A semi-quantitative approach to deriving a model structure for the uptake of organic chemicals by vegetation

An expert elicitation exercise was undertaken to determine those components and processes that are most important for modeling plant uptake of organic chemicals. The state of our knowledge of these processes was also assessed. This semi-quantitative analysis allowed the construction of an idealized model with seven compartments; soil bulk, soil water, roots, stem, leaves, fruit, and air. Three main areas were identified further research: 1) the uptake of organic chemicals by fruit; 2) the internal transfer of organic chemicals between plant structures (e.g., stem and leaves); and 3) the transfer via the soil-air-plant pathway. Until new data becomes available to quantify these processes, it is proposed that an equilibrium partitioning approach is used between plant components other than fruit or that models consist of both an edible and inedible compartment.

The changing structure of diets in the European Union in relation to healthy eating guidelines

Objective: Our objective in this paper is to assess diets in the European Union (EU) in relation to the recommendations of the recent World Health Organization/Food and Agriculture Organization expert consultation and to show how diets have changed between 1961 and 2001. Data and methods: Computations make use of FAOSTAT data on food availability at country level linked to a food composition database to convert foods to nutrients. We further explore the growing similarity of diets in the EU by making use of a consumption similarity index. The index provides a single number measure of dietary overlap between countries. Results: The data confirm the excessive consumption by almost all countries of saturated fats, cholesterol and sugars, and the convergence of nutrient intakes across the EU. Whereas in 1961 diets in several European countries were more similar to US diets than to those of other European countries, this is no longer the case; moreover, while EU diets have become more homogeneous, the EU as a whole and the USA have become less similar over time. Conclusions: Although the dominant cause of greater similarity in EU diets over the period studied is increased intakes in Mediterranean countries of saturated fats, cholesterol and sugar, also important are reductions in saturated fat and sugar in some Northern European countries. This suggests that healthy eating messages are finally having an impact on diets; a distinctly European diet may also be emerging.

Arthropod diversity and community structure in relation to land use in the mekong delta, vietnam

Declining biodiversity in agro-ecosystems, caused by intensification of production or expansion of monocultures, is associated with the emergence of agricultural pests. Understanding how land-use and management control crop-associated biodiversity is, therefore, one of the key steps towards the prediction and maintenance of natural pest-control. Here we report on relationships between land-use variables and arthropod community attributes (for example, species diversity, abundance and guild structure) across a diversification gradient in a rice-dominated landscape in the Mekong delta, Vietnam. We show that rice habitats contained the most diverse arthropod communities, compared with other uncultivated and cultivated land-use types. In addition, arthropod species density and Simpson's diversity in flower, vegetable and fruit habitats was positively related to rice cover in the local landscape. However, across the landscape as a whole, reduction in heterogeneity and the amount of uncultivated cover was associated, generally, with a loss of diversity. Furthermore, arthropod species density in tillering and flowering stages of rice was positively related to crop and vegetation richness, respectively, in the local landscape. Differential effects on feeding guilds were also observed in rice-associated communities with the proportional abundance of predators increasing and the proportional abundance of detritivores decreasing with increased landscape rice cover. Thus, we identify a range of rather complex, sometimes contradictory patterns concerning the impact of rice cover and landscape heterogeneity on arthropod community attributes. Importantly, we conclude that that land-use change associated with expansion of monoculture rice need not automatically impact diversity and functioning of the arthropod community.

The relation between content and structure in language production: an analysis of speech errors in semantic dementia

In order to explore the impact of a degraded semantic system on the structure of language production, we analysed transcripts from autobiographical memory interviews to identify naturally-occurring speech errors by eight patients with semantic dementia (SD) and eight age-matched normal speakers. Relative to controls, patients were significantly more likely to (a) substitute and omit open class words, (b) substitute (but not omit) closed class words, (c) substitute incorrect complex morphological forms and (d) produce semantically and/or syntactically anomalous sentences. Phonological errors were scarce in both groups. The study confirms previous evidence of SD patients’ problems with open class content words which are replaced by higher frequency, less specific terms. It presents the first evidence that SD patients have problems with closed class items and make syntactic as well as semantic speech errors, although these grammatical abnormalities are mostly subtle rather than gross. The results can be explained by the semantic deficit which disrupts the representation of a pre-verbal message, lexical retrieval and the early stages of grammatical encoding.

Gochnatia polymorpha (Less.) Cabrera (Asteraceae) changes in leaf structure due to differences in light and edaphic conditions

Gochnatia polymorpha (Less.) Cabrera é uma espécie de Asteraceae com ampla distribuição no bioma cerrado, sendo encontrada em diversas fisionomias florestais da região sudeste do Brasil. O presente estudo descreve alguns caracteres anatômicos foliares dessa espécie e os analisa quantitativamente em função de sua ocorrência nas formações florestais e também das diferenças de luminosidade. Foram encontradas diferenças quantitativas em todos os parâmetros anatômicos analisados. Os resultados demonstram que a alta plasticidade anatômica foliar nesta espécie pode ser considerada como uma vantagem adaptativa que a permite ocorrer em diversos ambientes do cerrado.

