Local Structural Differences Research Articles

PIP2 Phospholipid-Induced Aggregation of Tau Filaments Probed by Tip-Enhanced Raman Spectroscopy.

The morphology and secondary structure of peptide fibers formed by aggregation of tubulin-associated unit (Tau) fragments (K18), in the presence of the inner cytoplasmic membrane phosphatidylinositol component (PIP2 ) or heparin sodium (HS) as cofactors, are determined with nanoscale (<10 nm) spatial resolution. By means of tip-enhanced Raman spectroscopy (TERS), the inclusion of PIP2 lipids in fibers is determined based on the observation of specific C=O ester vibration modes. Moreover, analysis of amide I and amide III bands suggests that the parallel β-sheet secondary structure content is lower and the random coil content is higher for fibers grown from the PIP2 cofactor instead of HS. These observations highlight the occurrence of some local structural differences between these fibers. This study constitutes the first nanoscale structural characterization of Tau/phospholipid aggregates, which are implicated in deleterious mechanisms on neural membranes in Alzheimer's disease.

PIP2 Phospholipid‐Induced Aggregation of Tau Filaments Probed by Tip‐Enhanced Raman Spectroscopy

AbstractThe morphology and secondary structure of peptide fibers formed by aggregation of tubulin‐associated unit (Tau) fragments (K18), in the presence of the inner cytoplasmic membrane phosphatidylinositol component (PIP2) or heparin sodium (HS) as cofactors, are determined with nanoscale (&lt;10 nm) spatial resolution. By means of tip‐enhanced Raman spectroscopy (TERS), the inclusion of PIP2 lipids in fibers is determined based on the observation of specific C=O ester vibration modes. Moreover, analysis of amide I and amide III bands suggests that the parallel β‐sheet secondary structure content is lower and the random coil content is higher for fibers grown from the PIP2 cofactor instead of HS. These observations highlight the occurrence of some local structural differences between these fibers. This study constitutes the first nanoscale structural characterization of Tau/phospholipid aggregates, which are implicated in deleterious mechanisms on neural membranes in Alzheimer's disease.

The local structural differences in amorphous Ge-Sb-Te alloys

Chalcogenide alloys in pseudobinary line between Sb2Te3 and GeTe are extensively utilied in phase change memories for optical and electronic contrast between crystalline and amorphous phases. Different from the crystalline structure, the understanding of amorphous structures is still insufficient due to disorder and distortion. By employing first-principle molecular dynamics simulations and atomistic cluster alignment analysis, the short-range orders and the associated distortions of amorphous Sb2Te3, Ge1Sb2Te4, Ge2Sb2Te5, Ge3Sb2Te6 and GeTe are investigated to explore the origin of nature difference. The results reveal that GeGe and SbSb bonds present a notable competitive mechanism with GeTe content. The GeTe content has a great influence on Ge- and Te-centered short-range orders but little influence on the structures of Sb-centered clusters, especially for the octahedral sites and unidentified structures. The tetrahedrons in Ge-centered clusters of each alloy show a close proportion, but the fraction of tetrahedrons in total clusters increases with the increasing GeTe content due to the increase in the ratio of Ge atom. As for the distortions of clusters, the distorted tetrahedrons in Ge2Sb2Te5 are closest to the standard tetrahedron, the Peierls distortion of Ge-centered 6-fold octahedron reduces with an increase in GeTe content whereas that of Sb-centered 6-fold octahedron shows a little change. Additionally, it is found that GeTe content can inhibit the formation of nanocavity but contribute to the formation of the odd rings. Our findings deepens the understanding of amorphous structures, which can promote the design and application of phase-change materials.

The glass-forming ability explained from local structural differences by NMR between glasses and crystals in alkali metaphosphates

The glass forming ability of inorganic substances has traditionally been evaluated in kinetic terms related to the rate of spontaneous crystallization of their melts, which is related to viscosity from the macroscopic point of view. However, differences or similarities between the local structures of glasses and crystals of the same composition could have an additional influence on the kinetic ability to form a stable glass or a crystal from a melt. In this work, the local structure of alkali metaphosphate glasses and crystals has been analyzed by means of 31P MAS-NMR to demonstrate that the ability to form a glass is directly related to the differences between the atomic organization in the glassy states and the structure of the stable crystals at lower temperatures. This implies that chemical compositions having a similar atomic order in their glass and crystal structures will not easily develop the disordered long-range structure of glass.

