Distribution of ABCB1 polymorphisms among Brazilians: impact of population admixture

Introduction: Interethnic admixture is a source of cryptic population structure that may lead to spurious genotype-phenotype associations in pharmacogenomic studies. We studied the impact of population stratification on the distribution of ABCB1 polymorphisms (1236C > T, 2677G > T/A and 3435C > T) among Brazilians, a highly admixed population with Amerindian, European and African ancestral roots. Methods: Individual DNA from 320 healthy adults was genotyped with a panel of ancestry informative markers, and the proportions of African component of ancestry (ACA) were estimated. ABCB1 genotypes were determined by the single base extension/termination method. We describe the association between ABCB1 polymorphisms and ACA by fitting a linear proportional odds logistic regression model to the data. Results: The distribution of the ABCB1 2677G > T/A and 3435C > T, but not the 1236C > T, SNPs displayed a significant trend for decreasing frequency of the T alleles and TT genotypes from White to Intermediate to Black individuals. The same trend was observed in the frequency of the T/nonG/T haplotype at the 1236, 2677 and 3435 loci. When the population sample was proportioned in quartiles, according to the individual ACA estimates, the frequency of the T allele and TT genotype at each locus declined progressively from the lowest (< 0.25 ACA) to the highest (> 0.75 ACA) quartile. Linear proportional odds logistic regression analysis confirmed that the odds of having the T allele at each locus decreases in a continuous manner with the increase of the ACA, throughout the ACA range (0.13-0.94) observed in the overall population sample. A significant association was also detected between the individual ACA estimates and the presence of the T/nonG/T haplotype in the overall population. Conclusion: Self-identification according to the racial/color categories proposed by the Brazilian Census is insufficient to properly control for population stratification in pharmacogenomic studies of ABCB1.

Trace-metal biogeochemistry in the Mediterranean Thau Lagoon, a shellfish farming area

The present study contributes to the knowledge of the biogeochemistry of Pb, Cd, Cu, and Ni in the Mediterranean Than Lagoon, southern France, which is an important shellfish farming system. The concentrations of the metals were determined in sediment cores and the overlying waters using inductively coupled plasma mass spectrometry. Particular attention was given to the determination of dissolved Cu species because of their dual role as essential nutrient and toxicant to planktonic organisms. Dissolved Cu speciation was determined using the diffusive gradient in thin-film technique (DGT) and competitive ligand exchange-adsorptive cathodic stripping voltammetry (CLE-ACSV). Our data indicated a significant historical contamination of the sediments, which commenced in the second half of the 19th century, with trace metal inputs persisting until the end of the 20th century. In recent years a decrease in metal contamination has become apparent. The maxima observed for Pb, Cd, and Cu profiles probably indicate the occurence of anoxia crises. A strong complexation of the dissolved Cu species was observed in the waters of the Than Lagoon, which reduced the bioavailability of Cu. The dissolved Cu(2+) concentrations were probably too low to cause direct toxic effects on shellfish, but the highest concentration (5.29 pM) observed in this study can potentially influence phytoplankton communities. A comparison between the Cu speciation data indicates that up to 50% of the complexed Cu determined using CLE-ACSV was DGT labile.

Investigation of Iron (III) desferrioxamine B oxalate ligand exchange by UV-vis spectroscopy: the next step in developing a quantitative analytical method for measuring bioavailable iron in marine ecosystems

