Biology Commons^™

The Effects Of Anthropogenic Modification To The Landscape On Turtle Distribution And Health In South Dakota, Anna C. Kase

Dissertations and Theses

The Missouri River is a dynamic ecosystem that has been affected by anthropogenic modification and activity. The implementation of mainstem dams, reservoir formation, pollution, and non-native species invasions have greatly impacted this habitat and its constituents, particularly the false map turtle (Graptemys pseudogeographica). False map turtles are listed as a state threatened species in South Dakota and a focused large-scale assessment of their distribution and health has not been conducted since the 1960s. To address the gap in knowledge of how anthropogenic modifications to the Missouri River have impacted false map turtle distributions and health, the effect of a common …

Cop9 Signalosome Promotes Neointimal Hyperplasia Via Deneddyaltion And Csn5-Mediated Nuclear Export, Samiksha Giri

Dissertations and Theses

Neointimal hyperplasia (NH) is a common pathological response to vascular injury and mediated primarily by vascular smooth muscle cell (VSMC) migration and proliferation. The COP9 signalosome (CSN) is formed by 8 canonical subunits (CSN1 through CSN8) with its deneddylation activity residing in CSN5. Each or some of CSN subunits may have deneddylation-independent function but this is not well established. Despite the CSN being known to be a key regulator of protein degradation, its role in vascular biology remains obscure. The present study was conducted to fill these critical gaps.Our immunohistochemistry analyses revealed substantially higher CSN5 levels in the neointimal VSMCs …

Monitoring Movement And Range Expansion Of Silver And Bighead Carp (Hypophthalmichthys Molitrix, H. Nobilis) In South Dakota Tributaries Of The Missouri River, Lindsey Ann Pearl Labrie

Dissertations and Theses

Invasive species, climate change, human impacts on the landscape, flooding, and drought are all dynamic factors that greatly impact the Missouri River and its tributaries in eastern South Dakota. Invasive Carp, and more specifically, Bighead (Hypophthalmichthys nobilis) and Silver Carp (H. molitrix), first invaded the Missouri River watershed in eastern South Dakota in the late 1990s and have since spread throughout the basin downstream of Gavin’s Point Dam. The first chapter of this study uses environmental DNA (eDNA) in the context of two major barriers to fish movement in the Vermillion and Big Sioux Rivers to determine potential presence and …

Molecular Investigation Of Minor Genomic Populations And Biological Exposures In Human Health, Brandon Ned Johnson

Dissertations and Theses

The study of genetics has contributed to countless discoveries related to human health and disease. However, the complexities of human biology reside not only in the genome but also in the contributions from environmental exposures, as measured via the classical twin design. To understand the influence of biological exposures, I implemented study designs to explore both the health associations and propagation of foreign genetic material. Microchimerism has been studied for association with several clinical conditions, and I further investigated if male microchimerism could elucidate the etiology of Mayer-Rokitansky-Küster-Hauser syndrome. Prevalence of male microchimerism in women with no history of pregnancy …

Ser14-Rpn6 Phosphorylation Mediates The Activation Of 26s Proteasomes By Cyclic Amp And Protects Against Cardiac Proteotoxic Stress In Mice, Liuqing Yang

Dissertations and Theses

A better understanding of how proteasome activity is regulated can facilitate the search for proteasome enhancement strategies for disease treatment. A cell culture study shows cAMP-dependent protein kinase (PKA) activates 26S proteasomes by phosphorylating Ser14 of RPN6 (pS14-RPN6), but this discovery and its physiological significance remain to be established in vivo. To test the hypothesis that pS14-RPN6 mediates the activation of proteasomes by PKA and reduces proteotoxicity in animals, two knock-in mouse models with Ser14 of endogenous Rpn6 mutated to either Ala (S14A) or Asp (S14D) to respectively block or mimic pS14-Rpn6 were created. In a PKA-dependent manner, cAMP augmentation …

Of Transcription Factor And Transformation: Elucidating Gene Function In The Common Ice Plant, Mesembryanthemum Crystallinum, Chinenye Lilian Izuegbunam

Dissertations and Theses

Abiotic stresses negatively affect plant growth and development across the globe, which also affect the production of food, feed, biofuel, and fiber to meet the demands of a growing population. Thus, developing novel strategies to increase abiotic stress tolerance in crops is necessary. One of these strategies is exploring transcription factors (TFs) in Crassulacean Acid Metabolism (CAM) plants to improve plant abiotic stress tolerances. Therefore, the first objective of this dissertation determine the abiotic stress tolerance function of a CAM TF, McHB7opt in Arabidopsis. This study found that McHB7opt increased stress-responsive pathways related to seed germination and early seedling development. …

