bluuebunny/crossref_metadata_2025 huggingface dataset:
Effect of insulator sleeve material on the x-ray emission from a plasma focus device
Authors: Hussain S. , Shafiq M. , Badar M. A. , Zakaullah M.
Published: September 2010

The effect of insulator sleeve material on x-ray emission from a 2.3 kJ Mather type plasma focus device operated in argon-hydrogen mixture is investigated. The time and space resolved x-ray emission characteristics are studied by using a three channel p-i-n diode x-ray spectrometer and a multipinhole camera. The x-ray emission depends on the volumetric ratio of argon-hydrogen mixture as well as the filling pressure and the highest x-ray emission is observed for a volumetric ratio 40% Ar to 60% H2 at 2.5 mbar filling pressure. The fused silica insulator sleeve produces the highest x-ray emission whereas nonceramic insulator sleeves such as nylon, Perspex, or Teflon does not produce focus or x-rays. The pinhole images of the x-ray emitting zones reveal that the contribution of the Cu Kα line is weak and plasma x-rays are intense. The highest plasma electron temperature is estimated to be 3.3 and 3.6 keV for Pyrex glass and fused silica insulator sleeves, respectively. It is speculated that the higher surface resistivity of fused silica is responsible for enhanced x-ray emission and plasma electron temperature.
Diffusion dynamics and first passage time in a two-coupled pendulum system
Authors: Sakthivel G. , Rajasekar S.
Published: September 2010

We present the numerical investigation of diffusion process and features of first passage time (FPT) and mean FPT (MFPT) in a two-coupled damped and periodically driven pendulum system. The effect of amplitude of the external periodic force and phase of the force on diffusion constant, distribution of FPT, P(tFPT), and MFPT is analyzed. Normal diffusion is found. Diffusion constant is found to show power-law variation near intermittency and sudden widening crises while linear variation is observed in the quasiperiodic region. In the intermittency crisis the divergence of diffusion constant is similar to the divergence of mean bursting length. P(tFPT) of critical distances of state variable exhibit periodic multiple peaks with decaying amplitude. MFPT of critical distances also follows power-law variation. Diffusion constant and MFPT are sensitive to the phase factor of the periodic force.
Analysis of atomic and ion debris features of laser-produced Sn and Li plasmas
Authors: Coons R. W. , Harilal S. S. , Campos D. , Hassanein A.
Published: September 2010

Tin and lithium plasmas emit efficiently in the in-band region (13.5 nm with 2% bandwidth) necessary for extreme ultraviolet (EUV) lithography. We have made a detailed comparison of the atomic and ionic debris, as well as the emission features of Sn and Li plasmas under identical experimental conditions. Planar slabs of pure Sn and Li were irradiated with 1064 nm, 9 ns neodymium-doped yttrium aluminum garnet laser pulses for producing plasmas. A suite of diagnostics were used to analyze the emission and debris features, including optical emission spectroscopy (OES), a Faraday cup, an EUV pinhole camera, the absolute measurement of EUV conversion efficiency (CE), etc. Our results show that Sn plasmas provide a CE nearly twice that of Li. However, the kinetic energies of Sn ions are considerably higher, though with a lower flux. OES studies have showed that the kinetic energies of neutral species are substantially lower compared to that of the charged particle species.
Stride-to-stride energy regulation for robust self-stability of a torque-actuated dissipative spring-mass hopper
Authors: Ankarali M. Mert , Saranli Uluç
Published: September 2010

In this paper, we analyze the self-stability properties of planar running with a dissipative spring-mass model driven by torque actuation at the hip. We first show that a two-dimensional, approximate analytic return map for uncontrolled locomotion with this system under a fixed touchdown leg angle policy and an open-loop ramp torque profile exhibits only marginal self-stability that does not always persist for the exact system. We then propose a per-stride feedback strategy for the hip torque that explicitly compensates for damping losses, reducing the return map to a single dimension and substantially improving the robust stability of fixed points. Subsequent presentation of simulation evidence establishes that the predictions of this approximate model are consistent with the behavior of the exact plant model. We illustrate the relevance and utility of our model both through the qualitative correspondence of its predictions to biological data as well as its use in the design of a task-level running controller.
Self-consistent simulation of intermediate band solar cells: Effect of occupation rates on device characteristics
Authors: Yoshida Katsuhisa , Okada Yoshitaka , Sano Nobuyuki
Published: September 2010

In order to design optimum structures for intermediate band solar cells, simulations based on self-consistent drift-diffusion model with a suitable treatment of the intermediate band in device domain are necessary. In this work, we have included the dependence of occupation rate of intermediate band at each position on optical generation rate via the intermediate band. Typical material parameters of GaAs were used except for the absorption coefficient of each corresponding band-to-band transition. Simulation results using our model indicate that the dependence of occupation rate on device position strongly affect short-circuit currents and also electrostatic potentials of the cell.
Optimal causal inference: Estimating stored information and approximating causal architecture
Authors: Still Susanne , Crutchfield James P. , Ellison Christopher J.
Published: September 2010

