Biology Commons^™

Comparative Analysis Of Bacterial Recbcd And Sbcc-Sbcd Systems And The Yeast Mre11-Rad50 Complex During Dna Replication, Tannos Seyedjavadi

Dissertations and Theses

Accurate completion of DNA replication when forks converge is essential for genome stability. In Escherichia coli, several proteins have been identified including RecG, ExoI, RecBCD, and SbcCD, that contribute to completing replication, and loss of these factors causes genetic instability. Eukaryotes encode proteins with homology to several E. coli completion enzymes. Mre11–Rad50 complex is structurally and functionally conserved with bacterial SbcCD, and Rrm3 shares homologous motifs with bacterial RecBCD. These proteins are often described as being involved in homologous double strand break repair. Whether they are also conserved and play a similar role as their E. coli counterparts in …

Integrative Evidence For Cryptic Diversity In The Thomomys Mazama Species Complex: Phylogenetics, Cranial Morphometrics, And Ecological Niche Modeling, Jessica Kate St. Michael

Dissertations and Theses

The population genetic structure and geographic distribution of the pocket gopher genus Thomomys Wied-Neuwied, 1839, lends itself to speciation events. Conserved morphology, ecological specialization, and high rates of molecular evolution may increase the probability of allopatric speciation, thereby contributing to the presence of morphologically cryptic taxa. In light of these patterns of evolution, we assessed genetic divergence and phylogenetic relationships, cranial morphometric differentiation, and ecological divergence among taxa in the Thomomys mazama species complex to test the hypothesis that T. mazama is a single species. Species delimitation analysis using Bayesian Poisson Tree Processes (bPTP) and data from the mitochondrial cytochrome …

Thermal Sensitivity Of Native And Introduced Crabs: Implications For Reproductive Success, Keria Moritsugu-Vandehey

Dissertations and Theses

Temperature is a major driver of physiological and developmental processes in marine organisms, and continued climate warming is expected to affect reproduction and recruitment in estuarine species. Early life stages are often particularly sensitive to environmental stress, yet relatively little is known about how warming influences embryonic development, hatching success, and larval survival across co-occurring native and introduced crab species.

This study examined the effects of temperature on embryonic development, hatching success, and early larval survival in four estuarine crab species from the Pacific Northwest: the introduced European green crab, Carcinus maenas, and the native shore crabs Hemigrapsus nudus …

Growing Pains: The Loss Of Plasticity To Extreme Anoxia In Developing Embryos Of Austrofundulus Limnaeus, Patrick Ryan Clouser

Dissertations and Theses

Oxygen plays a pivotal role for most animal life on Earth, so much so that even short exposures to no oxygen, anoxia, can have severe effects on the animal's wellbeing. Conversely, aerobic recovery after anoxic insult can be just as detrimental. Some animals are the exception to this rule and demonstrate survival through anoxia and recovery. There has been a great deal of research around anoxia tolerant animals, but what remains unclear are the genetic underpinnings that determine the anoxia tolerant phenotype. RNA sequencing allows for the quantification of RNA transcripts within a sample, which can indicate if a gene …

Life Without Oxygen: Cellular Mechanisms Enabling Genome Maintenance And Proliferation In Cells From An Anoxia-Tolerant Vertebrate, Riley Asa Roth-Carter

Dissertations and Theses

When exposed to the complete loss of oxygen (anoxia) most organisms undergo rapid cellular deterioration driven by a range of metabolic dysfunctions associated with the loss of the terminal electron acceptor for aerobic respiration. This loss of ability to create and maintain necessary levels of cellular ATP through oxidative phosphorylation contributes to loss of membrane potentials, increase in the accumulation of acidic by-products of anaerobic metabolism, and a decrease in the ability to support other molecular processes that rely on a steady supply of ATP. While this extreme oxygen stress is lethal to a majority of vertebrate organisms there are …

