Classification of small molecules by two- and three-dimensional decomposition kernels

MOTIVATION: Several kernel-based methods have been recently introduced for the classification of small molecules. Most available kernels on molecules are based on 2D representations obtained from chemical structures, but far less work has focused so far on the definition of effective kernels that can also exploit 3D information. RESULTS: We introduce new ideas for building kernels on small molecules that can effectively use and combine 2D and 3D information. We tested these kernels in conjunction with support vector machines for binary classification on the 60 NCI cancer screening datasets as well as on the NCI HIV data set. Our results show that 3D information leveraged by these kernels can consistently improve prediction accuracy in all datasets. AVAILABILITY: An implementation of the small molecule classifier is available from http://www.dsi.unifi.it/neural/src/3DDK.     

Squamate richness in the Brazilian Cerrado and its environmental–climatic associations

We investigate patterns of species richness of squamates (lizards, snakes, and amphisbaenians) in the Brazilian Cerrado, identifying areas of particularly high richness, and testing predictions of large‐scale richness hypotheses by analysing the relationship between species richness and environmental climatic variables. We used point localities from museum collections to produce maps of the predicted distributions for 237 Cerrado squamate species, using niche‐modelling techniques. We superimposed distributions of all species on a composite map, depicting richness across the ecosystem. Then, we performed a multiple regression analysis using eigenvector‐based spatial filtering (Principal Coordinate of Neighbour Matrices) to assess environmental–climatic variables that are best predictors of species richness. We found that the environmental–climatic and spatial filters multiple regression model explained 78% of the variation in Cerrado squamate richness (r² = 0.78; F = 32.66; P < 0.01). Best predictors of species richness were: annual precipitation, precipitation seasonality, altitude, net primary productivity, and precipitation during the driest quarter. A model selection approach revealed that several mechanisms related to the different diversity hypothesis might work together to explain richness variation in the Cerrado. Areas of higher species richness in Cerrado were located mainly in the south‐west, north, extreme east, and scattered areas in the north‐west portions of the biome. Partitioning of energy among species, habitat differentiation, and tolerance to variable environments may be the primary ecological factors determining variation in squamate richness across the Cerrado. High richness areas in northern Cerrado, predicted by our models, are still poorly sampled, and biological surveys are warranted in that region. The south‐western region of the Cerrado exhibits high species richness and is also undergoing high levels of deforestation. Therefore, maintenance of existing reserves, establishment of ecological corridors among reserves, and creation of new reserves are urgently needed to ensure conservation of species in these areas.     

Oligopeptide uptake and aminoglycoside resistance in Escherichia coli K12

Previous reports have suggested that Escherichia coli K12 mutants defective in the expression of oligogopeptide permease protein A (OppA) exhibit reduced sensitivity to aminoglycosides due to altered permeability of the cell envelope. In this work, the role of the OppA protein, and the oligogopeptide permease (Opp) transport system has been evaluated, in the resistance to aminoglycosides using derivatives of the E. coli K12 SS320 strain selected for triornithine resistance or with a deletion of the complete opp operon. All tested mutants were defective in the uptake of tri- and tetra-peptides but did not expressed resistance to aminoglycosides. Additionally, complementation tests carried out with a plasmid encoding the OppA protein did not affect the sensitivity of the strains to these antibiotics. Taken together, these evidences indicate that the Opp uptake system, as well as the OppA protein, does not play a direct role in the sensitivity to aminoglycosides in E. coli K12.     

Effect of interleukin-10 on the Paracoccidioides brasiliensis killing by gamma-interferon activated human neutrophils

Paracoccidioidomycosis, a deep mycosis endemic in Latin America, is a chronic granulomatous disease caused by the fungus Paracoccidioides brasiliensis. Phagocytic cells play a critical role against this fungus, and several studies have shown the effects of activator and suppressive cytokines on macrophage and monocyte functions. However, studies on polymorphonuclear neutrophils (PMNs), that are the first cells recruited to the infection sites, are scarcer. Thus, the objective of this paper was to assess whether interleukin-10 (IL-10), a potent anti-inflammatory cytokine, is able to block the activity of IFN-gamma-activated human PMNs upon P. brasiliensis intracellular killing, in vitro. The results showed that IFN-gamma-activated PMNs have an effective fungicidal activity against the fungus. This activity was associated with the release of high levels of H(2)O(2), the metabolite involved in phagocytic cells antifungal activities. However, the concomitant incubation of these cells with IFN-gamma and IL-10 significantly blocked IFN-gamma activation. As a consequence, PMNs killing activity and H(2)O(2) release were inhibited. Together, our results show the importance of PMNs exposure to activator or suppressor cytokines in the early stages of paracoccidioidomycosis infection.     

