Thesis (M. Phil.)--University of Hong Kong, 2007. / Title proper from title frame. Also available in printed format.

Thesis (M.S.) in Oceanography--University of Maine, 2001. / Includes vita. Includes bibliographical references (leaves 100-105).

Thesis (Ph. D.)--University of Hong Kong, 1999. / Includes bibliographical references (leaves 147-165).

The primary purpose of this study was to deal with the taxonomy of the sand-dwelling dinoflagellates occurring in the North East Pacific Ocean. A preliminary examination of the community and the major ecological parameters affecting these organisms (exposure, grain size, temperature and salinity) was also undertaken. Although the study was mainly confined to those species inhabiting the inter-tidal zones of five marine beaches in British Columbia, some subtidal work was done. The conclusions are based on the analysis of approximately 120 samples from 15 field trips over a one year period. Forty-one species were recorded of which 12 could not be identified and may warrant being described as new species. In general, the number of both species and individual cells increased from winter to spring and summer with maximum comentrations between March and September. Out of the environmental parameters measured, grain size (which is primarily determined by tides and currents) is probably the most important factor in determining the distributions of these organisms in the summer months. / Science, Faculty of / Botany, Department of / Graduate

No description available.

published_or_final_version / Zoology / Doctoral / Doctor of Philosophy

published_or_final_version / abstract / Ecology and Biodiversity / Master / Master of Philosophy

No description available.

My dissertation focuses on genome and functional evolution of photosynthetic eukaryotes and the design and implementation of computational methods and tools to enable genome-wide studies to investigate these taxa. The work described here is grouped into two major topics, 1) endosymbiosis and genome evolution, and 2) harmful algal blooms. I discuss my work related to endosymbiosis and genome evolution in chapters 2-4. Chapters 5-6 cover the work related to harmful algal blooms. In chapter 1, I introduce the state-of-art of what is known about the history of plastids and evolution of photosynthesis in eukaryotes, an overview of marine harmful algae, and the specific aims of my dissertation. In chapter 2, I describe the design and implementation of the phylogenetic sorting tool, PhyloSort and the assembly of a high-throughput phylogenomic pipeline. Together, PhyloSort and the pipeline has become a key tool for multiple subsequent studies. chapter 2 also presents a case study using these tools in which we provide an estimate of the number of cyanobacterial genes that have been transferred to the nuclear genome of Plantae through primary endosymbiotic gene transfer; I use the model unicellular green alga Chlamydomonas reinhardtii for this purpose. In chapter 3, I discuss another case of prokaryotic contribution to the nucleus of photosynthetic eukaryotes. Here, the intriguing relationship of Chlamydiae-like bacteria and plants and algae is examined in a large-scale analysis, in which we scanned all available genomes of the primary photosynthetic organisms for genes of potential Chlamydiae origin. Surprisingly, we identified more than fifty Chlamydiae-derived genes in plants and algae. Here, we propose a model for the role that a Chlamydiae-like symbiont might have played in the establishment of the primary plastid in the common ancestor of Plantae. In chapter 4, I describe a study in which we explored the complete protein models of two diatom organisms as representative for photosynthetic chromalveolates and looked for genes that might have been acquired through endosymbiotic (secondary) or horizontal transfers from red or green algae. In contradiction of the “chromalveolate hypothesis” which states that photosynthesis in chromalveolates originated via the engulfment of a red alga symbiont, our study shows an unexpected green algal contribution that is fourfold greater than that of the canonical red algal symbiont. Our data suggest that the chromalveolate history includes a previously unrecognized green algal endosymbiont that was captured and lost prior to the more recent establishment of the red alga plastid, which is widespread in extant photosynthetic chromalveolates. In chapter 5, I discuss the identification of the phylogenetic origin of the genes involved in the biosynthetic pathway of saxitoxin in cyanobacteria. Here, we used a pyrosequencing approach to sequence de novo genomes of two strains of Anabaena circinalis, one of which is saxitoxin-producing and the other is non-toxic. Using comparative and phylogenetic analyses, I show that, within the saxitoxin gene cluster, genes that encode the key and unique enzymes in the pathway are of foreign origin that originated via horizontal transfer from non-cyanobacterial sources. These genes introduced the ability to produce saxitoxin in the ancestor of the toxic cyanobacterial clade. In chapter 6, I describe a gene expression study in which we used massively parallel signature sequencing (MPSS) to investigate RNA abundance patterns in the toxic dinoflagellate Alexandrium tamarense. This work provides the first clear evidence for the utilization by dinoflagellates of transcriptional to regulation. Moreover, using MPSS, we provide an estimate of the number of the distinct genes in Alexandrium tamarense; i.e., remarkably 40,000 loci. Taken together, our data indicate that dinoflagellates possess a great metabolic flexibility that allows them to efficiently toggle between photoautotrophy and heterotrophy based on the environmental conditions.

