bluuebunny/crossref_metadata_2025 huggingface dataset:
Intense 1.54 μm fluorescence of Er3+/Yb3+ codoped phosphate glass and the three-photon phenomenon of near infrared upconversion luminescence
Authors: Luo Lanjun , Song Feng , Yu Xiaochen , Wang Wentao , Ming Chengguo , Han Lin , Yu Yin , Wu Hao , Tian Jianguo
Published: February 2010

Transparent P2O5–CaO–Na2O glasses codoped with Er3+ and Yb3+ ions were fabricated by high-temperature melting technique. Strong near infrared and visible upconversion luminescence were observed under 975 nm laser diode excitation, and the luminescence processes were explained in details. For 1.54 μm band, the calculated peak emission cross sections is 1.04×10−20 cm2, and it is better than that in germinate, tellurite, silicate, and other phosphate glasses. The near infrared upconversion emission around 828 nm contains two-photon and three-photon processes, and it is attributed to the transition S43/2→I413/2, which enhances the population of the upper level for 1.54 μm laser emission and reduces the energy loss due to upconversion. Efficient near infrared fluorescence indicates Er3+/Yb3+ codoped phosphate glass is a promising laser and amplifier material.
Electronic structure and magnetism of the diluted magnetic semiconductor Fe-doped ZnO nanoparticles
Authors: Kataoka T. , Kobayashi M. , Sakamoto Y. , Song G. S. , Fujimori A. , Chang F.-H. , Lin H.-J. , Huang D. J. , Chen C. T. , Ohkochi T. , Takeda Y. , Okane T. , Saitoh Y. , Yamagami H. , Tanaka A. , Mandal S. K. , Nath T. K. , Karmakar D. , Dasgupta I.
Published: February 2010

We have studied the electronic structure of Fe-doped ZnO nanoparticles, which have been reported to show ferromagnetism at room temperature, by x-ray photoemission spectroscopy, resonant photoemission spectroscopy, x-ray absorption spectroscopy, and x-ray magnetic circular dichroism (XMCD). From the experimental and cluster-model calculation results, we find that Fe atoms are predominantly in the Fe3+ ionic state with mixture of a small amount of Fe2+ and that Fe3+ ions are dominant in the surface region of the nanoparticles. It is shown that the room temperature ferromagnetism in the Fe-doped ZnO nanoparticles primarily originated from the antiferromagnetic coupling between unequal amounts of Fe3+ ions occupying two sets of nonequivalent positions in the region of the XMCD probing depth of ∼2–3 nm.
Current noise correlations in double quantum dots asymmetrically coupled to external leads
Authors: Lü Hai-Feng , Zhang Jun-Rui , Wu Tao , Zu Xiao-Tao , Zhang Huai-Wu
Published: February 2010

We investigate the current noise autocorrelations and cross correlations through two interacting quantum dots coupled to four external leads. The results indicate sign reversal of the cross correlation in different tunneling regions, respect to competing or supporting processes. By adjusting the dot-lead coupling in one dot, shot noise in another system can be modulated from sub- to super-Poissonian in the Coulomb blockade regime. Furthermore, spin injection can induce super-Poissonian shot noises in both dots due to the corporation of spin blockade and Coulomb blockade.
Phase-dependent thermal conductivity of Ge1Sb4Te7 and N:Ge1Sb4Te7 for phase change memory applications
Authors: Shin Sangwoo , Kim Hyung Keun , Song Jiwoon , Choi Doo Jin , Cho Hyung Hee
Published: February 2010

We report the thermal conductivities of Ge1Sb4Te7 and nitrogen-doped Ge1Sb4Te7 thin films at temperatures ranging from 300 to 520 K using the 3ω method. Thermal conductivity of Ge1Sb4Te7 increases abruptly during the transition from the amorphous to crystalline phase. Nitrogen doping effectively suppresses the crystallization process, resulting reduction of lattice as well as electronic thermal conductivity. These behaviors are confirmed by x-ray diffraction, sheet conductance, and thermal conductivity measurements. Numerical modeling of phase change memory device shows that with nitrogen doping, performance increase in terms of lower reset current and faster reset time can be achieved.
High-pressure behavior of β-Ga2O3 nanocrystals
Authors: Wang H. , He Y. , Chen W. , Zeng Y. W. , Stahl K. , Kikegawa T. , Jiang J. Z.
Published: February 2010

Freestanding nanocrystalline β-Ga2O3 particles with an average grain size of 14 nm prepared by chemical method was investigated by angle-dispersive synchrotron x-ray diffraction in diamond-anvil cell up to 64.9 GPa at ambient temperature. The evolution of x-ray diffraction patterns indicated that nanocrystalline monoclinic β-Ga2O3 underwent a phase transition to rhombohedral α-Ga2O3. It was found that β- to α-Ga2O3 transition began at about 13.6–16.4 GPa, and extended up to 39.2 GPa. At the highest pressure used, only α-Ga2O3 was present, which remained after pressure release. A Birch–Murnaghan fit to the P-V data yielded a zero-pressure bulk modulus at fixed B0′=4: B0=228(9) GPa and B0=333(19) GPa for β-Ga2O3 and α-Ga2O3 phases, respectively. We compared our results with bulk β-Ga2O3, and concluded that the phase-transition pressure and bulk modulus of nanocrystalline β-Ga2O3 are higher than those of bulk counterpart.
Low-temperature solid phase epitaxy for integrating advanced source/drain metal-oxide-semiconductor structures
Authors: Gouyé A. , Berbezier I. , Favre L. , Amiard G. , Aouassa M. , Campidelli Y. , Halimaoui A.
Published: February 2010

