Interaction interfaces of protein domains are not topologically equivalent across families within superfamilies: Implications for metabolic and signaling pathways

Using a data set of aligned protein domain superfamilies of known three-dimensional structure, we compared the location of interdomain interfaces on the tertiary folds between members of distantly related protein domain superfamilies. The data set analyzed is comprised of interdomain interfaces, with domains occurring within a polypeptide chain and those between two polypeptide chains. We observe that, in general, the interfaces between protein domains are formed entirely in different locations on the tertiary folds in such pairs. This variation in the location of interface happens in protein domains involved in a wide range of functions, such as enzymes, adapters, and domains that bind protein ligands, or cofactors. While basic biochemical functionality is preserved at the domain superfamily level, the effect of biochemical function on protein assemblies is different in these protein domains related by superfamily. The divergence between proteins, in most cases, is coupled with domain recruitment, with different modes of interaction with the recruited domain. This is in complete contrast to the observation that in closely related homologous protein domains, almost always the interaction interfaces are topologically equivalent. In a small subset of interacting domains within proteins related by remote homology, we observe that the relative positioning of domains with respect to one another is preserved. Based on the analysis of multidomain proteins of known or unknown structure, we suggest that variation in protein-protein interactions in members within a superfamily could serve as diverging points in otherwise parallel metabolic or signaling pathways. We discuss a few representative cases of diverging pathways involving domains in a superfamily.     

Maternal, neonatal and community factors influencing neonatal mortality in Brazil

Child mortality (the mortality of children less than five years old) declined considerably in the developing world in the 1990s, but infant mortality declined less. The reductions in neonatal mortality were not impressive and, as a consequence, there is an increasing percentage of infant deaths in the neonatal period. Any further reduction in child mortality, therefore, requires an understanding of the determinants of neonatal mortality. 209,628 birth and 2581 neonatal death records for the 1998 birth cohort from the city of S?o Paulo, Brazil, were probabilistically matched. Data were from SINASC and SIM, Information Systems on Live Births and Deaths of Brazil. Logistic regression was used to find the association between neonatal mortality and the following risk factors: birth weight, gestational age, Apgar scores at 1 and 5 minutes, delivery mode, plurality, sex, maternal education, maternal age, number of prior losses, prenatal care, race, parity and community development. Infants of older mothers were less likely to die in the neonatal period. Caesarean delivery was not found to be associated with neonatal mortality. Low birth weight, pre-term birth and low Apgar scores were associated with neonatal death. Having a mother who lives in the highest developed community decreased the odds of neonatal death, suggesting that factors not measured in this study are behind such association. This result may also indicate that other factors over and above biological and more proximate factors could affect neonatal death.     

Toxoplasma gondii: isolation of tachyzoites rhoptries and incorporation into Iscom

Rhoptries have been isolated from Toxoplasma gondii tachyzoites by subcellular fractionation in isopynic density sucrose gradient. Five bands were observed, and transmission electron microscopy of these indicated that rhoptries were in band 3. This band had a density of 1.17 g/cm(3). Fraction 1 had membrane structures of the parasite. Fraction 2 contained membranes and mitochondria. Fraction 4 had mostly conoid structure and fraction 5 showed ghosts. The electrophoretic and Western blotting analysis of the fractions indicated the presence of a number of proteins. Iscoms were constructed from band 3, which contained the rhoptry structures. Iscom showed a only protein incorporated of 55 kDa. Isolation of the parasite organelles has got in this work is necessary to identification, characterization, and function elucidation of the organelle proteins.     

Effects of eicosanoid biosynthesis inhibitors on the prophenoloxidase-activating system and microaggregation reactions in the hemolymph of Rhodnius prolixus infected with Trypanosoma rangeli

Investigations on the effects of eicosanoid biosynthesis inhibitors on the hemocyte microaggregation and prophenoloxidase (proPO)-activating system in the hemolymph, parasitemia and mortality of Rhodnius prolixus infected with Trypanosoma rangeli were performed. Hemocoelic injection of live T. rangeli epimastigotes into fifth-instar larvae of R. prolixus that previously fed on blood containing an inhibitor of phospholipase A(2) (dexamethasone), a specific inhibitor of the cyclooxygenase pathway (indomethacin), and a non-selective lipoxygenase inhibitor (NDGA) (i) reduced the hemocyte microaggregation, (ii) attenuated the proPO system in the hemolymph and (iii) enhanced parasitemia and mortality induced by the parasite challenge in these insects. The effects obtained by dexamethasone administered orally were counteracted by inoculation of the insects with arachidonic acid. We suggest that the infectivity of T. rangeli can be increased by interference with the R. prolixus immune system. This is the first demonstration that the triatomine's immune responses to a parasite infection are modulated by a physiological system that includes eicosanoid biosynthesis.     

Calcium-regulated fusion of yolk granules during early embryogenesis of Periplaneta americana

This work reported membrane fusion of yolk granules (YGs) during early embryogenesis of the insect Periplaneta americana (P. americana). We showed that eggs from Day 5 of embryogenesis possess a greater amount of enlarged YGs in comparison with Day 1. Day 5 is also the period when the largest amount of free calcium is found (approximately 17 mM) within the oothecae from early embryogenesis. Treatment of Day 1-YGs fraction with 17 mM Ca2+ resulted in a YG size pattern very similar to the one observed in Day 5 eggs, where enlarged YGs were formed. YG membrane fusion was observed by fluorescent membrane dye transfer from previously labeled small YGs to larger ones and was also visualized by electron microscopy. We also showed that the small "in fusion" YGs seemed to be acidic, suggesting that acidification is correlated with YG membrane fusion. Hence, it was shown that YGs are capable of membrane fusion in a calcium-dependent manner and this process probably occurs in vivo during early embryogenesis of P. americana.     