Fine Characterization Of Leafing Phenology In The Brazilian Atlantic Forest By Optical And Microwave Remote Sensing, James B. Bell

Dissertations and Theses

Tropical forests provide important ecosystem functions in the global biosphere, but they remain among the most poorly understood elements of land surface models, especially with regard to their seasonal dynamics. For instance, in seasonally dry forests, the pattern of the annual green-up in their canopies closely follows annual patterns of rainfall. The same, however, does not occur in wet forest canopies which are dominated by evergreen trees. In the latter, water is not scarce enough to limit leaf photosynthetic function. Canopy leafing phenology in these forests is therefore poorly characterized by optical remote sensing methods which are not sensitive to …

Application Of Hierarchical Species Distribution Models To Avian Species Of South Dakota And The Upper Missouri River Basin, Reza Goljani Amirkhiz

Dissertations and Theses

Recognizing the distributional patterns of species can inform management actions and increase scientific knowledge about species. Habitat Suitability Models (HSMs) are valuable tools in modeling species’ niches and effects of climate change and anthropogenic and natural disturbances on species’ distributions and abundances. In this dissertation, I expanded the application of hierarchical HSMs for a rare bird (Virginia’s warbler) and an economically valuable bird (ring-necked pheasant) in South Dakota. Also, we developed multiscale HSMs for grassland birds in the Upper Missouri River Basin (UMRB) to quantify current habitat associations and predict the influences of climate and landcover change associated with the …

Unraveling The Regulatory Basis Of The Desiccation Tolerance Trait In Selaginella Lepidophylla, Madhavi Anuradha Ariyarathne Hewa Babarandhage

Dissertations and Theses

Desiccation tolerance was a crucial adaptation for plants during their transition to terrestrial environments. Some spike mosses, including S. lepidophylla, have evolved the remarkable ability to tolerate extreme desiccation, enabling survival in arid regions of the world. However, the regulatory basis of this trait remains unknown. This dissertation aims to unravel the genetic basis of desiccation tolerance in Selaginella lepidophylla and its potential for improving crop abiotic stress tolerance. To achieve this goal, three objectives were pursued. Objective 1 focused on determining the regulatory role of the SlbHLH transcription factor (TF) by overexpressing it in Arabidopsis thaliana to assess its …

Orthotrichum Lyellii As An Active Moss Biomonitor: Examining The Interplay Between Ambient Pm10, Bulk Deposition And Heavy Metals In An Urban Environment, Scott Bradley Kiel

Dissertations and Theses

The importance of monitoring and preventing pollution in the environment is a globally recognized issue. Of the criteria pollutants outlined by the United States Environmental Protection Agency, particulate matter is among these least understood in relation to toxicity and most wide-spread. Many governments have employed continuous air quality monitoring networks to track ambient levels of particulate matter, but are often too widespread to capture the heterogeneity of the urban environment, especially for heavy metal deposition. In Portland, OR, the epiphytic moss Orthotrichum lyellii was successfully used as a low-cost passive biomonitor to increase the spatial resolution of pollution around the …

Climate And Intraspecific Geographic Variation Of Nests And Eggs In The Eastern Kingbird Tyrannus Tyrannus, Samantha Marie Gillette

Dissertations and Theses

The reproductive success of birds is ultimately driven by the traits of nests, eggs, and incubation behavior and the interactions among them. Avian reproduction varies on large geographic scales, most prominently between tropic- vs. temperate-breeding species, but also on finer scales, such as along latitudinal and elevational geographic gradients. However, despite the importance of eggs and nests, how their traits vary geographically in response to differences in regional climate remains understudied.

