Thesis: Ph. D., Joint Program in Oceanography/Applied Ocean Science and Engineering (Massachusetts Institute of Technology, Department of Biology; and the Woods Hole Oceanographic Institution), 2014. / Cataloged from PDF version of thesis. / Includes bibliographical references (pages 113-127). / White sharks (Carcharodon carcharias) are highly migratory, ecologically important, vulnerable, and understudied marine predators. Ecogeochemistry, which takes advantage of natural variations in chemical signatures recorded in body tissues, can help determine lifetime movement, age, and ontogenetic diet history in difficult to study species. Shark vertebrae are constructed of distinct layers of tissue laid down sequentially over an individual's lifetime and may preserve a chemical record of environmental exposure. In this thesis, I investigate the ecology of the understudied northwest Atlantic (NWA) white shark population by applying several ecogeochemistry techniques to their vertebrae. I generate the first radiocarbon ([delta]¹⁴C) age estimates for adult white sharks, dramatically extending the maximum age and longevity compared to earlier age studies. [delta]¹⁴C results also verify a lack of reworking of vertebral material and hint at possible sexual dimorphism in growth rates. Using amino acid and bulk stable isotope analyses, I show that individual sharks have marked variation in feeding and movement, and that pinnipeds do not constitute a large portion of their diet. Finally, I explore the utility of elemental chemistry to retrospectively infer movement. This work provides an important informational baseline for future NWA white shark ecological studies and conservation and management efforts. / by Li Ling Hamady. / 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), 2011. / Cataloged from PDF version of thesis. / Includes bibliographical references (p. 147-166). / The ecological integrity of tropical habitats, including mangroves, seagrass beds and coral reefs, is coming under increasing pressure from human activities. Many coral reef fish species are thought to use mangroves and seagrass beds as juvenile nurseries before migrating to coral reefs as adults. Identifying essential habitats and preserving functional linkages among these habitats is likely necessary to promote ecosystem health and sustainable fisheries on coral reefs. This necessitates quantitative assessment of functional connectivity among essential habitats at the seascape level. This thesis presents the development and first application of a method for tracking fish migration using amino acid (AA) 13C analysis in otoliths. In a controlled feeding experiment with fish reared on isotopically distinct diets, we showed that essential AAs exhibited minimal trophic fractionation between consumer and diet, providing a 513C record of the baseline isoscape. We explored the potential for geochemical signatures in otoliths of snapper to act as natural tags of residency in seagrass beds, mangroves and coral reefs in the Red Sea, Caribbean Sea and Eastern Pacific Ocean. The 13C values of otolith essential AAs varied as a function of habitat type and provided a better tracer of residence in juvenile nursery habitats than conventional bulk stable isotope analyses (SIA). Using our otolith AA SIA approach, we quantified the relative contribution of coastal wetlands and reef habitats to Lutjanus ehrenbergii populations on coastal, shelf and oceanic coral reefs in the Red Sea. L. ehrenbergii made significant ontogenetic migrations, traveling more than 30 km from juvenile nurseries to coral reefs and across deep open water. Coastal wetlands were important nurseries for L. ehrenbergii; however, there was significant plasticity in L. ehrenbergii juvenile habitat requirements. Seascape configuration played an important role in determining the functional connectivity of L. ehrenbergii populations in the Red Sea. The compound-specific SIA approach presented in this thesis will be particularly valuable for tracking the movement of species and life-stages not amenable to conventional tagging techniques. This thesis provides quantitative scientific support for establishing realistic population connectivity models that can be used to design effective marine reserve networks. / by Kelton Wells McMahon. / Ph.D.

