Biology Commons^™

The Maintenance Of Cd4 And Cd8 T Cell Response To Persistent Antigens, Yu Xia

Arts & Sciences Graduate Student Theses and Dissertations

In response to transient antigen presence in the context of acute infections or vaccinations, antigen-specific naïve T cells clonally expand and differentiate. Most of the expanded cells undergo terminally differentiation and die following antigen clearance to re-establish immune homeostasis. In contrast, when the pathogen persists, such as in the context of chronic viral infections or anti-tumor immunity, while T cells undergo alternative differentiation known as exhaustion due to their reduced functionality, T cells still contribute to pathogen control and its response is sustained for longer duration due to unknown mechanisms. The goal of my thesis work is to understand how …

Multi-Omics Investigation Of Tumor Heterogeneity, Oncogenic Signaling, And Treatment Response In Human Cancers, Yige Wu

Arts & Sciences Graduate Student Theses and Dissertations

Cancer is a highly complex disease with aberrations at the genetic, epigenetic, transcriptomic, and protein levels that drove its phenotypic diversity. Clear cell renal cell carcinoma (ccRCC) is the most common form of kidney cancer, comprising roughly 80% of cases. To define the epigenetic and transcriptomic regulation of ccRCC at the single nucleus (sn) level, we performed snRNA-seq and snATAC-seq in 34 and 28 samples respectively, including primary tumors and normal adjacent tissues, and matched them with bulk proteogenomics data. We identified tumor-specific markers and tumor subpopulations using snRNA-seq, which demonstrated diverse pathway activity within and across patients. PBRM1 and …

Thermoregulation And Spatial Distribution Of Lizards In The Southwestern Usa: Adaptation To A Changing Climate, Caleb Lee Loughran

Biology ETDs

Lizards rely heavily on environmental temperatures to thermoregulate and maintain a body temperature (Tb) that optimizes physiological function and maximizes surface activity time. While early research noted the propensity for lizards to thermoregulate by shuttling between different thermal environments, it was long assumed that evaporative cooling via panting was an ineffective means of thermoregulation. However, evaporative cooling can potentially lower a lizard’s Tb significantly below air temperature, and thus allow lizards to extend activity periods during prolonged heat exposure. In this dissertation, I explore the varying abilities of lizards to thermoregulate while panting. I describe the metabolic and evaporative water …

Evaluating Threats To The Water Quality Of Little Buffalo Creek And Sarver Run Through Water Quality Analysis And Backpack Electrofishing Surveys, Riley Williams

Electronic Theses and Dissertations

Currently, 64.8% and 52.2% of Little Buffalo Creek and Sarver Run stream kilometers are impaired, respectively. Impairment sources to Little Buffalo Creek include agriculture, riparian deforestation, on-site wastewater, and urban runoff. Impairment sources to Sarver Run are unknown. Our goal was to understand sources of impairment through water quality analysis and fish surveys. Water samples were collected monthly and analyzed for cation and anion concentrations. Mass ratio analysis comparing Br/SO₄ and Mg/Li, Ca/Mg and Ca/Sr, Mg/Na and SO₄/Cl, and SO_4/Cl and Mg/Li suggests that mine drainage and conventional oil and gas may be impacting water …

A Review Of Current Methods In Avian Dietary Analysis And Their Integrated Application To Characterize The Trophic Niche Of Louisiana Waterthrush (Parkesia Motacilla)., Brandon Hoenig

Electronic Theses and Dissertations

Characterizing a species’ dietary composition presents an avenue to understand many facets of its ecological niche and can provide essential information for the species’ long-term conservation. To date, the vast majority of diet studies have relied on direct identification of prey during foraging observations or from diet samples to characterize the dietary habits of birds. However, advancements in laboratory-based approaches have revolutionized the field of trophic ecology by allowing researchers to indirectly infer dietary habits with higher resolution across greater time scales. Here, I apply two of these laboratory-based techniques, namely DNA metabarcoding and stable isotope analysis, to characterize the …

