bluuebunny/crossref_metadata_2025 huggingface dataset:
Master curves and radial distribution functions for shear dilatancy of liquid n-hexadecane via nonequilibrium molecular dynamics simulations
Authors: Tseng Huan-Chang , Wu Jiann-Shing , Chang Rong-Yeu
Published: April 2009

Shear dilatancy, a significant nonlinear behavior of nonequilibrium thermodynamics states, has been observed in nonequilibrium molecular dynamics (NEMD) simulations for liquid n-hexadecane fluid under extreme shear conditions. The existence of shear dilatancy is relevant to the relationship between the imposed shear rate γ̇ and the critical shear rate γ̇c. Consequently, as γ̇<γ̇c, the intermolecular equilibrium distance of the fluid remains unchanged, while the nonequilibrium state of the fluid approaches equilibrium. In contrast to γ̇>γ̇c, the intermolecular distance is lengthened substantially by strong shear deformation breaking the equilibrium thermodynamic state so that shear dilatancy takes place. Notably, a characteristic shear rate γ̇m, which depends on the root mean square molecular velocity and the average free molecular distance, is found in nonequilibrium thermodynamics state curves. Studies of the variations in the intermolecular radial distribution function (RDF) with respect to the shear rate provide a direct measure of the variation in the degree of intermolecular separation. Additionally, the variations of the RDF curve in the microscopic regime are consistent with those of the nonequilibrium thermodynamic state in the macroscopic world. By inspecting the overall shape of the RDF curve, it can be readily corroborated that the fluid of interest exists in the liquid state. More importantly, both primary characteristic values, the equilibrium thermodynamic state variable and a particular shear rate of γ̇p, are determined cautiously, with γ̇p depending on the γ̇m value and the square root of pressure. Thereby, the nonequilibrium thermodynamic state curves can be normalized as temperature-, pressure-, and density-invariant master curves, formulated by applying the Cross constitutive equation. Clearly, γ̇c occurs at which a reduced shear rate γ̇/γ̇p approaches 0.1. Furthermore, the trends in the rates of shear dilatancy in both the constant-pressure and constant-volume NEMD systems under isothermal conditions conform to the cyclic rule of pressure, as a function of density and shear rate.
Effect of localized magnetic field on the uniform ferromagnetic resonance mode in a thin film
Authors: Obukhov Yu. , Pelekhov D. V. , Nazaretski E. , Movshovich R. , Hammel P. C.
Published: April 2009

We theoretically analyze the influence of the micromagnetic probe used in ferromagnetic resonance force microscopy (FMRFM) on the ferromagnetic resonance (FMR) modes in a thin ferromagnetic film. Our analysis of the FMRFM force response reveals three regimes defined by the extent to which the probe perturbs the uniform FMR mode. With closer approach, the FMRFM force grows more slowly because the strengthening probe field suppresses the FMR response. Our analysis agrees well with experimental data and provides theoretical foundations for FMRFM imaging.
Stable T2Sin (T=Fe,Co,Ni,1≤n≤8) cluster motifs
Authors: Robles R. , Khanna S. N.
Published: April 2009

First principles studies on the geometry, electronic structure, and magnetic properties of neutral and anionic Fe2Sin, Co2Sin, and Ni2Sin (1≤n≤8) clusters have been carried out within a gradient corrected density functional framework. It is shown that these clusters display a variety of magnetic species with varying magnetic moment and different magnetic coupling between the two transition metal atoms. While Fe2Sin clusters are mostly ferromagnetic with large moments, Ni2Sin clusters are mostly nonmagnetic. Our studies of the variation of the binding energy upon addition of successive Si atoms and the gap between the highest occupied molecular orbital and the lowest unoccupied molecular orbital indicate that many of the motifs are quite stable and could be suitable as building blocks for generating magnetic cluster assembled materials. The studies also reveal motifs that could be used in molecular electronic devices to generate spin polarized currents or large magnetoresistance.
Stabilization and functional properties of La3NiAlMnO9 and La3CoAlMnO9 magnetoelectric triple perovskites
Authors: Singh M. P. , Truong K. D. , Jandl S. , Fournier P.
Published: April 2009

Ferromagnetic La3NiAlMnO9 (LNAMO) and La3CoAlMnO9 (LCAMO) triple-perovskite thin films are stabilized in the 750–860 °C temperature range in 100–900 mTorr O2 pressure range using pulsed-laser deposition. The LCAMO and LNAMO films exhibit ferromagnetism up to 190 and 130 K, respectively. The physical properties of these films demonstrate that the B-site 3d cations, Al, Mn, and Co or Ni ions, are structurally short-range ordered. A strong spin-lattice-polarization coupling in LCAMO is confirmed by a large dielectric constant and the onset of phonon softening in the vicinity of the ferromagnetic-to-paramagnetic phase transition.
Simple solutions for relativistic generalizations of the Child–Langmuir law and the Langmuir–Blodgett law
Authors: Zhang Yongpeng , Liu Guozhi , Yang Zhanfeng , Xing Qingzi , Shao Hao , Xiao Renzhen , Zhong Huaqiang , Lin Yuzheng
Published: April 2009

