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: 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.

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. / Cataloged from PDF version of thesis. / Includes bibliographical references (p. 158-160). / Quantifying uncertainty and error bounds is a key outstanding challenge in ocean state estimation and climate research. It is particularly difficult due to the large dimensionality of this nonlinear estimation problem and the number of uncertain variables involved. The "Estimating the Circulation and Climate of the Oceans" (ECCO) consortium has developed a scalable system for dynamically consistent estimation of global time-evolving ocean state by optimal combination of ocean general circulation model (GCM) with diverse ocean observations. The estimation system is based on the "adjoint method" solution of an unconstrained least-squares optimization problem formulated with the method of Lagrange multipliers for fitting the dynamical ocean model to observations. The dynamical consistency requirement of ocean state estimation necessitates this approach over sequential data assimilation and reanalysis smoothing techniques. In addition, it is computationally advantageous because calculation and storage of large covariance matrices is not required. However, this is also a drawback of the adjoint method, which lacks a native formalism for error propagation and quantification of assimilated uncertainty. The objective of this dissertation is to resolve that limitation by developing a feasible computational methodology for uncertainty analysis in dynamically consistent state estimation, applicable to the large dimensionality of global ocean models. Hessian (second derivative-based) methodology is developed for Uncertainty Quantification (UQ) in large-scale ocean state estimation, extending the gradient-based adjoint method to employ the second order geometry information of the model-data misfit function in a high-dimensional control space. Large error covariance matrices are evaluated by inverting the Hessian matrix with the developed scalable matrix-free numerical linear algebra algorithms. Hessian-vector product and Jacobian derivative codes of the MIT general circulation model (MITgcm) are generated by means of algorithmic differentiation (AD). Computational complexity of the Hessian code is reduced by tangent linear differentiation of the adjoint code, which preserves the speedup of adjoint checkpointing schemes in the second derivative calculation. A Lanczos algorithm is applied for extracting the leading rank eigenvectors and eigenvalues of the Hessian matrix. The eigenvectors represent the constrained uncertainty patterns. The inverse eigenvalues are the corresponding uncertainties. The dimensionality of UQ calculations is reduced by eliminating the uncertainty null-space unconstrained by the supplied observations. Inverse and forward uncertainty propagation schemes are designed for assimilating observation and control variable uncertainties, and for projecting these uncertainties onto oceanographic target quantities. Two versions of these schemes are developed: one evaluates reduction of prior uncertainties, while another does not require prior assumptions. The analysis of uncertainty propagation in the ocean model is time-resolving. It captures the dynamics of uncertainty evolution and reveals transient and stationary uncertainty regimes. The system is applied to quantifying uncertainties of Antarctic Circumpolar Current (ACC) transport in a global barotropic configuration of the MITgcm. The model is constrained by synthetic observations of sea surface height and velocities. The control space consists of two-dimensional maps of initial and boundary conditions and model parameters. The size of the Hessian matrix is 0(1010) elements, which would require 0(60GB) of uncompressed storage. It is demonstrated how the choice of observations and their geographic coverage determines the reduction in uncertainties of the estimated transport. The system also yields information on how well the control fields are constrained by the observations. The effects of controls uncertainty reduction due to decrease of diagonal covariance terms are compared to dynamical coupling of controls through off-diagonal covariance terms. The correlations of controls introduced by observation uncertainty assimilation are found to dominate the reduction of uncertainty of transport. An idealized analytical model of ACC guides a detailed time-resolving understanding of uncertainty dynamics. Keywords: Adjoint model uncertainty, sensitivity, posterior error reduction, reduced rank Hessian matrix, Automatic Differentiation, ocean state estimation, barotropic model, Drake Passage transport. / by Alexander G. Kalmikov. / Ph.D.

