A structure-activity relationship study of quinone compounds with trypanocidal activity

A set of 25 quinone compounds with anti-trypanocidal activity was studied by using the density functional theory (DFT) method in order to calculate atomic and molecular properties to be correlated with the biological activity. The chemometric methods principal component analysis (PCA), hierarchical cluster analysis (HCA), stepwise discriminant analysis (SDA), Kth nearest neighbor (KNN) and soft independent modeling of class analogy (SIMCA) were used to obtain possible relationships between the calculated descriptors and the biological activity studied and to predict the anti-trypanocidal activity of new quinone compounds from a prediction set. Four descriptors were responsible for the separation between the active and inactive compounds: T-5 (torsion angle), QTS1 (sum of absolute values of the atomic charges), VOLS2 (volume of the substituent at region B) and HOMO-1 (energy of the molecular orbital below HOMO). These descriptors give information on the kind of interaction that occurs between the compounds and the biological receptor. The prediction study was done with a set of three new compounds by using the PCA, HCA, SDA, KNN and SIMCA methods and two of them were predicted as active against the Trypanosoma cruzi. (c) 2005 Elsevier SAS. All rights reserved.

Automated NMR structure determination and disulfide bond identification of the myotoxin crotamine from Crotalus durissus terrificus

Crotamine is one of four major components of the venom of the South American rattlesnake Crotalus durissus terrificus. Similar to its counterparts in the family of the myotoxins, it induces myonecrosis of skeletal muscle cells. This paper describes a new NMR structure determination of crotamine in aqueous solution at pH 5.8 and 20 degrees C, using standard homonuclear (1)H NMR spectroscopy at 900 MHz and the automated structure calculation software ATNOS/CANDID/DYANA. The automatic NOESY spectral analysis included the identification of a most likely combination of the six cysteines into three disulfide bonds, i.e. Cys4-Cys36, Cys11-Cys30 and Cys18-Cys37; thereby a generally applicable new computational protocol is introduced to determine unknown disulfide bond connectivities in globular proteins. A previous NMR structure determination was thus confirmed and the structure refined. Crotamine contains an alpha-helix with residues 1-7 and a two-stranded anti-parallel beta-sheet with residues 9-13 and 34-38 as the only regular secondary structures. These are connected with each other and the remainder of the polypeptide chain by the three disulfide bonds, which also form part of a central hydrophobic core. A single conformation was observed, with Pro13 and Pro21 in the trans and Pro20 in the cis-form. The global fold and the cysteine-pairing pattern of crotamine are similar to the beta-defensin fold, although the two proteins have low sequence homology, and display different biological activities. (c) 2005 Elsevier Ltd. All rights reserved.

Flowering phenology, nectary structure and breeding system in Corymborkis flava (Spiranthoideae : Tropidieae), a terrestrial orchid from a Neotropical forest

Flowering phenology, breeding system and nectary structure of Corymborkis flava (Sw.) Kuntze were studied in a fragment of the Atlantic Forest in south-eastern Brazil. The flowering period extended from March (end of rainy season) to early June and seed dispersal occurred from June to September (dry season). Flowering peak occurred mainly in April, with up to 34 open flowers per plant being observed. The yellow, odourless and tubular flowers lasted similar to 7.8 days. The flowers present a perigonal nectary located in the basal lateral parts of the labellum; this is the first report on the nectary location and characterisation in the Tropidieae tribe. At the pre-anthesis stage, cells of both secretory parenchyma and epidermis of the nectary are filled with compound amyloplasts. However, starch grains were not observed in these tissues in senescent flowers, indicating that these starch grains are hydrolysed and used as source of sugars for nectar production. The nectar accumulates between the cuticle and the outer periclinal wall of the epidermal cells before. owing out into the nectar chamber. C. flava is a self-compatible species and spontaneous self-pollination does not occur because of hercogamy. The high pollinia removal (0.80) and insertion (0.82) per flower, as well as the high natural fruit-set indicate an efficient natural pollination system. The present study contributes for the knowledge of the diversity of reproductive strategies and nectary structures in Orchidaceae.