We introduce an approach to inferring the causal architecture of stochastic dynamical systems that extends rate-distortion theory to use causal shielding—a natural principle of learning. We study two distinct cases of causal inference: optimal causal filtering and optimal causal estimation. Filtering corresponds to the ideal case in which the probability distribution of measurement sequences is known, giving a principled method to approximate a system’s causal structure at a desired level of representation. We show that in the limit in which a model-complexity constraint is relaxed, filtering finds the exact causal architecture of a stochastic dynamical system, known as the causal-state partition. From this, one can estimate the amount of historical information the process stores. More generally, causal filtering finds a graded model-complexity hierarchy of approximations to the causal architecture. Abrupt changes in the hierarchy, as a function of approximation, capture distinct scales of structural organization. For nonideal cases with finite data, we show how the correct number of the underlying causal states can be found by optimal causal estimation. A previously derived model-complexity control term allows us to correct for the effect of statistical fluctuations in probability estimates and thereby avoid overfitting.
Do topological models provide good information about electricity infrastructure vulnerability?
Authors: Hines Paul , Cotilla-Sanchez Eduardo , Blumsack Seth
Published: September 2010

In order to identify the extent to which results from topological graph models are useful for modeling vulnerability in electricity infrastructure, we measure the susceptibility of power networks to random failures and directed attacks using three measures of vulnerability: characteristic path lengths, connectivity loss, and blackout sizes. The first two are purely topological metrics. The blackout size calculation results from a model of cascading failure in power networks. Testing the response of 40 areas within the Eastern U.S. power grid and a standard IEEE test case to a variety of attack/failure vectors indicates that directed attacks result in larger failures using all three vulnerability measures, but the attack-vectors that appear to cause the most damage depend on the measure chosen. While the topological metrics and the power grid model show some similar trends, the vulnerability metrics for individual simulations show only a mild correlation. We conclude that evaluating vulnerability in power networks using purely topological metrics can be misleading.
Numerical information processing under the global rule expressed by the Euler–Riemann ζ function defined in the complex plane
Authors: Chatelin Françoise
Published: September 2010

When nonzero, the ζ function is intimately connected with numerical information processing. Two other functions play a key role, namely, η(s)=∑n≥1(−1)n+1/ns and λ(s)=∑n≥01/(2n+1)s. The paper opens on a survey of some of the seminal work of Euler [Mémoires Acad. Sci., Berlin 1768, 83 (1749)] and of the amazing theorem by Voronin [Math. USSR, Izv. 9, 443 (1975)] Then, as a follow-up of Chatelin [Qualitative Computing. A Computational Journey into Nonlinearity (World Scientific, Singapore, in press)], we present a fresh look at the triple (η,ζ,λ) which suggests an elementary analysis based on the distances of the three complex numbers z, z/2, and 2/z to 0 and 1. This metric approach is used to contextualize any nonlinear computation when it is observed at a point describing a complex plane. The results applied to ζ, η, and λ shed a new epistemological light about the critical line. The suggested interpretation related to ζ carries computational significance.
Cross-validation of microfabricated atomic magnetometers with superconducting quantum interference devices for biomagnetic applications
Authors: Knappe Svenja , Sander Tilmann H. , Kosch Olaf , Wiekhorst Frank , Kitching John , Trahms Lutz
Published: September 2010

We compare the performance of a chip-scale atomic magnetometer (CSAM) with that of a superconducting quantum interference device (SQUID) sensor in two biomedical applications. Magnetocardiograms (MCGs) of healthy human subjects were measured simultaneously by a CSAM and a multichannel SQUID sensor in a magnetically shielded room. The typical features of MCGs are resolved by the CSAM, matching the SQUID results. Magnetorelaxometry (MRX) signals of iron nanoparticles were also obtained with the CSAM and compared to similar measurements with a SQUID.
Metal-enhanced chemiluminescence from chromium, copper, nickel, and zinc nanodeposits: Evidence for a second enhancement mechanism in metal-enhanced fluorescence
Authors: Weisenberg Micah , Zhang Yongxia , Geddes Chris D.
Published: September 2010

Over the past decade metal-fluorophore interactions, metal-enhanced fluorescence, have attracted significant research attention, with the technology now becoming common place in life science applications. In this paper, we address the underlying mechanisms of metal-enhanced fluorescence (MEF) and experimentally show using chemiluminescence solutions that MEF is indeed underpinned by two complimentary mechanisms, consistent with the recent reports by Geddes and co-workers [Zhang et al., J. Phys. Chem. C 113, 12095 (2009)] and their enhanced fluorescence hypothesis.
Three-color nonlinear optical mixing for the determination of the refractive index dispersion of a tellurite glass
Authors: Jin Zhian , Kan Carolyn , Szafruga Urszula B. , Toulouse Jean , Biaggio Ivan
Published: September 2010

We determine the refractive index dispersion of a quaternary tungsten-tellurite glass over a broad spectral range from 0.4 to 3 μm from the wavelength dependence of the phase matching conditions for third-order nonlinear optical frequency conversion. We discuss the optimum phase-matching geometries for this task and obtain the wavelength-dependence of the refractive index to within three significant digits by a least-squares fit of a Sellmeier-type equation to the phase-matching data.
Resonance frequency shift of a carbon nanotube with a silver nanoparticle adsorbed at various positions
Authors: Wang Shau-Chieh , Chang Yuan-Chih , Lien Der-Hsien , Hsu Tung , Chang Chia-Seng
Published: September 2010

