This thesis examined novel and previously utilised parameters of egg quality to determine and define reproductive success in farmed and wild salmonids. The effect of holding environment and inter-female variation on salmonid egg quality was also examined. Furthermore, two nutritional feed trials were undertaken to investigate whether organic Se, supplemented into salmonids broodstock diets, was vertically transferred to their eggs and what affect this dietary supplementation had on egg quality. Finally, the possibility that morphological and biochemical adaptations are present on the chorion of eggs from European whitefish (Coregonus lavaretus) was investigated in a resident Scottish population. Chapter 2 examined methods to determine egg quality using eggs from a single population of brown trout (Salmo trutta). Egg survival, provided a biologically relevant definition for egg quality, which was used throughout this study to assess the importance of selected egg quality parameters. Based on a review of the literature and the relationship between parameters of egg quality and egg survival rates, three determinants of egg quality were chosen for further examination. These were chorion breaking strength, elemental concentrations within the egg and the protein profile of the chorion. Brown trout broodstock from a single population were separated prior to spawning and exposed to two different holding units, ‘Ae system’ or ‘S.C.E.N.E. system’ at two sites. Eggs were stripped from females and 13 determinants of egg quality collected, analysed individually, combined by principle components analysis into an integrated egg quality score which was validated against egg survival. The multivariate egg quality score differed significantly between fish held in the Ae and S.C.E.N.E. systems. Egg survival, chorion breaking strength and Se chorion concentrations were higher in eggs produced by broodstock held in the S.C.E.N.E. system compared to those in the Ae system. Alternatively, chorion concentrations of P and K were higher in eggs from fish held in the raceway system. This data highlights the complex interactions between the holding environment and pre-ovulating fish and resultant egg quality. The variation in egg survival in individual Atlantic salmon (Salmo salar) reared in the same environment was assessed and used to examine the suitability of chorion measurements as parameters of egg quality. There was a significant difference in the egg survival rates between individual salmon. Results also show that there was also variation in egg survival, chorion breaking strength, chorion elemental concentrations and chorion protein concentrations and profiles between individual Atlantic salmon. Subsequent analysis of the data showed that there was no difference in these egg quality parameters between high and low egg survival rates. Furthermore, there was no correlation between egg survival and the chorion quality parameters recorded during this study. The results show that individual variation between fish is an important factor affecting egg quality. Broodstock Atlantic salmon were fed a standard commercial diet, with or without the addition of a supplemented nutritional mix, which included 0.5mg/kg of Sel-plex (organic Se). The Se content of the eggs and livers of each fish were assessed as was egg survival rates and proteomic analysis of the egg chorion. Concentrations of Se in the eggs of the individuals fed the supplemented diet were significantly higher than those fed the non-supplemented diet. However, the egg survival rate was also significantly lower in the supplemented group of fish. The assessment of the chorion protein profile and its proteomic structure was inconclusive. These results support the hypothesis that dietary selenium is vertically transferred to immature eggs during oocyte development. The lack of a linear relationship between Se egg concentrations and egg survival suggests that the lower survival rates of eggs from broodstock fed the supplemented diet in this trial was due to another nutritional component of the diet rather than the Se. Selenium enriched eggs from Atlantic salmon fed a supplemented diet and eggs from conspecifics fed a non-supplemented diet were tested for their ability to resist infection by Saprolegnia under incubation conditions similar to those used by the aquaculture industry. There was no significant difference in the presence/absence of infection, infection rate or survival between eggs produced by Atlantic salmon fed the supplemented and non-supplemented diet. Therefore, it was concluded that supplementation of broodstock diet does not alter the resistance of eggs to Saprolegnia. The presence of adhesive mechanisms on the surface of European whitefish eggs was examined from a population found within Loch Eck, Scotland. European whitefish eggs remain non-adhesive in a solution chemically similar to ovarian fluid, but become adhesive seconds after contact with water. Examination of the ultrastructure of the chorion showed that the morphology altered significantly after contact with water with nodule-like protuberances attached to connective filaments on the surface, present in water hardened but not non-water hardened eggs. Biochemical analysis also showed the presence of Chain A, RNase ZF-3e in the chorion of water hardened but not non water hardened eggs. Histochemical staining of the chorion showed that the externa, but not the interna stained positively for the presence of glycoproteins. Egg adhesive mechanisms allow European whitefish eggs to remain in optimal spawning grounds where factors such as mechanical damage, predation, desiccation and hypoxia are minimised.

