bluuebunny/crossref_metadata_2025 huggingface dataset:
An extended network of documentary data from South America and its potential for quantitative precipitation reconstructions back to the 16th century
Authors: Neukom Raphael , del Rosario Prieto María , Moyano Rodolfo , Luterbacher Jürg , Pfister Christian , Villalba Ricardo , Jones Philip D. , Wanner Heinz
Published: June 2009

In South America (SA) several documentary based climate time series exist, some of them extending back to the 16th century. Most of these records end in the 19th century, and can not be calibrated against instrumental data. Here, we used the newspaper “Los Andes” from Mendoza, Argentina, to extend documentary based indices of Mendoza precipitation and Central Andes snow depth to the late 20th century. A statistical approach to create “pseudo documentary” 20th century data was applied to prolong eight other documentary records. Increased variability of the hydrological cycle in the Central Andes and prevailing periods of wet and dry years in Mendoza suggest that the 20th century is extraordinary in the context of the last 400 years. The final set of extended documentaries explains significant portions of SA precipitation variability in large areas between 20°S and 40°S and can therefore improve the network of annually resolved precipitation proxies.
Severe convective storms initiated by intense wildfires: Numerical simulations of pyro‐convection and pyro‐tornadogenesis
Authors: Cunningham Philip , Reeder Michael J.
Published: June 2009

On the afternoon of 18 January 2003, wildfires swept through several outer suburbs of Canberra (Australia) producing, inter alia, a series of large pyro‐cumulonimbus cells and at least one tornado. The results of a large‐eddy simulation with a parameterized fire are reported here. The simulation, motivated by the Canberra wildfires and severe storms, captures the main characteristics of the observed pyro‐cumulonimbi, including the formation of a tornado close to where one was observed. In addition, the model develops prominent horizontally oriented vortices on the western side of the fire in the direction of the low‐level shear, and a series of horizontally oriented vortices on the upstream side of the convection column. The production of water by the fire is critical for the development of a pyro‐cumulonimbus cell intense enough to reach the tropopause as observed and plays a significant role in the associated tornadogenesis.
Comparison of rhizobacterial community composition in soil suppressive or conducive to tobacco black root rot disease
Authors: Kyselková Martina , Kopecký Jan , Frapolli Michele , Défago Geneviève , Ságová-Marečková Markéta , Grundmann Geneviève L , Moënne-Loccoz Yvan
Published: June 2009

Work on soils suppressive to Thielaviopsis basicola-mediated tobacco black root rot has focused on antagonistic pseudomonads to date. The role of non-Pseudomonas rhizosphere populations has been neglected, and whether they differ in black root rot-suppressive versus -conducive soils is unknown. To assess this possibility, tobacco was grown in a suppressive and a conducive soil of similar physicochemical properties, and rhizobacterial community composition was compared using a 16S rRNA taxonomic microarray. The microarray contains 1033 probes and targets 19 bacterial phyla. Among them, 398 probes were designed for Proteobacteria, Firmicutes, Actinomycetes, Cyanobacteria and Bacteroidetes genera/species known to include strains relevant for plant protection or plant growth promotion. Hierarchical clustering as well as principal component analysis of microarray data discriminated clearly between black root rot-suppressive and -conducive soils. In contrast, T. basicola inoculation had no impact on rhizobacterial community composition. In addition to fluorescent Pseudomonas, the taxa Azospirillum, Gluconacetobacter, Burkholderia, Comamonas and Sphingomonadaceae, which are known to comprise strains with plant-beneficial properties, were more prevalent in the suppressive soil. Mycobacterium, Bradyrhizobium, Rhodobacteraceae, Rhodospirillum and others were more prevalent in the conducive soil. For selected taxa, microarray results were largely corroborated by quantitative PCR and cloning/sequencing. In conclusion, this work identified novel bacterial taxa that could serve as indicators of disease suppressiveness in soil-quality assessments, and it extends the range of bacterial taxa hypothesized to participate in black root rot suppression.
Species-specific structural and functional diversity of bacterial communities in lichen symbioses
Authors: Grube Martin , Cardinale Massimiliano , de Castro João Vieira , Müller Henry , Berg Gabriele
Published: June 2009

Lichens are generally considered as mutualisms between fungi and green algae or cyanobacteria. These partnerships allow light-exposed and long-living joint structures. The unique organization of lichens provides still unexplored environments for microbial communities. To study lichen-associated bacterial communities, we analyze samples, by a polyphasic approach, from three lichen species (Cladonia arbuscula, Lecanora polytropa and Umbilicaria cylindrica) from alpine environments. Our results indicate that bacteria can form highly structured, biofilm-like assemblages on fungal surfaces and reach considerable abundances of up to 108 cells per gram fresh weight. Fluorescence in situ hybridization reveals the predominance of Alphaproteobacteria. Microbial fingerprints performed by PCR-single-strand conformation polymorphism analysis using universal and group-specific primers show distinct patterns for each lichen species. Characterization of cultivable strains and presence of functional genes in the total fraction suggest the involvement of associated bacteria in nutrient cycling. Ubiquitous nifH genes, which encode the nitrogenase reductase, show a high diversity and are assigned to Alphaproteobacteria and Firmicutes, for example, Paenibacillus. Cultivable strains mainly belonging to the genera Acinetobacter, Bacillus, Burkholderia, Methylobacterium and Paenibacillus show lytic (chitinolytic, glucanolytic, and proteolytic) activities, hormone production (indole-3-acetic acid) as well as phosphate mobilization and antagonistic activity toward other microorganisms. The traditional concept of lichens has to be expanded to consider multiple bacterial partners.
Exogenous glucosinolate produced by Arabidopsis thaliana has an impact on microbes in the rhizosphere and plant roots
Authors: Bressan Mélanie , Roncato Marie-Anne , Bellvert Floriant , Comte Gilles , Haichar Feth el Zahar , Achouak Wafa , Berge Odile
Published: June 2009