Bulliform cells in Loudetiopsis chrysothrix (Nees) Conert and Tristachya leiostachya Nees (Poaceae): structure in relation to function

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Surface structure and electronic properties of Pt-Fe/C nanocatalysts and their relation with catalytic activity for oxygen reduction

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Quantitative structural analysis of the transition from LT-LixCoO2 to HT-LixCoO2 using the rietveld method: correlation between structure and electrochemical performance

A quantitative phase analysis was made of LiXCoO2 powders obtained by two distinct chemical methodologies at different temperatures (from 400 to 700degreesC). A phase analysis was made using Rietveld refinements based on X-ray diffraction data, considering the LiXCoO2 powders as a multiphase system that simultaneously contained two main phases with distinct, layered and spinel-type structures. The sults showed the coexistence of both structures in LiXCoO2 obtained at low temperature (400 and 500degreesC), although only the layered structure was detected at higher temperatures (600 and 700degreesC, regardless of the chemical powder process employed. The electrochemical performance, evaluated mainly by the cycling reversibility of LiXCoO2 in the form of cathode insertion electrodes, revealed that there is a close correlation between structural features and the electrochemical response, with one of the redox processes (3.3 v/3.9 v) associated only with the presence of the spinel-type structure. (C) 2003 Elsevier B.V. All rights reserved.

Quantitative structural analysis of the transition from LT-Li xCoO2 to HT-LixCoO2 using the rietveld method: Correlation between structure and electrochemical performance

A quantitative phase analysis was made of LixCoO2 powders obtained by two distinct chemical methodologies at different temperatures (from 400 to 700°C). A phase analysis was made using Rietveld refinements based on X-ray diffraction data, considering the Li xCoO2 powders as a multiphase system that simultaneously contained two main phases with distinct, layered and spinel-type structures. The results showed the coexistence of both structures in LixCoO 2 obtained at low temperature (400 and 500°C), although only the layered structure was detected at higher temperatures (600 and 700°C), regardless of the chemical powder process employed. The electrochemical performance, evaluated mainly by the cycling reversibility of Li xCoO2 in the form of cathode insertion electrodes, revealed that there is a close correlation between structural features and the electrochemical response, with one of the redox processes (3.3 v/3.9 v) associated only with the presence of the spinel-type structure. © 2003 Elsevier B.V. All rights reserved.

Relation between green spaces and bird community structure in an urban area in Southeast Brazil

Increased urbanization typically leads to an increase in abundance of a few species and a reduction in bird species richness. Understanding the structure of biotic communities in urban areas will allow us to propose management techniques and to decrease conflicts between wild species and human beings. The objective of this study was to describe the structure of the bird community in an urban ecosystem. The study was carried out in the city of Taubaté in southeastern Brazil. Point-counts were established in areas with different levels of tree density ranging from urban green spaces to predominantly built-up areas. We looked for a correlation between the richness/abundance of birds and the size of the area surveyed, the number of houses, the number of tree species and the number of individual trees. The results of multiple regression showed that bird richness had a direct relationship with vegetation complexity. The abundance and diversity of tree species were better predictors of bird species than the number of houses and size of the area surveyed. We discuss implications of this study for conservation and management of bird diversity in urban areas, such as the need to increase green areas containing a large diversity of native plant species. © 2011 Springer Science+Business Media, LLC.

Echinococcus granulosus Antigen B Structure: Subunit Composition and Oligomeric States

Background: Antigen B (AgB) is the major protein secreted by the Echinococcus granulosus metacestode and is involved in key host-parasite interactions during infection. The full comprehension of AgB functions depends on the elucidation of several structural aspects that remain unknown, such as its subunit composition and oligomeric states. Methodology/Principal Findings: The subunit composition of E. granulosus AgB oligomers from individual bovine and human cysts was assessed by mass spectrometry associated with electrophoretic analysis. AgB8/1, AgB8/2, AgB8/3 and AgB8/4 subunits were identified in all samples analyzed, and an AgB8/2 variant (AgB8/2v8) was found in one bovine sample. The exponentially modified protein abundance index (emPAI) was used to estimate the relative abundance of the AgB subunits, revealing that AgB8/1 subunit was relatively overrepresented in all samples. The abundance of AgB8/3 subunit varied between bovine and human cysts. The oligomeric states formed by E. granulosus AgB and recombinant subunits available, rAgB8/1, rAgB8/2 and rAgB8/3, were characterized by native PAGE, light scattering and microscopy. Recombinant subunits showed markedly distinct oligomerization behaviors, forming oligomers with a maximum size relation of rAgB8/3 >rAgB8/2>rAgB8/1. Moreover, the oligomeric states formed by rAgB8/3 subunit were more similar to those observed for AgB purified from hydatid fluid. Pressure-induced dissociation experiments demonstrated that the molecular assemblies formed by the more aggregative subunits, rAgB8/2 and rAgB8/3, also display higher structural stability. Conclusions/Significance: For the first time, AgB subunit composition was analyzed in samples from single hydatid cysts, revealing qualitative and quantitative differences between samples. We showed that AgB oligomers are formed by different subunits, which have distinct abundances and oligomerization properties. Overall, our findings have significantly contributed to increase the current knowledge on AgB expression and structure, highlighting issues that may help to understand the parasite adaptive response during chronic infection.

