With the culture of marine fish species increasing, interest in ways to combat infection in these species has grown. One such avenue is the search for novel antimicrobials. Antimicrobial peptides (AMPs) are host derived molecules with a significant role in innate immune responses and have been studied extensively in mammals. Well known AMP families include β-defensins, cathelicidins, liver expressed antimicrobial peptides and, specific to fish, the piscidins. While these molecules have been found in some fish species mining of expressed sequence tag (EST) databases was carried out to identify them in other fishes. In this study we have found new members of the β-defensin, cathelicidin and piscidin families of AMPs, while also identifying new hepcidins and LEAP-2 molecules in a diverse range of fish species. The rest of this thesis focused on one major AMP family, the cathelicidins, which in fish have been mainly identified in salmonids. They are stored in secondary granules of neutrophils as inactive pro-peptides and when infection occurs, a cleavage event releases the active mature form that effects microbicidal activity. Characterization of the cathelicidin genes present in Atlantic cod (Gadus morhua) and haddock (Melanogrammus aeglefinus) was undertaken. A number of ESTs with significant homology to cathelicidins were found in Atlantic cod. Primers were designed to amplify these sequences by PCR in both gadoid species, and the gene products were cloned and sequenced. One and two cathelicidin genes were identified in cod (gmCath1) and haddock (maCath1; maCath2), respectively, which differ in the length of their active mature peptides. Gadoid cathelicidins were constitutively expressed in many tissues and were upregulated by a range of immunostimulants. Analysis of the gmCath1 promoter revealed numerous putative transcription factor binding sites, some of which were used in an expression vector construct to show upregulation of gene expression when stimulated with the viral RNA mimic Poly I:C. Synthetic and recombinant gadoid cathelicidins were produced but did not appear to display antimicrobial activity, so this requires further investigation. The discovery of new members of the major AMP families in such a diverse range of fish species bodes well for future research into the use of these antimicrobials as potential disease control molecules in the aquaculture industry. Particularly for Atlantic cod this is crucial as the major cod farms in Norway are experiencing difficulties with bacterial infections for which there is no vaccine at present.

This research investigated the ecological significance of GW-SW interactions in the hyporheic zone of two Scottish mountain rivers (the Girnock Burn and the River Feshie).  The research comprised three components: (i) an assessment of the influence of GW-SW interactions on the spatio-temporal variability of hyporheic hydrochemistry and macroinvertebrate community structure, (ii) an evaluation of the influence of GW-SW dynamics on small-scale spatio-temporal variability in hyporheic thermal regimes, and (iii) an investigation of the spatial relationship between Atlantic salmon <i>Salmo salar </i>(L.) spawning distributions and patterns of GW-SW exchange in a braided river reach. In the Girnock, marked inter- and intra-reach differences in hyporheic water quality were found and linked to spatio-temporal variability in GW-SW exchange.  Up to 25% of the spatial variability in invertebrate community structure could be accounted for by differences in hyporheic water quality.  Community composition varied markedly between winter, spring and summer seasons, with the relative importance of individual water quality variables differing between seasons. There was much heterogeneity in streambed temperature regimes across the study reaches, with data suggesting that long-residence groundwater contributed significantly to hyporheic exchange.  However, at small (cm to m) scales thermal variability was most likely explained by the interaction of reach-scale GW-SW exchanges with smaller-scale, current-bed form induced hyporheic exchange. In a braided section of the River Feshie, spatially complex and temporally dynamic GW-SW exchange patterns occurred.  Salmon spawning was concentrated in locations characterised by upwelling groundwater at depth, with up to 66% of spawning sites recorded in groundwater dominated channels.

