Viral and bacterial septicaemic infections modulate the expression of PACAP splicing variants and VIP/PACAP receptors in brown trout immune organs

Copyright © 2015. Published by Elsevier Ltd. Acknowledgments The authors thank Richard Paley, Georgina Rimmer and Tom Hill for their contribution during the brown trout infection challenges carried out in CEFAS-Weymouth biosecurity facilities. Bartolomeo Gorgoglione and Nick G. H. Taylor were supported by a DEFRA contract C3490

Catch and effort from a recreational trolling fishery in a large lake

Over recent decades recreational fisheries have grown substantially throughout the world. Despite this increase, catches from recreational fisheries have often been ignored in fisheries management, although this is now being remedied. Monitoring recreational fisheries can be expensive, and the primary means used for monitoring is angler (creel) surveys, typically funded from sales of fishing licences. The studies presented in this thesis examine different approaches to monitoring recreational trolling fisheries’ catch and effort, where fishing licenses are not required and there are no reporting requirements. I present results from a complemented roving/mail-in survey undertaken during 2013-2014 to estimate recreational effort and catch of Atlantic salmon (Salmo salar) and brown trout (S. trutta) in the largest lake in the European Union, Lake Vänern, Sweden. I also evaluate different angler catch reporting methods (mail-in, tournament reports and face-to-face interviews) and compare catch rates within and among spring and fall fishing periods. In addition, mail-in survey data are examined for recall bias.   I estimate that 28.7 tonnes of salmon and trout combined were harvested by the recreational trolling fishery in 2014, more than the commercial and subsistence fisheries combined. Seasonal differences in both recreational effort and catch were observed. Effort, in boat hours, was significantly higher in spring than in fall. Catch rates of trout were higher in fall than in spring, but there were no seasonal differences in catches of salmon. Harvest per boat day did not differ significantly among catch reporting methods, indicating that all three methods could be useful for managers interested in harvest rates. In contrast, total and released catch per boat day differed among reporting methods, with tournament anglers catching more fish in total. Finally, there was little evidence for recall bias in mail-in surveys, indicating that mail-in surveys are useful for collecting unbiased catch data. My study is the most comprehensive angler survey to date for Lake Vänern, and my results should be of immediate use to local fisheries managers and should also be of interest to researchers and managers interested in estimating catch and effort for fisheries at large spatial scales.

Annotation of Gyrodactylus salaris transcriptome

Relationship between organisms within an ecosystem is one of the main focuses in the study of ecology and evolution. For instance, host-parasite interactions have long been under close interest of ecology, evolutionary biology and conservation science, due to great variety of strategies and interaction outcomes. The monogenean ecto-parasites consist of a significant portion of flatworms. Gyrodactylus salaris is a monogenean freshwater ecto-parasite of Atlantic salmon (Salmo salar) whose damage can make fish to be prone to further bacterial and fungal infections. G. salaris is the only one parasite whose genome has been studied so far. The RNA-seq data analyzed in this thesis has already been annotated by using LAST. The RNA-seq data was obtained from Illumina sequencing i.e. yielded reads were assembled into 15777 transcripts. Last resulted in annotation of 46% transcripts and remaining were left unknown. This thesis work was started with whole data and annotation process was continued by the use of PANNZER, CDD and InterProScan. This annotation resulted in 56% successfully annotated sequences having parasite specific proteins identified. This thesis represents the first of Monogenean transcriptomic information which gives an important source for further research on this specie. Additionally, comparison of annotation methods interestingly revealed that description and domain based methods perform better than simple similarity search methods. Therefore it is more likely to suggest the use of these tools and databases for functional annotation. These results also emphasize the need for use of multiple methods and databases. It also highlights the need of more genomic information related to G. salaris.

Análise dos hábitos alimentares e de consumo de pescado das populações de Leiria e Peniche

Presentemente, o consumidor encontra à sua disposição uma diversidade de produtos alimentares que tornam a seleção dos alimentos uma tarefa muito mais complexa quando comparada com o passado. Diferenças culturais, sociais, pessoais e psicológicas influenciam o comportamento e as perceções dos consumidores. Sendo Peniche uma península com forte tradição piscatória procurou-se junto da população, perceber se as influências da região são refletidas nos seus hábitos de consumo e se diferem muito de uma região que não tenha as mesmas influências. Com base nas considerações acima referidas, o objetivo deste estudo foi avaliar os hábitos de consumo de pescado das populações de Leiria e Peniche através de um inquérito por questionário com apoio presencial, visando delinear o hábito de consumo, bem como a frequência, as preferências e restrições associadas ao consumo de pescado. Além disso, são relatadas as perceções dos consumidores em relação ao pescado selvagem e de aquacultura. Portugal é atualmente o país da União Europeia com o maior consumo anual de pescado por pessoa, e o terceiro do mundo, só ultrapassado pela Islândia e pelo Japão. O estudo foi realizado em 383 indivíduos residentes em Leiria e em 374 residentes em Peniche, maioritariamente do sexo feminino, com idades compreendidas entre os 30 e os 45 anos e detentores de grau de ensino superior. Os resultados mostram que os inquiridos consomem peixe, preferencialmente, cozido e grelhado, entre uma a três vezes por semana sendo que o bacalhau, o carapau, o salmão e a pescada estão entre as espécies mais consumidas. Devido à conveniência, pronta disponibilidade e preços acessíveis, os supermercados são os locais preferidos dos consumidores para comprarem peixe fresco e congelado. Além disso, a população de Peniche mantém o hábito de adquirir peixe fresco na peixaria e diretamente ao pescador. Apesar das duas populações exibirem uma maior propensão para consumir pescado selvagem, em Leiria o consumo de espécies de aquacultura aumenta com o grau de ensino. Por conseguinte, o pescado selvagem é considerado mais saudável, mais nutritivo, saboroso e mais seguro, sobretudo pela população que vive na zona costeira e que segue hábitos alimentares tradicionais. O pescado é percebido como um alimento saudável que possui alto teor em proteínas e ácidos gordos Omega-3, e baixo teor de gordura. No entanto, o preço elevado, a falta de disponibilidade para a sua confeção e as preocupações com os contaminantes presentes no pescado e consequentes riscos para a saúde são barreiras ao consumo de pescado. Os consumidores com mais idade mostram-se pouco recetivos à oferta de produtos inovadores à base de pescado por considerarem estes produtos de fraca qualidade. Com o avançar dos tempos, os habitantes de Peniche foram adquirindo novos hábitos de consumo e hoje em dia o consumo de pescado não difere muito da população de Leiria.

