Structure of tick anticoagulant peptide at 1.6 Å resolution complexed with bovine pancreatic trypsin inhibitor

The structure of tick anticoagulant peptide (TAP) has been determined by X-ray crystallography at t.6 Å resolution complexed with bovine pancreatic trypsin inhibitor (BPTI). The TAP-BPTI crystals are tetragonal, a = b = 46.87, c = 50.35 Å, space group P41, four complexes per unit cell. The TAP molecules are highly dipolar and form an intermolecular helical array along the c-axis with a diameter of about 45 Å. Individual TAP units interact in a head-to-tail fashion, the positive end of one molecule associating with the distal negative end of another, and vice versa. The BPTI molecules have a uniformly distributed positively charged surface that interacts extensively through 14 hydrogen bonds and two hydrogen bonded salt bridges with the helical groove around the helical TAP chains. Comparing the structure of TAP in TAP-BPTI with TAP bound to factor Xa(Xa) suggests a massive reorganization in the N-terminal tetrapeptide and the first disulfide loop of TAP (CyS5(T)- Cys 15(T)) upon binding to Xa. The Tyr1(T)OH atom of TAP moves 14.2 Å to interact with Asp189 of the S1 specificity site, Arg3(T)CZ moves 5.0 Å with the guanidinium group forming a cation-π-electron complex in the S4 subsite of Xa, while Lys7(T)NZ differs in position by 10.6 Å in TAP-BPTI and TAP-Xa, all of which indicates a different pre-Xa-bound conformation for the N- terminal of TAP in its native state. In contrast to TAP, the BPTI structure of TAP-BPTI is practically the same as all those of previously determined structures of BPTI, only arginine and lysine side-chain conformations showing significant differences.

Variation in mandible shape in Thrichomys apereoides (Mammalia: Rodentia): Geometric analysis of a complex morphological structure

The model of development and evolution of complex morphological structures conceived by Atchley and Hall in 1991 (Biol. Rev. 66:101-157), which establishes that changes at the macroscopic, morphogenetic level can be statistically detected as variation in skeletal units at distinct scales, was applied in combination with the formalism of geometric morphometrics to study variation in mandible shape among populations of the rodent species Thrichomys apereoides. The thin-plate spline technique produced geometric descriptors of shape derived from anatomical landmarks in the mandible, which we used with graphical and inferential approaches to partition the contribution of global and localized components to the observed differentiation in mandible shape. A major pattern of morphological differentiation in T. apereoides is attributable to localized components of shape at smaller geometric scales associated with specific morphogenetic units of the mandible. On the other hand, a clinal trend of variation is associated primarily with localized components of shape at larger geometric scales. Morphogenetic mechanisms assumed to be operating to produce the observed differentiation in the specific units of the mandible include mesenchymal condensation differentiation, muscle hypertrophy, and tooth growth. Perspectives for the application of models of morphological evolution and geometric morphometrics to morphologically based systematic biology are considered.

Morphology changes induced by laser irradiation on disperse red 13 films prepared by physical vapor deposition

Surface morphology changes induced by argon laser irradiation (514 nm) on disperse red 13 (DR13) films prepared by physical vapor deposition (PVD) were investigated. Atomic force microscopy was used to characterize the irradiated sample for different periods of irradiation. Needle-shape structures are observed which are attributed to the symmetry of DR13 molecules. The film becomes increasingly closely packed with the irradiation, with lower root mean square roughness for long exposure times. This is due to photoisomerization of DR13 molecules and probably heating of the sample, which can provide the required mobility for the molecular rearrangement. The rearrangement is such that voids in the film are filled in upon irradiating the sample, thus decreasing the film roughness and increasing the packing.