Thesis: Ph. D., Joint Program in Biological Oceanography (Massachusetts Institute of Technology, Department of Biology; and the Woods Hole Oceanographic Institution), 2017. / Cataloged from PDF version of thesis. / Includes bibliographical references (pages 159-168). / Thecosome pteropods are planktonic mollusks that form aragonite shells and that may experience increased dissolution and other adverse effects due to ocean acidification. This thesis focuses on assessing the possible biological effects of ocean acidification on the shells and locomotion of pteropods and examining the response of a local pteropod population to environmental change over time. I analyzed shell condition after exposing pteropods to elevated CO₂ as well as in natural populations to investigate the sensitivity of the shells of different species to aragonite saturation state ([omega][subscript A]). The pteropods (Limacina retroversa) from laboratory experiments showed the clearest pattern of shell dissolution in response to decreased [omega][subscript A], while wild populations either had non-significant regional trends in shell condition (Clio pyramidata) or variability in shell condition that did not match expectations due to regional variability in [omega][subscript A] (Limacina helicina). At locations with intermediate [omega][subscript A] (1.5-2.5) the variability seen in L. helicina shell condition might be affected by food availability more than tA. I examined sinking and swimming behaviors in the laboratory in order to investigate a possible fitness effect of ocean acidification on pteropods. The sinking rates of L. retroversa from elevated CO₂ treatments were slower in conjunction with worsened shell condition. These changes could increase their vulnerability to predators in the wild. Swimming ability was mostly unchanged by elevated CO₂ after experiments that were up to three weeks in duration. I used a long-term dataset of pteropods in the Gulf of Maine to directly test whether there has been a population effect of environmental change over the past several decades. I did not observe a population decline between 1977 and 2015, and L. retroversa abundance in the fall actually increased over the time series. Analysis of the habitat use of L. retroversa revealed seasonal associations with temperature, salinity, and bottom depths. The combination of laboratory experiments and field surveys helped to address gaps in knowledge about pteropod ecology and improve our understanding of the effects of ocean acidification on pteropods. / by Alexander Bergan. / Ph. D.

Thesis: Ph. D., Joint Program in Oceanography/Applied Ocean Science and Engineering (Massachusetts Institute of Technology, Department of Earth, Atmospheric, and Planetary Sciences; and the Woods Hole Oceanographic Institution), 2014. / Page 242 blank. Cataloged from PDF version of thesis. / Includes bibliographical references. / Recent work has documented dramatic changes in the West Antarctic Ice Sheet (WAIS) over the past 30 years (e.g., mass loss, glacier acceleration, surface warming) due largely to the influence of the marine environment. WAIS is particularly vulnerable to large-scale atmospheric dynamics that remotely influence the transport of marine aerosols to the ice sheet. Understanding seasonal- to decadal-scale changes in the marine influence on WAIS (particularly sea-ice concentration) is vital to our ability to predict future change. In this thesis, I develop tools that enable us to reconstruct the source and transport variability of marine aerosols to West Antarctica in the past. I validate new firn-core sea-ice proxies over the satellite era; results indicate that firn-core glaciochemical records from this dynamic region may provide a proxy for reconstructing Amundsen Sea and Pine Island Bay polynya variability prior to the satellite era. I next investigate the remote influence of tropical Pacific variability on marine aerosol transport to West Antarctica. Results illustrate that both source and transport of marine aerosols to West Antarctica are controlled by remote atmospheric forcing, linking local dynamics (e.g., katabatic winds) with large-scale teleconnections to the tropics (e.g., Rossby waves). Oxygen isotope records allow me to further investigate the relationship between West Antarctic firn-core records and temperature, precipitation origin, sea-ice variability, and large-scale atmospheric circulation. I show that the tropical Pacific remotely influences the source and transport of the isotopic signal to the coastal ice sheet. The regional firm-core array reveals a spatially varying response to remote tropical Pacific forcing. Finally, I investigate longer-term (-200 year) ocean and ice-sheet changes using the methods and results gleaned from the previous work. I utilize sea-ice proxies to reconstruct long-term changes in sea-ice and polynya variability in the Amundsen Sea, and show that the tropics remotely influence West Antarctica over decadal timescales. This thesis utilizes some of the highest-resolution, most coastal records in the region to date, and provides some of the first analyses of the seasonal- to decadal-scale controls on source and transport of marine aerosols to West Antarctica. / by Alison Sara Criscitiello. / Ph. D.