In this paper, the Child–Langmuir law and Langmuir–Blodgett law are generalized to the relativistic regime by a simple method. Two classical laws suitable for the nonrelativistic regime are modified to simple approximate expressions applicable for calculating the space-charge-limited currents of one-dimensional steady-state planar diodes and coaxial diodes under the relativistic regime. The simple approximate expressions, extending the Child–Langmuir law and Langmuir–Blodgett law to fit the full range of voltage, have small relative errors less than 1% for one-dimensional planar diodes and less than 5% for coaxial diodes.
Three-wave interactions between fast-ion driven modes in the National Spherical Torus Experiment
Authors: Crocker N. A. , Fredrickson E. D. , Kubota S. , Peebles W. A. , Bell R. E. , Kaye S. M. , LeBlanc B. P. , Menard J. E.
Published: April 2009

Experiments in the National Spherical Torus Experiment [M. Ono et al., Nucl. Fusion 40, 557 (2000)] have yielded new, unique observations of nonlinear three-wave interactions between compressional Alfvén eigenmodes (CAEs) and other fast-ion driven instabilities. Specifically, nonlinear interactions of CAEs have been conclusively identified with both energetic particle modes (EPMs) and toroidicity-induced Alfvén eigenmodes (TAEs). These nonlinear interactions occur simultaneously with other three-wave interactions observed between the TAEs and EPMs [N. A. Crocker et al., Phys. Rev. Lett. 97, 045002 (2006)]. The interaction between the CAEs and EPMs spatially redistributes the energy of the CAEs, concentrating it into a toroidally localized wave packet in the same way that the interaction between the TAEs and EPMs spatially concentrates the energy of the TAEs. The interaction between the CAEs and TAEs has been shown to further subdivide the CAE wave packet into a train of smaller wave packets. These nonlinear interactions occur during fast-ion loss events. The spatial redistribution of CAE fluctuation energy will modify the effect of the CAEs on fast-ion transport during these events.
Profiles of equilibrium constants for self-association of aromatic molecules
Authors: Beshnova Daria A. , Lantushenko Anastasia O. , Davies David B. , Evstigneev Maxim P.
Published: April 2009

Analysis of the noncovalent, noncooperative self-association of identical aromatic molecules assumes that the equilibrium self-association constants are either independent of the number of molecules (the EK-model) or change progressively with increasing aggregation (the AK-model). The dependence of the self-association constant on the number of molecules in the aggregate (i.e., the profile of the equilibrium constant) was empirically derived in the AK-model but, in order to provide some physical understanding of the profile, it is proposed that the sources for attenuation of the equilibrium constant are the loss of translational and rotational degrees of freedom, the ordering of molecules in the aggregates and the electrostatic contribution (for charged units). Expressions are derived for the profiles of the equilibrium constants for both neutral and charged molecules. Although the EK-model has been widely used in the analysis of experimental data, it is shown in this work that the derived equilibrium constant, KEK, depends on the concentration range used and hence, on the experimental method employed. The relationship has also been demonstrated between the equilibrium constant KEK and the real dimerization constant, KD, which shows that the value of KEK is always lower than KD.
Detailed plasma potential measurements in a radio-frequency expanding plasma obtained from various electrostatic probes
Authors: Lafleur T. , Charles C. , Boswell R. W.
Published: April 2009

On-axis plasma potential measurements have been made with an emissive probe in a low pressure (0.044 Pa) rf expanding plasma containing an ion beam. The beam is detected with a retarding field energy analyzer (RFEA), and is seen to disappear at high pressure (0.39 Pa). The emissive probe measurements are in very good agreement with corresponding measurements made with two separate RFEAs, and the results indicate that the floating potential of the strongly emitting probe gives an accurate measure of the plasma potential under the present conditions.
Synchrotron investigation on the sheared structure evolution of syndiotactic polypropylene crystallization process
Authors: Wen Huiying , Jiang Shichun , Men Yongfeng , Zhang Xuequan , An Lijia , Wu Zhonghua , Okuda Hiroshi
Published: April 2009

The final structure of molten syndiotactic polypropylene (sPP) sheared under different conditions was investigated by synchrotron small-angle x-ray scattering (SAXS) and wide-angle x-ray diffraction (WAXD) techniques to elucidate the shear effects on sPP crystalline structure. The results obtained from the WAXD show that there is no variation on crystalline form but a little difference on the orientation of the 200 reflection. The SAXS data indicate that the lamellar thickness and long period have not been affected by shear but the lamellar orientation is dependent on shear. The experimental data of sPP crystallization from sheared melt may indicate a mesophase structure that is crucial to the shear effects on the final polymer multiscale crystalline structures.
Gallium arsenide p-i-n radial structures for photovoltaic applications
Authors: Colombo C. , Heiβ M. , Grätzel M. , Fontcuberta i Morral A.
Published: April 2009

Gallium arsenide p-i-n radial junctions were fabricated by molecular beam epitaxy. The current-voltage characteristics of single nanowires were measured in the dark and under various illumination conditions including 1.5 AM. The total efficiency was 4.5%. Spatially resolved and power dependent photocurrent measurements indicate that the p-i-n junction is homogeneous along the nanowire. Electroluminescence measurements show an emission peak at about 1.4 eV, further corroborating the good quality of the nanowire. These results constitute an important progress for the use of nanowires in photovoltaic applications.
Coherence resonance induced by the deviation of non-Gaussian noise in coupled Hodgkin–Huxley neurons
Authors: Gong Yubing , Xie Yanhang , Hao Yinghang
Published: April 2009

