Coral reefs form marine-biodiversity hotspots of enormous ecological, economic, and aesthetic importance that rely energetically on a functional symbiosis between the coral animal and a photosynthetic alga. The ongoing decline of corals worldwide due to anthropogenic influences heightens the need for an experimentally tractable model system to elucidate the molecular and cellular biology underlying the symbiosis and its susceptibility or resilience to stress. The small sea anemone Aiptasia is such a model organism and the main aims of this dissertation were 1) to assemble and analyze its genome as a foundational resource for research in this area and 2) to investigate the role of miRNAs in modulating gene expression during the onset and maintenance of symbiosis. The genome analysis has revealed numerous features of interest in relation to the symbiotic lifestyle, including the evolution of transposable elements and taxonomically restricted genes, linkage of host and symbiont metabolism pathways, a novel family of putative pattern-recognition receptors that might function in host-microbe interactions and evidence for horizontal gene transfer within the animal-alga pair as well as with the associated prokaryotic microbiome. The new genomic resource was used to annotate the Aiptasia miRNA repertoire to illuminate the role of post-transcriptional regulatory mechanisms in regulating endosymbiosis. Aiptasia encodes a majority of species-specific miRNAs and first evidence is presented that even evolutionary conserved miRNAs are undergoing recent differentiations within the Aiptasia genome. The analysis of miRNA expression between different states of Symbiodinium infection further revealed that species-specific and conserved miRNAs are symbiotically regulated. In order to detect functional miRNA-mRNA interactions and to investigate the downstream effects of such miRNA action, a protocol for cross-linking immunoprecipitations of Argonaute, the central protein of the miRNA-induced silencing complex, was developed. This method identified binding sites of miRNAs on a transcriptome-wide scale and revealed target genes of symbiotically regulated miRNAs that were identified previously to be involved in the symbiosis. In summary, this dissertation provides novel insights into miRNA-mediated post-transcriptional modulation of the host transcriptome and by presenting a critically needed genomic resource, lays the foundation for the continued development of Aiptasia as a model for coral symbiosis.

Toxins produced by harmful algal blooms (HABs) are known to pose contamination risks to seafood products (e.g. fish and shellfish) consumed by human. In order to control contamination risks, monitoring regimes have to be performed rigorously. The effort to monitor the amount of toxins in consumable products has to rely on continuous supply to analytical standards. The current work presents the strategy in optimising the production of major diarrhetic shellfish poisoning (DSP) toxins, OA and DTX1, from Prorocentrum lima. The organism is also known to produce peridinin, a carotenoid pigment that has been found to have pharmaceutical potential. Results from this study showed that cultivation of P. lima CCAP 1136/11 was still, although not completely, reliant on supply of natural seawater. Characterisation of compounds produced by P. lima CCAP 1136/11 in batch culture identified three major bioactive compounds (OA, DTX1 and peridinin) and two minor OA-related compounds. Recovery of these major compounds was further optimised with two-stage extraction procedure. Several important considerations for the cultivation process include standardisation of inoculum age and initial cell density. These and several other growth parameters such as temperature, light and CO2 supplementation have been shown to affect the growth and production of DSP toxins and peridinin in the culture. One of the main highlights in this study revealed that providing culture with light and dark cycle at frequency of 0.5 hour benefit in the enhancement of OA, DTX1 and peridinin yield from P. lima CCAP 1136/11. As the last part of this study, a simple and scalable design of reactor has been proposed. Contrary to common observations for dinoflagellate culture, P. lima CCAP 1136/11 was found to be able to withstand increased sparging within the culture system, resulting in concomitant increased of growth and production of OA, DTX1 and peridinin. Future works have been suggested to focus on: (1) exploitation of different cultivation system, such as continuous or semicontinuous systems, and (2) exploration on genetic modification to enable commercial scale production of DSP toxins and peridinin.

<p>Through the analysis of the stratigraphic and spatial distribution of organic walled dinoflagellate cysts (dinocysts) from climatologically and oceanographically key sites, this project aims to contribute to a better understanding of the Eocene-Oligocene (E/O) environmental changes and their timing. A central issue is to identify the global environmental changes which are responsible for the Eocene cooling and its underlying mechanisms with the focus on the Oligocene isotope-1 (Oi-1) event, thought to mark the onset of major Antarctic glaciation.</p><p>Two low-latitude sites were selected, Blake Nose (western North Atlantic) and Massignano (central Italy). For the first time a coherent taxonomy and biostratigraphy of dinocysts was established for the late Eocene at these latitudes. A high resolution correlation was established between the Massignano E/O Stratotype Section and the stratigraphically more extended ‘Massicore’. The composite section was used to analyse sea surface temperature (SST) change across the greenhouse-icehouse transition by means of dinocyst distribution.</p><p>At Massignano, the Oi-1 event was recognised both qualitatively and quantitatively. In the power spectrum of the SST_dino the ~100 and ~400 kyr eccentricity cycles may be distinguished and correlated with La04. When orbitally tuned, the E/O GSSP dates ~100 kyr older than the Oi-1 event. The boundary’s age could either be ~33.75 or ~34.1 Ma, both differ significantly from the ~33.9 Ma age in the GTS 2004.</p><p>Furthermore, when the data from the low-latitude sites were combined with extensive datasets from the Proto North Atlantic and adjacent regions, a suite of species sensitive to changes in SST was recognised. Their first and last occurrences reflect seven distinct phases of decreasing SSTs during the Middle Eocene to earliest Oligocene.</p><p>These results clearly indicate that atmospheric cooling together with higher frequency orbital forcing played a key role in the transition from the Greenhouse to the Icehouse world.</p>

