Real-time PCR was utilised to measure the expression of several host immune genes in response to experimental infection with either ISAV or infectious pancreatic necrosis virus (IPNV). Probes targeting transcripts produced during type I and type II interferon (IFN) responses demonstrated these viruses induced both responses and peaked by day 6 post infection. The high mortality in ISAV infected fish highlighted the ineffective nature of the response and suggested the virus possesses IFN antagonistic capabilities to circumvent the host defence mechanisms. Viral proteins were studied using transfection-based methodologies to elucidate potential IFN antagonist capabilities with emphasis on the 7i protein as a putative analogue to the non-structural (NS1) protein of influenza. Results of two independent assays demonstrated the 7i protein caused a reduction induction of the interferon stimulated gene, Mx. In addition, RNA binding experiments suggested the 7i protein also possessed an RNA binding function. A surveillance programme with analysis by real-time PCR and sequencing looking for the presence of the putatively avirulent ISAV HPR0 strain, which contains an extra long highly polymorphic region (HPR) with the haemagglutinin-esterase (HE), was performed to demonstrate the extent of this strains presence in Scottish marine Atlantic salmon stocks. A transfection-based system combined with haemadsorption studies was utilised to examine differences in receptor binding and esterase activity of HE proteins obtained from an HPR0 type, a pathogenic virus and a specific combination of the two. The HPR0 HE protein was shown to be functional with respect to both receptor binding and esterase activity although no difference in function could be attributed to the presence of the full-length HPR in comparison to a protein from a pathogenic variant. This suggests the phenotypic variation of HPR0 may lie in another aspect of the viral life cycle.

Homogeneous models of the central and western North Atlantic circulations are investigated. A topographic interior model is analysed to determine its behaviour under certain conditions of wind stress and basin geometry. This leads to the recognition of the need for transport layers along the continental margins forming the western limits of the sea. The steeply inclined slope regions are found significant in this respect, provided that their widths are not less than O(E[sup]1/4) in magnitude, since if these become more narrow, the zones are not capable of transporting sufficient water volumes, without violating matching conditions demanded?y underlying lower Ekman layers. Steady models of the continental shelves off the eastern North American seaboard, with meridional coastlines, are considered. One of these permits the dominant alongshore velocity to equal a specified function of latitude along any chosen isoline of f/H. Another assumes that this current decays to zero on leaving the shelf region. This particular model is extended to remove the restriction of having a straight, north-south coast. In all cases, the direction in which information is transmitted has the coast to its right. Good qualitative agreement with observed current data from the area is noted. An O(E[sup]1/3)-wide, mildly topographic, abyssal depth layer located on the continental rise of the western Atlantic is analysed. This is found sufficient for completing the oceanic transport balance, and its proximity to the east of relatively narrow slopes off southern North America, makes it an attractive. model for the off-shelf behaviour of the Gulf Stream. The eastern North American coastline is approximated by an arc of a circle, with oceanic diameter, and a time-dependent model over its shelf zone is examined. This is capable of propagating low frequency continental shelf waves from the same, right-bounded direction as the aforementioned steady models.

Whole salmon scales were analysed using inductively coupled plasma mass spectrometry (ICP-MS) to test for differences in elemental compositions between salmon stocks. The investigation was structured to address stock variation based on fish origin (wild or farmed), farm populations, river origin of wild fish and sea fishery origin (Farces or Greenland). Initial studies were conducted to determine optimal analytical methods and to quantify the effects of fish size, sex, age and interannual variability on trace element composition within a single stock. Although a large number of trace elements were measured in fish scales, only a small number were found to be important predictor elements. The trace element composition of scale samples from wild and farmed fish enabled identification of origin (wild/farmed) to a high degree of accuracy (98 %), with Mn found in significantly higher concentrations in farmed fish and identified as the most influential element. Farmed fish taken from six sites around the west coast of Scotland were also correctly classified with a surprisingly high accuracy using discriminant analysis (87 %). The ability to discriminate between wild stocks was tested using scales from returning fish caught in 12 rivers from around Scotland. Overall classification success was 59 %, but this was found to depend on sample sizes, with elimination of samples comprised of small numbers of individuals improving the classification success to 90 %. The elements showing the highest predictive power differ according to the origin of fish, Mn carries most weight distinguishing farmed from wild fish, Ba, Mn, Zn, Co, Li, Ni and V are important in distinguishing between farms, Li, Sr and Ba strongly influence classification of wild wish and U was found to be the most important predictor element separating out samples recovered from the Farces and West Greenland fisheries. It is suggested that differences in Li and Ba i Abstract contents in scales reflect natural differences in river or catchment water chemistry, Zn, Ni, Co and V are likely to reflect differences in anthropogenic loading within industrialised settings and the high levels of Mn found in farmed fish scales predominantly reflects dietary uptake from supplementation of feed.