Thesis (S.M.)--Joint Program in Biological Oceanography (Massachusetts Institute of Technology, Dept. of Biology; and the Woods Hole Oceanographic Institution), 2008. / "February 2008." / Includes bibliographical references (p. 133). / I build on the deterministic phytoplankton growth model of Sosik et al. by introducing process error, which simulates real variation in population growth and inaccuracies in the structure of the matrix model. Adding a stochastic component allows me to use maximum likelihood methods of parameter estimation. I lay out the method used to calculate parameter estimates, confidence intervals, and estimated population growth rates, then use a simplified three-stage model to test the efficacy of this method with simulated observations. I repeat similar tests with the full model based on Sosik et al., then test this model with a set of data from a laboratory culture whose population growth rate was independently determined. In general, the parameter estimates I obtain for simulated data are better the lower the levels of stochasticity. Despite large confidence intervals around some model parameter estimates, the estimated population growth rates have relatively small confidence intervals. The parameter estimates I obtained for the laboratory data fell in a region of the parameter space that in general contains parameter sets that are difficult to estimate, although the estimated population growth rate was close to the independently determined value. / by Lorraine Thomas. / S.M.

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), 2013. / This electronic version was submitted by the student author. The certified thesis is available in the Institute Archives and Special Collections. / Cataloged from student-submitted PDF version of thesis. / Includes bibliographical references (p. 151-161). / Autonomous marine vehicles are increasingly used in clusters for an array of oceanographic tasks. The effectiveness of this collaboration is often limited by communications: throughput, latency, and ease of reconfiguration. This thesis argues that improved communication on intelligent marine robotic agents can be gained from acting on knowledge gained by improved awareness of the physical acoustic link and higher network layers by the AUV's decision making software. This thesis presents a modular acoustic networking framework, realized through a C++ library called goby-acomms, to provide collaborating underwater vehicles with an efficient short-range single-hop network. goby-acomms is comprised of four components that provide: 1) losslessly compressed encoding of short messages; 2) a set of message queues that dynamically prioritize messages based both on overall importance and time sensitivity; 3) Time Division Multiple Access (TDMA) Medium Access Control (MAC) with automatic discovery; and 4) an abstract acoustic modem driver. Building on this networking framework, two approaches that use the vehicle's "intelligence" to improve communications are presented. The first is a "non-disruptive" approach which is a novel technique for using state observers in conjunction with an entropy source encoder to enable highly compressed telemetry of autonomous underwater vehicle (AUV) position vectors. This system was analyzed on experimental data and implemented on a fielded vehicle. Using an adaptive probability distribution in combination with either of two state observer models, greater than 90% compression, relative to a 32-bit integer baseline, was achieved. The second approach is "disruptive," as it changes the vehicle's course to effect an improvement in the communications channel. A hybrid data- and model-based autonomous environmental adaptation framework is presented which allows autonomous underwater vehicles (AUVs) with acoustic sensors to follow a path which optimizes their ability to maintain connectivity with an acoustic contact for optimal sensing or communication. / by Toby Edwin Schneider. / Ph.D.

Thesis (Ph. D.)--Joint Program in Oceanography/Applied Ocean Science and Engineering (Massachusetts Institute of Technology, Dept. of Electrical Engineering and Computer Science; and the Woods Hole Oceanographic Institution), 2011. / Cataloged from PDF version of thesis. / Includes bibliographical references (p. 203-215). / Underwater wireless communication is quickly becoming a necessity for applications in ocean science, defense, and homeland security. Acoustics remains the only practical means of accomplishing long-range communication in the ocean. The acoustic communication channel is fraught with difficulties including limited available bandwidth, long delay-spread, time-variability, and Doppler spreading. These difficulties reduce the reliability of the communication system and make high data-rate communication challenging. Adaptive decision feedback equalization is a common method to compensate for distortions introduced by the underwater acoustic channel. Limited work has been done thus far to introduce the physics of the underwater channel into improving and better understanding the operation of a decision feedback equalizer. This thesis examines how to use physical models to improve the reliability and reduce the computational complexity of the decision feedback equalizer. The specific topics covered by this work are: how to handle channel estimation errors for the time varying channel, how to use angular constraints imposed by the environment into an array receiver, what happens when there is a mismatch between the true channel order and the estimated channel order, and why there is a performance difference between the direct adaptation and channel estimation based methods for computing the equalizer coefficients. For each of these topics, algorithms are provided that help create a more robust equalizer with lower computational complexity for the underwater channel. / by Ballard J. S. Blair. / Ph.D.