To date there are no analytical techniques designed to exclusively measure bioavailable iron in marine environments. The goal of this research is to develop such a technique by isolating the bioavailable iron using the terrestrial siderophore desferrioxamine B (DFB). This project contained many challenging aspects, but the specific goal of this study was to develop a robust analytical technique for quantification of Fe(III)-DFB complexes at nanomolar concentrations. Past work showed that oxalate (Ox) promotes photodissociation of Fe(III)-DFB to Fe(Il), and we are specifically interested in the mechanism of this process. A model was developed using known thermodynamic constants for Fe(III)-DFB and Fe(III) oxalato complexes and adjusting for ionic strength. The model was confirmed by monitoring the UV-VIS absorbance of the system at a variety of oxalate concentrations and pH. The model did not include ternary complexes. Next., the rate of Fe(1I) production during UV irradiation was examined. The results showed that the rate of Fe(II) production was based entirely on the [Fe(Ox)?]3- speciation, and that reoxidation of Fe(II) occurred via reactive oxygen intermediates. This reoxidation could be avoided by either decreasing the oxygen concentration or by adding a Fe(II) stabilizing reagent, such as ferrozine. Further studies need to be done to confirm that these results apply at sub nanomolar concentrations, and the issue of Fe(II) reoxidation at lower Fe concentrations needs to be addressed.

Biosystematics of the Genus Andryala L. (Asteraceae)

Andryala (Asteraceae: Cichorieae) is a little-known Mediterranean-Macaronesian genus whose taxonomy is much in need of revision. The aim of the present biosystematic study was to elucidate species relationships within this genus based on morphological and molecular data. In this study several taxa are recognised: 17 species, 14 subspecies, and 3 hybrids. Among these, 5 species are Macaronesian endemics (A. glandulosa, A. sparsiflora, A. crithmifolia Aiton, A. pinnatifida, and A. perezii), 4 species are Northwest African endemics (A. mogadorensis, A. maroccana, A. chevallieri, and A. nigricans) and one species is endemic to Romania (A. laevitomentosa). Historical background regarding taxonomic delimitation in the genus is addressed from Linnaean to present day concepts, as well as the origin of the name Andryala. The origin of Asteraceae and the systematic position of Andryala is shortly summarised. The morphological study was based on a bibliographic review and the revision of 1066 specimens of 13 herbaria as well as additional material collected during fieldwork. The variability of the morphological characters of the genus, including both vegetative taxonomic characters (root, stem, leaf and indumentum characters) and reproductive ones (inflorescence, floret, fruit and pappus characters), is assessed. Numerical analysis of the morphological data was performed using different similarity or dissimilarity measures and coefficients, as well as ordination and clustering methods. Results support the segregation of the recognised taxa and the congruence of the several analyses in the separation of the recognised taxa (using quantitative, binary or multi-state characters). The proposed taxonomy for Andryala includes a new infra-generic classification, new taxa and new combinations and ranks, typifications and diagnostic keys (one for the species and several for subspecies). For each taxon a list of synonyms, typification comments and a detailed description are provided, just as comments on taxonomy and nomenclature, and a brief discussion on karyology. Additionally, information on ecology and conservation status as well as on distribution and a list of studied material are also presented. Phylogenetic analyses based on different nuclear and chloroplast DNA markers, using Bayesian and maximum parsimony methods of inference, were performed. Results support three main lineages: separate ones for the relict species A. agardhii and A. laevitomentosa and a third including the majority of the Andryala species that underwent a relatively rapid and recent speciation. They also suggest a single colonization event of Madeira and the Canary Islands from the Mediterranean region, followed by insular speciation. Biogeography and speciation within the genus are briefly discussed, including a proposal for the centre of origin of the genus and possible dispersal routes.

Estudo da labilidade de Cu(II), Cd(II), Mn(II) e Ni(II) em substâncias húmicas aquáticas utilizando-se membranas celulósicas organomodificadas

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Diversificação evolutiva de gobídeos no litoral brasileiro: padrões citogenéticos e ecomorfológicos

