Fate of discards from deep water crustacean trawl fishery off the south coast of Portugal

Trawling for crustaceans takes place on the south coast of Portugal at depths between 200 and 800 m. Large amounts of discards are released back to sea, reaching the bottom in the general area where trawling occurs. The objective of this work was to study the time taken for decomposition of the discards, to identify the most important scavenging species involved, and to evaluate the impact on the species targeted by the fishery. We conducted a series of 22 trials, using traps baited with samples of the discards. The time of immersion varied between 1 and 40 h. The amount of tissue removed from the discards was evaluated on a qualitative scale of 1–3, and quantitatively. The species caught in the traps were identified. Considerable consumption of the bait had occurred after 5 h of immersion. After 24 h of immersion only fish bones were left; past 40 h, consumption was complete. The conger eel (Conger conger) was the most common fish species present in the traps. Two species, the amphipod Scopelocheirus hopei and the isopod Natatolana (Cirolana) borealis, were identified as most important for the recycling of organic matter in the system. The stomach contents of a sample of species caught in trawls were analysed for the presence of small scavengers. Preliminary results show that S. hopei and N. (C.) borealis are part of the diet of some of the target species of this fishery, such as the Norway lobster, Nephrops norvegicus and the rose shrimp Parapenaeus longirostris.

Risk assessment of the herbicide clomazone in the aquatic life.

Clomazone (2-(2-chlorophenyl)methyl-4.4-dimethyl-3-isoxazolidinone) is a post emergence herbicide widely used in rice fields in Rio Grande do Sul (Brazil) with high activity against Gramineae at the recommended application rate(AR).of 700g/ha. The herbicide input into the aquatic ecosystem may occur by aerial application or water drainage. The presence of this chemical in the water may affect non-target organisms leading to impairments in the aquatic food chain. Studies were conducted in this work to evaluate the risk of Clomazone using the estimated mean affective concentration (EC50) for the microalgae Selenastrum capricornutum(96h), the duckweed Lemna valdiviana(96h) and the crustacean Daphnia similis(48h). The EC50 values were 11.2; 31.7 and 13.8 mg/l, respectively. According to the obtained data, and considering a direct input of the herbicide in a 10cm column water, the estimated maximum application rate that doesn't cause acute effects is 5.3 AR for S. capricornutum, 6.5 AR for D. similis and 15.0 AR for L. valdiviana. The estimated maximum application rate that doesn't cause chronic effects is 2.0 AR for D. similis, 1.6 AR for S. capricornutum and 4.5 AR for L. valviana.

Humified fraction of organic matter due to plant mixture cultivation.

The aim of this study was to assess the organic matter changes in quantity and quality, particularly of the humic fraction in the surface layer (0?20 cm), of a Typic Plinthustalf soil under different management of plant mixtures used as green manure for mango (Mangifera indica L.) crops. The plant mixtures, which were seeded between rows of mango trees, were formed by two groups of leguminous and non -leguminous plants. Prior to sowing, seeds were combined in different proportions and compositions constituting the following treatments: 100% non-leguminous species (NL); 100% leguminous species (L); 75% L and 25% NL; 50% L and 50% NL; 25% L and 75% NL; and 100% spontaneous vegetation, considered a control. The plant mixtures that grew between rows of mango trees caused changes in the chemical composition of the soil organic matter, especially for the treatments 50% L and 50% NL and 25% L and 75% NL, which increased the content of humic substances in the soil organic matter. However, the treatment 25% L and 75% NL was best at minimising loss of total organic carbon from the soil. The humic acids studied have mostly aliphatic characteristics, showing large amounts of carboxylic and nitrogen groups and indicating that most of the organic carbon was formed by humic substances, with fulvic acid dominating among the alkali soluble fractions.

Numeric model to estimate pesticide deposition and losses from aerial spraying.

