125Te NMR for structural investigations in phase change materials: Optimization of experimental conditions coupled to NMR shift prediction.

Phase Change Materials as those of the Ge-Sb-Te ternary system are of great interest for technological applications. Properties of these compounds are strongly related to presence of vacancies and structural investigations remain challenging. In this paper we evidence that 125Te NMR in natural abundance and using commercial systems at intermediate field (14.1 â€‹T) together with NMR parameters prediction can contribute to improve understanding of electronic structure of such systems. GeTe is a typical phase change material, whose structure contains germanium vacancies, even in its stoichiometric form, giving it metallic properties. Here, we use nominal Ge50Te50 and Ge48Te52 crystalline samples as an example to optimize the WURST-CPMG technique, a powerful technique to record wide NMR spectra which has not yet been used on 125Te. The goal was to minimize the time devoted to experiments as well as maximize the signal-to-noise ratio in order to detect small intensity signals directly linked to vacancies. Virtual Crystal Approximation (VCA) calculations performed with WIEN2K helped to interpret the NMR spectra. For Te-based crystalline conducting samples the best experimental results were obtained using 3.2 â€‹mm thin wall rotors with diluted samples 40 â€‹vol% GeTe-60 â€‹vol% SiO2. In addition to the WURST-CPMG technique, high resolution spectra using MAS as implemented in the pj-MAT technique allowed us to identify the distributions of chemical shift parameters in the high intensity contribution of the 1D spectra. The NMR spectra recorded on the samples showed that an addition of Tellurium in the stoichiometric Ge50Te50 sample leads to an important broadening of the spectrum together with a shift of the lines. According to VCA calculations it could be attributed to a distribution of concentrations of germanium vacancies in the sample and it would appear that Knight Shift but also Chemical Shift could contribute in similar proportion to the NMR line position when metavalent bonding is invoked.

NMR shieldings from density functional perturbation theory: GIPAW versus all-electron calculations.

We present a benchmark of the density functional linear response calculation of NMR shieldings within the gauge-including projector-augmented-wave method against all-electron augmented-plane-wave+local-orbital and uncontracted Gaussian basis set results for NMR shieldings in molecular and solid state systems. In general, excellent agreement between the aforementioned methods is obtained. Scalar relativistic effects are shown to be quite large for nuclei in molecules in the deshielded limit. The small component makes up a substantial part of the relativistic corrections.

Running a 100-km ultra-marathon induces an inflammatory response but does not raise the level of the plasma iron-regulatory protein hepcidin.

AIM: Exercise may induce an inflammatory response that may lead to changes in iron metabolism. The aim of this study was to examine the relationship between the inflammation induced by a 100 km run and the level of hepcidin, which is a hormone regulating iron metabolism. METHODS: Six males, age 44.5±13.5 years, running 100 km. SETTING: the CRP protein, IL-6 and leucocyte count were measured as an index of inflammation. RESULTS: A 100 km run caused a progressive increase in blood IL-6 concentration, which reached the highest values after 75 km. Furthermore, an increase in levels of CRP, a marker of inflammation, was observed after the 100 km run and continued to increase after a 14 h recovery period. Leucocyte number and markers of muscle damage were significantly elevated after the 100 km run. This was accompanied by a decrease in transferrin saturation and an increase in blood haemoglobin and ferritin. Despite all these changes, the 100 km race did not affect blood hepcidin concentration either during the run or after a 14 h recovery period. CONCLUSION: The study shows that a 100 km run induces an inflammatory response but does not trigger changes in the blood hepcidin level. Thus it can be concluded that changes in IL-6 are not sufficient to increase the blood hepcidin level in runners.

Kinematic variables and blood Acid-base status in the analysis of collegiate swimmers' anaerobic capacity.

