Intakes and sources of isoflavones, lignans, enterolignans, coumestrol and soya-containing foods in the Norfolk arm of the European Prospective Investigation into Cancer and Nutrition (EPIC-Norfolk), from 7-day food diaries, using a newly updated database

Objective: A phytoestrogen-rich diet has been suggested to protect against a variety of common diseases but UK intake data on phytoestrogens or their food sources is sparse. This study aims to estimate the average intake of isoflavones, lignans, enterolignans and coumestrol from 7-day food diaries (7dFD), and to provide data on total isoflavone, lignan and phytoestrogen consumption by food group. Design: Development of a food composition database for twelve phytoestrogens and analysis of soya food and phytoestrogen consumption in a population-based study. Setting: Men and women, aged 40-79 years from the general population participating in EPIC-Norfolk between 1993 and 1997, with nutrient and food data from 7dFD. Subjects: A subset of 20 437 participants. Results: The median daily phytoestrogen intake for men was 1.20mg (interquartile range (IQR) 0.93-1.54 mg; mean 1.50 mg, SD 1.50 mg) and 0.89 mg for women (IQR 0.71-1.14 mg; mean 1.20 mg, SD 1.70 mg). In soya-consumers (SC), median daily intakes were higher: 2.86 mg in men (IQR – 1.30-7.27mg; mean 5.05 mg, SD 5.03 mg) and 3.14 mg in women (IQR – 1.09-7.33mg; mean 5.40 mg, SD 6.09 mg). In both men and women, bread made the greatest contribution to phytoestrogen intake – 40.7% and 35.7% respectively. In SC men and women, vegetable dishes and soya/goat’s/sheep’s milks were the main contributors – 42.6% and 18.9% in men and 38.8% and 29.1% in women, respectively. Conclusions: The ability to estimate phytoestrogen intake in Western populations more accurately will aid investigations into their suggested effects on health.

Processing reflexives in a second language: the timing of structural and discourse-level information

We report the results from two eye-movement monitoring experiments examining the processing of reflexive pronouns by proficient German-speaking learners of second language (L2) English. Our results show that the nonnative speakers initially tried to link English argument reflexives to a discourse-prominent but structurally inaccessible antecedent, thereby violating binding condition A. Our native speaker controls, in contrast, showed evidence of applying condition A immediately during processing. Together, our findings show that L2 learners’ initial focusing on a structurally inaccessible antecedent cannot be due to first language influence and is also independent of whether the inaccessible antecedent c-commands the reflexive. This suggests that unlike native speakers, nonnative speakers of English initially attempt to interpret reflexives through discourse-based coreference assignment rather than syntactic binding.

Structural features of condensed tannins affect in vitro ruminal methane production and fermentation characteristics

An in vitro study was conducted to investigate the effects of condensed tannins (CT) structural properties, i.e. average polymer size (or mean degree of polymerization); percentage of cis flavan-3-ols and percentage of prodelphinidins in CT extracts on methane production (CH4) and fermentation characteristics. CT were extracted from eight plants in order to obtain different CT types: black currant leaves, goat willow leaves, goat willow twigs, pine bark, red currant leaves, sainfoin plants, weeping willow catkins and white clover flowers. They were analysed for CT content and CT composition by thiolytic degradation, followed by HPLC analysis. Grass silage was used as a control substrate. Condensed tannins were added to the substrate at a concentration of 40 g/kg, with or without polyethylene glycol (+ or −PEG 6000 treatment) to inactivate tannins, and then incubated for 72 h in mixed buffered rumen fluid from three different lactating dairy cows per run. Total cumulative gas production (GP) was measured by an automated gas production system. During the incubation, 12 gas samples (10 μl) were collected from each bottle headspace at 0, 2, 4, 6, 8, 12, 24, 30, 36, 48, 56 and 72 h of incubation and analyzed for CH4. A modified Michaelis–Menten model was fitted to the CH4 concentration patterns and model estimates were used to calculate total cumulative CH4 production (GPCH4). Total cumulative gas production and GPCH4 curves were fitted using biphasic and monophasic modified Michaelis-Menten models, respectively. Addition of PEG increased GP, GPCH4, and CH4 concentration compared to the −PEG treatment. All CT types reduced GPCH4 and CH4 concentration. All CT increased the half time of GP and GPCH4. Moreover, all CT decreased the maximum rate of fermentation for GPCH4 and rate of substrate degradation. The correlation between CT structure and GPCH4 and fermentation characteristics showed that the proportion of prodelphinidins within CT had the largest effect on fermentation characteristics, followed by average 27 polymer size and percentage of cis-flavan-3-ols.

