Unexpected Diversity of Cellular Immune Responses against Nef and Vif in HIV-1-Infected Patients Who Spontaneously Control Viral Replication

Background: HIV-1-infected individuals who spontaneously control viral replication represent an example of successful containment of the AIDS virus. Understanding the anti-viral immune responses in these individuals may help in vaccine design. However, immune responses against HIV-1 are normally analyzed using HIV-1 consensus B 15-mers that overlap by 11 amino acids. Unfortunately, this method may underestimate the real breadth of the cellular immune responses against the autologous sequence of the infecting virus. Methodology and Principal Findings: Here we compared cellular immune responses against nef and vif-encoded consensus B 15-mer peptides to responses against HLA class I-predicted minimal optimal epitopes from consensus B and autologous sequences in six patients who have controlled HIV-1 replication. Interestingly, our analysis revealed that three of our patients had broader cellular immune responses against HLA class I-predicted minimal optimal epitopes from either autologous viruses or from the HIV-1 consensus B sequence, when compared to responses against the 15-mer HIV-1 type B consensus peptides. Conclusion and Significance: This suggests that the cellular immune responses against HIV-1 in controller patients may be broader than we had previously anticipated.

Characterization of Hepatitis B virus (HBV) genotypes in patients from Rondonia, Brazil

Background: Hepatitis B virus (HBV) can be classified into nine genotypes (A-I) defined by sequence divergence of more than 8% based on the complete genome. This study aims to identify the genotypic distribution of HBV in 40 HBsAg-positive patients from Rondonia, Brazil. A fragment of 1306 bp partially comprising surface and polymerase overlapping genes was amplified by PCR. Amplified DNA was purified and sequenced. Amplified DNA was purified and sequenced on an ABI PRISM (R) 377 Automatic Sequencer (Applied Biosystems, Foster City, CA, USA). The obtained sequences were aligned with reference sequences obtained from the GenBank using Clustal X software and then edited with Se-Al software. Phylogenetic analyses were conducted by the Markov Chain Monte Carlo (MCMC) approach using BEAST v.1.5.3. Results: The subgenotypes distribution was A1 (37.1%), D3 (22.8%), F2a (20.0%), D4 (17.1%) and D2 (2.8%). Conclusions: These results for the first HBV genotypic characterization in Rondonia state are consistent with other studies in Brazil, showing the presence of several HBV genotypes that reflects the mixed origin of the population, involving descendants from Native Americans, Europeans, and Africans.

Genetic Diversity on the Integrase Region of the pol Gene among HIV Type 1-Infected Patients Naive for Integrase Inhibitors in Sao Paulo City, Brazil

The presence of mutations associated with integrase inhibitor (INI) resistance among INI-naive patients may play an important clinical role in the use of those drugs Samples from 76 HIV-1-infected subjects naive to INIs were submitted to direct sequencing. No differences were found between naive (25%) subjects and subjects on HAART (75%). No primary mutation associated with raltegravir or elvitegravir resistance was found. However, 78% of sequences showed at least one accessory mutation associated with resistance. The analysis of the 76 IN sequences showed a high polymorphic level on this region among Brazilian HIV-1-infected subjects, including a high prevalence of aa substitutions related to INI resistance. The impact of these findings remains unclear and further studies are necessary to address these questions.

Placentation in Sigmodontinae: a rodent taxon native to South America

Background: Sigmodontinae, known as ""New World rats and mice,"" is a large subfamily of Cricetidae for which we herein provide the first comprehensive investigation of the placenta. Methods: Placentas of various gestational ages ranging from early pregnancy to near term were obtained for five genera, i.e. Necromys, Euryoryzomys, Cerradomys, Hylaeamys, and Oligoryzomys. They were investigated by means of histology, immunohistochemistry, a proliferation marker, DBA-lectin staining and transmission electron microscopy. Results: The chorioallantoic placenta was organized in a labyrinthine zone, spongy zone and decidua and an inverted yolk sac persisted until term. The chorioallantoic placenta was hemotrichorial. The interhemal barrier comprised fetal capillary endothelium and three layers of trophoblast, an outermost, cellular layer and two syncytial ones, with interspersed trophoblast giant cells (TGC). In addition, accumulations of TGC occurred below Reichert's membrane. The junctional zone contained syncytial trophoblast, proliferative cellular trophoblast, glycogen cells and TGC that were situated near to the maternal blood channels. In three of the genera, TGC were also accumulated in distinct areas at the placental periphery. PAS-positive glycogen cells derived from the junctional zone invaded the decidua. Abundant maternal uNK cells with positive response to PAS, vimentin and DBA-lectin were found in the decidua. The visceral yolk sac was completely inverted and villous. Conclusion: The general aspect of the fetal membranes in Sigmodontinae resembled that found in other cricetid rodents. Compared to murid rodents there were larger numbers of giant cells and in some genera these were seen to congregate at the periphery of the placental disk. Glycogen cells were found to invade the decidua but we did not identify trophoblast in the walls of the deeper decidual arteries. In contrast these vessels were surrounded by large numbers of uNK cells. This survey of wild-trapped specimens from five genera is a useful starting point for the study of placentation in an important subfamily of South American rodents. We note, however, that some of these rodents can be captive bred and recommend that future studies focus on the study of time dated pregnancies.

