bluuebunny/crossref_metadata_2025 huggingface dataset:
Low-order tensor approximations for electronic wave functions: Hartree–Fock method with guaranteed precision
Authors: Bischoff Florian A. , Valeev Edward F.
Published: March 2011

Here we report a formulation of the Hartree–Fock method in an adaptive multiresolution basis set of spectral element type. A key feature of our approach is the use of low-order tensor approximations for operators and wave functions to reduce the steep rise of storage and computational costs with the number of degrees of freedom that plague finite element computations. As a proof of principle we implemented Hartree–Fock method without explicit storage of the full-dimensional wave function and with guaranteed precision (microhartree precision for up to 14 electron systems is demonstrated). Even for the one-electron method the use of low-order tensor approximation reduces storage relative to the full representation, albeit with modest increase in cost. Preliminary tests for explicitly-correlated two-electron (six-dimensional) wave function suggest a factor of 50 savings in storage. At least correlated two-electron methods should be feasible with our approach on modern workstations with guaranteed precision.
Overlapping fragments method for electronic structure calculation of large systems
Authors: Vukmirović Nenad , Wang Lin-Wang
Published: March 2011

We present a method for the calculation of the electronic structure of systems that contain tens of thousands of atoms. The method is based on the division of the system into mutually overlapping fragments and the representation of the single-particle Hamiltonian in the basis of eigenstates of these fragments. In practice, for the range of the system size that we studied (up to tens of thousands of atoms), the dominant part of the calculation scales linearly with the size of the system when all the states within a fixed energy interval are required. The method is highly suitable for making good use of parallel computing architectures. We illustrate the method by applying it to diagonalize the single-particle Hamiltonian obtained using the density functional theory based charge patching method in the case of amorphous alkane and polythiophene polymers.
Tuning the hydrophobicity of mica surfaces by hyperthermal Ar ion irradiation
Authors: Keller Adrian , Fritzsche Monika , Ogaki Ryosuke , Bald Ilko , Facsko Stefan , Dong Mingdong , Kingshott Peter , Besenbacher Flemming
Published: March 2011

The hydrophobicity of surfaces has a strong influence on their interactions with biomolecules such as proteins. Therefore, for in vitro studies of bio-surface interactions model surfaces with tailored hydrophobicity are of utmost importance. Here, we present a method for tuning the hydrophobicity of atomically flat mica surfaces by hyperthermal Ar ion irradiation. Due to the sub-100 eV energies, only negligible roughening of the surface is observed at low ion fluences and also the chemical composition of the mica crystal remains almost undisturbed. However, the ion irradiation induces the preferential removal of the outermost layer of K+ ions from the surface, leading to the exposure of the underlying aluminosilicate sheets which feature a large number of centers for C adsorption. The irradiated surface thus exhibits an enhanced chemical reactivity toward hydrocarbons, resulting in the adsorption of a thin hydrocarbon film from the environment. Aging these surfaces under ambient conditions leads to a continuous increase of their contact angle until a fully hydrophobic surface with a contact angle >80° is obtained after a period of about 3 months. This method thus enables the fabrication of ultrasmooth biological model surfaces with precisely tailored hydrophobicity.
Nonequilibrium heat flows through a nanorod sliding across a surface
Authors: Popov Alexander V. , Viehman Douglas C. , Hernandez Rigoberto
Published: March 2011

The temperature-ramped irreversible Langevin equation [A. V. Popov and R. Hernandez, J. Chem. Phys. 134, 244506 (2007)] has been seen to describe the nonequilibrium atomic oscillations of a nanorod dragged across a surface. The nanorod and surface consist of hydroxylated α-Al2O3 layers as was studied earlier by Hase and co-workers [J. Chem. Phys. 122, 094713 (2005)]. The present approach corresponds to the reduced Frenkel–Kontorova–Tomlinson model in which only one element of the vibrational chain representing a surface layer is considered explicitly. The key new concept centers on a separation of the environment into two effective reduced-dimensional baths: an equilibrium bath arising from the thermostated vibrations of the crystal lattice and a nonequilibrium bath arising from driven oscillations at the contact between the nanorod and the surface. The temperature of the latter is defined by the mean energy of a representative atomic oscillator for a given layer. The temporal temperature fluctuations and the dependence of the static part of the temperature on the sliding velocity are close to those found in the MD simulations of Hase and co-workers.
Molecule–substrate interaction channels of metal-phthalocyanines on graphene on Ni(111) surface
Authors: Dou Weidong , Huang Shuping , Zhang R. Q. , Lee C. S.
Published: March 2011

Molecule–substrate interaction channels of metal-phthalocyanines (MPcs, including NiPc, CuPc, ZnPc, FePc, and CoPc) on graphene on Ni(111) were investigated by employing high-resolution electron energy loss spectroscopy (HREELS). Except the expected IR-active modes, some Raman-active modes were also observed in all of MPcs, which are considered in this study. From the origination of the Raman-active features, it was deduced that MPcs are coupled with the substrate mainly through their central metal atom. The Raman-active modes appear as symmetric peaks in the HREELS in the case of MPcs with Ni, Cu, and Zn, whereas they are asymmetric and appear as a Fano line shape in the case of MPcs with Fe and Co. This spectroscopic difference indicates that the molecule–substrate coupling is completely different in the two cases mentioned above. The molecule–substrate interaction strength is considerably weak and comparable with the π−π interaction between molecules in the case of MPcs with Ni, Cu, and Zn, whereas it is much stronger in the case of MPcs with Fe and Co. From the HREELS observations, it can be suggested that the whole molecule can be effectively decoupled from the underneath Ni(111) by inserting a single layer of graphene between them in the case of MPcs with Ni, Cu, and Zn, whereas only benzene rings can be completely decoupled in the case of MPcs with Fe and Co.
Theory and simulation on the kinetics of protein–ligand binding coupled to conformational change
Authors: Cai Lu , Zhou Huan-Xiang
Published: March 2011

