Detection of Leishmania DNA in phlebotomines captured in Campo Grande, Mato Grosso do Sul, Brazil

Over the past years, leishmaniases have become a public health issue in the Brazilian state of Mato Grosso do Sul, particularly in Campo Grande, the state capital. The purpose of this study was to detect the presence of Leishmania DNA in the population of phlebotomine sandflies using DNA amplification by PCR. Insect captures were carried out from 4 pm. to 7 am for 4 consecutive days each month from October 2005 to September 2006 in 16 neighborhoods located in 7 urban regions of Campo Grande. Traps were placed indoors and in the vicinity of households. As many as 971 males and 203 females were collected. One hundred and five naturally fed females were identified and grouped as 1- to 4-specimen pools. DNA extraction was carried out using whole insects. Lutzomyia longipalpis predominated, accounting for 99.15% of the phlebotomines captured. Also found was Nyssomyia whitmani, the vector of tegumentary leishmaniasis. Abundance was greatest in the vicinity of households (69.8% of the phlebotomines captured). As revealed by PCR, parasites were present in 1.9% of the Leishmania spp. specimens investigated and confirmed for visceral leishmaniasis.     

Structural basis for the interaction of isoDGR with the RGD-binding site of alphavbeta3 integrin

Asparagine deamidation at the NGR sequence in the 5th type I repeat of fibronectin (FN-I5) generates isoDGR, an alphavbeta3 integrin-binding motif regulating endothelial cell adhesion and proliferation. By NMR and molecular dynamics studies, we analyzed the structure of CisoDGRC (isoDGR-2C), a cyclic beta-peptide mimicking the FN-I5 site, and compared it with NGR, RGD, or DGR-containing cyclopeptides. Docking experiments show that isoDGR, exploiting an inverted orientation as compared with RGD, favorably interacts with the RGD-binding site of alphavbeta3, both recapitulating canonical RGD-alphavbeta3 contacts and establishing additional polar interactions. Conversely, NGR and DGR motifs lack the fundamental pharmacophoric requirements for high receptor affinity. Therefore, unlike NGR and DGR, isoDGR is a new natural recognition motif of the RGD-binding pocket of alphavbeta3. These findings contribute to explain the different functional properties of FN-I5 before and after deamidation, and provide support for the hypothesis that NGR --> isoDGR transition can work as a molecular timer for activating latent integrin-binding sites in proteins, thus regulating protein function.     

Vpr.A3A chimera inhibits HIV replication

Several APOBEC3 proteins (A3F and A3G), that are cytidine deaminases restrict human immunodeficiency virus (HIV) replication in the absence of the viral infectivity factor (Vif) protein. However, Vif leads to their degradation and counteracts their effects. Another member, A3A, restricts some retrotransposons and another virus but not HIV. We reasoned that this failure was due to the lack of appropriate targeting. Thus, we fused A3A to another viral protein, Vpr, which binds p6 in Gag and is incorporated into viral cores. Indeed, the Vpr.A3A chimera but not A3A was found abundantly in the viral core. It also restricted potently the replication of HIV and simian immunodeficiency virus in the presence and absence of Vif. Because we identified a high frequency of G to A mutations in viral cDNAs, this antiviral activity was mediated by DNA editing. Interestingly, our fusion protein did not restrict murine leukemia virus, which does not incorporate Vpr. Thus, by targeting appropriately a potent single domain cytidine deaminase, we rendered HIV and simian immunodeficiency virus restriction resistant to Vif.     

Caspase-3 activation triggers extracellular cathepsin L release and endorepellin proteolysis

Proteolysis of extracellular matrix components and the production of cryptic bioactive factors play key roles in vascular remodeling. We showed previously that extracellular matrix proteolysis is triggered by the apoptosis of endothelial cells (EC), resulting in the release of an anti-apoptotic C-terminal fragment of endorepellin (LG3). Here, we characterize the endorepellin-cleaving proteases released by apoptotic EC using a multifaceted proteomics strategy. Cathepsin L (CathL), a cysteine protease known to be associated with cardiovascular disease progression in animal models and humans, was isolated from medium conditioned by apoptotic EC. CathL cleaved recombinant endorepellin in vitro, leading to LG3 release. Inhibition of CathL activity in EC exposed to pro-apoptotic stimuli prevented LG3 release without modulating the development of apoptosis in EC. Inhibition of caspase-3 activation in EC with the biochemical inhibitor DEVD-fluoromethyl ketone or small interfering RNAs concomitantly prevented CathL release by EC, LG3 production, and the development of paracrine anti-apoptotic activity. These data demonstrate that caspase-3 activation is a novel pathway of importance for triggering extracellular CathL release and the cleavage of extracellular matrix components.     

