In silico screening of HIV-1 non-nucleoside reverse transcriptase and protease inhibitors

Two targets, reverse transcriptase (RT) and protease from HIV-1, were used during the past two decades to the discovery of non-nucleoside reverse transcriptase inhibitors (NNRTI) and protease inhibitors (PI) that belong to the arsenal of the antiretroviral therapy. Herein these enzymes were chosen as templates for conducting a computer-aided ligand design. Ligand and structure-based drug designs were the starting points to select compounds from a database bearing more than five million compounds by means of cheminformatic tools. New promising lead structures are retrieved from the database, which are open to acquisition and test. Classes of molecules already described as NNRTI or PI in the literature also came out and were useful to prove the reliability of the workflow, and thus validating the work carried out so far. (c) 2007 Elsevier Masson SAS. All rights reserved.

Persistent luminescence of Eu(2+) and Dy(3+) doped barium aluminate (BaAl(2)O(4):Eu(2+),Dy(3+)) materials

Polycrystalline Eu(2+) and Dy(3+) doped barium aluminate materials, BaAl(2)O(4):Eu(2+),Dy(3+), were prepared with solid state reactions at temperatures between 700 and 1500 degrees C. The influence of the thermal treatments on the stability, homogeneity and structure as well as to the UV-excited and persistent luminescence of the materials was investigated by X-ray powder diffraction, SEM imaging and infrared spectroscopies as well as by steady state luminescence spectroscopy and persistent luminescence decay curves, respectively. The IR spectra of the materials prepared at 250, 700, and 1500 degrees C follow the formation of BaAl(2)O(4) composition whereas the X-ray powder diffraction of compounds revealed how the hexagonal structure was obtained. The morphology of the materials at high temperatures indicated important aggregation due to sintering. The luminescence decay of the quite narrow Eu(2+) band at ca. 500 nm shows the presence of persistent luminescence after UV irradiation. The dopant (Eu(2+)) and co-clopant (Dy(3+)) concentrations affect the crystallinity and luminescence properties of the materials. (C) 2009 Elsevier B.V. All rights reserved.

The Human Figure in Drawing and Sculpture

My project as a Senior Scholar has been the study of the human figure through drawing and sculpture. I have worked directly from the model in order to understand the form and structure of the human body. The result of this concentrated study has been a sharpened sense of vision and an increased confidence in the use of materials for both two and three-dimensional representation.

Longitudinal distribution and lateral pattern of megalopal settlement and juvenile recruitment of Carcinus maenas (L.) (Brachyura, Portunidae) in the Mira River Estuary, Portugal

Settlement is a critical process in the life history of crabs, and thus affecting the abundance, distribution and structure of estuarine communities. The spatial pattern of settlement of megalopae of the shore crab Carcinus maenas along a longitudinal estuarine gradient (Mira River Estuary, Portugal) was examined, as well as its effects on the juvenile population. To measure megalopal settlement, four replicate collectors were deployed in six equally spaced stations along the estuarine axis. Juveniles were collected on the same locations with a quadrat randomly deployed on the substrate. To assess fine-scale megalopal settlement within a curved region of the estuary, replicate collectors were deployed on both margins along Moinho da Asneira curve. Megalopae settled differently along the six longitudinal points, with a tendency to attenuate their settlement upstream. Within the curved region, megalopae preferentially settled on the left margin collectors, probably due to the weaker velocity speeds felt on this margin. Concerning the overall juvenile density, there were significant differences among the stations distributed along the estuary, but they did no reflect a longitudinal dispersion attenuation pattern. Size-frequency distribution of the juvenile population showed that the average size is higher on the left margin. Recruits (carapace length between 1.0 mm and 3.4 mm) were more abundant on the upstream stations. Density of early juveniles (3.4 mm-6.5 mm) and juveniles (6.5 mm-10 mm) was more stable throughout the estuary axis than that of recruits. This distribution pattern may result from tidal excursion processes or mechanisms to avoid biotic interactions, such as predation and competition. (c) 2006 Elsevier Ltd. All rights reserved.

Insights into the Specificity of Thioredoxin Reductase-Thioredoxin Interactions. A Structural and Functional Investigation of the Yeast Thioredoxin System

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Bacterial diversity of terra preta and pristine forest soil from the Western Amazon

The survey presented here describes the bacterial diversity and community structures of a pristine forest soil and an anthropogenic, terra preta from the Western Amazon forest using molecular methods to identify the predominant phylogenetic groups. Bacterial community similarities and species diversity in the two soils were compared using oligonucleotide fingerprint grouping of 16S rRNA gene sequences for 1500 clones (OFRG) and by DNA sequencing. The results showed that both soils had similar bacterial community compositions over a range of phylogenetic distances, among which Acidobacteria were predominant, but that terra preta supported approximately 25% greater species richness. The survey provides the first detailed analysis of the composition and structure of bacterial communities from terra preta anthrosols using noncultured-based molecular methods. (c) 2006 Elsevier Ltd. All rights reserved.

