Thesis (Ph. D.)--Joint Program in Oceanography/Applied Ocean Science and Engineering (Massachusetts Institute of Technology, Dept. of Biology; and the Woods Hole Oceanographic Institution), 2008. / Includes bibliographical references. / In this thesis, I provide quantitative descriptions of toothed whale echolocation and foraging behavior, including assessment of the effects of noise on foraging behavior and the potential influence of ocean acoustic propagation conditions on biosonar detection ranges and whale noise exposure. In addition to presenting some novel basic science findings, the case studies presented in this thesis have implications for future work and for management. In Chapter 2, I describe the application of a modified version of the Dtag to studies of harbor porpoise echolocation behavior. The study results indicate how porpoises vary the rate and level of their echolocation clicks during prey capture events; detail the differences in echolocation behavior between different animals and in response to differences in prey fish; and show that, unlike bats, porpoises continue their echolocation buzz after the moment of prey capture. Chapters 3-4 provide case studies that emphasize the importance of applying realistic models of ocean acoustic propagation in marine mammal studies. These chapters illustrate that, although using geometric spreading approximations to predict communication/target detection ranges or noise exposure levels is appropriate in some cases, it can result in large errors in other cases, particularly in situations where refraction in the water column or multi-path acoustic propagation are significant. Finally, in Chapter 5, I describe two methods for statistical analysis of whale behavior data, the rotation test and a semi-Markov chain model. I apply those methods to test for changes in sperm whale foraging behavior in response to airgun noise exposure. Test results indicate that, despite the low-level exposures experienced by the whales in the study, some (but not all) of them reduced their buzz production rates and altered other foraging behavior parameters in response to the airgun exposure. / by Stacy Lynn DeRuiter. / Ph.D.

Thesis (Ph. D.)--Joint Program in Oceanography/Applied Ocean Science and Engineering (Massachusetts Institute of Technology, Dept. of Mechanical Engineering; and the Woods Hole Oceanographic Institution), 2009. / Includes bibliographical references (p. 271-277). / The Basin Acoustic Seamount Scattering Experiment (BASSEX) of 2004 was conducted to measure forward-scattering around the Kermit-Roosevelt Seamount Complex in the Northeast Pacific. The BASSEX experiment was focused on the bathymetric effects on acoustic propagation, in particular, on direct blockage, horizontal refraction, diffraction, and scattering by the seamounts. A towed hydrophone array, with 64 sensors cut for 250Hz (3m spacing), was used to measure the signals transmitted from the aforementioned broadband sources at many locations around the Kermit-Roosevelt and Elvis seamounts. Utilizing the measured broadband signals from the towed array, the size of the shadow zone was obtained. The measured data in the BASSEX experiment strongly support the understanding of the complicated phenomena of sound propagation around the seamounts. In addition, the experimental data could be used to validate current 2D and 3D theoretical models and develop new models to properly realize the sound propagation with such complicated phenomena. In this thesis, the reconciliation between the measured pulse arrivals from the BASSEX experiment and various two-dimensional (2D) and three-dimensional (3D) theoretical models is carried out to investigate the physical characteristics of the sound propagation around seamounts: First, the 2D Parabolic Equation (PE) model and the 2D ray tracing model are used to reconcile each ray arrival with the BASSEX experiment in terms of arrival time and grazing angle. / (cont.) We construct a sound speed field database based on the sound speed profiles from the BASSEX experiment, World Ocean Atlas (WOA) 2005, and CTD casts using the objective analysis. Second, 3D broadband sound propagation around a conical seamount is investigated numerically using the 3D spectral coupled-mode model (W. Luo, PhD Thesis, MIT, 2007). Since the calculation of 3D broadband pulses with the spectral coupled-mode model requires extensive computation time, a parallel program is developed with a clustered computing system to obtain results in reasonable time. The validation of the 3D spectral coupled-mode model is performed by a series of comparisons between the various 2D and 3D models for a shallow-water waveguide. The Kermit-Roosevelt seamount is modeled by a simple conical seamount for the 3D model. The computed 3D broadband pulses for the modeled conical seamount are compared with those from the BASSEX experiment and the 2D PE simulation. Through this analysis, we examine the limit of the application of the sound propagation models and improve the efficiency of the 3D sound propagation model using parallel computing to obtain a broadband pulse in a reasonable amount of time. / by Hyun Joe Kim. / Ph.D.