We show that chemical vapor deposition using trisilane decomposition opens capabilities for the deposition of amorphous silicon on Si substrate at low temperature. Based on this behavior we developed a process including amorphous silicon deposition and crystallization. Transmission electron microscopy observations prove that solid phase epitaxy (SPE) occurs and produces monocrystalline layers, free of extended defects and compatible with complementary metal-oxide-semiconductor technology. We also show that during SPE films remain amorphous on oxidized areas while they transform into single crystal on Si. This process opens promising perspectives for the fabrication of advanced MOS structures.
Cluster-glass-like state and exchange bias effect in spontaneously phase separated, Pr0.7Sr0.3CoO3
Authors: Patra M. , Majumdar S. , Giri S.
Published: February 2010

dc magnetization and ac susceptibility measurements were carried out in a polycrystalline compound with composition Pr0.7Sr0.3CoO3. Low-field dc magnetization and frequency-dependent ac susceptibility results suggest a cluster-glass-like transition at 165 K. When the sample was cooled in a static magnetic field, shifts in the magnetic hysteresis loop were observed at 5 K. Shifts in the hysteresis loop are the typical manifestation of exchange bias (EB) effect. Training effect observed at 5 K is one of the supportive experimental evidences of EB effect which could be satisfactorily analyzed by the relaxation model. EB effect is suggested due to the pinning effect at the ferromagnetic/spin-glass interface in a spontaneously phase separated cluster-glass compound.
Optical generation of surface acoustic waves guided at the linear boundary between two thin films
Authors: Maznev A. A. , Kelf Timothy A. , Tomoda Motonobu , Matsuda Osamu , Wright Oliver B.
Published: February 2010

Laser-induced transient grating measurements and ultrafast optical pump-probe imaging of surface acoustic waves near a linear boundary between copper and silica films on a silicon substrate indicate the presence of a boundary-localized mode with a phase velocity slightly below the Rayleigh wave velocity on the copper film. We analyze in detail the dispersion of this localized mode in comparison with that of the Rayleigh waves in the surrounding materials. The existence of the localized mode is ascribed to the nonuniformity of the copper film thickness near its edge resulting from polishing during fabrication.
Reactive radical facilitated reaction-diffusion modeling for holographic photopolymerization
Authors: Liu Jianhua , Pu Haihui , Gao Bin , Gao Hongyue , Yin Dejin , Dai Haitao
Published: February 2010

A phenomenological concentration of reactive radical is proposed to take the role of curing light intensity in explicit proportion to the reaction rate for the conventional reaction-diffusion model. This revision rationally eliminates the theoretical defect of null reaction rate in modeling of the postcuring process, and facilitates the applicability of the model in the whole process of holographic photopolymerizations in photocurable monomer and nematic liquid crystal blend system. Excellent consistencies are obtained in both curing and postcuring processes between simulated and experimentally measured evolutions of the first order diffraction efficiency of the formed composite Bragg gratings.
Exact Fermi coordinates for a class of space-times
Authors: Klein David , Collas Peter
Published: February 2010

We find exact Fermi coordinates for timelike geodesic observers for a class of space-times that includes anti-de Sitter space-time, de Sitter space-time, the constant density interior Schwarzschild space-time with positive, zero, and negative cosmological constant, and the Einstein static universe. Maximal charts for Fermi coordinates are discussed.
Measurement of the hot electron attenuation length of copper
Authors: Garramone J. J. , Abel J. R. , Sitnitsky I. L. , Zhao L. , Appelbaum I. , LaBella V. P.
Published: February 2010

Ballistic electron emission microscopy is utilized to investigate the hot-electron scattering properties of Cu through Cu/Si(001) Schottky diodes. A Schottky barrier height of 0.64±0.02 eV and a hot-electron attenuation length of 33.4±2.9 nm are measured at a tip bias of 1.0 eV and a temperature of 80 K. The dependence of the attenuation length with tip bias is fit to a Fermi liquid model that allows extraction of the inelastic and elastic scattering components. This modeling indicates that elastic scattering due to defects, grain boundaries, and interfaces is the dominant scattering mechanism in this energy range.
A microprobe technique for simultaneously measuring thermal conductivity and Seebeck coefficient of thin films
Authors: Zhang Yanliang , Hapenciuc Claudiu L. , Castillo Eduardo E. , Borca-Tasciuc Theodorian , Mehta Rutvik J. , Karthik Chinnathambi , Ramanath Ganpati
Published: February 2010

We demonstrate a microprobe technique that can simultaneously measure thermal conductivity κ and Seebeck coefficient α of thin films. In this technique, an alternative current joule-heated V-shaped microwire that serves as heater, thermometer and voltage electrode, locally heats the thin film when contacted with the surface. The κ is extracted from the thermal resistance of the microprobe and α from the Seebeck voltage measured between the probe and unheated regions of the film by modeling heat transfer in the probe, sample and their contact area, and by calibrations with standard reference samples. Application of the technique on sulfur-doped porous Bi2Te3 and Bi2Se3 films reveals α=−105.4 and 1.96 μV/K, respectively, which are within 2% of the values obtained by independent measurements carried out using microfabricated test structures. The respective κ values are 0.36 and 0.52 W/mK, which are significantly lower than the bulk values due to film porosity, and are consistent with effective media theory. The dominance of air conduction at the probe-sample contact area determines the microscale spatial resolution of the technique and allows probing samples with rough surfaces.
Electrically tunable electron g factors in coupled InAs/GaAs pyramid quantum dots
Authors: Wang Jiqing , Mao Huibing , Yu Jianguo , Zhao Qiang , Zhang Hongying , Yang Pingxiong , Zhu Ziqiang , Chu Junhao
Published: February 2010

