Search Results

Factors Affecting MeHg Contamination of Spiders and Insect-Mediated MeHg Flux from Human-Made Ponds
The present study focused on methylmercury (MeHg) in emergent aquatic insects and spiders from human-made ponds. This dissertation addresses two main topics: (1) factors affecting variation in spider MeHg concentrations around human-made ponds and (2) the magnitude of MeHg transported out of human-made ponds by emergent aquatic insects (insect-mediated MeHg flux). Spiders were specifically targeted in this study because they have been proposed as sentinels of MeHg contamination (organism whose tissue concentrations reflect the level of MeHg in the environment). Spider MeHg concentrations were related to spider diet, size, and proximity to waterbody, but affected individual spider taxa differently. In a second study, I found that only "large" spiders within a taxa had tissue concentrations positively related to prey MeHg concentrations. These results indicate that the relationship between spider and prey MeHg could be size-dependent and that "large" spiders within a taxa may better reflect ambient MeHg contamination. Finally, I tested a conceptual model hypothesizing insect-mediated MeHg flux from human-made ponds is controlled by pond permanence and fish presence. In agreement with the conceptual model, insect-mediated MeHg flux from ponds was suppressed by the presence of fish, likely due to fish predation on emergent insect larvae. I found the mean aggregate MeHg flux was approximately 6 times higher from ponds without fish than from ponds with fish. The suppression of insect flux by fish was stronger for large insect taxa than small insect taxa. Results of this study indicate that community structure can influence the cross-system transport of contaminants, like MeHg, from ponds to terrestrial food webs.
The Effect of Developmental Hypoxia on Cardiac Physiology in Three Species: Alligator mississippiensis, Chelydra serpentina, and Danio rerio
In this dissertation, I explored the effects of developmental hypoxia on heart contractility in three separate species of ectotherms: the common snapping turtle (Chelydra serpentina), the American alligator (Alligator mississippiensis), and the zebrafish (Danio rerio). I began with the common snapping turtle and tested whether the utilization of the sarcoplasmic reticulum was altered in response to developmental hypoxia. In the next two chapters, developmental hypoxia of the American alligator was explored studying how the cardiac tissue was affected, specifically in physiological stressors, sarcoplasmic reticulum utilization and sensitivity to pharmacological increases in contractility. The last chapter explored how zebrafish heart contractility was altered in response to chronic hypoxia from egg to adult. Findings from these chapters suggest that while developmental hypoxia did alter cardiac contractility, it did not alter the response of the heart to physiological stressors such as increased heart rate or under hypoxia. Overall, these findings contribute to increasing the current understanding of how developmental hypoxia alters the cardiovascular system but with an emphasis on the cardiac tissue level.
Suburban Succession and Stream Dynamics
Increasingly higher numbers of people are moving into urbanizing environments, yet our understanding of ecosystem consequences of rapid urbanization is still in its infancy. In this dissertation, I assessed dynamics of residential landscapes during suburban succession and consequences for ecosystem functioning. First, I used a space-for-time approach to quantify more than a century of suburban succession in the Dallas – Fort Worth metroplex (DFW). Attributes of residential landscape plant diversity and habitat complexity were quantified for 232 individual properties nested within 14 neighborhoods constructed between 1906 and 2020. Suburban succession progressed from simple turf lawns with limited habitat complexity to landscapes dominated by deciduous trees and high habitat complexity, but homeowner decisions related to landscape management affect the rate of that transition and the number of plants and taxa present. Next, I used the novel spatial construct of "neighborhoodsheds" to test for effects of suburban succession on carbon export, and found that the proportion of carbon derived from C3 vs. C4 plants was affected by neighborhood plant community structure (i.e. greater proportion of trees and shrubs primarily in later stages of suburban succession). Finally, I conducted a mesocosm experiment to test effects of changes in allochthonous inputs during suburban succession on aquatic ecosystem functioning. The proportion of carbon from C3 vs. C4 sources interacted with time to affect abundance of emergent mosquitoes and chironomids. This work sets the stage for further research on urban ecology in DFW and provides conceptual advances for the study of urban ecosystems more broadly.
Bottom-Up Impacts of Grazing Disturbance on Ground-Nesting Bee Assemblages: Do They Dig It?
In my thesis, I examined impacts of nesting and floral resources on ground-nesting bee assemblages at nine ranch sites with differing grazing histories. Because ecological disturbances can strongly affect the availability of foraging and nesting resources over time, I also examined the impacts of grazing history on nesting and floral resources for ground-nesting bees. I sampled bee assemblages, a comprehensive array of vegetation and soil measures, and floral abundance and richness. I used these data to determine (1) the importance of different nesting habitat resources and livestock grazing history for ground-nesting bees and (2) how livestock grazing history influenced the availability of nesting and floral resources. I found that sites with sandier soils had greater abundance and richness of ground-nesting bees, and sites with less compacted soils had greater bee abundance. Contrary to many other studies, the availability of bare ground was not important for ground-nesting bee abundance or richness. Grazing history did not affect any measures of nesting or floral habitat, and had negligible effects on ground-nesting bee abundance, richness, and community composition. My results suggest that the availability of sandier or less compacted soils may be limiting for ground-nesting bee abundance or richness, especially in areas with predominately clay soil types. In this context, the availability of such nesting resources may be more limiting than floral resource availability. More research is necessary to tease apart the effects of different nesting and floral resources for bees, and how different grassland management types affect bees through those resources. My findings highlight the importance of considering nesting habitat resources in bee conservation and restoration efforts.
Acute and Sublethal Impacts of Crude Oil Photo-Induced Toxicity in an Early Life Stage Marine Fish (Sciaenops ocellatus) and Invertebrate (Americamysis bahia)
We investigated the modifying effects of ultraviolet (UV) light and chemical dispersant (Corexit 9500A) on crude oil toxicity in juvenile mysids (≤ 24 h) (Americamysis bahia) and larval red drum (24-72 hpf) (Sciaenops ocellatus). These results demonstrate that crude oil toxicity significantly increases with co-exposure to environmentally relevant UV levels in both species, indicating photo-induced toxicity. This toxicity was further exacerbated by the application of chemical dispersants which increased the dissolution and concentration of oil-derived polycyclic aromatic hydrocarbons (PAHs) in test solutions. To better understand the mechanisms and initiating events of this observed photo-induced toxicity, the incidence of apoptotic cell death and global transcriptomic changes were assessed in larval red drum (24-72 hpf) following co-exposure to crude oil and UV. These results showed that co-exposure to UV and low concentrations of crude oil (<1 µg/L ∑PAH50) induced apoptotic cell death in skin and eye tissue and altered transcriptomic pathways related to visual processing and dermatological disease. To link these cellular and molecular impacts of photo-induced toxicity to apical endpoints of ecological performance, sublethal impacts to growth, metabolic rate, and visually mediated behaviors were explored in larval red drum at 2 developmental stages. These results suggested that earlier life stages may be more sensitive to photo-induced toxicity and that growth and development, particularly of sensory systems, can be sensitive targets of photo-induced toxicity. Together, these studies provide novel insights into the photo-induced toxicity of crude oil in aquatic organisms and can be used to inform future ecological risk assessments.
Hypoxia-Induced Cardiac Arrest Alters Central Nervous System Concentrations of the GLYT2 Glycine Transporter in Zebrafish (Danio rerio)
Hypoxia as a stressor has physiological implications that have been a focal point for many physiological studies in recent years. In some studies, hypoxia had large effects on the organ tissue degeneration, which ultimately effects multiple ecological processes. These organ tissue studies played a part in the development of new fields like neurocardiology, a specialty that studied the relationship between the brain and the heart. This thesis focuses on how hypoxia-induced cardiac arrest alters the amounts of GLYT2, a glycine reuptake transporter, in the central nervous system of zebrafish, Danio rerio. At 7 days post-fertilization (dpf), zebrafish were exposed to acute, severe hypoxia until they lost equilibrium, and minutes later, subsequent cardiac arrest occurred. Zebrafish were then placed into recovery groups to measure the GLYT2 levels at multiple points in zebrafish recovery. Fish were then sacrificed, and their brains dissected. Using immunofluorescence, the outer left optic tectum of the zebrafish was imaged, and mean image pixel fluorescent intensity was taken. There were significant changes (one-way ANOVA) in the levels of GLYT2 compared to that of the control groups during the course of recovery. GLYT2 levels continued to rise through the 24-hour recovery mark but did not show significant difference after 3 hours of recovery. This suggest that GLYT2 levels increased rapidly in the first 3 hours of recovery and continued to increase through 24 hours at a slower rate. Changes in GLYT2 levels may affect motor and sensory information, movement, visualization, and audition in these zebrafish. Further research should be conducted to determine how long it takes for GLYT2 levels to return to baseline, as well as behavioral measurements through each recovery period as it relates to glycine function.