Thesis (Ph. D.)--Joint Program in Oceanography/Applied Ocean Science and Engineering (Massachusetts Institute of Technology, Dept. of Biology; and the Woods Hole Oceanographic Institution), 2008. / Page 362 blank. / Includes bibliographical references. / Understanding how organisms deal with potentially toxic or fitness-reducing allelochemicals is important for understanding patterns of predation and herbivory in the marine environment. The ability of marine consumers to tolerate dietary toxins may involve biochemical resistance mechanisms, which increase the hydrophilicity of compounds and facilitate their active efflux out of sensitive cells and tissues. While several allelochemical-responsive detoxification enzymes have been sequenced and functionally characterized in terrestrial invertebrates feeding on chemically defended host plants, there is virtually no information concerning the role of these biotransformation enzymes that may mediate feeding tolerance in marine invertebrates. The objective of this research was to assess the diversity and dietary regulation of cytochrome P450s (CYP), glutathione S-transferases (GST) and ABC transporters in the generalist marine gastropod Cyphoma gibbosum feeding on a variety of chemically defended gorgonian corals, and to identify those dietary natural products that act as substrates for these proteins. Molecular and proteomic techniques identified both allelochemically-responsive CYPs, and constitutively expressed GSTs and transporters in Cyphoma digestive glands. Inhibition of Cyphoma GST activity by gorgonian extracts and selected allelochemicals (i.e., prostaglandins) indicated that gorgonian diets are likely to contain substrates for molluscan detoxification enzymes. In vitro metabolism studies with recombinant CYPs suggested those Cyphoma enzymes most closely related to vertebrate fatty acid hydroxylating enzymes may contribute to the detoxification ofichthyodeterrent cyclopentenone prostaglandins found in abundance in selected gorgonian species. / (cont.) Finally, the presence and activity of multixenobiotic resistance transporters in Cyphoma and the co-occurring specialist nudibranch, Tritonia hamnerorum, suggests these efflux transporters could function as a first line of defense against dietary intoxication. Together, these results suggest marine consumers that regularly exploit allelochemical-rich prey have evolved both general (GST and ABC transporters) and allelochemical-specific (CYP) detoxification mechanisms to tolerate prey chemical defenses. / by Kristen Elizabeth Whalen. / Ph.D.

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), 2006. / This electronic version was submitted by the student author. The certified thesis is available in the Institute Archives and Special Collections. / Includes bibliographical references (p. 155-162). / The oceanic response to overflows is explored using a two-layer isopycnal model. Overflows are a major source of the dense water of the global deep ocean, originating from only a few marginal seas. They enter the open ocean as dense gravity currents down a continental slope and play a crucial role in the deep ocean circulation. To understand the dynamics of these overflows, previous studies simplified their dynamics by treating the overlying ocean as inactive. This simplification may be a first approximation for the overflow but not for the overlying ocean. The Mediterranean overflow, for example, entrains about 2 Sv of overlying Atlantic water when it enters the Atlantic through Gibraltar Strait. The upper ocean must balance the mass loss and vortex stretching associated with entrainment. Thus for the upper ocean, overflows represent a localized region of intense mass and PV forcing. The simulations in this study show that in the upper layer, entrainment forces a cyclonic circulation along bathymetric contours. This is a topographic [beta]-plume and its transport depends on the entrainment region size and the topographic slope. / (cont.) Baroclinic instability also develops and creates eddy thickness flux to the in-shore direction, forcing a double gyre topographic [beta]-plume near the strait due to eddy PV flux convergence on the in-shore side of the continental slope and divergence on the offshore side. When the upper oceanic response to overflows is examined specifically for the Mediterranean overflow, the upper ocean is found to establish two trans-Atlantic zonal jets, analogous to the Azores current and the Azores Counter current. These two zonal jets are an extension of the topographic [beta]-plume driven by the overflow. Because the eddies in the steep slope region near Cape St. Vincent drive a mean flow across the slope, the topographic [beta]-plume connects to the Atlantic Ocean to become a basin scale flow. This thesis shows that overflows can induce a significant circulation in the upper ocean, and for the Mediterranean overflow, this circulation is a basin scale flow. / by Shinichiro Kida. / Ph.D.