The electron g factors of coupled InAs/GaAs quantum dots under external magnetic and electric fields are investigated by using the eight-band k•p model. The resonant coupling between the two dots remains under electric fields below 8.2 mV/nm, and is broken above the critical field due to the quantum Stark effect. By applying electric fields, a sign reverse of g factors is observed, and an electric field tunable zero g factor is found in the quantum dot molecules. Spin-orbit interactions nicely explain the transition mechanism of g factors under external electric fields.
Optical and electro-optic anisotropy of epitaxial Ba0.7Sr0.3TiO3 thin films
Authors: Wang D. Y. , Li S. , Chan H. L. W , Choy C. L.
Published: February 2010

The anisotropic optical and electro-optic properties of ferroelectric Ba0.7Sr0.3TiO3 thin films, deposited on highly transparent single-crystal MgO (001), (011), and (111) substrates using pulsed laser deposition, were investigated. The experimental results show a strong correlation between optical, electro-optic properties, and the orientation of Ba0.7Sr0.3TiO3 thin films. The linear electro-optic coefficient rc of the (001), (011), and (111)-oriented Ba0.7Sr0.3TiO3 thin films are 99.1, 15.7, and 87.8 pm/V, respectively. Such a correlation may be attributed to the orientation dependent distribution and magnitude of spontaneous polarization.
Intermittent convective transport carried by propagating electromagnetic filamentary structures in nonuniformly magnetized plasma
Authors: Xu G. S. , Naulin V. , Fundamenski W. , Rasmussen J. Juul , Nielsen A. H. , Wan B. N.
Published: February 2010

Drift-Alfvén vortex filaments associated with electromagnetic turbulence were recently identified in reversed field pinch devices. Similar propagating filamentary structures were observed in the Earth magnetosheath, magnetospheric cusp and Saturn’s magnetosheath by spacecrafts. The characteristics of these structures closely resemble those of the so-called mesoscale coherent structures, prevailing in fusion plasmas, known as “blobs” and “edge localized mode filaments” in the boundary region, and propagating avalanchelike events in the core region. In this paper the fundamental dynamics of drift-Alfvén vortex filaments in a nonuniformly and strongly magnetized plasma are revisited. We systemize the Lagrangian-invariant-based method. Six Lagrangian invariants are employed to describe structure motion and the resultant convective transport, namely, magnetic flux, background magnetic energy, specific entropy, total energy, magnetic momentum, and angular momentum. The perpendicular vortex motions and the kinetic shear Alfvén waves are coupled through the parallel current and Ampere’s law, leading to field line bending. On the timescale of interchange motion τ⊥, a thermal expansion force in the direction of curvature radius of the magnetic field overcomes the resultant force of magnetic tension and push plasma filament to accelerate in the direction of curvature radius resulting from plasma inertial response, reacted to satisfy quasineutrality. During this process the internal energy stored in the background pressure gradient is converted into the kinetic energy of convective motion and the magnetic energy of field line bending through reversible pressure-volume work as a result of the plasma compressibility in an inhomogeneous magnetic field. On the timescale of parallel acoustic response τ∥⪢τ⊥, part of the filament’s energy is transferred into the kinetic energy of parallel flow. On the dissipation timescale τd⪢τ⊥, the kinetic energy and magnetic energy are eventually dissipated, which is accompanied by entropy production, and in this process the structure loses its coherence, but it has already traveled a distance in the radial direction. In this way the propagating filamentary structures induce intermittent convective transports of particles, heat, and momentum across the magnetic field. It is suggested that the phenomena of profile consistency, or resilience, and the underlying anomalous pinch effects of particles, heat, and momentum in the fusion plasmas can be interpreted in terms of the ballistic motion of these solitary electromagnetic filamentary structures.
Parallel tempering Monte Carlo simulations of lysozyme orientation on charged surfaces
Authors: Xie Yun , Zhou Jian , Jiang Shaoyi
Published: February 2010

In this work, the parallel tempering Monte Carlo (PTMC) algorithm is applied to accurately and efficiently identify the global-minimum-energy orientation of a protein adsorbed on a surface in a single simulation. When applying the PTMC method to simulate lysozyme orientation on charged surfaces, it is found that lysozyme could easily be adsorbed on negatively charged surfaces with “side-on” and “back-on” orientations. When driven by dominant electrostatic interactions, lysozyme tends to be adsorbed on negatively charged surfaces with the side-on orientation for which the active site of lysozyme faces sideways. The side-on orientation agrees well with the experimental results where the adsorbed orientation of lysozyme is determined by electrostatic interactions. As the contribution from van der Waals interactions gradually dominates, the back-on orientation becomes the preferred one. For this orientation, the active site of lysozyme faces outward, which conforms to the experimental results where the orientation of adsorbed lysozyme is co-determined by electrostatic interactions and van der Waals interactions. It is also found that despite of its net positive charge, lysozyme could be adsorbed on positively charged surfaces with both “end-on” and back-on orientations owing to the nonuniform charge distribution over lysozyme surface and the screening effect from ions in solution. The PTMC simulation method provides a way to determine the preferred orientation of proteins on surfaces for biosensor and biomaterial applications.
Ultraviolet photorefraction at 325 nm in doped lithium niobate crystals
Authors: Xin Feifei , Zhang Guoquan , Bo Fang , Sun Haifeng , Kong Yongfa , Xu Jingjun , Volk Tatyana , Rubinina Natalia M.
Published: February 2010