Estimates of covariance functions for growth of Nelore cattle applying a parametric correlation structure to model within-animal correlations

A total of 20,065 weights recorded on 3016 Nelore animals were used to estimate covariance functions for growth from birth to 630 days of age, assuming a parametric correlation structure to model within-animal correlations. The model of analysis included fixed effects of contemporary groups and age of dam as quadratic covariable. Mean trends were taken into account by a cubic regression on orthogonal polynomials of animal age. Genetic effects of the animal and its dam and maternal permanent environmental effects were modelled by random regressions on Legendre polynomials of age at recording. Changes in direct permanent environmental effect variances were modelled by a polynomial variance function, together with a parametric correlation function to account for correlations between ages. Stationary and nonstationary models were used to model within-animal correlations between different ages. Residual variances were considered homogeneous or heterogeneous, with changes modelled by a step or polynomial function of age at recording. Based on Bayesian information criterion, a model with a cubic variance function combined with a nonstationary correlation function for permanent environmental effects, with 49 parameters to be estimated, fitted best. Modelling within-animal correlations through a parametric correlation structure can describe the variation pattern adequately. Moreover, the number of parameters to be estimated can be decreased substantially compared to a model fitting random regression on Legendre polynomial of age. © 2004 Elsevier B.V. All rights reserved.

Kinetics and crystal structure of human purine nucleoside phosphorylase in complex with 7-methyl-6-thio-guanosine

Purine nucleoside phosphorylase (PNP) catalyzes the reversible phosphorolysis of nucleosides and deoxynucleosides, generating ribose 1-phosphate and the purine base, which is an important step of purine catabolism pathway. The lack of such an activity in humans, owing to a genetic disorder, causes T-cell impairment, and drugs that inhibit this enzyme may have the potential of being utilized as modulators of the immunological system to treat leukemia, autoimmune diseases, and rejection in organ transplantation. Here, we describe kinetics and crystal structure of human PNP in complex with 7-methyl-6-thio-guanosine, a synthetic substrate, which is largely used in activity assays. Analysis of the structure identifies different protein conformational changes upon ligand binding, and comparison of kinetic and structural data permits an understanding of the effects of atomic substitution on key positions of the synthetic substrate and their consequences to enzyme binding and catalysis. Such knowledge may be helpful in designing new PNP inhibitors. © 2005 Elsevier Inc. All rights reserved.

Crystallographic structure of Ti-6Al-4V, Ti-HP and Ti-CP under high-pressure

The phase stability of a commercial purity (Ti-CP), high purity (Ti-HP) and Ti-6Al-4V alloy were investigated in a diamond anvil cell up to 32 GPa and 298 K using a polychromatic X-ray beam. The Ti-CP and Ti-HP shown the same HCP (c/a∼0.632) to Hexagonal (c/a∼1.63) non reversible martensitic transition at about 9 GPa. The as received Ti-6Al-4V shows a very low relative volume fraction β-Ti / α-Ti. No phase changes were observed in the Ti-6Al-4V alloy in the pressure range of this study. The α phase of the Ti-6Al-4V shows monotonic volume cell pressure dependence. This volume change is reversible and non-hysteretic. The cell of the a phase recovered its original volume when the pressure was released. © 2010 IOP Publishing Ltd.

Structure of a novel class II phospholipase D: Catalytic cleft is modified by a disulphide bridge

Phospholipases D (PLDs) are principally responsible for the local and systemic effects of Loxosceles envenomation including dermonecrosis and hemolysis. Despite their clinical relevance in loxoscelism, to date, only the SMase I from Loxosceles laeta, a class I member, has been structurally characterized. The crystal structure of a class II member from Loxosceles intermedia venom has been determined at 1.7. Å resolution. Structural comparison to the class I member showed that the presence of an additional disulphide bridge which links the catalytic loop to the flexible loop significantly changes the volume and shape of the catalytic cleft. An examination of the crystal structures of PLD homologues in the presence of low molecular weight compounds at their active sites suggests the existence of a ligand-dependent rotamer conformation of the highly conserved residue Trp230 (equivalent to Trp192 in the glycerophosphodiester phosphodiesterase from Thermus thermophofilus, PDB code: 1VD6) indicating its role in substrate binding in both enzymes. Sequence and structural analyses suggest that the reduced sphingomyelinase activity observed in some class IIb PLDs is probably due to point mutations which lead to a different substrate preference. © 2011 Elsevier Inc.