A specificity of Brassicaceous plants is the production of sulphur secondary metabolites called glucosinolates that can be hydrolysed into glucose and biocidal products. Among them, isothiocyanates are toxic to a wide range of microorganisms and particularly soil-borne pathogens. The aim of this study was to investigate the role of glucosinolates and their breakdown products as a factor of selection on rhizosphere microbial community associated with living Brassicaceae. We used a DNA-stable isotope probing approach to focus on the active microbial populations involved in root exudates degradation in rhizosphere. A transgenic Arabidopsis thaliana line producing an exogenous glucosinolate and the associated wild-type plant associated were grown under an enriched 13CO2 atmosphere in natural soil. DNA from the rhizospheric soil was separated by density gradient centrifugation. Bacterial (Alphaproteobacteria, Betaproteobacteria, Gammaproteobacteria and Acidobacteria), Archaea and fungal community structures were analysed by DGGE fingerprints of amplified 16S and 18S rRNA gene sequences. Specific populations were characterized by sequencing DGGE fragments. Roots of the transgenic plant line presented an altered profile of glucosinolates and other minor additional modifications. These modifications significantly influenced microbial community on roots and active populations in the rhizosphere. Alphaproteobacteria, particularly Rhizobiaceae, and fungal communities were mainly impacted by these Brassicaceous metabolites, in both structure and composition. Our results showed that even a minor modification in plant root could have important repercussions for soil microbial communities.
Proteomic Analysis of Human Adipose Tissue After Rosiglitazone Treatment Shows Coordinated Changes to Promote Glucose Uptake
Authors: Ahmed Meftun , Neville Matt J. , Edelmann Mariola J. , Kessler Benedikt M. , Karpe Fredrik
Published: June 2009

The aim of this study was to identify potential protein targets for insulin sensitization in human adipose tissue using unbiased proteomic approaches. Ten moderately obese, but otherwise healthy, subjects were treated with rosiglitazone 4 mg b.i.d. for 14 days and global protein and gene expression changes were monitored. Proteomic analysis revealed distinct up‐ or downregulation (greater than twofold) in 187 protein spots on the two‐dimensional (2‐D) gel images between day 0 and day 1 adipose tissue samples. When comparing the protein spots on the gels from day 0 with that of 14‐day‐treated samples, 122 spots showed differential expression. There was a striking increase in the expression of proteins involved in glucose transporter‐4 (GLUT4) granule transport and fusion (actin, myosin‐9, tubulin, vimentin, annexins, moesin, LIM, and SH3 domain protein‐1), signaling (calmodulin, guanine nucleotide–binding proteins), redox regulation (superoxide dismutase, catalase, ferritin, transferrin, heat shock proteins), and adipogenesis (collagens, galectin‐1, nidogen‐1, laminin, lamin A/C). However, there was an intriguing absence of correlated changes in mRNA expression, suggesting adaptation at a post‐transcriptional level in response to rosiglitazone. Thus, the major changes observed were among proteins involved in cytoskeletal rearrangement, insulin and calcium signaling, and inflammatory and redox signals that decisively upregulate GLUT4 granule trafficking in human adipose tissue. Such orchestrated changes in expression of multiple proteins provide insights into the mechanism underlying the increased efficiency in glucose uptake and improvement of insulin sensitivity in response to rosiglitazone treatment.
Ionic liquids as catalysts, solvents and conversion agents
Authors: Gujar Amit C. , White Mark G.
Published: June 2009

The literature of room temperature ionic liquids (RTILs) was reviewed to select and report on those RTILs involved directly in chemical reactions either as a solvent for a catalyst, a conversion agent, or a task specific ionic liquid. Special emphasis was placed on manuscripts appearing in the literature in the last ten years.
Defining Bilingualism: Factors Contributing to Variability in Language and Literacy Development of Spanish-English Bilingual Children
Authors: Davison Megan Dunn
Published: June 2009

Given the increasing number of children from homes in which a language other than English is the primary language, it is important for speech-language pathologists to understand how bilingualism is defined and the implications of different defining factors for language development and later literacy outcomes. The purpose of this paper is to explore the factors contributing to the differences observed across bilingual language and literacy development. Previous research suggests there are differences in the language and literacy development of bilingual children due to differing ages of exposure to each language and the context in which each language is then used. Implications for assessment and interventions are discussed.
Expository Text: Reading Comprehension, Bilingualism, and Instructional Strategies
Authors: Bejos Karla
Published: June 2009

