Analysis of floristic composition and structure as an aid to monitoring protected areas of dense rain forest in southeastern Brazil

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

Changes in the structure and pigmentation of the eyes of honeybee (Apis mellifera L.) queens with the limão mutation

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

Variations in tree community composition and structure in a fragment of tropical semideciduous forest in southeastern Brazil related to different human disturbance histories

In an area of tropical seasonal semideciduous forest, the soil characteristics, floristic composition, physiognomic structure, and the distribution of three regeneration and three dispersal guilds were studied for four stands within the forest that had documented histories of varying degrees of human disturbance. The aim was to study forest regeneration in areas of preserved forest and secondary forest, with parts of both types of forest experiencing either 'intensive' or 'occasional' cattle trampling. The study was carried out in the Sebastiao Aleixo da Silva Ecological Station, Bauru, São Paulo State, Brazil. Two stands were called 'secondary' because they corresponded to forest tracts that were felled and occupied by crops and pastures in the past and then abandoned to forest regeneration ca. 40 years before this study. The other two stands, called 'preserved', corresponded to areas of the fragment where the forest has been maintained with only minor human impacts. The arboreal component of the tree community (diameter at breast height or dbh greater than or equal to 5 cm) was sampled in 20 plots of 40 m x 40 m, and the subarboreal component (diameter at the base of the stem or dbs < 5 cm and height greater than or equal to 0.5 m) in subplots of 40 m x 2 m. Physiognomic features, such as canopy height and density of climbing plants, were registered all over a 5 m x 5 m gridline laid on the sample plots. Soil bulk samples were collected for chemical and textural analyses. Most detected differences contrasted the secondary to the preserved forest stands. The soils of the secondary stands showed higher proportions of sand and lower levels of mineral nutrients and organic matter than those of the preserved stands, probably due to higher losses by leaching and erosion. Compared to the secondary stands, the preserved ones had higher proportions of tall trees, higher mean canopy height, lower species diversity, higher abundance of autochorous and shade-tolerant climax species, and lower abundance of pioneer and light-demanding climax species. Despite the high proportion of species shared by the preserved and secondary stands (108 out of 139), they differed consistently in terms of density of the most abundant species. on the other hand, the secondary and preserved stands held similar values for tree density and basal area, suggesting that 40 years were enough to restore these features. Effects of cattle trampling on the vegetation were detected for the frequency of trees of anemochorous and zoochorous species, which were higher in the stands under occasional and intensive cattle trampling, respectively. The density of thin climbers was lower in the stands with intensive trampling. (C) 2004 Elsevier B.V. All rights reserved.

Structure of a lectin from Canavalia gladiata seeds: new structural insights for old molecules

Background: Lectins are mainly described as simple carbohydrate- binding proteins. Previous studies have tried to identify other binding sites, which possible recognize plant hormones, secondary metabolites, and isolated amino acid residues. We report the crystal structure of a lectin isolated from Canavalia gladiata seeds ( CGL), describing a new binding pocket, which may be related to pathogen resistance activity in ConA- like lectins; a site where a non- protein amino- acid, aaminobutyric acid ( Abu), is bound.Results: the overall structure of native CGL and complexed with alpha- methyl- mannoside and Abu have been refined at 2.3 angstrom and 2.31 angstrom resolution, respectively. Analysis of the electron density maps of the CGL structure shows clearly the presence of Abu, which was confirmed by mass spectrometry.Conclusion: the presence of Abu in a plant lectin structure strongly indicates the ability of lectins on carrying secondary metabolites. Comparison of the amino acids composing the site with other legume lectins revealed that this site is conserved, providing an evidence of the biological relevance of this site. This new action of lectins strengthens their role in defense mechanisms in plants.