Testing Evolutionary and Dispersion Scenarios for the Settlement of the New World

Background: Discussion surrounding the settlement of the New World has recently gained momentum with advances in molecular biology, archaeology and bioanthropology. Recent evidence from these diverse fields is found to support different colonization scenarios. The currently available genetic evidence suggests a ""single migration'' model, in which both early and later Native American groups derive from one expansion event into the continent. In contrast, the pronounced anatomical differences between early and late Native American populations have led others to propose more complex scenarios, involving separate colonization events of the New World and a distinct origin for these groups. Methodology/Principal Findings: Using large samples of Early American crania, we: 1) calculated the rate of morphological differentiation between Early and Late American samples under three different time divergence assumptions, and compared our findings to the predicted morphological differentiation under neutral conditions in each case; and 2) further tested three dispersal scenarios for the colonization of the New World by comparing the morphological distances among early and late Amerindians, East Asians, Australo-Melanesians and early modern humans from Asia to geographical distances associated with each dispersion model. Results indicate that the assumption of a last shared common ancestor outside the continent better explains the observed morphological differences between early and late American groups. This result is corroborated by our finding that a model comprising two Asian waves of migration coming through Bering into the Americas fits the cranial anatomical evidence best, especially when the effects of diversifying selection to climate are taken into account. Conclusions: We conclude that the morphological diversity documented through time in the New World is best accounted for by a model postulating two waves of human expansion into the continent originating in East Asia and entering through Beringia.

Beyond the Fragmentation Threshold Hypothesis: Regime Shifts in Biodiversity Across Fragmented Landscapes

Ecological systems are vulnerable to irreversible change when key system properties are pushed over thresholds, resulting in the loss of resilience and the precipitation of a regime shift. Perhaps the most important of such properties in human-modified landscapes is the total amount of remnant native vegetation. In a seminal study Andren proposed the existence of a fragmentation threshold in the total amount of remnant vegetation, below which landscape-scale connectivity is eroded and local species richness and abundance become dependent on patch size. Despite the fact that species patch-area effects have been a mainstay of conservation science there has yet to be a robust empirical evaluation of this hypothesis. Here we present and test a new conceptual model describing the mechanisms and consequences of biodiversity change in fragmented landscapes, identifying the fragmentation threshold as a first step in a positive feedback mechanism that has the capacity to impair ecological resilience, and drive a regime shift in biodiversity. The model considers that local extinction risk is defined by patch size, and immigration rates by landscape vegetation cover, and that the recovery from local species losses depends upon the landscape species pool. Using a unique dataset on the distribution of non-volant small mammals across replicate landscapes in the Atlantic forest of Brazil, we found strong evidence for our model predictions - that patch-area effects are evident only at intermediate levels of total forest cover, where landscape diversity is still high and opportunities for enhancing biodiversity through local management are greatest. Furthermore, high levels of forest loss can push native biota through an extinction filter, and result in the abrupt, landscape-wide loss of forest-specialist taxa, ecological resilience and management effectiveness. The proposed model links hitherto distinct theoretical approaches within a single framework, providing a powerful tool for analysing the potential effectiveness of management interventions.

Diversity of free-living marine nematodes (Enoplida) from Baja California assessed by integrative taxonomy