We studied Eastern Kingbirds (Tyrannus tyrannus), which have been previously demonstrated to alter incubation length in response to local climate conditions. Our study sites, Kansas (KS), New …

In Sickness And In Health: Parasites Of Stranded Pacific Harbor Seals (Phoca Vitulina Richardii) In Northern Oregon And Southern Washington, Cecily Douglas Bronson

Dissertations and Theses

Parasites have the capability to infect virtually every living organism on the planet and have adapted to infiltrate every trophic level. Many species have complex indirect life cycles and rely upon hosts at different levels of the food web for growth and reproduction. In the marine environment, having a high level of parasite diversity is thought to indicate a more stable ecosystem than an environment with low parasite diversity. As one of the top predators in their environment and because of their amphibious behaviors, pinnipeds (seals and sea lions) are exposed to a wide variety of parasites, making them ideal …

Helminths Of Thomomys Species (Rodentia: Geomyidae) Of Oregon, Malorri Rene Hughes

Dissertations and Theses

Although often viewed as inconsequential, parasites have significant ecological and evolutionary importance, and studying them can generate knowledge regarding their environments and their hosts. Helminths (intestinal parasites) infecting Western pocket gophers (Thomomys species) in Oregon had been documented based only on morphology prior to this study. Basing parasite identification solely on morphology is problematic because the characteristics used to identify species can be vague or similar, leading to misidentification or obscuring the true biodiversity present. Using molecular markers to verify species present not only is more reliable but also can be informative in terms of the host-parasite association. To …

Patterns And Process Of Sandbar Revegetation On The Missouri National Recreational Rive, Amena Begum Ruma

Dissertations and Theses

Decades of flow regulation have reduced sandbar area and recruitment of cottonwood and willow along the Missouri River. Conflicts exist between managing sandbars for habitat (removing vegetation) for threatened sandbar-nesting birds (i.e., Piping Plover) and allowing natural recruitment of early successional riparian woodland (set-aside bars) that may support other species and ecological values. Recent changes in topography, geomorphology, and vegetation were examined on sandbars that have been “set aside” from management within seven reaches of the Missouri National Recreational River (MNRR) in southeastern South Dakota, USA. An existing time series of maps of sandbar landcover, derived from satellite imagery, was …

Population Dynamics And Seasonal Movements Of Blue Suckers (Cycleptus Elongatus) In The James River, South Dakota, Tanner Leigh Carlson

Dissertations and Theses

Blue Suckers are a declining long lived catostomid, native to the large rivers and tributaries of the central United States. Currently in decline throughout their range due to anthropogenic impacts such as river channelization and dam construction, there are few stable Blue Sucker populations remaining. This study sought to describe population demographics of a stable population of Blue Suckers located in the unchannelized reach of the Missouri River below Gavins Point Dam. Year class strength, growth, and natural mortality was estimated based on aging data collected from lapillus otoliths. Previous research was conflicting as to what aging structure, pectoral fin …

The Role Of Rna Helicase Rhau In Immunoglobulin Class Switch Recombination, Sabine Jean Guillaume

Dissertations and Theses

B cells alter the expression of immunoglobulin isotypes through a process known as class switch recombination (CSR). In these cells, activation induced cytidine deaminase (AID) binds Gquadruplex (G4) switch transcripts, which serve as guide RNAs to target AID to the immunoglobulin heavy chain switch (S) regions in the DNA for CSR. Sequence alignment revealed homology between the AID G4 binding domain and the RNA helicase associated with AU-rich element (RHAU) specific motif (RSM), which allows RHAU binding to G4 RNAs and subsequent unwinding of G4 RNA into single-stranded transcripts. We hypothesize that RHAU functions in CSR by binding G4 S …

Exosome- And Microrna-Based Therapeutic Approach For Tendinopathy, Angela Wang Ilaltdinov

Dissertations and Theses

Tendinopathy, characterized by degeneration and chronic inflammation, is a significant clinical burden. Current treatments focus on symptom management but do not sufficiently address its underlying pathology; however, stem cell-based approaches aimed at repairing diseased tissues may overcome this limitation. Therapeutic effects of stem cells may be due in part to paracrine actions, including some mediated by exosomes – extracellular vesicles secreted by cells that play a role in cell communication. MicroRNA (miRNA), small non-coding RNA carried by exosomes, are likely responsible for many exosome effects. Exosomes and miRNA therapies show promise in treating diseases such as cancer and arthritis, but …

Modulation Of Stress-Induced Behaviors Through Orexinergic Signaling In The Basolateral Amygdala, Jazmine D W Yaeger

Dissertations and Theses

Stress initiates behavioral disturbances, which are often seen as symptoms of psychiatric disorders, like post-traumatic stress disorder (PTSD), depression, and anxiety. While stress is involved in the formation of disordered states, only certain individuals are vulnerable to, and therefore experience, these outcomes. Further, females are more likely to be diagnosed with stress-induced psychiatric disorders. Elements within stress neurocircuitry offer insight into differential behavioral outcomes associated with stressful experiences; and the basolateral amygdala (BLA), where pro- and anti-stress signals are integrated, is likely an important mediator in phenotype development. The orexin system, too, while being strongly associated with sleep, motivation, and …