Microstructural and optical characterization of CaWO4 and SrWO4 thin films prepared by a chemical solution method

Stoichiometric CaWO4 and SrWO4 thin films were synthesized using a chemical solution processing, the so-called polymeric precursor method. In this soft chemical method, soluble precursors such as strontium carbonate, calcium carbonate and tungstic acid, as starting materials, were mixed in an aqueous solution. The thin films were deposited on glass substrates by means of the spinning technique. The surface morphology and crystal structure of the thin films were investigated using X-ray diffraction (XRD), scanning electron microscopy (SEM), and atomic force microscopy (AFM). Nucleation stages and surface morphology evolution of the thin films on glass substrates were studied by atomic force microscopy. The films nucleate at 300 degreesC, after the coalescence of small nuclei into larger grains yielding a homogeneous dense surface. XRD characterization of these films showed that the CaWO4 and SrWO4 phases crystallize at 400 degreesC from an inorganic amorphous phase. No intermediate crystalline phase was identified. The optical properties were also studied. It was found that CaWO4 and SrWO4 thin films have an optical band gap, E-gap=5.27 and 5.78 eV, respectively, of a direct transition nature. The excellent microstructural quality and chemical homogeneity confirmed that this soft solution processing provides an inexpensive and environmentally friendly route for the preparation of CaWO4 and SrWO4 thin films. (C) 2003 Elsevier B.V. All rights reserved.

Experimental and theoretical study of the compound [Pd(dmba)(NCO)(imz)]

The compound [Pd(dmba)(NCO)(imz)] (dmba = N,N-dimethylbenzilamine; NCO = cyanate; imz = imidazole) was studied through experimental and theoretical methods. The complex was synthesized and characterized by IR and NMR spectroscopy. To an appropriate representation of the molecular environment, Gaussian basis sets for the constituent atoms of the compound were built and, after adequate supplementation with polarization and diffuse functions, they were used to study the molecule. Calculations of electronic and vibrational structure of two possible isomers were carried out, showing that the compound, which contains the NCO GROUP trans to the Pd-C bond, is 4.29 kcal/mol more stable than the analogous one, where the imz ligand is trans to the Pd-C bond. The calculated molecular parameters, bond distances, and bond angles showed that the geometry around the metallic center is square-planar with the cyanate being linear. The theoretical infrared spectrum of C(1) symmetry (electronic state (1)A) is in accordance with the experimental one. It also verified the contribution of Pd (4d(xz) + 4d(yz)) and Pd (4d(xy)) in the HOMO and LUMO orbitals, respectively. (c) 2006 Elsevier B.V. All rights reserved.

Development of successive cambia and structure of wood in Gallesia integrifolia (Spreng.) Harms (Phytolaccaceae)

Stem diameter in Gallesia integrifolia (Spreng.) Harms (Phytolaccaceae) increases by forming concentric rings of xylem alternating with phloem, which show frequent anastomoses. After a period of primary growth and the formation of first (normal) ring of vascular cambium, further successive rings are initiated outside this cambium. The second ring of cambium originates from the pericycle parenchyma located between the proto-phloem, and the pericycle fibres. Each cambium produces centripetally secondary xylem and centrifugally secondary phloem. Differentiation of xylem precedes that of phloem and the first elements formed are always xylem fibres. Structurally, the vascular cylinder is composed by successive rings of secondary xylem and phloem. These rings are separated by wide bands of conjunctive parenchyma tissue. Presence of collateral vascular bundles with irregular orientation is observed in the region of anastomoses of two or more bands of conjunctive tissue. These bundles are surrounded by isodiametric, lignified and thick-walled cells. In some of the cambial rings, occurrence of polycentric rays was also noticed; these rays are tall, and characterized by the presence of meristematic regions that differentiated into thick-walled elements of secondary xylem. Origin and development of the successive cambia and the structure of xylem are discussed.