Structure of magnetic poly(oxyethylene)-siloxane nanohybrids doped with Fe-II and Fe-III

Hybrid organic - inorganic nanocomposites doped with Fe-II and Fe-III ions and exhibiting interesting magnetic properties have been obtained by the sol - gel process. The hybrid matrix of these ormosils ( organically modified silicates), classed as di-ureasils and termed U( 2000), is composed of poly( oxyethylene) chains of variable length grafted to siloxane groups by means of urea crosslinkages. Iron perchlorate and iron nitrate were incorporated in the diureasil matrices, leading to compositions within the range 80 greater than or equal to n greater than or equal to 10, n being the molar ratio of ether-type O atoms per cation. The structure of the doped diureasils was investigated by small-angle X-ray scattering (SAXS). For Fe-II-doped samples, SAXS results suggest the existence of a two-level hierarchical structure. The primary level is composed of spatially correlated siloxane clusters embedded in the polymeric matrix and the secondary, coarser level consists of domains where the siloxane clusters are segregated. The structure of Fe-III-doped hybrids is different, revealing the existence of iron oxide based nanoclusters, identified as ferrihydrite by wide-angle X-ray diffraction, dispersed in the hybrid matrix. The magnetic susceptibility of these materials was determined by zero-field-cooling and field-cooling procedures as functions of both temperature and field. The different magnetic features between Fe-II- and Fe-III-doped samples are consistent with the structural differences revealed by SAXS. While Fe-II-doped composites exhibit a paramagnetic Curie-type behaviour, hybrids containing Fe-III ions show thermal and field irreversibilities.

Structure and electrical properties of potassium-doped siloxane-poly(oxypropylene) ormolytes

The structure and the ionic conduction properties of siloxane-poly(oxypropylene) (PPO) hybrids doped with different potassium salts (KCF3SO3, KI, KClO4 and KNO2) are reported for two polymer molecular weights (300 and 4000 g/mol), labelled PPO300 and PPO4000, respectively. The doping concentration, related to the concentration of the ether type oxygen of the PPO chain, is the same whatever the salt and verifies [O]/[K] = 20. Ionic room temperature conductivity shows the highest value for the KCF3SO3 doped PPO4000 hybrid (4 x 10(-7)Omega(-1).cm(-1)). The structure of these hybrids was investigated by X-ray powder diffraction (XRPD) and X-ray absorption spectroscopy (EXAFS and XANES) at the potassium K-edge (3607 eV). XRPD results show that the hybrid matrix is always amorphous and the formation of secondary potassium phases is observed for all the samples, except for the KCF3SO3 doped PPO4000 hybrid. EXAFS results evidence a good correlation between the ionic conductivity and the presence of oxygen atoms as first neighbours around potassium.

Synthesis, crystal structure and theoretical studies of aryltellurenyl tetramethylthiourea(tmtu) iodine complexes: Ph-Te(tmtu)I (1) and beta-naphtyl-Te(tmtu)I (2)

(1) C11H17IN2STe, Mr = 463.83, P2(1)/n, a 7.6582(8), b = 13.8008(9), c = 15.026(3) angstrom, beta = 96.233(12)degrees, Z = 4, R-1 = 0.0318. (2) C15H19IN2STe, Mr = 513.88, P2(1)/n, a = 8.434(5), b = 11.697(5), c = 18.472(5) angstrom, beta = 98.556(5)degrees, Z = 4, R-1 = 0.0236. The synthesis of the aryltellurenyl N,N',-tetramethylthiourea (tmtu) iodide has been performed by ligand exchange with potassium iodide and the corresponding aryltellurenyl(tmtu) bromide. In both structures the tellurium atom is primarily three-coordinated, being bonded to a carbon atom of the organic ring and, in directions nearly perpendicular to the Te-C bond, to one tmtu sulfur atom and one iodine. In addition there are Te...secondary bonds, joining the molecules in centrosymmetric dimers, which in turn are joined through C-H...1 and C-H... S interactions, in (1) and (2), respectively.

