Near full-length genome analysis of low prevalent human immunodeficiency virus type 1 subclade F1 in Sao Paulo, Brazil

Background: The genetic diversity of the human immunodeficiency virus type 1 (HIV-1) is critical to lay the groundwork for the design of successful drugs or vaccine. In this study we aimed to characterize and define the molecular prevalence of HIV-1 subclade F1 currently circulating in Sao Paulo, Brazil. Methods: A total of 36 samples were selected from 888 adult patients residing in Sao Paulo who had previously been diagnosed in two independent studies in our laboratory as being infected with subclade F1 based on pol subgenomic fragment sequencing. Proviral DNA was amplified from the purified genomic DNA of all 36 blood samples by 5 fragments overlapping PCR followed by direct sequencing. Sequence data were obtained from the 5 fragments of pure subclade F1 and phylogenetic trees were constructed and compared with previously published sequences. Subclades F1 that exhibited mosaic structure with other subtypes were omitted from any further analysis Results: Our methods of fragment amplification and sequencing confirmed that only 5 sequences inferred from pol region as subclade F1 also holds true for the genome as a whole and, thus, estimated the true prevalence at 0.56%. The results also showed a single phylogenetic cluster of the Brazilian subclade F1 along with non-Brazilian South American isolates in both subgenomic and the full-length genomes analysis with an overall intrasubtype nucleotide divergence of 6.9%. The nucleotide differences within the South American and Central African F1 strains, in the C2-C3 env, were 8.5% and 12.3%, respectively. Conclusion: All together, our findings showed a surprisingly low prevalence rate of subclade F1 in Brazil and suggest that these isolates originated in Central Africa and subsequently introduced to South America.

First Report of the Isolation and Molecular Characterization of Rickettsia amblyommii and Rickettsia felis in Central America

During 2010, 15 adult ticks, identified as Amblyomma cajennense, were collected from horses in Cahuita and Turrialba districts, whereas 7 fleas, identified as Ctenocephalides felis, were collected from a dog in San Jose city, Costa Rica. In the laboratory, three A. cajennense specimens, two from Cahuita and one from Turrialba, were individually processed for rickettsial isolation in cell culture, as was a pool of seven fleas. Rickettsiae were successfully isolated and established in Vero cell culture from the three ticks and from a pool of seven fleas in C6/36 cell culture. The three tick isolates were genotypically identified as Rickettsia amblyommii, and the flea isolate was identified as Rickettsia felis through DNA sequencing of portions of the rickettsial genes gltA, ompA, and ompB of each isolate. In addition, other seven ticks were shown to contain rickettsial DNA. Polymerase chain reaction products of at least two of these ticks were sequenced and also showed to correspond to R. amblyommii. Overall, 66.7% (10/15) of the A. cajennense adult ticks were found to be infected with rickettsiae. This is the first report of a successful isolation in cell culture of R. amblyommii and R. felis from Central America.

Molecular and geographic analyses of vampire bat-transmitted cattle rabies in central Brazil

Background: Vampire bats are important rabies virus vectors, causing critical problems in both the livestock industry and public health sector in Latin America. In order to assess the epidemiological characteristics of vampire bat-transmitted rabies, the authors conducted phylogenetic and geographical analyses using sequence data of a large number of cattle rabies isolates collected from a wide geographical area in Brazil. Methods: Partial nucleoprotein genes of rabies viruses isolated from 666 cattle and 18 vampire bats between 1987 and 2006 were sequenced and used for phylogenetic analysis. The genetic variants were plotted on topographical maps of Brazil. Results: In this study, 593 samples consisting of 24 genetic variants were analyzed. Regional localization of variants was observed, with the distribution of several variants found to be delimited by mountain ranges which served as geographic boundaries. The geographical distributions of vampire-bat and cattle isolates that were classified as the identical phylogenetic group were found to overlap with high certainty. Most of the samples analyzed in this study were isolated from adjacent areas linked by rivers. Conclusion: This study revealed the existence of several dozen regional variants associated with vampire bats in Brazil, with the distribution patterns of these variants found to be affected by mountain ranges and rivers. These results suggest that epidemiological characteristics of vampire bat-related rabies appear to be associated with the topographical and geographical characteristics of areas where cattle are maintained, and the factors affecting vampire bat ecology.