The primary purpose of the dissertation is to quantify the efficiency and operation of various types of fish passes for dams. This is achieved through a novel experiment of testing juvenile salmon in a scale model fish-passes with a range of small structures including vertical slots, orifices, weirs and combinations of all three. Direct comparisons of the efficiency of each type of fish pass in terms of upstream migration. Two identical physical models were constructed, one at the Fisheries Research Services Freshwater Laboratory at Almondbank, Perth, Scotland where observations were made of fish behaviour. The other model at the University of Glasgow, Glasgow tested only hydraulic conditions. The physical models were simplified representations of a reach of a river downstream of a dam, weir or any other obstruction to fish migration. A removable cross wall incorporating one of the types of pass tested divided the flume into two pools. A significantly higher proportion of fish moved through submerged orifices or vertical slots than through weirs for a given flow rate and velocity. The orifice and vertical slot passing efficiencies are directly correlated to the velocities existing in their vicinity. To reach the weir/slot/orifice devices, salmon parr tended also to stay near the bottom of the flume and followed a path along the sides of the arena, which provided them with low velocities and cover. In the vicinity of the weir/orifice/slot devices, the movements of salmon parr were consistent with energy-conserving strategies. Clearly, the extrapolations of results from the behaviour of small to large salmon remains cautious, the intention of this research being to characterise the behaviour of small salmon and to develop clear testable hypotheses about how large salmon may respond to water flow. Preliminary field tests were then conducted at Tongland Dam fish pass to test the main recommendation extrapolated from the parr behavioural study. The particular situation of this fish pass, which contains both weirs and orifices, allows a comparison between the two. Passive Integrated Transponder (PIT) tags together with antennae installed at a weir and an orifice were used to individually monitor the movement of wild spawning salmon passing through the fish pass. The results of the field test are as yet, inconclusive.

In 2005, Atlantic salmon (Salmo salar L.) migrating to the United Kingdom exhibited swollen, haemorrhagic vents, symptoms not previously recorded. The condition was latterly termed Red Vent Syndrome (RVS), and subsequently observed across the North Atlantic. RVS has been pathognomonically associated with one of the most abundant parasites within the marine environment, the ascaridoid nematode Anisakis simplex, which also causes Anisakiasis in humans. Although A. simplex is commonly found in Atlantic salmon, heavy infestation of the vent region is novel, and the expression of RVS has not been prevalent in other fish species. Red Vent Syndrome has been well studied, however, the causes of the condition, and the reasons driving the novel site of infestation exhibited by A. simplex, have not been clarified. The aim of this PhD therefore, is to provide new information regarding the underlying factors of the infestation of the vent region by A. simplex, and the emergence of RVS. This study therefore: i) assessed the relationship between nematode burdens within the viscera and musculature, in comparison to the vent in 117 adult Atlantic salmon; ii) compared the genetic structure of A. simplex present in the vent region and the viscera using the entire nuclear internal transcribed spacer (ITS) region; iii) investigated migratory route and feeding ground of Scottish salmon populations using stable isotope analysis of dorsal muscle tissue and parasite component communities and, iv) assessed the expression of the cytokine TNF-α1 within vent muscle tissue using (q)RT-PCR, in relation to RVS severity. Phylogenetic analyses have shown that it is A. simplex sensu stricto infesting the vent region. The results show that there is a significant positive relationship between the nematodue burden in the body (viscera and musculature) and in the vent region. Isotopic signatures of salmon populations showed no significant differences, however, A. simplex intensities between populations on the East and North coasts of Scotland suggest geographical differences in A. simplex transmission pathways. Finally, the expression of TNF-α1 is not significantly different between RVS severity, and nematode burden. Out of the four studied factors, increasing nematode intensities in Atlantic salmon populations, and the significant positive relationship of nematode intensities between the body (viscera and musculature) and the vent, are likely to explain the infestation of the vent by A. simplex. The underlying causes of RVS however remain uncertain and require further research. With incidences of RVS observed across a number of populations over a large spatial area, regional and global effectors such as warming sea surface temperatures, and the North Atlantic Oscillation are expected to play key roles in its aetiology.