Where Mussels Hang Out: A Multiscale Analysis Of Zebra Mussel (Dreissena Polymorpha) Spread In South Dakota, Justin Verner Sorensen

Dissertations and Theses

The spread of the invasive zebra mussel (Dreissena polymrpha) poses significant ecological and economic threats to freshwater systems across North America. Understanding population dynamics and how this aquatic invasive species spreads is essential for making natural resource management decisions. South Dakota represents an active frontline of the zebra mussel invasion, highlighting the importance of understanding the spread in this region. Statewide habitat suitability modeling of available aquatic habitat was performed using MaxEnt, a robust machine learning algorithm. Individual waterbody suitability means were also extracted to rank waterbodies within highly suitable regions. This work revealed that South Dakota possesses widespread suitable …

The Neuroprotective And Synergistic Effects Of Carbamoylated Erythropoietin And Insulin-Like Growth Factor-1 In Alzheimer's Disease, Morgan Jean Rothschadl

Dissertations and Theses

Alzheimer’s disease (AD) is a prominent neurodegenerative disease characterized by a decline in cognitive functioning. While current FDA-approved therapeutics exist, they fall short in creating significant and long-lasting improvements to cognition. A newer approach using neurotrophic factors has shown promising effects on improving cognition in clinical trials. Neurotrophic factors are secreted proteins that have multimodal effects in the brain, including supporting cell survival and functioning. Two neurotrophic factors of interest are carbamoylated erythropoietin (CEPO) and insulin-like growth factor-1 (IGF-1), and the goal of this study was to understand the synergistic and neuroprotective effects of CEPO and IGF-1 in AD. We …

Avian Use Of Early Successional Riparian Forest Along The Missouri River: What Do We Lose By Managing For Plovers And Terns?, Stephanie Nefas

Dissertations and Theses

Riparian ecosystems provide habitat for birds throughout their annual cycle, yet flow regulation along major rivers like the Missouri River has reduced early successional riparian forests. Following historic flooding in 2011, set-aside areas within the Missouri National Recreational River (MNRR) were established to allow natural riparian vegetation succession on newly created sandbars. I evaluated the value of these early successional forests for birds over three breeding seasons (2018–2020) and four migration periods (2020–2021). During migration, standardized point counts documented 7,462 individual birds representing 114 species across 828 surveys. Avian diversity was positively correlated with vertical habitat complexity, with the canopy …

Invasion Dynamics, Environmental Conditions, And Community Impacts Of Yellow Sweetclover (Melilotus Officinalis) Across The Northern Great Plains, Sakshi Saraf

Dissertations and Theses

Understanding how environmental conditions and invasion dynamics shape native plant Communities is critical for conserving and managing the semi-arid grasslands of the Northern Great Plains (NGP). Invasive plant species are increasingly altering ecosystem structure and function across this region, yet knowledge gaps remain regarding the drivers of invasion, their spatiotemporal dynamics, and their associations with native plant communities. This dissertation investigates three questions: (1) what environmental conditions are associated with the distribution and abundance of the invasive legume Melilotus officinalis (yellow sweetclover; MEOF), (2) how does MEOF vary across space and time under climatic conditions, and (3) how are environmental …

Hybridization And Introgression In Marine Invertebrates: Population Genomics Of Phymactis Papillosa And Asterias Sea Stars, Christopher J. Dookie

Dissertations and Theses

Hybridization and introgression are evolutionary significant processes in marine invertebrates (Sanford & Kelly,2011) yet genome-wide investigations of gene flow in these taxa remain limited relative to vertebrate systems (Marchi et al., 2021). This thesis presents genomic analyses of hybridization and introgression in two marine invertebrates occupying contrasting oceanographic settings and characterized by contrasting genomic datasets: restriction-site associated DNA sequencing (RADseq) SNP data for the eastern Pacific sea anemone Phymactis papillosa and whole genome sequencing (WGS) data for the North Atlantic sea stars Asterias rubens and Asterias forbesi. For each system, I applied coalescent-based species tree inference using CASTER (Zhang …