This literature review examines reading comprehension issues related to expository text. It describes what factors contribute to the complexity of expository text, what abilities and skills a reader must possess, and expository text structure. The review addresses influences of bilingualism on expository text comprehension. It discusses the relation of second language oral proficiency on reading, the complexity of the reading task for bilinguals, how they approach reading, and the transfer of literacy skills across languages. The final section reviews instructional strategies aimed at improving reading comprehension of expository text. This includes strategies to teach comprehension of the cause and effect concept, paraphrasing, and types of tasks to assess reading comprehension that are appropriate for bilingual readers.
Relationships between the third-order reactivity indicators in chemical density-functional theory
Authors: Cárdenas Carlos , Echegaray Eleonora , Chakraborty Debajit , Anderson James S. M. , Ayers Paul W.
Published: June 2009

Relationships between third-order reactivity indicators in the closed system [N, v(r)], open system [μ, v(r)], and density [ρ(r)] pictures are derived. Our method of derivation unifies and extends known results. Among the relationships is a link between the third-order response of the energy to changes in the density and the quadratic response of the density to changes in external potential. This provides a link between hyperpolarizability and the system’s sensitivity to changes in electron density. The dual descriptor is a unifying feature of many of the formulas we derive.
Ab initio study of valence and Rydberg states of CH3Br
Authors: Escure Christelle , Leininger Thierry , Lepetit Bruno
Published: June 2009

We performed configuration interaction ab initio calculations on the valence and 5s, 5pa1, and 5pe Rydberg bands of the CH3Br molecule as a function of the methyl-bromide distance for frozen C3v geometries. The valence state potential energy curves are repulsive, the Rydberg state ones are similar to the one of the CH3Br+ ion with a minimum at short distance. One state emerging from the 5pe band has valence and ion-pair characters as distance increases and the corresponding potential curve has a second minimum at large distance. This state has a very strong parallel electric dipole transition moment with the ground state and plays a central role in UV photon absorption spectra. It is also responsible for the parallel character of the anisotropy parameters measured in ion-pair production experiments. In each band, there is a single state, which has a non-negligible transition moment with the ground state, corresponding to a transition perpendicular to the molecular axis of symmetry, except for the 5pe band where it is parallel. The perpendicular transition moments between ground and valence states increase sharply as methyl-bromide distance decreases due to a mixing between valence and 5s Rydberg band at short distance. In each band, spin orbit interaction produces a pair of states, which have significant transition moments with the ground one. In the valence band, the mixing between singlet and triplet states is weak and the perpendicular transition to the Q11 state is dominant. In each Rydberg band, however, spin-orbit interaction is larger than the exchange interaction and the two significant transition moments with the ground state have comparable strengths. The valence band has an additional state (Q10) with significant parallel transition moment induced by spin-orbit interaction with the ground state at large distance.
Microphotoluminescence investigation on single ZnO microrods with different morphologies
Authors: Chu Xueying , Hong Xia , Li Xinghua , Li Yinghua , Zhang Xintong , Liu Yichun
Published: June 2009

Spatially resolved microphotoluminescence (μ-PL) was employed to investigate the photoluminescent properties of single ZnO microrods with three morphologies: fusiform, straight, and dumbbell. The morphology of ZnO microrods as well as the measurement region, both had great influence on the observed μ-PL. These were analyzed in terms of the defect density, the ionization effect of surface charges, and the thermal effect of laser. It was found that crystal defects favored the formation of bound excitons, which resulted in the redshift of ultraviolet bands in μ-PL. This redshift effect, however, could be submerged by the ionization of the bound excitons under the surface electric field, especially at the large surface-to-volume regions. The thermal effect of laser, an important factor for traditional photoluminescence characterization, can be neglected in the case of single rod μ-PL measurement.
Effect of Ag thickness on electrical transport and optical properties of indium tin oxide–Ag–indium tin oxide multilayers
Authors: Indluru A. , Alford T. L.
Published: June 2009

We report the dependence of electronic and optical properties on the Ag thickness in transparent conductive indium tin oxide (ITO)-Ag-ITO (IMI) multilayer films deposited on polyethylene naphthalate flexible substrate by sputtering at room temperature. The electrical properties (such as carrier concentration, mobility, and resistivity) changed significantly with incorporation of Ag between the ITO layers. Comparison of sheet resistance of the IMI multilayers and the calculated sheet resistance of the Ag midlayer indicates that most of the conduction is through the Ag film. The critical thickness of Ag to form a continuous conducting layer is found to be 8 nm using electrical and optical analysis. A conduction mechanism is proposed to elucidate the mobility variation with increased Ag thickness. Carrier transport is limited by either interface scattering or grain-boundary scattering depending on the thickness of the Ag midlayer. Interface scattering is dominant for thinner (5.5–7 nm) Ag and grain-boundary scattering is dominant for thicker (8–10.5 nm) Ag midlayers. In addition, the effect of varying Ag midlayer thickness on transmittance behavior is also discussed. A figure of merit is used to compare performance of the IMI multilayer systems as a function of Ag thickness.
Characteristics of photoluminescence due to exciton-exciton scattering in GaAs/AlAs multiple quantum wells
Authors: Nakayama M. , Hirao T. , Hasegawa T.
Published: June 2009