We positioned a single silver nanoparticle along the length of a carbon nanotube based resonator, and investigated the resonance frequency shift subject to the particle’s position. We found that a curve derived from the classical continuum model can fit well to our experimental data, implying the applicability of the analytical formula even in the nanometer range. We also used the finite element simulation to elicit the subtle frequency difference caused by the radial angle of nanoparticle’s position in reference to the vibrating plane of the resonator. This effect was found to have an insignificant correction to our measurement.
Fabrication of micropillars by laser-induced thermoplastic method
Authors: Wang Leyan , Zhang Dongxian , Zhang Haijun , Jiang J. Z.
Published: September 2010

A laser-induced thermoplastic formation technology for three dimension microstructure has been investigated theoretically and experimentally. An experimental system is built up and formation experiments are carried out on different kinds of thermoplastic materials. The appearance dependence of microstructures (micropillars) on the fabricating parameters has been discussed. Critical parameters for microstructure formation are concluded to be laser power, liquid temperature and material absorptance. By analyzing different melting-solidifying conditions, the balance between melting and solidifying velocities has been considered to be necessary for continuous micropillar growth. Based on theoretical analyses, micropillars with better HW ratio and better resolution are demonstrated.
Drooping as a simple characterization tool for extraction efficiency and optical losses in light emitting diodes
Authors: Oksanen Jani , Tulkki Jukka
Published: September 2010

We extend the previous droop models developed for InGaN light emitting diodes (LEDs) by accounting for the light extraction and show that drooping can be used to quantify both the extraction efficiency and the optical losses in LEDs. Our model allows very simple characterization of LEDs by an integrating sphere and therefore provides an attractive characterization tool to measure the most important loss parameters of various LED structures. In particular, the approach allows evaluation of the effects of various optical losses and photon recycling on the efficiency and consequently allows more efficient optimization of the LED structures. As an additional benefit, our measurement method does not necessarily require any fitting of the data.
Preparation of superhydrophobic nanodiamond and cubic boron nitride films
Authors: Zhou Y. B. , Yang Y. , Liu W. M. , Ye Q. , He B. , Zou Y. S. , Wang P. F. , Pan X. J. , Zhang W. J. , Bello I. , Lee S. T.
Published: September 2010

Superhydrophobic surfaces were achieved on the hardest and the second hardest materials, diamond and cubic boron nitride (cBN) films. Various surface nanostructures of nanocrystalline diamond (ND) and cBN films were constructed by carrying out bias-assisted reactive ion etching in hydrogen/argon plasmas; and it is shown that surface nanostructuring may enhance dramatically the hydrophobicity of ND and cBN films. Together with surface fluorination, superhydrophobic ND and cBN surfaces with a contact angle greater than 150° and a sliding angle smaller than 10° were demonstrated. The origin of hydrophobicity enhancement is discussed based on the Cassie model.
Time-resolved spectroscopy of InAsP/InP(001) quantum dots emitting near 2 μm
Authors: Elvira D. , Michon A. , Fain B. , Patriarche G. , Beaudoin G. , Robert-Philip I. , Vachtomin Y. , Divochiy A. V. , Smirnov K. V. , Gol’tsman G. N. , Sagnes I. , Beveratos A.
Published: September 2010

By using superconducting single photon detectors, we perform time-resolved characterization of a small ensemble of InAsP/InP quantum dots grown by metal organic vapor phase epitaxy, emitting at wavelengths between 1.6 and 2.2 μm. We demonstrate that alloying phosphorus with InAs allows to shift the emission wavelength toward higher wavelengths, while keeping the high optical quality of these quantum dots at room temperature, with no decrease in their radiative lifetime.
Spectroscopic characterization of bismuth embedded Y zeolites
Authors: Sun Hong-Tao , Sakka Yoshio , Miwa Yuji , Shirahata Naoto , Fujii Minoru , Gao Hong
Published: September 2010

Bismuth embedded Y zeolites were studied by using UV-vis- near infrared (NIR) diffuse reflectance, Raman, and steady-state NIR photoluminescence spectroscopy. The results suggest that Bi53+ and Bi+ active centers coexist in the dehydrated and hydrated zeolite framework, both of which contribute to NIR emission. Furthermore, it was revealed that the high-temperature annealing leads to the formation of Bi2O3 clusters, which act as blocks for selectively closing down the “in-out windows” of H2O and O2 molecules in the zeolites. It is believed that these materials can find a wide array of applications as active media of broadly tunable micro or nano-optical sources.
Influence of biochars on flux of N2O and CO2 from Ferrosol
Authors: van Zwieten L. , Kimber S. , Morris S. , Downie A. , Berger E. , Rust J. , Scheer C.
Published: September 2010

