Intergenic and external transcribed spacers of ribosomal RNA genes in lizard-infecting Leishmania: molecular structure and phylogenetic relationship to mammal-infecting Leishmania in the subgenus Leishmania (Leishmania)

To establish the relationships of the lizard- and mammal-infecting Leishmania, we characterized the intergenic spacer region of ribosomal RNA genes from L. tarentolae and L. hoogstraali. The organization of these regions is similar to those of other eukaryotes. The intergenic spacer region was approximately 4 kb in L. tarentolae and 5.5 kb in L. hoogstraali. The size difference was due to a greater number of 63-bp repetitive elements in the latter species. This region also contained another element, repeated twice, that had an inverted octanucleotide with the potential to form a stem-loop structure that could be involved in transcription termination or processing events. The ribosomal RNA gene localization showed a distinct pattern with one chromosomal band (2.2 Mb) for L. tarentolae and two (1.5 and 1.3 Mb) for L. hoogstraali. The study also showed sequence differences in the external transcribed region that could be used to distinguish lizard Leishmania from the mammalian Leishmania. The intergenic spacer region structure features found among Leishmania species indicated that lizard and mammalian Leishmania are closely related and support the inclusion of lizard-infecting species into the subgenus Sauroleishmania proposed by Saf'janova in 1982.

Structure and dynamics of a woody plant community of a tropical semi-deciduous seasonal forest in the "Estação Ecológica do Panga", municipality of Uberlândia, Minas Gerais, Brazil

Studies of plant community dynamics are essential in understanding the demographic patterns of species since changes in demographic rates can affect the floristic composition and future structure. The purpose of the present study was to analyze the changes in the community structure and floristic composition of woody plants in a tropical semi-deciduous forest in Uberlândia in central Brazil, during a 10-years period. The data were collected in 1989 and in 2000 in 50 quadrats (10 m x 10 m) where all trees with a minimum circumference at breast height of 10 cm were sampled. In 1989, 93 species and 1103 individuals were registered. Over a period of 10 years, seven new species were added to the community, although eight disappeared. The main change that occurred during this period in the floristic composition was the replacement of savannah species occurring in forest gaps by those from the forest understory.

Cloning and Molecular Characterization of the Schistosoma mansoni Genes RbAp48 and Histone H4

The human nuclear protein RbAp48 is a member of the tryptophan/aspartate (WD) repeat family, which binds to the retinoblastoma (Rb) protein. It also corresponds to the smallest subunit of the chromatin assembly factor and is able to bind to the helix 1 of histone H4, taking it to the DNA in replication. A cDNA homologous to the human gene RbAp48 was isolated from a Schistosoma mansoni adult worm library and named SmRbAp48. The full length sequence of SmRbAp48 cDNA is 1036 bp long, encoding a protein of 308 amino acids. The transcript of SmRbAp48 was detected in egg, cercariae and schistosomulum stages. The protein shows 84% similarity with the human RbAp48, possessing four WD repeats on its C-terminus. A hypothetical tridimensional structure for the SmRbAp48 C-terminal domain was constructed by computational molecular modeling using the b-subunit of the G protein as a model. To further verify a possible interaction between SmRbAp48 and S. mansoni histone H4, the histone H4 gene was amplified from adult worm genomic DNA using degenerated primers. The gene fragment of SmH4 is 294 bp long, encoding a protein of 98 amino acids which is 100% identical to histone H4 from Drosophila melanogaster.

Population structure and diversity of the pathogenic fungus Aspergillus fumigatus isolated from different sources and geographic origins

Fifty-five clinical and environmental Aspergillus fumigatus isolates from Mexico, Argentina, France and Peru were analyzed to determine their genetic variability, reproductive system and level of differentiation using amplified fragment length polymorphism markers. The level of genetic variability was assessed by measuring the percentage of polymorphic loci, number of effective alleles, expected heterozygocity and by performing an association index test (I A). The degree of genetic differentiation and variation was determined using analysis of molecular variance at three levels. Using the paired genetic distances, a dendrogram was built to detect the genetic relationship among alleles. Finally, a network of haplotypes was constructed to determine the geographic relationship among them. The results indicate that the clinical isolates have greater genetic variability than the environmental isolates. The I A of the clinical and environmental isolates suggests a recombining population structure. The genetic differentiation among isolates and the dendrogram suggest that the groups of isolates are different. The network of haplotypes demonstrates that the majority of the isolates are grouped according to geographic origin.