Thesis (Ph. D.)--Joint Program in Oceanography/Applied Ocean Science and Engineering (Massachusetts Institute of Technology, Dept. of Civil and Environmental Engineering; and the Woods Hole Oceanographic Institution), 2003. / Includes bibliographical references. / Sorption is a key factor in determining the fate of polycyclic aromatic hydrocarbons (PAHs) in the environment. Here, PAH sorption is proposed as the sum of two mechanisms: absorption into a biogenic, organic carbon (OC) fraction and adsorption onto a combustion-derived, black carbon (BC) fraction. To study BC adsorption, a 375ʻC thermal oxidation method was employed to remove OC and isolate the BC fraction. Test studies showed that nitrogen-containing macromolecules charred during this pretreatment causing a positive bias to the BC measurement. Meanwhile, the oxidation of relatively small BC particles underestimated the total BC content in non-charring samples. Models based on carbon oxidation were then proposed to estimate reasonably the total BC and OC contents of sediment samples. The adsorption of pyrene onto isolated BC particles was then studied by constructing a nonlinear isotherm, which was characterized with a BC-normalized distribution coefficient and a Freundlich exponent. Pyrene sorption to Boston Harbor sediment was then modeled as the sum of OC absorption and BC adsorption using the measured adsorption parameters and literature absorption values. Finally, literature reports of high PAH distribution coefficients from the field and nonlinear PAH isotherms from the laboratory were re-explained by considering BC adsorption. / by AmyMarie Accardi-Dey. / Ph.D.

Thesis (Ph. D.)--Joint Program in Oceanography/Applied Ocean Science and Engineering (Massachusetts Institute of Technology, Dept. of Biology; and the Woods Hole Oceanographic Institution), 2006. / This electronic version was submitted by the student author. The certified thesis is available in the Institute Archives and Special Collections. / Includes bibliographical references. / Cetacean blubber is a primary site for lipid storage, which the animal utilizes during periods of energetic stress. It is important to understand how the blubber responds to factors such as ontogeny, water temperature, reproductive status, and nutritional state because blubber is also the primary bioaccumulation site for persistent organic pollutants (POPs) such as polychlorinated biphenyls (PCBs). During periods of lipid mobilization such as lactation, PCBs from the blubber are mobilized into the circulatory system and may cause toxic effects. One particular toxic mechanism may include the induction of cytochrome P450 enzymes in the integument and liver, which could enhance the biotransformation of PCBs to hydroxylated metabolites (OH-PCBs). OH-PCBs may then interfere with thyroid hormone dependent neurodevelopment. The goals of these studies were to investigate the relationships between lipid dynamics and PCB effects and to devise a quantitative approach to assess neurodevelopment in delphinid cetaceans. Blubber morphology, cytochrome P450 1A1 (CYP1A1) expression in the skin-blubber biopsy, blubber and plasma PCBs, and plasma OH-PCBs were assessed in bottlenose dolphins (Tursiops truncatus). / (cont.) In addition, magnetic resonance (MR) images of the post-mortem brain in situ were obtained from Atlantic white-sided dolphin (Lagenorhynchus acutus) specimens. These results showed that: 1) Factors such as ontogeny, water temperature, and reproductive status affected blubber morphology in bottlenose dolphins. In response to warmer water, the lipid content of the blubber decreased and this appeared to involve loss of lipids from adipocytes in the middle blubber layer. Similar to the effects of starvation on blubber morphology, lactation decreased adipocyte size predominantly in the deeper blubber, 2) CYP1A1 levels in the deep blubber were significantly related to the total plasma TEQ98 concentrations, adipocyte shrinkage, and plasma OH-PCB levels, 3) Through in situ MR imaging of stranded, Atlantic white-sided dolphin specimens, the size of brain structures that depend on thyroid hormones for maturation could be measured accurately. Future studies can use this technique, coupled with chemical analysis of brain regions, to determine if thyroid hormone disrupting chemicals in delphinid cetaceans are associated with changes in the size of brain structures. / by Eric Wilson Montie. / Ph.D.

