Thesis (Ph. D.)--Joint Program in Biological Oceanography (Massachusetts Institute of Technology, Dept. of Ocean Engineering; and, the Woods Hole Oceanographic Institution), 2004. / Includes bibliographical references (leaves 169-180). / Toxic algae are a growing concern in the marine environment. One unique marine diatom, Pseudo-nitzschia multiseries (Hasle) Hasle, produces the neurotoxin domoic acid, which is the cause of amnesic shellfish poisoning. The molecular characterization of this organism has been limited to date. Therefore, the focus of this thesis was to identify and initiate characterization of actively expressed genes that control cell growth and physiology in P. multiseries, with the specific goal of identifying genes that may play a significant role in toxin production. The first step in gene discovery was to establish a complementary DNA (cDNA) library and a database of expressed sequence tags (ESTs) for P. multiseries. 2552 cDNAs were sequenced, generating a set of 1955 unique contigs, of which 21% demonstrated significant similarity with known protein coding sequences. Among the genes identified by sequence similarity were several involved in photosynthetic pathways, including fucoxanthin-chlorophyll a/c light harvesting protein and a C4-specific pyruvate, orthophosphate dikinase. Several genes that may be involved in domoic acid synthesis were also revealed through sequence similarity, for example, glutamate dehydrogenase and 5-oxo-L-prolinase. In addition, the identification of sequences that appear novel to Pseudo-nitzschia may provide insight into unique aspects of Pseudo-nitzschia biology, such as toxin production. Genes whose expression patterns were correlated with toxin production were identified by hybridization to a microarray manufactured from 5376 cDNAs. 121 cDNAs, representing 12 unique cDNA contigs or non-redundant cDNAs, showed significantly increased expression levels in P. multiseries cell populations that were actively producing toxin. / (cont.) The up-regulated transcripts included cDNAs with sequence similarity to 3-carboxymuconate cyclase, phosphoenolpyruvate carboxykinase, an amino acid transporter, a small heat shock protein, a long- chain fatty acid Co-A ligase, and an aldo/keto reductase. These results provide a framework for investigating the control of toxin production in P. multiseries. These transcripts may also be useful in ecological field studies in which they may serve as signatures of toxin production. Prospects for further application of molecular genetic technology to the understanding of the physiology and ecology of P. multiseries is discussed. / by Katie Rose Boissonneault. / Ph.D.

Thesis (S.M.)--Joint Program in Biological Oceanography (Massachusetts Institute of Technology, Dept. of Biology; and the Woods Hole Oceanographic Institution), 2010. / 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. 125-127). / In this thesis, I expand a spatially-explicit bioeconomic fishery model to include the negative effects of fishing effort on habitat quality. I consider two forms of effort driven habitat damage: First, fishing effort may directly increase individual mortality rates. Second, fishing effort may increase competition between individuals, thereby increasing density-dependent mortality rates. I then optimize effort distribution and fish stock density according to three management cases: (1) a sole owner, with jurisdiction over the entire fishery, who seeks to maximize profit by optimizing effort distribution; (2) a manager with limited control of effort and stock distributions, who seeks to maximize tax revenue by setting the length of a single, central reserve and a uniform tax per unit effort outside it; and (3) a manager with even more limited enforcement power, who can only set a tax per unit effort everywhere in the habitat space. I demonstrate that the economic efficiency of reserves depends upon model parameterization. In particular, reserves are most likely to increase profit (or tax revenue) when density-dependent fish mortality rates are affected. Interestingly, for large habitats that are sufficiently sensitive to density-dependent fish mortality effects, reserve networks (alternating fished and unshed areas of fixed periodicity) emerge. These results suggest that spatial forms of management which include marine reserves may enable signicant economic gains over nonspatial management strategies, in addition to the well-established conservation benefits provided by closed areas. / by Holly Villacorta Moeller. / S.M.

