Thesis (Ph. D.)--Joint Program in Oceanography/Applied Ocean Science and Engineering (Massachusetts Institute of Technology, Dept. of Earth, Atmospheric, and Planetary Sciences, and the Woods Hole Oceanographic Institution), 2003. / Includes bibliographical references (p. 132-139). / Iron (Fe) is an essential micronutrient for marine phytoplankton often limiting phytoplankton growth due to its low concentration in the ocean and thus playing a role in modulating the ocean's biological pump. In order to understand controls on global Fe distribution, the decoupling between Fe and P04 and the sensitivity of surface nutrient concentrations to changes in aeolian iron supply, I use a hierarchy of ocean circulation and biogeochemistry models. I formulate a mechanistic model of iron cycling which includes scavenging onto sinking particles and complexation with an organic ligand. The iron cycle is coupled to a model of the phosphorus cycle. The aeolian source of iron is prescribed. This system is examined in the context of a highly idealized box model. With appropriate choice of parameter values, the model can be brought into consistency with the relatively sparse ocean observations of iron in the oceans. I implement this biogeochemical scheme in a coarse resolution ocean general circulation model, guided by the box model sensitivity studies. This model is also able to reproduce the broad regional patterns of iron and phosphorus. In particular, the high macro-nutrient concentrations of the Southern Oceans result from iron limitation in the model. I define a tracer, Fe* that quantifies the degree to which a water mass is iron limited. Surface waters in high nutrient, low chlorophyll regions have negative Fe* values, indicating Fe limitation, because aeolian surface dust flux is not sufficient to / (cont.) compensate for the lack of iron in upwelled waters. The oceanic residence time of Fe is [approximately] 285 years in the model, confirming that transport plays an important role in controlling deep water [Fe[Tau]]. Globally, upwelling accounts for 40% of 'new' iron reaching the euphotic zone. Due to the potential ability of iron to change the efficiency of the carbon pump in the remote Southern Ocean, I study Southern Ocean surface P04 response to increased aeolian dust flux. My box model results suggest that a global ten fold increase in dust flux can support a P04 drawdown of [approximately]0.25[mu]M, while the GCM results suggest a P04 drawdown of 0.5 [mu]M. / by Payal Parekh. / Ph.D.

Thesis (M.S.)--Massachusetts Institute of Technology, Dept. of Mechanical Engineering, 1980. / MICROFICHE COPY AVAILABLE IN ARCHIVES AND ENGINEERING. / Includes bibliographical references. / by Vivék Ranadivé. / M.S.