Detection and Classification of Cancer and Other Noncommunicable Diseases Using Neural Network Models
Here, we show that training with multiple noncommunicable diseases (NCDs) is both feasible and beneficial to modeling this class of diseases. We first use data from the Cancer Genome Atlas (TCGA) to train a pan cancer model, and then characterize the information the model has learned about the cancers. In doing this we show that the model has learned concepts that are relevant to the task of cancer classification. We also test the model on datasets derived independently of the TCGA cohort and show that the model is robust to data outside of its training distribution such as precancerous legions and metastatic samples. We then utilize the cancer model as the basis of a transfer learning study where we retrain it on other, non-cancer NCDs. In doing so we show that NCDs with very differing underlying biology contain extractible information relevant to each other allowing for a broader model of NCDs to be developed with existing datasets. We then test the importance of the samples source tissue in the model and find that the NCD class and tissue source may not be independent in our model. To address this, we use the tissue encodings to create augmented samples. We test how successfully we can use these augmented samples to remove or diminish tissue source importance to NCD class through retraining the model. In doing this we make key observations about the nature of concept importance and its usefulness in future neural network explainability efforts.
Neurotoxic Effects of Polycyclic Aromatic Hydrocarbons in Vertebrates, from Behavioral to Cellular Levels
Polycyclic aromatic hydrocarbons (PAHs) are ubiquitous environmental toxicants found in anthropogenic mixtures such as crude oil, air pollution, vehicle exhaust, and in some natural combustion reactions. Single PAHs such as benzo[a]pyrene (BaP) also impact fish behavior when animals are exposed in early life stages and for short periods of time. Aquatic animals such as fish may encounter BaP through road runoff and oil spills, but few studies have examined the impact of aqueous exposure on adult fish, and fewer have examined the resulting fitness-relevant behavioral consequences of BaP and PAH mixtures and their long-term persistence. This dissertation targets this gap in the literature by examining how aqueous exposure to BaP influences anxiety-like behavior, learning, and memory in adult zebrafish, and how parental exposure to the PAH mixture, crude oil, combined with hypoxia affects social and exploratory behavior in unexposed larval zebrafish. We found that learning and memory were not affected by 24 hour exposure to BaP, that anxiety-like behavior was minimally affected, and that locomotor parameters such as distance moved and times spent in darting and immobile states were significantly altered by exposure to BaP. Additionally, we found that parental exposure to crude oil and hypoxia decreased larval velocity. Additionally, we examined how crude oil, BaP, and the detergent COREXIT influence a monolayer of mouse and fish endothelial cells, as an in vitro blood-brain barrier (BBB) model. We found that exposure to BaP in particular caused significant damage to both fish and mammal in vitro BBB models, and damage to the BBB is one potential mechanism by which neural integrity and behavior may be influenced. Understanding how these toxicants influence fish brains and behavior will give insight into how fish populations explore and interact with their environment and with predators, and how these interactions persist even when toxicants are no …
Air Breathing Fish: Development of Air Breathing in Bristlenose Plecos (Ancistrus cirrhosus)
The bristlenose pleco (Ancistrus cirrhosus) is a species of armored catfish in the Loricariidae family that breathes air facultatively when the aquatic environment becomes hypoxic. The bristlenose pleco uses its highly vascularized stomach as an air breathing organ. The two main goals of this developmental study were to determine the size of onset of air breathing and to determine the frequency of air breathing behavior in bristlenose plecos from juveniles to adults. Developing juveniles reach functional maturity within four to six months of hatching and grow to an adult size of eight to ten cm in length. To examine the developmental timing for the onset of air breathing, we tested different sized juveniles beginning at one cm up until 8 cm in length. The developmental timing for the onset of air breathing was measured by exposing each fish to a slowly decreasing aquatic oxygen content from 100% air saturation down to 8% air saturation. Fish were first able to breathe air at just over 2 cm and 1 gram in mass. There was a weak negative correlation between fish length and % air saturation at which air breathing began. When exposed to 15% air saturation, frequency of air breathing was negatively correlated with fish length. Armored catfish are becoming an invasive species in the southern US, outcompeting local fauna potentially because of this adaptation. This research provides important insight into the development of the air breathing adaptation that may allow these fish to outcompete the others.
Secondary Production of Dragonflies: Comparing Ecosystem Function of Ponds within an Urban Landscape in North Central Texas
The change of land use to include more urban areas is considered one of the main threats to biodiversity worldwide. Urban stormwater retention ponds have been built to collect storm runoff intensified by the increase in impervious surfaces. Although subject to environmental pressures like habitat degradation and pollution, these stormwater retention ponds are diversity hotspots by providing habitat for several aquatic and semi-aquatic species, including dragonflies. Previous research in Denton, Texas, has demonstrated that urban stormwater retention ponds support high taxa richness of adult dragonflies, but not for the aquatic nymphs. The current study builds on what we have seen by focusing on the immature aquatic stage as nymphs using secondary production of dominant dragonfly taxa and community structure to compare ecosystem function in three ponds with differing intensities of land use. Comparing communities and secondary production resulted in specific conductivity, dissolved oxygen, complex vegetation, and abundance explaining the differences between dragonfly communities. Secondary production was dependent on abundance which followed the intensity of urban land use surrounding the pond. This study supports that urban land use does have an effect on the functioning of the ponds and shows the importance of studying the communities over a year to get a clearer picture of what is happening in the ponds.
Developmental Effects of a Non-Dioxin-Like Polychlorinated Biphenyl Mixture on Zebrafish (Danio rerio)
PCBs are synthetic organic compounds known for their toxicity to many organisms and are notorious for having large discrepancies between measured and nominal concentrations. Historically thought to be less toxic, non-dioxin-like (NDL) PCBs represent the majority of congeners and are capable of eliciting neurotoxic effects. NDL-PCBs remain understudied, including their effects on aquatic organisms. In the first study, I collected extensive chemistry data and data on neurobehavioral and cardiac endpoints to test the acute effects of exposure to an NDL-PCB mixture on early life stage zebrafish. Neurobehavioral effects observed in the first study indicated a potential for longer term behavioral effects in these fish. In the second study, I collected data on feeding, social, and memory behavior of zebrafish at time points beyond the acute exposure from the first study. Acute and longer-term behavioral endpoints in the first and second studies demonstrated effects from PCB exposure but did not indicate mechanisms. In the third study, I collected untargeted and targeted metabolomic data on amino acid, sugar, anionic compound, and neurotransmitter profiles to determine the specific pathways affected by exposure to an NDL-PCB mixture. These combined data from these studies provide a unique insight into the chemical profile of an NDL-PCB mixture in biological applications and synthesize acute, longer-term, and mechanistic effects on developing zebrafish. These data fully illustrate an adverse outcome pathway from toxicokinetic to population level effects.