Thesis (Ph. D.)--Joint Program in Oceanography (Massachusetts Institute of Technology, Dept. of Biology; and the Woods Hole Oceanographic Institution), 2009. / This electronic version was submitted by the student author. The certified thesis is available in the Institute Archives and Special Collections. / "June 2009." / Includes bibliographical references. / Marine cyanobacteria in the genus Synechococcus are widely distributed and contribute significantly to global primary productivity. In many parts of the ocean their growth is limited by a lack of iron, an essential nutrient that is virtually insoluble in seawater. To overcome this, Synechococcus have evolved a number of strategies to acquire iron. Gene distribution, metagenomics and a novel immunological flow cytometry assay in the Costa Rica Upwelling Dome were used to estimate the importance of Fe stress. Genomic and metagenomic measures suggest that iron limitation is, paradoxically, more severe in coastal and upwelling areas than in the open ocean, where iron is less abundant. A serological assay found significant differences in the vertical distribution of the Fe stress protein IdiA over just a few meters. Despite average surface ocean iron concentrations of just 0.07 nM, most marine oligotrophic cyanobacteria lack iron-binding siderophores that are present in many heterotrophic marine bacteria. Siderophores are widely distributed in the surface ocean and compose an important portion of the pool of natural ligands that bind >99% of all soluble Fe. In bottle incubations from the Sargasso Sea we found the addition of Fe complexed to an excess of the siderophore desferrioxamine B (DFB) limited Synechococcus growth and stimulated the growth of heterotrophic bacteria in a concentration dependent manner. / (cont.) Laboratory work revealed that excess DFB decreased Synechococcus growth beyond Fe-limited controls at concentrations as low as 20-40 nM. The inhibition was aggravated by light but it could be reversed by the addition of Fe. The DFB inhibition could not be explained by thermodynamic or kinetic models of Fe' or co-limitation with other metals. DFB may interact with some aspect of cellular physiology to directly inhibit cyanobacterial growth. / by Adam R. Rivers. / Ph.D.

Thesis (Ph. D.)--Joint Program in Oceanography (Massachusetts Institute of Technology, Dept. of Civil and Environmental Engineering, and the Woods Hole Oceanographic Institution), 2002. / Vita. / Includes bibliographical references. / Photochemical transformations of chromophoric dissolved organic matter (CDOM) are one of the principal processes controlling its fate in coastal waters. The photochemical decomposition of CDOM leads to the formation of a variety of biologically available carbon substrates. Photomineralization of CDOM to dissolved inorganic carbon may constitute a significant flux in the global carbon cycle. Photoreactions ultimately lead to the destruction of the chromophores and hence to the loss of absorption and fluorescence (bleaching), thus acting as a sink for CDOM. Photodecomposition may proceed both via direct photochemical reactions, following absorption of photons by CDOM, or via indirect processes, involving DOM reactions with photochemically generated intermediates such as reactive oxygen species (ROS). The reactions of CDOM with two important ROS, superoxide (02-) and hydroxyl radical (OH), have different consequences. Superoxide reactions with CDOM did not appear to degrade the CDOM. Instead, CDOM catalysed the dismutation of 02- to 02 and HOOH. This reactivity has the effect of limiting the steady-state concentration of 02- in most coastal waters. In contrast, reactions of CDOM with radiolytically produced OH formed CO2 and several low molecular weight carboxylic acids, as well as bleached both the absorption and fluorescence at slow rates. These reactions did not increase the bioavailability of this material to a microbial consortium. Both direct and indirect photochemical processes are expected to be accelerated by the presence of iron. / (cont.) However, addition of iron to several coastal seawater samples neither increased the rate of photobleaching nor the apparent quantum yield (AQY) of CO. Similarly, the addition of the siderophore desferrioxamine B did not change the photobleaching rates or the CO AQYs. The addition of 2[mu]M Fe to solutions of Suwannee River Fulvic Acid did not increase the photobleaching rates. In combination with prior results, these findings suggest that indirect photoreactions do not increase the photobleaching rates of CDOM in coastal systems. A model of CDOM photobleaching based on the assumption of negligible indirect photobleaching processes and multiple non-interacting chromophores was created utilizing photobleaching data produced with monochromatic light to calculate the spectra and exponential decay rates of independent components. These components were then used to calculate bleaching spectra for broadband light and compared with actual bleaching spectra. / by Jared Verrill Goldstone. / Ph.D.