Habitat specialization and phylogenetic structure of tree species in a coastal Brazilian white-sand forest

Aims The coastal Brazilian rainforest on white-sand (restinga) ranks among the most fragmented forest types in the tropics, owing to both the patchy distribution of sandy soils and widespread coastal development activities. Here we study the environmental and evolutionary determinants of a forest tree assemblage at a single restinga forest in Southeastern Brazil. We also explore the ability of competing hypotheses to explain the maintenance of species diversity in this forest type, which includes contrasting extremes of edaphic conditions associated with flooding stress.Methods The study was conducted in a white-sand forest permanent plot of 10.24 ha on the coastal plain of Southeastern Brazil. This plot was divided into 256 quadrats of 20×20 m, which were classified into two main edaphic habitats (flooded and drained). Trees with a diameter ≥1cm at breast height were identified. We assembled DNA sequence data for each of the 116 morphospecies recognized using two chloroplast markers (rbcL and matK). A phylogenetic tree was obtained using the maximum likelihood method, and a phylogenetic distance matrix was produced from an ultrametric tree. We analyzed similarity in floristic composition and structure between habitats and related them to cross-plot distances using permutation procedures. Null model torus shift simulations were performed to obtain a statistical significance level for habitat association for each species. The phylogenetic structure for the two habitats and for each 20×20 m quadrat was calculated using the mean phylogenetic distance weighted by species abundance and checked for significance using the standardized effect size generated by 5000 randomizations of phylogenetic tip labels.Important findings Our results indicate that partitioning among edaphic habitats is important for explaining species distributions and coexistence in restinga forests. Species distributions within the plot were found to be non-random: there was greater floristic similarity within than between habitats, and>40% of the more abundant species were positively or negatively associated with at least one habitat. Patterns of habitat association were not independent of phylogenetic relatedness: the community was overdispersed with respect to space and habitat type. Closely related species tended to occur in different habitats, while neighboring trees tended to belong to more distantly related species. We conclude that habitat specialization is important for the coexistence of species in restinga forests and that habitat heterogeneity is therefore an essential factor in explaining the maintenance of diversity of this unique but fragile and threatened type of forest.     

Characterization of expressed Pgip genes in rice and wheat reveals similar extent of sequence variation to dicot PGIPs and identifies an active PGIP lacking an entire LRR repeat

Polygalacturonase-inhibiting proteins (PGIPs) are leucine-rich repeat (LRR) proteins involved in plant defence. A number of PGIPs have been characterized from dicot species, whereas only a few data are available from monocots. Database searches and genome-specific cloning strategies allowed the identification of four rice (Oryza sativa L.) and two wheat (Triticum aestivum L.) Pgip genes. The rice Pgip genes (Ospgip1, Ospgip2, Ospgip3 and Ospgip4) are distributed over a 30 kbp region of the short arm of chromosome 5, whereas the wheat Pgip genes, Tapgip1 and Tapgip2, are localized on the short arm of chromosome 7B and 7D, respectively. Deduced amino acid sequences show the typical LRR modular organization and a conserved distribution of the eight cysteines at the N- and C-terminal regions. Sequence comparison suggests that monocot and dicot PGIPs form two separate clusters sharing about 40% identity and shows that this value is close to the extent of variability observed within each cluster. Gene-specific RT-PCR and biochemical analyses demonstrate that both Ospgips and Tapgips are expressed in the whole plant or in a tissue-specific manner, and that OsPGIP1, lacking an entire LRR repeat, is an active inhibitor of fungal polygalacturonases. This last finding can contribute to define the molecular features of PG–PGIP interactions and highlights that the genetic events that can generate variability at the Pgip locus are not only limited to substitutions or small insertions/deletions, as so far reported, but can also involve variation in the number of LRRs.Electronic Supplementary Material Supplementary material is available to authorised users in the online version of this article at .     

On peptide de novo sequencing: a new approach.