We studied the photorefractive effect of lithium niobate (LiNbO3) doped with Mg, Zn, In, Hf, or codoped with Mg and Fe at an ultraviolet (UV) wavelength down to 325 nm. It is found that the UV photorefraction of LiNbO3 doped with Mg, Zn, In, or Hf was enhanced significantly as compared to that of the nominally pure LiNbO3. Our results show that the property of resistance against photorefraction in highly Mg, Zn, In, or Hf doped LiNbO3 is true only in the visible and near-infrared wavelength range. By contrast, these crystals exhibit excellent photorefractive characteristics at UV wavelength of 325 nm, even better than those at 351 nm. For example, the photorefractive two-wave coupling gain coefficient Γ and the photorefractive recording sensitivity at 325 nm were measured to be ∼38 cm−1 and 37.7 cm/J, respectively, in a LiNbO3 crystal doped with 9 mol % Zn. The photorefractive response time of a Mg:LiNbO3 with a 9 mol % Mg was measured to be 73 ms with a total recording intensity of 614 mW/cm2 at 325 nm. In highly Mg, Zn, In, or Hf doped LiNbO3 crystals, diffusion dominates over photovoltaic effect and electrons are the dominant charge carriers in UV photorefraction at 325 nm. The results are also of interest to the study on the defect structure of LiNbO3 near to the absorption edge.
Effects of additional Ce3+ doping on the luminescence of Li2SrSiO4:Eu2+ yellow phosphor
Authors: Kim Tae-Gon , Lee Hyo-Sug , Lin Chun Che , Kim Taehyung , Liu Ru-Shi , Chan Ting-Shan , Im Seoung-Jae
Published: February 2010

Additional Ce3+ doping improves the luminescence of Li2SrSiO4:Eu2+, a yellow phosphor for ultraviolet or blue light-emitting diodes. By examining the photoluminescence of Li2SrSiO4:Eu2+, Li2SrSiO4:Ce3+, and Li2SrSiO4:Ce3+,Eu2+, it was confirmed that the energy transfer from Ce3+ to Eu2+ ions contributes little to the enhanced luminescence of Li2SrSiO4:Ce3+,Eu2+. Alternatively, we suggested that Ce3+ ions could stabilize the Li vacancies, inhibit the oxidization of Eu2+ to Eu3+, and consequently increase emission intensity, based on the characterizations with decay time and synchrotron light source x-ray absorption measurements. The proposed argument was validated with first principle calculations of the defect formation energies.
Terahertz conductivity of doped silicon calculated using the ensemble Monte Carlo/finite-difference time-domain simulation technique
Authors: Willis K. J. , Hagness S. C. , Knezevic I.
Published: February 2010

We present terahertz-frequency characterization of doped silicon via a multiphysics numerical technique that couples ensemble Monte Carlo (EMC) simulation of carrier transport and a finite-difference time-domain (FDTD) solver of Maxwell’s curl equations. We elucidate the importance of rigorous enforcement of Gauss’s law, in order to avoid unphysical charge buildup and enhance solver accuracy. The calculated complex conductivity of doped bulk silicon shows excellent agreement with available experimental data. This comprehensive microscopic simulator is a valuable predictive tool in the terahertz frequency range, where experimental data are scarce and the Drude model inadequate.
High effective minority carrier lifetime on silicon substrates using quinhydrone-methanol passivation
Authors: Chhabra Bhumika , Bowden Stuart , Opila Robert L. , Honsberg Christiana B.
Published: February 2010

Iodine-methanol (I2/ME), a chemical passivation method, is extensively used in silicon (Si) solar cell fabrication for measuring minority carrier lifetime in bulk regions. We demonstrate that quinhydrone-methanol (QHY/ME) provides higher lifetimes than I2/ME. For 0.01 mol/dm−3 QHY/ME on float-zone (FZ) wafers at 1×1015 cm−3 injection level, a high lifetime of 3.3 ms and surface recombination velocity of 7 cm/sec on n-type (100 Ω cm) and 1.1 ms on p-type (2 Ω cm) is reported. The surface recombination velocity is also measured out of solution for several days. Chemical characterization results indicate increasing surface oxidation with decreasing passivation, consistent with proposed bonding mechanism.
Anisotropic transport in graphene on SiC substrate with periodic nanofacets
Authors: Odaka S. , Miyazaki H. , Li S.-L. , Kanda A. , Morita K. , Tanaka S. , Miyata Y. , Kataura H. , Tsukagoshi K. , Aoyagi Y.
Published: February 2010

Anisotropic transport in graphene field-effect transistors fabricated on a vicinal SiC substrate with a self-organized periodic nanofacet structure is investigated. Graphene thermally grown on a vicinal substrate contains two following regions: atomically flat terraces and nanofacets (atomically stepped slopes). The graphene film at a nanofacet is continuously connected between two neighboring terrace films. Anisotropic transport properties are clearly observed, indicating a difference in the graphene properties of the two regions. The observed anisotropic properties are discussed in terms of the effects of nanofacet structures on conductivity and electron mobility.
Structural defects in LiCoO2 studied by L7i nuclear magnetic relaxation
Authors: Kim J. S. , Lee K. W. , Kweon J. J. , Lee Cheol Eui , Kim K. , Lee J. , Noh S. J. , Kim H. S.
Published: February 2010