Neurons are noisy elements. Noise arises from both intrinsic and extrinsic sources. In this paper, we numerically study the effect of a particular kind of colored non-Gaussian noise (NGN), mainly of its deviation q from Gaussian noise, on the collective firing in bidirectionally coupled deterministic Hodgkin–Huxley neurons. It is found that the coefficient of variation (CV), characterizing the temporal regularity of the collective spikes, nonlinearly changes with increasing q and passes through a minimum at an intermediate optimal q where the collective spiking becomes most regular, which represents the presence of coherence resonance (CR). We also present a global view of CV as a function of q and neuron number N under various appropriate values of noise intensity. For each value of noise intensity, there is an island present in the contour plot, which sufficiently demonstrates the phenomenon of “q-induced CR.” This phenomenon, termed as q-induced CR, shows that there is an optimal deviation of the NGN by which the coupled neurons may behave most periodically in time. Our results provide a novel constructive role of the deviation of the NGN in information processing and signal transduction in real neural systems.
Measurements of plasma potential in high-pressure microwave plasmas
Authors: Tarasova A. V. , Podder N. K. , Clothiaux E. J.
Published: April 2009

Plasma potential of a high-pressure (∼1 Torr) microwave-generated argon plasma is measured using a Langmuir probe and a cold emissive probe. The operation of a hot emissive probe in a high-pressure plasma has been very difficult due to frequent burn-outs and significantly reduced lifetime of the probe filament, which, in turn, limits the possibility of collecting a wide range of data. The I-V characteristics from both Langmuir and emissive probes are interpreted using the collisionless probe theory since the collision correction factor is not very significant. The plasma potential determined from both Langmuir and cold emissive probe characteristics agrees well with one another and is observed to be dependent on the operating gas pressure but relatively unchanged as a function of the microwave power. An average plasma potential determined over the operating range of microwave powers varies nonlinearly with the gas pressure.
Enhanced UV photoresponse from heterostructured Ag–ZnO nanowires
Authors: Lin Dandan , Wu Hui , Zhang Wei , Li Heping , Pan Wei
Published: April 2009

Photoactive material consisting of heterogeneous Ag–ZnO nanowires (NWs) was prepared by electrospinning. Tunable UV photodetectors fabricated using Ag–ZnO NWs have shown high sensitivity up to over four orders of magnitude with relatively fast and stable response speed. The mechanism for this colossal photoconductivity is elucidated by means of the efficient exciton dissociation under UV illumination due to accelerated electron transfer from conduction band of ZnO to Ag nanoparticles. The facile process proposed here may pave the way for designing sensing and imaging systems.
Electrically tunable spatially variable switching in ferroelectric liquid crystal/water system
Authors: Choudhary A. , Coondoo I. , Prakash J. , Sreenivas K. , Biradar A. M.
Published: April 2009

An unusual switching phenomenon in the region outside conducting patterned area in ferroelectric liquid crystal (FLC) containing about 1–2 wt % of water has been observed. The presence of water in the studied heterogeneous system was confirmed by Fourier transform infrared spectroscopy. The observed optical studies have been emphasized on the “spatially variable switching” phenomenon of the molecules in the nonconducting region of the cell. The observed phenomenon is due to diffusion of water between the smectic layers of the FLC and the interaction of the curved electric field lines with the FLC molecules in the nonconducting region.
Grain boundary contribution to recoil loop openness of exchange-coupled nanocrystalline magnets
Authors: Rong Chuan-bing , Liu J. Ping
Published: April 2009

It has been well known that recoil loop openness is related to soft-phase presence in exchange-coupled hard-soft nanocomposite magnets. Our study on recoil loop openness of exchange-coupled nanocrystalline magnets (both single-phase and composite) using a micromagnetic finite-element method has revealed that the recoil loop openness is also due to decreased grain size. Open recoil loops exist in single-phase magnets as well. Simulation of magnetization distribution in both nanocrystalline single-phase magnets and nanocomposite magnets shows that the openness of the recoil loops is correlated with unstable magnetization behavior in grain boundary and soft-phase regions, which is attributed to high energy state caused by exchange coupling in these regions. The simulation results are supported by experimental data.
Scattering of surface and volume spin waves in a magnonic crystal
Authors: Chumak A. V. , Serga A. A. , Wolff S. , Hillebrands B. , Kostylev M. P.
Published: April 2009

The operational characteristics of a magnonic crystal, which was fabricated as an array of shallow grooves on a surface of a magnetic film, were compared for magnetostatic surface spin waves and backward volume magnetostatic spin waves. The rejection frequency bands formation was studied as a function of the grooves depth. It has been found that the rejection of the volume wave is considerably larger than of the surface one. The influences of the nonreciprocity of the surface spin waves, as well as of the scattering of the lowest volume spin-wave mode into higher ones on the rejection efficiency are discussed.
Selection of dopants to enhance hydrogen diffusion rates in MgH2 and NaMgH3
Authors: Hao Shiqiang , Sholl David S.
Published: April 2009