(R)-2,5-Dimethoxy-4-Iodoamphetamine [(R)-Doi] Influences Coping Strategies To An Escapable Social Stress, Kevin Thomas Krupp

Dissertations and Theses

Depressive mood disorders are a leading cause of disability worldwide and pharmacological treatments for these disorders are inadequate, requiring new compounds with greater efficacy be investigated. The etiology of depression is heterogeneous; however, it is well established that stress exposure, and the proinflammatory effects of stress have a major role. Psychedelic compounds have rapid and long-lasting anxiolytic and antidepressive effects in humans and animal models of stress induced affective behavior. However, it is not completely understood how these compounds produce such rapid effects. We investigated whether the psychedelic compound (R)-2,5-dimethoxy-4-iodoamphetamine [(R)-DOI], a selective 5-HT2A partial agonist with potent anti-inflammatory properties, …

Impacts Of Environmental And Anthropogenic Stressors On Amphibian Welfare, Diversity, And Distribution In The Upper Missouri River Basin, Kaitlyn Campbell

Dissertations and Theses

Climate change and anthropogenic stressors have contributed to rapid declines among various taxonomic groups; however, amphibian declines have been particularly intense and primarily stemmed from warming temperatures, habitat loss, exposure to contaminants, disease, and their subsequent interactions. Several climate mitigation strategies, like Bioenergy with Carbon Capture and Storage, have been proposed to alleviate the impact of rising temperatures; however, these proposals often fail to recognize and quantify the true impact on fauna, including changes in species distributions. To address this critical gap in knowledge, this research identified current amphibian distributions in the Upper Missouri River Basin and projected distribution changes …

A Bioinformatic And Biochemical Analysis Of Cruciviruses, George William Kasun

Dissertations and Theses

Cruciviruses are novel ssDNA viruses discovered through metagenomics and direct environmental DNA amplification and cloning. The genomes of cruciviruses suggest that gene transfer between RNA and DNA viruses occurred due to the presence of putative protein-encoding genes that are homologous to both ssRNA and ssDNA viruses. In order to gain a better understanding of this group of viruses both bioinformatic analyses and in vitro biochemical experiments were employed. The results of the bioinformatic analyses show that cruciviruses are a highly diverse group of ssDNA viruses. Their placement within established ssDNA phylogenies is difficult due to heterogeneity in their putative replication-associated …

Selenium Probes For The Detection Of Thioredoxin Reductase Activity, Tendai Joseph Mafireyi

Dissertations and Theses

The identification and quantification of proteins and enzymatic activity in living tissues frequently requires the use of invasive procedures such as biopsy. These techniques can inhibit measurements of protein levels in real-time, and the disruption of tissue can lead to the loss of important information concerning the spatial distribution and differential activities in various cell types. The use of small organic fluorescent probes that rely on activation or accumulation within a tissue embody robust methods of detection that address these issues. This dissertation describes the design, synthesis and evaluation of fluorescent probes that can detect the enzyme thioredoxin reductase (TrxR). …

Mitonuclear Mismatch Is Associated With Increased Male Frequency, Outcrossing, And Male Sperm Size In Experimentally-Evolved C. Elegans, Brent William Bever

Dissertations and Theses

We provide the first controlled study of how male frequencies and rates of outcrossing evolve in response to mitonuclear mismatch by allowing replicate lineages of C. elegans nematodes containing either mitochondrial or nuclear mutations of electron transport chain (ETC) genes to evolve under three sexual systems: facultatively outcrossing (wildtype), obligately selfing, and obligately outcrossing. In partial support of a tenet of the mitonuclear sex hypothesis, which predicts that outcrossing will be favored in cases of mitonuclear mismatch, we found evolution of increased male frequency in at least one replicate line of all four ETC mutant backgrounds tested--nuclear isp-1, mitochondrial …

Mechanisms Of Substrate Recognition By The Cul3-Based E3 Ligase, Katia Graziella De Oliveira Rebola

Dissertations and Theses

Cul3-based E3 ligase is responsible for regulating a variety of cellular pathways, many of which are known to have profound effects on the proper function of multicellular organisms. Although progress over the past years has been truly impressive, our understanding of the mechanisms of E2 recruitment and selection by the BCR complex and all the roles that Cul3 plays on kidneys remains in its infancy. To explore these aspects, this dissertation aims to analyze the Cul3 complex using two different approaches: (1) We used the powerful tool of chimeric analysis to map the essential domain binding characteristics of Cul3 taking …