Pre-Pulse Inhibition In Mutated Mice: Studying Compromised Microglial Cells To Discover New Genetic Connections To Autism, Bailey R. Kramarik

Senior Honors Projects, 2020-current

Microglial cells “play a pivotal role in refining neural networks during early critical periods” (Gabriele & Gray, 2020, p. 1). A disturbance in the functioning of these microglial cells contribute to specific characteristics of some neurodevelopmental disorders- including autism spectrum disorder. In this study, we used a mouse model to study disruptions in cell activity, as understanding the biological and genetic background of autism spectrum disorder could help us provide better treatment and therapy options to those diagnosed.

The mutated mice in this experiment have microglial cells with “compromised fractalkine signaling” (Gabriele & Gray, 2020, p. 4-5). We studied multimodal …

Biodiversity And Global Change In Terrestrial Ecosystems, Timothy John Ohlert

Biology ETDs

Terrestrial ecosystems are critical to human and ecological processes but many gaps in our knowledge remain regarding how terrestrial plant communities assemble and respond to global change. I used field experiments distributed around the world, including long-term experiments from the Sevilleta National Wildlife Refuge (SNWR) in New Mexico and deserts of the southwestern U.S., to evaluate the consequences of drought and other abiotic stressors on plant communities. Dominant grasses were particularly important for the productivity and structure of grasslands at SNWR. In general, the structure of desert plant communities had high resistance to extreme drought, though grasses and other perennial …

Procedures For Genetic Modification Of Miscanthus X Giganteus, A Biomass Crop, Anjali Arpan

Theses and Dissertations

Development of genetic improvement procedures for the bioenergy crop, Miscanthus × giganteus (M×g; triploid), are desired for trait improvement. Agrobacterium tumefaciens has been used in other Miscanthus spp. for genetic improvement, but not in M×g, nor have more than a few genes been introduced at a given time. Transformation procedures for M×g were developed; studies included use of A.tumefaciens (strain LBA4404) and A. rhizogenes (strain A4) for introduction of seven genes isolated (by other researchers) from Sorghum bicolor involved in sorgoleone biosynthesis (an allelopathic compound), and selectable marker gene neomycin phosphotransferase II. Procedural development included generation of …

Sprouting Systems, Abaigeal Aydt, Cassidy Smith

Honors Program: Expanded Learning Clubs

After taking a class at UNL about environmental awareness, two honors students paired up to start a hydroponics club at a local Lincoln school. In reaching out to the LPS director of sustainability, they were paired up with Prescott Elementary School. Over the course of a semester, they developed a club that got a hydroponic grow tower functioning for the school and taught students about nutrition and sustainability. This club is only in its beginning stages, but the impacts that it is making around the school can already be seen.

Classification Of Eurasian Watermilfoil (Myriophyllum Spicatum) Using Drone-Enabled Multispectral Imagery Analysis, Colin Brooks, Amanda Grimm, Amy Marcarelli, Nicholas Marion, Robert Shuchman, Michael Sayers

Michigan Tech Publications, Part 1

Remote sensing approaches that could identify species of submerged aquatic vegetation (SAV) and measure their extent in lake littoral zones would greatly enhance SAV study and management, especially if these approaches can provide faster or more accurate results than traditional field methods. Remote sensing with multispectral sensors can provide this capability, but SAV identification with this technology must address the challenges of light extinction in aquatic environments where chlorophyll, dissolved organic carbon, and suspended minerals can affect water clarity and the strength of the sensed light signal. Here, we present an uncrewed aerial system (UAS)-enabled methodology to identify the extent …

Physiological Costs Of Total Cholesterol In European Starlings Across An Urban To Rural Gradient, Courtney Linkous