Conformational change during protein–ligand binding may significantly affect both the binding mechanism and the rate constant. Most earlier theories and simulations treated conformational change as stochastic gating with transition rates between reactive and nonreactive conformations uncoupled to ligand binding. Recently, we introduced a dual-transition-rates model in which the transition rates between reactive and nonreactive conformations depend on the protein–ligand distance [H.-X. Zhou, Biophys. J. 98, L15 (2010)]. Analytical results of that model showed that the apparent binding mechanism switches from conformational selection to induced fit, when the rates of conformational transitions increase from being much slower than the diffusional approach of the protein–ligand pair to being much faster. The conformational-selection limit (kCS) and the induced-fit limit (kIF) provide lower and upper bounds, respectively, for the binding rate constant. Here we introduce a general model in which the energy surface of the protein in conformational space is coupled to ligand binding, and present a method for calculating the binding rate constant from Brownian dynamics simulations. Analytical and simulation results show that, for an energy surface that switches from favoring the nonreactive conformation while the ligand is away to favoring the reactive conformation while the ligand is near, kCS and kIF become close and, thus, provide tight bounds to the binding rate constant. This finding has significant mechanistic implications and presents routes for obtaining good estimates of the rate constant at low cost.
Correlation of photoconductivity response of amorphous In–Ga–Zn–O films with transistor performance using microwave photoconductivity decay method
Authors: Yasuno Satoshi , Kugimiya Toshihiro , Morita Shinya , Miki Aya , Ojima Futoshi , Sumie Shingo
Published: March 2011

The film quality of amorphous In–Ga–Zn–O (a-IGZO), an amorphous oxide semiconductor (AOS), was studied by the microwave photoconductivity decay (μ-PCD) method. Also, μ-PCD mappings over a 6 in. wafer were undertaken. It was found that the peak signal of the decay curve had a strong correlation with the a-IGZO transistor performance and hence the film quality. The film annealed under a wet condition showed the highest mobility and had the highest peak signal. The μ-PCD method was found to be a very useful tool to evaluate the film quality and predict the performance of AOS transistors fabricated under different process conditions.
Influence of GaAs surface structure on tunneling anisotropic magnetoresistance and magnetocrystalline anisotropy in epitaxial Co50Fe50/n-GaAs junctions
Authors: Uemura Tetsuya , Harada Masanobu , Akiho Takafumi , Matsuda Ken-ichi , Yamamoto Masafumi
Published: March 2011

An epitaxial Co50Fe50 layer was grown on As-terminated or Ga-terminated GaAs, and the influence of the termination species on both uniaxial-type tunneling anisotropic magnetoresistance (TAMR) characteristics and magnetocrystalline anisotropy was investigated. The magnetocrystalline anisotropy induced in the Co50Fe50 thin film was strongly dependent on the termination species of the GaAs surface, while the TAMR characteristics were almost unchanged. These experimental findings suggest that the TAMR effect is due to the anisotropy of electronic structure rather than the structural anisotropy.
Reduced Joule heating in nanowires
Authors: Léonard François
Published: March 2011

The temperature distribution in nanowires due to Joule heating is studied analytically using a continuum model and a Green’s function approach. We show that the temperatures reached in nanowires can be much lower than that predicted by bulk models of Joule heating, due to heat loss at the nanowire surface that is important at nanoscopic dimensions, even when the thermal conductivity of the environment is relatively low. In addition, we find that the maximum temperature in the nanowire scales weakly with length, in contrast to the bulk system. A simple criterion is presented to assess the importance of these effects. The results have implications for the experimental measurements of nanowire thermal properties, for thermoelectric applications, and for controlling thermal effects in nanowire electronic devices.
Energy channeling due to energetic-ion-driven instabilities in tokamak
Authors: Kuley Animesh , Liu C. S. , Tripathi V. K.
Published: March 2011

A kinetic formalism has been developed to study the emission of the destabilized ion Bernstein wave by the energetic α particles in the core region of the tokamak, with very peaked radial distribution. The destabilized waves are driven in the central region of the tokamak but are damped by the electrons in the outer due to the energy channeling.
Influence of electric field on persistent photoconductivity in unintentionally doped n-type GaN
Authors: Hou Qifeng , Wang Xiaoliang , Xiao Hongling , Wang Cuimei , Yang Cuibai , Yin Haibo , Deng Qingwen , Li Jinmin , Wang Zhanguo , Hou Xun
Published: March 2011

The influence of electric field on persistent photoconductivity in unintentionally doped n-GaN is investigated. It was found that under higher electric field the build-up course was slowed down while the decay course was accelerated. After a higher-voltage pulse, it was observed that the current dropped to a value lower than the dark current, and a current increase that lasted for thousands of seconds was observed. It is suggested that the above phenomena should be caused by the increase in capture rate of electron traps with electric field and are related to the Coulomb-repulsive characteristic of defects related to persistent photoconductivity.
C-doped ZnO nanowires: Electronic structures, magnetic properties, and a possible spintronic device
Authors: Dai Zhenxiang , Nurbawono Argo , Zhang Aihua , Zhou Miao , Feng Yuan Ping , Ho Ghim Wei , Zhang Chun
Published: March 2011