The transport properties of hydrogen in metal hydrides are crucial to the kinetics of H2 storage in these materials. Previous first-principles calculations and experiments have shown that H transport in MgH2 and NaMgH3 is dominated by charged defects. This creates the possibility of enhancing hydrogen diffusion in these materials by adding dopants that alter the population of the relevant charged defects. We describe a comprehensive set of first-principles calculations examining dopants in MgH2 and NaMgH3 for this purpose. Only a small number of elemental dopants are found to have favorable properties, but these dopants could increase the diffusivity of H by two to three orders of magnitude relative to the undoped materials.
Graphene nanoribbon array in a cellular automata architecture for propagation of binary information
Authors: León A. , Barticevic Z. , Pacheco M.
Published: April 2009

In this work we propose a cellular automata architecture using graphene nanoribbon arrays with spin polarization. We study the electronic and magnetic properties of the proposed structures by using first principles calculations and an algorithm based in the Glauber dynamic for simulating the cellular automata evolution. Our results show that the studied system can be scaled so that the propagation of digital information throughout the automata is possible at room temperature.
Phase-matched emission of few high-harmonic orders from a helium gas cell
Authors: Teichmann Sven , Hannaford Peter , Van Dao Lap
Published: April 2009

We report on femtosecond-laser-based generation of a few phase-matched high-order harmonics in a helium semi-infinite gas cell. The harmonic beam consists of effectively four to six intense orders with wavelengths around 9.5 nm. By varying the effective interaction length, we observe the effects of coherence length related to plasma formation and the Gouy phase shift on the output. The atomic scattering factors for photoabsorption, the effective propagation lengths (leff,He≈1 mm, leff,Ar≈7.2 mm), and the energy conversion efficiencies (εHe≈10−7, εAr≈5×10−7) are deduced for harmonic generation in helium (77th to 95th orders) and also argon (21st to 27th orders) for comparison.
Acoustic and radio-transmitter retention in common carp (Cyprinus carpio) in New Zealand
Authors: Daniel Adam J. , Hicks Brendan J. , Ling Nicholas , David Bruno O.
Published: April 2009

Common carp (Cyprinus carpio) are notoriously difficult to monitor in water temperatures above 20°C using telemetry owing to transmitter expulsion. To reduce transmitter loss, radio transmitters were anchored to the pelvic girdle and a polymer coating was applied to acoustic transmitters to reduce tissue irritation in two tank trials. Ten dummy transmitters were surgically implanted in each of four groups of adult koi carp, a highly coloured strain of C. carpio. Water temperatures ranged between 7 and 24°C. After 365 days, the control and test groups of each trial had similar expulsion rates (P ≥ 0.30; two-tailed Fisher’s exact probability test). Expulsion rates for uncoated acoustic transmitters were 60% (n = 6), coated acoustic transmitters 50% (n = 5), unanchored radio transmitters 60% (n = 6) and anchored radio transmitters 90% (n = 9). Expulsions occurred 15–362 days after implantation as a result of ulcers at or near the surgical wound. Bacterial infection of the wound appears to be the primary mechanism for transmitter expulsion.
Radio-tagging flexible-bodied fish: temporary confinement enhances radio-tag retention
Authors: Broadhurst Ben T. , Ebner Brendan C. , Clear Rhian C.
Published: April 2009

Animals that occupy holes or squeeze into interstitial spaces often have particularly flexible bodies and can be difficult to tag effectively. The present study evaluated three methods for radio-tagging the cryptic, eel-like fish Gadopsis bispinosus, a species that inhabits interstitial spaces among cobbles and boulders in streams. The three methods were an externally attached radio-tag with a whip antenna, an internally implanted coil radio-tag (internal coil) and an internally implanted radio-tag with an externally exited whip antenna (internal–external). Successful radio-tagging was determined in aquaria trials based on a combination of four indicators: (1) survival; (2) retention of the radio-tag; (3) healing of the surgical incision; and (4) rapid resumption of feeding. Externally attached radio-tags were shed and proved to be unsuitable (100%). Three of nine individuals with internal–external tagging completed the study with regular feeding, healed incisions and retained radio-tags. Conversely, five of nine individuals with internal coils were successful. This included two of three individuals held in either a simple environment for 3 days or for the duration of the trial and one of three individuals held in a complex environment. Temporary confinement following implantation with coil radio-tags offers a viable means of radio-tagging G. bispinosus. Temporary confinement following radio-tagging may also be useful for reducing radio-tag rejection and mortality for other fish species with similar body morphs and habitat use (e.g. eel species and sculpin).
Polar forests on the edge of extinction: what does the fossil spore and pollen evidence from East Antarctica say?
Authors: Truswell E. M. , Macphail M. K.
Published: April 2009