Fixed N (nitrate, nitrite, and ammonium) is a limiting nutrient for photosynthesis in the surface ocean. The rates and relative importance of N cycling processes, however, are temporally and spatially complex, which hamper their direct measurement and quantification. The South Atlantic subtropical front separates the Atlantic Ocean and the subantarctic, an area which can elucidate information about water masses both entering and leaving the basin. Through the GEOTRACES programme, an oceanographic section across 40°S in the South Atlantic is used to investigate biogeochemical cycling of nitrogen and carbon in this region. Hydrographic data, in combination with the isotopic composition of nitrate (NO3-), particulate organic carbon and particulate nitrogen (δ15NNO3, δ18ONO3, δ13CPOC, δ15NPN), is used to provide integrative measurements for temporally and spatially variable processes of the marine N-cycle and C-cycle. A thorough examination of the stable isotope cycling of particulate and dissolved N across the subtropical front is used to quantify the supply of fixed N to the mixed layer. The relative importance of nitrate from the subsurface, N2 fixation, terrestrial input and atmospheric deposition in supplying production is determined. Typically, 30-50% of the export flux in the subtropical water masses is sourced from N2 fixers and up to 75% within the Brazil Current. This finding suggests that diazotrophs may be abundant in the South West Atlantic providing a source of new N to this region. To assess the basin scale N-cycling processes, the deep water masses were analysed to reveal the origin and history of NO3-. Intermediate waters formed in the subantarctic are enriched in δ15NNO3 and δ18ONO3 from partial utilisation by algae. This enrichment in δ15NNO3 is not present in the subtropical North Atlantic or the return flow of the North Atlantic Deep Water (NADW), which decreases from ~5.9‰ in the newly formed intermediate waters to ~4.8‰ in the NADW at 40°S. The modification of isotopic signatures through the subtropical Atlantic can be calculated as an incorporation of 26-36 Tg N yr-1 of newly fixed N from an isotopic source of -1‰ (N2 fixation). The extent of N addition is higher than estimated rates of N loss within the Atlantic and surpasses the amount of N deficit supplied to the basin. Fixed N inputs and losses through the global ocean are investigated by the assessment of remineralised nitrate added to the ocean interior. A lower δ15N is observed in Atlantic remineralised nitrate in comparison to the Pacific. The relative importance of N2 fixation and pelagic denitrification within each ocean basin is quantified and through this approach, N2 fixation rates are estimated at 92-116 Tg N yr-1 in the Pacific and 24-32 Tg N yr-1 in the Indian Ocean. Combining Atlantic N2 fixation of ~32 Tg N yr-1 with Indo-Pacific, global N2 fixation rates can be estimated at 142-184 Tg N yr-1. The high inputs in the Pacific suggest that excess P is the dominant control on the success of N2 fixers. However, estimates of new N addition to the Atlantic indicate other mechanisms such as the recycling efficiency of P and supply of Fe to the surface ocean increase N2 fixation rates above this threshold. The organic matter supplied to sediments is principally derived from phytoplankton across the subtropical front. High organic content is associated with the productive Brazil-Malvinas Confluence region where a diverse supply of nutrients sustains elevated biomass. The Rio Plata outflow is characterised with high δ15NNO3 and δ15NPN, suggesting denitrification processes occur in the estuary. A low δ13C source associated with high Al concentrations is identified on the western slope, indicating a supply of terrestrial derived C to the deep ocean. The fractionation of C uptake by phytoplankton is assessed in subtropical and subantarctic waters. In the subantarctic, CO2[aq] and growth rates determine the extent of C isotope fractionation. In this region, low species diversity and a small range in cell size enable the fractionation from CO2[aq] and growth rate to be expressed in phytoplankton. In subtropical water masses a larger range of cell size is the principal determinant of C fractionation. Increased surface area to volume is the main mechanism for increasing C uptake, arguing against the use of δ13CPOC as a palaeoproxy. The low δ13CPOC and δ15NPN observed in the subtropics (from C fractionation and N2 fixation) contrast the heavier signatures in the subantarctic. These observations are propagated to the sediments, wherein organic matter shifts are determined by changes in the subtropical front over time. The results of this study have greatly improved knowledge of N and C cycling within the South Atlantic, providing new insight into the cycling of these two important elements in the surface and deep ocean, on a regional and global scale.