STEM ANATOMY and DEVELOPMENT of SUCCESSIVE CAMBIA IN THE NEOTROPICAL LIANA SECURIDACA RIVINIFOLIA (POLYGALACEAE)

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)

Expression, purification, and circular dichroism analysis of human CDK9

The human cyclin-dependent kinase 9 (CDK9) protein was expressed in E coli BL21 using the pET23a vector at 30 degrees C. Several milligrams of protein were purified from soluble fraction using ionic exchange and ATP-affinity chromatography. The structural quality of recombinant CDK9 and the estimation of its secondary structure were obtained by circular dichroism. Structural models of CDK9 presented 26% of helices in agreement with the spectra by circular dichroism analysis. This is the first report on human CDK9 expression in Escherichia coli and structure analysis and provides the first step for the development of CDK9 inhibitors. (c) 2006 Elsevier B.V. All rights reserved.

Synthesis, characterization and thermal behaviour of solid-state compounds of benzoates with some bivalent transition metal ions

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Forest natural regeneration and biomass production after slash and burn in a seasonally dry forest in the Southern Brazilian Amazon

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Development and characterization of 14 microsatellite loci from an enriched genomic library of Eucalyptus camaldulensis Dehnh

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Analysis of Bothrops jararacussu venomous gland transcriptome focusing on structural and functional aspects: I - gene expression profile of highly expressed phospholipases A(2)

Snake venom glands are a rich source of bioactive molecules such as peptides, proteins and enzymes that show important pharmacological activity leading to in local and systemic effects as pain, edema, bleeding and muscle necrosis. Most studies on pharmacologically active peptides and proteins from snake venoms have been concerned with isolation and structure elucidation through methods of classical biochemistry. As an attempt to examine the transcripts expressed in the venom gland of Bothrops jararacussu and to unveil the toxicological and pharmacological potential of its products at the molecular level, we generated 549 expressed sequence tags (ESTs) from a directional cDNA library. Sequences obtained from single-pass sequencing of randomly selected cDNA clones could be identified by similarities searches on existing databases, resulting in 197 sequences with significant similarity to phospholipase A(2) (PLA(2)), of which 83.2% were Lys49-PLA(2) homologs (BOJU-1), 0.1% were basic Asp49-PLA(2)s (BOJU-II) and 0.6% were acidic Asp49-PLA(2)s (BOJU-III). Adjoining this very abundant class of proteins we found 88 transcripts codifying for putative sequences of metalloproteases, which after clustering and assembling resulted in three full-length sequences: BOJUMET-I, BOJUMET-II and BOJUMET-III; as well as 25 transcripts related to C-type lectin like protein including a full-length cDNA of a putative galactose binding C-type lectin and a cluster of eight serine-proteases transcripts including a full-length cDNA of a putative serine protease. Among the full-length sequenced clones we identified a nerve growth factor (Bj-NGF) with 92% identity with a human NGF (NGHUBM) and an acidic phospholipase A2 (BthA-I-PLA(2)) displaying 85-93% identity with other snake venom toxins. Genetic distance among PLA(2)s from Bothrops species were evaluated by phylogenetic analysis. Furthermore, analysis of full-length putative Lys49-PLA(2) through molecular modeling showed conserved structural domains, allowing the characterization of those proteins as group II PLA(2)s. The constructed cDNA library provides molecular clones harboring sequences that can be used to probe directly the genetic material from gland venom of other snake species. Expression of complete cDNAs or their modified derivatives will be useful for elucidation of the structure-function relationships of these toxins and peptides of biotechnological interest. (C) 2004 Elsevier SAS. All rights reserved.