Thesis (S.M.)--Joint Program in Oceanography/Applied Ocean Science and Engineering (Massachusetts Institute of Technology, Dept. of Biology; and the Woods Hole Oceanographic Institution), 2008. / Includes bibliographical references (p. 54-59). / (cont) An increased understanding of heterotrophic bacterial strategies for acquiring nutrients and trace elements is critical for elucidating their impact on biogeochemical cycling in the ocean. It is estimated that iron is a limiting nutrient for phytoplankton growth in over 30% of the open ocean, but still little is known about bacterial strategies for iron acquisition. Siderophore (Fe ligand) production by bacteria may play a major role in influencing the bioavailability of iron in the ocean. Despite the importance of siderophores in the environment, only limited information from a select group of bacteria is available. On a cruise through the Costa Rica Dome (CRD) upwelling region in July 2005, a library of 867 isolates from five depth profiles inside and outside of the dome was obtained and screened for siderophore production using the Chrome Azurol-S (CAS) assay. Phylogenetic affiliation of 134 isolates was determined by sequencing the 16s rDNA gene, and determined that gamma proteobacteria such as Alteromonas, Pseudoalteromonas, Halomonas, and Marinobacter dominated the collection, while alpha-proteobacteria such as Roseobacter were also represented. The isolates obtained from stations in the CRD showed greater siderophore-producing capabilities between 55m and 100m while strains isolated from outside the CRD had shallower peak (-8-35m) production. Functional group determination showed that hydroxamate production dominated from 50-150m, while hydroxamate and catechol production is roughly equal in shallower waters. By characterizing the siderophores produced by these isolates and determining the genetic make-up of the population, these findings further our understanding of how heterotrophic microbes affect biogeochemical processes and the competitive nature of nutrient acquisition. / by Whitney B. Krey. / S.M.

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), 2004. / Includes bibliographical references. / Observations at mid-ocean ridges indicate that magmas are focused to the ridge axis by a network of porous dunites in near chemical isolation. This thesis investigates several of the outstanding questions regarding the mechanisms of melt transport and its effects on the shallow mantle. Chapter 1 details the current understanding of melt migration from observations at mid-ocean ridges and ophiolites. Chapter 2 uses the size distribution and abundance of dunites measured in the Oman ophiolite to place limits on the potential mechanisms by which dunites form and subsequently estimate the flux of chemically unequilibrated melt which a network of dunites can supply. Chapter 3 characterizes the chemical composition of dunites and harzburgites from Oman to further constrain the process by which dunites form and relates the observed trends within dunites to variations in the time-integrated melt/rock ratio. Chapter 4 examines the microstructures of peridotites in Oman to constrain the deformation mechanisms which determine the viscosity of shallow mantle. Chapter 5 is a numerical investigation of advection beneath ridges incorporating the rheology inferred from the observed microstructures. Chapter 6 integrates the conclusions of the previous chapters, reevaluating the potential melt flux through dunites and constraining the permeability of the shallow mantle. / by Michael Geoffrey Braun. / Ph.D.