Winter storms can have devastating social and economic impacts in Europe. The severity of storms and the region they influence (southern or northern Europe) is related to the index of the North Atlantic Oscillation (NAO). However recent findings indicate that over the last millennium the relationship between the NAO and storminess varied and the forcings over centennial timescales are debated. Therefore in this research storminess has been reconstructed from NAO-sensitive regions of southern Europe (Galicia, Spain) and northern Europe (Outer Hebrides, Scotland), to investigate the Late Holocene NAO-storminess relationship and the causes of observed variability. Reconstructions were based on measurements of aeolian sand deposits within ombrotrophic peat bogs and a lake sedimentary archive from the Hebrides. The elemental composition of the lake sediments were analysed (using ITRAX XRF core scanning) to identify aeolian/in-washed sediment resulting from storms, as confirmed by correlations with instrumental data. As this is a relatively new technique there was a methodological focus on assessing its applicability for storm reconstructions and the maximum resolution achievable. It is concluded the reconstruction had a 10-year resolution (equivalent to 2-5 mm sampling resolution). The peat bog reconstructions span 4000 cal yr BP to present and indicate that there was a Late Holocene northward storm track shift. The results suggest that storminess was high in Galicia between 4000-1800 cal yr BP, after which it decreased and then gradually increased in the Outer Hebrides after 1500 cal yr BP. Comparison with an NAO reconstruction supports a consistent NAO-storm relationship through the Late Holocene. Orbital forcing is suggested as causing a steepening of the latitudinal temperature gradient and increasingly zonal circulation. Superimposed on this trend are centennial variations, which spectral analysis and visual comparisons suggest are primarily the result of solar minima (suggested as causing a weakened latitudinal temperature gradient and meridional circulation patterns), with some additional forcing from volcanic and oceanic changes. Therefore there has been a consistent storm-NAO relationship through the Late Holocene; however there appear to have been millennial and centennial shifts as the result of hemispheric circulation reorganisations.

Over recent years geological, geochemical and geophysical surveys of mid-ocean ridges have revealed a significant degree of along-axis variability not only in seabed morphology, but also in crustal structure, particularly Numerous geophysical surveys of the Valu Fa Ridge, southwest Pacific, have mapped the extent of an axial mid-crustal reflector. This reflector has been interpreted as representing the top of a sill-like melt lens, comprising a high percentage of partial melt, lying at the top of a crustal magma chamber. In 1995, a controlled-source, wide-angle seismic dataset was acquired at the Valu Fa Ridge during RN Maurice Ewing cruise EW9512, to investigate the mid-deep crustal structure at this ridge, and particularly the crustal magma chamber associated with the melt lens beneath the ridge axis. The EW9512 acquisition geometry was primarily two-dimensional in design, and modelling of these 2-D profiles revealed the presence of an axial low velocity zone beneath the melt lens. This low velocity zone is thought to represent a region of crystal mush comprising a much lower percentage of partial melt than is present in the overlying melt lens. Similar structures have been modelled beneath a number of other mid-ocean ridges. The primary aim of this study was to build on this 2-D interpretation by taking advantage of three-dimensional ray coverage in the axial region in order to assess the along-axis continuity of the magmatic system, correlate this to any ridge segmentation apparent in the seabed morphology, and determine if ridge segmentation is related to the magma supply. The 3-D data were analysed using a tomographic inversion technique. The inversion results suggest that the axial low velocity zone may be segmented on a scale of 5-10 km, which correlates with the morphological segmentation of the ridge crest and is believed to reflect episodic magma supply with different ridge segments at different stages of a cycle of magmatic and amagmatic extension. However, three- dimensional ray coverage is not ideal owing to the dominantly 2-D acquisition geometry. Therefore a detailed assessment of data uncertainty and resolution was undertaken to enable a meaningful interpretation of the inversion results in terms of which features have a geological origin and which are artefacts of the inversion process. P-S mode converted arrivals arising from mid-crustal interfaces were also modelled in order to obtain improved geological constraints on the crustal structure than is possible from P-wave studies alone. This modelling indicates that the uppermost crust is pervaded by thin cracks. In addition, techniques were developed for modeling the polarisation of 5-wave arrivals with low signal strength. Application of these methods suggests that the thin cracks have a preferred orientation parallel to the ridge crest on-axis, and oblique to the ridge crest off-axis which is thought to reflect the pattern of southward propagation of the ridge system inferred from regional tectonic and bathymetric studies. Modelling of P-S mode converted arrivals arising from conversion at the top of the melt lens provided additional constraints on the properties of the melt lens. In conjunction with the 3-D tomographic results, this work suggests that the southernmost ridge segment in the study area has recently become magmatically active following a period of amagmatic extension suggested by its morphology, thus providing evidence for episodic melt supply at this ridge. As part of the suggestions for further work, a theoretical investigation of survey resolution was undertaken to test commonly adopted acquisition geometries with a view to optimising the design and cost-effectiveness of future 3-D controlled-source tomographic experiments.