Our knowledge of how oil spills affect coastal environments is severely limited by the shortage of research that addresses the impact of these events on phytoplankton, the single most important group of organisms in the marine ecosystem. This scarcity of knowledge is mainly attributed to the absence of baseline data, preventing the comparison of pre- and post-spill populations. This unique study aims to identify how dinoflagellates and diatoms, the two major groups of phytoplankton in coastal marine environments, have been affected by the 1989 Exxon Valdez oil spill in Prince William Sound (PWS), Alaska. To do this, sedimentary records of dinoflagellate cysts, produced during a dinoflagellate's life cycle and preserved in the sediment, and biogenic silica, a proxy for diatom abundance, were analyzed prior to, during and after the oil spill. The analysis of two well-dated cores in PWS reveals marked increases during the oil spill in the concentrations of total cysts of the species Operculodinium centrocarpum sensu Wall and Dale, (1966) and Dubridinium spp. Total cyst concentrations doubled in core P-10 from 362 to 749 per g, while in core P-12 the increase was from 1175 to 1771 cysts g-1. During this peak in cyst concentrations, total concentrations were 3 and 2 standard deviations greater than the mean in cores P-10 and P-12, respectively. Dubridinium spp. showed a five and sevenfold increase in concentrations in cores P-10 (4 to 20 cysts g-1) and P-12 (16 to 110 cysts g-1), respectively, while O. centrocarpum sensu Wall and Dale, (1966) doubled in concentrations in the two cores (P-10: 117 to 276 cysts g-1; P-12: 268 to 495 cysts g-1). Biogenic silica values did not show significant changes throughout the cores, with values varying between 8% and 9% in core P-10 and 9.0% to 10.9% in core P-12. These changes lie within or very close to the standard deviation of the analyzed standards, suggesting that much of the changes could be analytical noise. The dinoflagellate cyst signals seen in this study are comparable to those seen as a result of nutrient enrichment in estuarine systems, suggesting that the 1989 Exxon Valdez oil spill and its remediation had a stimulatory effect on some taxa of cyst- producing dinoflagellates. This impact appears to be short-lived, with cyst concentrations returning to pre-spill levels within two years of the event. The lack of change in diatom abundance, on the other hand, suggest that diatom abundance remained relatively constant during the entirety of the sample period. / Graduate / 2020-07-10

The first high resolution record of dinoflagellate cysts ~110-155 kyr over Termination II and the last interglacial in the Santa Barbara Basin, California from ODP Hole 893A details a complex paleoceanographic history. Changes in cyst abundances, concentrations, diversity, and assemblages reflect climatic and ocean circulation changes, and are successfully used to make quantitative reconstructions of past sea surface temperatures and annual primary productivity with the modern analogue technique based on a dinoflagellate cyst database from the northeast Pacific. The dominance of heterotrophic dinoflagellate cyst taxa Brigantedinium spp. throughout most of the section indicates coastal upwelling is an important influence on the basin. Based on the dinoflagellate cyst assemblages, five cyst zones are identified and approximately correspond to the marine isotope stage boundaries and their associated changes in sea surface temperatures and sea level. Cooler intervals, MIS 6 and MIS 5d, are characterized by cold-water indicator species Selenopemphix undulata whereas thermophyllic taxon Spiniferites mirabilis characterizes MIS 5e. In contrast to other studies in the Pacific, the data shows a one to two-thousand-year cooling event ~129 kyr that correlates to the Termination II sea level still-stand of the two-step deglaciation. A significant increase in cyst concentrations of heterotrophic and autotrophic taxa in the latest MIS 5e implies enhanced primary productivity as a result of increased seasonal upwelling and the warm, nutrient rich waters entering the basin after sea level stabilizes near modern levels. The hydrological evolution and cyst signal of the last interglacial is similar to the development of the Holocene in the Santa Barbara Basin, but the sustained presence of Spiniferites mirabilis across MIS 5e indicates sea surface temperatures were higher than modern conditions. The quantitative reconstructions appear to be less reliable, and show wide sea surface temperature changes across MIS 6 to 5d (~6.2-10.7°C in February; ~12.6-20.3°C in August) similar to modern ranges, while annual primary productivity was confined to a higher narrower range (~456-586 g C m-2 yr-1). / Graduate / 2020-04-18

