Reptiles can often experience perturbations that greatly influence their metabolic status (e.g., temperature, exercise, digestion, and ontogeny). The most common cause of fluctuations in metabolic status in post-embryonic reptiles is arguably digestion and physical activity (which will be further referred to as exercise). The objective of this thesis is to determine the mechanisms involved in CO2 transport during digestion, determine the mechanisms that allow for the maintenance of acid-base homeostasis during digestion, and observing the effect of an understudied form of exercise in semi-aquatic reptiles on the regulation of metabolic acidosis and base deficit. This dissertation provided evidence for potentially novel and under investigated mechanisms for acid-base homeostasis (e.g., small intestine and tissue buffering capacity; Chapters 3 & 4), while also debunking a proposed hypothesis for the function of an anatomical feature that still remains a mystery to comparative physiologist (Chapter 2). This thesis is far from systematic and exhaustive in its approach, however, the work accomplished in this dissertation has become the foundation for multiple distinct paths for ecologically relevant investigations of the regulation of metabolic acidosis/alkalosis in reptiles.

The present studies determine the accumulation of persistent organic pollutants (POPs) in three pinniped species, evaluate the relationship with relevant biomarkers of exposure, and calculate toxic effect thresholds. Stranded harp and hooded seals were found to be accumulating PBDEs at levels which could pose a based on threshold levels determined in this study. Northern fur seals are accumulating all three classes of POPs (PCBs, PBDEs, and OCPs) with significant relationships being seen with blubber percent lipid. Correlations between contaminant concentrations and expression levels of relevant biomarkers were seen potentially indicating an effect on multiple pathways. Overall risk can be hard to determine due to factors such as sex and age. Broad threshold response values and hazard quotients were calculated for toxic effect endpoints in pinnipeds. Overall these results suggest that certain populations of pinnipeds are at high risk of experiencing toxic effects due to POP exposure, but it is important to understand effects even at lower concentrations. The relationship between exposure, toxic effects, and other stressors, both environmental and physiological, can impact the overall fitness and survival of pinnipeds.

Microalgae being photosynthetic and having quick growth cycles can prove to be excellent candidates as biofactories for the production of aromatic compounds like para-hydroxybenzoic acid (pHBA) that act as a monomer in liquid crystal polymers. We developed transgenic lines of the model alga Chlamydomonas reinhardtii by performing nuclear transformation using electroporation. The transgenic cell lines expressed the ubiC gene that utilized chorismate from the shikimate pathway as a substrate to produce pHBA. The maximum yield of pHBA measured in these lines was 80 mg/L. Accruing pHBA can be toxic to the cells and the mechanism by which C. reinhardtii could detoxify pHBA is not known. C. reinhardtii genome was thus scanned for sequences similar to UDP-glucosyltransferase (UGT) that can transfer the glucose moiety to pHBA, rendering it non-toxic to the cell lines. Our analysis suggested the absence of any potential UGTs that could glycosylate pHBA and detoxify it. We further performed feeding experiments to test the ability of wt-type C. reinhardtii cells to detoxify pHBA and understand its fate. C. reinhardtii cells were fed with varying concentrations of pHBA and harvested at different time intervals. The HPLC chromatograms indicated a majority of the pHBA was catabolized. Based on these results, …

Trait-based approaches are useful in ecological research because of their potential ability to predict species responses from patterns present in the community and to infer mechanisms driving community assembly. Current approaches for fishes are lacking traits across all five fundamental niche dimensions (i.e. habitat, life history, trophic, metabolic and defense). This study quantified a broad range of fish functional traits across all five niche dimensions (commonly used traits and novel traits), quantified intra- and interspecific variation for each trait, tested for relationships among traits within and among niche dimensions, tested for phylogenetic conservatism of traits and assessed trait-environment relationships for a subset of these traits under two different contexts. Approximately one third of the quantified traits exhibited greater intraspecific variation than interspecific variation and were not included in subsequent analyses. There were similarities between phylogeny and trait dendrograms for all traits, and habitat, metabolic and defense traits. The traits identified in chapter 2 were able to explain species responses during different flow periods in two intermittent streams as well as species-specific differences in host microbiome at the onset of drought in one intermittent stream. The novel traits identified in chapter 2 did contribute to our understanding of the community assembly …

In the extensive and remote sub-Antarctic forests of South America, birds are the dominant terrestrial vertebrates. Despite considerable efforts to understand the ecology of birds breeding in these forests, our current knowledge for many species is still incomplete. During three breeding seasons (2014 – 2017), I studied the breeding ecology of the five most abundant open-cup forest-dwelling passerines in the sub-Antarctic forest of Navarino Island, Chile (55°04′S, 67°40′W). There were differences in some of the breeding strategies used by birds breeding on Navarino Island versus conspecific populations breeding at lower latitudes. Milvago chimango was the main nest predator of open-cup nesting forest passerines, and the main cause of nest failure. In addition, I found that species built their nests in sites with higher density and taller understory; however, these two factors decreased their nest survival. This mismatch could be due to a change in depredation risk on Navarino Island, and thus, passerines breeding there may be in an ecological trap. In addition, using light-level geolocators, I determined that the migratory connectivity of Elaenia albiceps is weak as a result of the large spatial spread of individuals on the wintering ground, and that the distances among individuals on the breeding grounds …

