Bacteriophage-encoded depolymerases: their diversity and biotechnological applications

Bacteriophages (phages), natural enemies of bacteria, can encode enzymes able to degrade polymeric substances. These substances can be found in the bacterial cell surface, such as polysaccharides, or are produced by bacteria when they are living in biofilm communities, the most common bacterial lifestyle. Consequently, phages with depolymerase activity have a facilitated access to the host receptors, by degrading the capsular polysaccharides, and are believed to have a better performance against bacterial biofilms, since the degradation of extracellular polymeric substances by depolymerases might facilitate the access of phages to the cells within different biofilm layers. Since the diversity of phage depolymerases is not yet fully explored, this is the first review gathering information about all the depolymerases encoded by fully sequenced phages. Overall, in this study, 160 putative depolymerases, including sialidases, levanases, xylosidases, dextranases, hyaluronidases, peptidases as well as pectate/pectin lyases, were found in 143 phages (43 Myoviridae, 47 Siphoviridae, 37 Podoviridae, and 16 unclassified) infecting 24 genera of bacteria. We further provide information about the main applications of phage depolymerases, which can comprise areas as diverse as medical, chemical, or food-processing industry.

Production and characterization of ZrCN-Ag coatings deposited by mganetron sputtering

Tese de Doutoramento (Programa doutoral em Engenharia de Materiais)

A critical evaluation of methods for the reconstruction of tissue-specific models

Under the framework of constraint based modeling, genome-scale metabolic models (GSMMs) have been used for several tasks, such as metabolic engineering and phenotype prediction. More recently, their application in health related research has spanned drug discovery, biomarker identification and host-pathogen interactions, targeting diseases such as cancer, Alzheimer, obesity or diabetes. In the last years, the development of novel techniques for genome sequencing and other high-throughput methods, together with advances in Bioinformatics, allowed the reconstruction of GSMMs for human cells. Considering the diversity of cell types and tissues present in the human body, it is imperative to develop tissue-specific metabolic models. Methods to automatically generate these models, based on generic human metabolic models and a plethora of omics data, have been proposed. However, their results have not yet been adequately and critically evaluated and compared. This work presents a survey of the most important tissue or cell type specific metabolic model reconstruction methods, which use literature, transcriptomics, proteomics and metabolomics data, together with a global template model. As a case study, we analyzed the consistency between several omics data sources and reconstructed distinct metabolic models of hepatocytes using different methods and data sources as inputs. The results show that omics data sources have a poor overlapping and, in some cases, are even contradictory. Additionally, the hepatocyte metabolic models generated are in many cases not able to perform metabolic functions known to be present in the liver tissue. We conclude that reliable methods for a priori omics data integration are required to support the reconstruction of complex models of human cells.

Effect of pH on Candida tropicalis virulence factors

Dissertação de mestrado em Bioengenharia

Clinical and echocardiographic predictors of mortality in chagasic cardiomyopathy - systematic review

Diagnosis, prognosis and evaluation of death risk in Chagas cardiomyopathy still constitute a challenge due to the diversity of manifestations, which determine the importance of using echocardiography, tissue Doppler and biomarkers. To evaluate, within a systematic review, clinical and echocardiographic profiles of patients with chronic chagasic cardiomyopathy, which may be related to worse prognosis and major mortality risk. To perform the systematic review, we used Medline (via PubMed), LILACS and SciELO databases to identify 82 articles published from 1991 to 2012, with the following descriptors: echocardiography, mortality and Chagas disease. We selected 31 original articles, involving diagnostic and prognostic methods. The importance of Chagas disease has increased due to its emergence in Europe and United States, but most evidence came from Brazil. Among the predictors of worse prognosis and higher mortality risk are morphological and functional alterations in the left and right ventricles, evaluated by conventional echocardiography and tissue Doppler, as well as the increase in brain natriuretic peptide and troponin I concentrations. Recently, the evaluations of dyssynchrony, dysautonomia, as well as strain, strain rate and myocardial twisting were added to the diagnostic arsenal for the early differentiation of Chagas cardiomyopathy. Developments in imaging and biochemical diagnostic procedures have enabled more detailed cardiac evaluations, which demonstrate the early involvement of both ventricles, allowing a more accurate assessment of the mortality risk in Chagas disease.