We have investigated photoluminescence (PL) properties of GaAs (15 nm)/AlAs (15 nm) and GaAs (20 nm)/AlAs (20 nm) multiple quantum wells at 10 K under high density excitation conditions at excitation energies in the region of the fundamental excitons. It has been found that the PL due to exciton-exciton scattering, the so-called P emission, is observed with a threshold nature in addition to the appearance of the biexciton PL. The energy spacing between the P-PL band and the heavy-hole exciton depends on the layer thickness, which reflects the change of the exciton binding energy by the quantum size effect. The intensity of the biexciton-PL band is saturated by the appearance of the P-PL band. Both the exciton-exciton scattering process and the biexciton formation process require the collision of two excitons. Thus, the exciton-exciton scattering process prevents the formation of biexcitons, which leads to the saturation behavior of the biexciton-PL intensity. Furthermore, we have confirmed the existence of optical gain leading to stimulated emission due to the exciton-exciton scattering process with use of a variable-stripe-length method.
A new class of highly efficient exact stochastic simulation algorithms for chemical reaction networks
Authors: Ramaswamy Rajesh , González-Segredo Nélido , Sbalzarini Ivo F.
Published: June 2009

We introduce an alternative formulation of the exact stochastic simulation algorithm (SSA) for sampling trajectories of the chemical master equation for a well-stirred system of coupled chemical reactions. Our formulation is based on factored-out, partial reaction propensities. This novel exact SSA, called the partial-propensity direct method (PDM), is highly efficient and has a computational cost that scales at most linearly with the number of chemical species, irrespective of the degree of coupling of the reaction network. In addition, we propose a sorting variant, SPDM, which is especially efficient for multiscale reaction networks.
Gyrokinetic equation in an exact canonical Hamiltonian coordinate system and its orbit-averaged form
Authors: Qi Lei , Wang Shaojie
Published: June 2009

A previous gauge-invariant gyrokinetic equation based on an approximate canonical Hamiltonian coordinate system is extended to an exact canonical Hamiltonian coordinate system with the time scale well separated. By using this formalism a new orbit-averaged gyrokinetic equation, which is valid for both trapped and passing particles, is established.
From power law intermittence to macroscopic coherent regime
Authors: Bologna Mauro , Budini Adrián A. , Giraldi Filippo , Grigolini Paolo
Published: June 2009

We address the problem of establishing which is the proper form of quantum master equation generating a survival probability identical to that corresponding to the nonergodic sequence of “light on” and “light off” fluorescence fluctuations in blinking quantum dots. We adopt a theoretical perspective based on the assumption that the abrupt transitions from the light on to light off state are the results of many collisions between system and environment, properly described by the Lindblad equation, and that between two consecutive collisions the system dynamics are frozen. This generates a quantum master equation belonging to the recently proposed class of generalized Lindblad equations, with a time convoluted structure, involving in the specific case of this paper both the unitary and the nonunitary contribution of the Lindblad equation. This is the property that under the low-frequency condition makes the new class of generalized Lindblad equation generates the required survival probability. We make the conjecture that this equation corresponds to the cooperative dynamics of many units that, in isolation, are described by the ordinary Lindblad equation. When the time scale of the unitary term of the Lindblad equation is shorter than the dephasing time, the cooperation generates a surprisingly extended macroscopic coherence.
Photon counting statistics of single molecule in solid matrix
Authors: Han Baiping , Ji Ziwu , Zheng Yujun
Published: June 2009

In this paper, we investigate the properties of photon emission statistics of single molecule in solid matrix. The influences of solid matrix surroundings on photon emission of single molecule system under the laser field and rf field for several examples, the single dibenzanthanthrene molecule in hexadecane, the spectral diffusion process, and the hidden two-state models and the Gaussian models of blinking behavior, are considered.
Potential measurement from a single lead ziroconate titanate nanofiber using a nanomanipulator
Authors: Chen Xi , Xu Shiyou , Yao Nan , Xu Weihe , Shi Yong
Published: June 2009

Direct piezoelectric potential measurement of single lead ziroconate titanate (PZT) nanofiber under bending using a nanomanipulator inside a scanning electron microscope chamber was presented. The PZT nanofibers, with the diameter and length around 100 nm and 70–100 μm, respectively, were aligned across trenches on a silicon substrate with a thermally grown oxide diffusion barrier and evaporated gold electrodes. A potential of ∼0.4 mV was generated when a bending moment was applied to a PZT nanofiber with an effective length of 4 μm by a tungsten tip of the nanomanipulator. The experiment demonstrated the feasibility of using these PZT nanofibers for nanoscale sensing, actuation, and energy harvesting.
Self-diffusion and macroscopic diffusion of hydrogen in amorphous metals from first-principles calculations
Authors: Hao Shiqiang , Sholl David S.
Published: June 2009

Diffusion of interstitial hydrogen plays a key role in potential uses for amorphous metals as membranes for hydrogen purification. We show how first principles-based methods can be used to characterize diffusion of interstitial H in amorphous metals using amorphous Fe3B as an example. Net transport of interstitial H is governed by the transport diffusion coefficient that appears in Fick’s law. This diffusion coefficient is strongly dependent on the interstitial concentration, and is not equal to the self-diffusion coefficient except at dilute interstitial concentrations. Under conditions of practical interest, the concentrations of interstitial H in amorphous metals are nondilute so methods to determine the transport diffusion coefficient must be used if net mass transport is to be described. We show how kinetic Monte Carlo simulations of interstitial H diffusion that use rates derived from first-principles calculations can be used to assess both self- and transport diffusion coefficients of H in amorphous metals. These methods will be helpful in efforts to screen amorphous metal alloys as potential membranes for hydrogen purification.
Temperature dependent charge-injection at the metal-organic semiconductor interface and density of states in pristine and doped pentacene
Authors: Vanoni Claudio , Jung Thomas A. , Tsujino Soichiro
Published: June 2009