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), 2013. / Cataloged from PDF version of thesis. / Includes bibliographical references. / Marine phytoplankton are the principal producers of oceanic dissolved organic matter (DOM), the organic substrate responsible for secondary production by heterotrophic microbes in the sea. Despite the importance of DOM in marine food webs, details regarding how marine microbes cycle DOM are limited, and few definitive connections have been made between specific producers and consumers. Consumption is thought to depend on the source of the DOM as well as the identity of the consumer; however, it remains unclear how phytoplankton diversity and DOM composition are related, and the metabolic pathways involved in the turnover of DOM by different microbial taxa are largely unknown. The motivation for this thesis is to examine the role of microbial diversity in determining the composition, lability, and physiological consumption of marine DOM. The chemical composition of DOM produced by marine phytoplankton was investigated at the molecular level using mass spectrometry. Results demonstrate that individual phytoplankton strains release a unique suite of organic compounds. Connections between DOM composition and the phylogenetic identity of the producing organism were identified on multiple levels, revealing a direct relationship between phytoplankton diversity and DOM composition. Phytoplankton-derived DOM was also employed in growth assays with oligotrophic bacterioplankton strains to examine effects on heterotrophic growth dynamics. Reproducible responses ranged from suppressed to enhanced growth rates and cell yields, and depended both on the identity of the heterotroph and the source of the DOM. Novel relationships between specific bacterioplankton types and DOM from known biological sources were found, and targets for additional studies on reactive DOM components were identified. The physiology of DOM consumption by a marine Oceanospirillales strain was studied using a combined transcriptomic and untargeted metabolomic approach. The transcriptional response of this bacterium to Prochlorococcus-derived DOM revealed an increase in anabolic processes related to metabolism of carboxylic acids and glucosides, increased gene expression related to proteorhodopsin-based phototrophy, and decreased gene expression related to motility. Putative identification of compounds present in Prochlorococcus-derived DOM supported these responses. Collectively, these findings highlight the potential for linking detailed chemical analyses of labile DOM from a known biological source with bacterioplankton diversity and physiology. / by Jamie William Becker. / 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. / Blooms of toxic species within the algal dinoflagellate species complex Alexandrium tamarense may cause Paralytic Shellfish Poisoning, a significant and growing environmental threat worldwide. However, blooms of closely related nontoxic A. tamarense also occur, sometimes in close geographical proximity to toxic blooms. This thesis explores the interactions between toxic and nontoxic blooms by examining sexual crosses between each of five ribosomal clades within the A. tamarense complex (termed Groups I-V). Several lines of evidence argue that these clades represent separate species. Particular emphasis was given to interactions between toxic Group I and nontoxic Group III species because they are among the most closely related A. tamarense clades and because they share a natural range boundary in several parts of the world. Interspecies hybridization appeared widespread between different clades and between geographically dispersed isolates. However, subsequent germination studies of hypnozygotes produced from combinations of Group I and Group III clones failed to yield new vegetative cultures in multiple trials. The possibility that these hypnozygotes were actually inbred (i.e. the result of pairs of only Group I or only Group III gametes) was considered and rejected using a nested PCR assay that was developed to assess the parentage of individual cysts. The assay was also suitable for analyzing cysts collected from the field and was applied to individual cysts collected from Belfast Lough, an area where both Group I and Group III blooms were known to occur. Two Group I/Group III hybrids were detected in fourteen successful assays from the Belfast sample, showing that hybridization does occur in nature. These findings have several important implications. First, the failure of Group I/Group III hybrids to produce new vegetative cultures serves as a proof that the A. tamarense clades represent cryptic species because they are unable to produce genetic intermediates. Second, the presence of hybrid cysts in Belfast Lough indicates ongoing displacement of a nontoxic population by a toxic one (or vice versa) in that region. Third, the inviability of toxic/nontoxic hybrids suggests a remediation strategy whereby the recurrence of toxic A. tamarense blooms might be combated through the introduction of nontoxic cells. The results from these experiments also highlighted several shortfalls in our understanding of the mechanisms governing sexual compatibility between clones and also our ability to replicate these organisms' sexual cycle in the laboratory. Two initiatives were begun with the ultimate goal of better characterizing sexual processes in natural populations. The first initiative was the application of an imaging flow cytometer to detect sexual events in natural blooms. An existing instrument, the Imaging FlowCytobot, was adapted to positively identify A. tamarense Group I cells in mixed species assemblages and measure cell DNA content. A collection of four samples were analyzed, three from the development and decline of a local Group I bloom and one from a Group I red tide that occurred near Portsmouth, NH and led to a major deposition of new cysts in the southern Gulf of Maine. Several unanticipated patterns were revealed including the discovery of a persistent layer of cells with 2c DNA content near the surface and disproportionately high rates of infection by an Amoebophrya sp. parasite in large A. tamarense planozygotes. The second initiative was the application of high throughput Illumina sequencing to define the transcriptomes of toxic Group I, nontoxic Group III, and toxic Group IV clones. Additional steps were taken to isolate RNA and prepare a cDNA library from a natural sample of Group I hypnozygotes. The applications for these data are expected to be extensive and include the discovery of sexual biomarkers and further characterization of the differences between toxic and nontoxic A. tamarense species. Preliminary results from the sequencing of these libraries and their initial assembly are described. / by Michael L. Brosnahan. / 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), 2016. / Cataloged