Short duration repeated maximal efforts are often used in swimming training to improve lactate tolerance, which gives swimmers the ability to maintain a high work rate for a longer period of time. The aim of the study was to examine the kinematics of swimming and its relation to the changes in blood acid-base status and potassium level. Seven collegiate swimmers, with at least 6 years of training experience, volunteered to participate in the study. The test consisted of 8 x 25 m front crawl performed with maximum effort. The rest period between repetitions was set to five seconds. Blood samples were taken from the fingertip at rest, after warm-up and in the 3rd minute after completion of the test. The swimming was recorded with a video recorder, for later analysis of time, velocity and technique (stroke index). Based on the swimming velocity results, the obtained curve can be divided into rapid decrease of velocity and relatively stable velocities. The breaking point of repetition in swimming velocity was assumed as the swimming velocity threshold and it was highly correlated with the decrease of the blood acid-base status (pH r=0.82, BE r=0.87, HCO3 (-) r=0.76; p<0.05 in all cases). There was no correlation between stroke index or fatigue index and blood acid-base status. Analysis of the swimming speed in the 8 x 25 m test seems to be helpful in evaluation of lactate tolerance (anaerobic capacity) in collegiate swimmers.

Allopurinol intake does not modify the slow component of V(.)O(2) kinetics and oxidative stress induced by severe intensity exercise.

The aim of this study was to test the hypothesis that allopurinol ingestion modifies the slow component of V(.)O(2) kinetics and changes plasma oxidative stress markers during severe intensity exercise. Six recreationally active male subjects were randomly assigned to receive a single dose of allopurinol (300 mg) or a placebo in a double-blind, placebo-controlled crossover design, with at least 7 days washout period between the two conditions. Two hours following allopurinol or placebo intake, subjects completed a 6-min bout of cycle exercise with the power output corresponding to 75 % V(.)O(2)max. Blood samples were taken prior to commencing the exercise and then 5 minutes upon completion. Allopurinol intake caused increase in resting xanthine and hypoxanthine plasma concentrations, however it did not affect the slow component of oxygen uptake during exercise. Exercise elevated plasma inosine, hypoxanthine, and xanthine. Moreover, exercise induced a decrease in total antioxidant status, and sulfhydryl groups. However, no interaction treatment x time has been observed. Short term severe intensity exercise induces oxidative stress, but xanthine oxidase inhibition does not modify either the kinetics of oxygen consumption or reactive oxygen species overproduction.

A single oral intake of arginine does not affect performance during repeated Wingate anaerobic test.

AIM: The ergogenic effect of arginine has been demonstrated in research focusing on its intake before exercise. However, in these studies, the effect of arginine in combination with other various metabolites were assessed. The aim of this study was to determine whether a single oral intake of arginine, without any other compounds, 60 minutes prior to exercise, modifies performance and exercise metabolism during a repeated Wingate anaerobic test. METHODS: Six healthy, active, but not highly trained volunteers participated in the study. Subjects performed three 30s all-out supramaximal Wingate Anaerobic Tests (WAnTs) with 4 minute-interval rest periods between WAnTs. RESULTS: Arginine ingestion before exercise did not influence physical performance. Triple WAnTs resulted in a marked increase in white blood cell (WBC) count, lactate and ammonia concentrations, however there were no differences between arginine and the placebo trials. CONCLUSION: Our data indicated that 2 g of arginine ingested in a single dose, neither induced nitrite/nitrate (NOx) concentrations changes, nor improved physical performance.

Density functional theory simulations of B K and N K NEXAFS spectra of h-BN/transition metal(111) interfaces.

The electronic structure and the corresponding B K and N K near-edge x-ray fine structure (NEXAFS) spectra of epitaxially grown h-BN on Ni(111), Pt(111), and Rh(111) surfaces are investigated by density functional theory. The calculations are carried out using the WIEN2k program package applying the augmented-plane-wave+local orbitals (APW+lo) method. The NEXAFS spectra are simulated using a 3 × 3 × 1 super cell and considering the final state rule by means of a (partial) core hole for the corresponding atom. The influence of a full or partial core hole is shown for the h-BN/Ni(111) system, for which the best agreement with the experimental spectra is found when half a core hole is assumed. All characteristic features of the experimental spectra are well reproduced by theory, including the angular dependences. The bonding effects are investigated by comparing the spectra of bulk h-BN with those of the h-BN/Ni(111) system. An analysis of both the density of states and charge densities reveals strong N-p(z)-Ni-d(z(2)) bonding/antibonding interactions. In the case of Pt(111) and Rh(111) surfaces, we discuss the effects of the nanomesh structures in terms of simple 1 × 1 commensurate models.