Results from the present study found for the first time that the use of bacterial strains of Lactobacillus acidophilus, Lactobacillus casei, Bifidobacterium thermophilum, and Enterococcus faecium from the commercial product PrimaLac® had the potential to act as a possible probiotic for juvenile red drum. The addition of PrimaLac® probiotics [whether as a water-soluble probiotic (WSP) or in a probiotic enhanced starter feed (PESF)] reduced mortality (%M), enhanced growth rates (MW, LT, SGR, and DGR), improved feed conversion efficiencies (FCEs), and physical condition factors in the juvenile red drum. Improvement was quantified using external morphological condition indices (MCIs) and blood physiological condition indices (PCIs). Results showed a strong positive relationship between MCIs and PCIs, which suggested that probiotics treated fish were in better health (lower MCIs) with lower fasting blood glucose and lactate levels than control fish. Addition of probiotics also resulted in improved water quality (lower nitrate, nitrite, and ammonia) in the treatment tanks compared to controls. Application of PrimaLac® probiotics on the morphology and histology of three different regions of the intestine (proximal, mid-and distal) improved intestinal length (Li), mass (Mi), and digesta mass (Md). In 5μm histological sections examined for differences among treatments (probiotics vs. controls), five variables …

To address the shortcomings in existing Markov model implementations in handling large amount of metagenomic data with comparable or better accuracy in classification, we developed a new algorithm based on pseudo-count supplemented standard Markov model (SMM), which leverages the power of higher order models to more robustly classify reads at different taxonomic levels. Assessment on simulated metagenomic datasets demonstrated that overall SMM was more accurate in classifying reads to their respective taxa at all ranks compared to the interpolated methods. Higher order SMMs (9th order or greater) also outperformed BLAST alignments in assigning taxonomic labels to metagenomic reads at different taxonomic ranks (genus and higher) on tests that masked the read originating species (genome models) in the database. Similar results were obtained by masking at other taxonomic ranks in order to simulate the plausible scenarios of non-representation of the source of a read at different taxonomic levels in the genome database. The performance gap became more pronounced with higher taxonomic levels. To eliminate contaminations in datasets and to further improve our alignment-free approach, we developed a new framework based on a genome segmentation and clustering algorithm. This framework allowed removal of adapter sequences and contaminant DNA, as well as generation …

In this work, we have performed comparative evolutionary analysis, functional genomics analysis, and machine learning analysis to identify the molecular factors that discriminate between multipartite and unipartite bacteria, with the goal to decipher taxon-specific factors and those that are prevalent across the taxa underlying the these traits. We assessed the roles of evolutionary mechanisms, namely, horizontal gene transfer and gene gain, in driving the divergence of bacteria with single and multiple chromosomes. In addition, we performed functional genomic analysis to garner support for our findings from comparative evolutionary analysis. We found genes such as those encoding conserved hypothetical protein DR_A0179 and hypothetical protein DR_A0109 in Deinococcus radiodurans R1, and Putative phage phi-C31 gp36 major capsid-like protein and hypothetical protein RSP_3729 in Rhodobacter sphaeroides 2.4.1, which are located on accessory chromosomes in both bacteria and were not found in the inferred ancestral sequences, and on the primary chromosomes, as well as were not found in their closest relatives with single chromosome within the same clade. These genes emphasize the important potential roles of the secondary chromosomes in helping multipartite bacteria to adapt to specialized environments or conditions. In addition, we applied machine learning algorithms to predict multipartite genomes based on gene …

We investigated the hypothesis that exposure to inhaled diesel exhaust PM can alter the gut microbiome and intestinal integrity, thereby promoting systemic inflammatory response and early CVD risk, which are exacerbated by HF diet. Furthermore, we investigated whether the observed exposure and diet-mediated outcomes could be mitigated through probiotic treatment. We performed an exposure study on C57Bl/6 male mice, placed on either a low fat (LF) diet or a high-fat (HF) diet, and exposed via oropharyngeal aspiration to 35 μg diesel exhaust particles (DEP) suspended in 35 μl of sterile saline or sterile saline controls (CON) twice a week for four weeks. A subset of mice on HF diet were dosed with 0.3 g/day (PRO, ~7.5x108 CFU/day) of probiotic Ecologic® Barrier 849 (Winclove Probiotics) in drinking water during the course of the study. For our first aim, we investigated the alterations in the gut microbiome, measured circulating cytokines and lipopolysaccharide (LPS), and measured CVD biomarkers in the heart. Our results revealed that exposure to inhaled DEP results in gut dysbiosis characterized by expansion of the phyla Verrucomicrobia and Proteobacteria and reduction in Actinobacteria, which was exacerbated by HF diet. Probiotics mitigated the DEP-mediated expansion of Proteobacteria and re-established Actinobacteria in …