Biochars produced by slow pyrolysis of greenwaste (GW), poultry litter (PL), papermill waste (PS), and biosolids (BS) were shown to reduce N2O emissions from an acidic Ferrosol. Similar reductions were observed for the untreated GW feedstock. Soil was amended with biochar or feedstock giving application rates of 1 and 5%. Following an initial incubation, nitrogen (N) was added at 165 kg/ha as urea. Microcosms were again incubated before being brought to 100% water-filled porosity and held at this water content for a further 47 days. The flooding phase accounted for the majority (<80%) of total N2O emissions. The control soil released 3165 mg N2O-N/m2, or 15.1% of the available N as N2O. Amendment with 1 and 5% GW feedstock significantly reduced emissions to 1470 and 636 mg N2O-N/m2, respectively. This was equivalent to 8.6 and 3.8% of applied N. The GW biochar produced at 350°C was least effective in reducing emissions, resulting in 1625 and 1705 mg N2O-N/m2 for 1 and 5% amendments. Amendment with BS biochar at 5% had the greatest impact, reducing emissions to 518 mg N2O-N/m2, or 2.2% of the applied N over the incubation period. Metabolic activity as measured by CO2 production could not explain the differences in N2O emissions between controls and amendments, nor could NH4+ or NO3– concentrations in biochar-amended soils. A decrease in NH4+ and NO3– following GW feedstock application is likely to have been responsible for reducing N2O emissions from this amendment. Reduction in N2O emissions from the biochar-amended soils was attributed to increased adsorption of NO3–. Small reductions are possible due to improved aeration and porosity leading to lower levels of denitrification and N2O emissions. Alternatively, increased pH was observed, which can drive denitrification through to dinitrogen during soil flooding.
An investigation into the reactions of biochar in soil
Authors: Joseph S. D. , Camps-Arbestain M. , Lin Y. , Munroe P. , Chia C. H. , Hook J. , van Zwieten L. , Kimber S. , Cowie A. , Singh B. P. , Lehmann J. , Foidl N. , Smernik R. J. , Amonette J. E.
Published: September 2010

Interactions between biochar, soil, microbes, and plant roots may occur within a short period of time after application to the soil. The extent, rates, and implications of these interactions, however, are far from understood. This review describes the properties of biochars and suggests possible reactions that may occur after the addition of biochars to soil. These include dissolution–precipitation, adsorption–desorption, acid–base, and redox reactions. Attention is given to reactions occurring within pores, and to interactions with roots, microorganisms, and soil fauna. Examination of biochars (from chicken litter, greenwaste, and paper mill sludges) weathered for 1 and 2 years in an Australian Ferrosol provides evidence for some of the mechanisms described in this review and offers an insight to reactions at a molecular scale. These interactions are biochar- and site-specific. Therefore, suitable experimental trials—combining biochar types and different pedoclimatic conditions—are needed to determine the extent to which these reactions influence the potential of biochar as a soil amendment and tool for carbon sequestration.
Microscopic characterisation of synthetic Terra Preta
Authors: Chia Chee Hung , Munroe Paul , Joseph Stephen , Lin Yun
Published: September 2010

Amazonian Dark Earths (Terra Preta) are anthropogenic soils with high organic carbon content and the ability to sustain higher fertility than adjacent, intensely weathered, acidic soils. Consequently, the microstructural development of biochar–mineral complexes, termed synthetic Terra Preta (STP), has been investigated. Here, biochar–mineral complexes are produced at elevated temperatures to mimic the structure of Terra Preta. These materials, if added to soils, may then also improve fertility. The raw materials used in STP were organic biowaste, such as sawdust, chicken manure, and blood and bone, and inorganic minerals such as kaolinite, bentonite, and cement kiln dust (which consists mainly of calcite). The STP samples were characterised using X-ray photoelectron spectroscopy, nuclear magnetic resonance, scanning electron microscopy (SEM), and transmission electron microscopy (TEM), and associated microchemical analytical methods, to gain an understanding of the interactions that occurred during processing between the organic and inorganic phases. The STP specimens exhibited microstructures that closely resemble Terra Preta. SEM and TEM revealed a complex aggregation of phases, together with evidence of the interfacial reactions, especially at higher processing temperatures. It is anticipated then that STP may be as effective in promoting plant growth and in sequestering carbon as Terra Preta
RETRACTED: Autophosphorylation of Tyr-610 in the receptor kinase BAK1 plays a role in brassinosteroid signaling and basal defense gene expression
Authors: Oh Man-Ho , Wang Xiaofeng , Wu Xia , Zhao Youfu , Clouse Steven D. , Huber Steven C.
Published: September 2010

BAK1 is a leucine-rich repeat receptor-like kinase that functions as a coreceptor with the brassinosteroid (BR) receptor BRI1 and the flagellin receptor FLS2, and as a negative regulator of programmed cell death. BAK1 has been shown to autophosphorylate on numerous serine/threonine sites in vitro as well as to transphosphorylate associated receptor kinases both in vitro and in planta. In the present study we identify Tyr-610 in the carboxyl-terminal domain of BAK1 as a major site of autophosphorylation that is brassinolide-induced in vivo and requires a kinase-active BAK1. Expression of BAK1(Y610F)-Flag in transgenic plants lacking the endogenous
bak1
and its functional paralogue,
bkk1
, produced plants that were viable but extremely small and generally resembled BR signaling mutants, whereas an acidic substitution for Tyr-610 to mimic phosphorylation restored normal growth. Several lines of evidence support the notion that BR signaling is impaired in the BAK1(Y610F)-Flag plants, and are consistent with the recently proposed sequential transphosphorylation model for BRI1/BAK1 interaction and activation. In contrast, the FLS2-mediated inhibition of seedling growth by the flg22 elicitor occurred normally in the Y610F-directed mutant. However, expression of many defense genes was dramatically reduced in BAK1(Y610F) plants and the nonpathogenic
hrpA
mutant of
Pseudomonas syringae
was able to grow rapidly in the mutant. These results indicate that phosphorylation of Tyr-610 is required for some but not all functions of BAK1, and adds significantly to the emerging notion that tyrosine phosphorylation could play an important role in plant receptor kinase signaling.
Strand- and site-specific DNA lesion demarcation by the xeroderma pigmentosum group D helicase
Authors: Mathieu Nadine , Kaczmarek Nina , Naegeli Hanspeter
Published: September 2010

