Re-mapping the molecular features of the human immunodeficiency virus type 1 and human T-cell lymphotropic virus type 1 Brazilian sequences using a bioinformatics unit established in Salvador, Bahia, Brazil, to give support to the viral epidemiology studies

The analysis of genetic data for human immunodeficiency virus type 1 (HIV-1) and human T-cell lymphotropic virus type 1 (HTLV-1) is essential to improve treatment and public health strategies as well as to select strains for vaccine programs. However, the analysis of large quantities of genetic data requires collaborative efforts in bioinformatics, computer biology, molecular biology, evolution, and medical science. The objective of this study was to review and improve the molecular epidemiology of HIV-1 and HTLV-1 viruses isolated in Brazil using bioinformatic tools available in the Laboratório Avançado de Sáude Pública (Lasp) bioinformatics unit. The analysis of HIV-1 isolates confirmed a heterogeneous distribution of the viral genotypes circulating in the country. The Brazilian HIV-1 epidemic is characterized by the presence of multiple subtypes (B, F1, C) and B/F1 recombinant virus while, on the other hand, most of the HTLV-1 sequences were classified as Transcontinental subgroup of the Cosmopolitan subtype. Despite the high variation among HIV-1 subtypes, protein glycosylation and phosphorylation domains were conserved in the pol, gag, and env genes of the Brazilian HIV-1 strains suggesting constraints in the HIV-1 evolution process. As expected, the functional protein sites were highly conservative in the HTLV-1 env gene sequences. Furthermore, the presence of these functional sites in HIV-1 and HTLV-1 strains could help in the development of vaccines that pre-empt the viral escape process.

Echovirus 30 associated with cases of aseptic meningitis in state of Pará, Northern Brazil

Investigation of the aetiology of viral meningitis in Brazil is most often restricted to cases that occur in the Southern and Southeastern Regions; therefore, the purpose of this study is to describe the viral meningitis cases that occurred in state of Pará, Northern Brazil, from January 2005-December 2006. The detection of enterovirus (EV) in cerebrospinal fluid was performed using cell culture techniques, RT-PCR, nested PCR and nucleotide sequencing. The ages of the 91 patients ranged from < one year old to > 60 years old (median age 15.90 years). Fever (87.1%), headache (77.0%), vomiting (61.5%) and stiffness (61.5%) were the most frequent symptoms. Of 91 samples analyzed, 18 (19.8%) were positive for EV. Twelve were detected only by RT- PCR followed by nested PCR, whereas six were found by both cell culture and RT-PCR. From the last group, five were sequenced and classified as echovirus 30 (Echo 30). Phylogenetic analyses revealed that Echo 30 detected in Northern Brazil clustered within a unique group with a bootstrap value of 100% and could constitute a new subgroup (4c) according to the phylogenetic tree described by Oberste et al. (1999). This study described the first molecular characterization of Echo 30 in Brazil and this will certainly contribute to future molecular analyses involving strains detected in other regions of Brazil.

Prevalence and genotyping of hepatitis C virus in blood donors in the state of Pará, Northern Brazil

Given the scarcity of epidemiological information on hepatitis C virus (HCV) infection in Northern Brazil, we determined the prevalence and genotypic frequency in blood donors in the state of Pará (PA). Blood samples from all of the blood donors at the Fundação HEMOPA (blood bank of PA) from 2004-2006 were screened for the presence of antibodies to anti-HCV and samples seroreactive to anti-HCV were further tested for HCV RNA using real-time PCR. In total, 116 HCV-RNA samples were genotyped, based on maximum likelihood phylogenetic analyses, using BioEdit, Modelgenerator, PHYML and FigTree software. The population consisted of 242,726 volunteers who donated blood from 2004-2006; the most common subgroup was males between the ages of 18-29 years old (37.30%). Within the whole group, 1,112 blood donors (0.46%) had indeterminate or positive serology; among these, 28.78% were males whose ages ranged from 18-29 years. A diagnosis of chronic HCV infection was confirmed for 304 donors (60.20% males; 66.45% were 30-49 years old), resulting in a prevalence of HCV RNA in 0.13% of the samples (304 of 242,726). HCV genotyping revealed a high frequency of genotype 1 (108/116) followed by genotype 3 (8/116). This study found HCV infection to be relatively infrequent in PA; genotype 1 was most commonly isolated. This information can help guide prevention and control policies aimed at efficient diagnosis and control measures.