Thesis (S.M.)--Joint Program in Oceanography/Applied Ocean Science and Engineering (Massachusetts Institute of Technology, Dept. of Ocean Engineering; and the Woods Hole Oceanographic Institution), 2005. / Includes bibliographical references (leaves 78-79). / The initial water impact of a free-falling object is primarily related to the fluid forces on the wetted surface of the object. The shape-dependent added-mass coefficients express the fluid forces integrated over the body, and thus physically represent the additional inertia of water accelerated with the body. The field of hydrodynamic impact has been primarily concerned with estimating the added-mass coefficients of various types of bodies for different water impact types, such as seaplane landings, torpedo drops, and ship slamming. In this study, a numerical model has been constructed to estimate the hydrodynamic impact loads of a REMUS dropped in free-fall from a helicopter in a low hover. Developed by von Alt and associates at Woods Hole Oceanographic Institution, the REMUS (Remote Environmental Monitoring UnitS) is a small, man-portable, torpedo shaped Autonomous Underwater Vehicle (AUV) that is normally operated from small boats for a variety of scientific, industrial, and military applications. Finite-element method software and computer aided drafting tools were used to create a simplified model of REMUS without fins, propeller, or transducers. / (cont.) This axisymmetric REMUS model was cut by a flat free surface at various pitch angles and submergence values, and a panel mesh of the wetted surface of the vehicle was created using an automatic mesh generator. Surface boundary conditions are enforced for the free surface by reflecting the body panels using the method of images. Each panel mesh was evaluated for its added- mass characteristics using a source collocation panel method developed by Dr. Yonghwan Kim, formerly of the Vortical Flow Research Laboratory (VFRL) at the Massachusetts Institute of Technology. Experimental impact tests were conducted with a specially-instrumented test vehicle to verify the initial impact accelerations. / by Stephen Michael Roe. / S.M.

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), 1997. / Includes bibliographical references (p. 411-422). / Pelagic sedimentation is the primary modifier of topography generated by ridge-associated volcanic and tectonic processes. This thesis represents an effort to understand the processes of, and the general distribution of, pelagic sedimentation on rough topography, particularly in the Atlantic Basin but with applications to the world ocean as a whole. This study utilizes a simple numerical model of sedimentation which, when applied to models of rough basement topography, allows us to study sedimentation effects in terms of commonly-measured stochastic parameters including seafloor RMS height, abyssal hill spacing, and slope distribution. We also address the effect of sediment compaction on seafloor morphology, and the impact of long-wavelength topography on stochastic measures of sedimented seafloor. Understanding gained allows the construction of inverse problems to obtain information about sediment distribution and basement morphology from multibeam bathymetric data in regimes where backscatter from rough, reflective basement highs obscures returns from wide-beam seismic systems. By using maximum likelihood estimation to compare slope distribution functions calculated from data to those from filtered model topographies, we estimate average sediment thickness L, basement RMS height H, and a measure of sediment mobility k. Using data from near-ridge surveys and off-axis transit lines, we invert for L, H, and K for 3-29 Ma seafloor from the western flank of the Mid-Atlantic Ridge (MAR) near 26* N, 2- 45 Ma seafloor from the western flank of the MAR near 260 S, 2-40 Ma seafloor from the eastern flank of the MAR near 25* S, and 1-38 Ma seafloor from the western flank of the MAR near 35* S. Variations in L with seafloor age allow us to constrain sediment rain rate and the corrosivity of bottom waters to calcite since the Oligocene. We hypothesize that sediment rain rates during much of the early and middle Miocene were only 10-50% of the average rate for the past -10 m.y. Variations in H suggest correlation between tectonic setting and topographic variability. A relatively narrow range of K is needed to describe intrahill sedimentation patterns. / by Helen Faith Webb. / Ph.D.