The Impact of Invasive Salmonids on Ecosystem Functioning in South America's Sub-Antarctic Inland and Marine Waters
Invasions from coho salmon were first reported in the Cape Horn Biosphere Reserve (CHBR) in 2019 which is the most southern distribution registered to date. The CHBR is known for its high number of endemic species and unique biodiversity, such as the native fishes Galaxias maculatus and Aplochiton taeniatus. There are now three invasive salmonid species in the rivers of CHBR and are a potential threat to the native fish taxa. Stable isotope and gut content analysis were used to understand resource utilization by both native galaxiid and invasive salmonid taxa, as well as aquatic macroinvertebrates and riparian spiders. The natural laboratory study approach applied to this research, allowed for comparisons of differences within streams that contain conditions in which fish do not occur naturally, to sites in which high densities of invasive salmonid exist. Analysis of the trophic niche and diet in this study showed the importance of marine resource use by the native galaxiid and coho salmon juveniles supported with elevated δ15N and δ34S ratios. Diet analysis also confirmed there was the highest similarity between the coho salmon juveniles and the native fish. Altered behavior and habitat use was shown through the isotope and diet analysis for the galaxiid in snow melt streams which could be due to the high density of invasive salmonids in these streams. The invasive salmonids were found to impact aquatic macroinvertebrate populations, specifically larger bodied Trichoptera abundance. Aquatic insect emergence was negatively correlated to salmonid densities. The aquatic insect emergence revealed alterations with significantly higher biomass of aquatic insect emergence in upstream sites without invasive fish. Lastly, aquatic insect predator (Hydrobiosidae: Rheochorema sp.) exhibited a suppressed trophic position in rivers with invasive salmonids. An unexpected finding from the study was the refugium stream habitat conditions that has been shown to be important for …
Conservation, Connectivity, and Coexistence: Understanding Corridor Efficacy in Fragmented Landscapes
Conservation corridors, areas of land connecting patches of natural land cover, are frequently cited and implemented as a restorative strategy to counteract fragmentation. Current corridor ecology focuses on experimental corridor systems or designed and built conservation corridors to assess functionality. Such systems and designs are typically short, straight swaths of homogenous land cover with unambiguous transitions between patches. Quantifying the degree to which amorphous landscape configurations, tortuosity, and heterogeneity of land cover and land uses within the corridor has on functional connectedness is a crucial yet overlooked component of corridor efficacy studies. Corridor literature lacks a robust and repeatable methodology for delineating existing landscape elements, recognizing arbitrary edges, and identifying the start and end of ambiguous transitions between the patches and corridor. Using a set of landscapes being studied as part of a global assessment of corridor efficacy, I designed a workflow that standardizes the boundary of corridor-patch interfaces. The proposed method is a quantitative and repeatable approach that minimizes the subjectivity in corridor delineations. This research investigates the degree to which the existence of a corridor modifies the structural and functional connectivity between patches connected by a corridor compared to an intact reference area.
Combined Effects of Polycyclic Aromatic Hydrocarbons and Ultraviolet Light on Benthic and Pelagic Macroinvertebrates
Crude oil commonly enters freshwater aquatic ecosystems as thin sheens forming on the water surface. Oil contains mixtures of toxic compounds called polycyclic aromatic hydrocarbons (PAHs), some of which are known to be photodynamic, increasing toxicity when combined with ultraviolet radiation. Benthic macroinvertebrate communities are commonly utilized as bioindicators, and as such rely on abundant data in literature concerning benthic macroinvertebrates' relative tolerances to a wide range of pollutants. A series of 10 plastic traps, half of which were filtered from UV radiation, were deployed in an urban pond for 27 days to determine colonization preferences of benthic macroinvertebrates to UV exposure. Results of this in situ experiment indicated that the majority of aquatic insects collected from traps inhabited the UV exposed treatment group, particularly the nonbiting midge, Chironomidae. A series of bioassays were then completed to investigate the sensitivities of a Chironomidae species to thin sheens of crude oil in the presence and absence of UV radiation. All bioassays were conducted using 10 day old Chironomus dilutus larvae cultured in the lab. The series of C. dilutus bioassays were all conducted under the same water quality parameters, temperatures, and oil sheen dosing methods, under a 16:8 photoperiod and exposed to 16 h UV per day. Five replicates (n = 20) were loaded into 350 mL glass crystallizing dishes and exposed to four treatments for 96 hours: no UV/with sheen, with UV/no sheen, both UV and oil sheen, and a control. Three assays with 175 mL water volume were completed, one with no sediment, one with silica sand, and one with fine sand. Sediment type had a significant effect on mortality (p < 0.0001), but significant effects of UV or PAHs were not found. Two more C. dilutus assays were completed with identical parameters as the latter two with sediment, …
Greater, Lesser, Guessers: A Look into the Hybridization of Greater and Lesser Prairie-Chickens
My thesis focuses on the conservation consequences of the hybridization of Lesser Prairie-Chickens in Kansas. Specifically, examining how past land management practices altering the species ranges impact the distinctiveness of Lesser Prairie-Chickens. Each chapter is an individual publication that addresses if the Greater and Lesser Prairie-Chicken are distinct when applying the morphological and biological species concepts. Chapter 2 compares the evolutionary history and morphological construct of Lesser Prairie-Chickens and other Galliformes using morphometric analysis. Chapter 3 uses low-resolution microsatellite data to reflect recent changes at the population level. This study aims to observe the Greater and Lesser Prairie-Chicken using the morphological and biological species concepts, two of the many species concepts, to determine the distinctiveness and rate of hybridization for these closely related species.
Data Mining Using Direct Injection Triple Quadrupole Mass Spectrometry, Infrared Spectroscopy, Inductively Coupled Plasma Optical Emission Spectroscopy, and Polymerase Chain Reaction for the Rapid Identification of Nutraceuticals and Contaminants
There has been a rapid surge toward "organic" products devoid of GMOs, MSGs, and other common compounds found in processed foods that continue to indicate an association with an increased risk for disease. These consumers seek nutrients and vitamins that are lacking in their diet and lifestyle in the form of nutraceuticals for disease prevention and treatment as well as overall lifestyle enhancement. However, these products generally lack clinical evidence as well as legal definition. Due to this ambiguity, nutraceuticals are neither considered a food product nor a pharmaceutical product. Furthermore, due to their alleged natural properties allowing for safe, therapeutic effects, nutraceuticals are being eagerly sought after by consumers in the place of pharmaceuticals. Additionally, since nutraceutical substances are "naturally" derived, there is a general lack of regulation regarding the manufacturing and distribution process. This mismanagement leads to lack of quality assurance (QA) and quality control (QC) protocols strictly implemented to define appropriate production and storage parameters. Without these critical measures, consumers are subjected to contamination of their products resulting from improper storage conditions and unmanaged production. These contaminants often include heavy metal impurities, pesticides, bacterial activity, and may also be adulterated with illicit drugs, all leading to detrimental health and environmental effects.
Migration Tracking, Survival, and Pairing Behavior of American Kestrels Wintering in North Central Texas
The American Kestrel (Falco sparverius) is the smallest and most abundant falcon in North America with a wide geographic range. Unfortunately, surveys have suggested that some kestrel populations have been in decline since the 1950s, though the nominal causes of this decline are unknown. Migratory movement patterns and connectivity have yet to be established for any population of migratory kestrels. In Chapter 2, I investigated methods for attaching migration trackers to kestrels. Specifically, I showed that leg-loop style harnesses may have negatively affected return rates whereas backpack harnesses did not. Based on these results, I recommend that backpack-style Teflon harnesses is the safest and most effective method for attaching tracking devices to small raptors. In Chapter 3, I quantified survivorship for kestrels wintering in north Texas to identify the timing of kestrel mortality. Notably, I found that juvenile kestrels had similar annual survival rates as adults (81.6% versus 79.5%). High overwintering survival in north Texas indicated that once kestrels arrived on their wintering grounds, they were highly likely to survive to spring migration. In Chapter 4, I investigated pairing behaviors previously undocumented in wintering kestrels. I found that winter pairing was relatively common, but more prevalent in urban environments than rural. My data suggested that pairing during the winter could be a coping mechanism to increase kestrel survival in stressful anthropic landscapes. Altogether, this research highlights that the documentation of migratory connectivity is essential to understanding how many processes affect kestrel population dynamics, as I found evidence of potential seasonal carryover effects.