The authors study temperature dependent electrical transport in pristine and tetrafluorotetracyanoquinodimethane (F4TCNQ)-doped pentacene to explore the physical mechanism of the doping-induced reduction in the contact resistance at the metal-organic semiconductor interface. It was found that the F4TCNQ-doping induces an apparent lowering of the hole injection barrier at gold-pentacene interfaces. In addition, characteristic changes in the density of states (DOS) induced by the F4TCNQ-doping in a thin-film transistor geometry have been observed. The correlation between the doping-induced DOS and the carrier injection process is discussed.
Effect of uniaxial pressure on metal-insulator transition in (Sm1−yNdy)0.52Sr0.48MnO3 single crystals
Authors: Murugeswari A. , Sarkar P. , Arumugam S. , Manivannan N. , Mandal P. , Ishida T. , Noguchi S.
Published: June 2009

We have investigated the effect of uniaxial pressure (P) on resistivity along the ab plane and c-axis in single crystals of (Sm1−yNdy)0.52Sr0.48MnO3 with y=0, 0.05, and 0.3. The application of pressure along the c-axis shifts the metal-insulator transition (MIT) to higher temperature, while MIT temperature decreases with P when it is applied perpendicular to the c-axis. This behavior is quite different from that observed in hydrostatic pressure and can be explained by considering the P dependence change in equatorial and apical Mn–O–Mn bond angles.
Gravitational-Wave Detection Using Pulsars: Status of the Parkes Pulsar Timing Array Project
Authors: Hobbs G. B. , Bailes M. , Bhat N. D. R. , Burke-Spolaor S. , Champion D. J. , Coles W. , Hotan A. , Jenet F. , Kedziora-Chudczer L. , Khoo J. , Lee K. J. , Lommen A. , Manchester R. N. , Reynolds J. , Sarkissian J. , van Straten W. , To S. , Verbiest J. P. W. , Yardley D. , You X. P.
Published: June 2009

The first direct detection of gravitational waves may be made through observations of pulsars. The principal aim of pulsar timing-array projects being carried out worldwide is to detect ultra-low frequency gravitational waves (f ∼ 10−9–10−8 Hz). Such waves are expected to be caused by coalescing supermassive binary black holes in the cores of merged galaxies. It is also possible that a detectable signal could have been produced in the inflationary era or by cosmic strings. In this paper, we review the current status of the Parkes Pulsar Timing Array project (the only such project in the Southern hemisphere) and compare the pulsar timing technique with other forms of gravitational-wave detection such as ground- and space-based interferometer systems.
Changing meaning causes coupling changes within higher levels of the cortical hierarchy
Authors: Schofield T. M. , Iverson P. , Kiebel S. J. , Stephan K. E. , Kilner J. M. , Friston K. J. , Crinion J. T. , Price C. J. , Leff A. P.
Published: June 2009

Processing of speech and nonspeech sounds occurs bilaterally within primary auditory cortex and surrounding regions of the superior temporal gyrus; however, the manner in which these regions interact during speech and nonspeech processing is not well understood. Here, we investigate the underlying neuronal architecture of the auditory system with magnetoencephalography and a mismatch paradigm. We used a spoken word as a repeating “standard” and periodically introduced 3 “oddball” stimuli that differed in the frequency spectrum of the word's vowel. The closest deviant was perceived as the same vowel as the standard, whereas the other 2 deviants were perceived as belonging to different vowel categories. The neuronal responses to these vowel stimuli were compared with responses elicited by perceptually matched tone stimuli under the same paradigm. For both speech and tones, deviant stimuli induced coupling changes within the same bilateral temporal lobe system. However, vowel oddball effects increased coupling within the left posterior superior temporal gyrus, whereas perceptually equivalent nonspeech oddball effects increased coupling within the right primary auditory cortex. Thus, we show a dissociation in neuronal interactions, occurring at both different hierarchal levels of the auditory system (superior temporal versus primary auditory cortex) and in different hemispheres (left versus right). This hierarchical specificity depends on whether auditory stimuli are embedded in a perceptual context (i.e., a word). Furthermore, our lateralization results suggest left hemisphere specificity for the processing of phonological stimuli, regardless of their elemental (i.e., spectrotemporal) characteristics.
Global distribution of conformational states derived from redundant models in the PDB points to non-uniqueness of the protein structure
Authors: Burra Prasad V. , Zhang Ying , Godzik Adam , Stec Boguslaw
Published: June 2009

