No description available.

Excess nutrients in the form of uneaten food or waste from intensive, monospecies aquaculture farms can have negative effects on the surrounding natural ecosystem, causing eutrophication and benthic habitat degradation. Biomitigative techniques such as Integrated Multi-Trophic Aquaculture (IMTA) are being investigated for their ability to reduce these negative environmental impacts. IMTA is the co-culture of multiple species from complementary trophic levels, physically orientated in such a way that excess waste nutrients from the fed component are intercepted by the extractive species. For IMTA systems to become a sustainable aquaculture design alternative, it is important to ensure that infrastructure orientation and stocking densities of the extractive species maximize the amount of excess nutrients intercepted and overall system efficiency. Previous research has shown that the majority of wastes from fed finfish are made up of large organic particulates which sink rapidly to the benthos underneath or near the fish cages and which would be available to benthic deposit-feeding species. The California sea cucumber (Parastichopus californicus) is a promising extractive species for IMTA on the west coast of Canada due to its deposit-feeding behaviour and its relatively high market price. Owing to the sea cucumber’s morphology and ability to move through restricted spaces, containment can be difficult without reducing nutrient transfer and overall IMTA system efficiency (i.e. mesh sizes needed to contain small sea cucumbers may restrict flow of farm particulates to them). The overall goal of the present work is to effectively contain juvenile sea cucumbers in such a way that maximizes benthic extraction of large-particulate nutrients within an IMTA system. / Graduate

Atualmente a ordem Dendrochirotida é composta por 800 espécies, sendo que metade destas estão entre as famílias Sclerodactylidae e Phyllophoridae. Todavia, a maior parte das informações acerca dos seus táxons é proveniente de revisões morfológicas muito antigas (Phyllophoridae em 1954, e Sclerodactylidae não revisada). Este estudo, portanto, se configura como o primeiro teste formal da monofilia das famílias Sclerodactylidae e Phylllophoridae e suas subfamílias. O presente trabalho constitui um estudo morfológico minucioso das estruturas que compõem o endoesqueleto dos Holothuroidea que são os ossículos dérmicos e anel calcário, vislumbrando alcançar através de uma análise cladística os objetivos descritos a seguir: (i) testar a monofilia de Phyllophoridae; (ii) testar a monofilia de Sclerodactylidae; (iii) testar a monofilia das subfamílias de Phyllophoridae e (iv) testar a monofilia das subfamílias de Sclerodactylidae. O material estudado foi obtido a partir de visitas e/ou empréstimos de museus nacionais e internacionais. Foram estudados espécimes de todas as ordens de Holothuroidea, à exceção de Elasipodida, totalizando 956 espécimes pertencentes a 78 espécies, das quais quatro foram delimitadas como grupo externo (i.e. Aspidochirotida, Apodida e Dendrochirotida [Cucumariidae e Psolidae]) e 44 delimitadas como grupo interno (todas as espécies tipo foram analisadas). Setenta e dois caracteres foram descritos e ilustrados através de fotografias ou microscopia eletrônica de varredura. As análises foram realizadas com o programa PAUP (v. 4.0), através do algoritmo de parcimônia Tree Bissection and Reconnection (TBR) de branch-swapping, com 5000 réplicas. O estudo morfológico detalhado permitiu elencar novos caracteres, bem como reinterpretar caracteres já estabelecidos, além de fornecer correções de interpretações equivocadas acerca de tais estruturas. Sclerodactylidae foi recuperada como monofilética e está composta por três subfamílias (todas foram recuperadas como monofiléticas), Clado I, Sclerodactylinae e Thyoninae. Phyllophoridae foi recuperada como monofilética e está composta por três subfamílias (todas foram recuperadas como monofiléticas), Cladolabinae, Phyllophorinae e Semperiellinae. / Currently, the order Dendrochirotida comprises about 800 species, half of these being within the families Sclerodactylidae and Phyllophoridae. Regardless, most information about these families is from old morphological revisions (Phyllophoridae in 1954 and Sclerodactylidae not reviewed). This study appears as the first formal test of the monophyly of the families Sclerodactylidae and Phylllophoridae and their respective subfamilies. The present work constituted a detailed morphological study of the structures that compose the Holothuroidea endoskeleton which are the dermal ossicles and calcareous ring to achieve through a cladistic analysis the following objectives: (i) to test the monophyly of Phyllophoridae; (ii) to test the monophyly of Sclerodactylidae; (iii) to test the monophyly of the Phyllophoridae subfamilies and iv) to test the monophyly of the subfamilies of Sclerodactylidae. The material studied was obtained from visits and/or loans from the national and international museums. Specimens of all orders of Holothuroidea were analyzed with the exception of Elasipodida, yielding 956 specimens belonging to 78 species, of which four were delimited as outgroups (i.e. Aspidochirotida, Apodida and Dendrochirotida [Cucumariidae and Psolidae]) and 44 delimited as internal groups (all type specimens were analyzed). A total of 72 morphological characters were described and illustrated through photographs or scanning electron microscopy images. The analyses were conducted with the aid of PAUP (v.4.0) using a parsimony algorithm Tree Bisection and Reconnection (TBR) branch-swapping (5000 replicates). This detailed morphological study allowed us to list new characters, to reinterpret. already established ones as well as providing corrections of misinterpretations about such structures. Sclerodactylidae was recovered as monophyletic and is composed of three subfamilies (all were recovered as monophyletic), Clade I, Sclerodactylinae and Thyoninae. Phyllophoridae was recovered as monophyletic and consists of three subfamilies (all were recovered as monophyletic), Cladolabinae, Phyllophorinae and Semperiellinae.