Master of Science in Integrative Biology Theses

Urban areas—characterized by high human densities and associated buildings and impermeable surfaces—are increasing globally and represents a leading threat to wildlife that is drastically altering the natural resources they are accustomed to. Prior studies suggest that living in urban habitats can cause wildlife to show increased cholesterol levels; in biomedical research, elevated cholesterol is linked to disease, but the consequence of elevated cholesterol in wildlife remains unclear. We measured total cholesterol in European starlings (Sturnus vulgaris)—an urban adapted species—across an urban and a rural site. We ask: (1) do urban starlings have elevated cholesterol, (2) does elevated cholesterol …

Pilfering Passerines? Inter-Class Competition: A New Direction In Foraging Ecology, Shannon Gillen

Masters Theses, 2020-current

Life in the epigeal layer below leaf litterfall often goes unexplored. Shrews (Soricidae, 1910) have foraged in this microhabitat for millions of years, carving out an existence in harsh habitats around the world, ranging from the tropics to subarctic boreal tundra. Two shrew species that inhabit the Shenandoah Valley of Virginia, the least shrew (Cryptotis parva) and northern short-tailed shrew (Blarina brevicauda), were the focus of this study. Shrews make epigeal foraging trails while they continually forage for food, and caching is a way to save this food for times of low and sporadic food availability. …

Does Manuka Honey Induce Antibiotic Resistant Bacterial Persisters And Viable But Non-Culturable Subpopulations?, Bryn Tennyson

2022 Symposium

Long-term antibiotic use has allowed microbes to develop resistance and cause chronic infectious diseases that were previously treatable. Resistance is phenomenon in which bacteria survive treatment with a concentration of antibiotics that was once lethal. Bacteria resist antibiotic treatment by genetic change or initiating states of dormancy called persisters or Viable but Non-Culturable (VBNCs) cells. These subpopulations of antibiotic resistant persisters and VBNCs increase with exposure to stresses, including antibiotic treatment, and are a major cause of reoccurring infections that result in significant morbidity and mortality. Manuka honey (MH), a well-known alternative broad-spectrum antimicrobial, is a promising treatment for cutaneous …

Clock-Linked Genes Underlie Seasonal Migratory Timing In A Diurnal Raptor, Christen M. Bossu, Julie A. Heath, Gregory S. Kaltenecker, Barbara Helm, Kristen C. Ruegg

Biology Faculty Publications and Presentations

Seasonal migration is a dynamic natural phenomenon that allows organisms to exploit favourable habitats across the annual cycle. While the morphological, physiological and behavioural changes associated with migratory behaviour are well characterized, the genetic basis of migration and its link to endogenous biological time-keeping pathways are poorly understood. Historically, genome-wide research has focused on genes of large effect, whereas many genes of small effect may work together to regulate complex traits like migratory behaviour. Here, we explicitly relax stringent outlier detection thresholds and, as a result, discover how multiple biological time-keeping genes are important to migratory timing in an iconic …

Traits And Functional Diversity Of A Hyperdiverse Bee Assemblage Are Linked To Aridity, Benjamin D. Turnley

Biology ETDs

Climate change in the American Southwest is altering the composition of species assemblages. However, the resulting patterns in mean trait values and functional diversity are poorly understood. Bees assemblages in Southwestern drylands are exceptionally diverse, and vary greatly in their morphologic traits. In this study we focused on two questions: Have community-weighted mean trait values shifted over time and/or with aridity, consistent with the hypothesis that aridification is driving bee assemblage change? Has the functional diversity of the Sevilleta bee assemblage declined over time and/or with aridity, consistent with the hypothesis that pollination services could be declining? To address these …

Ecology Of Texas Zebra Mussels, Heather Arterburn

Biology Datasets - Archive

Data analyzing the zebra mussel population dynamics in three Texas reservoirs over a period of 3-5 years. Data includes shell length of adult and planktonic larvae samples collected monthly, growth rates, reproductive periods, and settlement patterns. Additionally, water quality parameters are included for correlational analysis.