Diverse pollen and spore assemblages, spanning the Late Eocene preglacial–glacial transition, have been recovered from Ocean Drilling Program cores from Prydz Bay, East Antarctica. These microfloras are mostly in situ and provide an unparalleled record of terrestrial plant communities growing in Antarctica during the earliest stages of ice-cap formation. The evidence provides a basis for assessing the phytogeographic relationships of the Antarctic floras with other high-latitude floras in the southern hemisphere, including possible migration routes for some taxa. Preliminary studies (Macphail and Truswell 2004a) suggested the Late Eocene vegetation at Prydz Bay was floristically impoverished rainforest scrub, similar to Nothofagus–gymnosperm communities found near the climatic treeline in Patagonia and Tasmania. Re-evaluation of the microfloras indicates the diversity of shrubs, especially Proteaceae, was underestimated and the Late Eocene vegetation was a mosaic of dwarfed (krumholtz) trees, scleromorphic shrubs and wetland herbs, analogous to the taiga found in the transition zone between the boreal conifer forest and tundra biomes across the Arctic Circle. Microfloras similar to although much less diverse than the Prydz Bay assemblages occur in coreholes from the Ross Sea region on the opposite side of Antarctica. Interpretation of the latter is complicated by reworking and low yields but the combined evidence points to the collapse of taller woody ecosystems during the Eocene–Oligocene transition and their replacement by tundra-like or fell-field vegetation during the Oligocene and Neogene. This temperature-forced regression seems to have been broadly synchronous across the continent. The high-palaeolatitude location (~70°S) means that the Prydz Bay flora was adapted to several months of winter darkness and short-summer growing seasons. The nearest living relatives of identifiable woody taxa suggest year-round high humidity, with an annual precipitation between ~1200 and 1500 mm. Palaeotemperatures are more difficult to quantify although the inferred humid microtherm climate is consistent with mean annual temperatures less than 12°C and freezing winters.
α
5
β
1
-Integrin controls ebolavirus entry by regulating endosomal cathepsins
Authors: Schornberg Kathryn L. , Shoemaker Charles J. , Dube Derek , Abshire Michelle Y. , Delos Sue E. , Bouton Amy H. , White Judith M.
Published: April 2009

Integrins are involved in the binding and internalization of both enveloped and nonenveloped viruses. By using 3 distinct cell systems—CHO cells lacking expression of α
5
β
1
-integrin, HeLa cells treated with siRNA to α
5
-integrin, and mouse β
1
-integrin knockout fibroblasts, we show that α
5
β
1
-integrin is required for efficient infection by pseudovirions bearing the ebolavirus glycoprotein (GP). These integrins are necessary for viral entry but not for binding or internalization. Given the need for endosomal cathepsins B and L (CatB and CatL) to prime GPs for fusion, we investigated the status of CatB and CatL in integrin-positive and integrin-negative cell lines. α
5
β
1
-Integrin-deficient cells lacked the double-chain (DC) forms of CatB and CatL, and this correlated with decreased CatL activity in integrin-negative CHO cells. These data indicate that α
5
β
1
-integrin-negative cells may be refractory to infection by GP pseudovirions because they lack the necessary priming machinery (the double-chain forms of CatB and CatL). In support of this model, we show that GP pseudovirions that have been preprimed in vitro to generate the 19-kDa form of GP overcome the requirement for α
5
β
1
-integrin for infection. These results provide further support for the requirement for endosomal cathepsins for ebolavirus infection, identify the DC forms of these cathepsins as previously unrecognized factors that contribute to cell tropism of this virus, and reveal a previously undescribed role for integrins during viral entry as regulators of endosomal cathepsins, which are required to prime the entry proteins of ebolavirus and other pathogenic viruses.
Detection of circular polarization in light scattered from photosynthetic microbes
Authors: Sparks William B. , Hough James , Germer Thomas A. , Chen Feng , DasSarma Shiladitya , DasSarma Priya , Robb Frank T. , Manset Nadine , Kolokolova Ludmilla , Reid Neill , Macchetto F. Duccio , Martin William
Published: April 2009

The identification of a universal biosignature that could be sensed remotely is critical to the prospects for success in the search for life elsewhere in the universe. A candidate universal biosignature is homochirality, which is likely to be a generic property of all biochemical life. Because of the optical activity of chiral molecules, it has been hypothesized that this unique characteristic may provide a suitable remote sensing probe using circular polarization spectroscopy. Here, we report the detection of circular polarization in light scattered by photosynthetic microbes. We show that the circular polarization appears to arise from circular dichroism of the strong electronic transitions of photosynthetic absorption bands. We conclude that circular polarization spectroscopy could provide a powerful remote sensing technique for generic life searches.
Steroids are required for epidermal cell fate establishment in
Arabidopsis
roots
Authors: Kuppusamy Kavitha T. , Chen Andrew Y. , Nemhauser Jennifer L.
Published: April 2009

The simple structure of
Arabidopsis
roots provides an excellent model system to study epidermal cell fate specification. Epidermal cells in contact with 2 underlying cortical cells differentiate into hair cells (H cells; trichoblasts), whereas cells that contact only a single cortical cell differentiate into mature hairless cells (N cells; atrichoblasts). This position-dependent patterning, in combination with the constrained orientation of cell divisions, results in hair and nonhair cell files running longitudinally along the root epidermis. Here, we present strong evidence that steroid hormones called brassinosteroids (BRs) are required to maintain position-dependent fate specification in roots. We show that BRs are required for normal expression levels and patterns of
WEREWOLF
(
WER
) and
GLABRA2
(
GL2
), master regulators of epidermal patterning. Loss of BR signaling results in loss of hair cells in H positions, likely as a consequence of reduced expression of
CAPRICE
(
CPC
), a direct downstream target of WER. Our observations demonstrate that in addition to their well-known role in cell expansion, BRs play an essential role in directing cell fate.
MicroRNAs are essential for development and function of inner ear hair cells in vertebrates
Authors: Friedman Lilach M. , Dror Amiel A. , Mor Eyal , Tenne Tamar , Toren Ginat , Satoh Takunori , Biesemeier Deborah J. , Shomron Noam , Fekete Donna M. , Hornstein Eran , Avraham Karen B.
Published: April 2009