Phylogenetic position of the acariform mites: sensitivity to homology assessment under total evidence

Background: Mites (Acari) have traditionally been treated as monophyletic, albeit composed of two major lineages: Acariformes and Parasitiformes. Yet recent studies based on morphology, molecular data, or combinations thereof, have increasingly drawn their monophyly into question. Furthermore, the usually basal (molecular) position of one or both mite lineages among the chelicerates is in conflict to their morphology, and to the widely accepted view that mites are close relatives of Ricinulei. Results: The phylogenetic position of the acariform mites is examined through employing SSU, partial LSU sequences, and morphology from 91 chelicerate extant terminals (forty Acariformes). In a static homology framework, molecular sequences were aligned using their secondary structure as guide, whereby regions of ambiguous alignment were discarded, and pre-aligned sequences analyzed under parsimony and different mixed models in a Bayesian inference. Parsimony and Bayesian analyses led to trees largely congruent concerning infraordinal, well-supported branches, but with low support for inter-ordinal relationships. An exception is Solifugae + Acariformes (P. P = 100%, J. = 0.91). In a dynamic homology framework, two analyses were run: a standard POY analysis and an analysis constrained by secondary structure. Both analyses led to largely congruent trees; supporting a (Palpigradi (Solifugae Acariformes)) clade and Ricinulei as sister group of Tetrapulmonata with the topology (Ricinulei (Amblypygi (Uropygi Araneae))). Combined analysis with two different morphological data matrices were run in order to evaluate the impact of constraining the analysis on the recovered topology when employing secondary structure as a guide for homology establishment. The constrained combined analysis yielded two topologies similar to the exclusively molecular analysis for both morphological matrices, except for the recovery of Pedipalpi instead of the (Uropygi Araneae) clade. The standard (direct optimization) POY analysis, however, led to the recovery of trees differing in the absence of the otherwise well-supported group Solifugae + Acariformes. Conclusions: Previous studies combining ribosomal sequences and morphology often recovered topologies similar to purely morphological analyses of Chelicerata. The apparent stability of certain clades not recovered here, like Haplocnemata and Acari, is regarded as a byproduct of the way the molecular homology was previously established using the instrumentalist approach implemented in POY. Constraining the analysis by a priori homology assessment is defended here as a way of maintaining the severity of the test when adding new data to the analysis. Although the strength of the method advocated here is keeping phylogenetic information from regions usually discarded in an exclusively static homology framework; it still has the inconvenience of being uninformative on the effect of alignment ambiguity on resampling methods of clade support estimation. Finally, putative morphological apomorphies of Solifugae + Acariformes are the reduction of the proximal cheliceral podomere, medial abutting of the leg coxae, loss of sperm nuclear membrane, and presence of differentiated germinative and secretory regions in the testis delivering their products into a common lumen.

Severe Plasmodium vivax malaria exhibits marked inflammatory imbalance

Background: Despite clinical descriptions of severe vivax malaria cases having been reported, data regarding immunological and inflammatory patterns are scarce. In this report, the inflammatory and immunological status of both mild and severe vivax malaria cases are compared in order to explore immunopathological events in this disease. Methods and Results: Active and passive malaria case detections were performed during 2007 in Buritis, Rondonia, in the Brazilian Amazon. A total of 219 participants enrolled the study. Study individuals were classified according to the presence of Plasmodium vivax infection within four groups: non-infected (n = 90), asymptomatic (n = 60), mild (n = 50) and severe vivax infection (n = 19). A diagnosis of malaria was made by microscopy and molecular assays. Since at present no clear criteria define severe vivax malaria, this study adapted the consensual criteria from falciparum malaria. Patients with severe P. vivax infection were younger, had lived for shorter time in the endemic area, and recalled having experienced less previous malaria episodes than individuals with no malaria infection and with mild or asymptomatic infection. Strong linear trends were identified regarding increasing plasma levels of C reactive protein (CRP), serum creatinine, bilirubins and the graduation of disease severity. Plasma levels of tumour necrosis factor (TNF), interferon-gamma(IFN-gamma) and also IFN-gamma/interleukin-10 ratios were increased and exhibited a linear trend with gradual augmentation of disease severity. Both laboratory parameters of organ dysfunction and inflammatory cytokines were reduced during anti-parasite therapy in those patients with severe disease. Conclusion: Different clinical presentations of vivax malaria infection present strong association with activation of pro-inflammatory responses and cytokine imbalance. These findings are of utmost importance to improve current knowledge about physiopathological concepts of this serious widespread disease.