Model peptides mimic the structure and function of the N-terminus of the pore-forming toxin sticholysin II

To investigate the role of the N-terminal region in the lytic mechanism of the pore-forming toxin sticholysin II (St II), we studied the conformational and functional properties of peptides encompassing the first 30 residues of the protein. Peptides containing residues 1-30 (P1-30) and 11-30 (P11-30) were synthesized and their conformational properties were examined in aqueous solution as a function of peptide concentration, pH, ionic strength, and addition of the secondary structure-inducing solvent trifluoroethanol (TFE). CD spectra showed that increasing concentration, pH, and ionic strength led to aggregation of P1-30; as a consequence, the peptide acquired beta-sheet conformation. In contrast, P11-30 exhibited practically no conformational changes under the same conditions, remaining essentially structureless. Moreover, this peptide did not undergo aggregation. These differences clearly point to the modulating effect of the first 10 hydrophobic residues on the peptides aggregation and conformational properties. In TFE both the first ten hydrophobic peptides acquired alpha-helical conformation, albeit to a different extent, P11-30 displayed lower alpha-helical content. P1-30 presented a larger-fraction of residues in alpha-helical conformation in TFE than that found in St II's crystal structure for that portion of the protein. Since TFE mimics the membrane em,, such increase in helical content could also occur upon toxin binding to membranes and represent a step in the mechanism of pore formation. The peptides conformational properties correlated well with their functional behaviour. Thus, P1-30 exhibited much higher hemolytic activity than P11-30. In addition, P11-30 was able to block the toxin's hemolytic activity. The size of pores formed in red blood cells by P 1-30 was estimated by measuring the permeability PEGs of different molecular mass. The pore radius (0.95 +/- 0.01 nm) was very similar to that of the PEGs of different pore formed by the toxin. The results demonstrate that the synthetic peptide P1-30 is a good model of St 11 conformation and function and emphasize the contribution of the toxin's N-terminal region, and, in particular, the hydrophobic residues 1-10 to pore formation. (c) 2005 Wiley Periodicals, Inc.

Structure of luminescent mono and di-urethanesil nanocomposites doped with Eu3+ ions

A structure modeling of two families of sol-gel derived Eu3+-doped organic/inorganic hybrids based on the results of small-angle X-ray scattering experiments is reported. The materials are composed of poly(oxyethylene) chains grafted at one or both ends to siloxane groups and are called mono- and di-urethanesils, respectively. A theoretical function corresponding to a two-level hierarchical structure model fits well the experimental Scattering curves. The first level corresponds to small siloxane clusters embedded in a polymeric matrix. The secondary level is associated to the existence of siloxane cluster rich domains surrounded by a cluster-depleted polymeric matrix. Results show that increasing europium doping favors the growth of the secondary domains. (C) 2002 Elsevier B.V. B.V. 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.

Water regulation of actinomycin-D binding to DNA: the interplay among drug affinity, DNA long-range conformation, and hydration

Actiaomycin-D (actD) binds to natural DNA at two different classes of binding sites, weak and strong. The affinity for these sites is highly dependent on DNA se(sequence and solution conditions, and the interaction appears to be purely entropic driven Although the entropic character of this reaction has been attributed to the release of water molecules upon drug to DNA complex formation, the mechanism by which hydration regulates actD binding and discrimination between different classes of binding sites on natural DNA is still unknown. In this work, we investigate the role of hydration on this reaction using the osmotic stress method. We skew that the decrease of solution water activity, due to the addition of sucrose, glycerol ethylene glycol, and betaine, favors drug binding to the strong binding sites on DNA by increasing both the apparent binding affinity Delta G, and the number of DNA base pairs apparently occupied by the bound drug n(bp/actD). These binding parameters vary linearly with the logarithm of the molar fraction of water in solution log(X-w), which indicates the contribution of water binding to the energetic of the reaction. It is demonstrated that the hydration change measured upon binding increases proportionally to the apparent size of the binding site n(bp/uctD). This indicates that n(bp/actD) measured from the Scatchard plod is a measure of the size of the DNA molecule changing conformation due to ligand binding. We also find that the contribution of DNA deformation, gauged by n(bp/act) to the total free energy of binding Delta G, is given by Delta G = Delta G(local) + n(bp/actD) x delta G(DNA), where Delta G(local), = -8020 +/- 51 cal/mol of actD bound and delta G(DNa) = -24.1 +/- 1.7cal/mol of base pair at 25 degrees C. We interpret Delta G(local), as the energetic contribution due to the direct interactions of actD with the actual tetranucleotide binding site, and it n(bp/actB) X delta G(DNA) as that due to change inconformation, induced by binding, of it n(bp/actD) DNA base pairs flanking the local site. This interpretation is supported by the agreement found between the value of delta G(DNA) and the torsional free energy change measured independently. We conclude suggesting an allosteric model for ligand binding to DNA, such that the increase in binding affinity is achieved by increasing the relaxation of the unfavorable free energy of binding storage at the local site through a larger number of DNA base pairs. The new aspect on this model is that the size of the complex is not fixed but determined by solutions conditions, such as water activity, which modulate the energetic barrier to change helix conformation. These results may suggest that long-range allosteric transitions of duplex DNA are involved in the inhibition of RNA synthesis by actD, and more generally, in the regulation of transcription. (C) 2000 John Wiley & Sons, Inc.

