Crystal structure and statistical coupling analysis of highly glycosylated peroxidase from royal palm tree (Roystonea regia)

Royal palm tree peroxidase (RPTP) is a very stable enzyme in regards to acidity, temperature, H(2)O(2), and organic solvents. Thus, RPTP is a promising candidate for developing H(2)O(2)-sensitive biosensors for diverse applications in industry and analytical chemistry. RPTP belongs to the family of class III secretory plant peroxidases, which include horseradish peroxidase isozyme C, soybean and peanut peroxidases. Here we report the X-ray structure of native RPTP isolated from royal palm tree (Roystonea regia) refined to a resolution of 1.85 angstrom. RPTP has the same overall folding pattern of the plant peroxidase superfamily, and it contains one heme group and two calcium-binding sites in similar locations. The three-dimensional structure of RPTP was solved for a hydroperoxide complex state, and it revealed a bound 2-(N-morpholino) ethanesulfonic acid molecule (MES) positioned at a putative substrate-binding secondary site. Nine N-glycosylation sites are clearly defined in the RPTP electron-density maps, revealing for the first time conformations of the glycan chains of this highly glycosylated enzyme. Furthermore, statistical coupling analysis (SCA) of the plant peroxidase superfamily was performed. This sequence-based method identified a set of evolutionarily conserved sites that mapped to regions surrounding the heme prosthetic group. The SCA matrix also predicted a set of energetically coupled residues that are involved in the maintenance of the structural folding of plant peroxidases. The combination of crystallographic data and SCA analysis provides information about the key structural elements that could contribute to explaining the unique stability of RPTP. (C) 2009 Elsevier Inc. All rights reserved.

Short report: Historical analysis of a near disaster: Anopheles gambiae in Brazil

Attributed to human-mediated dispersal, a species of the Anopheles gambiae complex invaded northeastern Brazil in 1930. This event is considered unique among the intercontinental introductions of disease vectors and the most serious one: ""Few threats to the future health of the Americas have equalled that inherent in the invasion of Brazil, in 1930, by Anopheles gambiae."" Because it was only in the 1960s that An. gambiae was recognized as a species complex now including seven species, the precise species identity of the Brazilian invader remains a mystery. Here we used historical DNA analysis of museum specimens, collected at the time of invasion from Brazil, and aimed at the identification of the Brazilian invader. Our results identify the arid-adapted Anopheles arabiensis as being the actual invading species. Establishing the identity of the species, in addition to being of intrinsic historical interest, can inform future threats of this sort especially in a changing environment. Furthermore, these results highlight the potential danger of human-mediated range expansions of insect disease vectors and the importance of museum collections in retrieving historical information.

An event of stratospheric air intrusion and its associated secondary surface cyclogenesis over the South Atlantic Ocean

This work presents an analysis of a lowermost stratospheric air intrusion event over the coast of Brazil, which may have been responsible for a secondary surface cyclogenesis over the southwestern Atlantic Ocean. The surface cyclone initiated at 0600 UTC 17 April 1999 in a cold air mass in the rear of a cold front after a primary cyclone developed over the same region. The analysis of the secondary cyclone revealed the presence of lowermost stratospheric air intrusion characterized by anomalous potential vorticity (PV), dry air, and high concentration of ozone in atmospheric column. The system developed on the eastern side of an upper level core of PV anomaly, which induced a cyclonic wind circulation at lower levels and favored the onset of the secondary cyclone. In midlevels (500 hPa), the cutoff low development contributed to reduce the propagation speed of the wave pattern. This feature seemed to (1) allow the low-level cold/dry air to heat/moisten associated with sensible and latent fluxes transferred from the ocean to the atmosphere, which intensified a baroclinic zone parallel to the coast, and (2) contribute to the long duration of the system. The present analysis indicates that this secondary cyclone development could be the result of the coupling between the PV anomaly in the upper levels and low-level air-sea interaction.

An analysis of the environmental energetics associated with the transition of the first South Atlantic hurricane

This study presents the first analysis of the energetics associated with a hybrid cyclone`s transition in the Southern Hemisphere, Hurricane Catarina ( March 2004). Catarina has earned a place in history as the first documented South Atlantic hurricane, but its unusual tropical transition is still poorly understood. Here we show that Catarina`s transition was preceded by marked environmental changes in the Lorenz energy cycle, with an abrupt shift from a baroclinic to a predominantly barotropic state. Such changes help to explain the unusual vortex`s growth until its transition was completed. Although the vortex`s energy flux is not explicitly calculated, a likely mechanism linking the environmental energetics with Catarina is the extraction of eddy kinetic energy from horizontal momentum and heat transfers within the through component of the blocking. The results advance the understanding of this rare event and suggest that the technique has a great potential to study transitioning systems in general.