Microscopic environments and dynamics in LiCoO2 systems were probed by L7i nuclear magnetic relaxation measurements with regard to the structural defects as revealed by x-ray diffraction and electron spin resonance measurements. Thus, the structural defects of differing degrees, associated with Li vacancies, were well accounted for in the temperature-dependent spin-lattice relaxation rate analysis, and in the structural and dynamical inhomogeneity as derived from the relaxation patterns.
High current diffuse dielectric barrier discharge in atmospheric pressure air for the deposition of thin silica-like films
Authors: Starostin S. A. , Premkumar P. Antony , Creatore M. , de Vries H. , Paffen R. M. J. , van de Sanden M. C. M.
Published: February 2010

The diffuse dielectric barrier discharge in atmospheric pressure air was applied for the thin film deposition on polymeric web in industrially relevant roll-to-roll configuration. The silica-like film deposition was performed using the admixture of hexamethyldisiloxane precursor to air flow. Fast discharge imaging at 2 μs exposure time confirms plasma uniformity in a single current pulse time scale. Morphology and composition analyses indicate that the process results in ultrasmooth films (roughness comparable to initial substrate roughness) and shows the possibility to synthesize carbon-free layers.
High-Q silica microsphere by poly(methyl methacrylate) coating and modifying
Authors: Dong C.-H. , Sun F.-W. , Zou C.-L. , Ren X.-F. , Guo G.-C. , Han Z.-F.
Published: February 2010

We experimentally characterize the Q-factor in a silica microsphere with the poly(methyl methacrylate) coating. Experimental results demonstrated that the Q-factor of the coated microcavity is higher than 108. Moreover, this coating is able to eliminate scattering from the unsmoothed surface and tune the optical field in the cavity. In the cavity interaction with quantum dots, the coating can not only increase the Q-factor of the microsphere with deposited quantum dots but also draw the maximal field to the interface where the quantum dots exist. Therefore, this coating method can highly enhance the interaction strength, and it will contribute to the cavity quantum electrodynamics study.
Membrane-anchored serine protease matriptase regulates epithelial barrier formation and permeability in the intestine
Authors: Buzza Marguerite S. , Netzel-Arnett Sarah , Shea-Donohue Terez , Zhao Aiping , Lin Chen-Yong , List Karin , Szabo Roman , Fasano Alessio , Bugge Thomas H. , Antalis Toni M.
Published: February 2010

The intestinal epithelium serves as a major protective barrier between the mammalian host and the external environment. Here we show that the transmembrane serine protease matriptase plays a pivotol role in the formation and integrity of the intestinal epithelial barrier.
St14
hypomorphic mice, which have a 100-fold reduction in intestinal matriptase mRNA levels, display a 35% reduction in intestinal transepithelial electrical resistance (TEER). Matriptase is expressed during intestinal epithelial differentiation and colocalizes with E-cadherin to apical junctional complexes (AJC) in differentiated polarized Caco-2 monolayers. Inhibition of matriptase activity using a specific peptide inhibitor or by knockdown of matriptase by siRNA disrupts the development of TEER in barrier-forming Caco-2 monolayers and increases paracellular permeability to macromolecular FITC-dextran. Loss of matriptase was associated with enhanced expression and incorporation of the permeability-associated, “leaky” tight junction protein claudin-2 at intercellular junctions. Knockdown of claudin-2 enhanced the development of TEER in matriptase-silenced Caco-2 monolayers, suggesting that the reduced barrier integrity was caused, at least in part, by an inability to regulate claudin-2 expression and incorporation into junctions. We find that matriptase enhances the rate of claudin-2 protein turnover, and that this is mediated indirectly through an atypical PKCζ-dependent signaling pathway. These results support a key role for matriptase in regulating intestinal epithelial barrier competence, and suggest an intriguing link between pericellular serine protease activity and tight junction assembly in polarized epithelia.
Independent initiation of primary electron transfer in the two branches of the photosystem I reaction center
Authors: Müller Marc G. , Slavov Chavdar , Luthra Rajiv , Redding Kevin E. , Holzwarth Alfred R.
Published: February 2010

Photosystem I (PSI) is a large pigment-protein complex that unites a reaction center (RC) at the core with ∼100 core antenna chlorophylls surrounding it. The RC is composed of two cofactor branches related by a pseudo-C2 symmetry axis. The ultimate electron donor, P700(a pair of chlorophylls), and the tertiary acceptor, FX(a Fe4S4cluster), are both located on this axis, while each of the two branches is made up of a pair of chlorophylls (ec2 and ec3) and a phylloquinone (PhQ). Based on the observed biphasic reduction of FX, it has been suggested that both branches in PSI are competent for electron transfer (ET), but the nature and rate of the initial electron transfer steps have not been established. We report an ultrafast transient absorption study ofChlamydomonas reinhardtiimutants in which specific amino acids donating H-bonds to the 131-keto oxygen of either ec3A(PsaA-Tyr696) or ec3B(PsaB-Tyr676) are converted to Phe, thus breaking the H-bond to a specific ec3 cofactor. We find that the rate of primary charge separation (CS) is lowered in both mutants, providing direct evidence that the primary ET event can be initiated independently in each branch. Furthermore, the data provide further support for the previously published model in which the initial CS event occurs within an ec2/ec3 pair, generating a primary ec2+ec3-radical pair, followed by rapid reduction by P700in the second ET step. A unique kinetic modeling approach allows estimation of the individual ET rates within the two cofactor branches.
Heterospecies partition analysis reveals binding curve and stoichiometry of protein interactions in living cells
Authors: Wu Bin , Chen Yan , Müller Joachim D.
Published: February 2010