Pesticides applications have been described by many researches as a very inefficient process. In some cases, there are reports that only 0.02% of the applied products are used for the effective control of the problem. The main factor that influences pesticides applications is the droplet size formed on spraying nozzles. Many parameters affects the dynamic of the droplets, like wind, temperature, relative humidity, and others. Small droplets are biologically more active, but they are affected by evaporation and drift. On the other hand, the great droplets do not promote a good distribution of the product on the target. In this sense, associated with the risk of non target areas contamination and with the high costs involved in applications, the knowledge of the droplet size is of fundamental importance in the application technology. When sophisticated technology for droplets analysis is unavailable, is common the use of artificial targets like water-sensitive paper to sample droplets. On field sampling, water-sensitive papers are placed on the trials where product will be applied. When droplets impinging on it, the yellow surface of this paper will be stained dark blue, making easy their recognition. Collected droplets on this papers have different kinds of sizes. In this sense, the determination of the droplet size distribution gives a mass distribution of the material and so, the efficience of the application of the product. The stains produced by droplets shows a spread factor proportional to their respectives initial sizes. One of methodologies to analyse the droplets is a counting and measure of the droplets made in microscope. The Porton N-G12 graticule, that shows equaly spaces class intervals on geometric progression of square 2, are coulpled to the lens of the microscope. The droplet size parameters frequently used are the Volumetric Median Diameter (VMD) and the Numeric Median Diameter. On VMD value, a representative droplets sample is divided in two equal parts of volume, in such away one part contains droplets of sizes smaller than VMD and the other part contains droplets of sizes greater that VMD. The same process is done to obtaining the NMD, which divide the sample in two equal parts in relation to the droplets size. The ratio between VMD and NMD allows the droplets uniformity evaluation. After that, the graphics of accumulated probability of the volume and size droplets are plotted on log scale paper (accumulated probability versus median diameter of each size class). The graphics provides the NMD on the x-axes point corresponding to the value of 50% founded on the y-axes. All this process is very slow and subjected to operator error. So, in order to decrease the difficulty envolved with droplets measuring it was developed a numeric model, implemented on easy and accessfull computational language, which allows approximate VMD and NMD values, with good precision. The inputs to this model are the frequences of the droplets sizes colected on the water-sensitive paper, observed on the Porton N-G12 graticule fitted on microscope. With these data, the accumulated distribution of the droplet medium volumes and sizes are evaluated. The graphics obtained by plotting this distributions allow to obtain the VMD and NMD using linear interpolation, seen that on the middle of the distributions the shape of the curves are linear. These values are essential to evaluate the uniformity of droplets and to estimate the volume deposited on the observed paper by the density (droplets/cm2). This methodology to estimate the droplets volume was developed by 11.0.94.224 Project of the CNPMA/EMBRAPA. Observed data of herbicides aerial spraying samples, realized by Project on Pelotas/RS county, were used to compare values obtained manual graphic method and with those obtained by model has shown, with great precision, the values of VMD and NMD on each sampled collector, allowing to estimate a quantities of deposited product and, by consequence, the quantities losses by drifty. The graphics of variability of VMD and NMD showed that the quantity of droplets that reachs the collectors had a short dispersion, while the deposited volume shows a great interval of variation, probably because the strong action of air turbulence on the droplets distribution, enfasizing the necessity of a deeper study to verify this influences on drift.

Expression of rice genes homologous of Arabidopsis genes previously related to drought tolerance.

The identification and validation of candidate genes related to traits of interest is a time consuming and expensive process and the homology among genes from different species can facilitate the identification of genes of the target species from the genomic information of a model species. This study aimed to quantify the expression of homologous rice genes previously related to drought tolerance in Arabidopsis. Five genes (CPK6, PLDa, GluR2, CesA8, and EIN2) were identified in rice by the homology of the amino acid sequence between rice and Arabidopsis. The genotypes Douradão (drought tolerant) and Primavera (drought susceptible) were subjected to a water deficit experiment, and subsequently evaluated for gene expression by qPCR for the five homologous and Lsi1 genes. The qPCR analysis clearly showed that the five homologous genes were expressed in rice, which is an indication that these genes could preserve their function in rice as a response to drought. In Douradão, of the five homologous genes, all but OsGluR2 displayed an increase in the average expression in drought treatment when compared to the control, while in Primavera, the average expression of the five genes did not differ between the control and drought treatment. In Douradão, the OsPLDa1, which showed the higher expression level in drought in relation to the control (10.82), significantly increased the gene expression in the leaf and root tissues as a response to drought, in both vegetative and reproductive stages, whereas in Primavera, this gene was suppressed in both tissues and stages under drought. Therefore, the OsPLDa1 gene was the most important in relation to drought response and is an interesting candidate for further studies in developing rice cultivars that are more tolerant to this stress.

Neurophysiological, molecular and pathophysiological aspects of synthetic torpor

Synthetic torpor is a peculiar physiological condition resembling natural torpor, in which even non-hibernating species can be induced through different pharmacological approaches. The growing interest in the induction of a safe synthetic torpor state in non-hibernating species stems from the possible applications that it may have in a translational perspective. In particular, the deeper understanding of the functional changes occurring during and after synthetic torpor may lead to the standardization of a safe procedure to be used also in humans and to the implementation of new therapeutic strategies. Some of the most interesting and peculiar characteristics of torpor that should be assessed in synthetic torpor and may have a translational relevance are: the reversible hyperphosphorylation of neuronal Tau protein, the strong and extended neural plasticity, which may be related to Tau regulatory processes, and the development of radioresistance. In this respect, in the present thesis, rats were induced into synthetic torpor by the pharmacological inhibition of the raphe pallidus, a key brainstem thermoregulatory area, in order to assess: i) whether a reversible hyperphosphorylation of Tau protein occurs at the spinal cord level, also testing the possible involvement of microglia activation in this phenomenon; ii) sleep quality after synthetic torpor and its possible involvement in the process of Tau dephosphorylation; iii) whether synthetic torpor has radioprotective properties, by assessing histopathological and molecular features in animals exposed to X-rays irradiation. The results showed that: i) a reversible hyper-phosphorylation of Tau protein also occurs in synthetic torpor in the dorsal horns of the spinal cord; ii) sleep regulation after synthetic torpor seems to be physiological, and sleep deprivation speeds up Tau dephosphorylation; iii) synthetic torpor induces a consistent increase in radioresistance, as shown by analyses at both histological and molecular level.

