Genome-Wide Detection of Serpentine Receptor-Like Proteins in Malaria Parasites

Serpentine receptors comprise a large family of membrane receptors distributed over diverse organisms, such as bacteria, fungi, plants and all metazoans. However, the presence of serpentine receptors in protozoan parasites is largely unknown so far. In the present study we performed a genome-wide search for proteins containing seven transmembrane domains (7TM) in the human malaria parasite Plasmodium falciparum and identified four serpentine receptor-like proteins. These proteins, denoted PfSR1, PfSR10, PfSR12 and PfSR25, show membrane topologies that resemble those exhibited by members belonging to different families of serpentine receptors. Expression of the pfsrs genes was detected by Real Time PCR in P. falciparum intraerythrocytic stages, indicating that they potentially code for functional proteins. We also found corresponding homologues for the PfSRs in five other Plasmodium species, two primate and three rodent parasites. PfSR10 and 25 are the most conserved receptors among the different species, while PfSR1 and 12 are more divergent. Interestingly, we found that PfSR10 and PfSR12 possess similarity to orphan serpentine receptors of other organisms. The identification of potential parasite membrane receptors raises a new perspective for essential aspects of malaria parasite host cell infection.

Influence of the bacterioplankton community of a tropical eutrophic lagoon on the bacterial community of its neighbouring ocean

The Rodrigo de Freitas lagoon (RFL) is a tropical eutrophic coastal ecosystem located in the urban area of Rio de Janeiro, Brazil. This environment consists of freshwater but has communication with the ocean through a channel (Jardim de Alah`s Channel). The aim of this study was to evaluate the influence of lagoon water on the nearby ocean using molecular and traditional microbiological methods. We hypothesised that due to the eutrophic low-salinity environment, the bacterioplankton community from the RFL would have a native ""brackish"" composition influenced by both freshwater and marine phylotypes, and that bacterial phylotypes of this community would be detected in oceanic samples closer to the channel between the lagoon and the ocean. The cultivation and microscopy experiments clearly showed this influence. Bacterial cell counts revealed that the greater amounts of bacterial cells present in the lagoon increased the observed values seen at oceanic stations near the channel. The Denaturing gradient gel eletrophoresis community profiles also showed a clear influence of Rodrigo de Freitas lagoon waters on the adjacent beaches. The band patterns found for the stations near the channel showed that these communities were mixtures of the communities of the lagoon and sea, and as the distance from the channel increased, the samples became more similar to ocean bacterial communities. A 16S rRNA gene clone library was constructed using a sample acquired from the connection point between the lagoon and the ocean. Around 52% of the sequences in the library showed similarity to the genus Proteobacteria (1% Alpha, 21% Beta, 19% Gamma and 29% unclassified Proteobacteria), and the second most abundant genus was Bacteroidetes, with 15% of the total clones. The results showed that the structure of the bacterial community had both freshwater and marine characteristics.

Determination of uranium in phosphoric acid using neutron activation analysis

Phosphoric acid is generally obtained from an aqueous process starting with the reaction between phosphate rock and sulphuric acid. Due to their chemical similarity, uranium is usually associated with phosphate rock which during chemical processing is partitioned to phosphoric acid. Uranium determination in this matrix is a very important task because of its ingestion it could lead to radiological impact on the population. Therefore, a procedure was developed using an initial precipitation with calcium hydroxide and evaporation, followed by instrumental neutron activation analysis (INAA). The procedure was applied to analyse fourteen uranium enriched phosphoric acid samples.