Observações preliminares sôbre a longevidade dos "Seedlings" de feijoeiro - Phaseolus vulgaris : em função das reservas cotiledonares

According previous studies about longevity in maize by ACCORSI e ADÂMOLI DE BARROS, (1961) the authors presents in this paper the results of work on longevity of seedlings of beans. Seeds were separated in three groups according their weight, as followings: small 80-120 mg; medium 130-140 mg and big 150-200 mg. The sowing of the seeds was made in pure sand and the seedlings were distributed in distil. water and in complete solution of Arnon and Hoagland. Each treatment was made in two replications with eight seedlings by treatment. At present time the following conclusions can be related: 1.°) - Eight days after germination, the cotiledones of all the seedlings started to fell down, fourteen days after, all cotiledones had fell down. 2.°) - Fifteen days after germination, the seedlings in nutritive solution showed better development than those in distil. water. Table I e II gives results. 3.°) - All seedlings in distil. water showed symptoms of N, Ca, Fe deficiencies. 4.°) - Twenty nine days after germination the seedlings in distil. water manifested exhaust trace, by falling of the leaves and death of some plants although the aplicai buds keep green. 5.°) - After thirty-one days the plants in nutritives solution was in better condition than those in distil. water, although some alteration aboved mentioned was observed. The causes of this alteration are being studied. 6.°) - In many plants in complet solution the seminal leaves showed clorosis initial and some with necrosis, although apical buds keeps in ativity. 7.°) - Symptoms of clorosis and necrosis in diferents stages were observed in all leaflet; these symptoms were more strong in the groups of little seed and medium seeds.

Diet of the ichthyofauna associated with marginal vegetation of a mangrove forest in southeastern Brazil

The objective of this study was to analyze the diet of fish species that use the mangrove vegetation for shelter and feeding in a river southeastern Brazil. The fieldwork, including collecting and underwater observations, was carried out in the dry (July and August 2004) and in the rainy season (February and March 2005) in order to assess the existence of seasonal variation in the diets. Seven kinds of food items were consumed, two of plant origin and five of animal origin. Crustaceans predominated in the diet of most species, either in the form of unidentified fragments or discriminated in eight groups. The predominance of species using mainly a single food source (crustaceans, principally Ostracoda and Tanaidacea) and the existence of seasonal variation in the diets of some species became very evident in the analysis food niche breadth, with a predominance of dietary specialists. In the Rio da Fazenda mangrove, the submersed marginal vegetation was used by the ichthyofauna as a locale for foraging, and principally as cover by bottom-feeding species. These species may be using the vegetation for protection from aerial and aquatic predators, or even from the pull of the current during the turn of the tide. In the study area, the great diversity of crustaceans constitutes an important food source for most fish species which adjusted their diet according to seasonal changes in food availability and to interactions with other species.

Species richness, relative abundance, and habitat of reproduction of terrestrial frogs in the Triângulo Mineiro region, Cerrado biome, southeastern Brazil

Based on field observations and pitfall sampling, we determined the species richness, relative abundance, and reproductive habitat of terrestrial frogs in three municipalities in the Triângulo Mineiro region, south Cerrado biome, in southeastern Brazil. We found thirty-two species of terrestrial frogs, belonging to the families Brachycephalidae, Bufonidae, Cycloramphidae, Dendrobatidae, Leiuperidae, Leptodactylidae and Microhylidae. Most of the species were found in open areas and reproduced in human-generated environments, such as artificial lakes (10 species) and ponds (14 species). Dominance was high, with Physalaemus cuvieri Fitzinger, 1826 (Leiuperidae) representing 48% of sampled frogs. A larger number of individuals was captured in the wet season, when most of the species were reproducing. Compared to other areas of Cerrado biome, the Triângulo Mineiro sites presented a larger number of species, which may be attributed to the larger sampled area and greater sampling effort, lower altitude and presence of human generated habitats. The richness of terrestrial frogs was also larger than that in some forested localities in southeastern Brazil, indicating that the number of species cannot be explained only by precipitation and type of vegetation cover. The greater abundance of individuals during the wet season may be related to a greater movement of adults to breeding sites and to juvenile recruitment/dispersion. The heterogeneity of environments in the Cerrado biome, including its several isolated highlands, contributes to its high (local and regional) diversity of frogs.

