Worldwide molecular epidemiology of HIV

Human immunodeficiency virus (HIV) is the worldwide disseminated causative agent of acquired immunodeficiency syndrome (AIDS). HIV is a member of the Lentivirus genus of Retroviridae family and is grouped in two types named HIV-1 and HIV-2. These viruses have a notable ability to mutate and adapt to the new conditions of human environment. A large incidence of errors at the transcriptional level results in changes on the genetic bases during the reproductive cycle. The elevated genomic variability of HIV has carried important implications for the diagnosis, treatment and prevention as well as epidemiologic investigations. The present review describes important definitions and geographical distribution of subtypes, circulating recombinant forms and other genomic variations of HIV. The present study aimed at leading students of Biomedical Sciences and public health laboratory staff guidance to general and specific knowledge about the genomic variability of the HIV.

Temporal and spatial variability of fin whale's (Balaenoptera physalus) distribution in the Pelagos Sanctuary: Northwestern Mediterranean Sea

Dissertação de Mestrado, Estudos Integrados dos Oceanos, 20 de Março de 2014, Universidade dos Açores.

Shell variation in Patellid limpets: scales of spatial variability

World Congress of Malacology, Universidade dos Açores, Ponta Delgada, 21-28 de julho.

Intra- and interspecific mineral composition variability of commercial instant coffees and coffee substitutes: contribution to mineral intake

The present paper reports the amount and estimated daily mineral intake of nine elements (Ca, Mg, K, Na, P, Fe, Mn, Cr and Ni) in commercial instant coffees and coffee substitutes (n = 49). Elements were quantified by high-resolution continuum source flame (HR-CS-FAAS) and graphite furnace (HR-CS-GFAAS) atomic absorption spectrometry, while phosphorous was evaluated by a standard vanadomolybdophosphoric acid colorimetric method. Instant coffees and coffee substitutes are rich in K, Mg and P (>100 mg/100 g dw), contain Na, Ca and Fe in moderate amounts (>1 mg/100 g), and trace levels of Cr and Ni. Among the samples analysed, plain instant coffees are richer in minerals (p < 0.001), except for Na and Cr. Blends of coffee substitutes (barley, malt, chicory and rye) with coffee (20–66%) present intermediate amounts, while lower quantities are found in substitutes without coffee, particularly in barley. From a nutritional point of view the results indicate that the mean ingestion of two instant beverages per day (total of 4 g instant powder), either with or without coffee, cannot be regarded as important sources of minerals to the human diet, although providing a supplementation of some minerals, particularly Mg and Mn in instant coffees. Additionally, and for authentication purposes, the correlations observed between some elements and the coffee percentage in the blends, with particular significance for Mg amounts, provides a potential tool for the estimation of coffee in substitute blends.

Lipid content of frozen fish: comparison of different extraction methods and variability during freezing storage

In this work, a microwave-assisted extraction (MAE) methodology was compared with several conventional extraction methods (Soxhlet, Bligh & Dyer, modified Bligh & Dyer, Folch, modified Folch, Hara & Radin, Roese-Gottlieb) for quantification of total lipid content of three fish species: horse mackerel (Trachurus trachurus), chub mackerel (Scomber japonicus), and sardine (Sardina pilchardus). The influence of species, extraction method and frozen storage time (varying from fresh to 9 months of freezing) on total lipid content was analysed in detail. The efficiencies of methods MAE, Bligh & Dyer, Folch, modified Folch and Hara & Radin were the highest and although they were not statistically different, differences existed in terms of variability, with MAE showing the highest repeatability (CV = 0.034). Roese-Gottlieb, Soxhlet, and modified Bligh & Dyer methods were very poor in terms of efficiency as well as repeatability (CV between 0.13 and 0.18).

Epigenetic and transcriptional signatures of stable versus plastic differentiation of proinflammatory gd T cell subsets

Two distinct subsets of γδ T cells that produce interleukin 17 (IL-17) (CD27(-) γδ T cells) or interferon-γ (IFN-γ) (CD27(+) γδ T cells) develop in the mouse thymus, but the molecular determinants of their functional potential in the periphery remain unknown. Here we conducted a genome-wide characterization of the methylation patterns of histone H3, along with analysis of mRNA encoding transcription factors, to identify the regulatory networks of peripheral IFN-γ-producing or IL-17-producing γδ T cell subsets in vivo. We found that CD27(+) γδ T cells were committed to the expression of Ifng but not Il17, whereas CD27(-) γδ T cells displayed permissive chromatin configurations at loci encoding both cytokines and their regulatory transcription factors and differentiated into cells that produced both IL-17 and IFN-γ in a tumor microenvironment.