Measuring the binding curve and stoichiometry of protein complexes in living cells is a prerequisite for quantitative modeling of cellular processes. Dual-color fluorescence fluctuation spectroscopy provides a general framework for detecting protein interactions, but lacks suitable methods for quantifying protein heterointeractions in the cell. We address this challenge by introducing heterospecies partition (HSP) analysis for protein heterointeractions of the type D + 
n
A↔DA

n

. HSP directly identifies the heterointeracting species from the sample mixture and determines the binding curve and stoichiometry of the protein complex. The HSP method is applied to provide the first direct characterization of the ligand-dependent binding of the retinoic X receptor to the coactivator transcription intermediate factor 2. A previous study based on protein fragments observed a higher binding stoichiometry than biologically expected. We address this difference in stoichiometry by measuring the binding curves of the full-length proteins in living cells. This study provides proof-of-principle experiments that illustrate the potential of HSP as a general and robust analysis tool for the quantitative characterization of protein heterointeractions by dual-color fluorescence fluctuation spectroscopy in living cells.
Genetic approach for intracerebroventricular delivery
Authors: Regev Limor , Ezrielev Eli , Gershon Eran , Gil Shosh , Chen Alon
Published: February 2010

Administration of synthetic or purified peptides directly into the brain ventricles is a method commonly used by neuroscientists for exploring physiological and behavioral functions of gene products. i.v. administration is controlled by the blood–brain barrier, which limits its effectiveness, and current approaches for acute or chronic intracerebroventricular delivery have significant technical drawbacks resulting from both the chemical properties of the delivered substance and the experimental procedures. Here we describe a genetic approach for the delivery of secreted peptides or proteins into the cerebrospinal fluid (CSF). Using a choroid plexus-specific promoter, we established a lentiviral-based system, which offers inducible and reversible delivery of a gene product into the CSF. The functionality of this system was demonstrated by using the overexpression of the two established neuropeptides, corticotropin-releasing factor and gonadotropin-releasing hormone, modulating anxiety-like behavior and estrus cycle, respectively. We show that this choroid plexus-specific lentiviral-based system is a reliable, effective, and adaptable research tool for intracerebroventricular delivery.
Structural basis for the cooperative interplay between the two causative gene products of combined factor V and factor VIII deficiency
Authors: Nishio Miho , Kamiya Yukiko , Mizushima Tsunehiro , Wakatsuki Soichi , Sasakawa Hiroaki , Yamamoto Kazuo , Uchiyama Susumu , Noda Masanori , McKay Adam R. , Fukui Kiichi , Hauri Hans-Peter , Kato Koichi
Published: February 2010

Combined deficiency of coagulation factors V and VIII (F5F8D), an autosomal recessive disorder characterized by coordinate reduction in the plasma levels of factor V (FV) and factor VIII (FVIII), is genetically linked to mutations in the transmembrane lectin ERGIC-53 and the soluble calcium-binding protein MCFD2. Growing evidence indicates that these two proteins form a complex recycling between the endoplasmic reticulum (ER) and the ER-Golgi intermediate compartment and thereby function as a cargo receptor in the early secretory pathway of FV and FVIII. For better understanding of the mechanisms underlying the functional coordination of ERGIC-53 and MCFD2, we herein characterize their interaction by x-ray crystallographic analysis in conjunction with NMR and ultracentrifugation analyses. Inspection of the combined data reveals that ERGIC-53-CRD binds MCFD2 through its molecular surface remote from the sugar-binding site, giving rise to a 1∶1 complex in solution. The interaction is independent of sugar-binding of ERGIC-53 and involves most of the missense mutation sites of MCFD2 so far reported in F5F8D. Comparison with the previously reported uncomplexed structure of each protein indicates that MCFD2 but not ERGIC-53-CRD undergoes significant conformational alterations upon complex formation. Our findings provide a structural basis for the cooperative interplay between ERGIC-53 and MCFD2 in capturing FV and FVIII.
Nitrate-responsive miR393/
AFB3
regulatory module controls root system architecture in
Arabidopsis thaliana
Authors: Vidal Elena A. , Araus Viviana , Lu Cheng , Parry Geraint , Green Pamela J. , Coruzzi Gloria M. , Gutiérrez Rodrigo A.
Published: February 2010

One of the most striking examples of plant developmental plasticity to changing environmental conditions is the modulation of root system architecture (RSA) in response to nitrate supply. Despite the fundamental and applied significance of understanding this process, the molecular mechanisms behind nitrate-regulated changes in developmental programs are still largely unknown. Small RNAs (sRNAs) have emerged as master regulators of gene expression in plants and other organisms. To evaluate the role of sRNAs in the nitrate response, we sequenced sRNAs from control and nitrate-treated
Arabidopsis
seedlings using the 454 sequencing technology. miR393 was induced by nitrate in these experiments. miR393 targets transcripts that code for a basic helix-loop-helix (bHLH) transcription factor and for the auxin receptors TIR1, AFB1, AFB2, and AFB3. However, only
AFB3
was regulated by nitrate in roots under our experimental conditions. Analysis of the expression of this miR393/
AFB3
module, revealed an incoherent feed-forward mechanism that is induced by nitrate and repressed by N metabolites generated by nitrate reduction and assimilation. To understand the functional role of this N-regulatory module for plant development, we analyzed the RSA response to nitrate in
AFB3
insertional mutant plants and in miR393 overexpressors. RSA analysis in these plants revealed that both primary and lateral root growth responses to nitrate were altered. Interestingly, regulation of RSA by nitrate was specifically mediated by
AFB3
, indicating that miR393/
AFB3
is a unique N-responsive module that controls root system architecture in response to external and internal N availability in
Arabidopsis
.
Amygdala damage eliminates monetary loss aversion
Authors: De Martino Benedetto , Camerer Colin F. , Adolphs Ralph
Published: February 2010