Thesis (Ph. D.)--Joint Program in Biological Oceanography (Massachusetts Institute of Technology, Dept. of Biology; and the Woods Hole Oceanographic Institution), 2005. / Includes bibliographical references (p. 157-171). / Bacteriophage have been proposed to be the most abundant organisms on the planet, at an estimated 10³¹ particles globally (Hendrix et al., 1999). The majority of bacteriophage isolates (96%) are double-stranded DNA tailed phages (Caudovirales). These phages possess a distinctive icosehedral head, with a protein tail structure protruding from a single vertex. This organelle determines host specificity and provides the mechanism of passage of the phage genome into the host cell. Phages infecting differing microbial hosts may have access to a global pool of genes, albeit at different levels. Marine cyanobacteria of the genera Prochlorococcus and Synechococcus are numerically dominant photosynthetic cells in the large oligotrophic gyres of the open oceans, and contribute an estimated 30% to the oceanic photosynthetic budget. Cyanophages have been isolated which propagate on many strains of Synechococcus and Prochlorococcus. Cyanophages can effect community structure and succession through lytic infection of their hosts, and have implications in lateral gene transfer, mediated through lysogeny, mixed infections, pseudolysogeny, and transduction. / (cont.) The broad host ranges (between genera) observed in some phages indicates that lateral gene transfer is not confined to cells of the same strain. These phage/host interactions begin by host recognition by the tail of the infecting phage. Few studies have examined the structural proteins of cyanophage, partially due to the lack of a robust protocol for the growth and purification of phage particles. Cyanophage Syn5 is a short-tailed phage isolated from the Sargasso Sea by Waterbury and Valois (1993) which infects Synechococcus strain WH8109. Methods of growing the host cells and the phage, and concentrating the phage by PEG precipitation were developed. These methods led to highly concentrated purified phage stocks, to titers of 1012 particles/ml. Preliminary characterization of the growth of Syn5 gave a burst size of approximately 30 phage/cell and a lytic period of approximately 10 hours when inoculated into exponentially growing host cells acclimated to a temperature of 26⁰C and a light intensity of 50[mu]E m⁻² s⁻¹. Isolation of the phage nucleic acid yielded dsDNA molecules of approximately 40kb. The Syn5 particles were comprised of twelve structural proteins, as determined by SDS-PAGE. / (cont.) The most intense band on the gel was assigned to the capsid protein of Syn5 ([approx.] 35kDa). However, it was not possible to distinguish putative tail proteins via this method. Purified Syn5 particles were sent to the Pittsburgh Bacteriophage Institute for genome sequencing. The completed Syn5 genome was 46,214 bp long with a 237bp terminal repeat. Annotation of the completed Syn5 genome identified 61 putative ORFs, and revealed that Syn5 appeared closely related to the enteric phage T7 and cyanophages P-SSP7 and P60, as determined by gene similarity and synteny, although the genome was [approx.] 10kb longer than T7. Syn5 appeared to possess a more extensive DNA replisome that T7, containing copies of genes that encoded proteins of known T7 host co-factors, such as thioredoxin, utilized by the T7 DNAP. Several large ORFs were identified between the gene encoding the putative tail fiber and the gene encoding the putative terminase. These ORFs encoded proteins similar to some fibrous sequences within the NCBI non- redundant (nr) gene sequence database as of March, 2005; but had unknown functions within the phage. Unlike other recently sequenced cyanophages, SynS did not contain any photosynthetic genes. / (cont.) The structural proteins of SynS, as visualized by SDS-PAGE, were characterized by mass-spectroscopy and N-terminal sequencing. This allowed the assignment of sequences to putative ORFs within the Syn5 genome. The Syn5 particle was comprised of eleven discreet protein chains of molecular weight 152kDa, 139kDa, 99kDa, 90kDa, 66kDa, 60kDa, 47kDa, 35kDa, 22kDa, 21kDa, and 16kDa. The identified proteins included the portal, capsid, two tail tube proteins, and three internal virion proteins. Each of the genes encoding these proteins were found in the same gene order in the Syn5 genome as the corresponding genes were ordered in the T7 genome. There were three unidentifiable proteins within the particle (66kDa, 47kDa, and 16kDa). These mapped to the area of the SynS genome between the gene encoding the putative tail fiber and the gene encoding the putative terminase. No minor capsid or decorative capsid proteins were detected. The copy numbers of the corresponding protein chains were similar to those known for T7, with the exception of the tail fiber, which was present at a number of three chains per particle in comparison to T7's eighteen per particle. / (cont.) Polyclonal antibodies were raised against Syn5 particles. A Western blot with these antibodies showed that the tail fiber and the two unknown fibrous sequences were highly antigenic. This evidence implies that the unknown structures may act as host recognition proteins in addition to the tail fiber. Characterization of these novel proteins may provide insight to the host recognition abilities of cyanophages. An additional study was also carried out, investigating the high temperature limit of the growth of phage P22. The results revealed that the production of infectious particles was limited by the temperature sensitivity of the folding and assembly of the P22 tailspike protein. This work has been published and is included in the Appendix. / by Welkin Hazel Pope. / Ph.D.

