The South American Plasmodium falciparum var gene repertoire is limited, highly shared and possibly lacks several antigenic types

The Plasmodium falciparum var gene family encodes large variant antigens, which are important virulence factors, and also targets of the humoral host response. The frequently observed mild outcomes of falciparum malaria in many places of the Amazon area prompted us to ask whether a globally restricted variant (var) gene repertoire is present in currently circulating and older isolates of this area. By exhaustive analysis of var gene tags from 89 isolates and clones taken during many years from all over the Brazilian Amazon, we estimate that there are probably no more than 350-430 distinct sequence types, less than for any similar sized area studied so far. Detailed analysis of the var tags from genetically distinct clones obtained from single isolates revealed restricted and redundant repertoires suggesting either a low incidence of infective bites or restricted variant gene diversity in inoculated parasites. Additionally, we found a structuring of var gene repertoires observed as a higher pairwise typing sharing in isolates from the same microregion compared to isolates from different regions. Fine analysis of translated var tags revealed that certain Distinct Sequence Identifiers (DSIDs) were differently represented in Brazilian/South American isolates when compared to datasets from other continents. By global alignment of worldwide var DBL alpha sequences and sorting in groups with more than 76% identity, 125 clusters were formed and more than half of all genes were found in nine clusters with 50 or more sequences. While Brazilian/South American sequences were represented only in 64 groups, African sequences were found in the majority of clusters. DSID type 1 related sequences accumulated almost completely in one single cluster, indicating that limited recombination occurs in these specific var gene types. These data demonstrate the so far highest pairwise type sharing values for the var gene family in isolates from all over an entire subcontinent. The apparent lack of specific sequences types suggests that the P. falciparum transmission dynamics in the whole Amazon are probably different from any other endemic region studied and possibly interfere with the parasite`s ability to efficiently diversify its variant gene repertoires. (C) 2010 Elsevier B.V. All rights reserved.

Exciton behavior in GaAs/AlGaAs coupled double quantum wells with interface disorder

In this work, we present a detailed study on the optical properties of two GaAs/Al(0.35)Ga(0.65)As coupled double quantum wells (CDQWs) with inter-well barriers of different thicknesses, by using photoluminescence (PL) spectroscopy. The two CDQWs were grown in a single sample, assuring very similar experimental conditions for measurements of both. The PL spectrum of each CDQW exhibits two recombination channels which can be accurately identified as the excitonic e(1)-hh(1) transitions originated from CDQWs of different effective dimensions. The PL spectra characteristics and the behavior of the emissions as a function of temperature and excitation power are interpreted in the scenario of the bimodal interface roughness model, taking into account the exciton migration between the two regions considered in this model and the difference in the potential fluctuation levels between those two regions. The details of the PL spectra behavior as a function of excitation power are explained in terms of the competition between the band gap renormalization (BGR) and the potential fluctuation effects. The results obtained for the two CDQWs, which have different degrees of potential fluctuation, are also compared and discussed. (C) 2009 Elsevier B.V. All rights reserved.

Emergence and loss of assortative mating in sympatric speciation

We have studied an agent model which presents the emergence of sexual barriers through the onset of assortative mating, a condition that might lead to sympatric speciation. In the model, individuals are characterized by two traits, each determined by a single locus A or B. Heterozygotes on A are penalized by introducing an adaptive difference from homozygotes. Two niches are available. Each A homozygote is adapted to one of the niches. The second trait, called the marker trait has no bearing on the fitness. The model includes mating preferences, which are inherited from the mother and subject to random variations. A parameter controlling recombination probabilities of the two loci is also introduced. We study the phase diagram by means of simulations, in the space of parameters (adaptive difference, carrying capacity, recombination probability). Three phases are found, characterized by (i) assortative mating, (ii) extinction of one of the A alleles and (iii) Hardy-Weinberg like equilibrium. We also make perturbations of these phases to see how robust they are. Assortative mating can be gained or lost with changes that present hysteresis loops, showing the resulting equilibrium to have partial memory of the initial state and that the process of going from a polymorphic panmictic phase to a phase where assortative mating acts as sexual barrier can be described as a first-order transition. (C) 2009 Published by Elsevier Ltd.