It is commonly accepted that proteins have evolutionarily conserved 3-dimensional structures, uniquely defined by their amino acid sequence. Here, we question the direct association of structure to sequence by comparing multiple models of identical proteins. Rapidly growing structural databases contain models of proteins determined independently multiple times. We have collected these models in the database of the redundant sets of protein structures and then derived their conformational states by clustering the models with low root-mean-square deviations (RMSDs). The distribution of conformational states represented in these sets is wider than commonly believed, in fact exceeding the possible range of structure determination errors, by at least an order of magnitude. We argue that differences among the models represent the natural distribution of conformational states. Our results suggest that we should change the common notion of a protein structure by augmenting a single 3-dimensional model by the width of the ensemble distribution. This width must become an indispensible attribute of the protein description. We show that every protein contains regions of high rigidity (solid-like) and regions of high mobility (liquid-like) in different and characteristic contribution. We also show that the extent of local flexibility is correlated with the functional class of the protein. This study suggests that the protein-folding problem has no unique solution and should be limited to defining the folding class of the solid-like fragments even though they may constitute only a small part of the protein. These results limit the capability of modeling protein structures with multiple conformational states.
Continuous dissolution of structure during the unfolding of a small protein
Authors: Jha Santosh Kumar , Dhar Deepak , Krishnamoorthy Guruswamy , Udgaonkar Jayant B.
Published: June 2009

The unfolding kinetics of many small proteins appears to be first order, when measured by ensemble-averaging probes such as fluorescence and circular dichroism. For one such protein, monellin, it is shown here that hidden behind this deceptive simplicity is a complexity that becomes evident with the use of experimental probes that are able to discriminate between different conformations in an ensemble of structures. In this study, the unfolding of monellin has been probed by measurement of the changes in the distributions of 4 different intramolecular distances, using a multisite, time-resolved fluorescence resonance energy transfer methodology. During the course of unfolding, the protein molecules are seen to undergo slow and continuous, diffusive swelling. The swelling process can be modeled as the slow diffusive swelling of a Rouse-like chain with some additional noncovalent, intramolecular interactions. Here, we show that specific structure is lost during the swelling process gradually, and not in an all-or-none manner, during unfolding.
Locating the transition from periodic oscillations to spatiotemporal chaos in the wake of invasion
Authors: Sherratt Jonathan A. , Smith Matthew J. , Rademacher Jens D. M.
Published: June 2009

In systems with cyclic dynamics, invasions often generate periodic spatiotemporal oscillations, which undergo a subsequent transition to chaos. The periodic oscillations have the form of a wavetrain and occur in a band of constant width. In applications, a key question is whether one expects spatiotemporal data to be dominated by regular or irregular oscillations or to involve a significant proportion of both. This depends on the width of the wavetrain band. Here, we present mathematical theory that enables the direct calculation of this width. Our method synthesizes recent developments in stability theory and computation. It is developed for only 1 equation system, but because this is a normal form close to a Hopf bifurcation, the results can be applied directly to a wide range of models. We illustrate this by considering a classic example from ecology: wavetrains in the wake of the invasion of a prey population by predators.
An essential role for ATP binding and hydrolysis in the chaperone activity of GRP94 in cells
Authors: Ostrovsky Olga , Makarewich Catherine A. , Snapp Erik L. , Argon Yair
Published: June 2009

Glucose-regulated protein 94 (GRP94) is an endoplasmic reticulum (ER) chaperone for which only few client proteins and no cofactors are known and whose mode of action is unclear. To decipher the mode of GRP94 action in vivo, we exploited our finding that GRP94 is necessary for the production of insulin-like growth factor (IGF)-II and developed a cell-based functional assay.
Grp94
−/−
cells are hypersensitive to serum withdrawal and die. This phenotype can be complemented either with exogenous IGF-II or by expression of functional GRP94. Fusion proteins of GRP94 with monomeric GFP (mGFP) or mCherry also rescue the viability of transiently transfected, GRP94-deficient cells, demonstrating that the fusion proteins are functional. Because these constructs enable direct visualization of chaperone-expressing cells, we used this survival assay to assess the activities of GRP94 mutants that are defective in specific biochemical functions in vitro. Mutations that abolish binding of adenosine nucleotides cannot support growth in serum-free medium. Similarly, mutations of residues needed for ATP hydrolysis also render GRP94 partially or completely nonfunctional. In contrast, an N-terminal domain mutant that cannot bind peptides still supports cell survival. Thus the peptide binding activity in vitro can be uncoupled from the chaperone activity toward IGF in vivo. This mutational analysis suggests that the ATPase activity of GRP94 is essential for chaperone activity in vivo and that the essential protein-binding domain of GRP94 is distinct from the N-terminal domain.
α-Synuclein and Its A30P Mutant Affect Actin Cytoskeletal Structure and Dynamics
Authors: Sousa Vítor L. , Bellani Serena , Giannandrea Maila , Yousuf Malikmohamed , Valtorta Flavia , Meldolesi Jacopo , Chieregatti Evelina
Published: June 2009