Assessing protein stability of the dimeric DNA-binding domain of E2 human papillomavirus 18 with molecular dynamics

The objective of this study is to understand the structural flexibility and curvature of the E2 protein of human papillomavirus type 18 using molecular dynamics (6 ns). E2 is required for viral DNA replication and its disruption could be an anti-viral strategy. E2 is a dimer, with each monomer folding into a stable open-faced β-sandwich. We calculated the mobility of the E2 dimer and found that it was asymmetric. These different mobilities of E2 monomers suggest that drugs or vaccines could be targeted to the interface between the two monomers.

Spatial and temporal dynamics of drosophilid larval assemblages associated to fruits

The study of organisms and their resources is critical to further understanding population dynamics in space and time. Although drosophilids have been widely used as biological models, their relationship with breeding and feeding sites has received little attention. Here, we investigate drosophilids breeding in fruits in the Brazilian Savanna, in two contrasting vegetation types, throughout 16 months. Specifically, larval assemblages were compared between savannas and forests, as well as between rainy and dry seasons. The relationships between resource availability and drosophilid abundance and richness were also tested. The community (4,022 drosophilids of 23 species and 2,496 fruits of 57 plant taxa) varied widely in space and time. Drosophilid assemblages experienced a strong bottleneck during the dry season, decreasing to only 0.5% of the abundance of the rainy season. Additionally, savannas displayed lower richness and higher abundance than the forests, and were dominated by exotic species. Both differences in larval assemblages throughout the year and between savannas and gallery forests are consistent with those previously seen in adults. Although the causes of this dynamic are clearly multifactorial, resource availability (richness and abundance of rotten fruits) was a good predictor of the fly assemblage structure.

Land-use systems affect Archaeal community structure and functional diversity in western Amazon soils

The study of the ecology of soil microbial communities at relevant spatial scales is primordial in the wide Amazon region due to the current land use changes. In this study, the diversity of the Archaea domain (community structure) and ammonia-oxidizing Archaea (richness and community composition) were investigated using molecular biology-based techniques in different land-use systems in western Amazonia, Brazil. Soil samples were collected in two periods with high precipitation (March 2008 and January 2009) from Inceptisols under primary tropical rainforest, secondary forest (5-20 year old), agricultural systems of indigenous people and cattle pasture. Denaturing gradient gel electrophoresis of polymerase chain reaction-amplified DNA (PCR-DGGE) using the 16S rRNA gene as a biomarker showed that archaeal community structures in crops and pasture soils are different from those in primary forest soil, which is more similar to the community structure in secondary forest soil. Sequence analysis of excised DGGE bands indicated the presence of crenarchaeal and euryarchaeal organisms. Based on clone library analysis of the gene coding the subunit of the enzyme ammonia monooxygenase (amoA) of Archaea (306 sequences), the Shannon-Wiener function and Simpson's index showed a greater ammonia-oxidizing archaeal diversity in primary forest soils (H' = 2.1486; D = 0.1366), followed by a lower diversity in soils under pasture (H' = 1.9629; D = 0.1715), crops (H' = 1.4613; D = 0.3309) and secondary forest (H' = 0.8633; D = 0.5405). All cloned inserts were similar to the Crenarchaeota amoA gene clones (identity > 95 %) previously found in soils and sediments and distributed primarily in three major phylogenetic clusters. The findings indicate that agricultural systems of indigenous people and cattle pasture affect the archaeal community structure and diversity of ammonia-oxidizing Archaea in western Amazon soils.