A Neuromuscular Look Into Genetics Of Muscle Aging, Christina Talley

Master of Science in Integrative Biology Theses

As individuals age throughout their life, they experience muscle tissue loss that impacts their quality of life such as a decrease in their physical capabilities and sometimes even their mental capacity. The process of muscle aging is the key point of this study. This involves the individual’s muscles and the motor neurons that control them. Skeletal muscles are used daily to maintain posture, stand, walk, etc. Throughout a lifetime these muscles undergo damage and need to be repaired. When the muscles are repaired, they express physical changes. The tissue shrinks in size and eventually the composition of the tissue is …

Gene Expression Analysis Revealed The Activation Of Immune Responses During The Postnatal Development Of The Cerebellum In A Mouse Model Of Niemann-Pick Type C, Sierra Elizabeth Melli

Theses and Dissertations

Niemann-Pick Type C (NPC) is a recessive neurodegenerative lysosomal storage disorder that is caused by autosomal recessive mutations. The mutations result in the inactivation of NPC1 and NPC2 proteins. Inactivation of the NPC1 protein results in the accumulation of cholesterol within the endosomal and lysosomal compartments of cells including Cerebellar Purkinje cells. This accumulation of cholesterol leads to symptoms of dementia, neurodegeneration and potential of early childhood death in cases of early onset. In this study, we analyze the gene expression levels using the RNAseq technique in order to determine whether there is a significant difference between the expression of …

The Effects Of Disturbance Intensity On Total Bacteria Concentration In The Water Within Artificial Streams, Seth C. Davis

Honors College Theses

Bacterial communities persist longer in sediment than in the water because sediments offer beneficial conditions for proliferation and formation of self-sustaining colonies. However, environmental- and human-caused sediment disturbance may resuspend bacteria in the water, thus increasing the potential for harmful bacterial to interact with humans and other organisms. I tested the hypothesis that the level of sediment disturbance affects the abundance and duration of bacterial resuspension in artificial stream microcosms. Three treatments were administered: control (no disturbance), low intensity disturbance, and high intensity disturbance (n=5). Water samples were collected before disturbance treatment (P), and at 0, 6, 24, 48, and …

Type Of Synthetic Microfiber Influences Ingestion By Freshwater Worms, Sarah A. Martinez

Honors College Theses

Plastics enter the environment from many sources, including clothing made from synthetic textiles, which shed a form of microplastics (microfibers) during their production, use and disposal. The impacts of microfibers on freshwater organisms are relatively unknown, therefore we tested the hypothesis that short- and long-term effects of microfibers on the aquatic worm, Lumbriculus variegatus, depend on the type of synthetic microfiber present. Microcosms containing L. variegatus, sediment and water were exposed to either no fibers (control) or one of three microfiber treatments (nylon, polyester or olefin) at the same concentration for 48 hours or 28 days. At the …

Global Collision-Risk Hotspots Of Marine Traffic And The World’S Largest Fish, The Whale Shark, Freya C. Womersley, Nicolas E. Humphries, Nuno Queiroz, Marisa Vedor, Ivo Da Costa, Miguel Furtado, John P. Tyminski, Katya Abrantes, Gonzalo Araujo, Steffen S. Bach, Adam Barnett, Michael L. Berumen, Sandra Bessudo Lion, Camrin D. Braun, Elizabeth Clingham, Jesse E. M. Cochran, Rafael De La Parra, Stella Diamant, Alistair D. M. Dove, Christine L. Dudgeon, Mark V. Erdmann, Eduardo Espinoza, Richard Fitzpatrick, Jaime González Cano, Jonathan R. Green, Hector M. Guzman, Royale Hardenstine, Abdi Hasan, Fábio H. V. Hazin, Alex R. Hearn, Robert E. Hueter, Mohammed Y. Jaidah, Jessica Labaja, Felipe Ladino, Bruno C. L. Macena, John J. Morris Jr., Bradley M. Norman, Cesar Peñaherrera-Palma, Simon J. Pierce, Lina Maria Quintero, Dení Ramírez-Macías, Samantha D. Reynolds, Anthony J. Richardson, David P. Robinson, Christoph A. Rohner, David R. L. Rowat, Marcus Sheaves, Mahmood Shivji, Abraham B. Sianipar, Gregory B. Skomal, German Soler, Ismail Syakurachman, Simon R. Thorrold, D. Harry Webb, Bradley M. Wetherbee, Timothy D. White, Tyler Clavelle, David A. Kroodsma, Michele Thums, Luciana C. Ferreira, Mark G. Meekan, Lucy M. Arrowsmith, Emily K. Lester, Megan M. Meyers, Lauren R. Peel, Ana M. M. Sequeira, Victor M. Eguiluz, Carlos M. Duarte, David W. Sims

