Histogram-based DNA analysis for the visualization of chromosome, genome and species information

We describe a novel approach to explore DNA nucleotide sequence data, aiming to produce high-level categorical and structural information about the underlying chromosomes, genomes and species. The article starts by analyzing chromosomal data through histograms using fixed length DNA sequences. After creating the DNA-related histograms, a correlation between pairs of histograms is computed, producing a global correlation matrix. These data are then used as input to several data processing methods for information extraction and tabular/graphical output generation. A set of 18 species is processed and the extensive results reveal that the proposed method is able to generate significant and diversified outputs, in good accordance with current scientific knowledge in domains such as genomics and phylogenetics.

Polycyclic aromatic hydrocarbon levels in three pelagic fish species from Atlantic Ocean: inter-specific and inter-season comparisons and assessment of potential public health risks

The concentrations of 18 polycyclic aromatic hydrocarbons (PAHs) were determined in three commercially valuable fish species (sardine, Sardina pilchardus; chub mackerel, Scomber japonicus; and horse mackerel, Trachurus trachurus) from the Atlantic Ocean. Specimens were collected seasonally during 2007–2009. Only low molecular weight PAHs were detected, namely, naphthalene, acenaphthene, fluorene and phenanthrene. Chub mackerel (1.80–19.90 microg/kg ww) revealed to be significantly more contaminated than horse mackerel (2.73–10.0 microg/kg ww) and sardine (2.29–14.18 microg/kg ww). Inter-specific and inter-season comparisons of PAHs bioaccumulation were statistically assessed. The more relevant statistical correlations were observed between PAH amounts and total fat content (significant positive relationships, p < 0.05), and season (sardine displayed higher amounts in autumn–winter while the mackerel species showed globally the inverse behavior). The health risks by consumption of these species were assessed and shown to present no threat to public health concerning PAH intakes.

Biofiltration of Air/Styrene and Air/Styrene/Acetone mixtures in a bubble column reactor

The goal of this work was the treatment of polluted waste gases in a bubble column reactor (BCR), in order to determinate the maximum value of reactor’s efficiency (RE), varying the inlet concentration (C in) of the pollutants. The gaseous mixtures studied were: (i) air with styrene and (ii) air with styrene and acetone. The liquid phase used to contain the biomass in the reactor was a basal salt medium (BSM), fundamental for the microorganisms’ development. The reactor used in this project consists of a glass column of 620mm height and inside diameter 75mm. In all essays there were continually measured: pH, dissolved oxygen and liquid’s temperature. Temperature and pH were controlled (T=24ºC, 7.0 ≤ pH ≤ 7.7). In all experiments the liquid volume (including the biomass) used in the reactor was kept constant (1.5L) as well as the total gas flowrate (1 L/min). Concerning the goal of the work, some parameters were calculated: the organic load (OL), removal efficiency (RE), elimination capacity (EC), biomass concentration (xf) and dry biomass concentration (Xdw). In a first series of experiments, the gas mixture used was air with styrene, varying its concentration from 191 mg.m-3 to 6500 mg.m-3.It was concluded that the RE maximum value (97%) was obtained for C in Sty = 4200 mg.m-3. For the maximum tested value of C in Sty, RE obtained was 20%. In a second step, the gaseous mixture included acetone, varying C in Sty between 225 mg.m-3 and 2659 mg.m-3 and C in Ac between 153mg.m-3 and 1389 mg.m-3. The aim of these tests was the determination of C in Ac for which RE was maximum, obtaining C in Ac = 750 mg.m-3. A third series of experiments was performed, in which C in Ac was maintained equal to that value and C in Sty was varied until higher values (5422 mg.m-3). RE maximum values obtained in this last series were 100% for styrene and 40% for acetone. One important conclusion is the fact that the microorganisms available degrade better styrene than acetone. On the ambit of this study, it was possible to identify the species available in biomass: Xanthobacter antotrophicus py2, Enterobacter aerogenes, Nocardia, Corynebacterium Spp., Rhodococcus rhodochrous e Pseudomonas Sp.

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).

Serpentine bacteria influence metal translocation and bioconcentration of Brassica juncea and Ricinus communis grown in multi-metal polluted soils

The aim of this study was to assess the effects of inoculation of rhizosphere or endophytic bacteria (Psychrobacter sp. SRS8 and Pseudomonas sp. A3R3, respectively) isolated from a serpentine environment on the plant growth and the translocation and accumulation of Ni, Zn, and Fe by Brassica juncea and Ricinus communis on a multi-metal polluted serpentine soil (SS). Field collected SS was diluted to 0, 25, 50, and 75% with pristine soil in order to obtain a range of heavy metal concentrations and used in microcosm experiments. Regardless of inoculation with bacteria, the biomass of both plant species decreased with increase of the proportion of SS. Inoculation of plants with bacteria significantly increased the plant biomass and the heavy metal accumulation compared with non-inoculated control in the presence of different proportion of SS, which was attributed to the production of plant growth promoting and/or metal mobilizing metabolites by bacteria. However, SRS8 showed a maximum increase in the biomass of the test plants grown even in the treatment of 75% SS. In turn, A3R3 showed maximum effects on the accumulation of heavy metals in both plants. Regardless of inoculation of bacteria and proportion of SS, both plant species exhibited low values of bioconcentration factor (<1) for Ni and Fe. The inoculation of both bacterial strains significantly increased the translocation factor (TF) of Ni while decreasing the TF of Zn in both plant species. Besides this contrasting effect, the TFs of all metals were <1, indicating that all studied bacteria–plant combinations are suitable for phytostabilization. This study demonstrates that the bacterial isolates A3R3 and SRS8 improved the growth of B. juncea and R. communis in SS soils and have a great potential to be used as inoculants in phytostabilization scenarios of multi-metal contaminated soils.