Effects of stochastic hypoxia events on the benthic communities of transitional waters

Hypoxia is one of the most important and faster spreading threats to marine life and its occurrence has significantly increased in the last century. The effects of hypoxia on marine organisms and communities has mostly been studied in light of the intensity of the disturbance but not a lot of attention has been given to its interaction with other stressors and the timing of its appearance. In this thesis I started to explore these topics through laboratory and manipulative field experiments. I studied the interactive effects of thermal stress and hypoxia on a European native bivalve species (Cerastoderma edule; Linnaeus, 1758 ) and a non native one (Ruditapes philippinarum; Adams & Reeve, 1850) through a laboratory experiment performed in the Netherlands. The non native species displayed a greater tolerance to oxygen depletion than the native one. The first field experiment was performed in an Italian brackish coastal lagoon (Pialassa Baiona) and tested the effects of different timing regimes of hypoxia on the benthic community. It emerged that the main factor affecting the community is the duration of the hypoxia. The ability of the communities to recover after repeated hypoxic periods was explored in the second manipulative field experiment. We imposed three different timing regimes of hypoxia on sediment patches in Pialassa Baiona and we monitored the changes of both the benthic and the microbial communities after the disturbances. The preliminary analyses of the data from this last work suggest that the experimental manipulations caused limited detrimental effects on the communities. Overall this thesis work suggests that the duration of hypoxic events, their repetitive nature and the associated thermal stress are key factors in determining their effects on the communities and that management measures should point towards a reduction of the duration of the single hypoxic periods more than their frequency.

Bycatch and discard issues in the Adriatic demersal fisheries

Commercial fisheries exploiting the demersal resources of Western Adriatic Sea produce high bycatch and discard rates; the most important are bottom trawls, hydraulic dredges and passive nets. The five papers here published assess these fisheries’ impacts and investigate the potential of specific solutions to promote more sustainable exploitation. Papers I, II, III focused on bottom trawl fishery. Paper I compared the catch performance of the two legal codends by accounting for the entire species community in trawl catches. 50% of the catch in weight and 80% in count numbers consisted of discarded species, highlighting the severe impact of this fishery. Paper II estimated the selectivity of experimental codend having meshes turned 90° (T90) and of traditional diamond mesh codend with same mesh size. The T90 codend improved the size selection for all the target species. Paper III investigated the use of T90 meshes in the extension piece together with a reduction in mesh number at extension circumference. Results revealed that both these changes applied in the extension piece did not improve the selectivity of the main target species. Paper IV focused on hydraulic dredge fishery targeting the striped venus clam by assessing the clams’ size selection process operated by the dredge. 25% of the clams caught were not size selected due to clogging phenomenon in the dredge. The clam length with 50% retention probability was 18.9 mm, highlighting that the additional size selection process of sorting sieve is necessary to land only the legal clams >22 mm. Paper V compared the catch performance of innovative fish pots and of traditional trammel net. A similar catch efficiency between the two gears for the commercial portion was observed, while the trammel net produced significantly more discards in terms of species number and weight. All the results are discussed in fisheries management perspective.

A role for mammalian target of rapamycin (mTOR) pathway in non alcoholic steatohepatitis related-cirrhosis

Non-alcoholic fatty liver disease (NAFLD) encompasses the whole spectrum of steatosis, nonalcoholic steatohepatitis (NASH), and NASH-related cirrhosis (NASH/Cir). Although molecular advances have been made in this field, the pathogenesis of NAFLD is not completely understood. The gene expression profiling associated to NASH/Cir was assessed, in an attempt to better characterize the pathways involved in its etiopathogenesis. Methods: In the first step, we used cDNA microarray to evaluate the gene expression profiles in normal liver (n=3) and NASH/Cir samples (n=3) by GeneSifter (TM) analysis to identify differentially expressed genes and biological pathways. Second, tissue microarray was used to determine immunohistochemical expression of phosphorylated mTOR and 4E-BP1 in 11 normal liver samples, 10 NASH/Cir samples and in 37 samples of cirrhosis of other etiologies to further explore the involvement of the mTOR pathway evidenced by the gene expression analysis. Results: 138 and 106 genes were, respectively, up and down regulated in NASH/Cir in comparison to normal liver. Among the 9 pathways identified as significantly modulated in NASH/Cir, the participation of the mTOR pathway was confirmed, since expression of cytoplasmic and membrane phospho-mTOR were higher in NASH/Cir in comparison to cirrhosis of other etiologies and to normal liver. Conclusions: Recent findings have suggested a role for the cellular ""nutrient sensor"" mTOR in NAFLD and the present study corroborates the participation of this pathway in NASH/Cir. Phospho-mTOR evaluation might be of clinical utility as a potential marker for identification of NASH/Cir in cases mistakenly considered as cryptogenic cirrhosis owing to paucity of clinical data.

