Thesis. 1978. Ph.D.--Massachusetts Institute of Technology. Dept. of Earth and Planetary Science. / Microfiche copy available in Archives and Science. / Vita. / Bibliography: p. 333-347. / Ph.D.

Thesis (Ph.D.)--Massachusetts Institute of Technology, Dept. of Earth and Planetary Science, 1982. / Microfiche copy available in Archives and Science / Vita. / Bibliography: leaves 217-223. / by Frances Luellen Stephenson Hotchkiss. / Ph.D.

Thesis (Ph.D.)--Massachusetts Institute of Technology, Dept. of Earth and Planetary Sciences, 1980. / Microfiche copy available in Archives and Science. / Bibliography: leaves 206-211. / by Alexander N. Shor. / Ph.D.

Overfishing in the Benguela Current Large Marine Ecosystem (BCLME) resulted in degradation of the ecosystem. This study used the Driver-Pressure-State-Impact-Response (DPSIR) indicator framework to determine whether the ecosystem is now recovering. Indicator trends were analysed using various data sources that included government institutions and intergovernmental institutions. The results showed that the overall effect of Driver indicators was negative. This was mainly because of socio-economic pressure such as the need to create more jobs in light of rising national unemployment and the declining contribution of the fisheries sector to Gross Domestic Product (GDP). In addition to scientific advice, socio-economic factors also influenced the determination of Total Allowable Catches (TACs). The overall trend of Pressure indicators was positively influenced by the effect of TACs. The TACs reduced the quotas allocated for commercial fishing. Environmental factors did not seem to play a significant role in this study. State indicators had mixed results with the indicators assessed almost split in the middle between those showing a positive trend and those showing a negative trend. On the other hand, Impact and Response indicators showed overall positive results. Therefore, the conclusion of the study was that the degradation of the BCLME has slowed down and there are some signs of recovery. / Environmental Sciences / M.Sc. (Environmental Science)

Between 40 % and 50 % of the Earth’s primary production occurs in marine environments, primarily by phytoplankton. The trace metal micronutrients iron, zinc and cobalt are known to exert a significant biological control on phytoplankton productivity by serving as essential active centres in enzymatic processes such as inorganic carbon, nitrogen and phosphorus acquisition. The distributions and biogeochemistries of iron, zinc and cobalt therefore, have the potential to impact upon the global carbon cycle and hence climate. This research involves investigations into the biogeochemical cycling of iron, zinc and cobalt in the Atlantic Ocean. Iron measurements were conducted during October and November 2009 to determine the distribution and biogeochemistry of iron in the upper water column of the Atlantic Ocean along an Atlantic Meridional Transect (AMT-19). In addition, deck board incubation experiments were performed to establish the role of iron in controlling rates of di-nitrogen (N2) fixation in the North Atlantic. The distribution patterns and biogeochemistries of iron, zinc and cobalt in the South Atlantic at 40° S were determined during the UK GEOTRACES Section GA10 cruises of October 2010 and December 2011 to January 2012. Iron distributions in North Atlantic surface waters were primarily controlled by the transport and deposition of atmospheric dust particles. In the North Atlantic, elevated surface dissolved iron concentrations (0.50 - 1.65 nM) were associated with wet and dry deposition of Saharan dust between 4 and 29° N. To the south of 4° N, surface dissolved iron concentrations were markedly reduced (0.14 nM) indicating that high precipitation rates in the Inter-Tropical Convergence Zone (4 - 10° N) formed a barrier to the large-scale transport of Saharan dust particles, thus iron, to the South Atlantic. Here, the low surface dissolved iron concentrations were balanced by a total dissolvable iron flux out of the surface mixed layer (3.2 µmol m-2 y-1) that was comparable to atmospheric input estimates. Nitrogen fixation rates in the North Atlantic were highest (0.3 – 1.1 nmol L-1 d-1) where surface dissolved iron concentrations were elevated (1.02 nM) and decreased with increasing latitude as iron decreased. Hence, iron variability in the North Atlantic was sufficient to influence nitrogen fixation over a large spatial scale. In the South Atlantic Ocean at 40° S, the vertical and horizontal distributions of dissolved zinc and cobalt showed distinct gradients associated with the water masses present. Zinc concentrations ranged from 15 pM in open ocean surface waters to 8 nM in Antarctic Bottom Waters, whilst cobalt ranged from 2 pM to 80 pM in intermediate waters and was scavenged in deeper waters. Growth limiting mixed layer zinc concentrations resulted from the lack of a direct return path for zinc to the South Atlantic pycnocline with Sub-Antarctic Mode Water. Low zinc in this return path was identified by a linear correlation between zinc and soluble reactive phosphorus that showed a kink at ~ 500 m, much deeper than that observed in other oceanographic regimes. A seasonal study in the Southeast Atlantic revealed that the depletion of zinc over spring-summer periods resulted in an increase in the nutritional importance of cobalt and a shift towards phytoplankton with a cellular preference for cobalt over zinc and/or the ability to co-substitute these two trace metals at the molecular level. These key findings demonstrate the physico-chemical and biological influences that interact to control the distributions and biogeochemistries of iron, zinc and cobalt across diverse oceanographic regimes of the Atlantic Ocean, provide the first examination of zinc and cobalt biogeochemistries along the productive 40° S parallel and highlight the need for additional research in this region.