Effects of confinement on the electron-phonon interaction in Al(0.18)Ga(0.82)As/GaAs quantum wells

Photoluminescence measurements at different temperatures have been performed to investigate the effects of confinement on the electron-phonon interaction in GaAs/AlGaAs quantum wells (QWs). A series of samples with different well widths in the range from 150 up to 750 A was analyzed. Using a fitting procedure based on the Passler-p model to describe the temperature dependence of the exciton recombination energy, we determined a fit parameter which is related to the strength of the electron-phonon interaction. On the basis of the behavior of this fit parameter as a function of the well width thickness of the samples investigated, we verified that effects of confinement on the exciton recombination energy are still present in QWs with well widths as large as 450 angstrom. Our findings also show that the electron-phonon interaction is three times stronger in GaAs bulk material than in Al(0.18)Ga(0.82)As/GaAs QWs.

Synthetic spodumene polycrystals as a TL dosimetric material

Synthetic beta-spodumene polycrystals were produced by a devitrification method, undoped and doped with controlled concentration of the Ce3+ or Mn2+ impurities. The TL properties of these polycrystals and of a colourless natural spodumene were investigated. Some dosimetric properties of them were also discussed. The dopants do not affect the TL peak position with respect a pure beta-spodumene sample but the intensity of the TL peaks at 180 and 280 degrees C is improved in the Ce-doped one. The Ce3+ ions do not participate in the TL light emission; on the other hand, the presence of Mn2+ ions cause an emission band around 600-650 nm in the TL light emission spectrum. The emission around 400 nm appears in the TL emission spectrum of all the samples and it is believed to correspond to aluminium centre ([AlO4/hole](0)) recombination with an electron. The more sensitive samples to gamma-radiation are the colourless natural spodumene and the Ce-doped synthetic spodumene, respectively. The colourless natural spodumene crystal shows a TL peak at 180 degrees C suitable for dosimetry, while for Ce-doped beta-spodumene sample the TL peaks at 180 and 280 degrees C can be used. No fading of the TL emission was observed for Ce-doped beta-spodumene sample up to 80 days after irradiation. (C) 2007 Elsevier Ltd. All rights reserved.

TL dosimetry of natural quartz sensitized by heat-treatment and high dose irradiation

The aim of this paper is to report the sensitization of the TL peak appearing at 270 degrees C in the glow curve of natural quartz by using the combined effect of heat-treatments and irradiation with high gamma doses. For this, thirty discs with 6 x 1 mm(2) were prepared from plates parallell to a rhombolledral crystal face. The specimens were separated into four lots according to its TL read out between 160 and 320 degrees C. One lot was submitted to gamma doses of Co-60 radiation starting at 2 kGy and going up until a cumulative dose of 25 kGy. The other three lots were initially heal-treated at 500, 800 and 1000 degrees C and then irradiated with a single dose of 25kGy. The TL response of each lot was determined as a function of test-doses ranging from 0.1 to 30 mGy. As a result, it was observed that heat-treatments themselves did not produce the strong peak at 270 degrees C that was observed after the administration of high gamma doses. This peak is associated with the optical absorption band appearing at 470 rim which is due to the formation of [AlO4]degrees acting as electron-hole recombination centers. The formation of the 270 degrees C peak was preliminary analyzed in relation to aluminum- and oxygen-vacancy-related centers found in crystalline quartz. (C) 2008 Elsevier Ltd. All rights reserved.

TL, OSL and ESR studies on beryllium oxide

Electron spin resonance (ESR) studies were carried out to identify the defect centres responsible for the thermoluminescence (TL) and optically stimulated luminescence (OSL) processes in BeO phosphor. Two defect centres were identified in irradiated BeO phosphor by ESR measurements, which were carried out at room temperature and these were assigned to an O(-) ion and Al(2+) centre. The O(-) ion (hole centre) correlates with the main 190 degrees C TL peak. The Al(2+) centre (electron centre), which acts as a recombination centre, also correlates to the 190 degrees C TL peak. A third centre, observed during thermal annealing studies, is assigned to an O(-) ion and is related to the high temperature TL at 317 degrees C. This centre also appears to be responsible for the observed OSL process in BeO phosphor. (c) 2010 Elsevier B.V. All rights reserved.

The effect of the negative coupling parameter on the spectrum of a trapped Bose gas

The interest in attractive Bose-Einstein Condensates arises due to the chemical instabilities generate when the number of trapped atoms is above a critical number. In this case, recombination process promotes the collapse of the cloud. This behavior is normally geometry dependent. Within the context of the mean field approximation, the system is described by the Gross-Pitaevskii equation. We have considered the attractive Bose-Einstein condensate, confined in a nonspherical trap, investigating numerically and analytically the solutions, using controlled perturbation and self-similar approximation methods. This approximation is valid in all interval of the negative coupling parameter allowing interpolation between weak-coupling and strong-coupling limits. When using the self-similar approximation methods, accurate analytical formulas were derived. These obtained expressions are discussed for several different traps and may contribute to the understanding of experimental observations.