The fishes of the order Perciformes are characterized as an important model for understanding the genetic structure of marine populations, because besides they present examples of conservation chromosomal, also they present the karyotype diversification for some groups. Gobiidae family is the most specious in the marine environment. Among its representatives, many species are part of a cryptic fauna little noticed and studied, a wide distribution with behavioral and reproductive characteristics, that make them conducive to the action of biogeographical barriers. Morphologically this family presents reduced body structures through simplification and regressions. Despite their importance in evolutionary inferences, cytogenetics data are incipient facing their species diversity, especially with western Atlantic species. In order to estimate the evolutionary diversity in Gobiidae, it were developed cytogenetic analysis and the standards body, through geometric morphometrics in five species on the Brazilian coast, Coryphopterus glaucofraenum, Bathygobius mystacium, B. soporator, Ctenogobius smaragdus e C. Boleosoma. The data show significant karyotype and morphological diversity among the species. The pericentric inversions and mergers play an important role in chromosomal evolution of this family, causing karyotypic structural and numerical differences in all species. Karyotypic and morphological comparisons among geographic samples of B. soporator from the coast of Maranhão, Rio Grande do Norte and Bahia showed cytogenetics patterns commons, but different morphological patterns. A sample from the Atol das Rocas revealed conspicuous morphological and karyotypic differentiation of another continental populations, confirming the presence of a new island species. The approaches done reveal diversification consistent with characteristics of a group of low vagile and largely able to environmental selection due from peculiar ecological requirements

Ecologia trófica de anfíbios anuros: relações filogenéticas em diferentes escalas

Understand the origin, maintenance and the mechanisms that operate in the current biodiversity is the major goal of ecology. Species ecology can be influenced by different factors at different scales. There are three approaches about the ecological differences between species: the first brings that differences result from current processes on niche characteristics (e.g. diet, time, space); the second that species differences are explained by random patterns of speciation, extinction and dispersion, the third that historical events explain the formation and composition of species in communities. This study aims to evaluate the influence of phylogenetic relationships in determining ecological characteristics in amphibians (globally) and test with that, if ecological differences between species of frogs are the result of ancient pre-existing differences or as result of current interactions. Another objective of this study is to verify if ecological, historical or current characteristics determine the size of species geographical distribution. The diet data for analysis of trophic ecology were collected from published literature. We performed a non-parametric MANOVA to test the existence of phylogenetic effects in diet shifts on frogs history. Thus, it is expected to know the main factors that allow the coexistence of anuran species. We performed a phylogenetic regression to analyze if niche breadth, body size and evolutionary age variables determine the size of the geographical distribution of amphibians in the Amazon. In the present study, new contributions to knowledge of major ecological patterns of anurans are discussed under a phylogenetic perspective

Nickel in soil and maize plants grown on an oxisol treated over a long time with sewage sludge

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

The surprising evolutionary history of South American deer

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Identification of the endangered small red brocket deer (Mazama bororo) using noninvasive genetic techniques (Mammalia; Cervidae)

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Activity, movement and secretive behavior of a threatened arboreal folivore, the thin-spined porcupine, in the Atlantic forest of southern Bahia, Brazil

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Non invasive methods for genetic analysis applied to ecological and behavioral studies in Latino-America

Documenting the presence and abundance of the neotropical mammals is the first step for understanding their population ecology, behavior and genetic dynamics in designing conservation plans. The combination of field research with molecular genetics techniques are new tools that provide valuable biological information avoiding the disturbance in the ecosystems, trying to minimize the human impact in the process to gather biological information. The objective of this paper is to review the available non invasive sampling techniques that have been used in Neotropical mammal studies to apply to determine the presence and abundance, population structure, sex ratio, taxonomic diagnostic using mitochondrial markers, and assessing genetic variability using nuclear markers. There are a wide range of non invasive sampling techniques used to determine the species identification that inhabit an area such as searching for tracks, feces, and carcasses. Other useful equipment is the camera traps that can generate an image bank that can be valuable to assess species presence and abundance by morphology. With recent advances in molecular biology, it is now possible to use the trace amounts of DNA in feces and amplify it to analyze the species diversity in an area, and the genetic variability at intraspecific level. This is particularly helpful in cases of sympatric and cryptic species in which morphology failed to diagnose the taxonomic status of several species of brocket deer of the genus Mazama.