O açaí (Euterpe oleracea) é um fruto proveniente do açaizeiro, uma palmeira nativa da Amazônia Brasileira, considerado uma “superfruta” devido ao seu alto valor nutricional, com destaque para as antocianinas, associadas a efeitos benéficos à saúde. Uma vez que genótipos de frutos desenvolvidos por programas de melhoramento têm sido avaliados a fim de identificar frutos com composição fitoquímica melhorada e potencial antioxidante, o objetivo deste trabalho foi investigar o efeito do melhoramento genético na composição química, perfil de compostos bioativos e atividade antioxidante de seis genótipos de açaí (E. oleracea). Análises de composição química, perfil de antocianinas e carotenoides e de atividade antioxidante em diversos sistemas in vitro (método ABTS, oxidação da glutationa, teste da desoxirribose e células SH-SY5Y) foram realizadas em 6 genótipos e 1 amostra comercial utilizada como padrão. Com relação a composição química, de maneira geral, os genótipos apresentaram elevados teores de lipídeos (36,30 – 47,44%), fibras totais (11,31 – 15,88%), proteínas (7,78-9,50%) e cinzas (3,49 – 4,44%). Adicionalmente, as antocianinas cianidina 3-glicosídeo (12-43%) e cianidina 3-rutinosídeo (57-88%) foram identificadas nos genótipos avaliados e o genótipo L22P13 apresentou um incremento de 85% no teor de antocianinas totais. Com relação ao perfil de carotenoides, luteína, zeaxantina, α-caroteno e β-caroteno foram os principais carotenoides identificados nos genótipos avaliados, sendo que os genótipos BRS-PAMISTA e L22P13 apresentaram os teores mais elevados de carotenoides totais (125,39μg/g e 118μg/g). Com relação a atividade antioxidante, todos os genótipos reduziram a geração do radical ABTS em maior ou menor grau, embora diferenças significativas entre os genótipos e a amostra comercial não tenham sido observadas (IC50 = 73,98 – 175,7 vs. 121,7 μg/g). Entretanto, houve associação moderada e inversa entre a geração do radical ABTS e níveis de antocianinas e carotenoides. Ausência de diferenças significativas entre os extratos hidroetanólicos dos genótipos e a amostra comercial também foi observada no ensaio da desoxirribose (IC50 = 361,5 – 497,7 vs. 520,1 μg/g). Em cultura de células SH-SY5Y, os extratos hidroetanólicos na concentração de 50 μg/mL apresentaram um efeito protetor contra as espécies reativas geradas pelo H2O2 (ensaio DCFH-DA) e esse resultado foi associado ao teor de antocianinas dos extratos. Os resultados apontam genótipos promissores, com elevados teores de antocianinas e carotenoides, com potencial atividade antioxidante in vitro e um possível efeito protetor de células frente as espécies reativas. / The açaí (Euterpe oleracea) is a fruit of the açaizeiro, a native palm of the Brazilian Amazon, considered a "superfruit" due to its high nutritional value, especially anthocyanins, associated with beneficial health effects. Since fruit genotypes developed by breeding programs have been evaluated to identify fruits with improved phytochemical composition and antioxidant potential, the aim of this study was to investigate the effect of genetic improvement in the chemical composition, bioactive compounds profile and antioxidant activity of six açaí (E. oleracea) genotypes. The analysis of chemical composition, anthocyanins and carotenoids profile and antioxidant activity in various in vitro systems (ABTS method, glutathione oxidation, deoxyribose test and SH-SY5Y cells) were performed in six genotypes of açaí and one commercial sample that was used as standard. Regarding the chemical composition, in general, the genotypes showed high levels of lipids (36.30 – 47.44%), total fiber (11.31 – 15.88%), protein (7.78-9.50%) and ashes (3.49 – 4.44%). In addition, the anthocyanins cyanidin 3-glucoside (12-43%) and cyanidin 3-rutinoside (57-88%) were identified in evaluated genotypes and L22P13 genotype showed an increase of 85% in total anthocyanin content. Regarding the carotenoid profile, lutein, zeaxanthin, α-carotene and β-carotene were the main carotenoid identified in genotypes, being that BRS-PAMISTA and L22P13 genotypes showed the highest levels of total carotenoids (125.39 μg/g and 118 μg/g). Regarding the antioxidant activity, all genotypes reduced ABTS radical generation in greater or lesser extension, although there were no significant differences between hydroethanolic extracts of different genotypes and the commercial sample (IC50 = 73.98 - 175.7 vs. 121.7 μg/g). However, an inverse and moderate association between radical ABTS generation and anthocyanins and carotenoids content was observed. Absence of significant differences between hydroethanolic extracts of evaluated genotypes and the commercial sample was observed also in the deoxyribose assay (IC50 = 361.5 to 497.7 vs. 520.1 μg/g). In culture of SH-SY5Y cells, hydroethanolic extracts at concentration of 50 μg/mL had a protective effect against the reactive species generated by H2O2 (DCFH-DA assay) and this result was associated with the anthocyanins content of the extracts. The results showed promising genotypes with high levels of anthocyanins and carotenoids with antioxidant potential in vitro and a possible protective effect of cells against reactive species.