Evolução do rifteamento e paleogeografia da margem Atlântica Equatorial do Brasil: Triássico ao Holoceno

The Equatorial Atlantic Margin evolved from three rift systems recorded by a complex set of sedimentary basins developed since Upper Triassic to the Lower Cretaceous (Albian). The first rift system formed Foz do Amazonas Basin in Upper Triassic; the second phase formed Marajó Basin in Berriasian, a new rift in Foz do Amazonas Basin in Valanginian and Bragança-Viseu, Ilha Nova, São Luís e Barreirinhas basins in Aptian; the third phase formed Barreirinhas and Pará- Maranhão basins and a new rifting in the Foz do Amazonas Basin between the Aptian and Albian and evolved to continental break up. The main paleostress field during rift evolution was NE-SW and after the continental break up took the E-W direction, from the development of transform zones in the oceanic crust. From Miocene, South America was subjected to intraplate tectonics, which resulted in formation of E-W transcurrent faults that generated transtensive and transpressive segments that formed sedimentary basins and hills, resulting in changes in the drainage network. In Quaternary the landscape was modified by the last ice age that changed the sea level; the coastal drainage network was drowning resulting in the formation of the current line coast.

Synthesis, characterization and antifungal activity of quaternary derivatives of chitosan on Aspergillus flavus

Two series of new chitosan derivatives were synthesized by reaction of deacetylated chitosan (CH) with propyl (CH-Propyl) and pentyl (CH-Pentyl) trimethylammonium bromides to obtain derivatives with increasing degrees of substitution (DS). The derivatives were characterized by 1H NMR and potentiometric titration techniques and their antifungal activities on the mycelial growth of Aspergillus flavus were investigated in vitro. The antifungal activities increase with DS and the more substituted derivatives of both series, CH-Propyl and CH-Pentyl, exhibited antifungal activities respectively three and six times higher than those obtained with commercial and deacetylated chitosan. The minimum inhibitory concentrations (MIC) were evaluated at 24, 48 and 72h by varying the polymer concentration from 0.5 to 16g/L and the results showed that the quaternary derivatives inhibited the fungus growth at polymer concentrations four times lower than that obtained with deacetylated chitosan (CH). The chitosans modified with pentyltrimethylammonium bromide exhibited higher activity and results are discussed taking into account the degree of substitution (DS). © 2012 Elsevier GmbH.

Structural changes in soybean seed coat due to harvest time and storage

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

Structure control of poly(p-phenylene vinylene) in layer-by-layer films by deposition on a charged poly(o-methoxyaniline) cushion

In this paper, we demonstrate that the intrinsic electric field created by a poly(o-methoxyaniline) (POMA) cushion layer hinders the changes in molecular conformation of poly(p-phenylenevinylene) (PPV) in layer-by-layer with dodecylbenzene sulfonic acid (DBS). This was modeled with density functional theory (DFT) calculations where an energy barrier hampered molecular movements of PPV segments when they were subjected to an electric field comparable to that caused by a charged POMA layer. With restricted changes in molecular conformation, the PPV film exhibited Franck-Condon transitions and the photoexcitation spectra resembled the absorption spectra, in contrast to PPV/DBS films deposited directly on glass, with no POMA cushion. Other effects from the POMA cushion were the reduced number of structural defects, confirmed with Raman spectroscopy, and an enhanced PPV emission at high temperatures (300 K) in comparison with the films on bare glass. The positive effects from the POMA cushion may be exploited for enhanced opto-electronic devices, especially as the intrinsic electric field may assist in separating photoexcited electron-hole pairs in photovoltaic devices. © 2013 American Institute of Physics.

No changes in seedling recruitment when terrestrial mammals are excluded in a partially defaunated Atlantic rainforest

One of the most intriguing questions in ecology is how to identify which and how many species will be able to inhabit human-modified landscapes. Large-bodied mammals structure plant communities by trampling, herbivory, seed dispersal and predation, and their local extinction may have pervasive consequences in plant communities due to the breakdown of key interactions. Although much attention has been given to understanding the effects of defaunation on plant communities, information on the potential impacts on plant functional groups (seed dispersal, seed size and seedling leaves defense) inhabiting continuous forests after defaunation is scarce. We conducted mammal surveys (line transects and camera trapping) to determine the defaunation status of a continuous Atlantic forest in Brazil. Then, we evaluated the effects of defaunation on seedling diversity, richness and abundance of functional groups using 15 plot-pairs (each pair with one open and one exclusion plot) monitored over 36. months. We found that the studied area is partially defaunated because it exhibits high abundance of primates, while terrestrial mammals, such as large rodents and ungulates, are rare. We found no significant changes in either seedling richness and diversity or in the seedling composition of plant functional groups in response to mammal exclosure. Seedling mortality and recruitment were similar between plot types. Our findings suggest that at semi-defaunated areas, where arboreal species are still present, terrestrial mammals have low impacts on the plant community reassembly. © 2013 Elsevier Ltd.