Structure and Properties of Barium Bismuth Titanate Prepared by Mechanochemical Synthesis

Bi4Ti4O15 [BBT], a member of Aurivillius bismuth-based layer-structure perovskites, was prepared from stoichiometric amounts of BaTiO3 [BT] and Bi4Ti3O12 [BIT] obtained via mechanochemical synthesis. Mechanochemical synthesis was performed in air atmosphere in a planetary ball mill. BBT ceramics were sintered at 1100C for 4 h without pre-calcination step within heating rate 10C/min. The formation of phase and crystal structure of BT, BIT and BBT were approved using X-ray analysis. The morphology of obtained powders and microstructure were exhamined using scanning electron microscopy. The electrical properties of sintered samples were carried out.

Influence of silver additions on the structure and phase transformation of the Cu-13 wt % Al alloy

The influence of silver additions on the structure and phase transformation of the Cu-13 wt % Al alloy was studied by differential thermal analysis, X-ray diffraction, scanning electron microscopy and energy dispersive analysis of X-rays. The results indicate that the presence of silver modifies the phase-stability field, the transition temperature and the structure of the alloy. These effects are more pronounced for silver concentrations up to 8 wt %.

Initial description of the phylogeography, population structure and genetic diversity of Atlantic spotted dolphins from Brazil and the Caribbean, inferred from analyses of mitochondrial and nuclear DNA

We provide initial information regarding the population structure and genetic diversity of Stenella frontalis from the Caribbean and southeastern Brazil from analyses of mitochondrial control region sequences and sequences from the first intron of the α-lactalbumin gene. Comparisons with previously described S. frontalis sequences showed a high number of haplotypes shared between populations throughout their distribution range. High diversity was found for southeastern Brazil and Caribbean samples, and population structure analyses indicate significant differentiation among population units at the FST level, but not at the ΦST level. Significant differentiation at the FST level was found between the Caribbean population unit and all other populations units. These results suggest historical or present connectivity between the Azores and Madeira and the southeastern Brazil groups and population differentiation between the Caribbean and southeastern Brazil, supporting the notion of two separate stocks in the waters around the Atlantic coast of South America. © 2013 Elsevier Ltd.

Disentangling the influences of habitat structure and limnological predictors on stream fish communities of a coastal basin, southeastern Brazil

Em ambientes de riacho, fatores relacionados à estrutura dos habitats e limnologia interagem regulando os padrões de transferência de energia e matéria, afetando a composição da comunidade de peixes. Em bacias costeiras do sudeste do Brasil as características limnológicas e estrutura dos habitats diferem entre riachos de águas claras e pretas. Os primeiros são compostos por uma variedade de tipos de substrato, possuem velocidades de corrente mais elevadas e baixa condutividade, enquanto os últimos apresentam substrato arenoso, baixas velocidades de corrente e águas escuras e ácidas. Neste trabalho analisamos a importância relativa da estrutura dos habitats e das variáveis limnológicas como preditores dos padrões de composição em comunidades de peixes de riachos. Oito riachos de primeira a terceira ordem foram amostrados na planície costeira da bacia do rio Itanhaém. Capturamos 34 espécies e verificamos que a composição das comunidades foi influenciada por fatores estruturais e limnológicos, sendo os primeiros mais importantes. Uma fração de variação que não pode ser totalmente decomposta, deve-se à influência conjunta da limnologia e estrutura dos habitats. Algumas das espécies restritas aos riachos de águas pretas provavelmente apresentam adaptações fisiológicas e comportamentais para lidar com os baixos níveis de pH. Quando foram examinados somente os riachos de águas claras, toda a variação explicada na composição da comunidade de peixes foi atribuída aos fatores estruturais, devido a preferências específicas por diferentes características de hábitats.