The most detrimental responses of the UV-exposed skin are triggered by cyclobutane pyrimidine dimers (CPDs). Although placental mammals rely solely on nucleotide excision repair (NER) to eliminate CPDs, none of the core NER factors are apparently able to distinguish this hazardous lesion from native DNA, raising the question of how CPDs are circumscribed to define correct excision boundaries. A key NER intermediate involves unwinding of the damaged duplex by transcription factor TFIIH, a reaction that requires xeroderma pigmentosum group D (XPD) protein. This study was prompted by the observation that the ATPase/helicase activity of XPD is necessary for an effective anchoring of this subunit to UV lesions in mammalian nuclei. The underlying mechanism by which XPD impinges on damaged DNA has been probed with a monomeric archaeal homolog, thus revealing that the collision with a single CPD inhibits the helicase but stimulates its ATPase activity. Restriction and glycosylase protection assays show that the XPD helicase remains firmly bound to a CPD situated in the translocated strand along which the enzyme moves with 5′–3′ polarity. Competition assays confirm that a stable complex is formed when the XPD helicase encounters a CPD in the translocated strand. Instead, the enzyme dissociates from the substrate after running into a CPD in the complementary 3′–5′ strand. These results disclose a damage verification and demarcation process that takes place by strand-selective immobilization of the XPD helicase and its conversion to a site-specific ATPase at DNA lesions.
Predicting consumer behavior with Web search
Authors: Goel Sharad , Hofman Jake M. , Lahaie Sébastien , Pennock David M. , Watts Duncan J.
Published: September 2010

Recent work has demonstrated that Web search volume can “predict the present,” meaning that it can be used to accurately track outcomes such as unemployment levels, auto and home sales, and disease prevalence in near real time. Here we show that what consumers are searching for online can also predict their collective future behavior days or even weeks in advance. Specifically we use search query volume to forecast the opening weekend box-office revenue for feature films, first-month sales of video games, and the rank of songs on the Billboard Hot 100 chart, finding in all cases that search counts are highly predictive of future outcomes. We also find that search counts generally boost the performance of baseline models fit on other publicly available data, where the boost varies from modest to dramatic, depending on the application in question. Finally, we reexamine previous work on tracking flu trends and show that, perhaps surprisingly, the utility of search data relative to a simple autoregressive model is modest. We conclude that in the absence of other data sources, or where small improvements in predictive performance are material, search queries provide a useful guide to the near future.
Structures of the
Escherichia coli
ribosome with antibiotics bound near the peptidyl transferase center explain spectra of drug action
Authors: Dunkle Jack A. , Xiong Liqun , Mankin Alexander S. , Cate Jamie H. D.
Published: September 2010

Differences between the structures of bacterial, archaeal, and eukaryotic ribosomes account for the selective action of antibiotics. Even minor variations in the structure of ribosomes of different bacterial species may lead to idiosyncratic, species-specific interactions of the drugs with their targets. Although crystallographic structures of antibiotics bound to the peptidyl transferase center or the exit tunnel of archaeal (
Haloarcula marismortui
) and bacterial (
Deinococcus radiodurans
) large ribosomal subunits have been reported, it remains unclear whether the interactions of antibiotics with these ribosomes accurately reflect those with the ribosomes of pathogenic bacteria. Here we report X-ray crystal structures of the
Escherichia coli
ribosome in complexes with clinically important antibiotics of four major classes, including the macrolide erythromycin, the ketolide telithromycin, the lincosamide clindamycin, and a phenicol, chloramphenicol, at resolutions of ∼3.3 
Å
–3.4 
Å
. Binding modes of three of these antibiotics show important variations compared to the previously determined structures. Biochemical and structural evidence also indicates that interactions of telithromycin with the
E. coli
ribosome more closely resembles drug binding to ribosomes of bacterial pathogens. The present data further argue that the identity of nucleotides 752, 2609, and 2055 of 23S ribosomal RNA explain in part the spectrum and selectivity of antibiotic action.
Unraveling electronic energy transfer in single conjugated polyelectrolytes encapsulated in lipid vesicles
Authors: Karam Pierre , Ngo An Thien , Rouiller Isabelle , Cosa Gonzalo
Published: September 2010

A method for the study of conjugated polyelectrolyte (CPE) photophysics in solution at the single-molecule level is described. Extended observation times of single polymer molecules are enabled by the encapsulation of the CPEs within 200-nm lipid vesicles, which are in turn immobilized on a surface. When combined with a molecular-level visualization of vesicles and CPE via cryo-transmission electron microscopy, these single-molecule spectroscopy studies on CPEs enable us to directly correlate the polymer conformation with its spectroscopic features. These studies are conducted with poly[5-methoxy-2-(3-sulfopropoxy)-1,4-phenylene-vinylene] (MPS-PPV, a negatively charged CPE), when encapsulated in neutral and in negatively charged lipid vesicles. MPS-PPV exists as a freely diffusing polymer when confined in negatively charged vesicles. Individual MPS-PPV molecules adopt a collapsed-chain conformation leading to efficient energy migration over multiple chromophores. Both the presence of stepwise photobleaching in fluorescence intensity-time trajectories and emission from low-energy chromophores along the chain are observed. These results correlate with the amplified sensing potential reported for MPS-PPV in aqueous solution. When confined within neutral vesicles, single MPS-PPV molecules adopt an extended conformation upon insertion in the lipid bilayer. In this case emission arises from multiple chromophores within the isolated polymer chains, leading to an exponential decay of the intensity over time and a broad blue-shifted emission spectrum.
Local control of a disorder–order transition in 4E-BP1 underpins regulation of translation via eIF4E
Authors: Tait Shirley , Dutta Kaushik , Cowburn David , Warwicker Jim , Doig Andrew J. , McCarthy John E. G.
Published: September 2010