Thesis (Ph. D.)--Joint Program in Oceanography (Massachusetts Institute of Technology, Dept. of Biology; and Woods Hole Oceanographic Institution), 2000. / Includes bibliographical references. / The marine cyanobacteria Synechococcus and Prochlorococcus are important primary producers in oligotrophic oceans. The abundance and cell division rates of these cyanobacteria can be influenced by trace metals such as iron and copper. Iron is an essential trace metal that is present in the high nutrient, low chlorophyll waters of the equatorial Pacific in extremely low concentrations. When these waters were enriched with iron, Prochlorococcus chlorophyll fluorescence per cell and cell size increased. Cell division rates doubled inside the iron enriched patch and reached two divisions per day in bottle incubations with additional iron, indicating that Prochlorococcus were iron limited. However, cell numbers remained constant because mortality rates nearly doubled after the addition of iron and essentially matched the increases in cell division rate. Trace metals can also be present in toxic, rather than limiting concentrations. Copper is an essential trace element that is toxic to cyanobacteria in pM quantities. In stratified water columns in the Sargasso Sea, free Cu2+ concentrations are high in the mixed layer (up to 6pM) and most of the Prochlorococcus population is located below the thermocline where free Cu2+ concentrations are lower. The distribution of Synechococcus is more uniform with depth. Prochlorococcus isolates were more sensitive to copper than Synechococcus, but members of the low chi BIA (high light adapted) ecotype were less sensitive than strains with high chi BIA ratios (low light adapted). In the field, the in situ concentration of free Cu2+ had a strong effect on the copper sensitivity of Prochlorococcus. Net growth rates were substantially reduced when Prochlorococcus from environments where the in situ free Cu2+ was low (deep mixed layers and below the thermocline in stratified water) were exposed to copper. Prochlorococcus in shallow mixed layers where in situ Cu2 + was high were less sensitive to copper and may have been members of the copper resistant low chi B/ A ecotype. Synechococcus were relatively copper resistant across a range of environments. These data are consistent with the hypothesis that ambient copper levels may influence the relative abundance of Prochlorococcus and Synechococcus in the Sargasso Sea. / by Elizabeth Lowell Mann. / Ph.D.

Thesis (S.M.)--Joint Program in Chemical Oceanography (Massachusetts Institute of Technology, Dept. of Earth, Atmospheric, and Planetary Sciences; and the Woods Hole Oceanographic Institution), 2004. / Includes bibliographical references. / Paleoclimate records with sufficient length and temporal resolution to study the occurrence and causal mechanisms of abrupt climate change are exceedingly rare. Rapidly deposited ocean sediments provide the best archive for studying these events through geologic time, but such sites in the open ocean are limited to sediment drift deposits such as the Bermuda Rise in the northwest Atlantic. Using multiple climate proxies in a single core is becoming more common in high-resolution paleoclimate investigations, but a major potential concern for this approach arises from the possibility that the fine fraction of sediment (< 63 [micro]m), and the climate proxies within it, may represent conditions far from the deposition site. We hypothesize that hydrogen isotope ratios of alkenones, a class of lipids from phytoplankton, may provide insight into the source of fine fraction sediment. Because of their restricted sources, broad geographic distribution, and excellent preservation properties, alkenones are of particular interest in the emerging field of' compound-specific hydrogen isotopic analysis, and the sedimentary abundances, extents of unsaturations, and isotopic compositions of alkenones provide quantitative and near-continuous records. We isolated alkenones from cultured unicellular algae (haptophyte Emiliania huxleyi), surface ocean particulate material, and open ocean sediments to determine the extent and variability of hydrogen isotopic fractionation in the di-, tri-, and tetraunsaturated C₃₇ compounds. We then compared the [delta]D of the alkenones in surface sediments between the Bermuda Rise and the Scotian Margin above which a large ([approximately]20%) [delta]D gradient exists. We determined the fractionation between alkenones / (cont.) from suspended particulate samples and the water in which the phytoplanton lived, and examined the variability of alkenone 6D during key climate transitions at the Bermuda Rise. / by Amy C. Englebrecht. / S.M.

Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Earth, Atmospheric and Planetary Sciences and the Woods Hole Oceanographic Institution, 1986. / Microfiche copy available in Archives and Science. / Vita. / Bibliography: leaves 271-297. / by Bruce J. Brownawell. / Ph.D.

Thesis (Ph. D.)--Joint Program in Oceanographic Engineering (Massachusetts Institute of Technology, Dept. of Civil Engineering; and the Woods Hole Oceanographic Institution), 1989. / Includes bibliographical references (leaves 140-145). / The relationship between depth-averaged velocity and bottom stress for wind-driven flow in unstratified coastal waters is examined here. The adequacy of traditional linear and quadratic drag laws is addressed by comparison with a 2 1/2-D model. A 2 1/2-D model is one in which a simplified 1-D depth-resolving model (DRM) is used to provide an estimate of the relationship between the flow and bottom stress at each grid point of a depth-averaged model (DAM). Bottom stress information is passed from the DRM to the DAM in the form of drag tensor with two components: one which scales the flow and one which rotates it. This eliminates the problem of traditional drag laws requiring the flow and bottom stress to be collinear. In addition, the drag tensor field is updated periodically so that the relationship between the velocity and bottom stress can be time-dependent. However, simplifications in the 2 1/2-D model that render it computationally efficient also impose restrictions on the time-scale of resolvable processes. Basically, they must be much longer than the vertical diffusion time scale. Four progressively more complicated scenarios are investigated. The important factors governing the importance of bottom friction in each are found to be 1) non-dimensional surface Ekman depth ... is the surface shear velocity, f is the Coriolis parameter and h is the water depth 2) the non-dimensional bottom roughness, zo/h where zo is the roughness length and 3) the angle between the wind stress and the shoreline. Each has significant influence on the drag law. The drag tensor magnitude, r, and the drag tensor angle, 0 are functions of all three, while a drag tensor which scales with the square of the depth-averaged velocity has a magnitude, Cd, that only depends on zo/h. The choice of drag law is found to significantly affect the response of a domain. Spin up times and phase relationships vary between models. In general, the 2 1/2-D model responds more quickly than either a constant r or constant Cd model. Steady-state responses are also affected. The two most significant results are that failure to account for 0 in the drag law sometimes leads to substantial errors in estimating the sea surface height and to extremely poor resolution of cross-shore bottom stress. The latter implies that cross-shore near-bottom transport is essentially neglected by traditional DAMs. / by Harry Leonard Jenter, II. / Ph.D.

京都大学 / 0048 / 新制・課程博士 / 博士(理学) / 甲第18784号 / 理博第4042号 / 新制||理||1582(附属図書館) / 31735 / 京都大学大学院理学研究科物理学・宇宙物理学専攻 / (主査)准教授 中 暢子, 教授 田中 耕一郎, 教授 金光 義彦 / 学位規則第4条第1項該当 / Doctor of Science / Kyoto University / DGAM

京都大学 / 0048 / 新制・課程博士 / 博士(工学) / 甲第20381号 / 工博第4318号 / 新制||工||1669(附属図書館) / 京都大学大学院工学研究科電子工学専攻 / (主査)教授 木本 恒暢, 教授 白石 誠司, 准教授 浅野 卓 / 学位規則第4条第1項該当 / Doctor of Philosophy (Engineering) / Kyoto University / DGAM