Standard sampling and monitoring of fish populations are invasive and time- consuming techniques. The ongoing development of statistical techniques to analyze environmental DNA (eDNA) introduces a possible solution to these challenges. We analyzed and created statistical models for qPCR data obtained from two controlled experiments that were conducted on samples of Coho salmon at the Goldstream Hatchery. The first experiment analyzed was a density experiment whereby varying num- bers of Coho (1, 2, 4, 8, 16, 32 and 65 fish) were placed in separate tanks and eDNA measurements were taken. The second experiment dealt with dilution, whereby three Coho were placed into tanks, removed and eDNA was then sampled at dilution vol- umes of 20kL, 40kL, 80kL, 160kL and 1000kL. Finally, we analyzed a set of field data from several streams in the Pacific North West for the presence of Coho salmon. In the field models, we considered the impact of environmental covariates as well as eDNA concentrations. Our analysis suggests that eDNA concentration can be used as a reliable proxy to estimate Coho biomass. / Graduate / 2021-11-20

Mangrove forests have one of the highest capacities of any ecosystem to sequester carbon. Mangroves in the Red Sea exist in a uniquely saline, high temperature, nutrient limited environment and the effects on carbon storage and greenhouse gas (GHG) emissions from arid mangrove soils is understudied. The flux of carbon dioxide (CO2) and methane (CH4) has the potential to enhance or reduce the carbon storage capacity of mangroves, which is an important nature-based solution for carbon drawdown to limit global warming. To determine the magnitude of CO2 and CH4 flux from mangrove soil in the Red Sea, soil cores were incubated on a monthly basis for over a year in light and dark conditions. Soil properties such as salinity, organic carbon, water content, bulk density, and stable isotopes, along with environmental variables such as inundation frequency and temperature were measured to resolve the drivers and variation of GHG flux over time. Additionally, 16S and 18S rRNA metabarcoding was conducted to determine the relative influence of prokaryotes and eukaryotes in the microbial mat within this mangrove ecosystem, and the microbial contribution to GHG flux. Oxygen microsensors were used for fine-scale resolution of the microbial mat, to determine photosynthetic rates and oxygen profiles. Fluxes were found to be highly variable, with the highest correlation between GHG flux and soil water content (p<0.05). Both prokaryotic and eukaryotic components of the microbial mat had a significant relationship with GHG flux, with mixed impacts depending on the taxa. These findings show that Red Sea mangroves, despite their lower carbon storage capacity, are a negligible source of GHG to the atmosphere unlike other regions where GHG emissions offset a greater proportion of carbon storage potential. Additionally, the importance of the microbial mat in this ecosystem is demonstrated, and an important consideration for future studies on mangroves and their potential as a nature-based solution against global warming.

Staphylococcus aureus encodes two extracellular nuclease enzymes, Nuc and Nuc2. Nuc is a secreted enzyme that is cut by signal peptidase (SpsB) at the cell membrane and is further processed into two active forms, NucA and NucB, by an unknown protease. Nuc2 is predicted to be a second extracellular nuclease based on sequence homology to the staphylococcal nuclease (SNase) and is tethered to the membrane with a N-terminal anchor. At the beginning of these studies, little was understood about the biological and physiological roles of Nuc and Nuc2 in S. aureus. The goal of this dissertation was to characterize the extracellular nuclease activity of S. aureus in order to better understand the contributions of Nuc and Nuc2 to the S. aureus life cycle. The studies presented in Chapter II focus on the role of Nuc in regulating S. aureus biofilm growth. The secreted forms of Nuc, called NucA and NucB, were first identified as anti-biofilm agents present in spent media from a S. aureus alternative sigma factor B (sigB) mutant. Regulation studies identified the major repressors and activators of nuc expression and showed that nuc is repressed under biofilm-forming conditions. By bypassing the native regulatory mechanisms using a nuc inducible plasmid, biofilm growth could be inhibited in a dose-dependent manner. Biofilm testing of nuc mutant strains across genetic backgrounds led to the observation that biofilm thickness increased two-fold in the absence of Nuc. More high molecular weight extracellular DNA (eDNA) accumulated in the nuc mutant compared to wild-type cells, indicating a direct link between Nuc and the availability of eDNA to contribute to the biofilm matrix. These studies showed that nuc expression is tightly regulated in S. aureus biofilms, and Nuc activity can greatly impact biofilm formation and maturation. In Chapter III, studies were performed to determine whether Nuc2 is an active nuclease in S. aureus and where the protein is localized in the cell. Upon initial comparison to Nuc, Nuc2 has 42% amino acid identity in the proposed SNase domain, and 7 of 9 residues known to be required for Nuc activity are conserved in Nuc2. Fluorescence microscopy of a Nuc2-sGFP translational fusion demonstrated the protein is localized to the cell membrane, and alkaline phosphatase fusion studies showed that the C-terminus of Nuc2 faces out of the cell. Fluorescence resonance energy transfer (FRET) assays facilitated the detection of low levels of Nuc2 activity on the S. aureus cell surface, demonstrating for the first time the enzyme is a functional nuclease, and mutations in the nuc2 gene eliminated this activity. Purification of recombinant Nuc2 also showed that enzyme has DNase activity that is calcium-dependent. Through the construction of Nuc/Nuc2 chimeric proteins, it was determined that localization to the cell membrane does not impair nuclease activity, and the low levels measured for Nuc2 on S. aureus cells is likely due instead to weak expression. The knowledge that Nuc2 is an active nuclease, localized to the cell surface, provides insight into the potential roles Nuc2 may play in a biofilm environment and during S. aureus infection.