Losses are a possibility in many risky decisions, and organisms have evolved mechanisms to evaluate and avoid them. Laboratory and field evidence suggests that people often avoid risks with losses even when they might earn a substantially larger gain, a behavioral preference termed “loss aversion.” The cautionary brake on behavior known to rely on the amygdala is a plausible candidate mechanism for loss aversion, yet evidence for this idea has so far not been found. We studied two rare individuals with focal bilateral amygdala lesions using a series of experimental economics tasks. To measure individual sensitivity to financial losses we asked participants to play a variety of monetary gambles with possible gains and losses. Although both participants retained a normal ability to respond to changes in the gambles’ expected value and risk, they showed a dramatic reduction in loss aversion compared to matched controls. The findings suggest that the amygdala plays a key role in generating loss aversion by inhibiting actions with potentially deleterious outcomes.
A developmental framework for endodermal differentiation and polarity
Authors: Alassimone Julien , Naseer Sadaf , Geldner Niko
Published: February 2010

The endodermis is a root cell layer common to higher plants and of fundamental importance for root function and nutrient uptake. The endodermis separates outer (peripheral) from inner (central) cell layers by virtue of its Casparian strips, precisely aligned bands of specialized wall material. Here we reveal that the membrane at the Casparian strip is a diffusional barrier between the central and peripheral regions of the plasma membrane and that it mediates attachment to the extracellular matrix. This membrane region thus functions like a tight junction in animal epithelia, although plants lack the molecular modules that establish tight junction in animals. We have also identified a pair of influx and efflux transporters that mark both central and peripheral domains of the plasma membrane. These transporters show opposite polar distributions already in meristems, but their localization becomes refined and restricted upon differentiation. This “central–peripheral” polarity coexists with the apical–basal polarity defined by PIN proteins within the same cells, but utilizes different polarity determinants. Central–peripheral polarity can be already observed in early embryogenesis, where it reveals a cellular polarity within the quiescent center precursor cell. A strict diffusion block between polar domains is common in animals, but had never been described in plants. Yet, its relevance to endodermal function is evident, as central and peripheral membranes of the endodermis face fundamentally different root compartments. Further analysis of endodermal transporter polarity and manipulation of its barrier function will greatly promote our understanding of plant nutrition and stress tolerance in roots.
The structure of the harmonin/sans complex reveals an unexpected interaction mode of the two Usher syndrome proteins
Authors: Yan Jing , Pan Lifeng , Chen Xiuye , Wu Lin , Zhang Mingjie
Published: February 2010

The hereditary hearing-vision loss disease, Usher syndrome I (USH1), is caused by defects in several proteins that can interact with each other in vitro. Defects in USH1 proteins are thought to be responsible for the developmental and functional impairments of sensory cells in the retina and inner ear. Harmonin/USH1C and Sans/USH1G are two of the USH1 proteins that interact with each other. Harmonin also binds to other USH1 proteins such as cadherin 23 (CDH23) and protocadherin 15 (PCDH15). However, the molecular basis governing the harmonin and Sans interaction is largely unknown. Here, we report an unexpected assembly mode between harmonin and Sans. We demonstrate that the N-terminal domain and the first PDZ domain of harmonin are tethered by a small-domain C-terminal to PDZ1 to form a structural and functional supramodule responsible for binding to Sans. We discover that the SAM domain of Sans, specifically, binds to the PDZ domain of harmonin, revealing previously unknown interaction modes for both PDZ and SAM domains. We further show that the synergistic PDZ1/SAM and PDZ1/carboxyl PDZ binding-motif interactions, between harmonin and Sans, lock the two scaffold proteins into a highly stable complex. Mutations in harmonin and Sans found in USH1 patients are shown to destabilize the complex formation of the two proteins.
In situ measurements of gas/particle-phase transitions for atmospheric semivolatile organic compounds
Authors: Williams Brent J. , Goldstein Allen H. , Kreisberg Nathan M. , Hering Susanne V.
Published: February 2010

An understanding of the gas/particle-phase partitioning of semivolatile compounds is critical in determining atmospheric aerosol formation processes and growth rates, which in turn affect global climate and human health. The Study of Organic Aerosol at Riverside 2005 campaign was performed to gain a better understanding of the factors responsible for aerosol formation and growth in Riverside, CA, a region with high concentrations of secondary organic aerosol formed through the phase transfer of low-volatility reaction products from the oxidation of precursor gases. We explore the ability of the thermal desorption aerosol gas chromatograph (TAG) to measure gas-to-particle-phase transitioning for several organic compound classes (polar and nonpolar) found in the ambient Riverside atmosphere by using in situ observations of several hundred semivolatile organic compounds. Here we compare TAG measurements to modeled partitioning of select semivolatile organic compounds. Although TAG was not designed to quantify the vapor phase of semivolatile organics, TAG measurements do distinguish when specific compounds are dominantly in the vapor phase, are dominantly in the particle phase, or have both phases present. Because the TAG data are both speciated and time-resolved, this distinction is sufficient to see the transition from vapor to particle phase as a function of carbon number and compound class. Laboratory studies typically measure the phase partitioning of semivolatile organic compounds by using pure compounds or simple mixtures, whereas hourly TAG phase partitioning measurements can be made in the complex mixture of thousands of polar/nonpolar and organic/inorganic compounds found in the atmosphere.
Gas-phase water-mediated equilibrium between methylglyoxal and its geminal diol
Authors: Axson Jessica L. , Takahashi Kaito , De Haan David O. , Vaida Veronica
Published: February 2010