Differential proteome analysis of mature and germinated embryos of Araucaria angustifolia

Araucaria angustifolia is an endangered Brazilian native conifer tree. The aim of the present work was to identify differentially expressed proteins between mature and germinated embryos of A. angustifolia, using one and two dimensional gel electrophoresis approaches followed by protein identification by tandem mass spectrometry. The identities of 32 differentially expressed protein spots from two dimensional gel maps were successfully determined, including proteins and enzymes involved in storage mobilization such as the vicilin-like storage protein and proteases. A label free approach, based on spectral counts, resulted in detection of 10 and 14 mature and germinated enriched proteins, respectively. Identified proteins were mainly related to energetic metabolism pathways, translational processes. oxidative stress regulation and cellular signaling. The integrated use of both strategies permitted a comprehensive protein expression overview of changes in germinated embryos in relation to matures, providing insights into the this process in a recalcitrant seed species. Applications of the data generated on the monitoring and control of in vitro somatic embryos were discussed. Published by Elsevier Ltd.

Cell wall polysaccharides from cell suspension cultures of the Atlantic Forest tree Rudgea jasminoides (Rubiaceae)

Rudgea jasminoides (Rubiaceae) is a tropical tree species native of the Atlantic Forest in the south of Brazil. Previous studies with leaf cell walls of R. jasminoides showed a different proportion of cross-linked glycans compared to what is usually reported for eudicots. However, due to the difficulties of working with whole plant organs, cell suspensions of R. jasminoides, consisting of predominantly undifferentiated cells with mainly primary cell walls, were used to examine cell walls and extracellular soluble polysaccharides (EP) released into the culture medium. Sugar composition and linkage analysis showed homogalacturonans, xylogalacturonans and arabinogalactans to be the predominant EP. In the cell wall, homogalacturonans and arabinogalactans are the major pectins, and xyloglucans and xylans are the major cross-linking glycans. The presence of xylogalacturonans in the R. jasminoides cell cultures seems to be related to the occurrence of a homogeneous cell suspension with loosely attached cells. Although all alkali extractions from the cell walls yielded amounts of xyloglucan that exceed those of the xylans, the latter was found in a proportion that is higher than what has been usually reported for primary cell walls of most eudicots. The xyloglucan from cell walls of cell suspension cultures of R. jasminoides has low fucosylation levels and high proportion of galactosyl residues, a branching pattern commonly found in storage cell-wall xyloglucans.

A new species of Lauromacromia (Odonata: Corduliidae) from Southeastern Brazil, with a cladistic analysis of the genus and comments on Neotropical dragonfly biogeography

Lauromacromia melanica sp. nov. from Conceicao da Barra municipality, Espirito Santo State, Brazil, is described and illustrated based on two males (both in MNRJ n degrees 135). The new species is similar to L. picinguaba differing from it mainly by the absence of pale spots on S3-6 and by the ellipsoid shape of metepisternal pale stripe. A key for males of all species of the genus is provided. A cladistic analysis encompassing 43 external morphological male characters carried out in two distinct procedures, the first with all characters unordered and the second with two or three state characters ordered. The unordered analysis generated only one most-parsimonious tree (66 steps of length, CI = 0.69, RI = 0.62). The hypothesis of monophyly of Lauromacromia is supported and includes three groups, one formed by the Atlantic Forest species (L. melanica sp. nov. + L. picinguaba), and another by the Cerrado species (L. flaviae + (L. bedei + L. luismoojeni)), and L. dubitalis, positioned in polytomy with these two groups. The ordered analysis also generated only one most-parsimonious tree (68 steps of length, CI = 0.70, RI = 0.67), which maintained the monophyly of Lauromacromia but L. dubitalis positioned basally as sister-group to the Atlantic Forest + Cerrado species groups. The geographic distribution of Lauromacromia is updated with a new record of L. luismoojeni based on one adult male (Brazil: Mato Grosso do Sul State) and probable first Brazilian records for L. dubitalis (Amazonas and Para States) based on two larvae. A vicariance hypothesis is proposed to explain spatial evolution of Lauromacromia, and based on current biogeographical classifications we consider Gomphomacromia and Rialla apart from Neotropical biota. Some aspects of biology and ecology of Lauromacromia are also discussed.