The molecular mechanism underpinning regulation of eukaryotic translation initiation factor eIF4E by 4E-BP1 has remained unclear. We use isothermal calorimetry, circular dichroism, NMR, and computational modeling to analyze how the structure of the eIF4E-binding domain of 4E-BP1 determines its affinity for the dorsal face of eIF4E and thus the ability of this regulator to act as a competitive inhibitor. This work identifies the key role of solvent-facing amino acids in 4E-BP1 that are not directly engaged in interactions with eIF4E. These amino acid residues influence the propensity of the natively unfolded binding motif to fold into a conformation, including a stretch of α-helix, that is required for tight binding to eIF4E. In so doing, they contribute to a free energy landscape for 4E-BP1 folding that is poised so that phosphorylation of S65 at the C-terminal end of the helical region can modulate the propensity of folding, and thus regulate the overall free energy of 4E-BP1 binding to eIF4E, over a physiologically significant range. Thus, phosphorylation acts as an intramolecular structural modulator that biases the free energy landscape for the disorder–order transition of 4E-BP1 by destabilizing the α-helix to favor the unfolded form that cannot bind eIF4E. This type of order–disorder regulatory mechanism is likely to be relevant to other intermolecular regulatory phenomena in the cell.
Fundamental limit of nanophotonic light trapping in solar cells
Authors: Yu Zongfu , Raman Aaswath , Fan Shanhui
Published: September 2010

Establishing the fundamental limit of nanophotonic light-trapping schemes is of paramount importance and is becoming increasingly urgent for current solar cell research. The standard theory of light trapping demonstrated that absorption enhancement in a medium cannot exceed a factor of 4
n
2
/ sin
2
θ
, where
n
is the refractive index of the active layer, and
θ
is the angle of the emission cone in the medium surrounding the cell. This theory, however, is not applicable in the nanophotonic regime. Here we develop a statistical temporal coupled-mode theory of light trapping based on a rigorous electromagnetic approach. Our theory reveals that the conventional limit can be substantially surpassed when optical modes exhibit deep-subwavelength-scale field confinement, opening new avenues for highly efficient next-generation solar cells.
Calcium-sensing receptor is a physiologic multimodal chemosensor regulating gastric G-cell growth and gastrin secretion
Authors: Feng Jianying , Petersen Clark D. , Coy David H. , Jiang Jian-Kang , Thomas Craig J. , Pollak Martin R. , Wank Stephen A.
Published: September 2010

The calcium-sensing receptor (CaR) is the major sensor and regulator of extracellular Ca2+, whose activity is allosterically regulated by amino acids and pH. Recently, CaR has been identified in the stomach and intestinal tract, where it has been proposed to function in a non-Ca2+homeostatic capacity. Luminal nutrients, such as Ca2+and amino acids, have been recognized for decades as potent stimulants for gastrin and acid secretion, although the molecular basis for their recognition remains unknown. The expression of CaR on gastrin-secreting G cells in the stomach and their shared activation by Ca2+, amino acids, and elevated pH suggest that CaR may function as the elusive physiologic sensor regulating gastrin and acid secretion. The genetic and pharmacologic studies presented here comparing CaR-null mice and wild-type littermates support this hypothesis. Gavage of Ca2+, peptone, phenylalanine, Hepes buffer (pH 7.4), and CaR-specific calcimimetic, cinacalcet, stimulated gastrin and acid secretion, whereas the calcilytic, NPS 2143, inhibited secretion only in the wild-type mouse. Consistent with known growth and developmental functions of CaR, G-cell number was progressively reduced between 30 and 90 d of age by more than 65% in CaR-null mice. These studies of nutrient-regulated G-cell gastrin secretion and growth provide definitive evidence that CaR functions as a physiologically relevant multimodal sensor. Medicinals targeting diseases of Ca2+homeostasis should be reviewed for effects outside traditional Ca2+-regulating tissues in view of the broader distribution and function of CaR.
Serotonin selectively influences moral judgment and behavior through effects on harm aversion
Authors: Crockett Molly J. , Clark Luke , Hauser Marc D. , Robbins Trevor W.
Published: September 2010