Electronic structures, magnetic properties, and spin-dependent electron transport characteristics of C-doped ZnO nanowires have been investigated via first-principles method based on density functional theory and nonequilibrium techniques of Green's functions. Our calculations show that the doping of carbon atoms in a ZnO nanowire could induce strong magnetic moments in the wire, and the electronic structures as well as the magnetic properties of the system sensitively depend on partial hydrogenation. Based on these findings, we proposed a quasi-1d tunneling magnetic junction made of a partially hydrogenated C-doped ZnO nanowire, which shows a high tunneling magnetoresistance ratio, and could be the building block of a new class of spintronic devices.
Thermal conductivity of chalcogenide material with superlatticelike structure
Authors: Tong H. , Miao X. S. , Cheng X. M. , Wang H. , Zhang L. , Sun J. J. , Tong F. , Wang J. H.
Published: March 2011

Thermal conductivity of chalcogenide material with superlatticelike (SLL) structure is investigated using the 3ω method and the molecular dynamics method. Both the measured and calculated results show that the thermal conductivity of SLL is lower than those of conventional chalcogenide materials and will decrease to a minimum as the number of interfaces increases. The Raman spectrum is introduced to study the phonon behavior of SLL and the “phonon mode vanishing” is proposed to explain its lower thermal conductivity. Finite-element analysis and phase change memory cell testing confirm the enhancement of cell performance for SLL with minimum thermal conductivity.
Design of a hybrid battery charger system fed by a wind-turbine and photovoltaic power generators
Authors: Chang Chien Jia-Ren , Tseng Kuo-Ching , Yan Bo-Yi
Published: March 2011

This paper is aimed to develop a digital signal processor (DSP) for controlling a solar cell and wind-turbine hybrid charging system. The DSP consists of solar cells, a wind turbine, a lead acid battery, and a buck–boost converter. The solar cells and wind turbine serve as the system's main power sources and the battery as an energy storage element. The output powers of solar cells and wind turbine have large fluctuations with the weather and climate conditions. These unstable powers can be adjusted by a buck–boost converter and thus the most suitable output powers can be obtained. This study designs a booster by using a dsPIC30F4011 digital signal controller as a core processor. The DSP is controlled by the perturbation and observation methods to obtain an effective energy circuit with a full 100 W charging system. Also, this DSP can, day and night, be easily controlled and charged by a simple program, which can change the state of the system to reach a flexible application based on the reading weather conditions.
Laser ablation with resonance-enhanced multiphoton ionization time-of-flight mass spectrometry for determining aromatic lignin volatilization products from biomass
Authors: Mukarakate Calvin , Scheer Adam M. , Robichaud David J. , Jarvis Mark W. , David Donald E. , Ellison G. Barney , Nimlos Mark R. , Davis Mark F.
Published: March 2011

We have designed and developed a laser ablation/pulsed sample introduction/mass spectrometry platform that integrates pyrolysis (py) and/or laser ablation (LA) with resonance-enhanced multiphoton ionization (REMPI) reflectron time-of-flight mass spectrometry (TOFMS). Using this apparatus, we measured lignin volatilization products of untreated biomass materials. Biomass vapors are produced by either a custom-built hot stage pyrolysis reactor or laser ablation using the third harmonic of an Nd:YAG laser (355 nm). The resulting vapors are entrained in a free jet expansion of He, then skimmed and introduced into an ionization region. One color resonance-enhanced multiphoton ionization (1+1 REMPI) is used, resulting in highly selective detection of lignin subunits from complex vapors of biomass materials. The spectra obtained by py-REMPI-TOFMS and LA-REMPI-TOFMS display high selectivity and decreased fragmentation compared to spectra recorded by an electron impact ionization molecular beam mass spectrometer (EI-MBMS). The laser ablation method demonstrates the ability to selectively isolate and volatilize specific tissues within the same plant material and then detect lignin-based products from the vapors with enhanced sensitivity. The identification of select products observed in the LA-REMPI-TOFMS experiment is confirmed by comparing their REMPI wavelength scans with that of known standards.
Note: On the universality of proximal radial distribution functions of proteins
Authors: Lin Bin , Pettitt B. Montgomery
Published: March 2011

Protein hydration is important to protein structure and function. Molecular distribution functions have been an invaluable tool to study protein hydration. Proximal radial distribution functions (pRDFs) have been postulated as being transferable across proteins based on evidence collected from two proteins [V. A. Makarov, B. K. Andrews, and B. M. Pettitt, Biopolymers 45(7), 469 (1998)]. Here we selected nine proteins with different sizes as well as different secondary topologies. We show that pRDFs are universal for proteins with compact structures. We further compare these pRDFs with those calculated from polyglycines that have no defined structures to consider the extent of the validity of this approach.
Performance of Coopworth ewe lambs exposed to low levels of ryegrass endophyte (Neotyphodium lolii) alkaloids and allowed access to a mycotoxin deactivator
Authors: Reed K. F. M. , Cummins L. J. , Moore D. D. , Clark A. J.
Published: March 2011