Prevalence and genetic characterisation of HTLV-1 and 2 dual infections in patients with pulmonary tuberculosis in Central-West Brazil

Human T-cell lymphotropic virus (HTLV) may impact the clinical course of tuberculosis (TB). Both infections are highly endemic in Brazil. The aim of this study was to assess the prevalence of HTLV-1/2 in TB patients in Central-West Brazil and to perform a genetic characterisation of the respective isolates. Of the 402 patients, six (1.49%) were positive for anti-HTLV and five (1.24%; 95% confidence interval: 0.46-3.05) were infected with HTLV-1/2. Genetic characterisation demonstrated that the four HTLV-1 isolates belonged to the Transcontinental subgroup A of the Cosmopolitan subtype a and that the HTLV-2 isolate belonged to subtype a (HTLV-2a/c). The prevalence of HTLV infection observed in this study is higher than that observed in local blood donors and the HTLV-1 and 2 subtypes identified are consistent with those circulating in Brazil.

Phylogenetic relationships among four species of the guarani group of Drosophila (Diptera, Drosophilidae) as inferred by molecular and morphological analyses

Traditionally, the Drosophila guarani species group has been divided into two subgroups: the guarani and the guaramunu subgroups. Two, out of the four species included in this research, are members of the guarani subgroup (D. ornatifrons Duda, 1927 and D. subbadia Paterson & Mainland, 1943) and two are included in the guaramunu subgroup (D. maculifrons Duda, 1927 and D. griseolineata Duda, 1927). However, some authors have suggested that D. maculifrons and D. griseolineata are much closer to some species of the Drosophila tripunctata group than to some of the species of the guarani group. To add new data to the matter under dispute, Polyacrylamide Gel Eletrophoresis (PAGE-SDS) was used for the analysis and comparison of protein composition and Random Amplified Polymorphic DNA (RAPD) analysis to find differences in genomic DNA, in addition to the analysis of quantitative morphological characters previously described. Analysis of PAGE-SDS results in a dendrogram that pointed out D. subbadia as being the most distant within the Drosophila guarani group. However, these results were not supported either by RAPD analysis or by the analysis of continuous morphological characters, which supplied the clustering of D. subbadia with D. ornatifrons. Although our data give strong support to the clustering of D. subbadia and D. ornatifrons, none of the dendrograms provided a clade comprising D. maculifrons and D. griseolineata. Thus, this research does not support the traditional subdivision of the D. guarani group into those two subgroups.

Meliponini neotropicais: o gênero Partamona Schwarz, 1939 (Hymenoptera, Apidae, Apinae) - bionomia e biogeografia