Analyzing Changes In Russian Olive Distributions Along The Missouri River In Response To Flooding, Zachary Schild

Dissertations and Theses

Russian olive (Elaeagnus angustifolia; RO) is an invasive, nitrogen-fixing tree that has spread across riparian ecosystems in the western United States, potentially hindering native tree recruitment, reducing species richness, and impacting wildlife. RO has established within the Missouri National Recreational River (MNRR) in part due to modified flow regimes following dam construction. This study aimed to map the spread of RO using high-resolution National Agriculture Imagery Program (NAIP) imagery (2010, 2012, 2018, 2022) and evaluate the effects of the 2011 and 2019 floods on RO distributions in the Missouri National Recreational River (MNRR). RO cover in this area has expanded …

Orexin Receptor Modulation In Amygdalar Stress Circuitry Differentiates Resilient And Vulnerable Phenotypes, Megan Marie John

Dissertations and Theses

Social stress is important for evaluating threats and resource opportunities, however, chronic exposure initiates the onset of psychological disorders, such as anxiety, depression, and post-traumatic stress disorder (PTSD). Stress responsiveness varies between individuals and sexes, resulting in disproportionate diagnoses and ineffective treatment outcomes. Enhancing therapeutic efficacy requires understanding of stress responsivity, phenotype development, and neurocircuitry modifications. Key contributors to stress responsiveness, such as threat of aggression and motivational initiation, influence the development of resilient or vulnerable phenotypes through behavioral and molecular adaptations to stress-related neurocircuitry. The basolateral amygdala (BLA) is a brain region associated with fear learning and integrates stress …

Systematics And Phylogeography Of Mundochthonius Chamberlin, 1929, In The Pacific Northwest (Chelicerata, Pseudoscorpiones), Amanda Rai Montoya-Cowan

Dissertations and Theses

Understanding the processes that drive genetic divergence and species formation is central to evolutionary biology. Invertebrates with low dispersal ability, such as pseudoscorpions, are especially prone to cryptic diversification due to their occupancy of niche microhabitats and sensitivity to landscape barriers. Despite their ecological roles as predators and bioindicators, pseudoscorpions remain one of the least studied arachnid groups, with limited taxonomic resolution and few integrative studies. This research focuses on the genus Mundochthonius in the Pacific Northwest, particularly M. pacificus, a morphologically conserved species whose true diversity and distribution remain poorly understood.

Field surveys guided by a GIS-based habitat …

Functional Ecology Of Antarctic Flora, Zoie C. Yetley

Dissertations and Theses

Antarctic mosses play foundational roles in terrestrial ecosystem processes, yet their functional ecology remains poorly understood. This study developed a novel functional trait-based framework for dominant moss species across glacier retreat gradients in the South Shetland Islands, addressing a critical gap in Antarctic bryophyte ecology. Nutrient- and water-related traits were measured for four moss species--Polytrichastrum alpinum, Bryum pseudotriquetrum, Sanionia uncinata, and Syntrichia saxicola--along with Deschampsia antarctica, across nine sites spanning early to late successional stages. Results revealed strong interspecific trait differentiation: P. alpinum exhibited conservative nutrient-use and rapid water-uptake strategies; S. uncinata and B. pseudotriquetrum …

Recruitment, Reprogramming, And Function Of Trpv1+ Sensory Nerves In The Development And Progression Of Head And Neck Cancer, Anthony Restaino

Dissertations and Theses

Head and neck squamous cell carcinomas (HNSCC) are an epithelial cancer prevalent across the world and are divided into two subcategories: human papillomavirus-mediated (HPV+) and carcinogen-mediated (HPV-) HNSCC. These subgroups have distinct patient populations, divergent responses to therapy, and prognoses, however the foundational mechanisms that facilitate these differences are not well understood or defined. Recently, the presence and function of sensory neurons within the tumor environment of various solid tumors has been identified and investigated. Herein, we identify differences in the presence of TRPV1+ sensory neurons and neuron structures in the tumor environment of HPV+ and HPV- HNSCC, correlating with …

