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), 2002. / Includes bibliographical references (p. 130-138). / Mark-recapture analysis of populations is becoming an important tool in population biology. Mark-recapture methods can be used to estimate transition probabilities among life-stages from capture histories of marked individuals for which stages can be determined at each sampling occasion. This method is called a multi-stage mark-recapture (MSMR) method. In this thesis, I describe advances I made in the MSMR method and present analyses that apply this method to actual data. The advances I made in the MSMR method are motivated by a need to provide a link between mark-recapture data and demographic models such as matrix population models and integrodifference models. I resolve some issues that are commonly encountered during sampling, such as the fact that the sex or life-stage of some individuals is unknown during some sampling occasions and that individuals become unobservable during some life-stages. I introduce a stage-structure that permits simple conversion of estimated transition probabilities into a matrix population model. I describe an algorithm to simplify programming for parameter estimation. I also introduce a method to estimate the distribution of dispersal displacements (a dispersal kernel) from mark-recapture data. I apply some of the methods described above to data of the North Atlantic right whale (Eubalaena glacialis). The right whales are considered one of the most endangered mammals. The current population size is about 300 in the northwestern Atlantic, and the number is declining. I applied the multi-stage mark-recapture statistics to the 17-year in- dividual sighting history data. / (cont.) Using the estimated transition probabilities, I constructed a population projection matrix, which was used for further demographic analyses. I found that the population was slowly increasing in 1980, but it started to decline slowly around 1992. I show that (1) this change was caused by increased mortality of females that have just given birth, (2) protecting two females a year from the deaths is enough to prevent the declining trend, and (3) demographic stochasticity is a more important factor influencing their long-term viability than environmental stochasticity. / by Masami Fujiwara. / 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), 2003. / 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. 299-310). / Inertial terms dominate the single-gyre ocean model and prevent western-intensification when the viscosity is small. This occurs long before the oceanically-appropriate parameter range. It is demonstrated here that the circulation is controlled if a mechanism for ultimate removal of vorticity exists, even if it is active only in a narrow region near the boundary. Vorticity removal is modeled here as a viscosity enhanced very near the solid boundaries to roughly parameterize missing boundary physics like topographic interaction and three dimensional turbulence over the shelf. This boundary-enhanced viscosity allows western-intensified mean flows even when the inertial boundary width is much wider than the frictional region because eddies flux vorticity from within the interior streamlines to the frictional region for removal. Using boundary-enhanced viscosity, western-intensified calculations are possible with lower interior viscosity than in previous studies. Interesting behaviors result: a boundary-layer balance novel to the model, calculations with promise for eddy param- eterization, eddy-driven gyres rotating opposite the wind, and temporal complexity including basin resonances. / (cont.) I also demonstrate that multiple-gyre calculations have weaker mean circulation than single-gyres with the same viscosity and subtropical forcing. Despite traditional understanding, almost no inter-gyre flux occurs if no-slip boundary conditions are used. The inter-gyre eddy flux is in control only with exactly symmetric gyres and free slip boundaries. Even without the inter-gyre flux, the multiple-gyre circulation is weak because of sinuous instabilities on the jet which are not present in the single-gyre model. These modes efficiently flux vorticity to the boundary and reduce the circulation without an inter-gyre flux, postponing inertial domination to much smaller viscosities. / by Baylor Fix-Kemper. / Ph.D.