This work, dedicated to the study of nesting habits of the species of the Neotropical genus Partamona Schwarz, is a sequence to the taxonomic revision recently published elsewhere. A total of 214 nests and nest aggregations of 18 species [Partamona epiphytophila Pedro & Camargo, 2003; P. testacea (Klug, 1807); P. mourei Camargo, 1980; P. vicina Camargo, 1980; P. auripennis Pedro & Camargo, 2003; P. combinata Pedro & Camargo, 2003; P. chapadicola Pedro & Camargo, 2003; P. nhambiquara Pedro & Camargo, 2003; P. ferreirai Pedro & Camargo, 2003; P. pearsoni (Schwarz, 1938); P. gregaria Pedro & Camargo, 2003; P. batesi Pedro & Camargo, 2003; P. ailyae Camargo, 1980; P. cupira (Smith, 1863); P. mulata Moure in Camargo, 1980; P. seridoensis Pedro & Camargo, 2003; P. criptica Pedro & Camargo, 2003; P. helleri (Friese, 1900)] were studied , including data about habitat, substrate, structural characteristics, construction materials and behavior. The descriptions of the nests are illustrated with 48 drawings. Partial data of the nests of P. bilineata (Say, 1837), P. xanthogastra Pedro & Camargo, 1997, P. orizabaensis (Strand, 1919), P. peckolti (Friese, 1901), P. aequatoriana Camargo, 1980, P. musarum (Cockerell, 1917) and P. rustica Pedro & Camargo, 2003 are also presented. Nests of P. grandipennis (Schwarz, 1951), P. yungarum Pedro & Camargo, 2003, P. subtilis Pedro & Camargo, 2003, P. vitae Pedro & Camargo, 2003, P. nigrior (Cockerell, 1925), P. sooretamae Pedro & Camargo, 2003 and P. littoralis Pedro & Camargo, 2003 are unknown. The species of Partamona build notable nest entrance structures, with special surfaces for incoming / exiting bees; some of them are extremely well-elaborated and ornamented, serving as flight orientation targets. All species endemic to western Ecuador to Mexico with known nesting habits (P. orizabaensis, P. peckolti, P. xanthogastra, P. bilineata, P. aequatoriana and P. musarum) build their nests in several substrates, non-associated with termitaria, such as cavities and crevices in walls, among roots of epiphytes and in bases of palm leaves, in abandoned bird nests, under bridges, and in other protected places, except P. peckolti that occasionally occupies termite nests. In South America, on the eastern side of the Andes, only P. epiphytophila and P. helleri nest among roots of epiphytes and other substrates, non-associated with termitaria. All other species studied (P. batesi, P. gregaria, P. pearsoni, P. ferreirai, P. chapadicola, P. nhambiquara, P. vicina, P. mourei, P. auripennis, P. combinata, P. cupira, P. mulata, P. ailyae, P. seridoensis, P. criptica and P. rustica) nest inside active termite nests, whether epigeous or arboreous. The only species that builds obligate subterranean nests, associated or not with termite or ant nests (Atta spp.) is P. testacea. Nests of Partamona have one vestibular chamber (autapomorphic for the genus) closely adjacent to the entrance, filled with a labyrinth of anastomosing pillars and connectives, made of earth and resins. One principal chamber exists for food and brood, but in some species one or more additional chambers are filled with food storage pots. In nests of P. vicina, there is one atrium or "false nest", between the vestibule and the brood chamber, which contains involucral sheaths, cells and empty pots. All structures of the nest are supported by permanent pillars made of earth and resins (another autapomorphy of the genus). The characters concerning nesting habits were coded and combined with morphological and biogeographic data, in order to hypothesize the evolutive scenario of the genus using cladistic methodology. The phylogenetic hypothesis presented is the following: (((((P. bilineata (P. grandipennis, P. xanthogastra)) (P. orizabaensis, P. peckolti)) (P. aequatoriana, P. musarum)) P. epiphytophila, P. yungarum, P. subtilis, P. vitae) (((((P. testacea (P. mourei, P. vicina)) (P. nigrior (P. auripennis, P. combinata))) (P. ferreirai (P. pearsoni (P. gregaria (P. batesi (P. chapadicola, P. nhambiquara)))))) ((((P. ailyae, P. sooretamae) P. cupira, P. mulata) P. seridoensis) P. criptica, P. rustica, P. littoralis)) P. helleri))). One area cladogram is presented. Dates of some vicariance / cladogenesis events are suggested. For bilineata / epiphytophila group, which inhabits the Southwestern Amazonia and the Chocó-Mexican biogeographical components, the origin of ancestral species is attributed to the Middle Miocene, when the transgressions of the Maracaibo and Paranense seas isolated the tropical northwestern South America from the eastern continental land mass. The next cladogenic event in the history of the bilineata / epiphytophila group is attributed to the Plio-Pleistocene, when the Ecuadorian Andes reached more than 3000 m, and the ancestral species was fragmented in two populations, one occupying the western Andes (ancestral species of the bilineata subgroup) and other the southwestern Amazon (ancestral species of the epiphytophila subgroup). Other aspects of the history of Partamona are also discussed.

A new spot-thoraxed species of Drosophila from the Atlantic Forest of southeastern Brazil (Diptera, Drosophilidae)

Drosophila boraceia sp. nov. is described from a single male specimen collected at the Estação Biológica de Boracéia, Salesópolis, state of São Paulo, Brazil. At first inspection it looks like a species of Drosophila belonging to the fasciola subgroup of the repleta group, mainly because of the fasciola-like pattern of fused spots on the thorax. However, mostly due to the quite distinct structures of the male terminalia, it seems to be more similar to one ungrouped and also spot-thoraxed South American species, Drosophila atalaia Vilela & Sene, 1982. Illustrations of the terminalia are also provided.

Drosophila angustibucca Duda sensu Frota-Pessoa is an undescribed species (Diptera, Drosophilidae)

Drosophila nappae sp. nov. , belonging to the subgroup I of the Drosophila tripunctata species group of the subgenus Drosophila, is described from flies of one strain established from several females collected from July 1994 through April 1995 at Morro Santana, Porto Alegre, state of Rio Grande do Sul, Brazil. This species has been misidentified during the past fifty years as Drosophila angustibucca (sensu Frota-Pessoa, 1954; non Duda, 1925, described from Costa Rica). Illustrations of male and female terminalia are also provided.

Is Drosophila nasuta Lamb (Diptera, Drosophilidae) currently reaching the status of a cosmopolitan species?