Genetic structure and gene flow of Eugenia dysenterica natural populations

This study was carried out to assess the genetic variability of ten "cagaita" tree (Eugenia dysenterica) populations in Southeastern Goiás. Fifty-four randomly amplified polymorphic DNA (RAPD) loci were used to characterize the population genetic variability, using the analysis of molecular variance (AMOVA). A phiST value of 0.2703 was obtained, showing that 27.03% and 72.97% of the genetic variability is present among and within populations, respectively. The Pearson correlation coefficient (r) among the genetic distances matrix (1 - Jaccard similarity index) and the geographic distances were estimated, and a strong positive correlation was detected. Results suggest that these populations are differentiating through a stochastic process, with restricted and geographic distribution dependent gene flow.

Morphological and molecular diversity among cassava genotypes

The objective of this work was to characterize morphologically and molecularly the genetic diversity of cassava accessions, collected from different regions in Brazil. A descriptive analysis was made for 12 morphological traits in 419 accessions. Data was transformed into binary data for cluster analysis and analysis of molecular variance. A higher proportion of white or cream (71%) root cortex color was found, while flesh colors were predominantly white (49%) and cream (42%). Four accession groups were classified by the cluster analysis, but they were not grouped according to their origin, which indicates that diversity is not structured in space. The variation was greater within regions (95.6%). Sixty genotypes were also evaluated using 14 polymorphic microsatellite markers. Molecular results corroborated the morphological ones, showing the same random distribution of genotypes, with no grouping according to origin. Diversity indices were high for each region, and a greater diversity was found within regions, with: a mean number of alleles per locus of 3.530; observed and expected heterozygosity of 0.499 and 0.642, respectively; and Shannon index of 1.03. The absence of spatial structure among cassava genotypes according to their origins shows the anthropic influence in the distribution and movement of germplasm, both within and among regions.

Synthesis, structure and physicochemical properties of zinc and copper complexes based on sulfonamides containing 8-aminoquinoline ligands

Sulfonamides obtained by reaction of 8-aminoquinoline with 4-nitrobenzenesulfonylchloride and 2,4,6-triisopropylbenzenesulfonyl chloride were used to synthesize coordination compounds with CuII and ZnII with a ML2 composition. Determination of the crystal structures of the resulting zinc and copper complexes by X-ray diffraction show a distorted tetrahedral environment for the [Cu(qnbsa)2], [Cu(qibsa)2] and [Zn(qibsa)2] complexes in which the sulfonamide group acts as a bidentate ligand through the nitrogen atoms from the sulfonamidate and quinoline groups. The complex [Zn(qnbsa)2] crystallizes with a water molecule from the solvent and the Zn is five-coordinated and shows a bipyramidal-trigonal geometry. The electrochemical and electronic spectroscopy properties of the copper complexes are also discussed.

Effect of dye structure and redox mediators on anaerobic azo and anthraquinone dye reduction

We investigated the biological decolourisation of dyes with different molecular structures. The kinetic constant values (k1) achieved with azo dye Reactive Red 120 were 7.6 and 10.1 times higher in the presence of RM (redox mediators) AQDS and riboflavin, respectively, than the assays lacking RM. The kinetic constant achieved with the azo dye Congo Red was 42 times higher than that obtained with the anthraquinone dye Reactive Blue 4. The effect of RM on dye reduction was more evident for azo dyes resistant to reductive processes, and ineffective for anthraquinone dyes because of the structural stability of the latter.