A maturação em tonéis de carvalho é uma prática importante amplamente empregada na produção de uma bebida de alta qualidade. Porém, apesar da biodiversidade no Brasil, o envelhecimento da cachaça em tonéis de madeira não é uma prática comum. Os tonéis de carvalho são usualmente mais empregados para o processo de maturação da cachaça. Estes tonéis foram usados previamente por produtores para maturação de vinho, conhaque, e envelhecimento de whisky na Europa e América do Norte. Os apontamentos de alternativa para o carvalho apresentados neste trabalho reportam o perfil fenólico dos extratos de cachaça de espécies de madeira brasileiras em comparação com o carvalho. O método de HPLC foi usado para a análise simultânea de 16 compostos fenólicos de relevância para o sabor e aroma de bebidas envelhecidas. As separações cromatográficas foram realizadas usando uma coluna Shimadzu de C18 (2 mm x 3μm x 250 mm) com gradiente de eluição. As eluições dos compostos foram monitoradas em seu máximo de absorção especifico através de um espectrofotômetro de arranjo de diodo com exceção de catequina e epicatequina, as quais foram monitoradas usando um detector espectrofluorométrico com emissão fixada a 280 nm e excitação a 313 nm. Os 16 compostos fenólicos seguintes foram analisados: (ácido gálico, (+)catequina, ácido vanílico, vanilina, (-)epicatequina, ácido seríngico, seringaldeído, escopoletina, cumarina, sinapaldeído, coniferaldeído, trans-resveratrol, ácido elágico, mirecetina, quercetina e o eugenol) em extratos de cachaça de diferentes espécies de madeira. Os principais compostos fenólicos identificados e quantificados foram: ácido de vanílico (média 0.18 mg/L), seringaldeído (média 0.048 mg/L) e vanilina (média 0.47 mg/L). A cumarina apresenta maior concentração nos extratos de madeira brasileira do que nos extratos de carvalho nos níveis do composto supracitado. Nas amostras de carvalho o teor médio foi de 0,0054 mg/L e nas espécies de madeira brasileiras o teor médio foi de 1,2 mg/L. Também foi analisada a presença de compostos fenólicos em cachaça, rum e whisky onde o seringaldeído e a vanilina foram os compostos majoritários. / Maturation in oak barrels is an important widely spread pratice in the production of a high quality spirit. However, despite the biodiversity in Brazil, the cachaça aging in wodden barrels is not a commun pratice. The use mostly imported oak barrels for the cachaça maturation process. This producers barrel had been usual maturation previously for wine, cognac, and whisky aging in Europe and North America. The aiming to present alternative to oak the present work report the phenolics profile of cachaça extracts of Brazilian wood species in comparation with oak. A HPLC method was used for the simultaneous analysis of 16 phenolic compounds of importance for the flavor and aroma of aged spirits. The chromatographic separations were carried out using a Shimadzu C18 column (2 mm x 3μm x 250 mm) with for elution gradient. The eluting compounds were monitored at their specific maximum of absorption through a diode array spectrophotometric detector with exception of catechin and epicatechin which were probed using a spectrofluorometric detector with emission set at 280 nm and excitation at 313 nm. Follow 16 phenolics compounds have been analisys: ( gallic acid, (+)cathechin, vanillic acid, vanilin, (-)epicathechin, seringic acid, seringaldehyde, escopoletin, coumarin, sinapaldehyde, coniferaldehyde, trans-resveratrol, ellagic acid, mirecetin, quercetin and the eugenol) in cachaça extracts of different wood species. The major phenolic compounds identified and quantified are vanillc acid (medium 0.18 mg/L), seringaldehyde (medium 0.048 mg/L) and vanillin (medium 0.47 mg/L). The coumarin is on higher concentration in Brazilian wood extract then in oak the levels of the supracited compounds. In oak samples with medium values of 0.0054 mg/L and 1.2 mg/L for oak and Brazilian wood species respectively. Furthemore, the presence of phenolics were Abstract IQSC-USP iv investiged in cachaça, rum, and whisky revealing seringaldehyde and vanillin as the major components.

Thesis (Ph. D.)--Joint Program in Applied Ocean Physics and Engineering (Massachusetts Institute of Technology, Dept. of Ocean Engineering; and the Woods Hole Oceanographic Institution), 2000. / Includes bibliographical references (p. 255-264). / by Jason I. Gobat. / Ph.D.

Thesis (Ph. D.)--Joint Program in Biological Oceanography (Massachusetts Institute of Technology, Dept. of Biology; and the Woods Hole Oceanographic Institution), 1998. / "August, 1998." / Includes bibliographical references (p. 219-254). / Two cytochrome P4501A-dependent mechanisms of aryl hydrocarbon receptor (AhR) agonist toxicity were examined in the marine teleost scup (Stenotomus chrysops), alteration of arachidonic acid (AA) metabolism and production of reactive oxygen species (ROS). In scup hepatic microsomes, cytochrome P450s including CYP1A and CYP2B-like proteins catalyzed regioselective metabolism of AA to eicosatrienoic and hydroxyeicosatetraenoic acids. Benzo[a]pyrene (BP) treatment induced liver microsomal AA metabolism, but that effect varied with season. Endogenous AA epoxides were recovered from scup liver, heart, and kidney, and their composition in the liver was altered by treatment with BP or 2,3,7,8-tetrachlorodibenzo-p-dioxin. In scup and mammals, the formation of ROS was stimulated by binding of 3,3',4,4-tetrachlorobiphenyl (TCB) to CYP1A, apparently CYP1A1. Attack of that ROS inactivated scup CYP1A. ROS release and inactivation of CYPlA were stimulated only by substrates of CYP1A that are slowly metabolized. In vivo, 3,3',4,4',5- pentachlorobiphenyl (PeCB) potently induced CYPlA mRNA, protein and catalytic activity at low doses (0.01-0.1 mg/kg), suppressed induction of CYPlA protein and catalytic activity at a high dose (1 mg/kg) and transiently induced oxidative stress in scup liver. The suppression of CYP1A induction was organ-dependent, with hepatic CYP1A being most susceptible to inactivation. The results suggest that ROS could be involved in the in vivo suppression of scup liver CYP1A by planar halogenated aromatic hydrocarbons. The reactive oxygen sensitive transcription factor, nuclear factor-KB (NF-KB), was characterized in scup. An NF-KB consensus binding sequence bound specifically to 3 proteins in scup liver, heart and kidney. One protein was recognized by an antibody to mammalian p50. Injection alone appeared to activate NF-KB. BP did not increase the activation of NF-KB, and PeCB activated NF-KB in only 1 of 2 experiments. Last, CYP1A induction in endothelial cells of the American eel (Anguilla rostrata), a site which may be particularly susceptible to alterations in AA metabolism and ROS production, was described. Eel liver CYPlA responded to BP, 13-naphthoflavone and TCB in a dose-dependent fashion, and induction was correlated with hepatic inducer concentration. Endothelial CYP1A was inducible in a number of organs and was metabolically active. In the rete mirabile, penetration of endothelial CYP1A induction increased with increasing dose of AhR agonists, corresponding with an increase in inducer concentration. A transition from endothelial to epithelial staining occurred in the gill, heart and kidney at high inducer doses. / by Jennifer Joy Schlezinger. / Ph.D.