Exploring Mirna Function And Host Response To Coxiella Burnetii Infection, Madhur Sachan

Dissertations and Theses

Alveolar macrophages attempt to control bacterial infection through a spectrum of defense processes, including induction of apoptosis, autophagy, inflammatory response, and nutrient sequestration. MicroRNAs (miRNAs), a class of small non-coding RNAs, are involved in a spectrum of physiological processes, including immune response to intracellular infections. However, whether microRNAs have any functions in host response to Coxiella burnetii infection is unknown. Coxiella burnetii is a highly infectious intracellular pathogen that causes Q fever, a zoonosis with a worldwide occurrence. In this work, I investigated the functions of miRNAs in host response to C. burnetii infection and found that miRNAs are an …

Experiences Of Undergraduates And Graduate Teaching Assistants In Biology Course-Based Undergraduate Research Experiences, Emma Crystal Goodwin

Dissertations and Theses

Evidence of positive student outcomes from course-based undergraduate research experiences (CUREs) has sparked implementation of CUREs in introductory biology laboratory courses, as one approach to boosting student engagement in research. In a CURE, students collaborate with other students and instructors on a research project, where they conduct novel scientific research that has relevance to a local or scientific community. However, previous research rarely considers that graduate teaching assistants (GTAs) often teach introductory labs. The classroom role of GTAs expands in a CURE--they no longer need to simply teach a lab class, but also to serve as research mentors. GTAs, who …

Nesting Habits Of Cavity Nesting Bees And Wasps In Portland, Oregon, Stefanie Kay Steele

Dissertations and Theses

Native bees are threatened by habitat loss through urbanization, however, there is increasing interest in creating bee nesting habitat in urban areas. Few studies have determined what species are present in the region, or examined the role of nest height or cavity size in attracting the approximate one-third of native bees that nest in cavities. To determine what species were present, and whether they showed preferences for nesting at a certain height or cavity width, we set up artificial wooden cavity nest blocks across fourteen locations in the greater Portland, OR area. Wooden posts were erected with nest blocks at …

Temperature-Induced Activation Of The Reproductive Axis Through Melatonin-Mediated Changes In Thyrotropin, Treven J. Winters

Dissertations and Theses

An animal's ability to synchronize life-history events or stages with optimal environmental conditions is paramount to successfully reproducing and maximizing fitness. Additional events including migration, foraging, rearing of young, and emergence from hibernation are all examples of processes under environmental control in one species or another. An exciting new mechanism involving neural thyroid hormone metabolism has been elucidated that links environmental control to the neuroendocrine reproductive axis. In birds and mammals with seasonal breeding cycles, this neuroendocrine pathway is activated by photoperiod-induced changes in thyroid stimulating hormone (TSH, also known as thyrotropin) production within the pars tuberalis region of the …

Testing Functional Variation In Thermal Properties For Antarctic Mosses, Andrew Forrest Clements

Dissertations and Theses

As the maritime Antarctic ecosystem continues to warm, glacial retreat will further expose subterranean permafrost to warmer conditions. One of the most visible changes in the ecosystem is the colonization of the new ice-free areas by bryophytes, particularly mosses. These bryophytes are having important effects on terrestrial thermal properties, but little is known about differences among Antarctic moss species in their thermal properties. Here, I measured the thermal conductivity, specific heat capacity, and the water content of moss species on King George Island to understand the insulation ability of Antarctic mosses, Polytrichastrum alpinum, Sanionia georgicouncinata, Chorisodontium aciphyllum, …

Elucidating The Evolution And Function Of Srnas That Facilitate Bacterial Stress Tolerance, Madeline Claire Krieger

Dissertations and Theses

Non-coding small RNAs (sRNAs) are ubiquitous post-transcriptional regulators found in both gram-negative and gram-positive bacteria. Despite their integral role in many regulatory pathways, including those that facilitate stress-tolerance, little is known about the evolutionary forces that drive the emergence of novel sRNAs, how prevalent sRNAs are within bacterial species, or the functions of a majority of these transcripts. In this work, I first describe the evolution of OxyS, a well-characterized sRNA in gram-negative Enterobacteriaceae that is involved in coordinating the bacterial response to oxidative stress. Next, I identify novel sRNAs differentially produced by the gram-positive oral pathogen Streptococcus mutans in …