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Dissecting The Role Of Selenoprotein P And Thioredoxin Reductase In Pancreatic Cancer Metabolism, Alyssa A. Abbas

Dissertations, Master's Theses and Master's Reports

Pancreatic ductal adenocarcinoma (PDAC), the fourth leading cause of US cancer-related deaths, has a stark 5-year survival rate of 9%, emphasizing an urgent need for effective therapies. A well-established characteristic of cancer, metabolic dysregulation, presents an opportunity for developing therapies that target specific metabolic susceptibilities inherent in cancer cells. Our recent studies have discovered a susceptibility in PDAC; deprivation of cystine or blocking its uptake by erastin (a cystine transport inhibitor) triggers significant lipid peroxidation, thereby inducing ferroptosis specifically in the mesenchymal subtype of PDAC, but not in the epithelial subtype. This study aims to elucidate the roles of Selenoprotein …

Statistical Methods For Gwas And The Impact Of Diabetic Medication Adherence On Healthcare Costs, Meida Wang

Dissertations, Master's Theses and Master's Reports

This dissertation includes three Chapters. In Chapter One, we develop a computationally efficient clustering linear combination approach to jointly analyze multiple phenotypes for GWAS. In this paper, based on the existing CLC method and ACAT strategy, we develop the ceCLC method to test association between multiple phenotypes and a genetic variant. In Chapter Two, we develop a novel method called sCLC for association studies of multiple phenotypes and a genetic variant based on GWAS summary statistics. Simulation results show that sCLC can control Type I error rates well and has the highest power in most scenarios. In Chapter Three, we …

White-Tailed Deer In A Winter-Wonderland: Long-Term Deer Yard Use And Methodological Considerations For Ungulate Fecal Dna Metabarcoding, Melanie A. Ottino

Dissertations, Master's Theses and Master's Reports

Northern white-tailed deer (Odocoileus virginianus) mitigate the increased energetic costs of severe winter conditions through obligate migration to densely congregated areas with abundant conifer cover, a behavior referred to as yarding. “Deer yards” in the Western Upper Peninsula (UP) of Michigan are principally located within the reduced snowpack and increased ambient temperature microclimates of densely canopied eastern hemlock (Tsuga canadensis) stands, but specific drivers of long-term site fidelity and utilization are largely uncharacterized. As an important game species of high economic and cultural value and a keystone herbivore with critical impact of plant community composition and structure, identifying winter yarding …

Under Ice Photosynthetic Primary Production And Dark Carbon Fixation In A Temperate Freshwater System, Vanessa Cubillos Tellez

Dissertations, Master's Theses and Master's Reports

Ice-covered lakes are vulnerable to environmental change, especially those in the Northern Hemisphere where ice cover is rapidly declining due to global warming. These changes can alter metabolic processes and disrupt carbon cycling driven by primary producers who form the base of the food chain and are key to sustaining ecosystem function. Photosynthetic primary production and dark carbon fixation under the ice in the Keweenaw Waterway, a temperate freshwater system that is ice-covered for ~3 months out of the year, were studied using a carbon isotopic labeling (14C-bicarbonate) technique. Water samples were collected weekly during ice cover and monthly during …

Impacts Of Introduced Earthworms On Sugar Maple Sap Chemistry And The Discourse Of Invasion Ecology, Shelby Nicole Lane-Clark

Dissertations, Master's Theses and Master's Reports

To delve into further understanding of the relationships between introduced earthworms, forest ecosystems, and the human systems they impact, two approaches were taken. In the first approach, we seek to explore ways we can shift the discourse within and regarding the field of invasion ecology by re-framing how we approach discussion, management, and education regarding introduced species. Language issues surrounding introduced species through the example of earthworms in North America are described and potential solutions are provided, including a repositioned perspective that may facilitate better relationships with the natural world. The goal is to shift the language to be more …

Stamp Sand Along The Keweenaw Shoreline: Solid And Dissolved Copper & Effects On Biota, Gary Swain

Dissertations, Master's Theses and Master's Reports

Stamps sand refers to the regional colloquialism for the mine-tailing byproducts generated from copper (Cu) ore processing mills located in Michigan’s Keweenaw Peninsula. In the Keweenaw region, copper extracted from basalt ores resulted in a legacy of 100’s of millions of metric tonnes of stamp sand wastes, including 22.7 million metric tonnes at Gay, MI. Trace amounts of Cu persist in stamp sands and when leached have toxic enough concentrations to influence aquatic biota. To better understand stamp sands’ properties, we ran experiments and compiled data about the solid and dissolved phases of Cu. Solid phase concentration of Cu was …