Disparity between Multilocus Enzyme Electrophoresis, Microsatellite Markers and Pulsed-Field Gel Electrophoresis in epidemiological tracking of Candida albicans

Various molecular systems are available for epidemiological, genetic, evolutionary, taxonomic and systematic studies of innumerable fungal infections, especially those caused by the opportunistic pathogen C. albicans. A total of 75 independent oral isolates were selected in order to compare Multilocus Enzyme Electrophoresis (MLEE), Electrophoretic Karyotyping (EK) and Microsatellite Markers (Simple Sequence Repeats - SSRs), in their abilities to differentiate and group C. albicans isolates (discriminatory power), and also, to evaluate the concordance and similarity of the groups of strains determined by cluster analysis for each fingerprinting method. Isoenzyme typing was performed using eleven enzyme systems: Adh, Sdh, M1p, Mdh, Idh, Gdh, G6pdh, Asd, Cat, Po, and Lap (data previously published). The EK method consisted of chromosomal DNA separation by pulsed-field gel electrophoresis using a CHEF system. The microsatellite markers were investigated by PCR using three polymorphic loci: EF3, CDC3, and HIS3. Dendrograms were generated by the SAHN method and UPGMA algorithm based on similarity matrices (S(SM)). The discriminatory power of the three methods was over 95%, however a paired analysis among them showed a parity of 19.7-22.4% in the identification of strains. Weak correlation was also observed among the genetic similarity matrices (S(SM)(MLEE) x S(SM)(EK) x S(SM)(SSRs)). Clustering analyses showed a mean of 9 +/- 12.4 isolates per cluster (3.8 +/- 8 isolates/taxon) for MLEE, 6.2 +/- 4.9 isolates per cluster (4 +/- 4.5 isolates/taxon) for SSRs, and 4.1 +/- 2.3 isolates per cluster (2.6 +/- 2.3 isolates/taxon) for EK. A total of 45 (13%), 39(11.2%), 5 (1.4%) and 3 (0.9%) clusters pairs from 347 showed similarity (Si) of 0.1-10%, 10.1-20%, 20.1-30% and 30.1-40%, respectively. Clinical and molecular epidemiological correlation involving the opportunistic pathogen C. albicans may be attributed dependently of each method of genotyping (i.e., MLEE, EK, and SSRs) supplemented with similarity and grouping analysis. Therefore, the use of genotyping systems that give results which offer minimum disparity, or the combination of the results of these systems, can provide greater security and consistency in the determination of strains and their genetic relationships. (C) 2010 Elsevier B.V. All rights reserved.

Rare canopy species in communities within the Atlantic Coastal Forest in Rio de Janeiro State, Brazil

Rare species are one of the principal components of the species richness and diversity encountered in Dense Ombrophilous Tropical Forests. This study sought to analyze the rare canopy species within the Atlantic Coastal Forest in Rio de Janeiro State, Brazil. Six different communities were examined: Dense Ombrophilous alluvial Forest; Dense sub-montane Ombrophilous Forest; Dense Montane Ombrophilous in Serra do Mar and Serra da Mantiqueira. In each area the vegetation was sampled within forty 10 x 25 m plots alternately distributed along a linear transect. All trees with DBH (1.3 m above ground level) a parts per thousand yen5 cm were sampled. The canopy was characterized using the allometric relationship between diameter and height, and included all trees with BDH a parts per thousand yen10 cm and height a parts per thousand yen10 m. A total of 64 families, 206 genera, and 542 species were sampled, of which 297 (54.8%) represented rare species (less than one individual per hectare). The percentage of rare species varied from 34 to 50% in each of the different communities sampled. A majority of these rare trees belonged to the Rosidae, and a smaller proportion to the Dilleniidae. It was concluded that there was no apparent pattern to rarity among families, that rarity was probably derived from a number of processes (such as gap formation), and that a great majority of the rare species sampled were consistently rare. This indicates that the restricted geographic distribution and high degree of endemism of many arboreal taxa justifies the conservation of even small fragments of Atlantic Forest.