This thesis describes structural studies on the interactions between the fucosylated chondroitin sulfate (fCS) oligosaccharides and human proteins known as selectins. fCS is a carbohydrate obtained from sea cucumbers, that can be classified as a branched glycosaminoglycan (GAG). It has attracted much attention due to its anti-coagulant, anti-inflammatory, antimetastatic and anti-HIV properties and its structure was previously determined by NMR. Selectins constitute a family of proteins involved in cell adhesion processes, such as inflammation, attachment of viral particles and migration of tumour cells. fCS oligosaccharides have been shown to bind to selectins, which is likely a reason behind their biological activity. However, the mechanism of this interaction is currently unknown. The initial part of the thesis describes the experimental work on expression and purification of the recombinant L- and P-selectin constructs in Pichia pastoris, Escherichia coli and HEK 293 cells. The aim of these experiments was to produce two constructs for each selectin, a single domain construct, consisting of the C-type lectin domain only, and a double domain construct, consisting of both the C-type lectin and the EGF-like domains. The intention was that the recombinant proteins would be labelled with 13C and 15N to allow for the in-depth structural NMR studies on the fCS-selectin interaction. Various experimental approaches have been explored, including the use of different cell lines, modifications to construct design, as well as alterations to expression and purification conditions. Although it was not possible to produce soluble selectin constructs in either bacterial or yeast cells, protein expression tests in HEK293 cells, performed in collaboration with the Oxford Protein Production facility (OPPF), led to production of a soluble L-selectin construct, consisting of the L-selectin C-type lectin domain. The produced L-selectin construct, as well as two commercially available constructs of the Land P-selectin extracellular domains, were used in the Saturation Transfer Difference (STD) NMR experiments to provide new information about the nature of the fCS-selectin binding. The STD experiments allowed to identify the regions within the fCS oligosaccharides that are in direct contact with the protein and likely play an important role in this interaction. Experiments on different protein constructs allowed the comparison of fCS binding to P-selectin and to two different recombinant constructs of L-selectin. Results of these studies suggest that the binding occurs via a similar mechanism for both L- and P-selectins and that the fCS oligosaccharides bind to one-domain L-selectin construct with similar affinity as to a larger construct, consisting of the entire extracellular region of the protein. Alongside the experimental work, theoretical in silico studies on the fCS-selectin binding were undertaken as part of this project. The existing X-ray structures of selectin complexes were subjected to Molecular Dynamics (MD) simulations, which allowed to explore the dynamic behaviour of E-selectin upon binding to sialyl Lewis x (sLex). It was found that sLex forms a more favourable interaction with the extended conformation of E-selectin and that the protein in this conformation is characterised by a high degree of interdomain flexibility, with a new type of interdomain movement observed in the MD studies on this complex. In further in silico studies, the fCS oligosaccharides were docked to the existing P-selectin structures. The docking tests were performed on the computationally produced fCS trisaccharides with fucose branches either 2,4 or 3,4-sulfated. Results were evaluated with MD simulations and analysed in the light of current knowledge of selectin-ligand binding and the STD NMR experimental results. The in silico studies allowed to identify a subset of P-selectin residues that are likely involved in the interaction with fCS oligosaccharides in vivo. The conformational behaviour of P-selectin upon binding to fCS was also explored and it was found that the interdomain hinge is flexible during this interaction and allows transition from bent to extended conformational state. Finally, a new NMR method was developed to facilitate the studies of complex carbohydrates, incorporating the concepts of G-matrix Fourier Transform (GFT) NMR into 2D HSQC and 2D HSQC-TOCSY experiments. The method allows to separate peaks in the regions of high spectral overlap, providing information that can simplify the assignment process. The new experiments facilitated the structural evaluation of a sample containing a mixture of oligosaccharides resulting from the depolymerisation of fCS polysaccharide.