The arrival of a non-native species to has the potential to shape native communities by influencing ecological interactions such as predation, foraging, competition and disease transfer. A designation of invasive is applied to an introduced non-native species that has the potential to threaten the continued wellbeing of a native species, pose a risk to human health or negatively impact the economy. The European bullhead (Cottus perifretum) is a freshwater benthic-dwelling fish that is native to England but considered invasive in Scotland. The species was first reported in Scotland in the 1950's and thriving populations are now established in the waters of the Clyde, Forth and Tweed catchments. Bullhead presence is thought to negatively impact native stone loach (Barbatula barbatula) and brown trout (Salmo trutta) parr, due to shared preferences for habitat and prey resources. They are also thought to prey upon the eggs of native Atlantic salmon (Salmo salar) and brown trout, two species that are of high commercial value in Scotland. In other areas of introduction, bullheads have been found to increase parasite infection rates in native fishes. The species therefore has the capacity to incite competition and alter parasite/host interactions in areas of introduction, to the potential detriment of native fauna and the Scottish economy. The European bullhead has been the subject of considerable taxonomic scrutiny in recent years, resulting in its reclassification as a species complex. What was once considered a single species with a distribution encompassing Europe, Russia, Asia and Scandinavia, has been shown to consist of at least 15 distinct species. Genetic examination of bullheads from England confirmed the presence of Cottus perifretum, not Cottus gobio as traditionally listed in all UK literature and legislation. Native English bullhead is currently protected under Annex II of the European Commission Habitats Directive 92/43/EEC, based on the historic assumption that the species present is C. gobio. Analysis of the taxonomic identity of Scottish bullheads has remained outstanding. In this study the invasive status of bullhead was explored by examining feeding and parasitological interactions between bullheads and native freshwater communities in south-east Scotland. An assessment of the feeding preferences of native brown trout and stone loach in the presence and absence of bullheads tested competition for prey resources. Parasitological interactions were investigated by examining the shared parasite fauna of bullheads and native fish and invertebrate species. Bullheads from the Clyde and Forth catchments were analysed to provide a molecular and morphological description of this introduced species. Phylogenetic analysis of COX1 sequences obtained from Scottish bullheads, and a pair-wise distance calculation based on a Kimura 2-parameter model, showed that samples clustered in a distinct clade with English C. perifretum. Significant intraspecific variation was reported in all morphological features examined, but pooled data also revealed a resemblance to the published description provided for C. perifretum. Scottish bullhead is therefore confirmed to be an introduced pocket of the native English species, which is considered under threat in some areas due to habitat modifications and population decline. Comparisons between the dietary compositions of bullheads, brown trout and stone loach showed that the prey selection of brown trout and stone loach varied in the sample locations that contained co-occuring bullheads, when compared to locations where bullheads were absent. However, no direct evidence of trophic competition between bullheads and either brown trout or stone loach was reported. An examination of parasitological interactions recovered eight parasite species from four distinct taxonomic groups in total, of which four species (Echinorhynchus truttae, Apatemon gracilis, Diplostomum volvens and Raphidascaris acus) were shared between bullheads and one or more native fishes. Echinorhynchus truttae was also shared with gammarid crustaceans. Bullhead presence was found to coincide with D. volvens infections in European minnow (Phoxinus