Influence of current density on crystalline structure and magnetic properties of electrodeposited Co-rich CoNiW alloys

The influence of current density, at the interval 5-100 mA cm-2, on the structural and magnetic properties of electrodeposited (Co 100-xNix)100-yWy alloys (x = 23-33.5 at. % Ni, y = 1.7-7.3 at. % W) was studied from a glycine-containing bath. W-content decreases with the increase of the current density magnitude. X-ray data have shown stabilization of hexagonal close packed, face centered cubic or a mixture of these structures by modulating the applied cathodic current density, for values lower than 50 mA cm-2. Two structural phase transitions were observed: one from hexagonal close packed to face centered cubic structural transition occurring for a current density of 20 mA cm -2, and another one, from cubic crystalline phase to amorphous state, which happens for values higher than 50 mA cm-2. These structural phase transitions seem to be associated with the W-content as well as average crystalline grain sizes that reduce with increasing the current density value. The grain size effect may explain the face centered cubic stabilization in Co-rich CoNiW alloys, which was initially assumed to be basically due to H-adsorption/incorporation. Magnetic properties of Co-rich CoNiW alloys are strongly modified by the current density value; as a result of the changes on the W-content and their structural properties© 2013 Elsevier B.V. All rights reserved.

Role of acidic and basic electrolytes on the structure and morphology of cathodically reduced indium tin oxide (ITO) substrates

In this report we track the structural changes suffered by ITO along galvanostatic polarization at different current densities by X-ray diffraction and SEM micrographs. The XRD shown that cathodic treatment induces structural change in ITO, characterized by appearing peaks set distinct from ITO original structure associated to metallic phase of the solid solution of In-Sn. It is interesting to note that although the different ions present in the solution are not, at least to a noticeable degree, incorporated in the metallic phase, the SEM images show that they do influence its formation, pointing to some type of adsorptive mechanism of the inert ions during the lateral diffusion of the metallic ions. © 2013 Elsevier Ltd. All rights reserved.

Structure-function relationships of the peptide Paulistine: A novel toxin from the venom of the social wasp Polybia paulista

Background: The peptide Paulistine was isolated from the venom of wasp Polybia paulista. This peptide exists under a natural equilibrium between the forms: oxidised - with an intra-molecular disulphide bridge; and reduced - in which the thiol groups of the cysteine residues do not form the disulphide bridge. The biological activities of both forms of the peptide are unknown up to now. Methods: Both forms of Paulistine were synthesised and the thiol groups of the reduced form were protected with the acetamidemethyl group [Acm-Paulistine] to prevent re-oxidation. The structure/activity relationships of the two forms were investigated, taking into account the importance of the disulphide bridge. Results: Paulistine has a more compact structure, while Acm-Paulistine has a more expanded conformation. Bioassays reported that Paulistine caused hyperalgesia by interacting with the receptors of lipid mediators involved in the cyclooxygenase type II pathway, while Acm-Paullistine also caused hyperalgesia, but mediated by receptors involved in the participation of prostanoids in the cyclooxygenase type II pathway. Conclusion: The acetamidemethylation of the thiol groups of cysteine residues caused small structural changes, which in turn may have affected some physicochemical properties of the Paulistine. Thus, the dissociation of the hyperalgesy from the edematogenic effect when the actions of Paulistine and Acm-Paulistine are compared to each other may be resulting from the influence of the introduction of Acm-group in the structure of Paulistine. General significance: The peptides Paulistine and Acm-Paulistine may be used as interesting tools to investigate the mechanisms of pain and inflammation in future studies. © 2013 Elsevier B.V.