From individuals to communities: How singleton invasive pine saplings lead to biodiversity change in the Brazilian Cerrado hotspot

AbstractQuestionsHow do newly established species interact with existing assemblage members to alter local biodiversity? This question is especially topical given growing concerns about increased temporal turnover levels relative to background rates. Pine (Pinus spp.), a major invasive taxon in the Southern Hemisphere, is progressively dominating remaining fragments of the Brazilian savanna (Cerrado), a biodiversity hotspot. Because the Cerrado's diversity is linked to habitat heterogeneity we argue that the impact of these invasive singleton pines will be mediated by differences in local habitat structure. Here we use isolated invasive pines (Pinus elliottii) in the Cerrado as a study system to test the prediction that changes in the diversity of native communities, in the presence of newly established exotic individuals, will be greatest in the dominant vegetation layer of a habitat.LocationItirapina Ecological Station, southeast of Brazil.MethodsWe used a stratified random survey in 5 m × 5 m pairs of plots invaded by a single pine individual, each matched by control uninvaded plots; both shrub and grass vegetation layers were sampled in both habitats. In total, 300 plots were sampled, 114 in the shrub‐dominated campo sujo and 186 in the grass‐dominated campo úmido.ResultsOver 400 plant species were recorded. In both habitats, we detect marked shifts in species richness of the dominant vegetation layer. In line with our prediction, the nature of these changes is mediated by local habitat structure. We find significantly reduced species richness in the shrub layer of the shrub‐dominated habitat, but elevated species richness in the grass layer of the grass‐dominated habitat in invaded sites (vs. control). In the grass layer of campo úmido, pine initially decreases dominance thus allowing more species to colonize the plots.ConclusionsThe shape of the diversity vs. establishment time relationship is layer‐dependent, with a significant relationship between dominance/evenness and pine size in the grass layer but no relationship in the shrub layer. Our results show that, although complex, the consequences for local biodiversity of non‐native species establishment are not haphazard and thus contribute to the understanding of species co‐existence.

Solution structure of the N-terminal domain of proteasome lid subunit Rpn5

The 26S proteasome is the major protein degradation machinery in living cells. The Rpn5 protein is one scaffolding subunit in the lid subcomplex of the 19S regulatory particle in the proteasome holoenzyme. Herein we report the solution structure of the N-terminal domain (NTD) of yeast Rpn5 at high resolution by NMR spectroscopy. The results show that Rpn5 NTD adopts α-solenoid-like fold in right-handed superhelical configuration formed by a number of α-helices. Structural comparisons with currently available cryo-EM structures reveal local structural differences in the first three helices between yeast and human Rpn5. The results further highlight the conformational flexibility in three possible protein interaction sites. Moreover, the structures of the NTD show large variations among different PCI-containing Rpn subunits. Our current results provide atomic-level structural basis for further investigations of protein-protein interactions and the proteasome assembly pathway.

Microsecond MD simulations of human CYP2D6 wild-type and five allelic variants reveal mechanistic insights on the function.

Characterization of cytochrome P450 2D6 (CYP2D6) and the impact of the major identified allelic variants on the activity of one of the most dominating drug-metabolising enzymes is essential to increase drug safety and avoid adverse reactions. Microsecond molecular dynamics simulations have been performed to capture the dynamic signatures of this complex enzyme and five allelic variants with diverse enzymatic activity. In addition to the apo simulations, three substrates (bufuralol, veliparib and tamoxifen) and two inhibitors (prinomastat and quinidine) were included to explore their influence on the structure and dynamical features of the enzyme. Our results indicate that the altered enzyme activity can be attributed to changes in the hydrogen bonding network within the active site, and local structural differences in flexibility, position and shape of the binding pocket. In particular, the increased (CYP2D6*53) or the decreased (CYP2D6*17) activity seems to be related to a change in dynamics of mainly the BC loop due to a modified hydrogen bonding network around this region. In addition, the smallest active site volume was found for CYP2D6*4 (no activity). CYP2D6*2 (normal activity) showed no major differences in dynamic behaviour compared to the wild-type.