Evaluation of three brands of drug interaction software for use in intensive care units

Objective To evaluate drug interaction software programs and determine their accuracy in identifying drug-drug interactions that may occur in intensive care units. Setting The study was developed in Brazil. Method Drug interaction software programs were identified through a bibliographic search in PUBMED and in LILACS (database related to the health sciences published in Latin American and Caribbean countries). The programs` sensitivity, specificity, and positive and negative predictive values were determined to assess their accuracy in detecting drug-drug interactions. The accuracy of the software programs identified was determined using 100 clinically important interactions and 100 clinically unimportant ones. Stockley`s Drug Interactions 8th edition was employed as the gold standard in the identification of drug-drug interaction. Main outcome Sensitivity, specificity, positive and negative predictive values. Results The programs studied were: Drug Interaction Checker (DIC), Drug-Reax (DR), and Lexi-Interact (LI). DR displayed the highest sensitivity (0.88) and DIC showed the lowest (0.69). A close similarity was observed among the programs regarding specificity (0.88-0.92) and positive predictive values (0.88-0.89). The DIC had the lowest negative predictive value (0.75) and DR the highest (0.91). Conclusion The DR and LI programs displayed appropriate sensitivity and specificity for identifying drug-drug interactions of interest in intensive care units. Drug interaction software programs help pharmacists and health care teams in the prevention and recognition of drug-drug interactions and optimize safety and quality of care delivered in intensive care units.

Hydrogen production from soft-drink wastewater in an upflow anaerobic packed-bed reactor

The production of hydrogen from soft-drink wastewater in two upflow anaerobic packed-bed reactors was evaluated. The results show that soft-drink wastewater is a good source for hydrogen generation. Data from both reactors indicate that the reactor without medium containing macro- and micronutrients (R2) provided a higher hydrogen yield (3.5 mol H(2) mol(-1) of sucrose) as compared to the reactor (R1) with a nutrient-containing medium (3.3 mol H(2) mol(-1) of sucrose). Reactor R2 continuously produced hydrogen, whereas reactor R1 exhibited a short period of production and produced lower amounts of hydrogen. Better hydrogen production rates and percentages of biogas were also observed for reactor R2, which produced 0.4 L h(-1) L(-1) and 15.8% of H(2), compared to reactor R1, which produced 0.2 L h(-1) L(-1) and 2.6% of H(2). The difference in performance between the reactors was likely due to changes in the metabolic pathway for hydrogen production and decreases in bed porosity as a result of excessive biomass growth in reactor R1. Molecular biological analyses of samples from reactors R1 and R2 indicated the presence of several microorganisms, including Clostridium (91% similarity), Enterobacter (93% similarity) and Klebsiella (97% similarity). Copyright (C) 2011, Hydrogen Energy Publications, LLC. Published by Elsevier Ltd. All rights reserved.

Molecular characterization of a miraculin-like gene differentially expressed during coffee development and coffee leaf miner infestation

The characterization of a coffee gene encoding a protein similar to miraculin-like proteins, which are members of the plant Kunitz serine trypsin inhibitor (STI) family of proteinase inhibitors (PIs), is described. PIs are important proteins in plant defence against insects and in the regulation of proteolysis during plant development. This gene has high identity with the Richadella dulcifica taste-modifying protein miraculin and with the tomato protein LeMir; and was named as CoMir (Coffea miraculin). Structural protein modelling indicated that CoMir had structural similarities with the Kunitz STI proteins, but suggested specific folding structures. CoMir was up-regulated after coffee leaf miner (Leucoptera coffella) oviposition in resistant plants of a progeny derived from crosses between C. racemosa (resistant) and C. arabica (susceptible). Interestingly, this gene was down-regulated during coffee leaf miner herbivory in susceptible plants. CoMir expression was up-regulated after abscisic acid application and wounding stress and was prominent during the early stages of flower and fruit development. In situ hybridization revealed that CoMir transcripts accumulated in the anther tissues that display programmed cell death (tapetum, endothecium and stomium) and in the metaxylem vessels of the petals, stigma and leaves. In addition, the recombinant protein CoMir shows inhibitory activity against trypsin. According to the present results CoMir may act in proteolytic regulation during coffee development and in the defence against L. coffeella. The similarity of CoMir with other Kunitz STI proteins and the role of CoMir in plant development and plant stress are discussed.