Millay and Dickinson, born more than sixty years apart, were subject to vastly different influences and environments, although their homes were in the same geographic area. Their poetry reflects the difference of their times and their own temperament, but both wrote from a great depth and understanding of feeling and experience about subjects common to all mankind - death, love, anguish, the significance of nature.

Underwater visual censuses (UVCs) are one of the most widely used methods of studying species-rich coral reef fish assemblages. However, a considerable portion of reef fish diversity is missed or underrepresented by these traditional survey techniques. Environmental DNA (eDNA) sampling is an emerging technology that can detect traces of animal DNA from environmental samples, such as water and sediment, potentially including taxa that are missed by UVCs. Here, we assess the complementarity of eDNA to UVCs in surveying coral reef fish communities, particularly for cryptic and cryptobenthic taxa. We further investigate the effect of environmental sample source (water and sediment) and depth (10m and 30m). We conducted UVCs and eDNA sampling in three islands of the Farasan Banks, southern Saudi Arabia. A metabarcoding protocol was applied to environmental samples using a broad-spectrum fish assay targeting 16S mitochondrial DNA. Our eDNA surveys revealed 94 fish species, across 86 genera, 38 families, and 14 orders. Of the species detected by eDNA, 48.9% were also recorded on transects and 60.6% on roving diver surveys. eDNA also detected 6 cryptic, 10 cryptobenthic, and 13 pelagic species. Of these, only one (Eviota guttata) was recorded by UVCs. eDNA species composition was found to be significantly influenced by collection site (islands), and sample source (more species detected from water samples than sediment samples), but not by collection depth (10 versus 30 m depth). Our study provides further evidence that eDNA is an effective tool for the biomonitoring of tropical coral reef fish communities. However, we also stress that improvements are needed in methodology and reference sequence coverage for eDNA to realize its full potential of capturing cryptic and cryptobenthic diversity.

Seagrass, mangrove, saltmarshes and macroalgae - the coastal vegetated habitats, offer a promising nature-based solution to climate change mitigation, as they sequester carbon in their living biomass and in marine sediments. Estimation of the macrophyte organic carbon contribution to coastal sediments is key for understanding the sources of blue carbon sequestration, and for establishing adequate conservation strategies. Nevertheless,identification of marine macrophytes has been challenging and current estimations are uncertain. In this dissertation, time- and cost-efficient DNA-based methods were used to fingerprint marine macrophytes and estimate their contribution to the organic pool accumulated in blue carbon habitats. First, a suitable short-length DNA barcode from the universal 18S gene was chosen among six barcoding regions tested, as it successfully recovered degraded DNA from sediment samples and fingerprinted marine macrophyte taxa. Second, an experiment was performed to test whether the abundance of eDNA represents the content of organic carbon within the macrophytes; results supported this notion, indicating a positive correlation (R2 = 0.85) between eDNA and organic carbon. Third, using the chosen barcode, eDNA of marine macrophyte was identified from sediments of seagrass meadows and mangrove forests in the Arabian Red Sea, to further estimate contributions to the organic carbon pools. Estimations based on eDNA were compared against estimations of organic carbon based on stable isotope analyses from the same sediments; results from both methods were similar. In addition, this research provided the first quantitative evidence of the contribution of macroalgae to coastal and oceanic carbon pools. Hitherto, macroalgae have been ignored in blue carbon assessments because their fingerprinting was challenging and there was no evidence of their carbon export. The results of this dissertation demonstrate that eDNA offers an unprecedent taxonomic discrimination, and resolve the contribution of marine macrophytes to the organic pools in blue carbon sediments.

Thesis (M.A.)--Oregon State University, 2009. / Printout. Includes bibliographical references (leaves 128-142). Also available on the World Wide Web.

The central figure in The Awakening, Edna Pontellier, is shown in this thesis to pursue a narcissistic flight from existential reality. Following a review of contemporary criticism, Edna Pontellier's narcissism is discussed in connection with her sexuality and suicide. Sources cited range from biographies of Kate Chopin to scholarly articles to the works of modern psychologists. The emphasis throughout the thesis is on the wealth of interpretations that currently exist on The Awakening as well as the potential for further -study and interpretation in the future. Rather than viewing The Awakening as a purely feministic novel, it is stressed that The Awakening can transcend such categorization and be appreciated on many levels.

Thesis (M.A.)--Georgia State University, 2009. / Title from title page (Digital Archive@GSU, viewed July 27, 2010) Marti Singer, committee chair; Mary Hocks, Paul Schmidt, committee members. Includes bibliographical references (p. 62-64).

Thesis (M.A.)--West Virginia University, 2007. / Title from document title page. Document formatted into pages; contains vi, 82 p. : ill. Includes abstract. Includes bibliographical references (p. 79-82).