Cascade Reactions of α‐Phenylcinnamic Acid to Polycyclic Compounds Promoted by High Valent Transition Metal Halides

Abstractα‐Phenylcinnamic acid converts into polycyclic derivatives by interaction with high valent transition metal halides in chloroform at reflux temperature. Different products, featured by local structural differences depending on the nature of the metal halide system (i. e. WCl6, PCl5/NbF5 or PCl5/NbCl5), are easily isolable after treatment with water. In particular, WCl6 configures as an efficient multitasking agent, working as 1) chlorinator of the carboxylic acid function, 2) catalytic precursor for intra‐ and intermolecular rearrangements, and 3) catalytic precursor for Baeyer‐Villiger lactonization in water at ambient temperature, exploiting air as oxidant. The products have been purified by alumina chromatography, and identified by analytical and spectroscopic (IR, NMR) techniques, and by single crystal X‐ray diffraction in three cases. Their formation probably involves a common reaction pathway which has been rationalized by DFT calculations.

X-ray Scattering and O-O Pair-Distribution Functions of Amorphous Ices.

The structure factor and oxygen–oxygen pair-distribution functions of amorphous ices at liquid nitrogen temperature (T = 77 K) have been derived from wide-angle X-ray scattering (WAXS) up to interatomic distances of r = 23 Å, where local structure differences between the amorphous ices can be seen for the entire range. The distances to the first coordination shell for low-, high-, and very-high-density amorphous ice (LDA, HDA, VHDA) were determined to be 2.75, 2.78, and 2.80 Å, respectively, with high accuracy due to measurements up to a large momentum transfer of 23 Å–1. Similarities in pair-distribution functions between LDA and supercooled water at 254.1 K, HDA and liquid water at 365.9 K, and VHDA and high-pressure liquid water were found up to around 8 Å, but beyond that at longer distances, the similarities were lost. In addition, the structure of the high-density amorphous ices was compared to high-pressure crystalline ices IV, IX , and XII, and conclusions were drawn about the local ordering.

Evolution of the Local Structure within Chromophoric Mn-O5 Trigonal Bipyramids in YMn1- xIn xO3 with Composition.

We have investigated the local environment around Mn3+ and In3+ ions in YMn1- xIn xO3 chromophores to understand the origin of the intense blue color for small values of x in these solid solutions. While X-ray diffraction results provide an average description of the trigonal bipyramidal (TBP) units about Mn/In atoms with five oxygens surrounding the cation, the X-ray absorption near edge structure (XANES) as well as extended X-ray absorption fine structure (EXAFS) of these materials clearly suggest the presence of two different TBP environments, one of which is similar to MnO5 TBP in YMnO3. EXAFS in conjunction with first-principles calculations show that replacing larger In3+ ions by smaller Mn3+ ones additionally gives rise to another TBP strongly distorted along the axial direction, expanding one of the axial Mn-O bonds by ∼11%. The relative fraction of these two environments changes in close agreement with the global stoichiometry with the elongated TBP, therefore, being dominant in the regime of the low Mn content. This local structural difference is responsible for the intense, but relatively narrow, absorption feature in the red-yellow region of the absorption spectrum, and hence YMn1- xIn xO3 appears blue for small Mn dopings. This distortion is relatively less abundant in Mn-rich compositions, and therefore, such compositions appear black, controlled by the wide absorption feature of the trigonal bipyramid coordination with Mn-O bond lengths that are essentially the same as those in YMnO3, covering the entire visible range. The chromophore properties are, thus, governed by the ratio of these two MnO5 TBP environments, one with a characteristic optical absorption giving it a blue color and the other absorbing over the entire visible range.

Celebrating the 25th International Conference of The International Environmetrics Society

Celebrating the 25th International Conference of The International Environmetrics Society

Genome wide analyses uncover allele-specific RNA editing in human and mouse.

RNA editing is one of the most common RNA level modifications that potentially generate amino acid changes similar to those resulting from genomic nonsynonymous mutations. However, unlike DNA level allele-specific modifications such as DNA methylation, it is currently unknown whether RNA editing displays allele-specificity across tissues and species. Here, we analyzed allele-specific RNA editing in human tissues and from brain tissues of heterozygous mice generated by crosses between divergent mouse strains and found a high proportion of overlap of allele-specific RNA editing sites between different samples. We identified three allele-specific RNA editing sites cause amino acid changes in coding regions of human and mouse genes, whereas their associated SNPs yielded synonymous differences. In vitro cellular experiments confirmed that sequences differing at a synonymous SNP can have differences in a linked allele-specific RNA editing site with nonsynonymous implications. Further, we demonstrate that allele-specific RNA editing is influenced by differences in local RNA secondary structure generated by SNPs. Our study provides new insights towards a better comprehension of the molecular mechanism that link SNPs with human diseases and traits.

Protective Carbon Overlayers from 2,3-Naphthalenediol Pyrolysis on Mesoporous SiO₂ and Al₂O₃ Analyzed by Solid-State NMR.