Morphometric and genetic differentiation among populations of Eupemphix nattereri (Amphibia, Anura, Leiuperidae) from central Brazil

To assess genetic structure and phenotypic diversity of Eupemphix nattereri Steindachner, 1863, morphometric and molecular analyses were carried out for nine populations from the State of Goiás. A total of 11 morphometric traits were evaluated and genetic information was estimated using RAPD markers. Genetic and phenotypic distances were determined as a function of geographical origin. Correlation among genetic, morphometric, micro, and macroenviromental were analyzed by the Mantel test. Genetic data indicated high levels of genetic diversity (Φst= 0.3) among the nine populations. Mantel tests did not reveal a significant positive correlation between genetic and geographical distances, indicating that locally geographical populations were not genetically similar, even in distances smaller than 50 km. Discriminant analysis on 11 morphometric measurements showed a high divergence among the nine populations. However, a marginally significant correlation (P=0.08) between genetic and morphometric distances was found. The observed correlation was not causal in terms of the relationship between phenotype and genotype, but indicated common spatial structures. Thus, our results suggest that isolation-by-distance processes may explain population divergence in Eupemphix nattereri.

Reproductive modes and fecundity of an assemblage of anuran amphibians in the Atlantic rainforest, Brazil

Reproductive modes and size-fecundity relationships are described for anurans from Picinguaba, a region of Atlantic rainforest on the northern coast of the state of São Paulo, Brazil. We observed 13 reproductive modes, confirming a high diversity of modes in the Atlantic rainforest. This diversity of reproductive modes reflects the successful use of diversified and humid microhabitats by anurans in this biome. We measured the snout-vent length of 715 specimens of 40 species of anurans. The size-fecundity relationship of 12 species was analyzed. Female snout-vent lengths explained between 57% and 81% of clutch size variation. Anurans with aquatic modes laid more eggs than those with terrestrial or arboreal modes. Larger eggs were deposited by species with specialized reproductive modes.

The diet of the South American sea lion (Otaria flavescens) at Río Negro, Patagonia, Argentina, during the winter-spring period

The South American sea lion, Otaria flavescens (Shaw, 1800) population is steadily expanding along the Patagonian coast of Argentina in the last decades. However, little is known about the feeding ecology of the species in the area. The aim of this study was to analyze the food habits of O. flavescens from 91 scats collected at Río Negro province, during the winter and spring of 2005. Fish occurred in 96% of scats containing prey remains, followed by cephalopods (26%). Raneya brasiliensis (Kaup, 1856) was the most frequent and abundant species occurring in 58.6% of samples and constituting almost 50% of fish predated. Second in importance were Porichthys porosissimus (Cuvier, 1829) and Cynoscion guatucupa (Cuvier, 1830) in terms of occurrence (%FO 20.7) and numbers (29.6%) respectively. The squid Loligo gahi (d'Orbigny, 1835) was the most frequent cephalopod prey (42.1%), whereas Octopus tehuelchus (d'Orbigny, 1834) was the most abundant (77%). The higher amount and diversity of prey found in the spring in comparison with the winter season might be related to a higher feeding activity of seals or to a seasonal increase in food availability in the area.

Effects of anthropogenic impacts on benthic macroinvertebrates assemblages in subtropical mountain streams

The nature of the riparian and surrounding landscape has been modified by anthropogenic activities, which may subsequently alter the composition and functional structure of macroinvertebrate assemblages. The effect of these changes on function of benthic fauna is difficult to assess due to the scarce knowledge on functional structures in tropical streams. In this study we evaluate whether sites impacted and unimpacted by anthropogenic alterations differed in assemblage composition and density, richness and diversity of each functional feeding group. The selection of the sites was related to their distinct riparian characteristics, following the QBRy riparian quality index. Collector-gatherer was the dominant functional feeding group, comprising 91% of total density, whereas the proportion of shredders was very low, representing less of 0.5% of total density. Asemblage composition of macroinvertebrates differed between impacted and unimpacted sites. Predators were dominant in taxa number, representing about 60% of total taxa richness. In addition, the diversity and richness of collector-gatherers differed significantly between degraded and unimpacted sites, reflecting the sensitivity of this group to environmental changes and the utility to be used in the assessment of anthropogenic modifications. The results of this study reinforce the idea that riparian corridor management is critical for the distribution of macroinvertebrate assemblages as well as functional organization of lotic streams.