Changes in cardiac structure and function among elite judoists resulting from long-term judo practice.

AIM: The aim of this study was to investigate the character of changes in cardiac structure and function among elite judoists due to long-term judo practice. METHODS: A group of male (N = 20, average age: 22.1) and female (N = 15, average age: 19.4) athletes practising judo for about 10 years was subjected to echocardiographic tests carried out during rest (aorta diameter [AoD], diastolic dimension of the left ventricle [Dd], thickness of the interventricular septum [IVST], the thickness of the posterior wall of the left ventricle [LVPWT]), and to measurement of cardiovascular system's action parameters (heart rate [HR], stroke volume [SV], cardiac output [Q], blood pressure [BP]). Moreover, control non trained subjects were also studied, women (N = 30, average age: 19.1) and men (N = 30, average age: 21.4). In order to determine aerobic efficiency, the authors measured the maximal oxygen uptake (VO2max) using the direct method. The anaerobic capacity was estimated on the basis of the maximal anaerobic power, and the volume of the performed work was calculated by means of the 30s Wingate test. RESULTS: Echocardiographic test values imply that changes in heart morphology induced by long term judo training, such as increase diastolic dimension of the left ventricle, thickness of the interventricular septum and left ventricular posterior wall, resemble more the changes observed in endurance athletes than changes observed in strength athletes. CONCLUSION: The obtained data indicated that judo training improves both aerobic and anerobic performance and these changes were associated with changes in heart structure and function as compared to non trained control.

Unraveling the structure of the h-BN/Rh(111) nanomesh with ab initio calculations.

The properties of a single layer of h-BN on top of a Rh(111) surface are discussed in terms of an ab initio generated force field approach as well as by direct ab initio density-functional theory (DFT) calculations. A single-layer model for the h-BN/Rh(111) nanomesh, in contrast to a previously considered (incomplete) double-layer model of h-BN, can explain the experimental data. The main focus of this work is to compare a force field approach described earlier in (Laskowski et al 2007 Phys. Rev. Lett. 98 106802) with direct ab initio calculations. The calculated geometry of the h-BN layer is very similar to the structure predicted by the force field approach. The ab initio calculated density of states projected on N-p(x,y) of BN corresponding to 'low' and 'high' regions with respect to the Rh surface shows a 1 eV splitting and thus explains the observed σ-band splitting. Moreover, we find good agreement between calculated and experimental scanning tunneling microscope (STM) images of this system.

Increased respiration rate as a result of adaptation to copper in confused flour beetle, Tribolium confusum Jacquelin du Val.

Multi-generation exposure of organisms to toxicants may lead to adaptations increasing their resistance to a chemical. However, the increased tolerance may have a negative effect on fitness in uncontaminated environments due to increased maintenance costs in adapted individuals. Herein we present results of a multi-generation experiment on the flour beetle, Tribolium confusum, showing that animals bred for ca. 10-13 generations in copper-contaminated medium had higher maintenance costs then their counterparts originating from uncontaminated medium. The results show that significant changes in energy budgets may occur even after relatively short selection in small laboratory cultures.

SPINE bioinformatics and data-management aspects of high-throughput structural biology.

SPINE (Structural Proteomics In Europe) was established in 2002 as an integrated research project to develop new methods and technologies for high-throughput structural biology. Development areas were broken down into workpackages and this article gives an overview of ongoing activity in the bioinformatics workpackage. Developments cover target selection, target registration, wet and dry laboratory data management and structure annotation as they pertain to high-throughput studies. Some individual projects and developments are discussed in detail, while those that are covered elsewhere in this issue are treated more briefly. In particular, this overview focuses on the infrastructure of the software that allows the experimentalist to move projects through different areas that are crucial to high-throughput studies, leading to the collation of large data sets which are managed and eventually archived and/or deposited.

Increased adaptability of young judo sportsmen after protein supplementation.