Association of BoLA-DRB3.2 alleles with tick (Boophilus microplus) resistance in cattle

Losses caused by bovine tick burdens in tropical countries have a tremendous economic impact on production systems. Besides reducing production, this parasite can cause death in the most susceptible animals. The use of commercial acaricides has been the major method of control, but their misuse has led to tick resistance to many chemicals. More recently, vaccines have been used in some countries without solving the problem completely. An alternative could be the development of resistant animals and the use of genetic markers and candidate genes that could help with the enormous task of selecting resistant animals. The bovine lymphocyte antigen genes (BoLA) have been shown to be associated with some parasitic infestations and disease incidence. Thus, the objective of the present study was to determine the association of BoLA-DRB3.2 alleles with tick resistance in cattle. The study was conducted on 231 F2 (Gyr x Holstein) animals that were artificially infested with 10,000 tick larvae. Log of tick count +1 was used as the dependent variable in a mixed animal model with allele substitution effects in addition to fixed effects of year and season at tick count, sex of calves, age of animal at tick count, hair type (short-straight, short-curl, long-straight, and long-curl), coat color (white, >75% white, 50- 75% white, and 25-50% white), and additive genetic, permanent environmental and residual effects as random. Females showed fewer ticks than males. Animals with short-straight hair were more resistant to tick infestation than animals with long-curl hair, and animals with whiter coat color also had fewer ticks. An association between BoLA alleles and lower tick number was found for alleles DRB3.2 *18, *20 and *27 at the 5% significance level. Also, one allele (DRB3.2*16) showed an association at the 10% level. Allele *27 was the most frequent in the population (30.7%), followed by alleles *16 (10.8%), *20 (8.7%) and *18 (2.4%). These results suggest that BoLA-DRB3.2 alleles could be used to help in the selection of animals resistant to tick infestation. However, further studies involving a larger population of cattle in combination with other BoLA genes may help to understand the mechanisms of resistance to parasites.     

Prospective timing in pigeons: Isolating temporal perception in the time-left procedure

In the time-left procedure, a task used to study prospective timing, animals choose between two stimuli that signal different delays to reinforcement. Trials begin with one stimulus signaling C seconds to reinforcement and, at different moments since its onset, another stimulus, signaling S seconds to reinforcement, with C > S, is introduced. Optimal performance consists in choosing the stimulus signaling the shorter time to reinforcement. Animals have been found to perform in this optimal way. However, this procedure is complex and variables other than time may be responsible for the results. In two experiments with pigeons we sought to improve the time-left procedure to better isolate the effect of time in the animals’ behavior. We attempted to control for two confounding variables, the asymmetry in the time markers from training to testing and the cost of switching between the two response alternatives. We conclude that in the time-left task pigeons seem indeed to regulate their behavior based on time because, with our improved procedure, they still chose the stimulus associated with the shorter time to food. However, our version of the procedure created new interpretative difficulties, strengthening the idea that the time-left procedure may be too complex to study timing.     

Antiulcer activity of ethanolic extract of Encholirium spectabile Mart. ex Schult & Schult f. (Bromeliaceae) in rodents

This study evaluated the antiulcer activity of an ethanolic extract of Encholirium spectabile (ES-EtOH) by using different standard experimental models of induced acute gastric ulceration. ES-EtOH (100 mg/kg p.o) protected the gastric mucosa against ulceration that was induced by absolute ethanol (53%), ethanol/HCl (75%), ibuprofen (52 %) and ischemia/reperfusion (43 %). It also restored catalase activity and non-protein sulfhydryl group concentration in the gastric wall of mice that had been treated with ethanol. The pre-treatment of mice with N-nitro-L-arginine (70 mg/kg i.p.) abolished the protective activity of ES-EtOH, which indicates that prostaglandins, antioxidant compounds and nitric oxide synthase activity are involved in the gastroprotective activity of the extract.     

Variation in ostracod (Crustacea,Ostracoda) communities in the alluvial valley of the upper Paraná River (Brazil) in relation to substrate

Large river floodplains are convenient model systems to test for variation in animal and plant community structure, as they have a variety of habitats and substrates and are generally dynamic systems through the occurrence of flood pulses with varying intensity. South American floodplain systems furthermore have unique types of substrates, in the form of root systems of floating macrophytes. Here, we investigate the variation in ostracod (small, bivalved crustaceans) communities in relation to substrates and related environmental variables. Sampling was effected in 2004 in the alluvial valley of the upper Paraná River, Brazil, in the wet and dry seasons. Five different substrates, including littoral sediment and four macrophyte species root and leaf systems, in four hydrological systems and a variety of habitat types, were sampled. Fifty-four species of Ostracoda were found. Variation partitioning analysis (RDA) showed that ostracod communities significantly differed between different substrates, mainly between the littoral and plants with small root systems (Eichhornia azurea) on the one hand, and plants with large and complex root systems on the other hand (Eichhornia crassipes and Pistia stratiotes). RDA analyses indicated that the pleuston (biotic communities associated with root systems of floating plants) of E. crassipes comprised more non-swimming species than the pleuston of the smaller roots of P. stratiotes, but species-level Kruskal–Wallis analyses could not detect significant differences between both macrophyte species. Also habitat type and hydrological systems contributed to variation amongst ostracod communities, but less so than the factor substrate. Abiotic factors also contributed to variation, but the ranges of all measured water chemistry variables were narrow. This uniformity in abiotic factors, which might be owing to the occurrence of large flooding events, unites all water bodies, even those that are generally separated.