Three-dimensional visualization of human hemoglobin phenotypes with HPLC

Hemoglobinopathies were included in the Brazilian Neonatal Screening Program on June 6, 2001. Automated high-performance liquid chromatography (HPLC) was indicated as one of the diagnostic methods. The amount of information generated by these systems is immense, and the behavior of groups cannot always be observed in individual analyses. Three-dimensional (3-D) visualization techniques can be applied to extract this information, for extracting patterns, trends or relations from the results stored in databases. We applied the 3-D visualization tool to analyze patterns in the results of hemoglobinopathy based on neonatal diagnosis by HPLC. The laboratory results of 2520 newborn analyses carried out in 2001 and 2002 were used. The ""Fast"", ""F1"", ""F"" and ""A"" peaks, which were detected by the analytical system, were chosen as attributes for mapping. To establish a behavior pattern, the results were classified into groups according to hemoglobin phenotype: normal (N = 2169), variant (N = 73) and thalassemia (N = 279). 3-D visualization was made with the FastMap DB tool; there were two distribution patterns in the normal group, due to variation in the amplitude of the values obtained by HPLC for the F1 window. It allowed separation of the samples with normal Hb from those with alpha thalassemia, based on a significant difference (P < 0.05) between the mean values of the ""Fast"" and ""A"" peaks, demonstrating the need for better evaluation of chromatograms; this method could be used to help diagnose alpha thalassemia in newborns.

Electronic properties of liquid ammonia: A sequential molecular dynamics/quantum mechanics approach

The electronic properties of liquid ammonia are investigated by a sequential molecular dynamics/quantum mechanics approach. Quantum mechanics calculations for the liquid phase are based on a reparametrized hybrid exchange-correlation functional that reproduces the electronic properties of ammonia clusters [(NH(3))(n); n=1-5]. For these small clusters, electron binding energies based on Green's function or electron propagator theory, coupled cluster with single, double, and perturbative triple excitations, and density functional theory (DFT) are compared. Reparametrized DFT results for the dipole moment, electron binding energies, and electronic density of states of liquid ammonia are reported. The calculated average dipole moment of liquid ammonia (2.05 +/- 0.09 D) corresponds to an increase of 27% compared to the gas phase value and it is 0.23 D above a prediction based on a polarizable model of liquid ammonia [Deng , J. Chem. Phys. 100, 7590 (1994)]. Our estimate for the ionization potential of liquid ammonia is 9.74 +/- 0.73 eV, which is approximately 1.0 eV below the gas phase value for the isolated molecule. The theoretical vertical electron affinity of liquid ammonia is predicted as 0.16 +/- 0.22 eV, in good agreement with the experimental result for the location of the bottom of the conduction band (-V(0)=0.2 eV). Vertical ionization potentials and electron affinities correlate with the total dipole moment of ammonia aggregates. (c) 2008 American Institute of Physics.