Systematic revision and cladistic analysis of the Brazilian subfamily Sodreaninae (Opiliones: Gonyleptidae)

Sodreaninae is reviewed and all ten species are combined under its type genus, Sodreana Mello-Leitao, 1922, according to a cladistic analysis of morphological characters, which revealed a pectinate pattern of clades. The subfamily is endemic to the Brazilian Atlantic rainforest from Santa Catarina state to Rio de Janeiro state. Sodreana is herein considered a senior synonym of Stygnobates Mello-Leitao, 1927, Zortalia Mello-Leitao, 1936, Gertia B. Soares & H. Soares, 1946 and Annampheres H. Soares, 1979. The following new combinations are proposed: Sodreana barbiellinii (Mello-Leitao, 1927), Sodreana hatschbachi (B. Soares & H. Soares, 1946), Sodreana inscripta (Mello-Leitao, 1939), Sodreana leprevosti (B. Soares & H. Soares, 1947b), Sodreana bicalcarata (Mello-Leitao, 1936). Sodreana granulata (Mello-Leitao, 1937) is revalidated from the synonymy of Sodreana sodreana Mello-Leitao, 1922. Three new species are described: Sodreana glaucoi from Ilhabela and Boraceia, Sao Paulo state; S. curupira from Parque Nacional da Serra dos Orgaos, Rio de Janeiro state, and S. caipora from Ubatuba, Sao Paulo state. Sodreaninae species are restricted to forested areas and most occur in the southern part of the coastal Atlantic rainforest, one species occurs in interior Atlantic rainforest. The biogeographical analysis (Brooks Parsimony Analysis) resulted in a single and fully resolved most parsimonious tree with three main: components: northern (Bahia and Serra do Espinhaco), southern (Santa Catarina, Parana, Serra do Mar of Sao Paulo), and central (Espirito Santo, Serra da Bocaina, southern state of Rio de Janeiro, Serra dos Orgaos, Serra da Mantiqueira, Serra do Mar of Sao Paulo).

Taxonomy and cladistic analysis of the subgenus Xenomorellia Malloch (Diptera: Muscidae: Morellia Robineau-Desvoidy) with description of two new species

Xenomorellia Malloch, a subgenus of Morellia Robineau-Desvoidy, is revised to include two new species, Morellia (Xenomorellia) inca Nihei and Carvalho sp. nov. from South America, and M. (X.) maia Carvalho and Nihei sp. nov. from Costa Rica and Mexico. Diagnoses for M. (X.) holti (Malloch) and M. (X.) montanhesa (Albuquerque) are provided, as well as an identification key to the four species of the subgenus. A cladistic analysis was performed to test the monophyly of Xenomorellia and to recover the phylogenetic relationships among its species. Tree searches resulted in one single most-parsimonious cladogram, wherein the monophyly of Xenomorellia is supported, as well as a sister-group relationship with the Neotropical subgenus Trichomorellia Stein. Xenomorellia was divided into two clades: one with Caribbean-Andean species (maia + inca), and another with species from southeastern South America (holti + montanhesa).

Analysis of the genome of Spodoptera frugiperda nucleopolyhedrovirus (SfMNPV-19) and of the high genomic heterogeneity in group II nucleopolyhedroviruses

The genome of the most virulent among 22 Brazilian geographical isolates of Spodoptera frugiperda nucleopolyhedrovirus, isolate 19 (SfMNPV-1 9), was completely sequenced and shown to comprise 132 565 bp and 141 open reading frames (ORFs). A total of 11 ORFs with no homology to genes in the GenBank database were found. Of those, four had typical baculovirus; promoter motifs and polyadenylation sites. Computer-simulated restriction enzyme cleavage patterns of SfMNPV-1 9 were compared with published physical maps of other SfMNPV isolates. Differences were observed in terms of the restriction profiles and genome size. Comparison of SfMNPV-1 9 with the sequence of the SfMNPV isolate 3AP2 indicated that they differed due to a 1427 bp deletion, as well as by a series of smaller deletions and point mutations. The majority of genes of SfMNPV-1 9 were conserved in the closely related Spodoptera exigua NPV (SeMNPV) and Agrotis segetum NPV (AgseMNPV-A), but a few regions experienced major changes and rearrangements. Synthenic maps for the genomes of group 11 NPVs revealed that gene collinearity was observed only within certain clusters. Analysis of the dynamics of gene gain and loss along the phylogenetic tree of the NPVs showed that group 11 had only five defining genes and supported the hypothesis that these viruses form ten highly divergent ancient lineages. Crucially, more than 60% of the gene gain events followed a power-law relation to genetic distance among baculoviruses, indicative of temporal organization in the gene accretion process.