Em resposta à crescente perda de biodiversidade, diversos países adotam políticas de compensação que buscam equilibrar a destruição do habitat local restaurando, aprimorando e / ou protegendo áreas. Tais mecanismos são cada vez mais importantes no setor de mineração, onde a perda de habitat pode ser inevitável devido à rigidez locacional dos recursos minerais e com a coincidência com as áreas de importância da biodiversidade. Buscando contribuir para o avanço da compreensão da prática atual de compensação por perda de biodiversidade, investigamos as práticas adotadas em três minerações de calcário, em conformidade com a Lei da Mata Atlântica, lei federal que visa proteger este hotspot. Foram adotados os mecanismos de proteção e restauração em razões de área de 1: 1 a 1: 5. As principais dificuldades relatadas pelos atores chave foi encontrar áreas adequadas, métodos para calcular perdas residuais e incertezas sobre o sucesso da restauração. As melhores práticas recomendadas internacionalmente são parcialmente seguidas, com maior aderência observada para o caso cuja avaliação de impacto ambiental foi mais detalhada e forneceu uma base mais forte para planejar a compensação. Os resultados sugerem que a qualidade do planejamento e implementação de compensações está diretamente relacionada à qualidade da avaliação de impacto ambiental e, portanto, do licenciamento ambiental. / In response to the increasing loss of biodiversity, several countries have adopted offsetting policies that seek to balance local habitat destruction by restoring, enhancing and/or protecting equivalent values offsite. Such mechanisms are increasingly important in quarrying, where habitat loss may be unavoidable due to colocation of mineral resources and areas of biodiversity importance. Seeking to contribute to advance understanding of the current practice of biodiversity offsetting, we investigated actions required for environmental approval of three limestone quarries in compliance with Brazil\'s Atlantic Forest Act, a federal law that aims at protecting this biodiversity hotspot. Both protection and restoration offsets were applied at area ratios from 1:1.1 to 1:5. The main difficulties reported by practitioners are to find suitable areas, methods to calculate residual losses and uncertainties about the success of restoration. Internationally recommended best practices are partially followed with the highest adherence observed for the case whose environmental impact statement was more detailed and provided a stronger basis for designing the offset. Results suggest that the quality of offset planning and implementation is directly related to the quality of the environmental impact assessment.