Mercury, cadmium, lead and arsenic levels in three pelagic fish species from the Atlantic Ocean: intra- and inter-specific variability and human health risks for consumption

Three commonly consumed and commercially valuable fish species (sardine, chub and horse mackerel) were collected from the Northeast and Eastern Central Atlantic Ocean in Portuguese waters during one year. Mercury, cadmium, lead and arsenic amounts were determined in muscles using graphite furnace and cold vapour atomic absorption spectrometry. Maximum mean levels of mercury (0.1715 ± 0.0857 mg/kg, ww) and arsenic (1.139 ± 0.350 mg/kg, ww) were detected in horse mackerel. The higher mean amounts of cadmium (0.0084 ± 0.0036 mg/kg, ww) and lead (0.0379 ± 0.0303 mg/kg, ww) were determined in chub mackerel and in sardine, respectively. Intra- and inter-specific variability of metals bioaccumulation was statistically assessed and species and length revealed to be the major influencing biometric factors, in particular for mercury and arsenic. Muscles present metal concentrations below the tolerable limits considered by European Commission Regulation and Food and Agriculture Organization of the United Nations/World Health Organization (FAO/WHO). However, estimation of non-carcinogenic and carcinogenic health risks by the target hazard quotient and target carcinogenic risk, established by the US Environmental Protection Agency, suggests that these species must be eaten in moderation due to possible hazard and carcinogenic risks derived from arsenic (in all analyzed species) and mercury ingestion (in horse and chub mackerel species).

Assessment of the ensembles regional climate models in the representation of precipitation variability and extremes over Portugal

A new data set of daily gridded observations of precipitation, computed from over 400 stations in Portugal, is used to assess the performance of 12 regional climate models at 25 km resolution, from the ENSEMBLES set, all forced by ERA-40 boundary conditions, for the 1961-2000 period. Standard point error statistics, calculated from grid point and basin aggregated data, and precipitation related climate indices are used to analyze the performance of the different models in representing the main spatial and temporal features of the regional climate, and its extreme events. As a whole, the ENSEMBLES models are found to achieve a good representation of those features, with good spatial correlations with observations. There is a small but relevant negative bias in precipitation, especially in the driest months, leading to systematic errors in related climate indices. The underprediction of precipitation occurs in most percentiles, although this deficiency is partially corrected at the basin level. Interestingly, some of the conclusions concerning the performance of the models are different of what has been found for the contiguous territory of Spain; in particular, ENSEMBLES models appear too dry over Portugal and too wet over Spain. Finally, models behave quite differently in the simulation of some important aspects of local climate, from the mean climatology to high precipitation regimes in localized mountain ranges and in the subsequent drier regions.

Bisphenol A at the reference level counteracts doxorubicin transcriptional effects on cancer related genes in HT29 cells

Human exposure to Bisphenol A (BPA) results mainly from ingestion of food and beverages. Information regarding BPA effects on colon cancer, one of the major causes of death in developed countries, is still scarce. Likewise, little is known about BPA drug interactions although its potential role in doxorubicin (DOX) chemoresistance has been suggested. This study aims to assess potential interactions between BPA and DOX on HT29 colon cancer cells. HT29 cell response was evaluated after exposure to BPA, DOX, or co-exposure to both chemicals. Transcriptional analysis of several cancer-associated genes (c-fos, AURKA, p21, bcl-xl and CLU) shows that BPA exposure induces slight up-regulation exclusively of bcl-xl without affecting cell viability. On the other hand, a sub-therapeutic DOX concentration (40nM) results in highly altered c-fos, bcl-xl, and CLU transcript levels, and this is not affected by co-exposure with BPA. Conversely, DOX at a therapeutic concentration (4μM) results in distinct and very severe transcriptional alterations of c-fos, AURKA, p21 and CLU that are counteracted by co-exposure with BPA resulting in transcript levels similar to those of control. Co-exposure with BPA slightly decreases apoptosis in relation to DOX 4μM alone without affecting DOX-induced loss of cell viability. These results suggest that BPA exposure can influence chemotherapy outcomes and therefore emphasize the necessity of a better understanding of BPA interactions with chemotherapeutic agents in the context of risk assessment.

Probing key DNA contacts in AraR-mediated transcriptional repression of the Bacillus subtilis arabinose regulon.