Hydrothermally stable carbon overlayers can protect mesoporous oxides (SiO2 and Al2O3) from hydrolysis during aqueous-phase catalysis. Overlayers made at 800 °C by pyrolysis of 2,3-naphthalenediol deposited out of acetone solution were analyzed by solid-state 13C nuclear magnetic resonance (NMR) spectroscopy. Power absorption due to sample conductivity was prevented by diluting the sample in nonconductive and background-free tricalcium phosphate. While pyrolysis on SiO2 produced a predominantly aromatic carbon film, at least 15% of nonaromatic carbon (sp3-hybridized C as well as C=O) was observed on γ-Al2O3. These species were not derived from residual solvent, according to spectra of the same material treated at 400 °C. The sp3-hybridized C exhibited weak couplings to hydrogen, short spin-lattice relaxation times, and unusually large shift anisotropies, which are characteristics of tetrahedral carbon with high concentrations of unpaired electrons. Moderate heat treatment at 400 °C on SiO2 and Al2O3 resulted in yellow-brown and nearly black samples, respectively, but the darker color on Al2O3 did not correspond to more extensive carbonization. Aromatic carbon bonded to hydrogen remained predominant and the peaks of naphthalenediol were still recognizable; however, some of the chemical shifts differed by up to 5 ppm, indicating significant differences in local structure. On SiO2, additional sharp peaks were detected and attributed to 1/3 of the 2,3-naphthalene molecules undergoing fast, nearly isotropic motions.

Tracer Transport Probes Relaxation and Structure of Attractive and Repulsive Glassy Liquids.

Dynamic coupling of small penetrants to slow, cooperative relaxations within crowded cells, supercooled liquids, and polymer matrices has broad consequences for applications ranging from drug delivery to nanocomposite processing. Interactions between the constituents of these and other disordered media alter the cooperative relaxations, but their effect on penetrant dynamics remains incompletely understood. We use molecular dynamics simulations to show that the motions of hard-sphere tracer particles probe differences in local structure and cooperative relaxation processes in attractive and repulsive glassy liquid matrices with equal bulk packing fractions and long-time diffusivities. Coupling of the tracer dynamics to collective relaxations in each matrix affects the shape of tracer trajectories, which are fractal within the repulsive matrix and more compact in the attractive. These results reveal that the structure of relaxations controls penetrant transport and dispersion in cooperatively relaxing systems and provide insight into dynamical heterogeneity within glassy liquids.

The Network Structure of Childhood Psychopathology in International Adoptees

International adoptees are at an increased risk of emotional and behavioral problems, especially those who are adopted at an older age. We took a new approach in our study of the network structure and predictability of emotional and behavioral problems in internationally adopted children in Finland. Our sample was from the on-going adoption study and comprised 778 internationally adopted children (387 boys and 391 girls, mean age 10.5 (SD 3.4) years). Networks were estimated using Gaussian graphical models and lasso regularization for all the children, and separately for those who were adopted at different ages. The results showed that anxiety/depressive symptoms, social problems, and aggressiveness were the most central symptom domains. Somatic symptoms were the least central and had the weakest effect on the other domains. Similarly, aggressiveness, social problems, and attention problems were high in terms of predictability (73–65%), whereas internalizing problems were relatively low (28–56%). There were clear but local age-group differences in network structure, symptom centrality, and predictability. According to our findings, network models provide important additional information about the centrality and predictability of specific symptom domains, and thus may facilitate targeted interventions among international adoptees.

Structure activity relationship (SAR) toxicological assessments: The role of expert judgment

Structure activity relationships (SAR) and read-across are widely used animal alternative approaches for filling toxicological data gaps. A framework describing the use of expert judgment in evaluating analogs for SAR has been published and widely cited, however, reliance on expert judgment can introduce inconsistent results across experts and hinder transparency. Here we explore the use of a quantitative similarity score between an analog and a Structure of Interest (SOI) to see if these scores correlate with the expert judgement-based suitability rankings. We find these global similarity scores representing a “whole-molecule” view of similarity to be insensitive to differences in local structure which may be important for toxicity, and, therefore, cannot be substituted for expert judgement-based similarity rankings. In this paper, we suggest that the next step in the progression of SAR approaches retains the insights from expert judgment, but facilitates consistency and transparency through the development of rating “rules”. This report outlines and defines analog rating rules for several compound categories. While not comprehensive, the exercises demonstrate the development of rules for categories with a large spread in molecular weight and alkyl chain length and explains the advantages that we see in this approach compared to relying solely on a computational approach or an unstructured expert judgement approach. These rules may be incorporated into analog searching work flows to define boundaries for analogs “suitable” for read-across.