MicroRNAs (miRNAs) inhibit the translation of target mRNAs and affect, directly or indirectly, the expression of a large portion of the protein-coding genes. This study focuses on miRNAs that are expressed in the mouse cochlea and vestibule, the 2 inner ear compartments. A conditional knock-out mouse for
Dicer1
demonstrated that miRNAs are crucial for postnatal survival of functional hair cells of the inner ear. We identified miRNAs that have a role in the vertebrate developing inner ear by combining miRNA transcriptome analysis, spatial and temporal expression patterns, and bioinformatics. Microarrays revealed similar miRNA profiles in newborn-mouse whole cochleae and vestibules, but different temporal and spatial expression patterns of six miRNAs (miR-15a, miR-18a, miR-30b, miR-99a, miR-182, and miR-199a) may reflect their roles. Two of these miRNAs, miR-15a-1 and miR-18a, were also shown to be crucial for zebrafish inner ear development and morphogenesis. To suggest putative target mRNAs whose translation may be inhibited by selected miRNAs, we combined bioinformatics-based predictions and mRNA expression data. Finally, we present indirect evidence that Slc12a2, Cldn12, and Bdnf mRNAs may be targets for miR-15a. Our data support the hypothesis that inner ear tissue differentiation and maintenance are regulated and controlled by conserved sets of cell-specific miRNAs in both mouse and zebrafish.
Synergy between pathogen release and resource availability in plant invasion
Authors: Blumenthal Dana , Mitchell Charles E. , Pyšek Petr , Jarošík Vojtěch
Published: April 2009

Why do some exotic plant species become invasive? Two common hypotheses, increased resource availability and enemy release, may more effectively explain invasion if they favor the same species, and therefore act in concert. This would be expected if plant species adapted to high levels of available resources in their native range are particularly susceptible to enemies, and therefore benefit most from a paucity of enemies in their new range. We tested this possibility by examining how resource adaptations influence pathogen richness and release among 243 European plant species naturalized in the United States. Plant species adapted to higher resource availability hosted more pathogen species in their native range. Plants from mesic environments hosted more fungi than plants from xeric environments, and plants from nitrogen-rich environments hosted more viruses than plants from nitrogen-poor environments. Furthermore, plants classified as competitors hosted more than 4 times as many fungi and viruses as did stress tolerators. Patterns of enemy release mirrored those of pathogen richness: competitors and species from mesic and nitrogen-rich environments were released from many pathogen species, while stress tolerators and species from xeric and nitrogen-poor environments were released from relatively few pathogen species. These results suggest that enemy release contributes most to invasion by fast-growing species adapted to resource-rich environments. Consequently, enemy release and increases in resource availability may act synergistically to favor exotic over native species.
Functional electric field changes in photoactivated proteins revealed by ultrafast Stark spectroscopy of the Trp residues
Authors: Léonard Jérémie , Portuondo-Campa Erwin , Cannizzo Andrea , Mourik Frank van , van der Zwan Gert , Tittor Jörg , Haacke Stefan , Chergui Majed
Published: April 2009

Ultrafast transient absorption spectroscopy of wild-type bacteriorhodopsin (WT bR) and 2 tryptophan mutants (W86F and W182F) is performed with visible light excitation (pump) and UV probe. The aim is to investigate the photoinduced change in the charge distribution with 50-fs time resolution by probing the effects on the tryptophan absorption bands. A systematic, quantitative comparison of the transient absorption of the 3 samples is carried out. The main result is the absence in the W86F mutant of a transient induced absorption band observed at ≈300–310 nm in WT bR and W182F. A simple model describing the dipolar interaction of the retinal moiety with the 2 tryptophan residues of interest allows us to reproduce the dominant features of the transient signals observed in the 3 samples at ultrashort pump-probe delays. In particular, we show that Trp
86
undergoes a significant Stark shift induced by the transient retinal dipole moment. The corresponding transient signal can be isolated by direct subtraction of experimental data obtained for WT bR and W86F. It shows an instantaneous rise, followed by a decay over ≈500 fs corresponding to the isomerization time. Interestingly, it does not decay back to zero, thus revealing a change in the local electrostatic environment that remains long after isomerization, in the K intermediate state of the protein cycle. The comparison of WT bR and W86F also leads to a revised interpretation of the overall transient UV absorption of bR.
Cyp26 enzymes function in endoderm to regulate pancreatic field size
Authors: Kinkel Mary D. , Sefton Elizabeth M. , Kikuchi Yutaka , Mizoguchi Takamasa , Ward Andrea B. , Prince Victoria E.
Published: April 2009