AIM: The purpose of this study was to examine the effects of protein supplementation on adaptation process in young judoists. The assumption of this study was that young sportsmen would benefit from the protein supplements because of increased demand due to growth and training. METHODS: Twelve judoists were divided into two groups. One group received a soy protein supplement 0.5 g/kg body mass/day (P) and the second group (C) did not. Before and after 4 weeks of training the maximum oxygen uptake (VO(2max)) was evaluated in both groups. In addition, they performed Wingate test, where the maximal power output and the total work output were measured. RESULTS: The obtained results indicate that after 4 weeks of judo training the VO(2max) increase and Wingate test performance significantly improves. In both cases the increase was much higher in judoists who received the protein supplement, comparing to the control group. When the judoist were trained for another 3 months but without the protein supplementation, we observed disappearance of the differences in VO(2max) between the two studied groups. CONCLUSION: These data clearly indicate that the supplementation of a normal diet with soy protein (0.5 g per kg of body mass) is beneficial for a judoist. An increase in aerobic and anaerobic performance is higher in the protein supplemented group, despite the fact that the training protocol is the same for all the athletes. We conclude that it is possible to increase the adaptation to judo training by protein supplementation.

Frequency of three BRCA1 gene founder mutations in breast/ovarian cancer families from the Pomerania-Kujawy region of Poland.

A group of 63 families from the Pomerania-Kujawy region were analyzed for three BRCA1 gene Polish founder mutations, 5382insC, 300T>G, and 4153delA, because of breast (BrCa) and/or ovarian cancer (OvCa) history. The analysis was carried out by multiplex polymerase chain reaction method. BRCA1 mutation was revealed in nine (14%) families: in three (33%) of hereditary BrCa and OvCa families, in three (8%) of hereditary BrCa families, and in three (21%) of hereditary OvCa families. According to risk criteria, it was revealed in 45% of high-risk families with more than three cancers, 13% of moderate-risk families with two cancers, and 8% of families with sporadic OvCa. In six families, the mutation was found in a proband with BrCa or OvCa and in three families, the mutation was found in a healthy proband, first-degree relative of a patient deceased of BrCa or OvCa. 5382insC frameshift mutation accounted for 67% and 300T>G missense mutation for 33% of all identified familial mutations. 4153delA frameshift mutation was not found in analyzed sample of families. 5382insC mutation was found in 9% and 300T>G in 5% of all investigated families, and in 27 and 18%, respectively, of high-risk families. This underlines the importance of applying strict inclusion criteria to analyze mutation frequency in hereditary BrCa/OvCa families.

On the molecular discrimination between adenine and guanine by proteins.

The molecular recognition and discrimination of adenine and guanine ligand moieties in complexes with proteins have been studied using empirical observations on carefully selected crystal structures. The distribution of protein folds that bind these purines has been found to differ significantly from that across the whole PDB, but the most populated architectures and folds are also the most common in three genomes from the three different domains of life. The protein environments around the two nucleic acid bases were significantly different, in terms of the propensities of amino acid residues to be in the binding site, as well as their propensities to form hydrogen bonds to the bases. Plots of the distribution of protein atoms around the two purines clearly show different clustering of hydrogen bond donors and acceptors opposite complimentary acceptors and donors in the rings, with hydrophobic areas below and above the rings. However, the clustering pattern is fuzzy, reflecting the variety of ways that proteins have evolved to recognise the same molecular moiety. Furthermore, an analysis of the conservation of residues in the protein chains binding guanine shows that residues in contact with the base are in general better conserved than the rest of the chain.

Streptococcus pneumonia YlxR at 1.35 A shows a putative new fold.

The structure of the YlxR protein of unknown function from Streptococcus pneumonia was determined to 1.35 A. YlxR is expressed from the nusA/infB operon in bacteria and belongs to a small protein family (COG2740) that shares a conserved sequence motif GRGA(Y/W). The family shows no significant amino-acid sequence similarity with other proteins. Three-wavelength diffraction MAD data were collected to 1.7 A from orthorhombic crystals using synchrotron radiation and the structure was determined using a semi-automated approach. The YlxR structure resembles a two-layer alpha/beta sandwich with the overall shape of a cylinder and shows no structural homology to proteins of known structure. Structural analysis revealed that the YlxR structure represents a new protein fold that belongs to the alpha-beta plait superfamily. The distribution of the electrostatic surface potential shows a large positively charged patch on one side of the protein, a feature often found in nucleic acid-binding proteins. Three sulfate ions bind to this positively charged surface. Analysis of potential binding sites uncovered several substantial clefts, with the largest spanning 3/4 of the protein. A similar distribution of binding sites and a large sharply bent cleft are observed in RNA-binding proteins that are unrelated in sequence and structure. It is proposed that YlxR is an RNA-binding protein.