Structure and growth mechanism of CuO plates obtained by microwave-hydrothermal without surfactants

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

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.

Crystal structure of a novel myotoxic Arg49 phospholipase A(2) homolog (zhaoermiatoxin) from Zhaoermia mangshanensis snake venom: Insights into Arg49 coordination and the role of Lys122 in the polarization of the C-terminus

The venom of Zhaoermia mangshanensis, encountered solely in Mt Mang in China's Hunan Province, exhibits coagulant, phosphodiesterase, L-amino acid oxidase, kallikrein, phospholipase A(2) and myotoxic activities. The catalytically inactive PLA(2) homolog referred to as zhaoermiatoxin is highly myotoxic and displays high myonecrotic and edema activities. Zhaoermiatoxin possesses a molecular weight of 13,972 Da, consists of 121 amino-acid residues crosslinked by seven disulfide bridges and shares high sequence homology with Lys49-PLA(2)s from the distantly related Asian pitvipers. However, zhaoermiatoxin possesses an arginine residue at position 49 instead of a lysine, thereby suggesting a secondary Lys49 -> Arg substitution which results in a catalytically inactive protein. We have determined the first crystal structure of zhaoermiatoxin, an Arg49-PLA(2), from Zhaoermia mangshanensis venom at 2.05 A resolution, which represents a novel member of phospholipase A(2) family. In this structure, unlike the Lys49 PLA(2)s, the C-terminus is well ordered and an unexpected non-polarized state of the putative calcium-binding loop due to the flip of Lys122 towards the bulk solvent is observed. The orientation of the Arg-49 side chain results in a similar binding mode to that observed in the Lys49 PLA(2)s; however, the guadinidium group is tri-coordinated by carbonyl oxygen atoms of the putative calcium-binding loop, whereas the N zeta atom of lysine is tetra-coordinated as a result of the different conformation adopted by the putative calcium-binding loop. (c) 2008 Elsevier Ltd. All rights reserved.

Methyl- and phenylmercury(II) derivatives of 2-mercaptobenzothiazole. Crystal structure of (2-mercaptobenzothiazolato)methylmercury(II)

The complexes MeHgL and PhHgL (HL = 2-mercaptobenzothiazole) have been obtained from the reaction of the ligand with methylmercury hydroxide and phenylmercury acetate, respectively, in methanol. MeHgL, which has been characterized by single-crystal X-ray diffraction analysis (crystal data: triclinic, space group P1, with a = 8.009 (4) Å, b = 10.042 (4) Å, c = 13.074 (3) Å, α = 101.25 (2)°, β = 102.61(3)°, γ = 101.42 (3)°, R = 0.067), crystallizes with two independent molecules, I and I′, contained in each asymmetric unit with a coordination geometry based on the almost linear C-Hg-S group (Hg-S = 2.369 (6) Å, Hg-C = 2.06 (2) Å, and C-Hg-S = 177.7 (7)° for I; Hg-S = 2.375 (6) Å, Hg-C = 2.10 (3) Å, and C-Hg-S = 178.8 (6)° for I′). A secondary intramolecular interaction between the mercury atom and the C=N group of the ring and some weak intermolecular interactions between the metal and sulfur atoms were also found. The vibrational spectra of this compound and the phenylmercury(II) compound are discussed in light of the crystal structure. Diagnostic criteria of the bonding modes for the ligand are assessed. © 1985 American Chemical Society.