Unexpectedly high catch-and-release rates in European marine recreational fisheries: implications for science and management

While catch-and-release (C&R) is a well-known practice in several European freshwater recreational fisheries, studies on the magnitude and impact of this practice in Europeanmarine recreational fisheries are limited. To provide an overview of the practice andmagnitude of C&R among marine recreational anglers in Europe, the existing knowledge of C&R and its potential associated release mortality was collected andsummarized. The present study revealed that in several European countries over half of the total recreational catch is released by marine anglers. High release proportions of > 60% were found for Atlantic cod (Gadus morhua), European sea bass (Dicentrarchus labrax), pollack (Pollachius pollachius), and sea trout (Salmo trutta) in at least one of the studied European countries. In the case of the German recreational Baltic Sea cod fishery, release proportions varied considerably between years, presumably tracking a strong year class ofundersized fish. Reasons for release varied between countries and species, and included legal restrictions (e.g. minimumlanding sizes and daily bag limits) and voluntary C&R. Considering the magnitude of C&R practice among European marine recreational anglers, post-release mortalities of released fish may need to be accounted for in estimated fishingmortalities.However, as the survival rates of Europeanmarine species aremostly unknown, there is a need to conduct post-release survival studies and to identify factors affecting post-release survival. Such studies could also assist in developing species-specific, best-practice guidelines to minimize the impacts of C&R on released marine fish in Europe.

Life history & environmental effects on telomere dynamics in Atlantic salmon

While much of the study of molecular biology inevitably focuses on the parts of the genome that contain active genes, there are also non-coding regions that nonetheless play an essential role in maintaining genome integrity. One such region are telomeres, which cap the ends of all eukaryotic chromosomes and play an important role in chromosome protection. Telomere loss occurs at each cell division as a result of the ‘end replication problem’ and a relatively short telomere length is indicative of poor biological state. Thus far, the majority of studies on the dynamics and role of telomeres have been biased towards certain taxa. Research to date has mostly focussed on humans, other mammals and birds. There has been far less research on the telomere dynamics of ectotherms. It is important that we do so, especially since ectothermic vertebrates do not seem to down-regulate telomerase expression in the same way as endotherms, suggesting that their telomere dynamics may be less predictable in the later life stages. The main objective of this thesis was therefore to investigate how life history and environmental effects may influence telomere dynamics in Atlantic salmon Salmo salar. I carried out carefully designed experiments, both in the laboratory and in the wild, using a longitudinal approach where possible, in order to address a number of specific questions that are connected to this central theme. In chapter 2, I demonstrate that there can be significant links between parental life history and offspring telomere dynamics. Maternal life history traits, in particular egg size, were most strongly related to offspring telomere length at the embryonic stages. Paternal life history traits, such as early life growth rate, had a greater association with offspring telomere dynamics in the later stages of development. In chapter 3, using a wild Atlantic salmon population, I found that most individuals experienced a reduction in telomere length during the migratory phase of their life cycle; however the relative rate of telomere loss was dependent on sex, with males experiencing a relatively greater loss. Unexpectedly, I also found that juvenile salmon that had the shortest telomeres at the time of outward migration, had the greatest probability of surviving through to the return migration. In chapter 4, again using a wild system involving experimental manipulations of juvenile Atlantic salmon in Scottish streams, I found that telomere length in juvenile fish was influenced by parental traits and by direct environmental effects. Faster-growing fish had shorter telomeres and there was a greater cost (in terms of reduced telomere length) if the growth occurred in a harsher environment. I also found a positive association between offspring telomere length and the growth history of their fathers (but not mothers), represented by the number of years that fathers had spent at sea. Chapter 5 explored the hypotheses that oxidative DNA damage, catalase (CAT) antioxidant activity and cell proliferation rate are underlying mechanisms linking incubation temperature and telomere dynamics in salmon embryos. No evidence was found for any such effects, but telomere lengths in salmon embryos were found to be significantly affected by the temperature of the water in which they were living. There is also evidence that telomere length significantly increases during embryonic development. In summary, this thesis has shown that a complex mix of environmental and parental effects appear to influence telomere dynamics in Atlantic salmon, with parental effects especially evident during early life stages. It also demonstrated that telomeres lengthen through the embryo stages of development before reducing once the fry begin feeding, indicating that the patterns of telomere loss commonly found in endotherms may differ in ectotherms. Reasons for this variation in telomere dynamics are presented in the final Discussion chapter of the thesis.