The function of α-synuclein, a soluble protein abundant in the brain and concentrated at presynaptic terminals, is still undefined. Yet, α-synuclein overexpression and the expression of its A30P mutant are associated with familial Parkinson's disease. Working in cell-free conditions, in two cell lines as well as in primary neurons we demonstrate that α-synuclein and its A30P mutant have different effects on actin polymerization. Wild-type α-synuclein binds actin, slows down its polymerization and accelerates its depolymerization, probably by monomer sequestration; A30P mutant α-synuclein increases the rate of actin polymerization and disrupts the cytoskeleton during reassembly of actin filaments. Consequently, in cells expressing mutant α-synuclein, cytoskeleton-dependent processes, such as cell migration, are inhibited, while exo- and endocytic traffic is altered. In hippocampal neurons from mice carrying a deletion of the α-synuclein gene, electroporation of wild-type α-synuclein increases actin instability during remodeling, with growth of lamellipodia-like structures and apparent cell enlargement, whereas A30P α-synuclein induces discrete actin-rich foci during cytoskeleton reassembly. In conclusion, α-synuclein appears to play a major role in actin cytoskeletal dynamics and various aspects of microfilament function. Actin cytoskeletal disruption induced by the A30P mutant might alter various cellular processes and thereby play a role in the pathogenesis of neurodegeneration.
Clustering and Lateral Concentration of Raft Lipids by the MAL Protein
Authors: Magal Lee Goldstein , Yaffe Yakey , Shepshelovich Jeanne , Aranda Juan Francisco , de Marco Maria del Carmen , Gaus Katharina , Alonso Miguel Angel , Hirschberg Koret
Published: June 2009

MAL, a compact hydrophobic, four-transmembrane-domain apical protein that copurifies with detergent-resistant membranes is obligatory for the machinery that sorts glycophosphatidylinositol (GPI)-anchored proteins and others to the apical membrane in epithelia. The mechanism of MAL function in lipid-raft–mediated apical sorting is unknown. We report that MAL clusters formed by two independent procedures—spontaneous clustering of MAL tagged with the tandem dimer DiHcRED (DiHcRED-MAL) in the plasma membrane of COS7 cells and antibody-mediated cross-linking of FLAG-tagged MAL—laterally concentrate markers of sphingolipid rafts and exclude a fluorescent analogue of phosphatidylethanolamine. Site-directed mutagenesis and bimolecular fluorescence complementation analysis demonstrate that MAL forms oligomers via ϕxxϕ intramembrane protein–protein binding motifs. Furthermore, results from membrane modulation by using exogenously added cholesterol or ceramides support the hypothesis that MAL-mediated association with raft lipids is driven at least in part by positive hydrophobic mismatch between the lengths of the transmembrane helices of MAL and membrane lipids. These data place MAL as a key component in the organization of membrane domains that could potentially serve as membrane sorting platforms.
Investigating the link between Nephrops norvegicus burrow density and sediment composition in Scottish waters
Authors: Campbell Neil , Allan Lynda , Weetman Adrian , Dobby Helen
Published: June 2009

Campbell, N., Allan, L., Weetman, A., and Dobby, H. 2009. Investigating the link between Nephrops norvegicus burrow density and sediment composition in Scottish waters. – ICES Journal of Marine Science, 66: 2052–2059. Nephrops norvegicus is a burrowing decapod, found in the North Atlantic and Mediterranean Sea at depths of 10–1200 m, and currently the most valuable species taken by the commercial fishing industry in Scotland. It constructs and inhabits extensive burrow complexes in suitable muddy sediments. Owing to its variable emergence patterns, catch rates from traditional trawl surveys are not considered a good indicator of population size. Nephrops populations around Scotland are assessed using an underwater television (UWTV) survey method. Sediment samples are collected at the end of each UWTV deployment. This study focuses on two areas off the coast of Scotland and investigates the accuracy of the sediment maps used for assessment purposes, and the relationship between Nephrops burrow density and sediment composition, over the period 2002–2007. Nephrops have a stock-specific relationship with the sediment they inhabit, which retains the same form through fluctuations in population size.
Associations of lobsters (Homarus americanus) off southwestern Nova Scotia with bottom type from images and geophysical maps
Authors: Tremblay M. John , Smith Stephen J. , Todd Brian J. , Clement Pierre M. , McKeown David L.
Published: June 2009

Tremblay, M. J., Smith, S. J., Todd, B. J., Clement, P. M., and McKeown, D. L. 2009. Associations of lobsters (Homarus americanus) off southwestern Nova Scotia with bottom type from images and geophysical maps. – ICES Journal of Marine Science, 66: 2060–2067. Images from an underwater towed vehicle (Towcam) were used to estimate densities and to evaluate bottom-type associations of lobsters (Homarus americanus), crabs (Cancer spp.), and scallops (Placopecten magellanicus). Images were obtained in October 2006 along 14 line-transects off southwestern Nova Scotia in an area with productive lobster and scallop fisheries. Lobsters were observed in 4% of the 2044 images, crabs in 7%, and scallops in 40%. On sand, gravel, and cobble seabed, lobsters were readily observable. On rougher substrata with boulders, some lobsters were still evident either in the open or partially hidden in shelters. Estimated densities of lobsters from the images on some transects were 0.04 m−2, approximately half of the estimates of lobster density for adjacent inshore areas from scuba, but 34 times higher than estimates from scallop drags in the same area. Models of animal presence by bottom type were evaluated with categories that were (i) geophysically based (map of bottom type from geophysical characteristics) and (ii) image-based (sediment size from images). Significant relationships were evident with both types of seabed categorization, suggesting that it would be beneficial to stratify surveys using geophysical categories. Depth was also significant in determining presence/absence of lobsters and crabs. There is potential to develop indicators of lobster abundance using underwater imaging, and stratification by bottom type should be incorporated into surveys.
Capitalizing on nature: how to implement an ecosystem approach
Authors: Holt Alison R. , Hattam Caroline
Published: June 2009