Thesis (S.M. in Mechanical Engineering)--Joint Program in Ocean Engineering/Applied Ocean Physics and Engineering (Massachusetts Institute of Technology, Dept. of Mechanical Engineering; and the Woods Hole Oceanographic Institution), 2007. / Includes bibliographical references (p. 91-92). / Reducing the deleterious effect of Vortex Induced Vibrations (VIV) in marine risers is an important task for ocean engineers; and many competing factors exist in the design of VIV suppression devices. This thesis explores the experimental minimization of the drag force and the disruption of vortex formation by utilizing VIV suppression devices. Two series of tests are conducted-both utilizing separate testing designs. The first tests are the flexible cylinder experiments, detailed in Chapter 2, which determine the drag force and vibration amplitude of numerous, original testing configurations. The second series of tests are the rigid cylinder, PIV experiments, detailed in Chapter 3. These tests measure both the drag force on the cylinder and the oscillating component of the lift force, the latter of which is a good indication of vortex formation. The Chapter 3 tests also image the test section wake-providing helpful insight into the physical process of vortex formation. In brief, this thesis presents a detailed description and results of the two series of original VIV suppression tests. Many original configurations are tested, and the results are contained herein. / by David Emmanuel Farrell. / S.M.

Thesis (Ocean E)--Massachusetts Institute of Technology, Dept. of Ocean Engineering, 1980. / MICROFICHE COPY AVAILABLE IN ARCHIVES AND ENGINEERING. / Includes bibliographical references. / by Joseph Anthony Carnevale, Jr. / Ocean E

Thesis: Ph. D., Joint Program in Oceanography/Applied Ocean Science and Engineering (Massachusetts Institute of Technology, Department of Biology; and the Woods Hole Oceanographic Institution), 2018. / Cataloged from PDF version of thesis. / Includes bibliographical references. / Signaling pathways that respond to stress and sense nutrient availability are highly conserved throughout eukaryotes. In mammalian cells, these pathways have evolved to regulate immune responses, representing important therapeutic targets. Interestingly, components of these pathways can be found in plants, yeast and nematodes, where they also participate in response to abiotic and biotic stress. The Amino Acid Response (AAR) pathway, an ancient response to the cellular accumulation of uncharged tRNA, is part of the larger Integrated Stress Response (ISR) in mammals. The ISR consists of multiple branches, each one triggered by distinct stresses that produce phospho-eIF2x signal generation. Each ISR initiating stress results in a unique cellular response due to activation of both the ISR and additional parallel pathway(s) by the initiating stress, but, to date, no such alternate pathway has been identified for the AAR pathway. Despite its integral role in stress adaptation, the ISR has not been studied in early diverging animals. I have identified a highly conserved phosphorylation site in the protein eIF2a, the signature ISR effector, which allowed me to use a mammalian antibody to identify and characterize the ISR in the basal metazoan, Nematostella vectensis, revealing that the core components of the mammalian ISR were present over 550 million years ago in the common ancestor of cnidarians and bilaterians. Additionally, our lab has discovered a novel branch of the AAR pathway that regulates key tissue protective signals. Using evolutionary conservation of this pathway in model organisms, I have identified GCN1 as the branch point that links the signal generation components of the AAR pathway to downstream therapeutic effects. I then used transcriptomic and protein interaction analyses to begin to understand the scope of this pathway and identify key pathway regulators. / Funding for this research was provided by the National Science Foundation Graduate Research Fellowship Program, Allied Bristol Life Sciences (to Malcolm Whitman), the WHOI Academic Programs Office, and the WHOI Ocean Venture Fund / by Maja Lena Edenius. / Ph. D.