Least Tern Abundance, Nesting Productivity, And Dispersal Between Nesting And On- And Off-River Foraging Sites In The Missouri National Recreational River, Kyle Jorgensen

Dissertations and Theses

The Interior Least Tern (Sterna antillarum athalassos) has experienced significant conservation success, culminating in its removal from the federal endangered species list in 2021. However, the species remains state-endangered in South Dakota, and knowledge gaps persist regarding its foraging ecology and population dynamics along the Missouri National Recreational River (MNRR). This study aimed to address these gaps by quantifying Least Tern abundance, nesting productivity, and movement patterns between nesting and foraging sites during the 2024 and 2025 breeding seasons. We conducted surveys of Least Terns on riverine sandbars and off-river wetlands within a 30-km radius of the MNRR, employing both …

Body Size Distributions Of Riverine Freshwater Plankton Communities, Staci Ann Reynolds

Dissertations and Theses

The individual size distribution (ISD) is an individual based model that estimates the relative abundance of individual body sizes in a community. ISD’s slope or lambda (λ) gives insight into the communities’ food web and energy transfer. Climate change is expected to shift mean body sizes and λ as it increases individuals’ energy demands. Alterations in food webs and spatial distribution throughout the middle Missouri River basin may also have an impact on these communities λ. In a mesocosm experiment and field study, planktonic communities were sampled and had body sizes measured. Generalized linear mixed models were fit to calculate …

Elucidating The Non-Shivering Thermogenesis Response In The Black-Capped Chickadee (Poecile Atricapillus), Sweta Chand

Dissertations and Theses

The adaptation of small birds to cold environments involves mechanisms for both heat conservation and heat generation. While minimizing heat loss reduces the energy needed to maintain body temperature, thermogenesis remains essential. Shivering and non-shivering thermogenesis (NST) are two likely mechanisms supporting cold adaptation in small avian species. Although sarcolipin (SLN) aids NST in small mammals, studies in birds such as Dark- eyed Juncos have shown no increase or even a decrease in SLN expression during cold exposure, suggesting limited involvement. This may reflect biological differences or limitations of mRNA- focused sequencing, which excludes long non-coding RNAs (lncRNAs) capable of …

Periconceptual Nutrition And The Preimplantation Embryo: Approaches For Intervention And Generational Health, Abigail Klein

Dissertations and Theses

The typical American diet exceeds dietary fat recommendations, contributing to the rising rates of obesity. This negatively impacts fertility, pregnancy and fetal growth, and lifelong offspring health. During pregnancy, this also increases risk of co-morbidities like gestational diabetes. Despite this, lipids are not screened during pregnancy and limited research exists evaluating these co-exposures on offspring health. Our lab used a rat model of maternal high fat (HF) diet with late-gestation diabetes (DM) to demonstrate that mitochondrial dysfunction and oxidative stress incite lifelong cardiometabolic disease risk in offspring. To determine the timing of damage, we hypothesized that maternal overnutrition incites mitochondrial …

Investigation Of Rna-Binding Protein Expression Changes In The Hippocampus Following Doxorubicin And Cyclophosphamide Treatment, Lijie Chen

Dissertations and Theses

This study investigated the molecular mechanisms underlying chemotherapy-induced cognitive impairment (CICI) following doxorubicin and cyclophosphamide treatment in a rat model, revealing three significant alterations in hippocampal tissue: selective downregulation of heterogeneous nuclear ribonucleoprotein A1 (hnRNPA1) (21% decrease, p=0.0298), compromised astrocytic network integrity evidenced by reduced GFAP-positive area in cornu ammonis 3 (CA3) (24%, pB=0.026) and dentate gyrus (DG) (19%, pB=0.027) regions, and elevated cellular senescence marker p19Arf specifically in DG (69%, pB=0.033) and CA3 (27%, pB=0.024). The inverse relationship between hnRNPA1 reduction and p19Arf elevation suggests a potential mechanistic link between RNA dysregulation and senescence induction, with pronounced vulnerability in …