Analysis of differentially expressed genes in response to bacterial stimulation in hemocytes of the carpet-shell clam Ruditapes decussatus: identification of new antimicrobial peptides

Suppression subtractive hybridization was used to identify differentially expressed genes in hemocytes from carpet-shell clam Ruditapes decussatus stimulated with a mixture of dead bacterial strains. Putative function could be assigned to 100 of the 253 sequenced cDNAs. Based on sequence homologies, 3.16% of the total identified genes were possibly related to immune functions. Clam myticin isoforms 1, 2 and 3, and clam mytilin, with similarity with myticins and mytilins previously reported on Mytilus galloprovincialis were identified and characterized for the first time in clams. The analysis of their expression levels by quantitative PCR showed that they were induced by bacterial challenge. The results obtained in this work could be the first step leading to the understanding of molecular mechanisms by which these economically important marine bivalves respond to pathogens.     

Recent decrease in chinstrap penguin (<Emphasis Type="Italic">Pygoscelis antarctica</Emphasis>) populations at two of Admiralty Bay’s islets on King George Island,South Shetland Islands,Antarctica

We examined the breeding populations of chinstrap penguins (Pygoscelis antarctica) on Chabrier Rock and Shag Island within Admiralty Bay, King George Island, South Shetland Islands, Antarctica from 2002 to 2004. When comparing our results to historic data from 1979, we found an overall decline of 57% in the last 25 years, mirroring the population trend of this species in other regions of the Antarctic Peninsula. Our results are discussed in relation to factors hypothesized to be driving the declines found at other sites, as well as the importance of consistent annual censuses to accurately determine population trends.     

Proteome analysis of embryogenic cell suspensions of cowpea (<Emphasis Type="Italic">Vigna unguiculata</Emphasis>)

Using a combination of two-dimensional gel electrophoresis protein mapping and mass spectrometry analysis, we have established proteome reference maps of embryogenic cell suspensions of cowpea (Vigna unguiculata). The cell suspensions were generated from young primary leaves and contained basically pro-embryogenic masses, which enabled us to dissect their proteome composition while eliminating the complexity of too many cell types. Over 550 proteins could reproducibly be resolved over a pI range of 3–10. A total of 128 of the most abundant protein spots were excised, digested in-gel with trypsin and analyzed by tandem mass spectrometry. This enabled the identification of 67 protein spots. Two of the most abundant proteins were identified as a chitinase and as a ribonuclease belonging to the family of PR-4 and PR-10 proteins, respectively. The expression of the respective genes was confirmed by RT-PCR and the pattern of deposition of the PR-10 protein in cell suspensions as well as in developing cowpea seeds, roots, shoots and flowers were determined by Western blot experiments, using synthetic antibodies raised against a 14-amino acid synthetic peptide located close to the C-terminal region of the PR-10 protein.     

Adaptation of a Silica Membrane-based Kit for Purification of Sequencing-ready BAC DNA

We describe a modification of a protocol for the isolation of BAC DNA using a silica membrane-based kit designed for the isolation of plasmid DNA. The major advantages of this protocol are the expediency of the procedure, the high yield and purity, and the high quality of the BAC DNA that is suitable for direct sequencing.     

Geriatric dentistry: a new specialty in Brazil

Objective: To present the current status of geriatric dentistry in Brazil. Background: In 2001, the Brazilian Dental Council established a new specialty: geriatric dentistry. This decision was based on the increase in both the elderly population and the demand for dental treatment of this cohort. Materials and methods: Data were obtained through online searches of the Brazilian Dental Council and the Brazilian Institute of Geography and Statistics. Results: Brazil has 170 dental schools offering around 14 000 undergraduate vacancies every year. At the postgraduate level, there are 19 recognised dental specialties, one of which is geriatric dentistry, comprising 18 certificate programmes, with the potential to produce 216 new specialists every 18 months. The dentist/habitant ratio was 1:870, higher than that recommended by the Word Health Organization. The Brazilian population consists of around 14.5 million elderly people (8.6%). There were 124 specialists in geriatric dentistry distributed irregularly throughout the country. The specialist/elderly population rate was 1:117 249. At the undergraduate level, this new specialty is not included in the curricula of most dental schools in Brazil. Conclusions: Geriatric dentistry should be included in the undergraduate curricula of dental schools in Brazil. Postgraduate degree courses should be developed to produce more clinical academics and researchers in this field.