The mode of feeding exhibited by different organisms may influence the form or quantity of copper that is bioaccumulated. This hypothesis has been tested by exposing 2 species of sea cucumbers, Pentacta anceps and Stichopus chloronotus, which possess different feeding modes, to varying concentrations of copper. The digestive tract and body wall were dissected and analyzed for copper concentration using atomic absorption spectroscopy. A trend was present, exhibiting a small dose dependent curve. The results did not show a significant difference between species or treatments. This study indicates that feeding mode may influence the amount of copper accumulated but it could not be concluded because of a small sample size. The model used in this study demonstrated that copper was being actively precipitated out of the water and deposited into sediment. Future studies focusing on pollutant uptake may find this useful when evaluating the role of feeding mode or habitat.

While investigating the gruesome death of a marine biologist, a by-the-book biracial detective and a jaded Tribal officer uncover a conspiracy surrounding a sea cucumber poaching ring on the reservation. Inspired by actual events.

No description available.

To assess the spatial distribution of nutrient wastes around an open-water integrated fish/mollusk/kelp farm in-situ kelp bioassays were employed. Growth rates were measured over a four-month growing season and used as a proxy for relative nutrient concentrations. Seasonality and depth effects on growth rate were also assessed. Growth around the pens was 0.20 cm • day-1 higher than at the control, and reached a maximum of 1.4 cm • day-1. Optimal growth was achieved at 8 m. Growth at 8 m was significantly higher by 1.5 cm • day-1 compared to surface waters at 2 m. Early spring had the highest growth rates with a peak of 1.4 cm • day-1 recorded on June 21. This study re-iterates the fundamental benefits of IMTA and shows the potential of in-situ assay as an alternative to error-prone and costly water sampling to asses nutrient status in water. / Graduate

People are active participants in coral reef ecosystems. This ethnobiology study considers and contrasts folkbiological knowledge of people living in two groups of artisanal fishing villages in Kadavu Province, Fiji. The high level of biological diversity on the Astrolabe Reef provides insights into folk categorization and classification methods that include colour, shape, size, physical features, and habits of certain reef fish and marine animals. Surveying large numbers of experts and novices on defined groups of creatures yields more depth and range of responses allowing higher confidence levels in response accuracy. A comparison of the data with Berlins (1992) proposed principles yields mixed results. Sea cucumbers have high ecological salience and their identification requires attention to the affect of two centuries of trade on Fijian society. Effective ethnobiological research provides productive options to contribute to coral reef sustainability programs with long term benefits for local people and marine life. Key words: Kadavu, naming and classification of fish, coral reef ethnobiology.

No description available.