We used morphological and molecular approaches to evaluate the diversity of free-living marine nematodes (order Enoplida) at four coastal sites in the Gulf of California and three on the Pacific coast of Baja California, Mexico. We identified 22 morphological species belonging to six families, of which Thoracostomopsidae and Oncholaimidae were the most diverse. The genus Mesacanthion (Thoracostomopsidae) was the most widespread and diverse. Five allopatric species, genetically and morphologically differentiated, were found in two localities in the Gulf of California (M. sp1 and M. sp2) and three in the Pacific coast (M. sp3, M. sp4 and M. sp5). Overall, we produced 19 and 20 sequences for the 18S and 28S genes, respectively. Neither gene displayed intraspecific polymorphisms, which allowed us to establish that some morphological variation was likely either ontogenetic or due to phenotypic plasticity. Although 18S and 28S phylogenies were topologically congruent (incongruence length difference test, P > 0.05), divergences between species were much higher in the 28S gene. Moreover, this gene possessed a stronger phylogenetic signal to resolve relationships involving Rhabdodemania and Bathylaimus. On the other hand, the close relationship of Pareurystomina (Enchilidiidae) with oncholaimids warrants further study. The 28S sequences (D2D3 domain) may be better suited for DNA barcoding of marine nematodes than those from the 18S rDNA, particularly for differentiating closely related or cryptic species. Finally, our results underline the relevance of adopting an integrative approach encompassing morphological and molecular analyses to improve the assessment of marine nematode diversity and advance their taxonomy.

Nitrogen dynamics during ecosystem development in tropical forest restoration

We considered whether ecological restoration using high diversity of native tree species serves to restore nitrogen dynamics in the Brazilian Atlantic Forest. We measured delta(15)N and N content in green foliage and soil; vegetation N:P ratio; and soil N mineralization in a preserved natural forest and restored forests of ages 21 and 52 years. Green foliage delta(15)N values, N content, N:P ratio, inorganic N and net mineralization and nitrification rates were all higher, the older the forest. Our findings indicate that the recuperation of N cycling has not been achieved yet in the restored forests even after 52 years, but show that they are following a trajectory of development that is characterized by their N cycling intensity becoming similar to a natural mature forest of the same original forest formation. This study demonstrated that some young restored forests are more limited by N compared to mature natural forests. We document that the recuperation of N cycling in tropical forests can be achieved through ecological restoration actions. (C) 2011 Elsevier B.V. All rights reserved.

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.

Description of the Immatures of Workers of the Weaver Ant, Camponotus textor (Hymenoptera: Formicidae)

The weaver ants Camponotus textor (Forel) (Hymenoptera: Formicidae) are native to Central and South America, where they use their larvae to build silken nests by sewing tree leaves together. Few Studies have been conducted with this species, and little is known about the morphology of their larvae. Tie present paper estimated the number of larval instars of C. textor and presents a detailed morphological description of each immature stage based on light and electron microscopic observations. The number of larval in stars was estimated as four based oil the frequency distribution of larval head widths. Tic larvae of this species presented some typical characteristics of Camponotus (Mayr) larvae: body shape `pogonomyrmecoid`, ten pairs of spiracles, antennae with three sensilla, conspicuous `chiloscleres` on the labrum, and mature larvae with pronounced labial pseudopalps. Unprecedented characteristics would include: great diversity of body hair types, and `camponotoid` mandibles but with four medial denticles. This information can aid biological and taxonomic studies with these ants, and may be useful for ant systematics.

Native bromeliads as biomonitors of airborne chemical elements in a Brazilian restinga forest

Epiphytic bromeliads have been used as biomonitors of air pollution since they have specialized structures in leaves for absorbing humidity and nutrients available in the atmosphere. Leaves of five bromeliad species were collected in the conservation unit Parque Estadual Ilha do Cardoso, Sao Paulo State, Brazil, and analyzed by INAA. Vriesea carinata was the species showing most accumulation, with the highest mass fractions of K, Na, Rb and Zn. Similar results were previously found for the same species collected in the dense ombrophilous forest. Chemical composition of bromeliads provided an indication of the atmosphere status in the conservation unit.

Diversity and identification of methanogenic archaea and sulphate-reducing bacteria in sediments from a pristine tropical mangrove

Mangrove sediments are anaerobic ecosystems rich in organic matter. This environment is optimal for anaerobic microorganisms, such as sulphate-reducing bacteria and methanogenic archaea, which are responsible for nutrient cycling. In this study, the diversity of these two functional guilds was evaluated in a pristine mangrove forest using denaturing gradient gel electrophoresis (DGGE) and clone library sequencing in a 50 cm vertical profile sampled every 5.0 cm. DGGE profiles indicated that both groups presented higher richness in shallow samples (0-30 cm) with a steep decrease in richness beyond that depth. According to redundancy analysis, this alteration significantly correlated with a decrease in the amount of organic matter. Clone library sequencing indicated that depth had a strong effect on the selection of dissimilatory sulphate reductase (dsrB) operational taxonomic units (OTUs), as indicated by the small number of shared OTUs found in shallow (0.0 cm) and deep (40.0 cm) libraries. On the other hand, methyl coenzyme-M reductase (mcrA) libraries indicated that most of the OTUs found in the shallow library were present in the deep library. These results show that these two guilds co-exist in these mangrove sediments and indicate important roles for these organisms in nutrient cycling within this ecosystem.