The Natural Capital Initiative (
www.naturalcapitalinitiative.org.uk
) held its first conference ‘Valuing our life support systems’ at Savoy Place, London, from 29 April to 1 May 2009. The aim of the conference was to discuss different perspectives on, and solutions to, the conservation and sustainable use of ecosystem services. It particularly focused on the link between the environment and the economy, and how to implement an ecosystem approach to environmental management. This event brought together scientists across the natural and social sciences, alongside representatives from government, non-governmental organizations, business and industry.
Asymptotic expansions for solitary gravity-capillary waves in two and three dimensions
Authors: Ablowitz M. J. , Haut T. S.
Published: June 2009

High-order asymptotic series are obtained for two- and three-dimensional gravity-capillary solitary waves. In two dimensions, the first term in the asymptotic series is the well-known sech2solution of the Korteweg–de Vries equation; in three dimensions, the first term is the rational lump solution of the Kadomtsev–Petviashvili equation I. The two-dimensional series is used (with nine terms included) to investigate how small surface tension affects the height and energy of large-amplitude waves and waves close to the solitary version of Stokes’ extreme wave. In particular, for small surface tension, the solitary wave with the maximum energy is obtained. For large surface tension, the two-dimensional series is also used to study the energy of depression solitary waves. Energy considerations suggest that, for large enough surface tension, there are solitary waves that can get close to the fluid bottom. In three dimensions, analytic solutions for the high-order perturbation terms are computed numerically, and the resulting asymptotic series (to three terms) is used to obtain the speed versus maximum amplitude curve for solitary waves subject to sufficiently large surface tension. Finally, the above asymptotic method is applied to the Benney–Luke (BL) equation, and the resulting asymptotic series (to three terms) is verified to agree with the solitary-wave solution of the BL equation.
Simple conjugated polymer nanoparticles as biological labels
Authors: Green Mark , Howes Philip , Berry Catherine , Argyros Orestis , Thanou Maya
Published: June 2009

The use of nanoparticles in biology, especially in cellular imaging, is extremely promising and offers numerous advantages over existing organic dye systems. There are, however, constraints that need to be addressed before the use of such materials in mainstream clinical applications can be realized. One of the main concerns is the use of metal-containing particles that are potentially toxic or interfere with other diagnostic processes. Here, we present the use of simple conjugated polymer nanoparticles as alternative photostable cellular optical imaging agents.
Forecasting the limits of resilience: integrating empirical research with theory
Authors: Thrush Simon F. , Hewitt Judi E. , Dayton Paul K. , Coco Giovanni , Lohrer Andrew M. , Norkko Alf , Norkko Joanna , Chiantore Mariachiara
Published: June 2009

Despite the increasing evidence of drastic and profound changes in many ecosystems, often referred to as regime shifts, we have little ability to understand the processes that provide insurance against such change (resilience). Modelling studies have suggested that increased variance may foreshadow a regime shift, but this requires long-term data and knowledge of the functional links between key processes. Field-based research and ground-truthing is an essential part of the heuristic that marries theoretical and empirical research, but experimental studies of resilience are lagging behind theory, management and policy requirements. Empirically, ecological resilience must be understood in terms of community dynamics and the potential for small shifts in environmental forcing to break the feedbacks that support resilience. Here, we integrate recent theory and empirical data to identify ways we might define and understand potential thresholds in the resilience of nature, and thus the potential for regime shifts, by focusing on the roles of strong and weak interactions, linkages in meta-communities, and positive feedbacks between these and environmental drivers. The challenge to theoretical and field ecologists is to make the shift from hindsight to a more predictive science that is able to assist in the implementation of ecosystem-based management.
The MrpA, MrpB and MrpD subunits of the Mrp antiporter complex in Bacillus subtilis contain membrane-embedded and essential acidic residues
Authors: Kajiyama Yusuke , Otagiri Masato , Sekiguchi Junichi , Kudo Toshiaki , Kosono Saori
Published: June 2009

Bacillus subtilis Mrp is a unique Na+/H+ antiporter with a multicomponent structure consisting of the mrpABCDEFG gene products. We have previously reported that the conserved and putative membrane-embedded Glu-113, Glu-657, Asp-743 and Glu-747 of MrpA (ShaA) are essential for the transport function. In this study, we further investigated the functional involvement of the equivalent conserved acidic residues of other Mrp proteins in heterologous Escherichia coli and natural B. subtilis backgrounds. Asp-121 of MrpB and Glu-137 of MrpD were additionally identified to be essential for the transport function in both systems. Glu-137 of MrpD and Glu-113 of MrpA were found to be conserved in the homologous MrpD/MrpA proteins as well as in the homologous subunits of H+-translocating primary active transporters such as Nuo and Mbh, suggesting their critical role in ion binding. The remaining essential acidic residues clustered in the C-terminal domain of MrpA (Glu-657, Asp-743 and Glu-747) and MrpB (Asp-121); these subunits are fused in some Gram-negative species. It is possible that the MrpA, MrpB and MrpD subunits, which contain essential transmembrane acidic residues, form the ion translocation site(s) of the Mrp antiporter complex.