Theoretical study on the molecular and electronic properties of some substances used for diabetes mellitus treatment

Diabetes mellitus (DM) is a disease that affects a large number of people, and the number of problems associated with the disease has been increasing in the past few decades. These problems include cardiovascular disorders, blindness and the eventual need to amputate limbs. Therefore, the quality of life for people living with DM is less than it is for healthy people. In several cases, metabolic syndrome (MS), which can be considered a disturbance of the lipid metabolism, is associated with DM. In this work, two drugs used to treat DM, pioglitazone and rosiglitazone, were studied using theoretical methods, and their molecular properties were related to the biological activity of these drugs. From the results, it was possible to correlate the properties of each substance-particularly electronic properties-with the biological interactions that are linked to their pharmacological effects. These results suggest that there are future prospects for designing or developing new drugs based on the correlation between theoretical and experimental properties.

EVOLUTION AND LIFETIME OF TRANSIENT CLUMPS IN THE TURBULENT INTERSTELLAR MEDIUM

We study the evolution of dense clumps and provide an argument that the existence of the clumps is not limited by their crossing times. We claim that the lifetimes of the clumps are determined by turbulent motions on a larger scale, and we predict the correlation of clump lifetime with column density. We use numerical simulations to successfully test this relation. In addition, we study the morphological asymmetry and the magnetization of the clumps as functions of their masses.

Assessment of the Performance of Acoustic and Mass Balance Methods for Leak Detection in Pipelines for Transporting Liquids

On-line leak detection is a main concern for the safe operation of pipelines. Acoustic and mass balance are the most important and extensively applied technologies in field problems. The objective of this work is to compare these leak detection methods with respect to a given reference situation, i.e., the same pipeline and monitoring signals acquired at the inlet and outlet ends. Experimental tests were conducted in a 749 m long laboratory pipeline transporting water as the working fluid. The instrumentation included pressure transducers and electromagnetic flowmeters. Leaks were simulated by opening solenoid valves placed at known positions and previously calibrated to produce known average leak flow rates. Results have clearly shown the limitations and advantages of each method. It is also quite clear that acoustics and mass balance technologies are, in fact, complementary. In general, an acoustic leak detection system sends out an alarm more rapidly and locates the leak more precisely, provided that the rupture of the pipeline occurs abruptly enough. On the other hand, a mass balance leak detection method is capable of quantifying the leak flow rate very accurately and of detecting progressive leaks.

Methane generation in tropical landfills: Simplified methods and field results

This paper deals with the use of simplified methods to predict methane generation in tropical landfills. Methane recovery data obtained on site as part of a research program being carried Out at the Metropolitan Landfill, Salvador, Brazil, is analyzed and used to obtain field methane generation over time. Laboratory data from MSW samples of different ages are presented and discussed: and simplified procedures to estimate the methane generation potential, L(o), and the constant related to the biodegradation rate, k are applied. The first order decay method is used to fit field and laboratory results. It is demonstrated that despite the assumptions and the simplicity of the adopted laboratory procedures, the values L(o) and k obtained are very close to those measured in the field, thus making this kind of analysis very attractive for first approach purposes. (C) 2008 Elsevier Ltd. All rights reserved.

EFFECT OF THERMAL TREATMENT ON PHENOLIC COMPOUNDS AND FUNCTIONALITY LINKED TO TYPE 2 DIABETES AND HYPERTENSION MANAGEMENT OF PERUVIAN AND BRAZILIAN BEAN CULTIVARS (PHASEOLUS VULGARIS L.) USING IN VITRO METHODS

The effect of thermal treatment on phenolic compounds and type 2 diabetes functionality linked to alpha-glucosidase and alpha-amylase inhibition and hypertension relevant angiotensin I-converting enzyme (ACE) inhibition were investigated in selected bean (Phaseolus vulgaris L,) cultivars from Peru and Brazil using in vitro models. Thermal processing by autoclaving decreased the total phenolic content in all cultivars, whereas the 1,1-diphenyl-2-picrylhydrazyl radical scavenging activity-linked antioxidant activity increased among Peruvian cultivars, alpha-Amylase and alpha-glucosidase inhibitory activities were reduced significantly after heat treatment (73-94% and 8-52%, respectively), whereas ACE inhibitory activity was enhanced (9-15%). Specific phenolic acids such as chlorogenic and caffeic acid increased moderately following thermal treatment (2-16% and 5-35%, respectively). No correlation was found between phenolic contents and functionality associated to antidiabetes and antihypertension potential, indicating that non phenolic compounds may be involved. Thermally processed bean cultivars are interesting sources of phenolic acids linked to high antioxidant activity and show potential for hypertension prevention.