from PDF version of thesis. / Includes bibliographical references. / The role of oxylipins in ocean biogeochemistry was investigated using microcosm amendment experiments, environmental lipidomics, and culture based studies. Oxylipins are a bioactive class of secondary metabolites produced by diatoms and other eukaryotic phytoplankton. Previous research has focused mainly on one class of oxylipins, polyunsaturated aldehydes (PUAs), and their impacts on copepods. And few studies have looked at the impacts of oxylipins in situ. Here I show that oxylipins have the potential to impact carbon flux attenuation, oxylipin production in situ is linked to diatom bloom decline and viruses, and oxylipins deter microzooplankton grazing. Sinking particles collected in the North Atlantic were determined to be hot spots for PUAs with concentrations in the micromolar range. Natural particle associated microbial communities exhibited a dose dependent response to PUAs. Stimulatory PUA concentrations ranged from 1-10 ptM, resulting in enhanced remineralization of organic matter by particle associated microbes. Thus, PUAs produced during bloom decline may lead to greater flux attenuation and nutrient recycling. A novel lipidomics approach was applied along a cruise track in the California Coastal System revealing that canonical diatom free fatty acids and oxylipins dominated the dissolved lipidome and oxylipin abundance was correlated with diatom bloom demise as assessed by phaeophytin and biogenic Si. RNA viruses were likely the cause of diatom bloom demise and may have induced oxylipin production. The link between viruses and oxylipins represents a new infochemical signaling pathway in the ocean. Many oxylipins that are novel to the marine environment were also identified. The dissolved lipidome was sampled during grazing experiments with the microzooplankton grazer Oxyrrhis marina and both wild type Phaeodactylum tricornutum and a chronically stressed, transgenic strain (PtNOA). Grazing was suppressed in the PtNOA treatments compared to the WT, likely due to upregulation of small unknown lipophilic molecules. This suggests that cellular stress and oxylipin production may deter microzooplankton grazing in the environment potentially altering the transfer of energy through the microbial food web. By employing interdisciplinary approaches, we have learned that oxylipins production in situ is linked to bloom decline and the bioactivity of these compounds has significant implications for ocean biogeochemical cycles. / by Bethanie Rachele Edwards. / 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), 2016. / Cataloged from PDF version of thesis. / Includes bibliographical references. / Ocean waves are a powerful sediment transport mechanism in the coastal zone. This thesis investigates how waves shape deltaic landforms and how small scale river mouth processes affect large-scale delta morphology. I have developed and applied models of plan-view delta shape and their channel dynamics. Simple parameterizations and key insights from these models have allowed us to transcend spatial scales from river mouths to delta plains and make morphologic predictions around the globe for every delta on Earth. I have applied models of delta morphology to backtrack the late Holocene evolution of the Ebro River delta in Spain and estimate timescales and magnitude of past climate change and human impacts. Currently, many deltas around the world face large sediment deficits because of river damming. I model deltaic response to reductions in sediment load and offer frameworks to predict future deltaic change in these dynamic and threatened coastal regions. / by Jaap H. Nienhuis / 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), 2016. / 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. / This thesis examines the structure of Pacific oceanic lithosphere that has been modified by post-formation magmatism in order to better understand the processes of secondary magmatic evolution of the lithosphere, which can have global-scale implications for oceanic and atmospheric chemistry. In the western Pacific, widespread Cretaceous magmatism has modified oceanic lithosphere over hundreds of millions of square kilometers. Seismic models of the upper crust from within the Jurassic Quiet Zone and the crust and upper mantle near the Mariana Trench reveal crust that is locally thickened via focused extrusive volcanism and crust that is modestly but uniformly thickened over broad regions. These distinct modes of magmatic emplacement suggest the operation of both focused and diffuse modes of melt transport through the lithosphere. Analysis of seismic observations from Guaymas Basin, in the Gulf of California, endeavor to advance our understanding of sill-driven alteration of sediments, an important consequence of secondary magmatism. We show that seismically imaged physical disruption to sediments due to igneous sill intrusion can be related to changes in sediment physical properties that reflect alteration processes. We also show how sill thickness can be estimated, enabling alteration intensity to be related to sill thickness in a variety of settings. / by Helen Shao-Hwa Feng. / 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), 2005. / Handwritten on CDROMS: v. [1]. Appendix, histological images -- v. [2]. CT images. -- Table of contents refers to CDROMS as: Appendix and CT and histological images for all species, attached CD) / Includes bibliographical references (v. 2, leaves 216-247). / In this thesis, the relationships of olfactory sensitivity to three biological variables were tested. The sensitivity of a marine mammal, the sea otter (Enhydra lutris) was measured in order to determine whether a marine lifestyle results in impaired olfaction. The effect of dietary relevance on sensitivity to specific odorants was evaluated. Finally, a new morphometric model of olfactory uptake efficiency was developed and tested against behavioral measurements of olfactory sensitivity in twelve mammalian species from five orders. Olfactory thresholds were obtained for the first time from two sea otters for seven odorant compounds from various natural sources. Otters were trained using operant conditioning to participate in direct behavioral testing. Sea otter olfactory sensitivity was comparable to that of previously studied terrestrial mammals. The incidence of an odorant in the diet of the olfactor was found to influence specific sensitivity to that compound but to varying degrees among different mammalian orders. Nasal cavity specimens were measured using radiologic (CT scan) and histologic (light microscopy) techniques. Surface areas and volumes of the nasal cavity were used to calculate the Olfactory Uptake Efficiency (OUE). OUE is significantly related to olfactory bulb volume. A possible relationship was found between OUE and general olfactory sensitivity. / by Jennifer Hammock. / Ph.D.