Aversive emotional reactions to real or imagined social harms infuse moral judgment and motivate prosocial behavior. Here, we show that the neurotransmitter serotonin directly alters both moral judgment and behavior through increasing subjects’ aversion to personally harming others. We enhanced serotonin in healthy volunteers with citalopram (a selective serotonin reuptake inhibitor) and contrasted its effects with both a pharmacological control treatment and a placebo on tests of moral judgment and behavior. We measured the drugs' effects on moral judgment in a set of moral 'dilemmas' pitting utilitarian outcomes (e.g., saving five lives) against highly aversive harmful actions (e.g., killing an innocent person). Enhancing serotonin made subjects more likely to judge harmful actions as forbidden, but only in cases where harms were emotionally salient. This harm-avoidant bias after citalopram was also evident in behavior during the ultimatum game, in which subjects decide to accept or reject fair or unfair monetary offers from another player. Rejecting unfair offers enforces a fairness norm but also harms the other player financially. Enhancing serotonin made subjects less likely to reject unfair offers. Furthermore, the prosocial effects of citalopram varied as a function of trait empathy. Individuals high in trait empathy showed stronger effects of citalopram on moral judgment and behavior than individuals low in trait empathy. Together, these findings provide unique evidence that serotonin could promote prosocial behavior by enhancing harm aversion, a prosocial sentiment that directly affects both moral judgment and moral behavior.
Secretion of a bacterial virulence factor is driven by the folding of a C-terminal segment
Authors: Peterson Janine H. , Tian Pu , Ieva Raffaele , Dautin Nathalie , Bernstein Harris D.
Published: September 2010

Autotransporters are bacterial virulence factors consisting of an N-terminal “passenger domain” that is secreted in a C- to-N-terminal direction and a C-terminal “β domain” that resides in the outer membrane (OM). Although passenger domain secretion does not appear to use ATP, the energy source for this reaction is unknown. Here, we show that efficient secretion of the passenger domain of the
Escherichia coli
O157:H7 autotransporter EspP requires the stable folding of a C-terminal ≈17-kDa passenger domain segment. We found that mutations that perturb the folding of this segment do not affect its translocation across the OM but impair the secretion of the remainder of the passenger domain. Interestingly, an examination of kinetic folding mutants strongly suggested that the ≈17-kDa segment folds in the extracellular space. By mutagenizing the ≈17-kDa segment, we also fortuitously isolated a unique translocation intermediate. Analysis of this intermediate suggests that a heterooligomer that facilitates the membrane integration of OM proteins (the Bam complex) also promotes the surface exposure of the ≈17-kDa segment. Our results provide direct evidence that protein folding can drive translocation and help to clarify the mechanism of autotransporter secretion.
Cooperativity between
trans
and
cis
interactions in cadherin-mediated junction formation
Authors: Wu Yinghao , Jin Xiangshu , Harrison Oliver , Shapiro Lawrence , Honig Barry H. , Ben-Shaul Avinoam
Published: September 2010

Intercellullar junctions formed by cadherins, including desmosomes and adherens junctions, comprise two dimensional arrays of “
trans
” dimers formed between monomers emanating from opposing cell surfaces. Lateral “
cis
” interfaces between cadherins from the same cell surface have been proposed to play a role in cadherin clustering. Although the molecular details of
cis
interactions remain uncertain, they must define an anisotropic arrangement where binding is favorable only in certain orientations. Here we report Monte Carlo simulations performed on a 2D lattice constructed to account for the anisotropy in cadherin
cis
interactions. A crucial finding is that the “phase transition” between freely diffusing cadherin monomers and dimers and a condensed ordered 2D junction formed by dimers alone is a cooperative process involving both
trans
and
cis
interactions. Moreover,
cis
interactions, despite being too weak to be measured in solution, are critical to the formation of an ordered junction structure. We discuss these results in light of available experimental information on cadherin binding free energies that are transformed from their bulk solution values to interaction energies on a 2D lattice.
Structure-function study of the fourth transmembrane segment of the GABAρ1 receptor
Authors: Estrada-Mondragón Argel , Reyes-Ruiz Jorge Mauricio , Martínez-Torres Ataúlfo , Miledi Ricardo
Published: September 2010

The Cys-loop family of receptors mediates synaptic neurotransmission in the central nervous system of vertebrates. These receptors share several structural characteristics and assemble in the plasma membrane as multimers with fivefold symmetry. Of these, the ionotropic GABA receptors are key players in the pathogenesis of diseases like epilepsy, anxiety, and schizophrenia. Different experimental approaches have shed some light on the mechanisms behind the function of these receptors; but little is known about their structure at high resolution. Sequence homology with the nicotinic acetylcholine receptor predicts that ionotropic GABA receptors possess four transmembrane segments (TM1–4) and that TM2 forms the wall of the ion channel. However, the role of the other three segments is unclear. The GABAρ1 receptor plays a fundamental role in the regulation of neurotransmission along the visual pathway, is highly sensitive to GABA, and exhibits little desensitization. In our recent investigations of the role of TM4 in receptor function, a key residue in this domain (W475) was found to be involved in activation of the receptor. Here we have generated a structural model of the GABAρ1 receptor in silico and assessed its validity by electrophysiologically testing nine amino acid substitutions of W475 and deletions of the neighboring residues (Y474 and S476). The results identify a critical linkage between the ligand-binding domain and the TM4 domain and provide a framework for more detailed structure-function analyses of ionotropic GABA receptors.
Neonicotinoid insecticides induce salicylate-associated plant defense responses
Authors: Ford Kevin A. , Casida John E. , Chandran Divya , Gulevich Alexander G. , Okrent Rachel A. , Durkin Kathleen A. , Sarpong Richmond , Bunnelle Eric M. , Wildermuth Mary C.
Published: September 2010