X-ray photoelectron spectroscopy, x-ray absorption spectroscopy, and x-ray diffraction characterization of CuO-TiO2-CeO2 catalyst system

X-ray photoelectron spectroscopy (XPS), x-ray diffraction (XRD), and x-ray absorption spectroscopy (XAS) techniques have been applied to characterize the surface composition and structure of a series of CuO-TiO2-CeO2 catalysts. For a small loading of cerium, ceria was mainly dispersed on the titania surface and a minor amount of CeO2 crystallite appeared. At higher loading of cerium, the CeO2 phase increased and the atomic Ce/Ti ratio values were smaller than the nominal composition, as a consequence of cerium agglomeration. This result suggests that only a fraction of cerium can be spread on the titania surface. For titanium-based mixed oxide, we observed that cerium is found as Ce3+ uniquely on the surface. The atomic Cu/(Ce+Ti) ratio values showed no influence from cerium concentration on the dispersion of copper, although the copper on the surface was shown to be dependent on the cerium species. For samples with a high amount of cerium, XPS analysis indicated the raise of second titanium species due cerium with spin-orbit components at higher binding energies than those presented by Ti4+ in a tetragonal structure. The structural results obtained by XAS are consistent with those obtained by XRD and XPS. (C) 2001 American Vacuum Society.

Seed rain and seed limitation in a planted gallery forest in Brazil

With seeds collected monthly during one year from 53 1-m(2) seed traps, we investigated the seed rain and seed limitation in a gallery forest planted in 1994 in SE Brazil. Contrasting animal- (zoochorous) and wind-dispersed (anemochorous) plants we investigated (1) which aspects of the composition and structure of the vegetation influence the abundance and species richness of the seed rain; (2) if such influences differ between zoochorous and anemochorous seeds; (3) if the abundance and richness of the seed rain sampled under zoochorous and nonzoochorous plant species differ; and (4) if seed limitation (given by the proportion of sites to which seeds were not dispersed) differs between zoochorous and anemochorous plant species, and also between species that have been planted and those that further colonized the area (colonists). Seed rain was intense and dominated by anemochorous species. The overall seed rain was not influenced by the vegetation parameters we analyzed (canopy height and cover, plant size, abundance, and richness) or by the plant species above the seed trap. The abundance and richness of zoochorous seeds in a given spot was influenced by the abundance and richness of zoochorous plants in its immediate vicinity. Seed limitation was higher for anemochorous than zoochorous species and higher for planted than for colonist species. We concluded with recommendations for the initial establishment of a planted forest, including the homogeneous distribution of zoochorous plants to permit a spatially homogeneous zoochorous seedfall, which will likely enhance the chances of survival and successful establishment of seeds.

The use of biodiversity as source of new chemical entities against defined molecular targets for treatment of malaria, tuberculosis, and T-cell mediated diseases: a review

The modern approach to the development of new chemical entities against complex diseases, especially the neglected endemic diseases such as tuberculosis and malaria, is based on the use of defined molecular targets. Among the advantages, this approach allows (i) the search and identification of lead compounds with defined molecular mechanisms against a defined target (e.g. enzymes from defined pathways), (ii) the analysis of a great number of compounds with a favorable cost/benefit ratio, (iii) the development even in the initial stages of compounds with selective toxicity (the fundamental principle of chemotherapy), (iv) the evaluation of plant extracts as well as of pure substances. The current use of such technology, unfortunately, is concentrated in developed countries, especially in the big pharma. This fact contributes in a significant way to hamper the development of innovative new compounds to treat neglected diseases. The large biodiversity within the territory of Brazil puts the country in a strategic position to develop the rational and sustained exploration of new metabolites of therapeutic value. The extension of the country covers a wide range of climates, soil types, and altitudes, providing a unique set of selective pressures for the adaptation of plant life in these scenarios. Chemical diversity is also driven by these forces, in an attempt to best fit the plant communities to the particular abiotic stresses, fauna, and microbes that co-exist with them. Certain areas of vegetation (Amazonian Forest, Atlantic Forest, Araucaria Forest, Cerrado-Brazilian Savanna, and Caatinga) are rich in species and types of environments to be used to search for natural compounds active against tuberculosis, malaria, and chronic-degenerative diseases. The present review describes some strategies to search for natural compounds, whose choice can be based on ethnobotanical and chemotaxonomical studies, and screen for their ability to bind to immobilized drug targets and to inhibit their activities. Molecular cloning, gene knockout, protein expression and purification, N-terminal sequencing, and mass spectrometry are the methods of choice to provide homogeneous drug targets for immobilization by optimized chemical reactions. Plant extract preparations, fractionation of promising plant extracts, propagation protocols and definition of in planta studies to maximize product yield of plant species producing active compounds have to be performed to provide a continuing supply of bioactive materials. Chemical characterization of natural compounds, determination of mode of action by kinetics and other spectroscopic methods (MS, X-ray, NMR), as well as in vitro and in vivo biological assays, chemical derivatization, and structure-activity relationships have to be carried out to provide a thorough knowledge on which to base the search for natural compounds or their derivatives with biological activity.