Structure and Ionic Conductivity in the Mixed-Network Former Chalcogenide Glass System [Na2S](2/3)[(B2S3)(x)(P2S5)(1-x)](1/3)

Glasses in the system [Na2S](2/3)[(B2S3)(x)(P2S5)(1-x)](1/3) (0.0 <= x <= 1.0) were prepared by the melt quenching technique, and their properties were characterized by thermal analysis and impedance spectroscopy. Their atomic-level structures were comprehensively characterized by Raman spectroscopy and B-11, P-31, and Na-23 high resolution solid state magic-angle spinning (MAS) NMR techniques. P-31 MAS NMR peak assignments were made by the presence or absence of homonuclear indirect P-31-P-31 spin-spin interactions as detected using homonuclear J-resolved and refocused INADEQUATE techniques. The extent of B-S-P connectivity in the glassy network was quantified by P-31{B-11} and B-11{P-31} rotational echo double resonance spectroscopy. The results clearly illustrate that the network modifier alkali sulfide, Na2S, is not proportionally shared between the two network former components, B and P. Rather, the thiophosphate (P) component tends to attract a larger concentration of network modifier species than predicted by the bulk composition, and this results in the conversion of P2S74-, pyrothiophosphate, Na/P = 2:1, units into PS43-, orthothiophosphate, Na/P = 3:1, groups. Charge balance is maintained by increasing the net degree of polymerization of the thioborate (B) units through the formation of covalent bridging sulfur (BS) units, B S B. Detailed inspection of the B-11 MAS NMR spectra reveals that multiple thioborate units are formed, ranging from neutral BS3/2 groups all the way to the fully depolymerized orthothioborate (BS33-) species. On the basis of these results, a comprehensive and quantitative structural model is developed for these glasses, on the basis of which the compositional trends in the glass transition temperatures (T-g) and ionic conductivities can be rationalized. Up to x = 0.4, the dominant process can be described in a simplified way by the net reaction equation P-1 + B-1 reversible arrow P-0 + B-4, where the superscripts denote the number of BS atoms for the respective network former species. Above x = 0.4, all of the thiophosphate units are of the P-0 type and both pyro-(B-1) and orthothioborate (B-0) species make increasing contributions to the network structure with increasing x. In sharp contrast to the situation in sodium borophosphate glasses, four-coordinated thioborate species are generally less abundant and heteroatomic B-S-P linkages appear to not exist. On the basis of this structural information, compositional trends in the ionic conductivities are discussed in relation to the nature of the charge-compensating anionic species and the spatial distribution of the charge carriers.

Local order and electronic structure of Pb1-xLaxZr0.40Ti0.60O3 materials and its relation with ferroelectric properties

The knowledge of electronic and local structures is a fundamental step towards understanding the properties of ferroelectric ceramics. X-ray absorption near-edge structure (XANES) of Pb1-xLaxZr0.40Ti0.60O3 ferroelectric samples was measured in order to know how the local order and electronic structure are related to their ferroelectric property, which was tailored by the substitution of lead by lanthanum atoms. The analysis of XANES spectra collected at Ti K- and L-edges XANES showed that the substitution of Pb by La leads to a decrement of local distortion around Ti atoms on the TiO6 octahedron. The analysis of O K-edge XANES spectra showed that the hybridization between O 2p and Pb 6sp states is related to the displacement of Ti atoms in the TiO6 octahedra. Based on these results, it is possible to determine that the degree of ferroelectricity in these samples and the manifestation of relaxor behavior are directly related to the weakening of O 2p and Pb 6sp hybridization. (C) 2012 American Institute of Physics. [http://dx.doi.org/10.1063/1.4720472]