Thesis (Ph. D.)--Joint Program in Biological Oceanography (Massachusetts Institute of Technology, Dept. of Ocean Engineering; and the Woods Hole Oceanographic Institution), February 2001. / Includes bibliographical references. / by Nicole Jane Poulton. / Ph.D.

Thesis (S.M.)--Joint Program in Biological Oceanography (Massachusetts Institute of Technology, Dept. of Biology; and the Woods Hole Oceanographic Institution), 2011. / Cataloged from PDF version of thesis. / Includes bibliographical references (p. 27-33). / The colonization dynamics and life histories of pioneer species are vital components in understanding the early succession of nascent hydrothermal vents. The reproductive ecology of pioneer species at deep-sea hydrothermal vents may provide insight into their dispersal, population connectivity, and ability to colonize after disturbance. An opportunity to study the reproductive traits of two pioneer gastropod species, Ctenopelta porfera and Lepetodrilus tevnianus, presented itself in 2006 after an eruption on the East Pacific Rise (EPR) eliminated vent communities near 9°50'N. Standard histological techniques were used to determine whether reproductive characteristics, such as timing of gamete release, fecundity, or time to maturation, differed from other vent gastropods in ways that might explain arrival of these two species as early colonizers. Both species exhibited two-component oocyte size frequency distributions that indicated they were quasi-continuous reproducers with high fecundity. In C. porifera, the oocyte size distributions differed slightly between two collection dates, suggesting that environmental cues may introduce some variability in gamete release. In samples collected within one year of the estimated eruption date, individuals in populations of both C. porfera and L. tevnianus were reproductively mature. The smallest reproducing C. porifera were 4.2 mm (males) and 5.4 mm (females) in shell length, whereas reproductive L. tevnianus were smaller (2.3 and 2.4 mm in males and females respectively). Most Cporifera in the population were large (> 6.0 mm) compared to their settlement size and reproductively mature. In contrast, most L tevnianus were small (< 1.0 mm) and immature. Reproductive traits of the two species are consistent with opportunistic colonization, but are also similar to those of other Lepetodrilus species and peltospirids at vents, and do not explain why these particular two species were the dominant pioneers. It is likely that their larvae were in high supply immediately after the eruption due to oceanographic transport processes from remote source populations. / by Skylar Bayer. / S.M.

Thesis (Ph. D.)--Joint Program in Oceanography (Massachusetts Institute of Technology, Dept. of Earth, Atmospheric, and Planetary Sciences; and the Woods Hole Oceanographic Institution), 1987. / MICROFICHE COPY AVAILABLE IN ARCHIVES AND LINDGREN. / Vita. / Includes bibliographies. / by Leslie Karen Rosenfeld. / Ph.D.

Thesis (Ph. D.)--Joint Program in Biological Oceanography (Massachusetts Institute of Technology, Dept. of Biology; and the Woods Hole Oceanographic Institution), 1998. / Includes bibliographical references. / by Gorka Sancho. / Ph.D.

Thesis (Ph. D.)--Joint Program in Biological Oceanography (Massachusetts Institute of Technology, Dept. of Biology; and the Woods Hole Oceanographic Institution), 1998. / Includes bibliographical references (leaves 179-199). / by Marjorie Frances Oleksiak. / Ph.D.