phoxinus) and a reduced prevalence of E. truttae in brown trout. Diplostomum volvens was only reported from minnow found in sites with bullheads, strongly suggesting bullheads were responsible for introducing this parasite to native minnows. Bullheads functioned as an alternative host for E. truttae, diluting brown trout parasite loads and reducing overall infection rates in sites where bullhead and brown trout co-exist. The findings reported for both feeding preference and parasite burdens in the presence and absence of bullheads suggest that bullheads do have some effect on the ecology of native species, but these are considered minimal and unlikely to impact the long-term survival of native species. Eradication of Scottish bullhead may contradict the conservation effort that is currently in place. Given the current lack of evidence to validate bullhead's invasive qualities and the recent confirmation of its genetic lineage, revisiting the designation of the bullhead as invasive is warranted. Active eradication should be treated with caution until a significant negative impact can be proven.

This thesis is based on eighteen months' fieldwork in Tissana: a bustling multi-ethnic fishing town on Sierra Leone's southern coast. It tells the story of the successive waves of young migrants who, for several decades, have been arriving on the coast from rural areas seeking an alternative to the indentured labour conditions of a farming economy still shaped by the legacy of domestic slavery. Set against the backdrop of a rapidly changing post­‐war economy, and in an ecological context in which fish stocks are in treacherous decline, I explore the intersection between people's everyday struggles for economic survival and their taken-for-granted knowledge of the substance of the world within which those fragile livelihoods play out. In a region in which we have come to correlate ‘memory' with the collective scars of slavery and civil war, Tissana's older residents look back with nostalgia and remember the youthful energy, conspicuous consumption and seemingly easy ‘freedom' of their town's early boom years. In some respects, the pattern is familiar from accounts of resource rushes all across Africa: the convergence of large numbers of young strangers in an unfamiliar landscape far from the authority of village elders opened up a space in which a new kind of moral economy emerged. However, within just a few decades of its initial boom, the fluidity of Sierra Leone's fishing economy is already under intense pressure. Fish stocks have suffered a noticeable decline and, as catches become smaller and more erratic, people find themselves drawn once more into networks of dependency and reciprocity that offer their only viable hope of material security. A constant tension animating everyday life in Tissana is how people are able to work, through the strategic deployment of material gifts, to nurture the relationships that they rely upon for their subsistence, whilst simultaneously attempting to protect themselves from becoming entangled in other, less appealing social bonds. At its core, then, this is a work about the materiality of human relationships; of social bonds formed and lived under conditions of such stark economic uncertainty that, very often, ‘love' and ‘livelihoods' are difficult to disaggregate — and even more difficult to trust. Here relationships often have a peculiarly fleshy, ethnographically observable aspect. One can go a long way towards mapping the town's fluctuating networks of friendship, love, debt, and obligation simply by watching the gifts of fish exchanging hands on the wharf. The town also raises a quite particular set of problems for an anthropologist interested in the materiality of social life. I explore how the lived experience of poverty, and the anxiety of stretched livelihoods are entangled with quotidian discussions of blessings, swears, initiation societies, and ‘fetish' medicines: elements of social life that we might intuitively gloss as ‘ritual', but that are, in fact, integral to the everyday economic order. Here, my work builds on a long literature in Sierra Leonean ethnography. Anthropologists working in this region have often revealed how their interlocutors do not draw any sharp distinction between ‘material' and ‘immaterial' elements of the physical environment and the agencies that inhabit it (Ferme 2001; Tonkin 1979; Bellman 1984). My contribution to this literature is to explore how such apparently abstruse questions of im/materiality become relevant in people's lives through economic practice: through the everyday decisions people make, and the work they invest, in fishing, trading, and gift-exchange.

