaling maintains presynaptic function of parallel fiber–Purkinje cell synapses via BDNF
Authors: Furutani Kazuharu , Okubo Yohei , Kakizawa Sho , Iino Masamitsu
Published: May 2006

The maintenance of synaptic functions is essential for neuronal information processing, but cellular mechanisms that maintain synapses in the adult brain are not well understood. Here, we report an activity-dependent maintenance mechanism of parallel fiber (PF)–Purkinje cell (PC) synapses in the cerebellum. When postsynaptic metabotropic glutamate receptor (mGluR) or inositol 1,4,5-trisphosphate (IP
3
) signaling was chronically inhibited
in vivo
, PF–PC synaptic strength decreased because of a decreased transmitter release probability. The same effects were observed when PF activity was inhibited
in vivo
by the suppression of NMDA receptor-mediated inputs to granule cells. PF–PC synaptic strength similarly decreased after the
in vivo
application of an antibody against brain-derived neurotrophic factor (BDNF). Furthermore, the weakening of synaptic connection caused by the blockade of mGluR–IP
3
signaling was reversed by the
in vivo
application of BDNF. These results indicate that a signaling cascade comprising PF activity, postsynaptic mGluR–IP
3
signaling and subsequent BDNF signaling maintains presynaptic functions in the mature cerebellum.
Conformation of the synaptobrevin transmembrane domain
Authors: Bowen Mark , Brunger Axel T.
Published: May 2006

The synaptic vesicle protein synaptobrevin (also called VAMP, vesicle-associated membrane protein) forms part of the SNARE (soluble
N
-ethylmaleimide sensitive factor attachment protein receptor) complex, which is essential for vesicle fusion. Additionally, the synaptobrevin transmembrane domain can promote lipid mixing independently of complex formation. Here, the conformation of the transmembrane domain was studied by using circular dichroism and attenuated total reflection Fourier-transform infrared spectroscopy. The synaptobrevin transmembrane domain has an α-helical structure that breaks in the juxtamembrane region, leaving the cytoplasmic domain unstructured. In phospholipid bilayers, infrared dichroism data indicate that the transmembrane domain adopts a 36° angle with respect to the membrane normal, similar to that reported for viral fusion peptides. A conserved aromatic/basic motif in the juxtamembrane region may be causing this relatively high insertion angle.
Distinct p53 acetylation cassettes differentially influence gene-expression patterns and cell fate
Authors: Knights Chad D. , Catania Jason , Giovanni Simone Di , Muratoglu Selen , Perez Ricardo , Swartzbeck Amber , Quong Andrew A. , Zhang Xiaojing , Beerman Terry , Pestell Richard G. , Avantaggiati Maria Laura
Published: May 2006

The activity of the p53 gene product is regulated by a plethora of posttranslational modifications. An open question is whether such posttranslational changes act redundantly or dependently upon one another. We show that a functional interference between specific acetylated and phosphorylated residues of p53 influences cell fate. Acetylation of lysine 320 (K320) prevents phosphorylation of crucial serines in the NH2-terminal region of p53; only allows activation of genes containing high-affinity p53 binding sites, such as p21/WAF; and promotes cell survival after DNA damage. In contrast, acetylation of K373 leads to hyperphosphorylation of p53 NH2-terminal residues and enhances the interaction with promoters for which p53 possesses low DNA binding affinity, such as those contained in proapoptotic genes, leading to cell death. Further, acetylation of each of these two lysine clusters differentially regulates the interaction of p53 with coactivators and corepressors and produces distinct gene-expression profiles. By analogy with the “histone code” hypothesis, we propose that the multiple biological activities of p53 are orchestrated and deciphered by different “p53 cassettes,” each containing combination patterns of posttranslational modifications and protein–protein interactions.
Paradigm lost: milton connects kinesin heavy chain to miro on mitochondria
Authors: Rice Sarah E. , Gelfand Vladimir I.
Published: May 2006