Thesis (Ph. D.)--Joint Program in Oceanography (Massachusetts Institute of Technology, Dept. of Earth, Atmospheric and Planetary Sciences; and the Woods Hole Oceanographic Institution), 1999. / Includes bibliographical references. / This study is a geochemical investigation of the evolution of the Kerguelen plume, on the basis of upper mantle and lower crustal xenoliths. Ultramafic xenoliths include harzburgites predominant, a lherzolite, dunites and pyroxenites, whereas lower crustal xenoliths are cumulate gabbros recrystallized under granulite facies conditions. On the basis of the whole rock major element characteristics and trace element abundance patterns in clinopyroxenes, the harzburgites were found to be residues of extensive melting at high pressures within the Kerguelen plume. These were then recrystallized at low pressures and metasomatized by plume generated melts. Details of the metasomatic process were determined from trace element variations in clinopyroxene in connection to texture. This demonstrated that meltrock reaction and the precipitation of new clinopyroxenes occurred by metasomatic carbonatitic melts. It was also found that some of the harzburgites had distinctly unradiogenic Os isotopic compositions and were identified as originating from the sub-Gondwanaland lithosphere. On the basis of major and trace element compositions, the granulite xenoliths were found to be originally gabbroic cumulates formed from plume-derived basaltic melts emplaced at the base of the crust by underplating and subsequently recrystallized isobarically under granulite conditions. The Sr, Nd and Os isotopic compositions of the peridotite and granulite xenoliths demonstrate that the Kerguelen plume is isotopically heterogeneous and displays a temporal progression toward more enriched Sr and Nd isotopic compositions from the Ninetyeast Ridge to granulite xenoliths to Kerguelen basalts and Heard Island basalts. / by Deborah Renee Hassler. / Ph.D.

The objective of this research was to examine bottlenose dolphin (Tursiops truncatus) habitat use in the Indian River Lagoon (IRL) based on monthly relocation of photo-identified individuals, prey availability and environmental factors from 2003-2015. We focused on the variation of spatial and temporal abiotic and biotic factors and their influence on bottlenose dolphin habitat use patterns. Harbor Branch Oceanographic Institute (HBOI) conducted monthly photo-identification surveys along the length of the IRL and GPS locations of photographed dolphins were collected at the time of surveying. Stratified random samples of prey and environmental variables were collected monthly by the Florida Fish and Wildlife Conservation Commission (FWC) as part of the Fisheries-Independent Monitoring (FIM) program. Kernel density estimation was used to determine the magnitude-per-unit area of dolphins across a continuous raster surface of the IRL by wet and dry seasons each year, the values of which were used as a response variable in Classification and regression tree (CART) analyses with FIM fish community and environmental factors as predictors. Understanding how dolphins respond to environmental factors over time in the IRL could be used to predict future responses in estuaries and prioritize conservation and restoration actions. / Includes bibliography. / Thesis (M.S.)--Florida Atlantic University, 2019. / FAU Electronic Theses and Dissertations Collection