During February–April, Coopworth ewe lambs grazing a pasture dominated by naturalised perennial ryegrass (PRG) exhibited slight signs of ill-thrift and heat stress. PRG represented 85% of the herbage; 90% of the PRG population was infected with Neotyphodium endophyte. Concentrations of ergovaline and lolitrem B in perennial ryegrass were each within the range 0.5–1.0 mg/kg DM during this period. Two groups of 30 lambs rotated weekly between two paddocks that offered 6 t DM/ha of mature, low-quality pasture. They received an allowance of crushed barley and peas (80 : 20) at 100 g/head per day. One group was treated with a mycotoxin deactivator, Mycofix® Plus, mixed into their mash during processing (5 g/100 g). No sign of ‘staggers’ was observed in the lambs at any time. Lambs with access to Mycofix Plus made great use of shade; their occupancy of shade increased steeply with ambient temperature over the range 18−38°C (P < 0.001). For the control group, occupancy of shade was low (P < 0.001) and independent of temperature (P < 0.001). Instead of using shade on hot days, the control lambs whose respiration rate was higher than treated ewes (P < 0.001) commonly stood by the wire fence, huddled in the open. Over the first 56 days of treatment, while pasture remained dry, weight change in control and treated lambs was –13 and +16 g/day, respectively (P < 0.010). The need for greater investigation of the effects of endophyte alkaloids on livestock is discussed.
Tracking livestock using global positioning systems - are we still lost?
Authors: Swain D. L. , Friend M. A. , Bishop-Hurley G. J. , Handcock R. N. , Wark T.
Published: March 2011

Since the late 1980s, satellite-based global positioning systems (GPS) have provided unique and novel data that have been used to track animal movement. Tracking animals with GPS can provide useful information, but the cost of the technology often limits experimental replication. Limitations on the number of devices available to monitor the behaviour of animals, in combination with technical constraints, can weaken the statistical power of experiments and create significant experimental design challenges. The present paper provides a review and synthesis of using GPS for livestock-based studies and suggests some future research directions. Wildlife ecologists working in extensive landscapes have pioneered the use of GPS-based devices for tracking animals. Wildlife researchers have focussed efforts on quantifying and addressing issues associated with technology limitations, including spatial accuracy, rate of data collection, battery life and environmental factors causing loss of data. It is therefore not surprising that there has been a significant number of methodological papers published in the literature that have considered technical developments of GPS-based animal tracking. Livestock scientists have used GPS data to inform them about behavioural differences in free-grazing experiments. With a shift in focus from the environment to the animal comes the challenge of ensuring independence of the experimental unit. Social facilitation challenges independence of the individual in a group. The use of spatial modelling methods to process GPS data provides an opportunity to determine the degree of independence of data collected from an individual animal within behavioural-based studies. By using location and movement information derived from GPS data, researchers have been able to determine the environmental impact of grazing animals as well as assessing animal responses to management activities or environmental perturbations. Combining satellite-derived remote-sensing data with GPS-derived landscape preference indices provides a further opportunity to identify landscape avoidance and selection behaviours. As spatial livestock monitoring tools become more widely used, there will be a greater need to ensure the data and associated processing methods are able to answer a broader range of questions. Experimental design and analytical techniques need to be given more attention if GPS technology is to provide answers to questions associated with free-grazing animals.
Why Do Some Alkoxybromothiophenes Spontaneously Polymerize?
Authors: Wagner Pawel , Jolley Kenneth W. , Officer David L.
Published: March 2011

Neat liquid 3-alkoxy-2-bromothiophenes such as 2-bromo-EDOT have been shown to autopolymerize at room temperature and above, depending on their proton acidity and the nature and arrangement of substituents.
Effect of combined soil water and external load on soil compaction
Authors: Hamza M. A. , Al-Adawi S. S. , Al-Hinai K. A.
Published: March 2011

Reducing soil compaction is now an important issue in agriculture due to intensive use of farm machinery in different farm operations. This experiment was designed to study the influence of combinations of external load and soil water on soil compaction. Four soil water levels were combined with four external loads as follows: soil water—air-dry, 50% of field capacity, field capacity, and saturation; external load using different-sized tractors—no load (0 kg), small tractor (2638 kg), medium tractor (3912 kg), and large tractor (6964 kg). Soil bulk density, soil strength, and soil water infiltration rate were measured at 0–100, 100–200, and 200–300 mm soil depths. The 16 treatments were set up in a randomised block design with three replications.
Combined increases in soil water and external load increased soil compaction, as indicated by increasing soil bulk density and soil strength and decreasing soil water infiltration rate. There was no significant interaction between soil water and external load for bulk density at all soil depths, but the interaction was significant for soil strength and infiltration rates at all soil depths. The ratio between the weight of the external load and the surface area of contact between the external load and the ground was important in determining the degree of surface soil compaction. Least compaction was produced by the medium tractor because it had the highest tyre/ground surface area contact. In general, the effects of soil water and external load on increasing soil bulk density and soil strength were greater in the topsoil than the subsoil.
Cell-ECM traction force modulates endogenous tension at cell–cell contacts
Authors: Maruthamuthu Venkat , Sabass Benedikt , Schwarz Ulrich S. , Gardel Margaret L.
Published: March 2011

