Thesis (M.A. in International Security and Civil-Military Relations)--Naval Postgraduate School, December 2003. / Thesis advisor(s): Donald Abenheim, Robert E. Looney. Includes bibliographical references (p. 105-112). Also available online.

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Yeast cell wall (YCW) extracts have long been regarded as beneficial supplements in aquaculture feeds, especially with respect to immunomodulation. Previous studies have shown that supplementing salmon diets with YCW extracts increases resistance to sea lice. During the series of three trials, different sea lice challenge models and YCW extracts were studied. In Trial 1, fish fed a diet containing 0.4% YCW #a exhibited a significant reduction in sea lice burden of 23% compared to the control diet. The skin and skin mucus samples from Trial 1 were hence used for high-throughput screening of altered transcripts and proteins, while searching for candidate biomarkers for YCW extracts. Samples from Trials 2 and 3 were used for testing the candidate transcripts in independent biological samples, hence confirming or otherwise their suitability as biomarkers. Due to the lack of skin-specific libraries in the salmonid EST database, Roche-454 sequencing was used to describe the skin transcriptome of Atlantic salmon and form the basis of successive experiments. The resulting transcriptome assembly included 4,108 transcripts that were previously unknown for salmon, which include both skin-specific and low-expression transcripts. Analysis of the mucus proteome by 2D gels of Trials 1 and 2 samples showed that 27 and 49 proteins, respectively, exhibited a change in expression due to dietary treatment (p<0.05). Of these, calreticulin-like protein showed greatest potential as a biomarker since its expression was changed in both Trials 1 and 2 at the proteomic level and Trials 2 and 3 at the transcriptomic level. RNAseq was carried out on Trial 1 skin samples and 375 transcripts were significantly altered in expression across dietary treatments (p<0.05). Validation of this data by qPCR was successful and yielded similar fold changes to the RNAseq output. However, when the expression of a selection of genes was studied in Trial 2 samples, no correlation was found and hence, no candidate biomarker molecules were discovered. While further work is required to deduce the underlying mechanisms of immunomodulation due to dietary YCW extracts, this project has yielded two skin-specific transcriptomic databases which may be used to enhance the genomic data for salmonids.

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This study documents the marine sponge fauna (Phylum Porifera) in the Northwest Atlantic, through the used of fishermen’s local ecological knowledge, fisheries observer data, trawl survey data and in situ exploration. A review of the role of structural benthic species, including ascidians, bryozoans, corals, hydroids and sponges as ecosystem engineers provides the context within which to discuss the contribution of sponges to seafloor habitat heterogeneity. Fishermen’s knowledge is useful in identifying areas of high concentration of benthic structural species, but is not particularly useful in determining the distribution of specific sponge species, with the exception of glass sponges, with the common name “Russian Hat”. Fisheries observer data from the Scotia Fundy Region and trawl survey data from the Newfoundland Region were obtained from the years 1977-2001 and 1973-2007 respectively. Despite the lack of systematic collection of information on sponge catches, prior to 2002, the information recorded show broad scale patterns of sponge distribution from the Scotian Shelf to the Eastern Arctic, and this thesis brings this information together for the first time. The move to deeper and more northern waters following the groundfish collapse in 1992 resulted in large catches of sponges, up to 5000kg per set, on the Labrador Shelf and Eastern Arctic. The combination of fishermen’s information, observer data and in situ research on the Scotian Shelf resulted in the identification of a previously undescribed and globally unique population of Vazella pourtalesi, a Hexactinellid sponge, in the Family Rossellidae. The impacts of fishing on the sponge community of the Gulf of Maine were examined by quantifying the sponge community inside and outside of the Western Gulf of Maine Closed Area. After two years, the sponge community within the closed area was dominated by the demosponge, Iophon sp. while the area that remained open to fishing had a higher diversity of sponges. The information presented in this thesis can inform marine ecosystem management, particularly in light of international obligations to protect vulnerable marine ecosystems.