This thesis reviews archaeological material, medieval literature, place-names and palaeoenvironmental data cited in explorations of the early Viking Age North Atlantic area, and proposes a reassessment of chronology for the earliest settlement of Iceland. After analysing previous scholarship and discussing the problems inherent in study of early North Atlantic settlement, it is suggested that a multi-disciplinary approach is needed and can be articulated (by drawing upon Karl Popper’s ideas) to foster a fruitful conversation between disciplines. This methodology for engaging with multi-disciplinary materials is then presented. Three sections follow, tackling in turn three areas of Viking Age scholarship that have caused difficulty and frustration in the past: the toponymy of Hebridean Pap-islands (Chapter Three); the chronology of carve construction, occupation and human-environmental interactions at Seljaland in southern Iceland (Chapters Four, Five, Six, and Seven); and the İrland et mikla tradition of medieval literature, including discussion of the views of the largely forgotten nineteenth-century scholar Eugène Beauvois (Chapter Eight). Couched in a Popperian methodology, the new archaeological and palaeoenvironmental research that forms the bulk of the thesis is integrated with small-scale studies of place-names and medieval literature. Tephronchronology plays a large part in the Seljaland section. Chapter Six, for instance, introduces the tephra contours technique for study of past environments. The thesis concludes with a new proposal for the first settlement of Iceland and its connections to Atlantic Scotland, arrived at by considering the archaeological and tephra deposits at Seljaland, in conjunction with art-historical, toponymic and literary material. The thesis proposes that southern Iceland’s Seljaland caves were built c. AD 800 – earlier than the traditional Norse foundation of settlement on the island – and that cross sculpture in these caves suggests a connection with Gaelic monasticism found across the Scottish islands in this period.

Aquaculture is known as a major food-producing industry and Atlantic salmon (Salmo salar) and rainbow trout (Oncorhynchus mykiss) are the major cultured species in Scotland. However, disease outbreaks in aquaculture have been reported and are commonly associated with intensive fish farming, which results in a tremendous cost in the industry. Hence, understanding what immune-related genes and cells are present, their responses, mechanisms and functions in these farmed animals is a first requirement for potent vaccine design, selection of disease-resistant breeds and disease outbreak prevention. The innate immune system is the first line of defence against microbes which use germline-encoded pattern recognition receptors (PRRs) to recognise specific, conserved and constitutive products of invading pathogens, called pathogen-associated molecular patterns (PAMPs) that are important for survival of the microorganism and are thus hard for the microorganism to change. This thesis focuses on the identification and characterisation of a family of PRR called toll-like receptors (TLRs) and a TLR accessory protein UNC93B1 using different approaches. In Chapters 2, 3 and 5, eleven TLR genes and UNC93B1 were identified from Atlantic salmon whole-genome shotgun (WGS) contigs. These genes were cloned and sequenced and their putative domain structure, gene synteny and homology to other genes were determined by bioinformatics analysis. In addition, the constitutive expression profile of these genes was examined in different tissues from healthy salmon using real-time PCR. The potential modulation of these genes was examined in different in vitro and in vivo models which provide information to help understand the role(s) of these genes during inflammation or in the immune responses against pathogens. Several of these TLRs are so-called non-mammalian TLRs (TLR19, TLR20a and TLR20d) and are therefore particularly interesting to study. The sub-cellular localization was also investigated in TLR-GFP expression plasmid transfected Salmon Head Kidney-1 (SHK-1) cells. Lastly, attempts were made to develop a Human Embryonic Kidney (HEK) 293T cell line based platform to study TLR signalling and ligand specificity (Chapter 4).

The present study investigated spatial and temporal relationships between fluctuations in the abundance of Atlantic salmon (Salmo salar L.) and plankton records from the Continuous Plankton Recorder (CPR) in the North Atlantic Ocean. Analyses that examined co-variation in time series of salmon pre-fishery abundance (PFA) from fishing nations on both sides of the North Atlantic revealed a high degree of common variation between neighbouring nations for abundance of one sea winter salmon (1SW) and a common decline in the long-term abundance trends for multi-sea winter salmon (MSW). An appraisal of the data attributes for a selection of plankton taxa sampled by the CPR, corresponding to seasonal abundance in specific regions, indicated that these data capture useful spatial and temporal information on the abundance of the sampled taxa. Spatial interpolations were carried out using Data-Interpolating Variational Analysis (DIVA) for planktonic taxa that have been proven to relate to Atlantic salmon in previous studies, namely Calanus finmarchicus, Euphausiacea and Hyperiidae. Geographical boundaries were established for distinct populations of Calanus finmarchicus and for distinct aggregations of species in the cases of the Euphausiacea and the Hyperiidae. This knowledge was enhanced with information on the likelihood of persistence of these populations obtained by analysing the coherency of their seasonal cycles of abundance. This study detected strong relationships, in the form of long-term correlations, between the three selected plankton taxa (Calanus finmarchicus, Euphausiacea, Hyperiidae) and the diatom component of phytoplankton. These results indicated that the population dynamics of plankton species assemblages in these regions are influenced by common biotic and abiotic factors. Significant relationships were found between pre-fishery abundance PFA estimates for post-smolt salmon and Hyperiid amphipods. The relationships detected were particularly strong for 1SWsalmon of British and Icelandic origin at a lag of 1 year, i.e. corresponding to effects on the early phase of migration at sea. Relationships detected corresponding to the Euphausiacea and Calanus finmarchicus were more prevalent at lag-0 after the first winter at sea i.e. they relate to effects on the adult salmon. The results corresponding to MSW salmon also provided some indication of carry-over effects from the early phase of migration on adult survival. This work provided support for the hypothesis that early marine mortality is critical to the overall dynamics of salmon populations. Such information on ecosystem interactions is needed to improve the current knowledge on factors relating to salmon survival at sea. This information can be used to fine-tune important parameters of predictive models for stock management or conservation of salmon, especially in the face of the pressures of climate change.

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