SAXS Studies of the Endoglucanase Cel12A from Gloeophyllum trabeum Show Its Monomeric Structure and Reveal the Influence of Temperature on the Structural Stability of the Enzyme

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

Population structure, sex ratio and growth of the seabob shrimp Xiphopenaeus kroyeri (Decapoda, Penaeidae) from coastal waters of southern Brazil

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

Local structure and hybridization states in Ba0.9Ca0.1Ti1-xZrxO3 ceramic compounds: Correlation with a normal or relaxor ferroelectric character

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

New insights regarding HCV-NS5A structure/function and indication of genotypic differences

Abstract Background HCV is prevalent throughout the world. It is a major cause of chronic liver disease. There is no effective vaccine and the most common therapy, based on Peginterferon, has a success rate of ~50%. The mechanisms underlying viral resistance have not been elucidated but it has been suggested that both host and virus contribute to therapy outcome. Non-structural 5A (NS5A) protein, a critical virus component, is involved in cellular and viral processes. Methods The present study analyzed structural and functional features of 345 sequences of HCV-NS5A genotypes 1 or 3, using in silico tools. Results There was residue type composition and secondary structure differences between the genotypes. In addition, second structural variance were statistical different for each response group in genotype 3. A motif search indicated conserved glycosylation, phosphorylation and myristoylation sites that could be important in structural stabilization and function. Furthermore, a highly conserved integrin ligation site was identified, and could be linked to nuclear forms of NS5A. ProtFun indicated NS5A to have diverse enzymatic and nonenzymatic activities, participating in a great range of cell functions, with statistical difference between genotypes. Conclusion This study presents new insights into the HCV-NS5A. It is the first study that using bioinformatics tools, suggests differences between genotypes and response to therapy that can be related to NS5A protein features. Therefore, it emphasizes the importance of using bioinformatics tools in viral studies. Data acquired herein will aid in clarifying the structure/function of this protein and in the development of antiviral agents.

Phylogeography of the neotropical Anopheles triannulatus complex (Diptera: Culicidae) supports deep structure and complex patterns

Abstract Background The molecular phylogenetic relationships and population structure of the species of the Anopheles triannulatus complex: Anopheles triannulatus s.s., Anopheles halophylus and the putative species Anopheles triannulatus C were investigated. Methods The mitochondrial COI gene, the nuclear white gene and rDNA ITS2 of samples that include the known geographic distribution of these taxa were analyzed. Phylogenetic analyses were performed using Bayesian inference, Maximum parsimony and Maximum likelihood approaches. Results Each data set analyzed septely yielded a different topology but none provided evidence for the seption of An. halophylus and An. triannulatus C, consistent with the hypothesis that the two are undergoing incipient speciation. The phylogenetic analyses of the white gene found three main clades, whereas the statistical parsimony network detected only a single metapopulation of Anopheles triannulatus s.l. Seven COI lineages were detected by phylogenetic and network analysis. In contrast, the network, but not the phylogenetic analyses, strongly supported three ITS2 groups. Combined data analyses provided the best resolution of the trees, with two major clades, Amazonian (clade I) and trans-Andean + Amazon Delta (clade II). Clade I consists of multiple subclades: An. halophylus + An. triannulatus C; trans-Andean Venezuela; central Amazonia + central Bolivia; Atlantic coastal lowland; and Amazon delta. Clade II includes three subclades: Panama; cis-Andean Colombia; and cis-Venezuela. The Amazon delta specimens are in both clades, likely indicating local sympatry. Spatial and molecular variance analyses detected nine groups, corroborating some of subclades obtained in the combined data analysis. Conclusion Combination of the three molecular markers provided the best resolution for differentiation within An. triannulatus s.s. and An. halophylus and C. The latest two species seem to be very closely related and the analyses performed were not conclusive regarding species differentiation. Further studies including new molecular markers would be desirable to solve this species status question. Besides, results of the study indicate a trans-Andean origin for An. triannulatus s.l. The potential implications for malaria epidemiology remain to be investigated.