Toxin-Like Proteins In The Venom Of Drosophila Parasitoids, Lady V. Cardenas

Dissertations and Theses

The figitid parasitoid wasps of Drosophila are gaining importance in agriculture due to their ability to kill the resilient soft-fruit pest Drosophila suzukii. Their success and infection strategies vary, and the mechanisms underlying these differences are largely unknown. Some of their venom proteins have been shown to be important in suppressing host defense. Here, we report that Ganaspis brasiliensis, a parasitoid of D. suzukii survives well on Drosophila yakuba, a host species with a strong cellular immunity, and infected flies are unable to mount a strong immune response. To predict possible toxin-like proteins in Ganaspis venoms that might suppress cellular …

Blattella Germanica As A Vector Of Salmonella Typhimurium, Matthew Turner

Dissertations and Theses

The following investigates the role of the German cockroach (Blattella germanica) as a vector of the bacterium Salmonella enterica subspecies enterica serovar Typhimurium (S. Typhimurium). As such, this work examines various host-pathogen-microbiome interactions that define the vectorial capacity of the German cockroach for Salmonella. To date, the majority of literature focuses on the general association of the German cockroach with various human pathogens, claiming any dissemination to be carried out via passive mechanical transmission. This project recognizes those claims, while expanding to include the possibility of biological transmission, involving active and complex host-pathogen interactions, including mechanisms like replication within the …

Dietary Saturated Fatty Acids Modulate Host Innate Immunity, Amy Lorraine Seufert

Dissertations and Theses

Nutrition, cellular metabolism, and inflammatory regulation of the immune system are interconnected, and advancing our understanding of this will greatly improve treatment of metabolic and inflammatory disease. Specifically, dietary saturated fats are becoming increasingly appreciated for their ability to modify innate immune cell function in mammals following absorption into the blood and lymphatic circulation systems. The work herein focuses on the capacity for lipids in the diet to modulate innate immune memory. My thesis first broadly outlines fundamental background, including: the evolution of human nutrition, the discovery of innate immune memory, and key topics that reoccur throughout the text surrounding …

Varecia Rubra (Red Ruffed Lemur) Diel Activity And Calling At Andranobe, Masoala National Park, Madagascar, Hannah Elena Hilden-Reid

Dissertations and Theses

With respect to the natural variation in abiotic and biotic conditions present between daytime and nighttime periods, many animal species show evolutionary adaptations specialized for diurnality, nocturnality, or crepuscularity. Biologists have traditionally viewed categorizations of this kind as fixed within taxonomic groups, emphasizing how intricately species’ survival is contingent on the ability to adapt to low light, high light, or twilight conditions. However, movement away from such distinct temporal niche categories began within chronobiological studies following the discovery of more flexible patterns of activity in numerous taxa during the late 1970s. This shift generated increased interest in elucidating the complex …

Deepwhalenet: A Climate Change-Aware Fft-Based Neural Network For Underwater Passive Acoustic Monitoring, Nicholas Ryan Rasmussen

Dissertations and Theses

In the face of escalating climate threats, the conservation of whale species has become increasingly critical. Traditional acoustic monitoring methods, burdened by extensive pre-processing and post-processing, need more adaptability and efficiency for effective marine mammal surveillance. This study introduces DeepWhaleNet, a novel deep-learning framework tailored for Underwater Passive Acoustic Monitoring (UPAM). DeepWhaleNet is designed to streamline whale detection by directly analyzing raw log-power spectrograms, thus extracting essential acoustic features to conserve these endangered species. The framework employs an extensive short-time Fourier transform (STFT) for input processing and a customized ResNet-18 architecture for classification, distinguishing whale vocalizations from ambient noise and …