Working Memory and Decision-Making in a Frontoparietal Circuit Model.

Working memory (WM) and decision-making (DM) are fundamental cognitive functions involving a distributed interacting network of brain areas, with the posterior parietal cortex (PPC) and prefrontal cortex (PFC) at the core. However, the shared and distinct roles of these areas and the nature of their coordination in cognitive function remain poorly understood. Biophysically based computational models of cortical circuits have provided insights into the mechanisms supporting these functions, yet they have primarily focused on the local microcircuit level, raising questions about the principles for distributed cognitive computation in multiregional networks. To examine these issues, we developed a distributed circuit model of two reciprocally interacting modules representing PPC and PFC circuits. The circuit architecture includes hierarchical differences in local recurrent structure and implements reciprocal long-range projections. This parsimonious model captures a range of behavioral and neuronal features of frontoparietal circuits across multiple WM and DM paradigms. In the context of WM, both areas exhibit persistent activity, but, in response to intervening distractors, PPC transiently encodes distractors while PFC filters distractors and supports WM robustness. With regard to DM, the PPC module generates graded representations of accumulated evidence supporting target selection, while the PFC module generates more categorical responses related to action or choice. These findings suggest computational principles for distributed, hierarchical processing in cortex during cognitive function and provide a framework for extension to multiregional models.SIGNIFICANCE STATEMENT Working memory and decision-making are fundamental "building blocks" of cognition, and deficits in these functions are associated with neuropsychiatric disorders such as schizophrenia. These cognitive functions engage distributed networks with prefrontal cortex (PFC) and posterior parietal cortex (PPC) at the core. It is not clear, however, what the contributions of PPC and PFC are in light of the computations that subserve working memory and decision-making. We constructed a biophysical model of a reciprocally connected frontoparietal circuit that revealed shared and distinct functions for the PFC and PPC across working memory and decision-making tasks. Our parsimonious model connects circuit-level properties to cognitive functions and suggests novel design principles beyond those of local circuits for cognitive processing in multiregional brain networks.

Disconnecting structure and dynamics in glassy thin films

Nanometrically thin glassy films depart strikingly from the behavior of their bulk counterparts. We investigate whether the dynamical differences between a bulk and thin film polymeric glass former can be understood by differences in local microscopic structure. Machine learning methods have shown that local structure can serve as the foundation for successful, predictive models of particle rearrangement dynamics in bulk systems. By contrast, in thin glassy films, we find that particles at the center of the film and those near the surface are structurally indistinguishable despite exhibiting very different dynamics. Next, we show that structure-independent processes, already present in bulk systems and demonstrably different from simple facilitated dynamics, are crucial for understanding glassy dynamics in thin films. Our analysis suggests a picture of glassy dynamics in which two dynamical processes coexist, with relative strengths that depend on the distance from an interface. One of these processes depends on local structure and is unchanged throughout most of the film, while the other is purely Arrhenius, does not depend on local structure, and is strongly enhanced near the free surface of a film.

Testing for local structure in spatiotemporal point pattern data

The detection of clustering structure in a point pattern is one of the main focuses of attention in spatiotemporal data mining. Indeed, statistical tools for clustering detection and identification of individual events belonging to clusters are welcome in epidemiology and seismology. Local second‐order characteristics provide information on how an event relates to nearby events. In this work, we extend local indicators of spatial association (known as LISA functions) to the spatiotemporal context (which will be then called LISTA functions). These functions are then used to build local tests of clustering to analyse differences in local spatiotemporal structures. We present a simulation study to assess the performance of the testing procedure, and we apply this methodology to earthquake data.

Effect of doping concentration on Nd-related photoluminescence in TiO2 with Al co-doping

Nd doped, Nd-Al co-doped anatase phase TiO2 thin films were fabricated on silicon substrates by laser ablation and post annealing. The result of measuring PL spectra showed intense emissions from a luminescent centre of Nd3+ ions in these thin films. The luminescence of Nd-Al co-doped samples were stronger and broader than only Nd doped samples. Doping concentration of Nd determined suitable co-doping concentration of Al and post annealing temperature. Also there is the difference of shape of the PL spectra which indicates that the difference of local fine structure around Nd. Based on these facts, XAFS spectra was measured and suggested that the coordination around Nd was changed by this Al-co-doping.