Stoicheiometric analysis in studies of metabolism

Stoicheiometric analysis of metabolic pathways provides a systematic way of determining which metabolite concentrations are subject to constraints, information that may otherwise be very difficult to recognize in a large branched pathway. The procedure involves representing the pathway structure in the form of a matrix and then carrying out row operations to convert the matrix into "row echelon form": this is a form in which as many as possible of the elements on the main diagonal are non-zero, and all of the elements below the main diagonal are zero. If exactly the same operations are carried out on a unit matrix of order equal to the number of intermediate metabolites in the pathway, the resulting matrix allows the stoicheiometric constraints to be read off directly.     

Uncertainties regarding dengue modeling in Rio de Janeiro, Brazil

Dengue fever is currently the most important arthropod-borne viral disease in Brazil. Mathematical modeling of disease dynamics is a very useful tool for the evaluation of control measures. To be used in decision-making, however, a mathematical model must be carefully parameterized and validated with epidemiological and entomological data. In this work, we developed a simple dengue model to answer three questions: (i) which parameters are worth pursuing in the field in order to develop a dengue transmission model for Brazilian cities; (ii) how vector density spatial heterogeneity influences control efforts; (iii) with a degree of uncertainty, what is the invasion potential of dengue virus type 4 (DEN-4) in Rio de Janeiro city. Our model consists of an expression for the basic reproductive number (R0) that incorporates vector density spatial heterogeneity. To deal with the uncertainty regarding parameter values, we parameterized the model using a priori probability density functions covering a range of plausible values for each parameter. Using the Latin Hypercube Sampling procedure, values for the parameters were generated. We conclude that, even in the presence of vector spatial heterogeneity, the two most important entomological parameters to be estimated in the field are the mortality rate and the extrinsic incubation period. The spatial heterogeneity of the vector population increases the risk of epidemics and makes the control strategies more complex. At last, we conclude that Rio de Janeiro is at risk of a DEN-4 invasion. Finally, we stress the point that epidemiologists, mathematicians, and entomologists need to interact more to find better approaches to the measuring and interpretation of the transmission dynamics of arthropod-borne diseases.     

Hydrosoluble formazan XTT: its application to natural products drug discovery for Leishmania

A colorimetric method for measuring the viability of Leishmania promastigotes is described that is based on the reduction of the tetrazolium salt, XTT, to a water-soluble formazan. Values obtained by the XTT method correlated well with parasite number (r=0.965) and with methods that rely upon the reduction of MTT or MTS (r=0.96 and 0.97, respectively). The IC(50) values obtained by XTT method with amphotericin-B, miltefosine and ketoconazole were similar to those previously reported by other methods. The XTT method proved to be a reliable and convenient method for the screening of methanolic extracts from 1059 plants and was used for the bioassay-guided fractionation of the alkaloid aegeline from Sarcorhachis naranjoana.     

Seasonal changes in lipid classes and fatty acid composition in the digestive gland of Pecten maximus

Seasonal variations in lipid classes and fatty acid composition of triacylglycerols and phospholipids in the digestive gland of Pecten maximus were studied over a period of 16 months. Acylglycerols predominated (19-77% of total lipids), in accordance with the role of the digestive gland as an organ for lipid storage in scallops. Seasonal variations were mainly seen in the acylglycerol content, while phospholipids (2.5-10.0% of total lipids) and sterols (1.9-7.4% of total lipids) showed only minor changes. The most abundant fatty acids were 14:0, 16:0, 18:0, 16:1(n-7), 18:1(n-9), 18:1(n-7), 18:4(n-3), 20:5(n-3) and 22:6(n-3) and these showed similar seasonal profiles in both, triacylglycerol and phospholipid fractions. In contrast to the phospholipid fraction, the triacylglycerol fraction contained more 20:5(n-3) than 22:6(n-3). In three phospholipid samples we noted a high percentage of a 22-2-non-methylene-interrupted fatty acid, previously described to have a structural role in several bivalve species. The main polyunsaturated fatty acids displayed important seasonal variations parallel to those of the acylglycerols, suggesting good nutritional conditions. A positive correlation existed between the level of saturated fatty acids and temperature, whereas the levels of polyunsaturated fatty acids correlated negatively with temperature.     

Molecular evidence for a single taxon, Anopheles nuneztovari s.l., from two endemic malaria regions in Colombia

To elucidate the Anopheles nuneztovari s.l. taxonomic status at a microgeographic level in four malaria endemic localities from Antioquia and Córdoba, Colombia, fragments of the cytochrome oxidase subunit I (COI) and the white gene were used. The COI analysis showed low genetic differentiation with fixation index (F(ST)) levels between -0.02-0.137 and Nm values between 3-∞, indicating the presence of high gene flow among An. nuneztovari s.l. populations from the four localities. The COI network showed a single most common haplotype, type 1 (n = 55), present in all localities, as the likely ancestral haplotype. Analysis of the white gene showed that An. nuneztovari s.l. populations from both departments grouped with haplotypes 19 and 20, which are part of lineage 3 reported previously. The results of the present study suggest that An. nuneztovari s.l. is a single taxon in the area of the present study.     

Late pleistocene paleoclimates of the South Pacific based on statistical analysis of planktonic foraminifers

Statistical analysis applied to foraminiferal data from 78 South Pacific core tops enables the derivation of a transfer function that relates sea surface temperature to foraminiferal assemblages. Application of this transfer function to eight cores from the southern part of the East Pacific Rise yields estimates of the sea surface temperatures of the last glacial maximum, as well as the paleotemperature record of the past 150,000 years. Comparison of the last glacial temperature estimates with the recent sea surface temperature shows that the greatest change between glacial and present conditions (about 5°C) occurs in a climatically sensitive area near 50°S. Stratigraphic correlation of two cores from this area suggests that the last glacial started in this area with rapid cooling, and that the climate stayed generally cold until the end of the glacial. Similar general shape of the climatic record is found in the high latitudes of the North Atlantic as well as in the ice sheets of Greenland and Antarctica. In contrast to the similarity in the shape of these high-latitude records, they differ distinctly from the foraminiferal oxygen isotope record of several deep-sea cores which indicates a general gradual increase of ice volume from the beginning of the last glacial to the maximum glaciation which occurred about 18,000 years B.P.In the study area the rate of sediment accumulation during the last glacial is about two to three times less than in the last interglacial. There is no indication of increased carbonate solution during the glacial, and it is suggested that the change in the accumulation rate results from a reduction in the supply of calcareous shells to the sediment. It seems that with cooling, the environment becomes less favorable to organisms producing calcium carbonate tests, and therefore carbonate production decreases during the glacial.     

The role of Y84 on domain 1 and Y87 on domain 2 of Paragonimus westermani taurocyamine kinase: Insights on the substrate binding mechanism of a trematode phosphagen kinase

The two-domain taurocyamine kinase (TK) from Paragonimus westermani was suggested to have a unique substrate binding mechanism. We performed site-directed mutagenesis on each domain of this TK and compared the kinetic parameters Km^Tc and Vmax with that of the wild-type to determine putative amino acids involved in substrate recognition and binding. Replacement of Y84 on domain 1 and Y87 on domain 2 with R resulted in the loss of activity for the substrate taurocyamine. Y84E mutant has a dramatic decrease in affinity and activity for taurocyamine while Y87E has completely lost catalytic activity. Substituting H and I on the said positions also resulted in significant changes in activity. Mutation of the residues A59 on the GS region of domain 1 also caused significant decrease in affinity and activity while mutation on the equivalent position on domain 2 resulted in complete loss of activity.