The control of organ size and position relies, at least in part, upon appropriate regulation of the signals that specify organ progenitor fields. Pancreatic cell fates are specified by retinoic acid (RA), and proper size and localization of the pancreatic field are dependent on tight control of RA signaling. Here we show that the RA-degrading Cyp26 enzymes play a critical role in defining the normal anterior limit of the pancreatic field. Disruption of Cyp26 function causes a dramatic expansion of pancreatic cell types toward the anterior of the embryo. The
cyp26a1
gene is expressed in the anterior trunk endoderm at developmental stages when RA is signaling to specify pancreas, and analysis of
cyp26a1/giraffe
(
gir
) mutant zebrafish embryos confirms that
cyp26a1
plays the primary role in setting the anterior limit of the pancreas. Analysis of the
gir
mutants further reveals that
cyp26b1
and
cyp26c1
function redundantly to partially compensate for loss of Cyp26a1 function. We used cell transplantation to determine that Cyp26a1 functions directly in endoderm to modulate RA signaling and limit the pancreatic field. Taken together with our finding that endodermal expression of
cyp26
genes is subject to positive regulation by RA, our data reveal a feedback loop within the endoderm. Such feedback can maintain consistent levels of RA signaling, despite environmental fluctuations in RA concentration, thus ensuring a consistent size and location of the pancreatic field.
Evidence for an ancient adaptive episode of convergent molecular evolution
Authors: Castoe Todd A. , de Koning A. P. Jason , Kim Hyun-Min , Gu Wanjun , Noonan Brice P. , Naylor Gavin , Jiang Zhi J. , Parkinson Christopher L. , Pollock David D.
Published: April 2009

Documented cases of convergent molecular evolution due to selection are fairly unusual, and examples to date have involved only a few amino acid positions. However, because convergence mimics shared ancestry and is not accommodated by current phylogenetic methods, it can strongly mislead phylogenetic inference when it does occur. Here, we present a case of extensive convergent molecular evolution between snake and agamid lizard mitochondrial genomes that overcomes an otherwise strong phylogenetic signal. Evidence from morphology, nuclear genes, and most sites in the mitochondrial genome support one phylogenetic tree, but a subset of mostly amino acid-altering substitutions (primarily at the first and second codon positions) across multiple mitochondrial genes strongly supports a radically different phylogeny. The relevant sites generally evolved slowly but converged between ancient lineages of snakes and agamids. We estimate that ≈44 of 113 predicted convergent changes distributed across all 13 mitochondrial protein-coding genes are expected to have arisen from nonneutral causes—a remarkably large number. Combined with strong previous evidence for adaptive evolution in snake mitochondrial proteins, it is likely that much of this convergent evolution was driven by adaptation. These results indicate that nonneutral convergent molecular evolution in mitochondria can occur at a scale and intensity far beyond what has been documented previously, and they highlight the vulnerability of standard phylogenetic methods to the presence of nonneutral convergent sequence evolution.
A chemical screen for biological small molecule–RNA conjugates reveals CoA-linked RNA
Authors: Kowtoniuk Walter E. , Shen Yinghua , Heemstra Jennifer M. , Agarwal Isha , Liu David R.
Published: April 2009

Compared with the rapidly expanding set of known biological roles for RNA, the known chemical diversity of cellular RNA has remained limited primarily to canonical RNA, 3′-aminoacylated tRNAs, nucleobase-modified RNAs, and 5′-capped mRNAs in eukaryotes. We developed two methods to detect in a broad manner chemically labile cellular small molecule–RNA conjugates. The methods were validated by the detection of known tRNA and rRNA modifications. The first method analyzes small molecules cleaved from RNA by base or nucleophile treatment. Application to
Escherichia coli
and
Streptomyces venezuelae
RNA revealed an RNA-linked hydroxyfuranone or succinyl ester group, in addition to a number of other putative small molecule–RNA conjugates not previously reported. The second method analyzes nuclease-generated mononucleotides before and after treatment with base or nucleophile and also revealed a number of new putative small molecule–RNA conjugates, including 3′-dephospho-CoA and its succinyl-, acetyl-, and methylmalonyl-thioester derivatives. Subsequent experiments established that these CoA species are attached to
E. coli
and
S. venezuelae
RNA at the 5′ terminus. CoA-linked RNA cannot be generated through aberrant transcriptional initiation by
E. coli
RNA polymerase in vitro, and CoA-linked RNA in
E. coli
is only found among smaller (≲200 nucleotide) RNAs that have yet to be identified. These results provide examples of small molecule-RNA conjugates and suggest that the chemical diversity of cellular RNA may be greater than previously understood.
mTOR supports long-term self-renewal and suppresses mesoderm and endoderm activities of human embryonic stem cells
Authors: Zhou Jiaxi , Su Pei , Wang Lu , Chen Joanna , Zimmermann Maike , Genbacev Olga , Afonja Olubunmi , Horne Mary C. , Tanaka Tetsuya , Duan Enkui , Fisher Susan J. , Liao Jiayu , Chen Jie , Wang Fei
Published: April 2009

Despite the recent identification of the transcriptional regulatory circuitry involving SOX2, NANOG, and OCT-4, the intracellular signaling networks that control pluripotency of human embryonic stem cells (hESCs) remain largely undefined. Here, we demonstrate an essential role for the serine/threonine protein kinase mammalian target of rapamycin (mTOR) in regulating hESC long-term undifferentiated growth. Inhibition of mTOR impairs pluripotency, prevents cell proliferation, and enhances mesoderm and endoderm activities in hESCs. At the molecular level, mTOR integrates signals from extrinsic pluripotency-supporting factors and represses the transcriptional activities of a subset of developmental and growth-inhibitory genes, as revealed by genome-wide microarray analyses. Repression of the developmental genes by mTOR is necessary for the maintenance of hESC pluripotency. These results uncover a novel signaling mechanism by which mTOR controls fate decisions in hESCs. Our findings may contribute to effective strategies for tissue repair and regeneration.
An age-related homeostasis mechanism is essential for spontaneous amelioration of hemophilia B Leyden
Authors: Kurachi Sumiko , Huo Jeffrey S. , Ameri Afshin , Zhang Kezhong , Yoshizawa Akiyasu C. , Kurachi Kotoku
Published: April 2009