Site-directed mutagenesis and structural modeling of Coq10p indicate the presence of a tunnel for coenzyme Q6 binding

Coq10p is a protein required for coenzyme Q function, but its specific role is still unknown. It is a member of the START domain superfamily that contains a hydrophobic tunnel implicated in the binding of lipophilic molecules. We used site-directed mutagenesis, statistical coupling analysis and molecular modeling to probe structural determinants in the Coq10p putative tunnel. Four point mutations were generated (coq10-K50E, coq10-L96S, coq10-E105K and coq10-K162D) and their biochemical properties analysed, as well as structural consequences. Our results show that all mutations impaired Coq10p function and together with molecular modeling indicate an important role for the Coq10p putative tunnel. (C) 2010 Federation of European Biochemical Societies. Published by Elsevier B.V. All rights reserved.

The CATH Hierarchy Revisited-Structural Divergence in Domain Superfamilies and the Continuity of Fold Space

This paper explores the structural continuum in CATH and the extent to which superfamilies adopt distinct folds. Although most superfamilies are structurally conserved, in some of the most highly populated superfamilies (4% of all superfamilies) there is considerable structural divergence. While relatives share a similar fold in the evolutionary conserved core, diverse elaborations to this core can result in significant differences in the global structures. Applying similar protocols to examine the extent to which structural overlaps occur between different fold groups, it appears this effect is confined to just a few architectures and is largely due to small, recurring super-secondary motifs (e.g., alpha beta-motifs, alpha-hairpins). Although 24% of superfamilies overlap with superfamilies having different folds, only 14% of nonredundant structures in CATH are involved in overlaps. Nevertheless, the existence of these overlaps suggests that, in some regions of structure space, the fold universe should be seen as more continuous.

The CATH classification revisited-architectures reviewed and new ways to characterize structural divergence in superfamilies

The latest version of CATH (class, architecture, topology, homology) (version 3.2), released in July 2008 (http://www.cathdb.info), contains 1 14215 domains, 2178 Homologous superfamilies and 1110 fold groups. We have assigned 20 330 new domains, 87 new homologous superfamilies and 26 new folds since CATH release version 3.1. A total of 28 064 new domains have been assigned since our NAR 2007 database publication (CATH version 3.0). The CATH website has been completely redesigned and includes more comprehensive documentation. We have revisited the CATH architecture level as part of the development of a `Protein Chart` and present information on the population of each architecture. The CATHEDRAL structure comparison algorithm has been improved and used to characterize structural diversity in CATH superfamilies and structural overlaps between superfamilies. Although the majority of superfamilies in CATH are not structurally diverse and do not overlap significantly with other superfamilies, similar to 4% of superfamilies are very diverse and these are the superfamilies that are most highly populated in both the PDB and in the genomes. Information on the degree of structural diversity in each superfamily and structural overlaps between superfamilies can now be downloaded from the CATH website.

Structural analysis of fertilization in the fish Brycon orbignyanus

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

Structural and ultrastructural characteristics of the yolk syncytial layer in Prochilodus lineatus (Valenciennes, 1836) (Teleostei; Prochilodontidae)

The yolk syncytial layer (YSL) has been regarded as one of the main obstacles for a successful cryopreservation of fish embryos. The purpose of this study was to identify and characterize the YSL in Prochilodus lineatus, a fish species found in southeastern Brazil and considered a very important fishery resource. Embryos were obtained through artificial breeding by hormonal induction. After fertilization, the eggs were incubated in vertical incubators with a controlled temperature (28 degrees C). Embryos were collected in several periods of development up to hatching and then fixed with 2% glutaralclehyde and 4% paraformaldehyde in 0.1 M sodium phosphate buffer (pH 7.3). Morphological analyses were carried out under either light, transmission or scanning electron microscopy. The formation of the YSL in P. lineatus embryos starts at the end of the cleavage stage (morula), mainly at the margin of the blastoderm, and develops along the embryo finally covering the entire yolk mass (late gastrula) and producing a distinct intermediate zone between the yolk and the endodermal cells. The YSL was characterized by the presence of microvilli on the contact region with the yolk endoderm. A cytoplasmic mass, full of mitochondria, vacuoles, ribosomes, endomembrane nets and euchromatic nuclei, indicated a high metabolic activity. This layer is shown as an interface between the yolk and the embryo cells that, besides sustaining and separating the yolk, acts as a structure that makes it available for the embryo. The structural analyses identified no possible barriers to cryoprotectant penetration.