1973 was a period in the history of the Atlantic Alliance when United States and European interests diverged to an unprecedented degree. Kissinger's Year of Europe initiative (1973/74) and the associated proposal, originally for a new Atlantic Charter and later for a less far-reaching declaration of principles, was an American attempt to inspire an explicit restatement of Alliance obligations. The intention was to take account of changes in the Atlantic relationship consequent upon EEC enlargement, economic pressures, and a dwindling of US domestic support for commitments to Europe at a time of detente with the USSR and the Watergate debacle. But the problems which the US sought to resolve were exacerbated by events, by different priorities in Europe, and by the attitude of France, which chose to interpret American proposals as a diplomatic offensive rather than an attempt to address Alliance problems. Closer US-Soviet relations, the eclipse of European interests during the 1973 Middle East war, and different approaches to the energy crisis created real tension between the allies. It increased - temporarily - the rival attractions of greater European cooperation before leading to recriminations within the Nine members of the EEC and eventual French isolation in the face of Paris's continued hostility to Kissinger's prescription for renewed cooperation. This thesis re-evaluates these events. It looks at the background to 1973 and the prevailing wisdom on such concepts as Atlantic partnership and interdependence. It examines the view that the US initiative was misinterpreted because of unwillingness to jeopardise newly-established European objectives for greater cooperation. It describes how the difficulties were resolved by enhancing - albeit only marginally - the importance of consultation within the Alliance and permitting a degree of US influence within European political cooperation on issues affecting US interests. Finally, it touches on possible comparisons with the early 1990s.

The North Atlantic Oscillation (NAO) is the major mode of atmospheric winter variability over the North Atlantic. Its current state has long been described by the station‐based NAO Index. This index has been shown to represent winter temperature anomalies over Northern Europe well. Nonetheless, its positions of measurement are stationary and may not catch the moving NAO-pattern’s characteristics sufficiently well to best represent the Scandinavian winter temperature anomalies. A new index based on North Atlantic maximum and minimum sea level pressure (SLP) is introduced in this study (called NAOE Index). The points of NAOE Index are therefore moving over the North Atlantic SLP‐field and may better catch atmospheric processes affecting Scandinavian winter temperature anomalies. NAOE Index correlation with Scandinavian winter temperature anomalies is analyzed through NASA’s (National Aeronautics and Space Administration) MERRA‐data (Modern Era‐Retrospective analysis forResearch and Applications). This study shows that NAOE Index represents the Scandinavian winter temperature anomalies almost as well as NAO Index from observed values does. The indices are alsowell correlated with each other. The direct difference between maximum and minimum SLP is also analyzed with regard to the Scandinavian winter temperature anomalies. The SLP‐differences are class‐divided and their correlations to the class‐mean temperature anomaly are shown to be very high. This correlation issignificantly higher than the correlations of temperature and each index. Hence, the results from this study suggest that an index based on the direct extreme‐SLP‐difference is preferred for representing the NAO’s impact on Scandinavian winter temperature anomalies. This study gives additionally a comprehensive view of NAO. Studies concerning the NAO’s history of research, dynamics, temperature connections and secondary impacts are reviewed.

This study examined three aspects of the processes of host location and initial attachment of the infective copepodid stage of the sea louse, <i>Lepeophtheirus salmonis</i> Krøyer 1838, to its host Atlantic salmon, <i>Salmo salar </i>(L.). The role of host and non-host odours and derived chemicals in modifying copepodid behaviour was identified in laboratory bioassays. Seasonal and stage-specific changes in the energetics of the eggs and the free-living larval stages were investigated through respiration experiments and chemical analyses. The influence of realistic physical factors, light intensity, salinity and host swimming speed, on determining the sites of initial copepodid attachment were identified in flowing water conditions, by the use of flume studies. Exposure to original odours and extracts of host odours resulted in significant changes in non-oriented behaviour and movement patterns which would increase the probability of host encounter, whilst exposure to original and extracts of host odour gave near-significant levels of oriented movement to the odour source. The host-derived chemicals isophorone and 1-octen-3-ol appeared to induce activated and limited arrested behaviours in the copepodid, respectively. During all stages of embryonic and larval development a gradual reduction in weight and energy content with developmental stage of larvae was noted, as lipid and protein stores were preferentially catabolised to provide energy for morphological changes and increased locomotion of the later larval stages, as revealed by an observed increase in respiration rates with developmental stage. Seasonal changes in embryonic dry weight, energy and biochemical composition were masked by the presence of seasonally variable proteinaceous egg cases. The free living stages showed a mixed trend in reproductive strategy, similar to previous studies of <i>L. salmonis </i>eggs in response to seasonal changes in temperature and photoperiod, but also similar to trends observed in food-unlimited holopelagic copepod species. Light intensity, salinity and host swimming speed independently and interactively altered the distribution and total initial attachment of <i>L. salmonis</i> copepodids on host Atlantic salmon smolts.