Regulation of age-related changes in gene expression underlies many diseases. We previously discovered the first puberty-onset gene switch, the age-related stability element (ASE)/age-related increase element (AIE)-mediated genetic mechanism for age-related gene regulation. Here, we report that this mechanism underlies the mysterious puberty-onset amelioration of abnormal bleeding seen in hemophilia B Leyden. Transgenic mice robustly mimicking the Leyden phenotype were constructed. Analysis of these animals indicated that ASE plays a central role in the puberty-onset amelioration of the disease. Human factor IX expression in these animals was reproducibly nullified by hypophysectomy, but nearly fully restored by administration of growth hormone, being consistent with the observed sex-independent recovery of factor IX expression. Ets1 was identified as the specific liver nuclear protein binding only to the functional ASE, G/CAGGAAG, and not to other Ets consensus elements. This study demonstrates the clinical relevance of the first discovered puberty-onset gene switch, the ASE/AIE-mediated regulatory mechanism.
Folding energy landscape of cytochrome
cb
562
Authors: Kimura Tetsunari , Lee Jennifer C. , Gray Harry B. , Winkler Jay R.
Published: April 2009

Cytochrome
cb
562
is a variant of an
Escherichia coli
four-helix bundle
b
-type heme protein in which the porphyrin prosthetic group is covalently ligated to the polypeptide near the terminus of helix 4. Studies from other laboratories have shown that the apoprotein folds rapidly without the formation of intermediates, whereas the holoprotein loses heme before native structure can be attained. Time-resolved fluorescence energy transfer (TRFET) measurements of cytochrome
cb
562
refolding triggered using an ultrafast continuous-flow mixer (150 μs dead time) reveal that heme attachment to the polypeptide does not interfere with rapid formation of the native structure. Analyses of the TRFET data produce distributions of Trp-59–heme distances in the protein before, during, and after refolding. Characterization of the moments and time evolution of these distributions provides compelling evidence for a refolding mechanism that does not involve significant populations of intermediates. These observations suggest that the cytochrome
b
562
folding energy landscape is minimally frustrated and able to tolerate the introduction of substantial perturbations (i.e., the heme prosthetic group) without the formation of deep misfolded traps.
Design of anti- and pro-aggregation variants to assess the effects of methionine oxidation in human prion protein
Authors: Wolschner Christina , Giese Armin , Kretzschmar Hans A. , Huber Robert , Moroder Luis , Budisa Nediljko
Published: April 2009

Prion disease is characterized by the α→β structural conversion of the cellular prion protein (PrP
C
) into the misfolded and aggregated “scrapie” (PrP
Sc
) isoform. It has been speculated that methionine (Met) oxidation in PrP
C
may have a special role in this process, but has not been detailed and assigned individually to the 9 Met residues of full-length, recombinant human PrP
C
[rhPrP
C
(23-231)]. To better understand this oxidative event in PrP aggregation, the extent of periodate-induced Met oxidation was monitored by electrospray ionization-MS and correlated with aggregation propensity. Also, the Met residues were replaced with isosteric and chemically stable, nonoxidizable analogs, i.e., with the more hydrophobic norleucine (Nle) and the highly hydrophilic methoxinine (Mox). The Nle-rhPrP
C
variant is an α-helix rich protein (like Met-rhPrP
C
) resistant to oxidation that lacks the in vitro aggregation properties of the parent protein. Conversely, the Mox-rhPrP
C
variant is a β-sheet rich protein that features strong proaggregation behavior. In contrast to the parent Met-rhPrP
C
, the Nle/Mox-containing variants are not sensitive to periodate-induced in vitro aggregation. The experimental results fully support a direct correlation of the α→β secondary structure conversion in rhPrP
C
with the conformational preferences of Met/Nle/Mox residues. Accordingly, sporadic prion and other neurodegenerative diseases, as well as various aging processes, might also be caused by oxidative stress leading to Met oxidation.
Thermal transport due to turbulence including magnetic fluctuation in externally heated plasma
Authors: Ishizawa A. , Nakajima N.
Published: April 2009

A new three-dimensional numerical simulation of turbulent transport phenomena in an open system controlled by an external heat source and a sink is proposed by virtue of self-consistent calculation of the multi-scale interactions. External heating is applied to an equilibrium including micro-turbulence, and thermal transport due to the turbulence is investigated for a case including small-scale magnetic fluctuation and for a case including not only small-scale but also large-scale magnetic fluctuation by numerically solving a reduced set of two-fluid equations. In the first case turbulent transport controlled by external heating is calculated and profile stiffness in electromagnetic turbulence is examined. In the second case a change in turbulent transport in the presence of a tearing mode, which is large-scale magnetic fluctuation, is examined. In this case multi-scale interactions between micro-turbulence and the tearing mode play the key role in thermal transport. When the tearing mode appears in a quasi-equilibrium including micro-turbulence and zonal flow, the energy spectrum of micro-turbulence is changed so that the energy of the dominant toroidal mode representing micro-turbulence is reduced and the energy of the small toroidal mode increases. At the same time the gradient of ion temperature is reduced and the heat flux increases around the magnetic islands due to the tearing mode.