Five-year evaluation of bloodstream yeast infections in a tertiary hospital: the predominance of non-C. albicans Candida species

This is a retrospective observational study of clinical and epidemiologic data from bloodstream yeast infections over 5 years (2004-2008) in a tertiary-care hospital. During this period, there were 52 such infections, at a rate of 2.4 per 1,000 hospital admissions. Non-C. albicans Candida species and other genera were responsible for 82% of infections, with C. tropicalis and C. parapsilosis being the most common. In 2008 no C. albicans infections occurred. Several uncommon fungal pathogens were observed, including Trichosporon asahii, Rhodotorula spp. and Candida zeylanoides. Of 16 isolates tested, 3 (19%) were resistant to fluconazole, including one C. zeylanoides (MIC 8 mu g/ml) and one C. tropicalis (MIC 16 mu g/ml) isolate, as well as intrinsically resistant C. krusei. All isolates tested were susceptible to itraconazole (n = 7) and amphotericin B (n = 8). Yeast infections were associated with severe underlying diseases, mainly hematological/solid cancers (71%), hospitalization in the ICU (41%), central venous catheters (80%), and use of antimicrobials (94%). The overall mortality rate was 50%. Our finding of a predominance of non-C. albicans Candida species infection with uncommon yeasts, and fluconazole resistance, suggests the need for continuous surveillance of fungemia and of antibiotic susceptibility trends, in order to adopt treatment strategies applicable to particular healthcare institutions.

Gene expression profile analysis of primary glioblastomas and non-neoplastic brain tissue: identification of potential target genes by oligonucleotide microarray and real-time quantitative PCR

The prognosis of glioblastomas is still extremely poor and the discovery of novel molecular therapeutic targets can be important to optimize treatment strategies. Gene expression analyses comparing normal and neoplastic tissues have been used to identify genes associated with tumorigenesis and potential therapeutic targets. We have used this approach to identify differentially expressed genes between primary glioblastomas and non-neoplastic brain tissues. We selected 20 overexpressed genes related to cell cycle, cellular movement and growth, proliferation and cell-to-cell signaling and analyzed their expression levels by real time quantitative PCR in cDNA obtained from microdissected fresh tumor tissue from 20 patients with primary glioblastomas and from 10 samples of non-neoplastic white matter tissue. The gene expression levels were significantly higher in glioblastomas than in non-neoplastic white matter in 18 out of 20 genes analyzed: P < 0.00001 for CDKN2C, CKS2, EEF1A1, EMP3, PDPN, BNIP2, CA12, CD34, CDC42EP4, PPIE, SNAI2, GDF15 and MMP23b; and NFIA (P: 0.0001), GPS1 (P: 0.0003), LAMA1 (P: 0.002), STIM1 (P: 0.006), and TASP1 (P: 0.01). Five of these genes are located in contiguous loci at 1p31-36 and 2 at 17q24-25 and 8 of them encode surface membrane proteins. PDPN and CD34 protein expression were evaluated by immunohistochemistry and they showed concordance with the PCR results. The present results indicate the presence of 18 overexpressed genes in human primary glioblastomas that may play a significant role in the pathogenesis of these tumors and that deserve further functional investigation as attractive candidates for new therapeutic targets.

Accessing Planktothrix species diversity and associated toxins using quantitative real-time PCR in natural waters

Tese de Doutoramento em Biologia apresentada à Faculdade de Ciências da Universidade do Porto, 2015.

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).

Diversity of non-clinical Acinetobacter species in a sub-saharan Africa region: evidence of carbapenem-hydrolysing class D-β-lactamase producers

[Excerpt] Although Acinetobacter baumannii has been the main agent for healthcare infections, recent reports suggest that some Acinetobacter environmental species should be considered as a potential cause of disease. In Angola, there are no previous data on its environmental reservoirs and resistance features. We aimed to unveil the occurrence and diversity of Acinetobacter species and the presence of resistance mechanisms in different non-clinical settings in Angola.