Cells in tissues are mechanically coupled both to the ECM and neighboring cells, but the coordination and interdependency of forces sustained at cell-ECM and cell–cell adhesions are unknown. In this paper, we demonstrate that the endogenous force sustained at the cell–cell contact between a pair of epithelial cells is approximately 100 nN, directed perpendicular to the cell–cell interface and concentrated at the contact edges. This force is stably maintained over time despite significant fluctuations in cell–cell contact length and cell morphology. A direct relationship between the total cellular traction force on the ECM and the endogenous cell–cell force exists, indicating that the cell–cell tension is a constant fraction of the cell-ECM traction. Thus, modulation of ECM properties that impact cell-ECM traction alters cell–cell tension. Finally, we show in a minimal model of a tissue that all cells experience similar forces from the surrounding microenvironment, despite differences in the extent of cell-ECM and cell–cell adhesion. This interdependence of cell–cell and cell-ECM forces has significant implications for the maintenance of the mechanical integrity of tissues, mechanotransduction, and tumor mechanobiology.
Universal rule for the symmetric division of plant cells
Authors: Besson Sébastien , Dumais Jacques
Published: March 2011

The division of eukaryotic cells involves the assembly of complex cytoskeletal structures to exert the forces required for chromosome segregation and cytokinesis. In plants, empirical evidence suggests that tensional forces within the cytoskeleton cause cells to divide along the plane that minimizes the surface area of the cell plate (Errera’s rule) while creating daughter cells of equal size. However, exceptions to Errera’s rule cast doubt on whether a broadly applicable rule can be formulated for plant cell division. Here, we show that the selection of the plane of division involves a competition between alternative configurations whose geometries represent local area minima. We find that the probability of observing a particular division configuration increases inversely with its relative area according to an exponential probability distribution known as the Gibbs measure. Moreover, a comparison across land plants and their most recent algal ancestors confirms that the probability distribution is widely conserved and independent of cell shape and size. Using a maximum entropy formulation, we show that this empirical division rule is predicted by the dynamics of the tense cytoskeletal elements that lead to the positioning of the preprophase band. Based on the fact that the division plane is selected from the sole interaction of the cytoskeleton with cell shape, we posit that the new rule represents the default mechanism for plant cell division when internal or external cues are absent.
Understanding vision in wholly empirical terms
Authors: Purves Dale , Wojtach William T. , Lotto R. Beau
Published: March 2011

This article considers visual perception, the nature of the information on which perceptions seem to be based, and the implications of a wholly empirical concept of perception and sensory processing for vision science. Evidence from studies of lightness, brightness, color, form, and motion all indicate that, because the visual system cannot access the physical world by means of retinal light patterns as such, what we see cannot and does not represent the actual properties of objects or images. The phenomenology of visual perceptions can be explained, however, in terms of empirical associations that link images whose meanings are inherently undetermined to their behavioral significance. Vision in these terms requires fundamentally different concepts of what we see, why, and how the visual system operates.
Stepwise assembly of the
Nova
-regulated alternative splicing network in the vertebrate brain
Authors: Irimia Manuel , Denuc Amanda , Burguera Demián , Somorjai Ildiko , Martín-Durán Jose M. , Genikhovich Grigory , Jimenez-Delgado Senda , Technau Ulrich , Roy Scott W. , Marfany Gemma , Garcia-Fernàndez Jordi
Published: March 2011

Novel organismal structures in metazoans are often undergirded by complex gene regulatory networks; as such, understanding the emergence of new structures through evolution requires reconstructing the series of evolutionary steps leading to these underlying networks. Here, we reconstruct the step-by-step assembly of the vertebrate splicing network regulated by
Nova
, a splicing factor that modulates alternative splicing in the vertebrate central nervous system by binding to clusters of YCAY motifs on pre-RNA transcripts. Transfection of human HEK293T cells with
Nova
orthologs indicated vertebrate-like splicing regulatory activity in bilaterian invertebrates, thus
Nova
acquired the ability to bind YCAY clusters and perform vertebrate-like splicing modulation at least before the last common ancestor of bilaterians. In situ hybridization studies in several species showed that
Nova
expression became restricted to CNS later on, during chordate evolution. Finally, comparative genomics studies revealed a diverse history for
Nova
-regulated exons, with target exons arising through both de novo exon creation and acquisition of YCAY motifs by preexisting exons throughout chordate and vertebrate history. In addition, we find that tissue-specific
Nova
expression patterns emerged independently in other lineages, suggesting independent assembly of tissue-specific regulatory networks.
Holliday junction-containing DNA structures persist in cells lacking Sgs1 or Top3 following exposure to DNA damage
Authors: Mankouri Hocine W. , Ashton Thomas M. , Hickson Ian D.
Published: March 2011

The Sgs1–Rmi1–Top3 “dissolvasome” is required for the maintenance of genome stability and has been implicated in the processing of various types of DNA structures arising during DNA replication. Previous investigations have revealed that unprocessed (X-shaped) homologous recombination repair (HRR) intermediates persist when S-phase is perturbed by using methyl methanesulfonate (MMS) in
Saccharomyces cerevisiae
cells with impaired Sgs1 or Top3. However, the precise nature of these persistent DNA structures remains poorly characterized. Here, we report that ectopic expression of either of two heterologous and structurally unrelated Holliday junction (HJ) resolvases,
Escherichia coli
RusA or human GEN1
1-527
, promotes the removal of these X-structures in vivo. Moreover, other types of DNA replication intermediates, including stalled replication forks and non-HRR-dependent X-structures, are refractory to RusA or GEN1
1-527
, demonstrating specificity of these HJ resolvases for MMS-induced X-structures in vivo. These data suggest that the X-structures persisting in cells with impaired Sgs1 or Top3 contain HJs. Furthermore, we demonstrate that Sgs1 directly promotes X-structure removal, because the persistent structures arising in Sgs1-deficient strains are eliminated when Sgs1 is reactivated in vivo. We propose that HJ resolvases and Sgs1–Top3–Rmi1 comprise two independent processes to deal with HJ-containing DNA intermediates arising during HRR in S-phase.
Tradeoffs associated with constitutive and induced plant resistance against herbivory
Authors: Kempel Anne , Schädler Martin , Chrobock Thomas , Fischer Markus , van Kleunen Mark
Published: March 2011