Invasive Buckthorn Mapping: A Uav-Based Approach Utilizing Machine Learning, Gis, And Remote Sensing Techniques In The Upper Peninsula Of Michigan, Vikranth Madeppa

Dissertations, Master's Theses and Master's Reports

An Invasive species is a species that is alien or non-native to the ecosystem which causes harm to economic, environmental, or human health (E.O. 13112 of Feb 3, 1999). Invasive species have posed a serious threat to ecosystems across the globe. These invasive species have impacts on the biodiversity and productivity of invaded forests. Remotely sensed data is a valuable resource for understanding and addressing issues related to invasive species. This study presents a novel approach for mapping the distribution of two invasive plant species, Common and Glossy Buckthorn, using unmanned aerial vehicles (UAVs), machine learning algorithms, geographic information systems …

Statistical Methods For Gene Selection And Genetic Association Studies, Xuewei Cao

Dissertations, Master's Theses and Master's Reports

This dissertation includes five Chapters. A brief description of each chapter is organized as follows.

In Chapter One, we propose a signed bipartite genotype and phenotype network (GPN) by linking phenotypes and genotypes based on the statistical associations. It provides a new insight to investigate the genetic architecture among multiple correlated phenotypes and explore where phenotypes might be related at a higher level of cellular and organismal organization. We show that multiple phenotypes association studies by considering the proposed network are improved by incorporating the genetic information into the phenotype clustering.

In Chapter Two, we first illustrate the proposed GPN …

Fine Root Respiration In Quercus Rubra Is Influenced By Multidimensional Trade-Offs In Root Trait Space, Emma L. Shedd

Dissertations, Master's Theses and Master's Reports

Economic theory is often applied to plant strategies, arguing that trade-offs exist between maximizing quick returns on investment within short lifespans or producing longer-lived tissues with slower returns. While these trade-offs are well-studied aboveground, their influence on belowground traits, including root respiration, remains unclear. Resource heterogeneity and symbioses with mycorrhizal fungi may complicate root trade-off axes beyond those predicted by economics theory alone. Investigating fine root trade-offs in Quercus rubra populations along a latitudinal gradient in the Midwest, USA, we identified two distinct axes of variation in root traits: one related to a potential “fungal symbiosis” trade-off and another representing …

The Art And Science Of Wood: From Pyrography To Termites And Wood Decomposition, Joanna D. Walitalo

Dissertations, Master's Theses and Master's Reports

Wood is vital to many natural ecosystems, as it provides energy, nutrients, and habitat for organisms from the micro- to the macro- scale. Wood is also critical to humans for similar reasons, and can be an important medium of art and education. This dissertation addresses three diverse aspects of wood with the contexts of science, art, and education. First, we explored the impact of timber harvest techniques and site preparation on microbial wood decay and subterranean termite responses on a forest-stand scale. The amount of coarse woody debris removed post-harvest, coupled with the location and species of the test wood …

Eutrophication On Twin Lakes: Applying A Phosphorus Budget And Shoreline Surveys To Assess Current & Historical Lake Health, Tyler K. Lemahieu

Dissertations, Master's Theses and Master's Reports

The Twin Lakes system, a series of lakes including Lake Gerald and Lake Roland, was historically categorized as oligotrophic but is now mesotrophic having experienced cultural eutrophication. A mass balance phosphorus budget model was constructed for the Twin Lakes system in Houghton, Co. Michigan for the 2022 stratified season. Additional spatial insights were gleaned through a survey of shoreline water quality, which corroborated the model results. The lakes currently experience substantial depletion of hypolimnetic dissolved oxygen during late summer stratification. A budget reveals approximately 22% (6.6 kg) of the current 29.5 kg total phosphorus inputs to Twin Lakes (during the …

Prediction Of Sumoylation Sites In Proteins From Language Model Representations, Evgenii Sidorov

Dissertations, Master's Theses and Master's Reports

Sumoylation is an essential post-translational modification intimately involved in a diverse range of eukaryotic cellular mechanisms and plays a significant role in DNA repair. Some researchers hypothesize that a high level of SUMOylation events in cancer cells improves cells' chances for survival under stress conditions by regulating tumor-related proteins.