Nematode community, trophic structure and population fluctuation in soybean fields

Temporal (monthly in three fields for 12 months) and spatial (once in 23 fields during March-April) samplings were conducted in the major soybean (Glycine max)-growing region of the Brazilian Federal District. Fifty-three nematode genera were found in both samplings, but 13 were detected only by the temporal sampling, and one only by the spatial sampling. Fifty-three percent were plant-parasites, 35% were bacterivores, and about 12% were fungivores, predators and omnivores constituted the community that was dominated by the genera Helicotylenchus (40% of total abundance), Acrobeles (15%), Cephalobus (7.6%), Meloidogyne(5.6%) and Pratylenchus (4.9%). Heterodera glycines was not found in this study. There were no differences in ten ecological measurements [Ds, H', Es, T, FF/BF, (FF+BF)/PP, MI, PPI, mMI, and Dorylaimida (%)] between the two sampling types, but differences in indexes d and J'. Plant parasite populations dropped at the end of the crop cycle, remained at low levels during the dry season and the seedling period, then increased again in the crop-growing season. Fungivores maintained their low populations throughout the year, increasing only in June and July, the post-harvest period, when soil fungi decomposed root tissue. The population of bacterivores slightly declined during the dry season and the initial rainy season, but peaked in the middle of the rainy season, apparently associated with soil humidity. In the five most abundant nematodes, those of Acrobeles and Pratylenchus were more populous in wet soils, Cephalobus and Meloidogyne adapted well in dry soils, but Helicotylenchus survived abundantly in a wide range of soil moisture.

Analysis of the structure and vibrational spectra of glucose and fructose

Molecular modelling using semiempirical methods AM1, PM3, PM5 and, MINDO as well as the Density Functional Theory method BLYP/DZVP respectively were used to calculate the structure and vibrational spectra of d-glucose and d-fructose in their open chain, alpha-anomer and beta-anomer monohydrate forms. The calculated data show that both molecules are not linear; ground state and the number for the point-group C is equal to 1. Generally, the results indicate that there are similarities in bond lengths and vibrational modes of both molecules. It is concluded that DFT could be used to study both the structural and vibrational spectra of glucose and fructose.

Insights into the role of hydration in protein structure and stability obtained through hydrostatic pressure studies

A thorough understanding of protein structure and stability requires that we elucidate the molecular basis for the effects of both temperature and pressure on protein conformational transitions. While temperature effects are relatively well understood and the change in heat capacity upon unfolding has been reasonably well parameterized, the state of understanding of pressure effects is much less advanced. Ultimately, a quantitative parameterization of the volume changes (at the basis of pressure effects) accompanying protein conformational transitions will be required. The present report introduces a qualitative hypothesis based on available model compound data for the molecular basis of volume change upon protein unfolding and its dependence on temperature.

Eccentric and concentric cardiac hypertrophy induced by exercise training: microRNAs and molecular determinants

Among the molecular, biochemical and cellular processes that orchestrate the development of the different phenotypes of cardiac hypertrophy in response to physiological stimuli or pathological insults, the specific contribution of exercise training has recently become appreciated. Physiological cardiac hypertrophy involves complex cardiac remodeling that occurs as an adaptive response to static or dynamic chronic exercise, but the stimuli and molecular mechanisms underlying transduction of the hemodynamic overload into myocardial growth are poorly understood. This review summarizes the physiological stimuli that induce concentric and eccentric physiological hypertrophy, and discusses the molecular mechanisms, sarcomeric organization, and signaling pathway involved, also showing that the cardiac markers of pathological hypertrophy (atrial natriuretic factor, β-myosin heavy chain and α-skeletal actin) are not increased. There is no fibrosis and no cardiac dysfunction in eccentric or concentric hypertrophy induced by exercise training. Therefore, the renin-angiotensin system has been implicated as one of the regulatory mechanisms for the control of cardiac function and structure. Here, we show that the angiotensin II type 1 (AT1) receptor is locally activated in pathological and physiological cardiac hypertrophy, although with exercise training it can be stimulated independently of the involvement of angiotensin II. Recently, microRNAs (miRs) have been investigated as a possible therapeutic approach since they regulate the translation of the target mRNAs involved in cardiac hypertrophy; however, miRs in relation to physiological hypertrophy have not been extensively investigated. We summarize here profiling studies that have examined miRs in pathological and physiological cardiac hypertrophy. An understanding of physiological cardiac remodeling may provide a strategy to improve ventricular function in cardiac dysfunction.