A procedure is presented for the automatic determination of the amino acid sequence of peptides by processing data obtained from mass spectrometry analysis. This is a basic and relevant problem in the field of proteomics. Furthermore, it has an even higher conceptual and applicative interest in peptide research, as well as in other connected fields. The analysis does not rely on known protein databases, but on the computation of all amino acid sequences compatible with the given spectral data. By formulating a mathematical model for such combinatorial problems, the structural limitations of known methods are overcome, and efficient solution algorithms can be developed. The results are very encouraging both from the accuracy and computational points of view.     

Amino acid anthranilamide derivatives as a new class of glycogen phosphorylase inhibitors

A series of amino acid anthranilamide derivatives identified from a high-throughput screening campaign as novel, potent, and glucose-sensitive inhibitors of human liver glycogen phosphorylase a are described. A solid-phase synthesis using Wang resin was also developed which provided efficient access to a variety of analogues, and resulted in the identification of key structure–activity relationships, and the discovery of a potent exemplar (IC₅₀ = 80 nM). The SAR scope, synthetic strategy, and in vitro results for this series are presented herein.     

The genome of Rhodobacter sphaeroides strain 2.4.1 encodes functional cobinamide salvaging systems of archaeal and bacterial origins

Bacteria and archaea use distinct pathways for salvaging exogenous cobinamide (Cbi), a precursor of adenosylcobalamin (coenzyme B(12)). The bacterial pathway depends on a bifunctional enzyme with kinase and guanylyltransferase activities (CobP in aerobic adenosylcobalamin synthesizers) to convert adenosylcobinamide (AdoCbi) to AdoCbi-guanosine diphosphate (AdoCbi-GDP) via an AdoCbi-phosphate intermediate. Archaea lack CobP, and use a different strategy for the synthesis of AdoCbi-GDP. Archaea cleave off the aminopropanol group of AdoCbi using the CbiZ AdoCbi amidohydrolase to generate adenosylcobyric acid, which is converted to AdoCbi-phosphate by the CbiB synthetase, and to AdoCbi-GDP by the CobY guanylyltransferase. We report phylogenetic, in vivo and in vitro evidence that the genome of Rhodobacter sphaeroides encodes functional enzymes for Cbi salvaging systems of both bacterial and archaeal origins. Products of the reactions were identified by high-performance liquid chromatography, UV-visible spectroscopy and bioassay. The cbiZ genes of several bacteria and archaea restored Cbi salvaging in a strain of Salmonella enterica unable to salvage Cbi. Phylogenetic data led us to conclude that CbiZ is an enzyme of archaeal origin that was horizontally transferred to bacteria. Reasons why some bacteria may contain both types of Cbi salvaging systems are discussed.     

The effect of epibionts on the susceptibility of the red seaweed Cryptonemia seminervis to herbivory and fouling

Epibiosis or fouling on living organisms can have direct and indirect detrimental effects, in particular on photosynthetic organisms such as seaweeds. It thus seems reasonable to hypothesize that macroalgae have been selected for the presence or induction of antifouling (AF) defences. The red seaweed Cryptonemia seminervis is usually found in nature with an elevated cover of epibionts. To assess the effect of epibiosis on the susceptibility of this seaweed to herbivory and fouling, the abundance of fouling was evaluated and compared to herbivore consumption (by amphipods and sea urchins) of fouled (bryozoan and sponge) and non-fouled C. seminervis. Attachment of the mussel Perna perna to surfaces treated with extracts from seaweeds with and without epibionts was also assessed. Epibiosis corresponded to ca. 51% of the blade surface of C. seminervis, sometimes covering as much as 90% and up to 51% of the thallus weight, encompassing mainly the bryozoan Membranipora membranacea and an unidentified sponge. Algae colonized by M. membranacea were preferred compared to algae devoid of epibionts, a 'shared doom' effect, either by the amphipod Elasmopus brasiliensis or by the urchin Lytechinus variegatus (p < 0.01). Sponge epibiosis also increased consumption by both herbivores (p < 0.001), suggesting that epibionts may act as lures to herbivores, attracting consumers that otherwise would not feed significantly on the seaweed. Foods containing extracts from fouled C. seminervis were preferred by urchins over the alga devoid of epibionts. However, extracts from fouled alga inhibited mussel attachment when compared to epibiont-free alga. Differences might be a direct detrimental effect of the presence of epibionts. On the other hand, epibiosis may induce the production of AF defences in C. seminervis.