Several prominent hypotheses have been posed to explain the immense variability among plant species in defense against herbivores. A major concept in the evolutionary ecology of plant defenses is that tradeoffs of defense strategies are likely to generate and maintain species diversity. In particular, tradeoffs between constitutive and induced resistance and tradeoffs relating these strategies to growth and competitive ability have been predicted. We performed three independent experiments on 58 plant species from 15 different plant families to address these hypotheses in a phylogenetic framework. Because evolutionary tradeoffs may be altered by human-imposed artificial selection, we used 18 wild plant species and 40 cultivated garden-plant species. Across all 58 plant species, we demonstrate a tradeoff between constitutive and induced resistance, which was robust to accounting for phylogenetic history of the species. Moreover, the tradeoff was driven by wild species and was not evident for cultivated species. In addition, we demonstrate that more competitive species—but not fast growing ones—had lower constitutive but higher induced resistance. Thus, our multispecies experiments indicate that the competition–defense tradeoff holds for constitutive resistance and is complemented by a positive relationship of competitive ability with induced resistance. We conclude that the studied genetically determined tradeoffs are indeed likely to play an important role in shaping the high diversity observed among plant species in resistance against herbivores and in life history traits.
Cleavage and activation of a Toll-like receptor by microbial proteases
Authors: de Zoete Marcel R. , Bouwman Lieneke I. , Keestra A. Marijke , van Putten Jos P. M.
Published: March 2011

Toll-like receptors (TLRs) are innate receptors that show high conservation throughout the animal kingdom. Most TLRs can be clustered into phylogenetic groups that respond to similar types of ligands. One exception is avian TLR15. This receptor does not categorize into one of the existing groups of TLRs and its ligand is still unknown. Here we report that TLR15 is a sensor for secreted virulence-associated fungal and bacterial proteases. Activation of TLR15 involves proteolytic cleavage of the receptor ectodomain and stimulation of NF-κB–dependent gene transcription. Receptor activation can be mimicked by the expression of a truncated TLR15 of which the entire ectodomain is removed, suggesting that receptor cleavage alleviates receptor inhibition by the leucine-rich repeat domain. Our results indicate TLR15 as a unique type of innate immune receptor that combines TLR characteristics with an activation mechanism typical for the evolutionary distinct protease-activated receptors.
Axial
Hox9
activity establishes the posterior field in the developing forelimb
Authors: Xu Ben , Wellik Deneen M.
Published: March 2011

Current models hold that the early limb field becomes polarized into anterior and posterior domains by the opposing activities of
Hand2
and
Gli3
. This polarization is essential for the initiation of
Shh
expression in the posterior margin of the limb bud, but how this polarity is established is not clear. Here we show that initial anteroposterior polarization of the early forelimb field requires the function of all four
Hox9
paralogs (
Hoxa9
,
Hoxb9
,
Hoxc9
, and
Hoxd9
). This is unexpected, given that only
HoxA
and
HoxD AbdB
group genes have been shown to play a role in forelimb patterning, regulating the activation and maintenance of
Shh
expression and subsequent proximal-distal patterning of the forelimb. Our analysis of
Hox9
quadruple mutants demonstrates that
Hox9
function is required for the expression of
Hand2
in the posterior limb field. Subsequently,
Gli3
expression is not repressed posteriorly,
Shh
expression is not initiated, and collinear expression of
HoxA/D10–13
is not established, resulting in severely malformed forelimbs lacking all posterior,
Shh
-regulated elements. This
Hox9
mutant phenotype is restricted to the forelimbs; mutant hindlimbs are normal, revealing fundamental differences in the patterning mechanisms governing the establishment of forelimb and hindlimb fields.
Recruitment of a species-specific translational arrest module to monitor different cellular processes
Authors: Chiba Shinobu , Kanamori Takashi , Ueda Takuya , Akiyama Yoshinori , Pogliano Kit , Ito Koreaki
Published: March 2011

Nascent chain-mediated translation arrest serves as a mechanism of gene regulation. A class of regulatory nascent polypeptides undergoes elongation arrest in manners controlled by the dynamic behavior of the growing chain;
Escherichia coli
SecM monitors the Sec protein export pathway and
Bacillus subtilis
MifM monitors the YidC membrane protein integration/folding pathway. We show that MifM and SecM interact with the ribosome in a species-specific manner to stall only the ribosome from the homologous species. Despite this specificity, MifM is not exclusively designed to monitor membrane protein integration because it can be converted into a secretion monitor by replacing the N-terminal transmembrane sequence with a secretion signal sequence. These results show that a regulatory nascent chain is composed of two modular elements, one devoted to elongation arrest and another devoted to subcellular targeting, and they imply that physical pulling force generated by the latter triggers release of the arrest executed by the former. The combinatorial nature may assure common occurrence of nascent chain-mediated regulation.
Remotely sensed evidence of tropical peatland conversion to oil palm
Authors: Koh Lian Pin , Miettinen Jukka , Liew Soo Chin , Ghazoul Jaboury
Published: March 2011