Alterations in the Expression of Proteins Associated with Non-Alcoholic Fatty Liver Disease Observed in the Liver of the C57Bl/6 Wild-Type Male Mouse in Response to Exposure of Mixed Vehicle Emissions and/or High Fat Diet Consumption
Recent epidemiological studies have demonstrated a correlation between the manifestation of non-alcoholic fatty liver disease (NAFLD) and ambient air pollution levels, which is exacerbated by the presence of other risk factors, such as diabetes, dyslipidemia, obesity, and hypertension. We investigated the hypothesis that exposure to a mixture of gasoline and diesel engine emissions (MVE) coupled with the concurrent consumption of a high-fat (HF) diet promotes the development of a NAFLD phenotype within the liver. Three-month-old male C57Bl/6 mice were placed on either a low fat or HF diet and exposed via whole-body inhalation to either filtered (FA) air or MVE (30 µg PM/m3 gasoline engine emissions + 70 µg PM/m3 diesel engine emissions) 6 hr/day for 30 days. Histology revealed mild microvesicular steatosis and hepatocyte hypertrophy in response to MVE exposure alone, compared to FA controls, yielding a classification of "borderline NASH" under the criteria of the modified NAFLD active score (NAS) system. As anticipated, animals on a HF diet exhibited moderate steatosis; however, we also observed inflammatory infiltrates, hepatocyte hypertrophy, and increased lipid accumulation, with the combined effect of HF diet and MVE exposure. Immunofluorescence staining and RT-qPCR of the liver revealed the presence of lipid peroxidation, altered expression of inflammatory markers, induction of hepatic stellate cell activation biomarkers, and conversion to pyroptosis in response to MVE exposure and/or consumption of a HF diet. Our results indicate that inhalation exposure to traffic-generated air pollution initiates hepatocyte injury within the liver, exacerbates lipid accumulation and hepatocyte injury induced by the consumption of a HF diet, and alters molecular pathways associated with inflammation, fibrogenesis, and cell death, thereby contributing to the progression of NAFLD-related pathologies.
Multi-Level Effects of Oxygen Exposure in Endothermic Insects
This dissertation examined the phenotypic plasticity of endothermic, flight and respiratory physiology in response to developmental oxygen exposure in the moth Manduca sexta. Development in both 10% O2 hypoxia and 30% O2 hyperoxia treatments were used to look at the physiological consequence on both ends of the oxygen spectrum. Hypoxic insects reached smaller sizes as adults and had longer pupation lengths than controls. Hyperoxic insects were larger at the end of the larval stage, had increased larval growth rates, but also had longer developmental larval developmental times and pupation lengths than controls. There was a decrease in both metabolic rate and thorax temperatures of hypoxic reared insects at normoxic levels. In flight trials hypoxic insects had the lowest critical flight PO2, and the hyperoxic insects had the highest PO2. There was an increase in hypoxic insect flight muscle mitochondria oxygen consumption in permeabilized fibers, but this did not translate to the isolated flight muscle mitochondria metabolic rates. Rearing oxygen level did not significantly affect mitochondrial density and size; myofibril density and size, or tracheal density and size in flight muscle. Overall, I found that higher levels of organization were more susceptible to the effects of chronic oxygen exposure and found more effects of hypoxia than hyperoxia.
Inferring a Network of Horizontal Gene Flow among Prokaryotes Using Complementary Approaches
Horizontal gene transfer (HGT), a mechanism that facilitates exchange of genetic material between organisms from different lineages, has a profound impact on prokaryotic evolution. To infer HGT, we first developed a comparative genomics-based tool, APP, which can perform phyletic pattern analysis using completely sequenced genomes to identify genes are unique to a genome or have sporadic distribution in its close relatives. Performance assessment against currently available tools on a manually created 18-genome dataset and 2 benchmarking datasets revealed the superior accuracy of APP over other methods. We then utilized a parametric method to construct a gene exchange network. The composition-based method, Jenson-Shannon Codon Bias (JS-CB), groups genes into clusters based on similar codon usage bias. These clusters were analyzed using APP and examined for the enrichment HGT associated marker genes, then annotated as of native or alien origin based on these multiple lines of evidence. Intergenome clustering enabled identification of genes mobilized across alien components of the genomes (alien-alien transfer) and from native components of donor genomes to the recipient genomes (native-alien transfer). Functional classification of alien gene clusters revealed that metabolism associated genes are most frequently mobilized, in concurrence with previous reports, and additionally, a large number of genes with yet unknown functions were found to have been horizontally transferred, a important finding that needs to be further investigated.
Regulation of Receptors in Neuronal Cilia with Development, Seizures, and Knockouts: Implications for Excitability
Neurons commonly have a primary cilium, which is a non-motile organelle extending from the centrosome into the extracellular space. In most brain regions, neuronal cilia are enriched in either somatostatin receptor type 3 (SstR3) or melanin concentrating hormone receptor type 1 (MCHR1), or both. The present immunohistochemical study provides novel evidence that primary cilia regulate neuronal excitability via G-protein coupled receptors (GPCRs), and that their identity is governed by brain region and by competition, both in adulthood and in postnatal development. The hippocampus, which is particularly vulnerable to seizures, has opposing gradients of SstR3(+) and MCHR1(+) ciliary GPCRs. We hypothesized that there is a competition between these two ciliary GPCRs, which might take place on any level from gene expression to presence in the cilium. We examined whether receptor colocalization occurs transiently in development before ciliary GPCR dominance is established in neurons in the CNS. In postnatal CA1 and CA3, the first GPCR to appear in cilia was the one that will dominate in adults: MCHR1 in CA1 and SstR3 in CA3. Some days later, the second GPCR was expressed along with the first; dual-receptor cilia were the exclusive type until single-receptor cilia emerged again around P14. Single-receptor cilia then increased in numbers through adulthood. By identifying ciliary receptors that modulate seizure activity in mice, the present study lays a foundation for therapeutic approaches to reduce neuronal excitotoxicity underlying cell death in epilepsy, CNS injury, and neurodegenerative diseases.
Temperature Change and Its Consequences for the Physiology of the Eurythermic Sheepshead Minnow (Cyprinodon variegatus)
The estuarine sheepshead minnow (Cyprinodon variegatus) is the most eurythermic fish species, with a thermal tolerance window between 0.6°C and 45.1°C. However, little is known about the physiological mechanisms that allow this species to survive this temperature range. In order to understand how sheepshead minnow physiology is affected by temperature acclimation and acute changes in temperature, I conducted research on this species using a multi-level approach. I began at the organismal level, and examined the effects of these temperature changes on the sheepshead minnow's metabolic rate and swimming performance. The next chapter investigated the effects of changing temperatures on cardiac function (i.e., tissue/organ specific effects). In the final chapter, I conducted research at the sub-cellular level, and determined how mitochondrial bioenergetics / function is impacted by changing temperatures. This research shows that while sheepshead minnows are able to sustain heart function and mitochondrial respiration over a broad range of temperatures; they also display a plastic temperature response which is associated with the downregulation of standard metabolic rate and cardiac remodeling to maintain force generation. Collectively, these physiological responses may contribute to the sheepshead minnow's ability to maintain physiological and organismal function across a large temperature range.
Influence of Hypoxia on Acute Lead Toxicity and Calcium Homeostasis in Early Life Stage Zebrafish (Danio rerio)
The purpose of this study was to investigate the effects of Pb and hypoxia co-exposure on Pb toxicity and Ca homeostasis in early life stage (ELS) zebrafish (Danio rerio). Previous evidence indicates that exposure of ELS zebrafish to hypoxia (~20% air saturation) reduces Ca uptake, likely through down-regulation of the apical epithelial Ca channel (ECaC). Considering that Pb and Ca are known antagonists and compete for uptake pathways, it was hypothesized that co-exposure of Pb with hypoxia would decrease Pb toxicity by reducing Pb uptake (likely mediated through a reduced number of ECaCs). However, it was shown that at 96 hpf, whole body accumulation of both Pb and Ca was lower at 40% air saturation compared to 100% and 20% air saturation. This result closely aligned with the 96h LC50 results which showed the highest mortality of zebrafish at 40% compared to the other air saturation levels. This suggests that toxicity is likely the result of exacerbated hypocalcemia at 40% air saturation due to both Pb competition for Ca binding to Ca uptake channels/transporters, such as ECaC, and potentially reduced expression of such channels/transporters in response to this level of hypoxia. Overall, it appears that ELS zebrafish respond differentially to the 40% and 20% hypoxia levels when co-exposed with Pb. Further investigation is needed to illustrate the physiological and molecular mechanisms underlying this response.