ABSTRACT In early March 2015, three males and two females of one unknown species of Drosophila were collected from a compost pile and some garbage cans in the west region of the city of São Paulo, state of São Paulo, Brazil. Morphologically it is easily identified by the presence of the following conspicuous features: a brownish dorsal stripe along pleura, an entirely iridescent silvery-whitish frons when seen directly from the front, and a row of cuneiform setae on anteroventral side of femur of foreleg; the former two traits being more evident in males. The species was easily reared in a modified banana-agar medium and two isofemale lines were established allowing to obtain mitotic cells showing a diploid chromosome number of 2n = 8. Based both on morphological and chromosomal features, in addition to the geographical distribution, we concluded that the unknown flies belong to Drosophila nasuta Lamb, 1914, a tropical species of the nasuta subgroup of the Drosophila immigrans species group. Photomicrographs of male imagines, terminalia, mitotic and meiotic metaphase plates, as well as of female mitotic metaphase, are included.

Kinetics of K release from soils of Brazilian coffee regions: effect of organic acids

Kinetic studies on soil potassium release can contribute to a better understanding of K availability to plants. This study was conducted to evaluate K release rates from the whole soil, clay, silt, and sand fractions of B-horizon samples of a basalt-derived Oxisol and a sienite-derived Ultisol, both representative soils from coffee regions of Minas Gerais State, Brazil. Potassium was extracted from each fraction after eight different shaking time periods (0-665 h) with either 0.001 mol L-1 citrate or oxalate at a 1:10 solid:solution ratio. First-order, Elovich, zero-order, and parabolic diffusion equations were used to parameterize the time dependence of K release. For the Oxisol, the first-order equation fitted best to the experimental data of K release, with similar rates for all fractions and independent of the presence of citrate or oxalate in the extractant solution. For all studied Ultisol fractions, in which K release rates increased when extractions were performed with citrate solution, the Elovich model described K release kinetics most adequately. The highest potassium release rate of the Ultisol silt fraction was probably due to the transference of "non-exchangeable" K to the extractant solution, whereas in the Oxisol exchangeable potassium represented the main K source in all studied fractions.

Characterization and classification of soils in the Taquari river basin - Pantanal region, state of Mato Grosso do Sul, Brazil

Among the soils in the Mato Grosso do Sul, stand out in the Pantanal biome, the Spodosols. Despite being recorded in considerable extensions, few studies aiming to characterize and classify these soils were performed. The purpose of this study was to characterize and classify soils in three areas of two physiographic types in the Taquari river basin: bay and flooded fields. Two trenches were opened in the bay area (P1 and P2) and two in the flooded field (P3 and P4). The third area (saline) with high sodium levels was sampled for further studies. In the soils in both areas the sand fraction was predominant and the texture from sand to sandy loam, with the main constituent quartz. In the bay area, the soil organic carbon in the surface layer (P1) was (OC) > 80 g kg-1, being diagnosed as Histic epipedon. In the other profiles the surface horizons had low OC levels which, associated with other properties, classified them as Ochric epipedons. In the soils of the bay area (P1 and P2), the pH ranged from 5.0 to 7.5, associated with dominance of Ca2+ and Mg2+, with base saturation above 50 % in some horizons. In the flooded fields (P3 and P4) the soil pH ranged from 4.9 to 5.9, H+ contents were high in the surface horizons (0.8-10.5 cmol c kg-1 ), Ca2+ and Mg² contents ranged from 0.4 to 0.8 cmol c kg-1 and base saturation was < 50 %. In the soils of the bay area (P1 and P2) iron was accumulated (extracted by dithionite - Fed) and OC in the spodic horizon; in the P3 and P4 soils only Fed was accumulated (in the subsurface layers). According to the criteria adopted by the Brazilian System of Soil Classification (SiBCS) at the subgroup level, the soils were classified as: P1: Organic Hydromorphic Ferrohumiluvic Spodosol. P2: Typical Orthic Ferrohumiluvic Spodosol. P3: Typical Hydromorphic Ferroluvic Spodosol. P4: Arenic Orthic Ferroluvic Spodosol.

Genesis, Characterization, and Classification of Mangrove Soils in the Subaé River Basin, Bahia, Brazil