Rising global demands for food and biofuels are driving forest clearance in the tropics. Oil-palm expansion contributes to biodiversity declines and carbon emissions in Southeast Asia. However, the magnitudes of these impacts remain largely unquantified until now. We produce a 250-m spatial resolution map of closed canopy oil-palm plantations in the lowlands of Peninsular Malaysia (2 million ha), Borneo (2.4 million ha), and Sumatra (3.9 million ha). We demonstrate that 6% (or ≈880,000 ha) of tropical peatlands in the region had been converted to oil-palm plantations by the early 2000s. Conversion of peatswamp forests to oil palm led to biodiversity declines of 1% in Borneo (equivalent to four species of forest-dwelling birds), 3.4% in Sumatra (16 species), and 12.1% in Peninsular Malaysia (46 species). This land-use change also contributed to the loss of ≈140 million Mg of aboveground biomass carbon, and annual emissions of ≈4.6 million Mg of belowground carbon from peat oxidation. Additionally, the loss of peatswamp forests implies the loss of carbon sequestration service through peat accumulation, which amounts to ≈660,000 Mg of carbon annually. By 2010, 2.3 million ha of peatswamp forests were clear-felled, and currently occur as degraded lands. Reforestation of these clearings could enhance biodiversity by up to ≈20%, whereas oil-palm establishment would exacerbate species losses by up to ≈12%. To safeguard the region's biodiversity and carbon stocks, conservation and reforestation efforts should target Central Kalimantan, Riau, and West Kalimantan, which retain three-quarters (3.9 million ha) of the remaining peatswamp forests in Southeast Asia.
A role for UDP-glucose glycoprotein glucosyltransferase in expression and quality control of MHC class I molecules
Authors: Zhang Wei , Wearsch Pamela A. , Zhu Yajuan , Leonhardt Ralf M. , Cresswell Peter
Published: March 2011

UDP-glucose:glycoprotein glucosyltransferase 1 (UGT1) serves as a folding sensor in the calnexin/calreticulin glycoprotein quality control cycle. UGT1 recognizes disordered or hydrophobic patches near asparagine-linked nonglucosylated glycans in partially misfolded glycoproteins and reglucosylates them, returning folding intermediates to the cycle. In this study, we examine the contribution of the UGT1-regulated quality control mechanism to MHC I antigen presentation. Using UGT1-deficient mouse embryonic fibroblasts reconstituted or not with UGT1, we show that, although formation of the peptide loading complex is unaffected by the absence of UGT1, the surface level of MHC class I molecules is reduced, MHC class I maturation and assembly are delayed, and peptide selection is impaired. Most strikingly, we show using purified soluble components that UGT1 preferentially recognizes and reglucosylates MHC class I molecules associated with a suboptimal peptide. Our data suggest that, in addition to the extensively studied tapasin-mediated quality control mechanism, UGT1 adds a new level of control in the MHC class I antigen presentation pathway.
Defining the earliest step of cardiovascular progenitor specification during embryonic stem cell differentiation
Authors: Bondue Antoine , Tännler Simon , Chiapparo Giuseppe , Chabab Samira , Ramialison Mirana , Paulissen Catherine , Beck Benjamin , Harvey Richard , Blanpain Cédric
Published: March 2011

During embryonic development and embryonic stem cell (ESC) differentiation, the different cell lineages of the mature heart arise from two types of multipotent cardiovascular progenitors (MCPs), the first and second heart fields. A key question is whether these two MCP populations arise from differentiation of a common progenitor. In this paper, we engineered Mesp1–green fluorescent protein (GFP) ESCs to isolate early MCPs during ESC differentiation. Mesp1-GFP cells are strongly enriched for MCPs, presenting the ability to differentiate into multiple cardiovascular lineages from both heart fields in vitro and in vivo. Transcriptional profiling of Mesp1-GFP cells uncovered cell surface markers expressed by MCPs allowing their prospective isolation. Mesp1 is required for MCP specification and the expression of key cardiovascular transcription factors. Isl1 is expressed in a subset of early Mesp1-expressing cells independently of Mesp1 and acts together with Mesp1 to promote cardiovascular differentiation. Our study identifies the early MCPs residing at the top of the cellular hierarchy of cardiovascular lineages during ESC differentiation.
Loss of mitochondrial complex I activity potentiates dopamine neuron death induced by microtubule dysfunction in a Parkinson’s disease model
Authors: Choi Won-Seok , Palmiter Richard D. , Xia Zhengui
Published: March 2011

Mitochondrial complex I dysfunction is regarded as underlying dopamine neuron death in Parkinson’s disease models. However, inactivation of the Ndufs4 gene, which compromises complex I activity, does not affect the survival of dopamine neurons in culture or in the substantia nigra pars compacta of 5-wk-old mice. Treatment with piericidin A, a complex I inhibitor, does not induce selective dopamine neuron death in either Ndufs4+/+ or Ndufs4−/− mesencephalic cultures. In contrast, rotenone, another complex I inhibitor, causes selective toxicity to dopamine neurons, and Ndufs4 inactivation potentiates this toxicity. We identify microtubule depolymerization and the accumulation of cytosolic dopamine and reactive oxygen species as alternative mechanisms underlying rotenone-induced dopamine neuron death. Enhanced rotenone toxicity to dopamine neurons from Ndufs4 knockout mice may involve enhanced dopamine synthesis caused by the accumulation of nicotinamide adenine dinucleotide reduced. Our results suggest that the combination of disrupting microtubule dynamics and inhibiting complex I, either by mutations or exposure to toxicants, may be a risk factor for Parkinson’s disease.
miR-24 inhibits apoptosis and represses Bim in mouse cardiomyocytes
Authors: Qian Li , Van Laake Linda W. , Huang Yu , Liu Siyuan , Wendland Michael F. , Srivastava Deepak
Published: March 2011