Production and Optimization of Para-Hydroxybenzoic Acid (pHBA) in Algae Using Metabolic Engineering and Genomics Approaches
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, literature was reviewed to find a suitable UGT candidate to enable the engineering of the glycosylation mechanism in the alga. A transgenic algal line with gene encoding UGT89B1 was created and fed with varying concentrations of pHBA. HPLC chromatograms from the extracts revealed the presence of phenolic glucoside. Following this, C. reinhardtii was co-transformed with ubiC and gene encoding UGT89B1; this led to the production of pHBA and further glycosylation to pHBA glucoside (phenolic glucoside). The maximum yield of pHBA yields in these cell lines was 180 mg/L. Growing C. reinhardtii lines producing pHBA on a large scale can lead …
Reduced Visceral Fat and Biological Indices of Inflammation Following Combined Prebiotic/Probiotic Supplementation in Free Living Adults
Probiotics/prebiotic supplementation represents a viable option for addressing systemic inflammation and chronic disease risk resulting from excessive body weight. The purpose of this feasibility study was to determine if 90-d of supplementation with prebiotic and probiotic could alter mRNA responsible for inflammation and subsequently metabolic health in weight stable overweight adults. Participants were advised to not change their diet or exercise habits during the study. All protocols were approved by the University IRB and participants gave written informed consent. Participants were randomly assigned to either placebo (N=7; rice flour) or combined (N=8) prebiotic (PreticX® Xylooligosaccharide; 0.8 g/d; ADIP) and probiotic (MegaDuo® Bacillus subtilis HU58 and Bacillus coagulans SC-208; 3 Billion CFU/d) and measurements were made at baseline, 30, 60, and 90-d. Whole body DXA scans (GE iDXA®) and blood 574-plex mRNA analysis (Nanostring®) were used to generate primary outcomes. Compared to placebo, supplementation was associated with a 36% reduction in visceral adipose tissue (p = 0.001). Supplement resulted in significant, differential expression of 15 mRNA associated with adipose tissue inflammation, systemic inflammation, and/or chronic disease risk. The key findings support that 90-d prebiotic/probiotic supplementation may be associated with an improved metabolic health, reduced adipose tissue inflammation, reduced systemic inflammation, and reduced chronic disease risk. Collectively these findings demonstrate the potential of a prebiotic/probiotic supplement to impact metabolic health risk independent of weight loss in free-living individuals.
CO2 Transport and Acid-Base Status during Fluctuations in Metabolic Status in Reptiles
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.
Investigating the Effects of Inhaled Diesel Exhaust Particles on Gut Microbiome, Intestinal Integrity, Systemic Inflammation, and Biomarkers of Cardiovascular Disease in Wildtype Mice
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 the intestine of HF animals. Furthermore, we determined that exposure to inhaled DEP increases systemic LPS and inflammatory markers IL-1α, IL-3, G-CSF, and TNF-α. Furthermore, we found that inhaled DEP exposure results in increased CVD biomarkers sICAM-1, sP-selectin, and thrombomodulin in the heart. Probiotic treatment was effective in attenuating LPS, inflammatory responses, and CVD biomarkers in HF animals, validating the involvement of the microbiome in mediating inhaled DEP-mediated responses. Considering the effects we observed in the microbiota and systemically of the HF and probiotic treatment animals, we investigated the effects of inhaled DEP on intestinal integrity and inflammation in HF …
Multiple Dimensions of Fish Functional Traits, Trait Relationships, and Associations with Community Structure and Dynamics
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 dynamics in chapter 3.
Flow-Recruitment Relationships of Smallmouth Buffalo (Ictiobus bubalus) in Three Texas River Basins
This project focused on the relationship between instream flows and smallmouth buffalo (Ictiobus bubalus) recruitment in the Gulf Coastal Plain of Texas. The flow regime is the dominant factor in lotic systems and, consequently, the relationship between instream flows, including impacts to natural flow regimes, and life-history is a subject of growing interest. Smallmouth buffalo is a good model to investigate the relationship between river flows and variable interannual recruitment success of periodic life-history strategist fish species. Smallmouth buffalo were collected from the Brazos, Colorado, and Guadalupe Rivers of Texas, U.S.A., and otoliths were extracted from individuals in the field and sectioned and photographed in the lab. Photographs of sectioned otoliths were used to estimate age and thus the year in which the individual was spawned by counting back from the time of capture. Population age structure (i.e. a ‘state' or condition at a point in time) was used to infer effects of flow variation on a rates-based process (i.e. recruitment). After controlling for mortality using recruitment index values, interannual variation in recruitment was modeled using multiple components of the flow regime quantified as indicators of hydrologic alteration (IHA) variables based on daily discharge data from USGS gaging stations in each river system. Model selection followed a two-tier approach, first fitting models using only flow attributes associated with the spawning season then adding additional informative parameters from the pre-spawn and post-spawn periods. The primary finding from model selection was that duration of high flow pulses during the spawning season is a critical component of the flow regime associated with successful Smallmouth Buffalo recruitment. These findings have implications for river management and conservation of ecological integrity, in particular populations of periodic life-history strategist species.
Analysis of the Accumulation, Toxic Effects, and Risk of Persistent Organic Pollutants in Pinnipeds
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.
Analysis of Multipartite Bacterial Genomes Using Alignment-Free and Alignment-Based Pipelines
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 content of multipartite genomes and their unipartite relatives, and leveraged this to identify genes that are deemed important by machine learning in discriminating between multipartite and unipartite genomes. This approach led to the identification of marker genes that could be used in discriminating between bacteria with multipartite genomes and. bacteria with single chromosome genomes Furthermore, we examined modules in gene co-expression networks of multipartite Rhodobacter sphaeroides 2.4.1 and its close unipartite relative Rhodobacter capsulatus SB 1003 that were enriched in genes differentially expressing under stressful conditions representing different experiments. This led to the identification of 6 modules in the Rhodobacter …
Sociality in Harris's Hawks Revisited: Patterns of Reproductive Output and Delayed Dispersal
In the lower Rio Grande Valley of south Texas, more than half the nesting groups of Harris's hawks (Parabuteo unicinctus) include at least one auxiliary group member in addition to a breeding pair. To provide further insight into cooperatively breeding raptors, I evaluated sociality in Harris's hawks through the dual benefits framework. I explored the formation, structure, and stability of cooperative group formation across a spatially variable study area, which includes high levels of urbanization and development as well as remote, undisturbed native habitats with low anthropogenic impact. I used color banding, regular censuses of active territories, and a microsatellite relatedness analysis to examine patterns of sociality, including delayed dispersal, the effect of auxiliary group members on reproductive output, parentage of broods, and the relatedness of auxiliaries compared to the nestlings in their territories. I confirmed cooperative polygamy with genetic techniques for the first time in Harris's hawks and found 58% of juvenile hawks delayed dispersal for at least 6 mo. Using the dual benefits framework, I found social associations that formed through delayed dispersal followed predictions for resource-defense benefits, but sociality among mature non-related hawks more closely followed predictions associated with collective action benefits, specifically reproductive output was significantly reduced in undeveloped habitats, presumably due to a less predictable prey-base.
Benefits of Probiotics on Mortality, Growth Performance, Physiological Condition and Gut Histomophology of Juvenile Red Drum (Sciaenops ocellatus)
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 within each intestinal region were also quantified: (i) perimeter ratio (PR) between the internal perimeter (IP) of the intestinal lumen and the external perimeter (EP) of the intestine where, PR = IP/EP; (ii) width of lamina propria (wLP); (iii) thickness of the muscle layer (tM); (iv) the number of goblet cells per segments (GC); and (v) height of enterocytes (hE). Overall, Li and Mi significantly increased by 13.4 ± 1.2% and 11.8 ± 0.9%, respectively, and Md decreased by 33.2 ± 1.21% compared to controls. Significant increases in microvilli heights, PR (by 21.3 ± 1.2%), tM (by 18.4 ± 0.9%), …
Breeding Ecology and Migratory Connectivity of Passerines in the World's Southernmost Forests
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 are not maintained in the wintering grounds. My study opens further questions about the mechanisms driving differences in breeding strategies among populations. In addition, further research is needed to assess hypotheses that could explain the mismatch between nest-site selection and nest survival and to understand what drives elaenias' movements, not only during winter but throughout their annual cycle.