Structural and optical properties on thulium-doped LHPG-grown Ta(2)O(5) fibres

Structural, spectroscopic and dielectric properties of thulium-doped laser-heated pedestal Ta(2)O(5) as-grown fibres were studied. Undoped samples grow preferentially with a single crystalline monoclinic structure. The fibre with the lowest thulium content (0.1 at%) also shows predominantly a monoclinic phase and no intra-4f(12) Tm(3+) recombination was observed. For sample with the highest thulium amount (1.0 at%), the appearance of a dominant triclinic phase as well as intraionic optical activation was observed. The dependence of photoluminescence on excitation energy allows identification of different site locations of Tm(3+) ions in the lattice. The absence of recombination between the first and the ground-state multiplets as well as the temperature dependence of the observed transitions was justified by an efficient energy transfer between the Tm(3+) ions. Microwave dielectric properties were investigated using the small perturbation theory. At a frequency of 5 GHz, the undoped material exhibits a dielectric permittivity of 21 and for thulium-doped Ta(2)O(5) samples it decreases to 18 for the highest doping concentration. Nevertheless, the dielectric losses maintain a very low value. (C) 2008 Elsevier Ltd. All rights reserved.

Joint Experimental and Theoretical Analysis of Order Disorder Effects in Cubic BaZrO(3) Assembled Nanoparticles under Decaoctahedral Shape

Periodic first-principles calculations based on density functional theory at the B3LYP level has been carried out to investigate the photoluminescence (PL) emission of BaZrO(3) assembled nanoparticles at room temperature. The defect created in the nanocrystals and their resultant electronic features lead to a diversification of electronic recombination within the BaZrO(3) band gap. Its optical phenomena are discussed in the light of photoluminescence emission at the green-yellow region around 570 nm. The theoretical model for displaced atoms and/or angular changes leads to the breaking of the local symmetry, which is based on the refined structure provided by Rietveld methodology. For each situation a band structure, charge mapping, and density of states were built and analyzed. X-ray diffraction (XRD) patterns, UV-vis measurements, and field emission scanning electron microscopy (FE-SEM) images are essential for a full evaluation of the crystal structure and morphology.

Zirconium oxide anodic films: Optical and structural properties

The photoluminescence of anodically prepared ZrO(2) films was investigated. Morphological and microstructural analyses reveal an oxide surface covered by a high distribution of blisters and the major crystallographic structure is the monoclinic phase with small quantities of tetragonal phase. The photoluminescence reveals a broad emission band in the range between 350 and 650 nm. It was proposed that the photoluminescence mechanism is originated from the emission of a recombination center related to defects (oxygen vacancies) formed during Zr anodization. (C) 2008 Elsevier B.V. All rights reserved.

Influence of chromium concentration on the optical-electronic properties of ruby microstructures

Films of amorphous aluminium nitride (AlN) were prepared by conventional radio frequency sputtering of an Al + Cr target in a plasma of pure nitrogen. The Cr-to-Al relative area determines the Cr content, which remained in the similar to 0-3.5 at% concentration range in this study. Film deposition was followed by thermal annealing of the samples up to 1050 degrees C in an atmosphere of oxygen and by spectroscopic characterization through energy dispersive x-ray spectrometry, photoluminescence and optical transmission measurements. According to the experimental results, the optical-electronic properties of the Cr-containing AlN films are highly influenced by both the Cr concentration and the temperature of the thermal treatments. In fact, thermal annealing at 1050 degrees C induces the development of structures that, because of their typical size and distinctive spectral characteristics, were designated by ruby microstructures (RbMSs). These RbMSs are surrounded by a N-rich environment in which Cr(3+) ions exhibit luminescent features not present in other Cr(3+)-containing systems such as ruby, emerald or alexandrite. The light emissions shown by the RbMSs and surroundings were investigated according to the Cr concentration and temperature of measurement, allowing the identification of several Cr(3+)-related luminescent lines. The main characteristics of these luminescent lines and corresponding excitation-recombination processes are presented and discussed in view of a detailed spectroscopic analysis.