Acute myocardial infarction (MI) involves necrotic and apoptotic loss of cardiomyocytes. One strategy to salvage ischemic cardiomyocytes is to modulate gene expression to promote cell survival without disturbing normal cardiac function. MicroRNAs (miRNAs) have emerged as powerful regulators of multiple cellular processes, including apoptosis, suggesting that regulation of miRNA function could serve a cardioprotective function. In this study, we report that miR-24 (miRNA-24) expression is down-regulated in the ischemic border zone of the murine left ventricle after MI. miR-24 suppresses cardiomyocyte apoptosis, in part by direct repression of the BH3-only domain–containing protein Bim, which positively regulates apoptosis. In vivo expression of miR-24 in a mouse MI model inhibited cardiomyocyte apoptosis, attenuated infarct size, and reduced cardiac dysfunction. This antiapoptotic effect on cardiomyocytes in vivo was partially mediated by Bim. Our results suggest that manipulating miRNA levels during stress-induced apoptosis may be a novel therapeutic strategy for cardiac disease.
A simple fabrication method of randomly oriented polycrystalline zinc oxide nanowires and their application to gas sensing
Authors: Hung Nguyen Le , Kim Hyojin , Hong Soon-Ku , Kim Dojin
Published: March 2011

Randomly oriented polycrystalline ZnO nanowires with a mean diameter of 100–150 nm have been successfully synthesized on SiO
2/Si substrates through the thermal oxidation of sputtered Zn nanowires in dry air at 400 °C. Structural characterization by x-ray diffraction (XRD), scanning electron microscopy (SEM) and transmission electron microscopy (TEM) revealed that each ZnO nanowire consisted of a chain of ZnO nanocrystallites. From gas sensing measurements for CO, H
2 and NO gases, the polycrystalline ZnO nanowires showed a highly sensitive and fast response to both reducing and oxidizing gases in dry air at relatively low concentrations and operating temperatures, indicating potential applications of polycrystalline ZnO nanowires as sensing materials for gas sensors.
Epitaxial Pb(Zr,Ti)O
3 thin films for a MEMS application
Authors: Nguyen Minh D , Vu Hung N , Blank Dave H A , Rijnders Guus
Published: March 2011

This research presents the deposition and device fabrication of epitaxial Pb(Zr,Ti)O
3 (PZT) thin films for applications in microelectromechanical systems (MEMS). A piezoelectric micro-membrane is described as an example. Using the pulsed laser deposition (PLD) technique and the MEMS microfabrication process, the piezo-membranes with diameters ranging from 200 to 500 μm were obtained. The displacement of piezo-membranes increased from 5.1 to 17.5 nm 
V
−1 with a piezoelectric-membrane diameter in the range of 200–500 μm. Furthermore, the effect of PZT film-thickness on the mechanical properties has been investigated. By using the conductive-oxide SrRuO
3 (SRO) layers as the electrodes, the degradation of both ferroelectric and piezoelectric properties is prevented up to 1010 switching cycles.
Nuclear envelope dispersion triggered by deregulated Cdk5 precedes neuronal death
Authors: Chang Kuei-Hua , Multani Parminder Singh , Sun Kai-Hui , Vincent Fabien , de Pablo Yolanda , Ghosh Soumitra , Gupta Ritika , Lee Hyun-Pil , Lee Hyoung-gon , Smith Mark A. , Shah Kavita
Published: March 2011

Nuclear fragmentation is a common feature in many neurodegenerative diseases, including Alzheimer’s disease (AD). In this study, we show that nuclear lamina dispersion is an early and irreversible trigger for cell death initiated by deregulated Cdk5, rather than a consequence of apoptosis. Cyclin-dependent kinase 5 (Cdk5) activity is significantly increased in AD and contributes to all three hallmarks: neurotoxic amyloid-β (Aβ), neurofibrillary tangles (NFT), and extensive cell death. Using Aβ and glutamate as the neurotoxic stimuli, we show that deregulated Cdk5 induces nuclear lamina dispersion by direct phosphorylation of lamin A and lamin B1 in neuronal cells and primary cortical neurons. Phosphorylation-resistant mutants of lamins confer resistance to nuclear dispersion and cell death on neurotoxic stimulation, highlighting this as a major mechanism for neuronal death. Rapid alteration of lamin localization pattern and nuclear membrane change are further supported by in vivo data using an AD mouse model. After p25 induction, the pattern of lamin localization was significantly altered, preceding neuronal death, suggesting that it is an early pathological event in p25-inducible transgenic mice. Importantly, lamin dispersion is coupled with Cdk5 nuclear localization, which is highly neurotoxic. Inhibition of nuclear dispersion rescues neuronal cells from cell death, underscoring the significance of this event to Cdk5-mediated neurotoxicity.