Fiedler trees for multiscale surface analysis

In this work we introduce a new hierarchical surface decomposition method for multiscale analysis of surface meshes. In contrast to other multiresolution methods, our approach relies on spectral properties of the surface to build a binary hierarchical decomposition. Namely, we utilize the first nontrivial eigenfunction of the Laplace-Beltrami operator to recursively decompose the surface. For this reason we coin our surface decomposition the Fiedler tree. Using the Fiedler tree ensures a number of attractive properties, including: mesh-independent decomposition, well-formed and nearly equi-areal surface patches, and noise robustness. We show how the evenly distributed patches can be exploited for generating multiresolution high quality uniform meshes. Additionally, our decomposition permits a natural means for carrying out wavelet methods, resulting in an intuitive method for producing feature-sensitive meshes at multiple scales. Published by Elsevier Ltd.

Thermodynamic characterization of the palm tree Roystonea regia peroxidase stability

The structural stability of a peroxidase, a dimeric protein from royal palm tree (Roystonea regia) leaves, has been characterized by high-sensitivity differential scanning calorimetry, circular dichroism, steady-state tryptophan fluorescence and analytical ultracentifugation under different solvent conditions. It is shown that the thermal and chemical (using guanidine hydrochloride (Gdn-HCl)) folding/unfolding of royal palm tree peroxidase (RPTP) at pH 7 is a reversible process involving a highly cooperative transition between the folded dimer and unfolded monomers, with a free stabilization energy of about 23 kcal per mol of monomer at 25 degrees C. The structural stability of RPTP is pH-dependent. At pH 3, where ion pairs have disappeared due to protonation, the thermally induced denaturation of RPTP is irreversible and strongly dependent upon the scan rate, suggesting that this process is under kinetic control. Moreover, thermally induced transitions at this pH value are dependent on the protein concentration, allowing it to be concluded that in solution RPTP behaves as dimer, which undergoes thermal denaturation coupled with dissociation. Analysis of the kinetic parameters of RPTP denaturation at pH 3 was accomplished on the basis of the simple kinetic scheme N ->(k) D, where k is a first-order kinetic constant that changes with temperature, as given by the Arrhenius equation; N is the native state, and D is the denatured state, and thermodynamic information was obtained by extrapolation of the kinetic transition parameters to an infinite heating rate. Obtained in this way, the value of RPTP stability at 25 degrees C is ca. 8 kcal per mole of monomer lower than at pH 7. In all probability, this quantity reflects the contribution of ion pair interactions to the structural stability of RPTP. From a comparison of the stability of RPTP with other plant peroxidases it is proposed that one of the main factors responsible for the unusually high stability of RPTP which enhances its potential use for biotechnological purposes, is its dimerization. (c) 2008 Elsevier Masson SAS. All rights reserved.

Dynamic Changes in the Mental Rotation Network Revealed by Pattern Recognition Analysis of fMRI Data

We investigated the temporal dynamics and changes in connectivity in the mental rotation network through the application of spatio-temporal support vector machines (SVMs). The spatio-temporal SVM [Mourao-Miranda, J., Friston, K. J., et al. (2007). Dynamic discrimination analysis: A spatial-temporal SVM. Neuroimage, 36, 88-99] is a pattern recognition approach that is suitable for investigating dynamic changes in the brain network during a complex mental task. It does not require a model describing each component of the task and the precise shape of the BOLD impulse response. By defining a time window including a cognitive event, one can use spatio-temporal fMRI observations from two cognitive states to train the SVM. During the training, the SVM finds the discriminating pattern between the two states and produces a discriminating weight vector encompassing both voxels and time (i.e., spatio-temporal maps). We showed that by applying spatio-temporal SVM to an event-related mental rotation experiment, it is possible to discriminate between different degrees of angular disparity (0 degrees vs. 20 degrees, 0 degrees vs. 60 degrees, and 0 degrees vs. 100 degrees), and the discrimination accuracy is correlated with the difference in angular disparity between the conditions. For the comparison with highest accuracy (08 vs. 1008), we evaluated how the most discriminating areas (visual regions, parietal regions, supplementary, and premotor areas) change their behavior over time. The frontal premotor regions became highly discriminating earlier than the superior parietal cortex. There seems to be a parcellation of the parietal regions with an earlier discrimination of the inferior parietal lobe in the mental rotation in relation to the superior parietal. The SVM also identified a network of regions that had a decrease in BOLD responses during the 100 degrees condition in relation to the 0 degrees condition (posterior cingulate, frontal, and superior temporal gyrus). This network was also highly discriminating between the two conditions. In addition, we investigated changes in functional connectivity between the most discriminating areas identified by the spatio-temporal SVM. We observed an increase in functional connectivity between almost all areas activated during the 100 degrees condition (bilateral inferior and superior parietal lobe, bilateral premotor area, and SMA) but not between the areas that showed a decrease in BOLD response during the 100 degrees condition.