Exploring The Role Of Nonmuscle Myosin Ii In Renal Thick Ascending Limb Epithelial Cell Protein Trafficking And Organelle Architecture, Brook Busselman

Dissertations and Theses

The traditional functional roles of the actin associated motor protein nonmuscle myosin II (NM2) have been thoroughly studied. However, the nontraditional roles for NM2 in the context of membrane remodeling and protein trafficking events in cells have just recently been unraveled. Our work has found that genetic inactivation of NM2 protein isoforms MYH9 and MYH10 in the renal epithelium of adult mice leads to progressive kidney disease. Aberrant protein transport and localization in cells of the thick ascending limb (TAL) of the kidney nephron is accompanied by upregulation of endoplasmic reticulum (ER) stress and the unfolded protein response (UPR) pathway. …

The Role Of The Vibrio Cholerae Type Vi Secretion System During Kin Cell Interaction, Biofilm Formation And Priority Effects, Karen A. Castro

Dissertations and Theses

Vibrio cholerae’s Type VI secretion system (T6SS) is one of the arsenals used by the bacteria for its long-term survival in different environments, against a variety of opponents, and for its maintained pathogenicity in vulnerable regions of the world. Therefore, the more we understand about the activity of the T6SS, the closer we get to understanding its role in bacterial competition; inter-and-intra, and how this shapes a bacterial niche. Further, although the probiotic-like effect in the V. cholerae vaccine is described to work fast due to niche uptake hindering colonization of toxigenic strains, it is not yet clear if there …

Impacts Of Environmental Stressors On Native South Dakota Amphibian Physiology And Survival, Danielle Jean Galvin

Dissertations and Theses

Amphibian populations around the world are declining, with some of the most likely drivers behind these declines including emerging infectious diseases and environmental contaminants. To address major gaps in the current literature, I sought to evaluate the effect of two major environmental stressors on various aspects of amphibian physiology: emerging infectious diseases and environmental contaminants. Emerging infectious diseases of amphibians include fungal, viral, and parasitic pathogens which have expanded in host range, either geographically or in competent host species. Environmental contaminants include chemicals which may be naturally occurring in the environment, or which may be introduced to the environment, often …

Comparative Skull Morphology Of California Sea Lions (Zalophus Californianus) And Steller Sea Lions (Eumetopias Jubatus) In The Pacific Northwest And Implications For Hybridization, Ada Iris Garcia Garcia

Dissertations and Theses

Eumetopias jubatus (Steller sea lions) that breed on the Oregon coast are smaller than those found both in Alaska and California. During the breeding season, male Zalophus californianus (California sea lions) move past E. jubatus rookeries in Oregon on their way to their breeding rookeries in Southern California. Introgression potentially could explain the difference in size of Oregon E. jubatus relative to remaining populations. At Portland State University (PSU), the marine mammal collection of the Museum of Vertebrate Biology has over 200 skulls of Z. californianus and E. jubatus from throughout northern Oregon and southern Washington. To assess whether morphologically …

Resistance To Dna Interstrand Crosslinks In Escherichia Coli Arises Through Prevention Rather Than Repair, Travis Kim Worley

Dissertations and Theses

DNA interstrand crosslinks are particularly lethal lesions that form in DNA when certain molecules intercalate between complementary strands of DNA and form covalent bonds with both strands. Once formed, these lesions present an absolute block to replication and transcription, ultimately resulting in cell death. Because of this lethality, chemicals that form DNA interstrand crosslinks are found in nature as defensive chemicals produced by plants and microbes. Moreover, crosslinking agents have proven effective the treatment of dysplastic conditions and are often first line chemotherapeutics.

However, cancer cells can become resistant to DNA interstrand crosslinks. Unlike other DNA lesions, the double-stranded nature …