Application of molecular techniques to evaluate the methanogenic archaea and anaerobic bacteria in the presence of oxygen with different COD : sulfate ratios in a UASB reactor

In this paper, the microbial characteristics of the granular sludge in the presence of oxygen (3.0 +/- 0.7 mg O-2 1(-1)) were analyzed using molecular biology techniques. The granules were provided by an upflow anaerobic sludge blanket (UASB) operated over 469 days and fed with synthetic substrate. Ethanol and sulfate were added to obtain different COD/SO42- ratios (3.0, 2.0, and 1.6). The results of fluorescent in situ hybridization (FISH) analyses showed that archaeal cells, detected by the ARC915 probe, accounted for 77%, 84%, and 75% in the COD/SO42- ratios (3.0, 2.0, and 1.6, respectively). Methanosaeta sp. was the predominant acetoclastic archaea observed by optical microscopy and FISH analyses, and confirmed by sequencing of the excised bands of the DGGE gel with a similarity of 96%. The sulfate-reducing bacterium Desulfovibrio vulgaris subsp. vulgaris (similarity of 99%) was verified by sequencing of the DGGE band. Others identified microorganism were similar to Shewanella sp. and Desulfitobacterium hafniense, with similarities of 95% and 99%, respectively. These results confirmed that the presence of oxygen did not severely affect the metabolism of microorganisms that are commonly considered strictly anaerobic. We obtained mean efficiencies of organic matter conversion and sulfate reducing higher than 74%. (C) 2008 Elsevier Ltd. All rights reserved.

Sphericity of apatite particles determined by gas permeability through packed beds

Because shape is an assessment of the three-dimensional form of a particle, it may be described in terms of sphericity (Psi), which is a measure of how closely a particle approaches a spherical configuration. In this study, Darcy`s law and the Kozeny-Carman model for fluid flow through porous media were applied to packed beds to determine the sphericity (Psi) of apatite particles. The beds were composed of glass spheres or particles of apatite (igneous from Brazil and sedimentary from the United States) of three classes of size (Class 1: -297 +210 mu m; Class 2: -210 +149 mu m; Class 3: -149 +105 mu m). Glass spheres were used to validate the model because of its known sphericity (Psi = 1.00). Apatite particles, either igneous or sedimentary, showed very close values for particle sphericity (Psi approximate to 0.6). Observations on particle images conducted by scanning electron microscopy illustrated that igneous (Psi = 0.623) and sedimentary (Psi = 0.644) particles of apatite of Class 2 predominantly exhibit elongated shape. The close value of particle sphericity (Psi approximate to 0.6) showed by either igneous or sedimentary apatite may be justified by the similarity in particle shape.

Spontaneous vegetation on overburden piles in the Coal Basin of Santa Catarina, Brazil

The objective of this work was to select indigenous vegetal species for restoration programs aiming at the regeneration of ombrophilous dense forest. Thirty-five spoil piles located in the county of Sideropolis, Santa Catarina, that received overburden disposal for 39 years (1950-1989) were selected for study because they exhibited remarkable spontaneous regrowth of trees compared to surrounding spoil piles. Floristic inventory covered the whole area of the 35 piles, whereas survey on phytosociology and natural regeneration studies were conducted in 70 plots distributed along the 35 piles. Floristic inventory recorded 83 species from 28 botanical families. Herbaceous terricolous plants constituted the predominant species (47.0%), followed by shrubs (26.5%), trees (19.3%), and vines (7.2%). Results from surveys on phytosociology and natural regeneration, focused on shrubs and trees, recorded incipient ecological succession. In addition, the most adapted species recorded on the overburden piles, as ranked by index of natural regeneration (RNT) plus importance value index (IVI), were as follows: Clethra scabra (RNT = 23.93%; IVI = 17.28%), Myrsine coriacea (RNT = 20.93%, IVI = 11.26%), Eupatorium intermedium (RNT 7.56%, IVI 0.40%), Miconia ligustroides (RNT 5.84%, IVI 2.37%), Ossaea amygdaloides (RNT 3.84%, IVI 1.30%), Tibouchina sellowiana (RNT 3.29%, M 1.94%), Eup. inulaefolium (RNT = 2.65%, IVI = 0.80%), and Baccharis dracunculifolia (RNT = 2.28%; IVI = 0.56%). High values of IVI and RNT exhibited by the exotic species Eucalyptus saligna (IVI = 21.73%, RNT = 51.41%) indicated strong competition between exotic and indigenous species. Severe chemical (acidic pH and lack of nutrients) and physical (coarse substrate and slope angle of 40-50 degrees) characteristics displayed by the overburden piles constituted limitations to floristic diversity and size of indigenous trees, indicating the need for substrate reclamation prior to forest restoration.