The kinesin motor typically binds to cargo through its light chains. In this issue Glater et al. (p. 545) demonstrate a new type of linkage through the adapter protein, milton, and the mitochondrial membrane GTPase, miro. This is an important result because it represents a new mechanism of cargo binding and because miro's ability to bind GTP and calcium suggests that it is involved in the regulation of mitochondrial transport.
TRFMA: a web-based tool for terminal restriction fragment length polymorphism analysis based on molecular weight
Authors: Nakano Yoshio , Takeshita Toru , Yamashita Yoshihisa
Published: May 2006

Summary: TRFMA provides a Web environment for analyzing T-RFLP results based on molecular weights of the fragments, rather than the numbers of nucleotides, to increase accuracy. The 16S rRNA data are saved as an XML file containing around 650 sequences (light version) and a MySQL database containing around 50 000 sequences (full version), which are connected to Web server via PHP5 and manipulated on an Internet browser.

Availability: TRFMA is freely available at and can be downloaded from the same site.

Contact:  yosh@dent.kyushu-u.ac.jp
Combo: a whole genome comparative browser
Authors: Engels Reinhard , Yu Tamara , Burge Chris , Mesirov Jill P. , DeCaprio David , Galagan James E.
Published: May 2006

Summary: Combo is a comparative genome browser that provides a dynamic view of whole genome alignments along with their associated annotations. Combo provides two different visualization perspectives. The perpendicular (dot plot) view provides a dot plot of genome alignments synchronized with a display of genome annotations along each axis. The parallel view displays two genome annotations horizontally, synchronized through a panel displaying local alignments as trapezoids. Users can zoom to any resolution, from whole chromosomes to individual bases. They can select, highlight and view detailed information from specific alignments and annotations. Combo is an organism agnostic and can import data from a variety of file formats.

Availability: Combo is integrated as part of the Argo Genome Browser which also provides single-genome browsing and editing capabilities. Argo is written in Java, runs on multiple platforms and is freely available for download at .

Contact:  reinhard@broad.mit.edu
INFO-RNA—a fast approach to inverse RNA folding
Authors: Busch Anke , Backofen Rolf
Published: May 2006

Motivation: The structure of RNA molecules is often crucial for their function. Therefore, secondary structure prediction has gained much interest. Here, we consider the inverse RNA folding problem, which means designing RNA sequences that fold into a given structure.

Results: We introduce a new algorithm for the inverse folding problem (INFO-RNA) that consists of two parts; a dynamic programming method for good initial sequences and a following improved stochastic local search that uses an effective neighbor selection method. During the initialization, we design a sequence that among all sequences adopts the given structure with the lowest possible energy. For the selection of neighbors during the search, we use a kind of look-ahead of one selection step applying an additional energy-based criterion. Afterwards, the pre-ordered neighbors are tested using the actual optimization criterion of minimizing the structure distance between the target structure and the mfe structure of the considered neighbor.

We compared our algorithm to RNAinverse and RNA-SSD for artificial and biological test sets. Using INFO-RNA, we performed better than RNAinverse and in most cases, we gained better results than RNA-SSD, the probably best inverse RNA folding tool on the market.

Availability:  

Contact:  backofen@informatik.uni-freiburg.de

Supplementary information: Supplementary data are available on Bioinformatics online.
Comparative gene marker selection suite
Authors: Gould Joshua , Getz Gad , Monti Stefano , Reich Michael , Mesirov Jill P.
Published: May 2006

Motivation: An important step in analyzing expression profiles from microarray data is to identify genes that can discriminate between distinct classes of samples. Many statistical approaches for assigning significance values to genes have been developed. The Comparative Marker Selection suite consists of three modules that allow users to apply and compare different methods of computing significance for each marker gene, a viewer to assess the results, and a tool to create derivative datasets and marker lists based on user-defined significance criteria.