Thesis advisor: Noah P. Snyder / Substrate size and mobility are important to Atlantic salmon (Salmo salar) spawning and rearing success. Channel geometry is a control on bedload mobility in streams. It is believed that channel morphology in many Maine rivers has been altered by land use practices, creating wider and shallower channels, and lowering stream competence. If correct, these changes may be partially responsible for the limited number of returning salmon currently observed in Maine coastal rivers. To evaluate the magnitude of these changes, I performed a statistical comparison of channel morphology between two Atlantic coastal streams: the Narraguagus River in Downeast Maine and the Jacquet River in northern New Brunswick, Canada. Compared to the Narraguagus River, the Jacquet River has relatively healthy returns of adult salmon. Both watersheds have similar drainage areas (Narraguagus 588 km²; Jacquet 510 km²;) and mean annual precipitation (1244 mm; 1200 mm), but differing average channel gradients (0.16%; 0.51%) and longitudinal profiles. During the summer of 2007, I surveyed a 13.6-km section of the Narraguagus with a drainage area range of 129-247 km², and a 10.4-km section of the Jacquet with a drainage area range of 94-265 km². I made measurements of active and bankfull width and depth, and channel gradient at 100-m intervals, and performed grain-size counts at 200-m intervals. I also measured gradient and width in a GIS-based analysis. Results of my analysis show that channel gradient is likely the most influential factor on Atlantic salmon habitat as it relates to sediment size. The two rivers exhibit no significant difference in width-to-depth ratio, when low-gradient outliers in the Narraguagus River are removed. Predicted median riverbed grain sizes were calculated using two methods: (1) from the empirical relationship between basal shear stress and measured grain size; and (2) using the Shields parameter and remote sensing data only. Measured and predicted grain sizes reveal finer river-bed sediments on the Narraguagus River, however, Shields parameter calculations show that sediment should be mobile in both streams. I compare these predictions to field-based habitat mapping on the Narraguagus River. Based on predicted grain sizes, I expect nearly continuous Atlantic salmon spawning (28-95%) and rearing (95-100%) habitat on the Jacquet, and much less spawning (47-62%) and rearing (57-68%) habitat on the Narraguagus. This is likely because the Narraguagus River is segmented into reaches of steeper gradient (S < 0.002) with potentially good habitat, and flatter reaches (S < 0.0005) of poor habitat. The long flat reaches (several km) likely act as sediment sinks, preventing the continuity of downstream sediment transport and causing sediment to be sourced from localized glacial deposits. / Thesis (MS) — Boston College, 2009. / Submitted to: Boston College. Graduate School of Arts and Sciences. / Discipline: Geology and Geophysics.

Thesis advisor: Noah P. Snyder / Dam-influenced streambank morphology has not been studied extensively in rivers in deglaciated landscapes with high densities of colonial-era milldams. Fluvial restoration in the eastern U.S. often focuses on understanding pre-Colonial floodplain processes. Recent work by Walter and Merritts (2008a) in the Piedmont of the U.S. mid-Atlantic region suggests milldams significantly impact sedimentation by creating surfaces composed of post-dam legacy sediment that are often abandoned by the river and function as fill terraces. I analyze channel morphology and sedimentation patterns upstream of two breached dams on the Sheepscot River in mid-coastal Maine using lidar digital elevation models, historical aerial photographs, radiocarbon dating, and hydraulic modeling. In the past several decades, observable channel morphologic changes occurred at the two study sites: Maxcy's Mills dam (built in 1809, it was 2-m high and breached in the late 1950s), and at Head Tide dam (built in the 1760s, it is 4-m high and was partially breached in 1952). The Sheepscot River has a native population of Atlantic salmon, which is a federally listed endangered species. Understanding the existence and transport of legacy sediment has become an important component of habitat restoration efforts in the region. The goal of this investigation is to determine the extent and morphologic function of legacy sediment in order to better understand how historical dam sites affect channel morphology and sediment transport in a post-glacial, low-gradient river system. Field and remote sensing analyses indicate that surfaces (up to 2.65 m high) composed of mud and sand function as floodplains 1 km upstream from Head Tide dam and surfaces 90 cm high continue 2.5 km upstream from Maxcy's Mills. Analysis of seven radiocarbon dates from pieces of tree bark sampled from the stratigraphy (58-187 cm below the surface) of the two study sites suggest up to 1.8 m of sediment upstream of the two study sites was deposited within the past 300 years and is therefore a legacy of the dams. Quantification of the total volume of stored legacy sediment is on the same scale as volumes observed in the mid-Atlantic Piedmont region, leading to the conclusion that post-glacial rivers in northern New England store milldam sediment in similar fashion to streams analyzed in the Walter and Merritts (2008a) study. / Thesis (MS) — Boston College, 2013. / Submitted to: Boston College. Graduate School of Arts and Sciences. / Discipline: Earth and Environmental Sciences.