Probabilistic Modeling for Whole Metagenome Profiling
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 of clusters of similar segments, which were then used to sample representative read fragments to constitute training datasets. The parameters of a logistic regression model were learnt from these training datasets using a Bayesian optimization procedure. This allowed us to establish thresholds for classifying metagenomic reads by SMM. This led to the development of a Python-based frontend that combines our SMM algorithm with the logistic regression optimization, named POSMM (Python Optimized Standard Markov Model). POSMM provides a much-needed alternative to metagenome profiling programs. Our algorithm that builds the genome models on the fly, and thus obviates the need to build …
A Genetic Assessment of the Mating System of a Suburban Red-Shouldered Hawk Population in Southwest Ohio
Considering the high reproductive investment of the social male and the cost to the female of losing this benefit by soliciting copulations outside the social pair bond, it is expected that most raptor populations would exhibit low to no occurrence of extra-pair paternity (EPP). This holds true for the majority of raptor species studied to date with only one exception of an urban Cooper's hawk (Accipiter cooperii) study which reported an unexpectedly high extra-pair young frequency of 19.29%. In our study we examined the frequency of EPP within a red-shouldered hawk (Buteo lineatus) population residing in the suburban/urban matrix of southwest Ohio. During the breeding seasons of 2018 and 2019, 181 breeding age and nestling individuals were color-banded and sampled for genetic analysis using nine microsatellite loci. After genotyping a total of 40 broods (with at least two nestlings per brood) and both presumptive parents of each brood, no clear evidence of EPP was detected. However, at one nest site, the entire brood of four chicks was not sired by the adult male observed during the courtship period, nor another adult male observed tending the chicks later in the season. We suspect that this particular nest represented two instances of rapid mate replacement rather than extra-pair fertilization by a third unsampled male, because none of the chicks were sired by either of the two adult males observed at the nest. We also reviewed potential factors contributing to our finding of overall genetic monogamy in our study population in comparison to other raptor taxa EPP studies. Our results suggested that factors other than habitat composition alone play an important role in determining the type of breeding strategy exhibited by different raptor populations.
A Test of the Female Mimicry Hypothesis in Painted Buntings (Passerina ciris)
While female mimicry and lower status signaling hypotheses of delayed plumage maturation have received much discussion in the literature, the experimental tests of these hypotheses have been infrequent. Those experimental tests often use a simulated intruder method with artificial model intruders rather than using live conspecific birds as intruders. Subadult male painted buntings (Passerina ciris) possess delayed plumage maturation where they appear visually identical to adult females during their first potential breeding season, while adult males are strikingly different in plumage coloration. Here I test the behavioral responses in a territorial population of painted buntings that exhibits extreme delayed plumage maturation using a simulated territorial intrusion experiment to measure territorial male behavioral response when presented with live caged intruders of both subadult and adult males. Territorial adult males were significantly more likely to initiate an attack and continue to attack caged adult male intruders than compared to caged subadult male intruders. This result supports both the female mimicry and status signaling hypotheses, and does not support the cryptic hypothesis. Additionally, in anecdotal observations, territorial males occasionally performed mating display behaviors to caged subadult male intruders. These results further suggest that territorial male painted buntings may identify subadult males as potential mates, supporting the female mimicry hypothesis for subadult males in this species. To what degree subadult males may benefit from DPM deserves further study.
Traffic-Generated Air Pollution-Exposure Mediated Expression of Factors Associated with Progression of Multiple Sclerosis in a Female Polipoprotein E Knockout Mouse Model
Environmental air pollution is one risk factor associated with the onset and progression of multiple sclerosis (MS). In this project, we investigated the effects of ubiquitous traffic-generated pollutants, namely a mixture of gasoline and diesel vehicle exhaust (MVE), on signaling pathways associated with the pathophysiology of MS in the central nervous system (CNS) of either ovary intact (ov+) or ovariectomized (ov-) female Apolipoprotein (Apo) E-/-. Specifically, we investigated whether a subchronic inhalation exposure to MVE (200 PM μg/m3; 6 hr/d, 7d/wk, 30d) vs. filtered air (FA) controls altered myelination, T cell infiltration, blood-brain barrier (BBB) integrity, or production of reactive oxygen species (ROS) and expression of neuroinflammation markers in the CNS ov+ and ov- Apo E-/- mice. Our results revealed that inhalation exposure to MVE resulted in increased demyelination and CD4+ and CD8+ T cell infiltration, associated with alterations in BBB integrity. Disruption of the BBB was evidenced by decreased tight junction (TJ) protein expression, increased matrix metalloproteinase (MMPs) activity, and increased permeability of immunoglobin (Ig) G, which were more pronounced in the MVE ov- group. Moreover, MVE-exposure also promoted ROS and neuroinflammatory signaling in the CNS of ov+ and ov- mice, compared to FA groups. To analyze mechanisms that may contribute to MVE-exposure mediated inflammatory signaling in the CNS, we examined the NF-κB signaling pathway components, namely IKK subunits, IKKα, and IKKβ, as well as RelA. MVE -exposure did not alter the expression of either IKKα and IKKβ or RelA. However, increased expression of IKKα and IKKβ mRNA was observed in both FA ov- and MVE ov- groups, indicating female sex steroid hormone signaling involvement. Investigation of hormone receptors expression revealed a reduction in cerebral ERα mRNA expression, compared to ov+ mice; however, MVE-exposure resulted in an even further decrease in expression of ERα mRNA, while ERβ and PRO …
Investigating the Effects of Traffic-Generated Air-Pollution on the Microbiome and Immune Responses in Lungs of Wildtype Mice
There is increasing evidence indicating that exposure to air pollutants may be associated with the onset of several respiratory diseases such as allergic airway disease and chronic obstructive pulmonary disorder (COPD). Many lung diseases demonstrate an outgrowth of pathogenic bacteria belonging to the Proteobacteria phylum, and the incidence of occurrence of these diseases is higher in heavily polluted regions. Within the human body, the lungs are among the first to be exposed to the harmful effects of inhaled pollutants and microbes. Research in the past few decades have expounded on the air-pollution-induced local and systemic inflammatory responses, but the involvement of the lung microbial communities has not yet been well-characterized. Lungs were historically considered to be sterile, but recent advances have demonstrated that the lower respiratory tract is replete with a wide variety of microorganisms - both in health and disease. Recent studies show that these lung microbes may play a significant role in modulating the immune environment by inducing IgA and mucus production. Air pollutants have previously been shown to alter intestinal bacterial populations that increase susceptibility to inflammatory diseases; however, to date, the effects of traffic-generated air pollutants on the resident microbial communities on the lungs have not been explored. The microbiome is influenced by several factors, including diet and environmental exposures. A large percentage of the Western world population consumes a high-fat (HF) diet which has resulted in the epidemic of obesity. Consumption of an HF diet has been shown to alter the intestinal microflora and increase baseline inflammation. We aimed to understand whether diet might also contribute to the alteration of the commensal lung microbiome, either alone or related to exposure. Thus, we investigated the hypothesis that exposure to air pollutants can alter the commensal lung microbiota, thereby promoting alterations in the lung's immune and inflammatory …
Peregrine Falcon (Falco peregrinus) Subspecies Phylogenomics Using Whole Genome Re-Sequencing
Peregrine falcon subspecies taxonomy is widely debated due to uncertainty in their evolutionary history and unresolved phylogenetic reconstruction using both morphological and molecular data. Previous genetic work has shown limited support for subspecies taxonomy largely as a result of molecular markers used, potential contemporary gene flow, incomplete lineage sorting, and ancestral polymorphisms. With the advent of next-generation sequencing, the cost of generating large amounts of sequence data has dropped significantly, making whole genome re-sequencing (WGR) studies of non-model organisms more tangible. In this study, WGR methods have been utilized to investigate the phylogenetic relationships among all 20 currently recognized peregrine falcon subspecies. By generating whole-genome data for all 20 subspecies, subspecies specific diagnostic SNPs have been identified to aid in subspecies delimitation. Results of this study broadly support current subspecies, however, reveal that further study is needed to investigate regional relationships among subspecies in Asia, Australia, and western North America. With these results, conservation efforts can be further supported by allowing for accurate delimitation of local subspecies and subspecies boundaries.