Structural analysis of the embryonic development in Brycon cephalus (Gunther, 1869)

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

Molecular adaptability of nucleoside diphosphate kinase b from trypanosomatid parasites: stability, oligomerization and structural determinants of nucleotide binding

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

On the photoluminescence behavior of samarium-doped strontium titanate nanostructures under UV light. A structural and electronic understanding

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)

Structural modelling of Eu3+-based siloxane-poly( oxyethylene) nanohybrids

The modelling of the local structure of sol-gel derived Eu3+-based organic/inorganic hybrids is reported, based on Small-Angle X-ray Scattering (SAXS), photoluminescence and mid-infrared spectroscopy. The hybrid matrix of these organically modified silicates, classed as di-ureasils and termed U(2000) and U(600), is formed by poly( oxyethylene) (POE) chains of variable length grafted to siloxane domains by means of urea cross-linkages. Europium triflate, Eu(CF3SO3)(3), was incorporated in the two di-ureasil matrices with compositions 400 greater than or equal ton greater than or equal to 10, n is the molar ratio of ether oxygens per Eu3+. The SAXS data for undoped hybrids (n=infinity) show the presence of a well-defined peak attributed to the existence of a liquid-like spatial correlation of siloxane rich domains embedded in the polymer matrix and located at the ends of the organic segments. The obtained siloxane particle gyration radius Rg(1) is around 5 Angstrom (error within 10%), whereas the interparticle distance d is 25 +/-2 Angstrom and 40 +/-2 Angstrom, for U(600) and U(2000), respectively. For the Eu3+-based nanocomposites the formation of a two-level hierarchical local structure is discerned. The primary level is constituted by strongly spatially correlated siloxane particles of gyration radius Rg(1) (4-6 and 3-8 Angstrom, errors within 5%, for U(600())n Eu(CF3SO3)(3), 200 greater than or equal ton greater than or equal to 40, and U(2000)(n)Eu(CF3SO3)(3), 400 greater than or equal ton greater than or equal to 40, respectively) forming large clusters of gyration radius Rg(2) (approximate to 75 +/- 10 Angstrom). The local coordination of Eu3+ in both di-ureasil series is described combining the SAXS, photoluminescence and mid-infrared results. In the di-ureasils containing long polymer chains, U(2000)(n)Eu(CF3SO3)(3), the cations interact exclusively with the carbonyl oxygens atoms of the urea bridges at the siloxane-POE interface. In the hybrids containing shorter chains, U(600)(n)Eu(CF3SO3)(3) with n ranging from 200 to 60, the Eu3+ ions interact solely with the ether-type oxygens of the polymer chains. Nevertheless, in this latter family of hybrids a distinct Eu3+ local site environment involving the urea cross-linkages is detected when the europium content is increased up to n=40.

Hydration effects on the structural properties and haem-haem interaction in haemoglobin

Direct and simultaneous measurements of hydration water content and protein conformation have been performed using quartz crystal microbalance and visible absorption spectroscopy. Equilibrium and kinetics of methaemoglobin/haemichrome transition induced by the alteration of the degree of hydration was investigated in thin films exposed to controlled humidity. The kinetics experiment show that the conversion of species achieve the equilibrium more rapidly that the amount of sorbed water by the protein. The transition shows a sigmoid behaviour and suggest cooperative phenomena manifested by haem-haem interaction. The water hydration network contributing to the haem haem interaction advise that water acts as allosteric effectors for the conversion between species. Irreversible changes produced by complete drying are clearly shown.

Structural and ultrastructural analysis of embryonic development of Prochilodus lineatus (Valenciennes, 1836) (Characiforme ; Prochilodontidae)

This survey was performed to characterize the embryogenesis of Prochilodus lineatus. Seven stages of embryo development were identified - zygote, cleavage, blastula, gastrula, segmentation, larval and hatching - after a period of incubation of 22h (24 degrees C) or 14h (28 degrees C). The following cleavage pattern was identified: the first plane was vertical (2 blastomeres); the second was vertical and perpendicular to the first (4 blastorneres); the third was vertical and parallel to the first (4 x 2); the fourth cleavage was vertical and parallel to the second (4 x 4); the fifth was vertical and parallel to the first (4 x 8); and the sixth cleavage was horizontal (64 blastomeres). At the blastula stage (3.0-4.0 h (24 degrees C); 1.66-2.0h (28 degrees C) irregular spaces were detected and periblast structuring was initiated. At the gastrula stage (4.0-8.0 h (24 degrees C); 3.0-6.0 h (28 degrees C) the epiboly, convergence and cell movements, as well as the formation of embryonic layers, had begun. The segmentation stage (10.0-15.0h (24 degrees C); 7.0-10.0h (28 degrees C)) was characterized by a rudimentary formation of organs and systems (somites, optic vesicle and intestinal delimitation). The embryo at the larval stage (16.0-21.0 h (24 degrees C); 11.0-13.0 h (28 degrees C)) showed a free tail, more than 25 somites, an optic vesicle and a ready-to-hatch larval shape. The blastomeres at cleavage stage had disorganized nuclei indicating high mitotic activity. At gastrula, the blastomeres and the periblast had euchromatic nuclei and a large number of mitochondria and vesicles. The yolk was organized into globose sacs, which were dispersed into small pieces prior to absorption.