Orientador: Daniel Carneiro Carrettiero / Dissertação (mestrado) - Universidade Federal do ABC, Programa de Pós-Graduação em Biossistemas, 2012

Orientador: Daniel Carneiro Carrettiero. / Dissertação (mestrado) - Universidade Federal do ABC, Programa de Pós-Graduação em Biossistemas, 2012.

Assessment of disease status in fish is used as an indicator of the biological effects of contaminants in the marine environment. At some UK offshore sites the prevalence of liver tumours in Limanda limanda (dab) exceeds 20%. However, the molecular mechanisms of tumour formation and the causative agents are not known. The contribution of epigenetic mechanisms, although well-established in human tumourigenesis, is under-studied in tumours of aquatic species. In this thesis, alteration in the DNA methylation patterns in tumours of two fish species, the model species zebrafish (Danio rerio) and the un-sequenced marine flatfish dab, were investigated. The data presented provided a comprehensive characterisation of DNA methylation pattern in zebrafish liver and the first evidence of alterations in DNA methylation profiles of key genes in tumourigenesis pathways in any aquatic species. A statistically significant lower level of global DNA methylation was demonstrated in hepatocellular adenoma (HCA) and non-cancerous surrounding liver tissue (ST) compared to liver of non-cancer bearing dab. The evidence presented in this thesis suggests that chronic exposure to a mixture of pollutants contribute to global DNA hypomethylation followed by further epigenetic and genomic changes, leading to the development of tumours in dab. These findings suggest a link between the environment, epigenome and cancer in fish tumours in the wild.

<p>Neuroblastoma is a malignant childhood cancer, originating from sympathetic neuroblasts of the peripheral nervous system. Neuroblastoma is a heterogenous group of tumours, while some are highly malignant others can spontaneosly mature into a more benign form or regress. Less than half of the patients survive and this statistics has improved only modestly over the past 20 years. </p><p>SH-SY5Y is a human neuroblastoma cell line established from a highly malignant tumour. The cells have retained a capacity to differentiate <i>in vitro</i> in response to low concentrations of the phorbolester 12-O-tetradecanoylphorbol-13-acetate (TPA) in the presence of serum or defined growth factors. Differentiated cells are characterised by neurite formation and upregulation of neuronal marker genes. SH-SY5Y are unresponsive to nerve growth factor (NGF), but when transfected to express the NGF-receptor TrkA, they differentiate in response to NGF. Protein kinase C (PKC) is pivotal for the differentiation response to take place.</p><p>We have investigated the role of signaling through the Ras-MAPK pathway in differentiating SH-SY5Y, with respect to neurite formation, expression of neuronal marker genes and growth control. Our results show that differentiation-promoting treatment induced a sustained activation and nuclear accumulation of the MAPK ERK in SH-SY5Y. The nuclear accumulation of ERK was PKC-dependent. However, nuclear accumulation of ERK was not sufficient for a differentiation response to take place in these cells, but ERK activity was needed for the characteristic upregulation of <i>NPY</i> and <i>GAP-43</i> induced by TPA. ERK activity did not induce neurite formation, neither was it necessary for TPA-induced neurite formation. Instead, stimulation of a pathway distinct from MEK/ERK, but downstream of Ras, was needed for morphological differentiation. We could also show that differentiated cells still entered S-phase and that there was no correlation between expression of the CKI p21_cip1 (an ERK target), BrdU-incorporation or neurite formation. </p>