Scaling of structures subject to impact loads when using a power law constitutive equation

It is well known that structures subjected to dynamic loads do not follow the usual similarity laws when the material is strain rate sensitive. As a consequence, it is not possible to use a scaled model to predict the prototype behaviour. In the present study, this problem is overcome by changing the impact velocity so that the model behaves exactly as the prototype. This exact solution is generated thanks to the use of an exponential constitutive law to infer the dynamic flow stress. Furthermore, it is shown that the adopted procedure does not rely on any previous knowledge of the structure response. Three analytical models are used to analyze the performance of the technique. It is shown that perfect similarity is achieved, regardless of the magnitude of the scaling factor. For the class of material used, the solution outlined has long been sought, inasmuch as it allows perfect similarity for strain rate sensitive structures subject to impact loads. (C) 2009 Elsevier Ltd. All rights reserved.

Ciratefi: An RST-invariant template matching with extension to color images

Template matching is a technique widely used for finding patterns in digital images. A good template matching should be able to detect template instances that have undergone geometric transformations. In this paper, we proposed a grayscale template matching algorithm named Ciratefi, invariant to rotation, scale, translation, brightness and contrast and its extension to color images. We introduce CSSIM (color structural similarity) for comparing the similarity of two color image patches and use it in our algorithm. We also describe a scheme to determine automatically the appropriate parameters of our algorithm and use pyramidal structure to improve the scale invariance. We conducted several experiments to compare grayscale and color Ciratefis with SIFT, C-color-SIFT and EasyMatch algorithms in many different situations. The results attest that grayscale and color Ciratefis are more accurate than the compared algorithms and that color-Ciratefi outperforms grayscale Ciratefi most of the time. However, Ciratefi is slower than the other algorithms.

Self-organized criticality and the predictability of human behavior

The behavior of normal individuals and psychiatric patients vary in a similar way following power laws. The presence of identical patterns of behavioral variation occurring in individuals with different levels of activity is suggestive of self-similarity phenomena. Based on these findings, we propose that the human behavior in social context can constitute a system exhibiting self-organized criticality (SOC). The introduction of SOC concept in psychological theories can help to approach the question of behavior predictability by taking into consideration their intrinsic stochastic character. Also, the ceteris paribus generalizations characteristic of psychological laws can be seen as a consequence of individual level description of a more complex collective phenomena. Although limited, this study suggests that, if an adequate level of description is adopted, the complexity of human behavior can be more easily approached and their individual and social components can be more realistically modeled. (C) 2009 Elsevier Ltd. All rights reserved.

Generation of self-similar Gaussian time series by means of the DWT and DWPT variance maps

Due to the several kinds of services that use the Internet and data networks infra-structures, the present networks are characterized by the diversity of types of traffic that have statistical properties as complex temporal correlation and non-gaussian distribution. The networks complex temporal correlation may be characterized by the Short Range Dependence (SRD) and the Long Range Dependence - (LRD). Models as the fGN (Fractional Gaussian Noise) may capture the LRD but not the SRD. This work presents two methods for traffic generation that synthesize approximate realizations of the self-similar fGN with SRD random process. The first one employs the IDWT (Inverse Discrete Wavelet Transform) and the second the IDWPT (Inverse Discrete Wavelet Packet Transform). It has been developed the variance map concept that allows to associate the LRD and SRD behaviors directly to the wavelet transform coefficients. The developed methods are extremely flexible and allow the generation of Gaussian time series with complex statistical behaviors.