Availability: The Comparative Marker Selection application suite is freely available as a GenePattern module. The GenePattern analysis environment is freely available at

Contact:  jgould@broad.mit.edu
Mid-Pleistocene divergence of Cuban and North American ivory-billed woodpeckers
Authors: Fleischer Robert C , Kirchman Jeremy J , Dumbacher John P , Bevier Louis , Dove Carla , Rotzel Nancy C , Edwards Scott V , Lammertink Martjan , Miglia Kathleen J , Moore William S
Published: May 2006

We used ancient DNA analysis of seven museum specimens of the endangered North American ivory-billed woodpecker (
Campephilus principalis
) and three specimens of the species from Cuba to document their degree of differentiation and their relationships to other
Campephilus
woodpeckers. Analysis of these mtDNA sequences reveals that the Cuban and North American ivory bills, along with the imperial woodpecker (
Campephilus imperialis
) of Mexico, are a monophyletic group and are roughly equidistant genetically, suggesting each lineage may be a separate species. Application of both internal and external rate calibrations indicates that the three lineages split more than one million years ago, in the Mid-Pleistocene. We thus can exclude the hypothesis that Native Americans introduced North American ivory-billed woodpeckers to Cuba. Our sequences of all three woodpeckers also provide an important DNA barcoding resource for identification of non-invasive samples or remains of these critically endangered and charismatic woodpeckers.
Clonal reproduction and genetic caste differences in a queen-polymorphic ant,
Vollenhovia emeryi
Authors: Ohkawara Kyohsuke , Nakayama Megumi , Satoh Atsumi , Trindl Andreas , Heinze Jürgen
Published: May 2006

Most social Hymenoptera are characterized by simple haploid sex determination and environment-based caste differentiation. This appears to be strikingly different in the queen-polymorphic ant
Vollenhovia emeryi
. Almost all long- and short-winged queens from a population in Central Japan were homozygous at three microsatellite loci, whereas workers were mostly heterozygous, suggesting either a complex system of genetic caste determination or, more likely, the production of female sexuals from unfertilized eggs by thelytokous parthenogenesis and of workers from fertilized eggs. Furthermore, male genotypes were not compatible with those of the queens and had exclusively the paternal allele found in the sterile, heterozygous workers, probably because males are produced from fertilized eggs after the exclusion of maternal nuclear DNA as recently reported for
Wasmannia auropunctata
. The genus
Vollenhovia
might provide an interesting model system to trace the evolution of unusual caste and sex determination systems.
Orthogonal (transverse) arrangements of actin in endothelia and fibroblasts
Authors: Curtis Adam , Aitchison Gregor , Tsapikouni Theodora
Published: May 2006

Though actin filaments running across the cell (transverse actin) have been occasionally reported for epithelial cells in groups and for cells growing on fibres, there has been no report heretofore of transverse actin in cells grown on planar substrata. This paper describes evidence in support of this possibility derived from actin staining, polarization microscopy and force measurements. The paper introduces two new methods for detecting the orientation and activity of contractile elements in cells. The orthogonal actin is most obvious in cells grown on groove ridge structures, but can be detected in cells grown on flat surfaces.
Anisotropic elastic materials that have one or two sheets of spherical slowness surface
Authors: Ting T.C.T
Published: May 2006

It is shown that certain anisotropic elastic materials can have one or two sheets of spherical slowness surface. The waves associated with a spherical slowness sheet can be longitudinal, transverse or neither. However, a longitudinal wave can propagate in any direction if and only if the slowness sheet is a sphere

. The same cannot be said of transverse waves. A transverse wave can propagate in any direction without having a spherical slowness sheet. If a spherical slowness sheet

exists, the waves need not be transverse. The existence of a spherical slowness sheet means that the associated velocity surface and the wave surface also have a sphere. Thus, one sheet of the wave front due to a point source is a sphere, a rather unusual phenomenon for anisotropic elastic materials. Particularly interesting anisotropic elastic materials are the ones in which one longitudinal and two transverse waves can propagate in any direction. They have one spherical slowness sheet

for the longitudinal waves. In the special case, they have a second spherical slowness sheet

which is disjoint from the spherical slowness sheet

. The third slowness sheet

is a spheroid.