Ocean circulation is a fundamental component of the Earth's climate system. The Atlantic thermohaline circulation, driven by deep convection at high latitudes, has a central role in regulating European climate through its transport and redistribution of heat. Either directly or indirectly, Mediterranean Water (MW) provides the high salinities found in the Nordic Seas which are required to precondition for deep convection. The precise mechanisms and pathways remain undetermined and yet are fundamental to understanding the effect that any change in the Mediterranean Outflow may have on circulation and ultimately on climate. This thesis investigates the transport of MW in the North Atlantic Ocean using hydrographic and model data. The primary objective is to quantify how much MW flows northwards and how much flows westwards from its source in the Gulf of Cadiz. Two boxes (Med Boxes) were constructed using hydrographic sections in the eastern North Atlantic enclosing the Strait of Gibraltar and Mediterranean Outflow. Inverse methods were used to determine the velocity field from which volume transports and salt fluxes were calculated. The main northward flow of MW across 41°N occurs east of 12°W, at depths of 500 to 1500 m, and transports 50 to 75% of the MW. An advective westward pathway across 20°W transports MW at similar depths into the ocean interior between 35°N and 40°N. Insignificant salt fluxes across the southern section (24°N) at MW depths confirm that no MW crosses the southern Med Box boundary. The net overturning circulation of the Med Box, with inflowing surface waters and outflowing intermediate waters, is attributed both to the exchange at the Strait of Gibraltar and also to water mass transformation associated with entrainment of North Atlantic Water into the Mediterranean Outflow. The magnitude of the circulation provides an estimate of this entrainment of 1.6 ± 0.6 Sv, within the Med Box boundaries. For comparison with these observational estimates, the model used is OCCAM, a level model from the Ocean Circulation and Climate Advance Modelling Project. The primary reason for choosing this model is that experiments have been undertaken with the Strait of Gibraltar both open and closed, enabling a new approach to the investigation of MW transport. MW is identified using the salinity difference between the two model experiments. Although the model circulation (in the open-Strait run) has a similar net overturning to the hydrography, different MW transport pathways are observed. A weak and variable northward pathway along the Iberian Peninsula and a strong southwestward flow from the Gulf of Cadiz result in a higher proportion of MW flowing westwards (61%) than northwards (39%). Seasonal variability is observed, with maximum westward flow in Autumn (70%) and minimum in Spring (50%). There is no evidence in the model that the northward boundary current provides a direct route for Mediterranean salt to reach the Nordic Seas.

Thesis (M. Ed.)--College of William and Mary. / Typescript. Vita. Includes bibliographical references (leaves [71]-73). Also available via the World Wide Web.

This dissertation aims at understanding ocean-atmosphere interactions in the Atlantic basin, and how this coupling may lead to increased climate predictability on seasonal-to-interannual time scales. Two regions are studied: the South Atlantic convergence zone (SACZ), and the tropical Atlantic. We studied the SACZ during austral summer and separated its variability into forced and internal components. This was done by applying a signal-to-noise optimization procedure to an ensemble of integrations of the NCAR Community Climate Model (CCM3)forced with observed Sea Surface Temperature (SST). The analysis yielded two dominant responses: (1) a response to local Atlantic SST consisting of a dipole-like structure in precipitation close to the coast of South America; (2) a response to Pacific SST which manifests mainly in the upper-level circulation consisting of a northeastward shift of the SACZ during El Niño events. The land portion of the SACZ was found to be primarily dominated by internal variability, thereby having limited potential predictability at seasonal time scales. We studied two aspects of tropical Atlantic Variability (TAV). First, we investigated the effect of extratropical variability on the gradient mode. We found that the intensive Southern Hemisphere (SH) winter variability can play a pre-conditioning role in the onset of the interhemispheric anomalies in the deep tropics during boreal spring. This SH influence on TAV is contrasted with its northern counterpart that primarily comes from the North Atlantic Oscillation during boreal winter. Second, we explored the importance of ocean dynamics in the predictability of TAV. We used the CCM3 coupled to a slab ocean as a tier-one prediction system. The ocean processes are included as a statistical correction that parameterizes the heat transport due to anomalous linear ocean dynamics. The role of ocean dynamics was studied by comparing prediction runs with and without the correction. We showed that in the corrected region the corrected model outperforms the non-corrected one particularly at long lead times. Furthermore, when the model was initialized with global initial conditions, tropical Atlantic SST anomalies are skillfully predicted for lead times of up to six months. As result, the corrected model showed high skill in predicting rainfall in the ITCZ during boreal spring.

Thesis (M.Sc.)--Memorial University of Newfoundland, 2001. / Bibliography: leaves 165-177.

Thesis (M.A.)--Naval Postgraduate School, 2002. / Thesis advisor(s): Donald Abenheim, David Yost. Includes bibliographical references. Also available online.

Thesis (Ph. D.)--University of Texas at Austin, 2002. / Vita. Includes bibliographical references. Available also from UMI Company.

Thesis (M.A. in National Security Affairs)--Naval Postgraduate School, December 2003. / Thesis advisor(s): David S. Yost, Hans-Eberhard Peters. Includes bibliographical references. Also available online.