GRASSIUS: A Platform for Comparative Regulatory Genomics across the Grasses

Transcription factors (TFs) are major players in gene regulatory networks and interactions between TFs and their target genes furnish spatiotemporal patterns of gene expression. Establishing the architecture of regulatory networks requires gathering information on TFs, their targets in the genome, and the corresponding binding sites. We have developed GRASSIUS (Grass Regulatory Information Services) as a knowledge-based Web resource that integrates information on TFs and gene promoters across the grasses. In its initial implementation, GRASSIUS consists of two separate, yet linked, databases. GrassTFDB holds information on TFs from maize (Zea mays), sorghum (Sorghum bicolor), sugarcane (Saccharum spp.), and rice (Oryza sativa). TFs are classified into families and phylogenetic relationships begin to uncover orthologous relationships among the participating species. This database also provides a centralized clearinghouse for TF synonyms in the grasses. GrassTFDB is linked to the grass TFome collection, which provides clones in recombination-based vectors corresponding to full-length open reading frames for a growing number of grass TFs. GrassPROMDB contains promoter and cis-regulatory element information for those grass species and genes for which enough data are available. The integration of GrassTFDB and GrassPROMDB will be accomplished through GrassRegNet as a first step in representing the architecture of grass regulatory networks. GRASSIUS can be accessed from www.grassius.org.

Inhibition of myeloperoxidase-mediated protein nitration by tempol: Kinetics, mechanism, and implications

Despite the therapeutic potential of tempol (4-hydroxy-2,2,6,6-tetra-methyl-1-piperidinyloxy) and related nitroxides as antioxidants, their effects on peroxidase-mediated protein tyrosine nitration remain unexplored. This posttranslational protein modification is a biomarker of nitric oxide-derived oxidants, and, relevantly, it parallels tissue injury in animal models of inflammation and is attenuated by tempol treatment. Here, we examine tempol effects on ribonuclease (RNase) nitration mediated by myeloperoxidase (MPO), a mammalian enzyme that plays a central role in various inflammatory processes.. Some experiments were also performed with horseradish peroxidase (HRP). We show that tempol efficiently inhibits peroxidase-mediated RNase nitration. For instance, 10 mu M tempol was able to inhibit by 90% the yield of 290 mu M 3-nitrotyrosine produced from 370 mu M RNase. The effect of tempol was not completely catalytic because part of it was consumed by recombination with RNase-tyrosyl radicals. The second-order rate constant of the reaction of tempol with MPO compound I and 11 were determined by stopped-flow kinetics as 3.3 x 10(6) and 2.6 x 10(4) M-1 s(-1), respectively (pH 7.4, 25 degrees C); the corresponding HRP constants were orders of magnitude smaller. Time-dependent hydrogen peroxide and nitrite consumption and oxygen production in the incubations were quantified experimentally and modeled by kinetic simulations. The results indicate that tempol inhibits peroxidase-mediated RNase nitration mainly because of its reaction with nitrogen dioxide to produce the oxammonium cation, which, in turn, recycles back to tempol by reacting with hydrogen peroxide and superoxide radical to produce oxygen and regenerate nitrite. The implications for nitroxide antioxidant mechanisms are discussed.

Trypanosoma cruzi MSH2: Functional analyses on different parasite strains provide evidences for a role on the oxidative stress response

Components of the DNA mismatch repair (MMR) pathway are major players in processes known to generate genetic diversity, such as mutagenesis and DNA recombination. Trypanosoma cruzi, the protozoan parasite that causes Chagas disease has a highly heterogeneous population, composed of a pool of strains with distinct characteristics. Studies with a number of molecular markers identified up to six groups in the T. cruzi population, which showed distinct levels of genetic variability. To investigate the molecular basis for such differences, we analyzed the T. cruzi MSH2 gene, which encodes a key component of MMR, and showed the existence of distinct isoforms of this protein. Here we compared cell survival rates after exposure to genotoxic agents and levels of oxidative stress-induced DNA in different parasite strains. Analyses of msh2 mutants in both T. cruzi and T. brucei were also used to investigate the role of Tcmsh2 in the response to various DNA damaging agents. The results suggest that the distinct MSH2 isoforms have differences in their activity. More importantly, they also indicate that, in addition to its role in MMR, TcMSH2 acts in the parasite response to oxidative stress through a novel mitochondrial function that may be conserved in T. brucei. (C) 2010 Elsevier B.V. All rights reserved.