Neonicotinoid insecticides control crop pests based on their action as agonists at the insect nicotinic acetylcholine receptor, which accepts chloropyridinyl- and chlorothiazolyl-analogs almost equally well. In some cases, these compounds have also been reported to enhance plant vigor and (a)biotic stress tolerance, independent of their insecticidal function. However, this mode of action has not been defined. Using
Arabidopsis thaliana
, we show that the neonicotinoid compounds, imidacloprid (IMI) and clothianidin (CLO), via their 6-chloropyridinyl-3-carboxylic acid and 2-chlorothiazolyl-5-carboxylic acid metabolites, respectively, induce salicylic acid (SA)-associated plant responses. SA is a phytohormone best known for its role in plant defense against pathogens and as an inducer of systemic acquired resistance; however, it can also modulate abiotic stress responses. These neonicotinoids effect a similar global transcriptional response to that of SA, including genes involved in (a)biotic stress response. Furthermore, similar to SA, IMI and CLO induce systemic acquired resistance, resulting in reduced growth of a powdery mildew pathogen. The action of CLO induces the endogenous synthesis of SA via the SA biosynthetic enzyme ICS1, with ICS1 required for CLO-induced accumulation of SA, expression of the SA marker
PR1
, and fully enhanced resistance to powdery mildew. In contrast, the action of IMI does not induce endogenous synthesis of SA. Instead, IMI is further bioactivated to 6-chloro-2-hydroxypyridinyl-3-carboxylic acid, which is shown here to be a potent inducer of
PR1
and inhibitor of SA-sensitive enzymes. Thus, via different mechanisms, these chloropyridinyl- and chlorothiazolyl-neonicotinoids induce SA responses associated with enhanced stress tolerance.
Proteolytic processing of protocadherin proteins requires endocytosis
Authors: Buchanan Sean M. , Schalm Stefanie S. , Maniatis Tom
Published: September 2010

The α-, β-, and γ-protocadherins (Pcdhα, Pcdhβ, and Pcdhγ) comprise a large family of single-pass transmembrane proteins predominantly expressed in the nervous system. These proteins contain six cadherin-like extracellular domains, and proteolysis of Pcdhα and Pcdhγ by the γ-secretase complex releases their intracellular domains into the cytoplasm where they may function locally and/or enter the nucleus and affect gene expression. Thus, cleavage of Pcdhs may function to link intercellular contacts and intracellular signaling. Here we report that shedding of the Pcdhα extracellular domain and subsequent processing by γ-secretase require endocytosis and that Pcdhs interact with the regulator of vesicular sorting ESCRT-0 in undifferentiated cells. We also find that the accumulation of Pcdh cleavage products is regulated during development. Differentiation leads to an increase in the interactions between Pcdh proteins and a decrease in the accumulation of cleavage products. We conclude that Pcdh processing requires endocytosis and that the level of cleavage products is regulated during neuronal differentiation.
Not all nuclear pores created equal
Authors: Leslie Mitch
Published: September 2010

Pore-making process isn't identical in interphase and mitosis.
Sam68 regulates EMT through alternative splicing–activated nonsense-mediated mRNA decay of the SF2/ASF proto-oncogene
Authors: Valacca Cristina , Bonomi Serena , Buratti Emanuele , Pedrotti Simona , Baralle Francisco Ernesto , Sette Claudio , Ghigna Claudia , Biamonti Giuseppe
Published: September 2010

Epithelial-to-mesenchymal transition (EMT) and its reversal (MET) are crucial cell plasticity programs that act during development and tumor metastasis. We have previously shown that the splicing factor and proto-oncogene SF2/ASF impacts EMT/MET through production of a constitutively active splice variant of the Ron proto-oncogene. Using an in vitro model, we now show that SF2/ASF is also regulated during EMT/MET by alternative splicing associated with the nonsense-mediated mRNA decay pathway (AS-NMD). Overexpression and small interfering RNA experiments implicate the splicing regulator Sam68 in AS-NMD of SF2/ASF transcripts and in the choice between EMT/MET programs. Moreover, Sam68 modulation of SF2/ASF splicing appears to be controlled by epithelial cell–derived soluble factors that act through the ERK1/2 signaling pathway to regulate Sam68 phosphorylation. Collectively, our results reveal a hierarchy of splicing factors that integrate splicing decisions into EMT/MET programs in response to extracellular stimuli.
Imaging proprotein convertase activities and their regulation in the implanting mouse blastocyst
Authors: Mesnard Daniel , Constam Daniel B.
Published: September 2010

Axis formation and allocation of pluripotent progenitor cells to the germ layers are governed by the TGF-β–related Nodal precursor and its secreted proprotein convertases (PCs) Furin and Pace4. However, when and where Furin and Pace4 first become active have not been determined. To study the distribution of PCs, we developed a novel cell surface–targeted fluorescent biosensor (cell surface–linked indicator of proteolysis [CLIP]). Live imaging of CLIP in wild-type and Furin- and Pace4-deficient embryonic stem cells and embryos revealed that Furin and Pace4 are already active at the blastocyst stage in the inner cell mass and can cleave membrane-bound substrate both cell autonomously and nonautonomously. CLIP was also cleaved in the epiblast of implanted embryos, in part by a novel activity in the uterus that is independent of zygotic Furin and Pace4, suggesting a role for maternal PCs during embryonic development. The unprecedented sensitivity and spatial resolution of CLIP opens exciting new possibilities to elucidate PC functions in vivo.