Evaluation of the microbial diversity in a horizontal-flow anaerobic immobilized biomass reactor treating linear alkylbenzene sulfonate

The purpose of this work was to assess the degradation of linear alkylbenzene sulfonate (LAS) in a horizontal-flow anaerobic immobilized biomass (HAIB) reactor. The reactor was filled with polyurethane foam where the sludge from a sanitary sewage treatment was immobilized. The hydraulic detention time (HDT) used in the experiments was of 12 h. The reactor was fed with synthetic substrate (410 mg l(-1) of meat extract, 115 mg l(-1) of starch, 80 mg l(-1) of saccharose, 320 mg l(-1) of sodium bicarbonate and 5 ml l(-1)of salt solution) in the following stages of operation: SI-synthetic substrate, SII-synthetic substrate with 7 mg l(-1) of LAS, SIII-synthetic substrate with 14 mg l(-1) of LAS and SIV-synthetic substrate containing yeast extract (substituting meat extract) and 14 mg l(-1) of LAS, without starch. At the end of the experiment (313 days) a degradation of similar to 35% of LAS was achieved. The higher the concentration of LAS, the greater the amount of foam for its adsorption. This is necessary because the isotherm of LAS adsorption in the foam is linear for the studied concentrations (2 to 50 mg l(-1)). Microscopic analyses of the biofilm revealed diverse microbial morphologies, while Denaturing Gradient Gel Eletrophoresis (DGGE) profiling showed variations in the population of total bacteria and sulphate-reducing bacteria (SRB). The 16S rRNA gene sequencing and phylogenetic analyses revealed that the members of the order Clostridiales were the major components of the bacterial community in the last reactor operation step.

Native tree seedling growth when fertilized with different amounts of dry sewage sludge and mineral fertilizer

The increasing volume of urban sewage nowadays generates considerable amount of sludge to be disposed of. One environmentally adequate destination could be the application of treated and stabilized sludge (biosolids) to forest plantations as fertilizer and soil conditioner. The purpose of this study was to analyze the feasibility of applying sewage sludge, evaluating its effects on native tree seedlings. The species evaluated were aroeira-pimenteira (Schinus terebinthifolia Raddi), cabreuva-vermelha (Myroxy-Ion peruiferum L. f.), pau-de-viola (Cytarexyllum myrianthum Cham), unha-de-vaca (Bauhinia forficata Link), which are usually planted in forest restoration. Seedlings were cultivated in pots, containing a volume of 4 dm(3) of soil, within a greenhouse. The study was developed in the proximity of Campinas, SP, Brazil, and installed in November, 2003. The design was entirely randomized including seven treatments: control; mineral fertilization; and different doses of sewage sludge (biosolids) complemented with potassium, due to the low concentration of this element in the sludge produced by the wastewater treatment plant of Barueri (Metropolitan region of Sao Paulo city). The results showed that the application of different dosages of biosolids promoted different responses in stem height and biomass production. The treatment with 20 g/dm(3) of dry sewage sludge promoted both the highest growth and the highest seedling biomass production, compared to the control treatment. All native tree species treated with the highest dosage of sewage sludge showed a growth similar to that of mineral fertilization. The seedlings of aroeira-pimenteira, pau-de-viola, and unha-de-vaca, all typical species of the initial succession in natural forest ecosystems, grew and produced more biomass than cabreuva-vermelha, a typical species of the final forest succession.

Fruit flies (Diptera, Tephritidae) and their associations with native host plants in a remnant area of the highly endangered Atlantic Rain Forest in the State of Espirito Santo, Brazil

The results presented in this paper refer to a host survey, lasting approximately three and a half years (February 2003-july 2006), undertaken in the Vale do Rio Doce Natural Reserve, a remnant area of the highly endangered Atlantic Rain Forest located in Linhares County, State of Espirito Santo, Brazil. A total of 330 fruit samples were collected from native plants, representing 248 species and 51 plant families. Myrtaceae was the most diverse family with 54 sampled species. Twenty-eight plant species, from ten families, are hosts of ten Anastrepha species and of Ceratitis capitata (Wiedemann). Among 33 associations between host plants and fruit flies, 20 constitute new records, including the records of host plants for A. fumipennis Lima and A. nascimentoi Zucchi. The findings were discussed in the light of their implications for rain forest conservation efforts and the study of evolutionary relationships between fruit flies and their hosts.