Investigating the Mechanisms involved in Traffic-Generated Air Pollution: Mediated Disruption of the Blood-Brain Barrier in a Wild Type Mouse Model using a Pharmaceutical Intervention Approach
This study investigated whether oxLDL and/or angiotensin (Ang) II signaling pathways mediate traffic-generated air pollution- exposure induced alterations in blood-brain barrier (BBB) integrity and permeability in a healthy wild type (C57Bl/6) mouse model; additionally, whether these outcomes are exacerbated by a high fat-diet investigated. An environmentally relevant concentration of a mixture of vehicle engine exhaust (MVE) was used. To investigate the hypotheses, 12 wk old male C57Bl/6 mice on either a high fat (HF) or low fat (LF) diet were randomly assigned to inhalational exposure of either filtered-air (FA) or 30 µg PM/m3 diesel exhaust + 70 µg PM/m3 gasoline exhaust (MVE) for 6 hr/day for 30 days. Additionally, we examined mechanisms involved in MVE-mediated alterations BBB integrity using a novel BBB co-culture in vitro model, consisting of mouse primary cerebral vascular endothelial cells on an apical transwell and astrocytes in the basal compartment, which was treated with plasma from the mice on our exposure study. Our in vivo exposure study results showed that MVE inhalation resulted in increased circulating plasma oxLDL and Ang II, compared to FA controls. Additionally, we observed increased cerebral microvascular expression of oxLDL receptors, LOX-1 and CD-36, and Ang II receptor subtype 1 (AT1) in MVE-exposed C57Bl/6 mice, which was further exacerbated with consumption of an HF diet. Increased signaling of both Ang II and oxLDL was associated with decreased BBB integrity, as evidenced by the concurrent reduction in expression of tight junction (TJ) protein claudin-5 and increased permeability of sodium fluorescein (Na-F) from the blood into the cerebral parenchyma. Our results suggest that possible mechanisms involved in oxLDL and/or Ang II-mediated alterations in BBB integrity include oxidative stress and upregulated expression and activity of matrix metalloproteinase (MMP)-9, which is associated with degradation of TJ proteins in the BBB. Our in vitro BBB co-culture results …
Metabolic Responses to Crude Oil during Very Early Development in the Zebrafish (Danio rerio)
The present study sought to determine some morphological and physiological critical windows during very early development in zebrafish exposed to crude oil. I hypothesized that exposed zebrafish would present a decrease in survival rate and body mass, and an increase in routine oxygen consumption (ṀO2), and critical oxygen tension (PCrit). To test these hypotheses, zebrafish were acutely exposed (24 h) during different days of development (1 to 6 days post-fertilization, dpf) to different concentrations of high-energy water-accommodated fractions (HEWAFs). The endpoints of survival, body mass, routine oxygen consumption, and critical oxygen partial pressure were measured at 7 dpf. Survival rate decreased based on the exposure concentration but not as a function of the day of crude oil exposure. No significant effects were found in PCrit. Body mass was reduced by the different concentrations of HEWAF, with the size of the effect varying with exposure day, with the effect strongest on when exposure occurred at 2 and 3 dpf. Oxygen consumption (ṀO2) differed significantly depending upon the day of exposure in fish exposed to crude oil. Specifically, HEWAF exposure significantly increased ṀO2 in larvae exposed at 3 dpf (9.081 µmol O2/g/h, ±0.559) versus 2 dpf (6.068 µmol O2/g/h, ±0.652) and 6 dpf (6.485 µmol O2/g/h, ±0.609). Overall, the main effects on body mass and ṀO2 occurred at crude oil exposures during 3 dpf. The presence of a critical window in fish is proposed at this developmental time, which coincides with the hatching period.
The Consequences of Early Life Stage Thyroid Suppression on Immune Function in the Fathead Minnow (Pimephales promelas)
Current evidence suggests that thyroid hormones (THs) may impact development of the immune system. However, studies that explore the role of THs in immune development are limited, and the mechanisms leading to alterations in immune function are poorly understood. It is important to elucidate the role of THs in immune development given that many environmental contaminants have been shown to disrupt TH homeostasis and may also have negative impacts on the immune system. As such, the main goal of this study was to determine the long-term consequences of early life stage (ELS) hypothyroidism on immune function. To achieve this goal, it was first necessary to further characterize basic immune function in the selected model species, the fathead minnow (FHM, Pimephales promelas). Preliminary studies were conducted to describe the transcriptomic response to Yersinia ruckeri and adapt assays for the assessment of respiratory burst and phagocytic cell activity. To determine the long-term effects of ELS hypothyroidism, FHMs were exposed to the model thyroid suppressant propylthiouracil (PTU) from <1 to 30 days post hatch and reared under normal conditions. Upon reaching adulthood, ex vivo immune cell function and the in vivo immune response to Y. ruckeri were assessed. Fish exposed to PTU experienced significant alterations in gene networks associated with immune cell function as well as significant decreases in phagocytic cell activity. However, immune-related alterations at the molecular and cellular levels did not manifest themselves at higher levels of organization as ELS hypothyroidism did not affect any other immune-related endpoints, including pathogen resistance. To our knowledge, this is the first study to provide evidence that ELS hypothyroidism causes long-term effects on the immune system in fish.
The Effects of Probiotics on Growth, and Metabolism in Juvenile Oreochromis mossambicus (Mozambique Tilapia)
Improving growth, lowering mortality rates, and having a faster turnaround to harvest is essential for the future of commercial aquaculture. The primary goal of this study was to determine if introducing a single strain probiotic Lactobacillus rhamnosus IMC 501 into the feed regimen of a commercially important aquaculture freshwater fish, Mozambique tilapia (Oreochromis mossambicus), would decrease mortality; change metabolic rates; and increase tissue wet mass (MW), standard length, growth rate and feed conversion rate (FCRs). IMC501 was added to the fishmeal in four increasing concentrations and compared to a control without probiotics. Results from two-way ANOVAs showed that both treatment levels and elapsed time had a significant effect on both mean standard length and wet mass; in the latter case, time points and treatments interacted with one another, showing that tilapia grew best with a moderate level of probiotics present. The growth benefits of probiotics continued for months after the initial treatments. Oxygen consumption (metabolic rate) was measured using closed respirometry and resulted in recording the first values for juvenile tilapia treated with probiotics. For oxygen consumption, there were significant treatment and time effects with significant interactions, indicating that metabolism increased with probiotics once the dosage exceeded three times the industry level. These results are consistent with the observed increases in mass, length and growth rates. These results demonstrate the importance of conducting dose-response experiments in order to determine the most effective concentration of probiotics in juvenile freshwater fish. Importantly, probiotics at the right concentration increase metabolic rates and can positively influence tilapia growth, which is of interest for the optimization of Mozambique tilapia production in aquaculture.