Amino acid-base interactions: a three-dimensional analysis of protein-DNA interactions at an atomic level.

To assess whether there are universal rules that govern amino acid-base recognition, we investigate hydrogen bonds, van der Waals contacts and water-mediated bonds in 129 protein-DNA complex structures. DNA-backbone interactions are the most numerous, providing stability rather than specificity. For base interactions, there are significant base-amino acid type correlations, which can be rationalised by considering the stereochemistry of protein side chains and the base edges exposed in the DNA structure. Nearly two-thirds of the direct read-out of DNA sequences involves complex networks of hydrogen bonds, which enhance specificity. Two-thirds of all protein-DNA interactions comprise van der Waals contacts, compared to about one-sixth each of hydrogen and water-mediated bonds. This highlights the central importance of these contacts for complex formation, which have previously been relegated to a secondary role. Although common, water-mediated bonds are usually non-specific, acting as space-fillers at the protein-DNA interface. In conclusion, the majority of amino acid-base interactions observed follow general principles that apply across all protein-DNA complexes, although there are individual exceptions. Therefore, we distinguish between interactions whose specificities are 'universal' and 'context-dependent'. An interactive Web-based atlas of side chain-base contacts provides access to the collected data, including analyses and visualisation of the three-dimensional geometry of the interactions.

Time to death response in carabid beetles exposed to multiple stressors along a gradient of heavy metal pollution.

We investigated the responses of invertebrates inhabiting polluted environments to multiple stressors. Carabid beetles (Pterostichus oblongopunctatus F.) were subjected to food deprivation and insecticide treatment (dimethoate) to resolve trends associated with a gradient of heavy metal pollution. Metal concentrations along the gradient of five sites ranged from approximately 150 to 10,500 mg/kg Zn, 136 to 2600 mg/kg Pb, and 0.84 to 81.9 mg/kg Cd. There was no difference in body mass along the pollution gradient. However, the beetles originating from the most contaminated sites were significantly less tolerant to food deprivation than beetles from the reference site. Median survival time was 120 h for the two most polluted sites, compared with 168 h at the reference site. Beetles from the two most polluted sites were also significantly more susceptible to dimethoate at 0.1 microgram active ingredient/beetle. Median survival times were 12 and 123 h for beetles from the two most polluted sites and 359 h for the reference site. Carabid beetles exposed to chronic pollution, therefore, exhibit elevated susceptibility to additional stressors.

Why short-term bioassays are not meaningful--effects of a pesticide (Imidacloprid) and a metal (cadmium) on pea aphids (Acyrthosiphon pisum Harris).

The life-table study on effects of a heavy metal, Cd (100 and 200 mg kg-1 soil), and an insecticide, imidacloprid (4 and 40 g a.i. ha-1), on pea aphids revealed significant effects of both chemicals on life history traits and population dynamics. Substantial differences in the action of the two chemicals and between the two doses of imidacloprid were observed. The pesticide caused high mortality at the beginning of the experiment, however some aphids were able to live for as long as control insects. In contrast, Cd-induced mortality was low at the beginning but increased during the experiment. Analysis of data collected during the first 10 days of the experiment, the first 20 days, or for the whole life-time of the cohort gave different results. While highly significant effects of imidacloprid were detected already after 10 days of the experiment, Cd treatment resulted in no effect for this time of exposure. Higher dose of imidacloprid decreased growth and development rates along with delayed reproduction (9th or 10th day). In contrast, the aphids treated with the low dose of imidacloprid and with both concentrations of Cd started their reproduction at the same day as untreated insects (6th or 7th day), but the reproduction tended to cease earlier. This indicates that too short ecotoxicological tests may result in serious underestimation of some effects, while overestimating others.