Through the analysis of the stratigraphic and spatial distribution of organic walled dinoflagellate cysts (dinocysts) from climatologically and oceanographically key sites, this project aims to contribute to a better understanding of the Eocene-Oligocene (E/O) environmental changes and their timing. A central issue is to identify the global environmental changes which are responsible for the Eocene cooling and its underlying mechanisms with the focus on the Oligocene isotope-1 (Oi-1) event, thought to mark the onset of major Antarctic glaciation. Two low-latitude sites were selected, Blake Nose (western North Atlantic) and Massignano (central Italy). For the first time a coherent taxonomy and biostratigraphy of dinocysts was established for the late Eocene at these latitudes. A high resolution correlation was established between the Massignano E/O Stratotype Section and the stratigraphically more extended ‘Massicore’. The composite section was used to analyse sea surface temperature (SST) change across the greenhouse-icehouse transition by means of dinocyst distribution. At Massignano, the Oi-1 event was recognised both qualitatively and quantitatively. In the power spectrum of the SSTdino the ~100 and ~400 kyr eccentricity cycles may be distinguished and correlated with La04. When orbitally tuned, the E/O GSSP dates ~100 kyr older than the Oi-1 event. The boundary’s age could either be ~33.75 or ~34.1 Ma, both differ significantly from the ~33.9 Ma age in the GTS 2004. Furthermore, when the data from the low-latitude sites were combined with extensive datasets from the Proto North Atlantic and adjacent regions, a suite of species sensitive to changes in SST was recognised. Their first and last occurrences reflect seven distinct phases of decreasing SSTs during the Middle Eocene to earliest Oligocene. These results clearly indicate that atmospheric cooling together with higher frequency orbital forcing played a key role in the transition from the Greenhouse to the Icehouse world.

Thesis (Ph. D.)--Biology, Georgia Institute of Technology, 2008. / Committee Chair: Kubanek, Julia; Committee Member: Hay, Mark; Committee Member: Jiang, Lin; Committee Member: Pavia, Henrik; Committee Member: Snell, Terry.

Thesis (M. Sc.), Memorial University of Newfoundland, 1998. / Restricted until June 1999. Bibliography: leaves 84-95.

Polyether compounds are a subgroup of natural products with regular occurrence of multiple C-O-C motifs. The biosynthetic origin of polycylic polethers has been studied and the majority of them are derived from polyketide or terpene pathways. Normally, the polycyclic polyethers can be divided into two groups based on their structural features: the first group features multiple rings that are interconnected by carbon-carbon single bond, which are produced by a biosynthetic cascade of exo epoxide-opening reactions; the other group has multiple fused cyclic ethers and are formed by an cascade of endo epoxide-opening reactions. Karenia brevis (K. brevis) is known as principle harmful bloom (HAB) organism of the Gulf of Mexico which can cause red tides. Brevetoxins (PbTx) are a suit of cyclic polyether ladder compounds produced by K. brevis. Brevetoxins are neurotoxins that can bind to voltage-gated sodium channels in nerve and muscle cells, resulting in disruption of normal neurological processes causing the human illness which is clinically described as neurotoxic shellfish poisoning (NSP). Inspired by Cane-Celmer-Wesley’s proposal regarding monensin biosynthesis, Nakanishi and Shimizu proposed a biosynthetic pathway for brevetoxin which suggests that PKS-mediated synthesis of the polyene is followed by epoxidation to afford a polyepoxide which then undergoes an epoxide-opening cascade, catalyzed by an epoxide hydrolase (EH). To find evidence to support the hypothesis that an epoxide hydrolase from polyether ladder producing dinoflagellates will catalyze the construction of the polyether ladder framework from polyepoxide substrates, and to study the role of epoxide hydrolase in the biosynthesis of polyether ladder compounds, it is necessary to identify and produce one or more epoxide hydrolase from dinoflagellates. The methods to detect epoxide hydrolase activity in K. brevis and different techniques to obtain epoxide hydrolases from K. brevis are discussed. A microsomal EH identified from a K. brevis EST library was cloned and expressed. The characterization of this EH, including substrate selectivity and enantioselectivity as well as its potential to catalyze the critical ento-tet cyclization epoxy alcohol, is discussed.

Animal and plant genomes produce numerous small RNAs (smRNAs) that regulate gene expression post-transcriptionally affecting metabolism, development, and epigenetic inheritance. In order to characterize the repertoire of endogenous microRNAs and potential gene targets, we conducted smRNA and mRNA expression profiling over nine experimental treatments of cultures from the dinoflagellate Symbiodinium sp. A1, a photosynthetic symbiont of scleractinian corals. We identified a total of 75 novel smRNAs in Symbiodinum sp. A1 that share stringent key features with functional microRNAs from other model organisms. A subset of 38 smRNAs was predicted independently over all nine treatments and their putative gene targets were identified. We found 3,187 animal-like target sites in the 3’UTRs of 12,858 mRNAs and 53 plantlike target sites in 51,917 genes. Furthermore, we identified the core RNAi protein machinery in Symbiodinium. Integration of smRNA and mRNA expression profiling identified a variety of processes that could be under microRNA control, e.g. regulation of translation, DNA modification, and chromatin silencing. Given that Symbiodinium seems to have a paucity of transcription factors and differentially expressed genes, identification and characterization of its smRNA repertoire establishes the possibility of a range of gene regulatory mechanisms in dinoflagellates acting post-transcriptionally.