Nucleic Acid Research (2007) Vol.37 N. 14 4755-4766

Octopus Lipid and Vitamin E Composition: Interspecies, Interorigin, and Nutritional Variability

Octopus vulgaris, Octopus maya, and Eledone cirrhosa from distinct marine environments [Northeast Atlantic (NEA), Northwest Atlantic (NWA), Eastern Central Atlantic, Western Central Atlantic (WCA), Pacific Ocean, and Mediterranean Sea] were characterized regarding their lipid and vitamin E composition. These species are those commercially more relevant worldwide. Significant interspecies and interorigin differences were observed. Unsaturated fatty acids account for more than 65% of total fatty acids, mostly ω-3 PUFA due to docosahexaenoic (18.4−29.3%) and eicosapentanoic acid (11.4− 23.9%) contributions. The highest ω-3 PUFA amounts and ω-3/ω-6 ratios were quantified in the heaviest specimens, O. vulgaris from NWA, with high market price, and simultaneously in the lowest graded samples, E. cirrhosa from NEA, of reduced dimensions. Although having the highest cholesterol contents, E. cirrhosa from NEA and O. maya from WCA have also higher protective fatty acid indexes. Chemometric discrimination allowed clustering the selected species and several origins based on lipid and vitamin E profiles.

Post-transcriptional regulation of HFE gene expression

Thesis presented to obtain the Ph.D. degree in Biology (Molecular Genetics), by the Universidade Nova de Lisboa, Faculdade de Ciências e Tecnologia.

Giardia duodenalis: INTER-STRAIN VARIABILITY OF PROTEINS, ANTIGENS, PROTEASES, ISOENZYMES AND NUCLEIC ACIDS

Giardia duodenalis isolates from asymptomatic or symptomatic patients and from animals present similarities and differences in the protein composition, antigenic profile, pattern of proteases and isoenzymes, as well as in nucleic acids analysis. In the present overview, these differences and similarities are reviewed with emphasis in the host-parasite interplay and possible mechanisms of virulence of the protozoon.

Predictivity Strength of the Spatial Variability of Phenanthrene Sorption Across Two Sandy Loam Fields

Sorption is commonly agreed to be the major process underlying the transport and fate of polycyclic aromatic hydrocarbons (PAHs) in soils. However, there is still a scarcity of studies focusing on spatial variability at the field scale in particular. In order to investigate the variation in the field of phenanthrene sorption, bulk topsoil samples were taken in a 15 × 15-m grid from the plough layer in two sandy loam fields with different texture and organic carbon (OC) contents (140 samples in total). Batch experiments were performed using the adsorption method. Values for the partition coefficient K d (L kg−1) and the organic carbon partition coefficient K OC (L kg−1) agreed with the most frequently used models for PAH partitioning, as OC revealed a higher affinity for sorption. More complex models using different OC compartments, such as non-complexed organic carbon (NCOC) and complexed organic carbon (COC) separately, performed better than single K OC models, particularly for a subset including samples with Dexter n < 10 and OC <0.04 kg kg−1. The selected threshold revealed that K OC-based models proved to be applicable for more organic fields, while two-component models proved to be more accurate for the prediction of K d and retardation factor (R) for less organic soils. Moreover, OC did not fully reflect the changes in phenanthrene retardation in the field with lower OC content (Faardrup). Bulk density and available water content influenced the phenanthrene transport mechanism phenomenon.

Genetic variability of Triatoma flavida and Triatoma bruneri (Hemiptera: Reduviidae) by RAPD-PCR technique

The Triatominae (Hemiptera:Reduviidae) contains the principal and potential Chagas disease vectors present in Mexico, Central America and South America. Triatoma flavida and T. bruneri are Cuban species. These species are closely related according to morphology and were considered synonyms until 1981, when they were separated on the grounds of external characters of the body and the morphology of male genitalia. The present study seeks to analyze genetic polymorphism of T. flavida and T. bruneri populations using RAPD techniques, and to assess the genetic relationship between these species. Ten random primers were used to evaluate the genetic variability among species using RAPD-PCR. The genetic flow among them was calculated. The dendrogram based on calculated Jaccard distances showed two clearly distinguishable clusters which coincided with the studied species. Within each species, moderate genetic differentiation (Fst 0.05-0.15) and migration rates (N > 1) were found among populations, that reveal gene flow and genetic homogeneity. Between species, the Fst value showed a high genetic differentiation and the migration rate was insufficient to maintain genetic homogeneity, and confirmed the absence of gene flow between them. Our results confirm the genetic variability among T. flavida and T. bruneri species.