Thesis (Ph. D.)--Joint Program in Chemical Oceanography (Massachusetts Institute of Technology, Dept. of Earth, Atmospheric and Planetary Sciences; and the Woods Hole Oceanographic Institution), 1999. / Includes bibliographical references. / The goal of this thesis was to use high resolution analytical techniques coupled with molecular level analyses to chemically characterize high molecular weight (> 1 k Da (HMW)) dissolved organic matter (DOM) isolated from seawater in an attempt to provide new insights in to the cycling of DOM in the ocean. While a variety of sites spanning different environments (fluvial, coastal and oceanic) and ocean basins were examined, the chemical structure of the isolated HMW DOM varied little at both the polymer and monomer levels. All samples show similar ratios of carbohydrate:acetate:lipid carbon (80±4:10±2:9±4) indicating that these biochemicals are present within a family of related polymers. The carbohydrate fraction shows a characteristic distribution of seven major neutral monosaccharides: rhamnose, fucose, arabinose, xylose, mannose, glucose and galactose; and additionally contains Nacetylated amino sugars as seen by Nuclear Magnetic Resonance Spectroscopy (NMR). This family of compounds, consisting of a specifically linked polysaccharide backbone that is acylated at several positions, has been termed acylated polysaccharides (APS) by our laboratory. APS accounts for 50% of the carbon in HMW DOM isolated from the surface ocean and 20% of the carbon in HMW DOM isolated from the deep ocean. In order to identify a possible source for APS three species of phytoplankton, Thalassiossira weissflogii, Emiliania huxleyi and Phaeocystis, were cultured in seawater and their HMW DOM exudates examined by variety of analytical techniques. Both the T. weissflogii and E. huxleyi exudates contain compounds that resemble APS indicating that phytoplankton are indeed a source of APS to the marine environment. Furthermore, the degradation of the T. weissflogii exudate by a natural assemblage of microorganisms indicates that the component resembling APS is more resistant to microbial degradation compared to other polysaccharides present in the culture. Molecular level analyses show the distribution of monosaccharides to be conservative in surface and deep waters suggesting that APS is present throughout the water column. In order to determine the mechanism by which APS is delivered to the deep ocean the [delta]14C value of APS in the deep ocean was compared to the A14C value of the dissolved inorganic carbon (DIC) at the same depth. If the formation of deep water is the dominant mode of transport then both the DIC and APS will have similar [delta]14C values. However, if APS is injected into the deep ocean from particles or marine snow then the [delta]14C value of APS will be higher than the DIC at the same depth. Our results indicate that APS in the deep Pacific Ocean carries a modem [delta]14C value and is substantially enriched in 14C relative to the total HMW DOM and the DIC at that depth. Thus, particle dissolution appears to be the most important pathway for the delivery of APS to the deep ocean. / by Lihini I. Aluwihare. / Ph.D.

Thesis (Ph. D.)--Joint Program in Oceanography (Massachusetts Institute of Technology, Dept. of Earth, Atmospheric, and Planetary Sciences; and the Woods Hole Oceanographic Institution), 1998. / Includes bibliographical references (v. 2, leaves 423-433). / The goal of this thesis is to develop a methodology to interpret sound scattered from the seafloor in terms of seafloor structure and subseafloor geological properties. Specifically, this work has been directed towards the interpretation of matched-filtered, beam-formed monostatic acoustic reverberation data acquired on the west flank of the Mid-Atlantic Ridge when the seafloor is insonified by a band-limited, lowgrazing- angle acoustic pulse. This research is based on the hypothesis that observed backscatter signals are produced by a combination.of seafloor (interface) scattering and subseafloor (volume) scattering from structure having variations at scale lengths similar to the wavelength of the insonifying acoustic field. Analysis of monostatic reverberation data acquired during the Site A experiment (Run 1) of the Acoustic Reverberation Special Research Program 1993 Acoustics Cruise suggests that the scattered signals cannot be accounted for quantitatively in terms of large-scale slope, even though a strong correspondence between high intensity backscatter and seafloor ridges is observed. In order to investigate and quantify the actual sources of seafloor scattering, a numerical modeling study of seafloor models is undertaken using a finitedifference solution to the elastic wave equation. Geological data available at Site A and published reports describing geological properties of similar deep ocean crustal regions are used to develop a realistic seafloor model for the study area with realistic constraints on elastic parameters. Wavelength-scale heterogeneity in each model, in the form of seafloor roughness and subseafloor volume heterogeneity is defined using stochastic distributions with Gaussian autocorrelations. These distributions are quantified by their correlation lengths and standard deviation in amplitude. In order to incorporate all seafloor structure in a single parameterization of seafloor scattering, large-scale slope and wavelength-scale seafloor spatial parameters (rms height and correlation length), are included, along with the acoustic beam grazing-angle relative to a horizontal seafloor, in the definition of an 'effective grazing angle'. The Rayleigh roughness parameter, which depends on grazing angle of the insonification, is then redefined using the effective grazing angle and calculated for a variety of seafloor models. Scattering strengths are shown to vary systematically but nonlinearly with the 'effective Rayleigh roughness parameters' of horizontal rough seafloor models. This leads to an approximate interpretation scheme for backscatter intensity. In general, variation in backscattering is found to be dominated by the scattering from rough seafloor. If the seafloor is smooth or very low velocity (e.g., sediment), then scattering from volume heterogeneity becomes an important factor in the backscattered field. Both wavelength-scale seafloor roughness and volume heterogeneity are shown to be capable of producing the levels of variation in intensity observed in monostatic reverberation experiments. Variations in large-scale seafloor slope and subseafloor average velocity are shown to influence the backscatter response of seafloor models. / by Robert John Greaves. / Ph.D.