Only the B biotype of Bemisia tabaci is present on vegetables in São Paulo State, Brazil

Bemisia tabaci (Genn.) é considerada uma das mais importantes pragas em cultivos de hortaliças e ornamentais em todo o mundo. Baseado na análise da seqüência mitocondrial (citocromo oxidase I - mtCOI) foi proposto recentemente que B. tabaci deva ser considerado um complexo críptico de espécies, contendo 11 grupos e 24 espécies. Dois destes grupos: Middle East-Asia Minor e Mediterranean englobam os biótipos B e Q, respectivamente. Avaliou-se a sequência mtCOI de espécimes de B. tabaci coletados em regiões do estado de São Paulo, Brasil. Por PCR-RFLP utilizando-se a enzima Taq I, pôde-se observar somente o padrão típico de clivagem para o biótipo B. Comparando-se com sequências consenso, todas as moscas brancas foram classificadas no grupo Middle East-Asia Minor e puderam ser separadas em quatro haplótipos, indicando prevalência do biótipo B em áreas de pimentão (Capsicum annuum L.), tomate (Solanum lycopersicum L.), cucurbitáceas e berinjela (Solanum melongena L.) do Estado de São Paulo.

DNA bar-coding reveals source and patterns of Thaumastocoris peregrinus invasions in South Africa and South America

Thaumastocoris peregrinus is a recently introduced invertebrate pest of non-native Eucalyptus plantations in the Southern Hemisphere. It was first reported from South Africa in 2003 and in Argentina in 2005. Since then, populations have grown explosively and it has attained an almost ubiquitous distribution over several regions in South Africa on 26 Eucalyptus species. Here we address three key questions regarding this invasion, namely whether only one species has been introduced, whether there were single or multiple introductions into South Africa and South America and what the source of the introduction might have been. To answer these questions, bar-coding using mitochondrial DNA (COI) sequence diversity was used to characterise the populations of this insect from Australia, Argentina, Brazil, South Africa and Uruguay. Analyses revealed three cryptic species in Australia, of which only T. peregrinus is represented in South Africa and South America. Thaumastocoris peregrinus populations contained eight haplotypes, with a pairwise nucleotide distance of 0.2-0.9% from seventeen locations in Australia. Three of these haplotypes are shared with populations in South America and South Africa, but the latter regions do not share haplotypes. These data, together with the current distribution of the haplotypes and the known direction of original spread in these regions, suggest that at least three distinct introductions of the insect occurred in South Africa and South America before 2005. The two most common haplotypes in Sydney, one of which was also found in Brisbane, are shared with the non-native regions. Sydney populations of T. peregrinus, which have regularly reached outbreak levels in recent years, might thus have served as source of these three distinct introductions into other regions of the Southern Hemisphere.

Soil Solution as Affected by Plant Residues and Nitrogen Rates

Cation mobility in acidic soils with low organic-matter contents depends not only on sorption intensity but also on the solubility of the species present in soil solution. In general, the following leaching gradient is observed: potassium (K+) magnesium (Mg2+) calcium (Ca2+) aluminum (Al3+). To minimize nutrient losses and ameliorate the subsoil, soil solution must be changed, favoring higher mobility of M2+ (metal ions) forms. This would be theoretically possible if plant residues were kept on the soil surface. An experiment was conducted in pots containing a Distroferric Red Latosol, with soil solution extractors installed at two depths. Pearl millet, black oat, and oilseed radish residues were laid on the soil surface, and nitrogen (as ammonium nitrate) was applied at rates ranging from 0 to 150mgkg-1. Corn was grown for 52 days. Except for K+ and ammonium (NH4 +), nitrogen rates and plant residues had little effect upon the concentrations and forms of the elements in the soil solution. Presence of cover crop residues on soil surface decreased the effect of nitrogen fertilizer on Ca leaching. More than 90% of the Ca2+, Mg2+, and K+ were found as free ions. The Al3+ was almost totally complexed as Al(OH3)0. Nitrogen application increased the concentrations of almost all the ions in soil solution, including Al3+, although there was no modification in the leaching gradient.