A new species of Leiostracus from Bahia, Brazil (Gastropoda, Pulmonata, Orthalicidae)

A remarkable new species of pulmonate snail was recently collected in a small Atlantic Rainforest fragment near the city of Canavieiras, state of Bahia, Brazil, an area known for a high diversity of land snails. It is described herein as Leiostracus fetidus sp. nov. and can be easily identified by its color pattern of irregular brown to black axial stripes on a white to yellow background, a reddish axial band "separating" the white peristome from the rest of the shell and a broad brown spiral band surrounding the umbilical region. Other diagnostic features include a relatively small size, a proto columellar fold and two very weak folds delimiting the basal region of the aperture. This discovery is a reminder of how little this fauna is known and also an alarm for proper conservation of these forest fragments.

Bird-habitat associations in coastal rangelands of southern Brazil

Nearly all remnants of temperate grasslands in southeastern South America are used for livestock ranching and are subject to habitat degradation resulting from this activity. Exploring how habitat features affect the composition of grassland avifaunal communities is a first step to understand how current cattle-ranching management practices impact avian diversity. We used canonical ordination to test for relationships between five habitat variables and the composition of the bird community in coastal grasslands in southern Brazil. We sampled pastures with different heights, from overgrazed short-grass to tall herbaceous vegetation. We recorded 1,535 individuals and 27 species of birds. The first ordination axis indicated a strong contribution of mean vegetation height on the composition of the bird community, whereas the second axis revealed the influence of herbaceous vegetation patchiness and woody vegetation cover. Three groups of species were revealed by the ordination: one more diffuse associated with intermediate and tall herbaceous vegetation, another with short grass, and a third with vegetation patchiness and woody vegetation. Species restricted to tall herbaceous vegetation are negatively impacted from habitat degradation resulting from overgrazing and trampling by livestock, and mowing and burning of tall plants. Occurrence of these species in our study area is related with the presence of swales immediately behind the dune system and where remnants of tall vegetation persist. Birds of pastures with ample cover of short herbaceous plants, including one globally threatened species and six other restricted to short-grass habitat, apparently benefit from local livestock management practices. Woody vegetation possibly functions as a keystone structure, enabling the occurrence in grasslands of avian species that rely on shrubby habitat. Although livestock ranching promotes the diversity of habitats by creating distinct patches of vegetation height in grasslands, current management practices directed to the maintenance of short grass pastures may eliminate an entire subset of species, including regionally threatened taxa, and reduce avian diversity. The maintenance of large patches of tall herbaceous plants is needed to ensure the survival of species reliant on this type of grassland structure in our study area.

Geographic variation in ectoparasitic mites diversity in Tadarida Brasiliensis (Chiroptera, Molossidae)

Tadarida brasiliensis (Geoffroy, 1824), the Brazilian free-tailed bat, is an insectivorous bat that occurs from southern United States of America to southern South America. In this study we present the first data on diversity of ectoparasitic mites of T. brasiliensis in Brazil. A compilation and analysis of the studies of mite diversity conducted in different points the geographic distribution this bat species are provided. The mites were collected from March 2010 to November 2011 on 160 T. brasiliensis adult bats captured in southern Brazil. Four species of mites have been found: Chiroptonyssus robustipes (Ewing, 1925), Ewingana longa (Ewing, 1938), Ewingana inaequalis (Radford, 1948), and specimens of Cheyletidae. Chiroptonyssus robustipes was the most prevalent species (100%), followed by E. longa (20%), E. inaequalis (10%), and specimens of Cheyletidae (1.25%). The data currently available show that C. robustipes parasitizes T. brasiliensis throughout its region of occurrence, and this mite is highly prevalent and abundant. The two species of Ewingana accompany the geographical distribution of T. brasiliensis, but with much lower prevalence and abundance.