This study belongs to a booming field of harnessing computational power to the domain of life. Prediction of protein structure, its molecular function, and the design of new drugs are just a few examples of the applications within this exciting area of research. By leveraging computational power, researchers can analyze vast …

Multiscale Molecular Modeling Studies Of The Dynamics And Catalytic Mechanisms Of Iron(Ii)- And Zinc(Ii)-Dependent Metalloenzymes, Sodiq O. Waheed

Dissertations, Master's Theses and Master's Reports

Enzymes are biological systems that aid in specific biochemical reactions. They lower the reaction barrier, thus speeding up the reaction rate. A detailed knowledge of enzymes will not be achievable without computational modeling as it offers insight into atomistic details and catalytic species, which are crucial to designing enzyme-specific inhibitors and impossible to gain experimentally. This dissertation employs advanced multiscale computational approaches to study the dynamics and reaction mechanisms of non-heme Fe(II) and 2-oxoglutarate (2OG) dependent oxygenases, including AlkB, AlkBH2, TET2, and KDM4E, involved in DNA and histone demethylation. It also focuses on Zn(II) dependent matrix metalloproteinase-1 (MMP-1), which helps …

Comparison Of Cell Cycle Gene Expression Between Ovarian Cancer Cell Line Skov3 And Non-Cancerous Cell Lines, Akayla Weatherby

Dissertations, Master's Theses and Master's Reports

Roughly 1% of women will be diagnosed with ovarian cancer during their lifetime. There are many different factors that impact how likely someone is to develop ovarian cancer including age, lifestyle, and family history. Ovarian cancer, like all cancers, occurs due to the accumulation of cancer cells that result from errors in the cell cycle or its regulation. Here, we studied how cell cycle gene expression was altered in the epithelial-like ovarian cancer cell line SKOV3, as compared to the pre-cancerous ovarian cell line FT282, and the non-cancerous foreskin fibroblast cell line BJ5Ta. The three cell lines were synchronized into …

Tropical Plant Physiological Responses To Experimental Warming And Hurricane Disturbance, Robert Tunison

Dissertations, Master's Theses and Master's Reports

Tropical forests exchange more carbon with the atmosphere than any other biome, but their responses to climate change are largely understudied. The work presented in this dissertation uses a tropical understory warming experiment that was hit by a hurricane disturbance to investigate how plant physiology responds to multiple types of climate change pressures. We measured the potential for root respiration, leaf photosynthesis & respiration, and leaf thermotolerance acclimation to experimental warming while recovering from hurricane disturbance. We found there was thermal acclimation via decreased ecosystem root respiration, increased photosynthetic thermal niche breadth, and decreased quantum efficiency for some species at …

Cancer/Testis Gene Expression Changes In Metastatic Cancer, Clara M. Mosentine

Dissertations, Master's Theses and Master's Reports

Metastasis is the movement of cancerous cells to new parts of the body, often through the blood or lymph systems. Metastasis is classified as stage IV cancer, a prognosis that is significantly more difficult to effectively treat compared to earlier cancer stages. We are interested in assessing whether expression of Cancer/testis (CT) genes, a class of genes that are predominantly expressed in germ cells while also being abnormally expressed in a large percentage of cancers, is associated with cancer metastasis. Germ cells make up an organism’s reproductive system, such as the testis and ovaries, and exhibit cellular immortality and, in …

Characterization Of Vernal Pools Across National Parks In The Great Lakes Region, Samantha R. Kurkowski

Dissertations, Master's Theses and Master's Reports

Vernal pools are small, ephemeral wetlands that become inundated each spring and provide many ecosystem services to the surrounding upland forests. They also provide critical habitat for amphibians and invertebrates, as their temporary nature keeps them free of fish and reduces predator populations. As part of a mapping project, we collected baseline field data on vernal pool characteristics throughout five Great Lakes National Parks: Pictured Rocks National Lakeshore, Sleeping Bear Dunes National Lakeshore, Apostle Islands National Lakeshore, Isle Royale National Park, and Voyagers National Parks. Our goals were to characterize and assess how vernal pools vary within and across the …

Bioaccumulation Of Polychlorinated Biphenyl Compounds And Mercury In A Mining Impacted Aquatic Ecosystem, Michelle Bollini