Computational analyses on the structure-function relation in ion channels

Ion channels are protein molecules, embedded in the lipid bilayer of the cell membranes. They act as powerful sensing elements switching chemicalphysical stimuli into ion-fluxes. At a glance, ion channels are water-filled pores, which can open and close in response to different stimuli (gating), and one once open select the permeating ion species (selectivity). They play a crucial role in several physiological functions, like nerve transmission, muscular contraction, and secretion. Besides, ion channels can be used in technological applications for different purpose (sensing of organic molecules, DNA sequencing). As a result, there is remarkable interest in understanding the molecular determinants of the channel functioning. Nowadays, both the functional and the structural characteristics of ion channels can be experimentally solved. The purpose of this thesis was to investigate the structure-function relation in ion channels, by computational techniques. Most of the analyses focused on the mechanisms of ion conduction, and the numerical methodologies to compute the channel conductance. The standard techniques for atomistic simulation of complex molecular systems (Molecular Dynamics) cannot be routinely used to calculate ion fluxes in membrane channels, because of the high computational resources needed. The main step forward of the PhD research activity was the development of a computational algorithm for the calculation of ion fluxes in protein channels. The algorithm - based on the electrodiffusion theory - is computational inexpensive, and was used for an extensive analysis on the molecular determinants of the channel conductance. The first record of ion-fluxes through a single protein channel dates back to 1976, and since then measuring the single channel conductance has become a standard experimental procedure. Chapter 1 introduces ion channels, and the experimental techniques used to measure the channel currents. The abundance of functional data (channel currents) does not match with an equal abundance of structural data. The bacterial potassium channel KcsA was the first selective ion channels to be experimentally solved (1998), and after KcsA the structures of four different potassium channels were revealed. These experimental data inspired a new era in ion channel modeling. Once the atomic structures of channels are known, it is possible to define mathematical models based on physical descriptions of the molecular systems. These physically based models can provide an atomic description of ion channel functioning, and predict the effect of structural changes. Chapter 2 introduces the computation methods used throughout the thesis to model ion channels functioning at the atomic level. In Chapter 3 and Chapter 4 the ion conduction through potassium channels is analyzed, by an approach based on the Poisson-Nernst-Planck electrodiffusion theory. In the electrodiffusion theory ion conduction is modeled by the drift-diffusion equations, thus describing the ion distributions by continuum functions. The numerical solver of the Poisson- Nernst-Planck equations was tested in the KcsA potassium channel (Chapter 3), and then used to analyze how the atomic structure of the intracellular vestibule of potassium channels affects the conductance (Chapter 4). As a major result, a correlation between the channel conductance and the potassium concentration in the intracellular vestibule emerged. The atomic structure of the channel modulates the potassium concentration in the vestibule, thus its conductance. This mechanism explains the phenotype of the BK potassium channels, a sub-family of potassium channels with high single channel conductance. The functional role of the intracellular vestibule is also the subject of Chapter 5, where the affinity of the potassium channels hEag1 (involved in tumour-cell proliferation) and hErg (important in the cardiac cycle) for several pharmaceutical drugs was compared. Both experimental measurements and molecular modeling were used in order to identify differences in the blocking mechanism of the two channels, which could be exploited in the synthesis of selective blockers. The experimental data pointed out the different role of residue mutations in the blockage of hEag1 and hErg, and the molecular modeling provided a possible explanation based on different binding sites in the intracellular vestibule. Modeling ion channels at the molecular levels relates the functioning of a channel to its atomic structure (Chapters 3-5), and can also be useful to predict the structure of ion channels (Chapter 6-7). In Chapter 6 the structure of the KcsA potassium channel depleted from potassium ions is analyzed by molecular dynamics simulations. Recently, a surprisingly high osmotic permeability of the KcsA channel was experimentally measured. All the available crystallographic structure of KcsA refers to a channel occupied by potassium ions. To conduct water molecules potassium ions must be expelled from KcsA. The structure of the potassium-depleted KcsA channel and the mechanism of water permeation are still unknown, and have been investigated by numerical simulations. Molecular dynamics of KcsA identified a possible atomic structure of the potassium-depleted KcsA channel, and a mechanism for water permeation. The depletion from potassium ions is an extreme situation for potassium channels, unlikely in physiological conditions. However, the simulation of such an extreme condition could help to identify the structural conformations, so the functional states, accessible to potassium ion channels. The last chapter of the thesis deals with the atomic structure of the !- Hemolysin channel. !-Hemolysin is the major determinant of the Staphylococcus Aureus toxicity, and is also the prototype channel for a possible usage in technological applications. The atomic structure of !- Hemolysin was revealed by X-Ray crystallography, but several experimental evidences suggest the presence of an alternative atomic structure. This alternative structure was predicted, combining experimental measurements of single channel currents and numerical simulations. This thesis is organized in two parts, in the first part an overview on ion channels and on the numerical methods adopted throughout the thesis is provided, while the second part describes the research projects tackled in the course of the PhD programme. The aim of the research activity was to relate the functional characteristics of ion channels to their atomic structure. In presenting the different research projects, the role of numerical simulations to analyze the structure-function relation in ion channels is highlighted.