The Ecological Importance and Population Structure of Magellanic Woodpeckers (Campephilus magellanicus) in the World's Southernmost Forests
The Magellanic woodpecker (Campephilus magellanicus), the largest woodpecker in Central and South America, is declining throughout its range. Notably, limited research has been conducted on the Campephilus genus, especially for island populations. Mostly during austral summers 2015-2017, I explored the ecological importance and population structure of Magellanic woodpeckers on Navarino Island, Chile (55°04′S, 67°40′W). First, I assessed how coleopteran larval density and distribution within trees may influence Magellanic woodpecker foraging behavior. Second, I designed an experiment to determine which of three detection methods would best elicit a woodpecker detection. Third, I conducted a population genetics study to elucidate trends within and among Magellanic woodpecker populations to better inform management decisions. I identified two coleopteran species: one lucanid (Erichius femoralis) and one cerambycid (Microplophorus magellanicus) within two lenga (Nothofagus pumilio) trees foraged on by Magellanic woodpeckers. Maximum woodpecker excavation depths were 71-90 mm; most larval gallery depths were 51-70 mm. The drumming device most effectively influenced the likelihood of a woodpecker detection. The odds of a woodpecker responding were 2.14 times more likely than responding to either a playback or control. On Navarino Island, I observed a pattern of isolation by distance among sampled woodpeckers, slight female sex-biased dispersal, and family groups likely consisted of nuclear families with partner replacement. Genetic diversity estimates were lower for Navarino woodpeckers than for mainland populations. Future research should build upon these results to better understand Magellanic woodpecker life history characteristics and its role in the ecosystem.
Storm Water Retention Ponds: An Important Source of Aquatic Macroinvertebrate Diversity in a Semi-Arid Urban Landscape of Denton, Texas
The City of Denton, located in a semi-arid region of Texas, has over 200 manmade ponds within its city limits. Many of these ponds, located in densely populated areas, are engineered to control storm water runoff. There is a general lack of recognition of the value these waters contribute to regional biodiversity and as greenspaces. This study, conducted in Denton, is monitoring habitat variables and macroinvertebrate diversity in a series of ponds selected to represent a gradient of urban influences. The objective of this study is to identify the variables associated with the highest diversity. Using drone imagery and a meter square box sampler, the quantitative approach allowed for delineation of three habitat types and area. The macroinvertebrates where identified to the genus level which allowed for higher resolution and resulted in stronger comparisons of the communities and conditions of the ponds. Taxa richness was positively correlated to pond size and trees along shoreline and negatively associated with average depth. Overall, submerged vegetation supported highest diversity and abundance, especially genera of Chironomidae (Diptera). Conductivity was associated with urban influences and the most urban influenced pond had the lowest taxa richness, but also reduced habitat area. Results of this study conclude that these stormwater ponds benefit to the ecology of the city and provide beautiful, green spaces. If managed correctly, these systems can be incorporated into sustainable development in the future of the City of Denton.
Transgenerational Responses to Environmental Stressors in Vertebrates: From Organisms to Molecules
Genomic modifications occur slowly across generations, whereas short-term epigenetic transgenerational inheritance of adaptive phenotypes may be immediately beneficial to large numbers of individuals, acting as a bridge for survival when adverse environments occur. In this study we used dietary exposure to crude oil as an example of an environmental stressor to assess its effects from the molecular to the organismal levels in piscine and avian animal models. In addition, we assessed the role of the parental exposures on their offspring F1 generation. The research developed in this dissertation has contributed to several areas of investigation including molecular biology, animal physiology, and evolutionary biology. The quantitative information from these studies may be utilized to supplement information regarding the proximate and ultimate effects of environmental stressors on fish and bird populations. Furthermore, this information may be used as additional support for understanding the conservation of the responses from the molecular to the whole organismal levels across the vertebrate taxa, as well as their implications for population survival and maintenance. Additionally, the zebrafish (Danio rerio), the Siamese fighting fish (Betta splendens) and the king quail (Coturnix chinensis) have proven to be excellent models to start building a strong basis for understanding the effects of environmental stressors and transgenerational epigenetic phenomena using a multi-level approach. Furthermore, as more raw data and information is discovered, the concatenation of development, organismal variation, epigenetics inheritance, natural selection, speciation and evolution is being slowly decrypted.
Optical Brain Imaging of Motor Cortex to Decode Movement Direction using Cross-Correlation Analysis
The goal of this study is to determine the intentional movement direction based on the neural signals recorded from the motor cortex using optical brain imaging techniques. Towards this goal, we developed a cross-correlation analysis technique to determine the movement direction from the hemodynamic signals recorded from the motor cortex. Healthy human subjects were asked to perform a two-dimensional hand movement in two orthogonal directions while the hemodynamic signals were recorded from the motor cortex simultaneously with the movements. The movement directions were correlated with the hemodynamic signals to establish the cross-correlation patterns of firings among these neurons. Based on the specific cross-correlation patterns with respect to the different movement directions, we can distinguish the different intentional movement directions between front-back and right-left movements. This is based on the hypothesis that different movement directions can be determined by different cooperative firings among various groups of neurons. By identifying the different correlation patterns of brain activities with each group of neurons for each movement, we can decode the specific movement direction based on the hemodynamic signals. By developing such a computational method to decode movement direction, it can be used to control the direction of a wheelchair for paralyzed patients based on the changes in hemodynamic signals recorded using non-invasive optical imaging techniques.
Phenotype Analysis of the CISD Gene Family Relative to Mitochondrial Function in Caenorhabditis elegans
NEET proteins belong to a unique class of [2Fe-2S] cluster proteins that have been shown to participate in various biological processes such as regulating iron, reactive oxygen species and apoptosis within the cell and are localized to the mitochondria. Disruption of the mitochondrial NEET proteins are associated with different human diseases such as obesity, neurodegeneration, cancer and diabetes. In humans, a missense mutation in the CISD2 gene results in a heritable multisystem disorder termed Wolfram syndrome 2 (WFS2), a disease which displays an early onset of juvenile diabetes and various neuropsychiatric disorders. The C. elegans genome contains three previously uncharacterized cisd genes: cisd-1, which has homology to the human CISD1 and CISD2, and cisd-3.1 and cisd-3.2, both of which have homology to the human CISD3. Disruption of the cisd-3 gene(s) function results in mis-regulation of proteostasis in the mitochondria, whereas cisd-1 and cisd-3.1 disruption impacts proteostasis in the endoplasmic reticulum. Reduction of cisd-3.2 gene function also leads to a developmental delay in C. elegans. A knockout mutation of the cisd-3.2(pn68) gene function results in various germline defects including delayed development progression and morphological defects. Furthermore, I show the cisd gene(s) and protein expression profiles is present relative to sex, tissue type and developmental stages. This work is significant because it provides further insight of the essential role of CISD-3 relative to C. elegans. Furthermore, my studies can contribute to new genetic discoveries that will widen the scientific research relative to NEET protein family studies.
The Metabolic Physiology of Planarian Flatworms
Using a high throughput closed respirometry method to measure oxygen consumption, I determined metabolic rates in asexual and sexual Schmidtea mediterranea and Girardia dorotocephala, as a function of temperature, taxon, stressors, reproductive mode, age, regeneration, and specific dynamic action. This study has shown that oxygen consumption can reliably be measured in planaria using optode closed respirometry, and also provided a reliable method for measuring wet mass in planaria, which has been a challenge to researchers in the past. This research revealed that oxygen consumption in S. mediterranea is 1.5-2.1X greater in the sexual strain over the asexual strain at 13-18°C. Within the sexual strain, oxygen consumption is 1.5 -2.2X greater in sexually mature adults over the sexually immature groups (hatchlings, juveniles, and regenerating sexuals). Furthermore, I was able to quantify differences in sexual morphology between these groups exhibiting significant differences in oxygen consumption. The results of this research supports a theory of higher metabolic costs with sexual maturity in S. mediterranea. Therefore, this study has established sexual and asexual S. mediterranea as simple, yet attractive models for investigating energetic costs between sexual and asexual phenotypes. This research also provided quantitative values for specific dynamic action in planaria, with a maximum increase in oxygen consumption of 160% induced by feeding, as well as metabolic relationships in planaria involving temperature, age, and regeneration. These values establish planaria as one of the simplest animal models in which common metabolic patterns, such as SDA and poikilothermic temperature sensitivity, have been demonstrated. Therefore, this research has contributed to the overall knowledge of the basic physiology in this animal, providing the framework for future metabolic studies in planaria involving environmental factors, reproduction, regeneration, development, and aging. Information from this study may supplement interpretation and understanding of modern cellular, molecular, and genomic studies in planaria.
Back to Top of Screen