Synthetic peptides as an antigenic base in an ELISA for laboratory diagnosts of schistosomiasis mansoni

A pool of five synthetic peptides was used as an antigenic base in an ELISA (ELISA-Pp) for laboratory diagnosis of Schistosoma mansoni. Serum samples were obtained from individuals with acute (n = 23) and chronic (n = 30) schistosomiasis, with other parasitoses (n = 39) or without parasitic infections (n = 100). ELISA-Pp was compared with other immunoenzymatic methods for detection of IgM (IgM-ELISA) or IgG (IgG-ELISA) as well as an immunofluorescence test for detection of IgM antibodies (IgM-IFT). The sensitivity and specificity of ELISA-Pp was 86.8% and 94.2% when tested on the schistosomiasis group and the non-schistosomiasis group, respectively. Comparison of ELISA-Pp with other serological methods resulted in K concordance indices varying from 0.59 to 0.75. Evaluation of anti-peptide IgG antibodies showed higher Levels in patients with acute compared with chronic schistosomiasis (P = 0.001). ELISA-Pp showed satisfactory sensitivity and high specificity and may constitute a potentially useful method for laboratory diagnosis of schistosomiasis mansoni. (c) 2007 Royal Society of Tropical Medicine and Hygiene. Published by Elsevier Ltd. All rights reserved.

Biotype stability of Candida albicans isolates after culture storage determined by randomly amplified polymorphic DNA and phenotypical methods

P>Typing methods to evaluate isolates in relation to their phenotypical and molecular characteristics are essential in epidemiological studies. In this study, Candida albicans biotypes were determined before and after storage in order to verify their stability. Twenty C. albicans isolates were typed by Randomly Amplified Polymorphic DNA (RAPD), production of phospholipase and proteinase exoenzymes (enzymotyping) and morphotyping before and after 180 days of storage in Sabouraud dextrose agar (SDA) and sterilised distilled water. Before the storage, 19 RAPD patterns, two enzymotypes and eight morphotypes were identified. The fragment patterns obtained by RAPD, on the one hand, were not significantly altered after storage. On the other hand, the majority of the isolates changed their enzymotype and morphotype after storage. RAPD typing provided the better discriminatory index (DI) among isolates (DI = 0.995) and maintained the profile identified, thereby confirming its utility in epidemiological surveys. Based on the low reproducibility observed after storage in SDA and distilled water by morphotyping (DI = 0.853) and enzymotyping (DI = 0.521), the use of these techniques is not recommended on stored isolates.

A chemometric study on the analgesic activity of cannabinoid compounds using SDA, KNN and SIMCA methods

The supervised pattern recognition methods K-Nearest Neighbors (KNN), stepwise discriminant analysis (SDA), and soft independent modelling of class analogy (SIMCA) were employed in this work with the aim to investigate the relationship between the molecular structure of 27 cannabinoid compounds and their analgesic activity. Previous analyses using two unsupervised pattern recognition methods (PCA-principal component analysis and HCA-hierarchical cluster analysis) were performed and five descriptors were selected as the most relevants for the analgesic activity of the compounds studied: R (3) (charge density on substituent at position C(3)), Q (1) (charge on atom C(1)), A (surface area), log P (logarithm of the partition coefficient) and MR (molecular refractivity). The supervised pattern recognition methods (SDA, KNN, and SIMCA) were employed in order to construct a reliable model that can be able to predict the analgesic activity of new cannabinoid compounds and to validate our previous study. The results obtained using the SDA, KNN, and SIMCA methods agree perfectly with our previous model. Comparing the SDA, KNN, and SIMCA results with the PCA and HCA ones we could notice that all multivariate statistical methods classified the cannabinoid compounds studied in three groups exactly in the same way: active, moderately active, and inactive.