University of Technology, Sydney. Faculty of Science. / Global climate change is leading to the rise of ocean temperatures and is triggering mass coral bleaching events on reefs around the world. This involves the expulsion of the symbiotic dinoflagellate algae, known as zooxanthellae, from the coral host. Coral bleaching is believed to occur as a result of damage to the photosynthetic apparatus of these symbionts, although the specific site of initial impact is yet to be conclusively resolved. This thesis examined a number of sites within the light reactions of photosynthesis and evaluated the efficiency of photoprotective heat dissipating pathways. Upon expulsion, the capacity for long-term survivorship of expelled zooxanthellae in the water column was also assessed. A reduction in photosystem II (PSII) photochemical efficiency during exposure to elevated temperature and high light (bleaching conditions) was found to be highly dependent upon the increase in abundance of QB non-reducing PSII centres (inactive PSII centres), indicating damage to the site of the secondary electron acceptor, QB, resulting in a limited capacity for its reduction. Therefore, this reduced the rate of the reoxidation of the primary electron acceptor, QA-. Fast induction curve (FIC) analysis of the rise from minimum fluorescence to maximum fluorescence revealed a lower amplitude in the J step along this curve, which was consistent with a reduction in the rate of QA reoxidation. This photoinhibition of PSII was found to occur once the effectiveness of excess energy dissipation through energy-dependent quenching and state-transition quenching was exceeded, suggesting that these mechanisms were incapable of preventing photodamage. Antenna size heterogeneity showed little change under bleaching conditions with a significant increase in PSIIbeta only apparent in one species of coral. The thermostability of the oxygen evolving complex (OEC) and thylakoid membrane were found to increase during exposure to bleaching conditions and exceeded bleaching thresholds of corals. This rapid rise in temperature-dependent thermostability also occurred over seasons, where variation in ocean temperatures was matched by gradual shifts in OEC and thylakoid membrane thermotolerance. Variation in thermostability between species was not found to be linked to zooxanthellae genotype, and instead was related to the bleaching susceptibility of the host. Despite this capacity for resilience to bleaching conditions, the PSII reaction centres did not exhibit such a mechanism for rapid acclimatisation. Corals can only be as tolerant to bleaching conditions as their most sensitive component allows. The formation of nonfunctional PSII centres is therefore suggested to be involved in the initial photochemical damage to zooxanthellae which leads to a bleaching response. Zooxanthellae were found to be expelled irrespective of OEC function and thylakoid membrane integrity, as these sites of the photosynthetic apparatus were still intact when cells were collected from the water column. Although zooxanthellae were photosynthetically competent and morphologically intact upon expulsion, their longevity in the water column was dependent on the time of expulsion following the onset of bleaching and the ambient water temperatures. The survivorship of these zooxanthellae was restricted to a maximum of 5 days in the water column which suggests that unless expelled zooxanthellae inhabit other environs of coral reefs which may be more favourable for survival, their capacity for persistence in the environment is extremely limited. Chlorophyll a fluorescence measurements are a common tool for investigating photosynthetic impacts to in hospite zooxanthellae of corals. Pathways causing dark-reduction of the plastoquinone pool are shown to be active in corals and affect measurements which require dark-adaptation. Pre-exposure to far-red light was found to be an effective procedure to oxidise the inter-system electron transport chain and ensure determination of the true maximum quantum yield of PSII and accurate FICs. It is concluded that the trigger for coral bleaching lies in the photosynthetic apparatus of zooxanthellae and evidence is presented in support of this impact site not being the OEC or thylakoid membrane.