ABSTRACT Preservation of mangroves, a very significant ecosystem from a social, economic, and environmental viewpoint, requires knowledge on soil composition, genesis, morphology, and classification. These aspects are of paramount importance to understand the dynamics of sustainability and preservation of this natural resource. In this study mangrove soils in the Subaé river basin were described and classified and inorganic waste concentrations evaluated. Seven pedons of mangrove soil were chosen, five under fluvial influence and two under marine influence and analyzed for morphology. Samples of horizons and layers were collected for physical and chemical analyses, including heavy metals (Pb, Cd, Mn, Zn, and Fe). The moist soils were suboxidic, with Eh values below 350 mV. The pH level of the pedons under fluvial influence ranged from moderately acid to alkaline, while the pH in pedons under marine influence was around 7.0 throughout the profile. The concentration of cations in the sorting complex for all pedons, independent of fluvial or marine influence, indicated the following order: Na+>Mg2+>Ca2+>K+. Mangrove soils from the Subaé river basin under fluvial and marine influence had different morphological, physical, and chemical characteristics. The highest Pb and Cd concentrations were found in the pedons under fluvial influence, perhaps due to their closeness to the mining company Plumbum, while the concentrations in pedon P7 were lowest, due to greater distance from the factory. For containing at least one metal above the reference levels established by the National Oceanic and Atmospheric Administration (United States Environmental Protection Agency), the pedons were classified as potentially toxic. The soils were classified as Gleissolos Tiomórficos Órticos (sálicos) sódico neofluvissólico in according to the Brazilian Soil Classification System, indicating potential toxicity and very poor drainage, except for pedon P7, which was classified in the same subgroup as the others, but different in that the metal concentrations met acceptable standards.

Evaluation of preoperative computed tomography angiography in association with conventional angiography versus computed tomography angiography only, in the endovascular treatment of aortic diseases

Objective To evaluate the association of conventional angiography (AG) with computed tomography angiography (CTA) as compared with CTA only, preoperatively, in the treatment of aortic diseases. Materials and Methods Retrospective study involving patients submitted to endovascular treatment of aortic diseases, in the period from January 2009 to July 2010, with use of preoperative CTA + conventional AG or CTA only. The patients were divided into two groups, namely: G1 – thoracic aortic diseases; and G2 – abdominal aortic diseases. G1 was subdivided into 1A (preoperative AG + CTA) and 1B (preoperative CTA). G2 was subdivided into 2C (CTA + AG) and 2D (CTA only). Results The authors evaluated 156 patients. In subgroups 1A and 1B, the rate of technical success was, respectively, 100% and 94.7% (p = 1.0); and the rate of therapeutic success was, respectively, 81% and 58% (p = 0.13). A higher number of complications were observed in subgroup 1B (p = 0.057). The accuracy in the calculation of the prosthesis was higher in subgroup 1A (p = 0.065). In their turn, the rate of technical success in subgroups 2C and 2D was, respectively, 92.3% and 98.6% (p = 0.17). The rate of therapeutic success was 73% and 98.6% (p = 0.79). Conclusion Preoperative conventional AG should be reserved for cases where CTA cannot provide all the information in the planning of a therapeutic intervention.

O emprego de quitosana quimicamente modificada com anidrido succínico na adsorção de azul de metileno

The adsorption capacity of alpha-chitosan and its modified form with succinic anhydride was compared with the traditional adsorbent active carbon by using the dye methylene blue, employed in the textile industry. The isotherms for both biopolymers were classified as SSA systems in the Giles model, more specifically in L class and subgroup 3. The dye concentration in the supernatant in the adsorption assay was determined through electronic spectroscopy. By calorimetric titration thermodynamic data of the interaction between methyene blue and the chemically modified chitosan at the solid/liquid interface were obtained. The enthalpy of the dye/chitosan interaction gave 2.47 ± 0.02 kJ mol-1 with an equilibrium constant of 7350 ± 10 and for the carbon/dye interaction this constant gave 5951 ± 8. The spontaneity of these adsorptions are reflected by the free Gibbs energies of -22.1 ± 0.4 and -21.5 ± 0.2 kJ mol-1, respectively, found for these systems. This new adsorbent derived from a natural polysaccharide is as efficient as activated carbon. However 97% of the bonded dye can be eluted by sodium chloride solution, while this same operation elutes only 42% from carbon. Chitosan is efficient in dye removal with the additional advantage of being cheap, non-toxic, biocompatible and biodegradable.

Obtenção de filmes espessos de seleneto de cobre sobre carbono vítreo, ouro, titânio e cobre

Copper selenide (berzelianite) films were prepared on the title substrates using the chemical bath deposition technique (CBD). Film composition was determined by energy dispersion of x-rays. The kinetics of film growth is parabolic and film adherence limits the film thickness. On titanium, copper selenide forms islands that do not completely cover the surface, unless the substrate is prepared with a tin oxide layer; film composition also depends on the titanium oxide layer. On vitreous carbon, CBD and mechanical immobilization techniques lead to films with similar resistances for the electron transfer across the film/substrate interface. On gold, composition studies revealed that film composition is always the same if the pH is in the range from 8 to 12, in contrast to films prepared by an ion-ion combination route. On copper, a new procedure for obtaining copper selenide films as thick as 5 µm has been developed.