Wave Energy Converters (WECs) promise to be a viable alternative to current electrical generation methods. However, these WECs must become more efficient before wide-scale industrial use can become cost-effective. The efficiency of a WEC is primarily dependent upon its geometry and ballast configuration which are both difficult to evaluate, due to slow computation time and high computation cost of current models. In this thesis, we use evolutionary algorithms to optimize the ballast geometry of a wave energy generator using a two step process. First, we generate a function approximator (neural network) to predict wave energy converter power output with respect to key geometric design variables. This is a critical step as the computation time of using a full model (e.g., AQWA) to predict energy output prohibits the use of an evolutionary algorithm for design optimization. The function approximator reduced the computation time by over 99% while having an average error of only 3.5%. The evolutionary algorithm optimized the weight distribution of a WEC, resulting in an 84% improvement in power output over a ballast-free WEC. / Graduation date: 2012

<p>Oceanographic features, such as fronts, eddies, and upwellings, provide important foraging areas for marine predators. These areas serve as important "hotspots" of marine life, by aggregating weakly swimming lower and mid-trophic level species which, in turn, attract foraging predators. Despite the importance of these dynamic features, we lack a comprehensive understanding of how they create foraging habitat for seabirds and other marine predators. In the first part of this dissertation, I review current knowledge of how seabirds use oceanographic features with an emphasis on developing a more mechanistic understanding of these features, and identify important considerations for future studies. I use the findings of this review to inform two field research projects in the Bay of Fundy, Canada and Onslow Bay, North Carolina. In these two projects, I examined seabird abundance and distribution in relation to oceanographic features that occur at different spatial and temporal scales. In the first project, I examined foraging habitat of red-necked phalaropes (<italic>Phalaropus lobatus</italic>) in relation fine-scale tidal forcing near the Brier Island ledges in the Bay of Fundy. This research demonstrated the importance of biophysical interactions in creating phalarope habitat, and characterized red-necked phalarope habitat in both space and time. In Onslow Bay, I investigated the effects of Gulf Stream fronts and eddies on the abundance and distribution of seabirds using both remotely sensed and in situ data. I used fisheries acoustics surveys to investigate prey distribution within Gulf Stream frontal eddies. I then developed habitat models for the six most commonly sighted species or species groups (Cory's shearwaters, <italic>Calonectris diomedea</italic>; greater shearwaters (<italic>Puffinus gravis</italic>; Wilson's storm petrel, <italic>Oceanites oceanicus</italic>; Audubon's shearwaters, <italic>Puffinus lherminieri</italic>; black-capped petrels, <italic>Pterodrama hasitata</italic>; and red and red-necked phalaropes, grouped together as <italic>Phalaropus</italic> spp.) using multivariate modeling techniques. Gulf Stream frontal eddies influenced the abundance and distribution of seabirds in Onslow Bay, although frontal features were not as important in predicting seabird habitat as demonstrated in previous studies in the South Atlantic Bight. Prey availability in Gulf Stream frontal eddies was highest in eddy cold core regions, particularly in those regions close to the Gulf Stream. Taken together, the results of my dissertation: underscore the importance of conducting standardized surveys to assess dynamic environmental variables; demonstrate the use of multivariate methods to examine seabird foraging in relation to oceanographic features; emphasize the need to evaluate both prey distributions and physical regimes within oceanographic features at depth; and highlight the importance of temporal aspects of oceanographic features, such as the persistence and age of the features, when assessing the role that these features play in creating seabird foraging habitat.</p> / Dissertation

Thesis (M.S. in Computer Science)--Naval Postgraduate School, December 2003. / Thesis advisor(s): Neil Rowe, Carlyle Wash. Includes bibliographical references (p. 95). Also available online.