In aqueous solution, aldehydes, and to a lesser extent ketones, hydrate to form geminal diols. We investigate the hydration of methylglyoxal (MG) in the gas phase, a process not previously considered to occur in water-restricted environments. In this study, we spectroscopically identified methylglyoxal diol (MGD) and obtained the gas-phase partial pressures of MG and MGD. These results, in conjunction with the relative humidity, were used to obtain the equilibrium constant,
K

P

, for the water-mediated hydration of MG in the gas phase. The Gibbs free energy for this process, Δ
G
°
, obtained as a result, suggests a larger than expected gas-phase diol concentration. This may have significant implications for understanding the role of organics in atmospheric chemistry.
Amoeboid organism solves complex nutritional challenges
Authors: Dussutour Audrey , Latty Tanya , Beekman Madeleine , Simpson Stephen J.
Published: February 2010

A fundamental question in nutritional biology is how distributed systems maintain an optimal supply of multiple nutrients essential for life and reproduction. In the case of animals, the nutritional requirements of the cells within the body are coordinated by the brain in neural and chemical dialogue with sensory systems and peripheral organs. At the level of an insect society, the requirements for the entire colony are met by the foraging efforts of a minority of workers responding to cues emanating from the brood. Both examples involve components specialized to deal with nutrient supply and demand (brains and peripheral organs, foragers and brood). However, some of the most species-rich, largest, and ecologically significant heterotrophic organisms on earth, such as the vast mycelial networks of fungi, comprise distributed networks without specialized centers: How do these organisms coordinate the search for multiple nutrients? We address this question in the acellular slime mold
Physarum polycephalum
and show that this extraordinary organism can make complex nutritional decisions, despite lacking a coordination center and comprising only a single vast multinucleate cell. We show that a single slime mold is able to grow to contact patches of different nutrient quality in the precise proportions necessary to compose an optimal diet. That such organisms have the capacity to maintain the balance of carbon- and nitrogen-based nutrients by selective foraging has considerable implications not only for our understanding of nutrient balancing in distributed systems but for the functional ecology of soils, nutrient cycling, and carbon sequestration.
Uridylation of mature miRNAs and siRNAs by the MUT68 nucleotidyltransferase promotes their degradation in
Chlamydomonas
Authors: Ibrahim Fadia , Rymarquis Linda A. , Kim Eun-Jeong , Becker James , Balassa Eniko , Green Pamela J. , Cerutti Heriberto
Published: February 2010

Regulation of gene expression by small RNAs (∼20–30 nucleotides in length) plays an essential role in developmental pathways and defense responses against genomic parasites in eukaryotes. MicroRNAs (miRNAs) and small interfering RNAs (siRNAs) commonly direct the inactivation of cognate sequences through a variety of mechanisms, including RNA degradation, translation inhibition, and transcriptional repression. Recent studies have provided considerable insight into the biogenesis and the mode of action of miRNAs and siRNAs. However, relatively little is known about mechanisms of quality control and small RNA decay in RNA interference (RNAi) pathways. Here we show that deletion of
MUT68
, encoding a terminal nucleotidyltransferase in the alga
Chlamydomonas reinhardtii
, results in elevated miRNA and siRNA levels. We found that MUT68 plays a role in the untemplated uridylation of the 3′ ends of small RNAs in vivo and stimulates their degradation by the RRP6 exosome subunit in vitro. Moreover, RRP6 depletion also leads to accumulation of small RNAs in vivo. We propose that MUT68 and RRP6 cooperate in the degradation of mature miRNAs and siRNAs, as a quality control mechanism to eliminate dysfunctional or damaged small RNA molecules.
Loss of myeloid cell-derived vascular endothelial growth factor accelerates fibrosis
Authors: Stockmann Christian , Kerdiles Yann , Nomaksteinsky Marc , Weidemann Alexander , Takeda Norihiko , Doedens Andrew , Torres-Collado Antonio X. , Iruela-Arispe Luisa , Nizet Victor , Johnson Randall S.
Published: February 2010

Tissue injury initiates a complex series of events that act to restore structure and physiological homeostasis. Infiltration of inflammatory cells and vascular remodeling are both keystones of this process. However, the role of inflammation and angiogenesis in general and, more specifically, the significance of inflammatory cell-derived VEGF in this context are unclear. To determine the role of inflammatory cell-derived VEGF in a clinically relevant and chronically inflamed injury, pulmonary fibrosis, we deleted the VEGF-A gene in myeloid cells. In a model of pulmonary fibrosis in mice, deletion of VEGF in myeloid cells resulted in significantly reduced formation of blood vessels; however, it causes aggravated fibrotic tissue damage. This was accompanied by a pronounced decrease in epithelial cell survival and a striking increase in myofibroblast invasion. The drastic increase in fibrosis following loss of myeloid VEGF in the damaged lungs was also marked by increased levels of hypoxia-inducible factor (HIF) expression and Wnt/β-catenin signaling. This demonstrates that the process of angiogenesis, driven by myeloid cell-derived VEGF, is essential for the prevention of fibrotic damage.