Thesis advisor: John E. Ebel / The seismicity of the mid Atlantic Ridge (MAR) was compared in space and time with the seismicity along the Atlantic continental margins of Europe, Africa, North America, the Carribean and South America in a bid to appraise the level of influence of the ridge push force at the MAR on the Atlantic coastal seismicity. By analyzing the spatial and temporal patterns of many earthquakes (along with the patterns in their stress directions) in diverse places with similar tectonic settings, it is hoped that patterns that might be found indicate some of the average properties of the forces that are causing the earthquakes. The spatial analysis of the dataset set used shows that areas with higher seismic moment release along the north MAR spatially correlate with areas with relatively lower seismic moment release along the north Atlantic continental margins (ACM) and vice versa. This inverse spatial correlation observed between MAR seismicity and ACM seismicity might be due to the time (likely a long time) it takes stress changes from segments of the MAR currently experiencing high seismic activity to propagate to the associated passive margin areas presently experiencing relatively low seismic activity. Furthermore, the number of Atlantic basin and Atlantic coast earthquakes occurring away from the MAR is observed to be independent of the proximity of earthquake’s epicenters from the MAR axis. The effect of local stress as noted by Wysession et al. (1995) might have contributed to the independence of Atlantic basin and Atlantic coast earthquake proximity from the MAR. The Latchman (2011) observation of strong earthquakes on a specific section of the MAR being followed by earthquakes on Trinidad and Tobago was tested on other areas of the MAR and ACM. It was found that that the temporal delay observed by Latchman does not exist for the seismicity along other areas along the MAR and ACM. Within the time window used for this study, it appears that seismicity is occurring randomly in space away from the MAR. The weak anticorrelations between ACM and MAR seismicity show that the ridge push force probably has some level of influence on the ACM seismicity. However, as revealed from previous research on the study area, the forces resulting from lateral density contrasts related to topographic features and lateral density variations between oceanic and continental crust also appear to significantly influence the seismicity of the Atlantic coastal margins. / Thesis (MS) — Boston College, 2015. / Submitted to: Boston College. Graduate School of Arts and Sciences. / Discipline: Geology and Geophysics.

The type of Atlantic salmon immune response to amoebic gill disease was investigated by analysis of cytokine genes possibly related to the TH1, TH17 and Treg pathways, which were significantly down regulated, while il-4/13 isoforms, possibly related to the TH2 pathway, were found to be significantly up regulated. Moreover, the injection of Atlantic salmon with rIfn-γ, which might initiate the TH1 immune pathway, did not reduce infection load of Paramoeba perurans or severity of gill pathology in challenged fish. Different arginase isoforms present in salmonids were also characterised and the data supported the concept that arginase type II may be a more relevant marker of alterantive activate macrophages in teleost fish induced by rIl-4/13. Regarding the biology of P. perurans, the susceptibility of amoebae to different environmental conditions showed that amoebae exposed to salinities lower than 3 ppt were disrupted or did not recover after 16 days, while all amoebae cultures showed a significant difference between the two temperatures (10°C and 15°C) studied over time. Significant differences were also found in relative abundance of the 30 most prevalent bacterial genera present in the isolated P. perurans cultures (16S rRNA). The impact of stress on the host response to AGD was tested for the presence of an association between temperature (10°C and 15°C) and variation in severity of AGD in Atlantic salmon. This association was demonstrated for the histopathology and P. perurans load analysis, reflecting an earlier and stronger AGD infection at the higher temperature (15°C) treatment. No significant difference between the two temperature treatments was shown in hormonal and molecular responses. Therefore, temperature might not act as a chronic stressor but its effect could be linked to the higher amoebae attachment seen at higher temperatures in the in vitro experiment reported.