Dissertations, Master's Theses and Master's Reports

The Keweenaw area continues to be influenced by the century of copper mining that ended nearly 50 years ago. This project is focused on Torch Lake, an aquatic ecosystem that has been heavily impacted by mining waste disposal. The watershed has been impaired by mine discharge and tailings, smelter and smokestack plumes, and poor waste disposal practices. The lake is listed as a Great Lakes Area of Concern with beneficial use impairments of restrictions on fish consumption and a degraded benthic community. Polychlorinated biphenyl compounds (PCBs) and methylmercury (MeHg) are persistent, bioaccumulative, and toxic substances (PBTs). These contaminants pose threats …

Near-Surface Soil Nitrogen And Vegetation Response To Invasive Emerald Ash Borer In Forested Black Ash Wetlands Of The Western Upper Peninsula, Michigan, Usa, Daniel A. Beyer

Dissertations, Master's Theses and Master's Reports

Invasive emerald ash borer (EAB) (Agrilus planipennis Fairmaire) poses an imminent threat to the structure and function of North American hardwood forests, particularly black ash (Fraxinus nigra Marshall), and alters the hydrologic and ecological services of their wetlands. Black ash trees regularly grow in seasonally saturated soils and are responsible for hydrologic regulation and nutrient cycling. In this study, a gradient of black ash wetlands impacted by EAB were monitored to assess vegetation changes and near-surface soil nitrogen availability. Vegetation community changes were intertwined with nitrogen cycle disturbances following EAB infestation. As black ash died and fell to …

Sequencing Antisense Transcriptome Of Populus Through Antisense/Sense Transcript Pair Enrichment, Emma V. Burke

Dissertations, Master's Theses and Master's Reports

Past transcriptome research on plants focused primarily on protein coding genes, and only recently researchers began looking into the non-protein coding regions that may play significant roles in gene regulation. Antisense RNA transcripts that are found naturally in the cell share complementary sequence with sense transcripts and have been shown to regulate expression of their sense counterparts. Since antisense RNA has been largely under-studied and difficult to sequence because of their low relative abundance, new methods are needed to target antisense RNA for efficient genome-wide profiling. To address this gap in methods to efficiently and cost effectively enrich antisense RNA …

Changes In Poplar Digestibility Due To Overexpression Of Laccase Genes, Fnu Arunima

Dissertations, Master's Theses and Master's Reports

Woody biomass, particularly poplar, is a sought-after feedstock for lignocellulosic biofuels because of its year-round availability and high productivity. Because of cell wall components like lignin, poplar is inherently resistant to enzymatic saccharification. The experiment aims to determine whether the controlled overexpression of laccase genes alters the biomass composition and whether it can create poplar that is more digestible than the wildtype.

Three sets of transgenic poplar (Populus tremula x alba) samples were evaluated: laccase 18, laccase 27, and STTM. Laccase 18 samples, an target of miRNA397a was overexpressed along with Laccase 27. Short Tandem target Mimic (STTM) technology …

Machine Learning Methods For Prediction Of Human Infectious Virus And Imputation Of Hla Alleles, Xiaoqing Gao

Dissertations, Master's Theses and Master's Reports

This dissertation contains three Chapters. The following is a concise description of each Chapters.

In Chapter 1, we introduced the Random Forest, a machine learning method, to foresee whether a virus is capable of infecting humans. The Covid pandemic informs us the importance of predicting the ability of a zoonotic virus that can infect humans from its genomic sequence. We used the -mer with and as features of a virus to predict if it can affect humans. We further employed the Boruta algorithm to select the important features, then fed those important features into the Random Forest method to train …

Exploring Ph Gradient Phenomena In Non-Linear Electrokinetic Microfluidic Devices, Azade Tahmasebi

Dissertations, Master's Theses and Master's Reports

Electrokinetic microfluidics is a versatile technology utilized within lab on a chip (LOC) devices for diagnostic and analytical applications; advantages include reduced resource demands, flexibility, and simplicity of use. Dielectrophoresis (DEP) is a precision nonlinear electrokinetic tool utilized within microfluidic microdevices to induce polarization and control bioparticle motions for applications that range from hemoglobin separations to cancer cell isolation and detection. Despite promising results, undesired side phenomena can occur in electrokinetic systems which impede reproducibility and accuracy. These unfavorable phenomena have not been comprehensively explored in the literature. Prior preliminary research suggests the fundamental phenomena originate from microelectrodes utilized in …