Biology Faculty Articles

Marine traffic is increasing globally yet collisions with endangered megafauna such as whales, sea turtles, and planktivorous sharks go largely undetected or unreported. Collisions leading to mortality can have population-level consequences for endangered species. Hence, identifying simultaneous space use of megafauna and shipping throughout ranges may reveal as-yet-unknown spatial targets requiring conservation. However, global studies tracking megafauna and shipping occurrences are lacking. Here we combine satellite-tracked movements of the whale shark, Rhincodon typus, and vessel activity to show that 92% of sharks’ horizontal space use and nearly 50% of vertical space use overlap with persistent large vessel (>300 …

The Synthesis And Characterization Of Ionic Liquids Using Nitrogen-Based Cations For Transdermal Delivery, Jo Galloway

Honors Theses

The purpose of this research was to explore the synthesis mechanisms of water-soluble ionic liquids with nitrogen-containing cationic bases for future use in transdermal drug delivery and forensic science applications. Ionic liquids are salts with an organic cation and either an organic or inorganic anion. They have asymmetric structures, which means that the molecules don’t pack together as neatly as other salts do, therefore, they don’t crystallize as easily, and their melting points are lower. Ionic liquids have melting points below 100°C, and many are liquid at room temperature. Mechanistic studies reveal that the potency of ILs in enhancing transdermal …

Developing A Novel Place Preference Assay To Compare Drosophila Species Over Time, Martha M. Brinson

Honors Theses

Across phylogeny, integration of external factors, memory, and internal states of the organism dictate organismal behavior and mechanisms. The underlying genetic components can affect these behaviors such as in genomic changes arising from speciation. In this thesis, a new place preference assay was evaluated in the analysis and investigation of two species of Drosophila flies (D. melanogaster and D. simulans) to measure similarities and differences and their attraction to two different food substrates. Sleep and circadian measurements were also recorded during experimentation. The Drosophila Activity Monitor 5M (DAM5M) System and Sleep Circadian Analysis MATLAB Program (SCAMP) analysis were …

Invasion Of The Northeastern United States By The Southern Pine Beetle, Dendroctonus Frontalis, And The Impacts On Signatures Of Isolation By Distance Assessed Using Mitochondrial Dna, Lora Grace Holman

Honors Theses

The southern pine beetle (SPB) is a small, black beetle that parasitizes pine trees across the United States and Central America. Recently it has been recognized that the range of SPB is not limited to the southern United States, but rather extends northward across the eastern United States, which raises concerns for pine trees that have never encountered the pest before. Using mitochondrial DNA sequences from a section of the cytochrome oxidase I gene and four different measures of genetic distance compared to geographic distance, we tested for evidence of isolation by distance (IBD) among sampled SPB to see whether …

Investigating The Role Of Small Rna Pathways In Arabidopsis Shoot Gravitropism, Julia Lott

Honors Theses

The plant stem grows against the gravitational force, a phenomenon called negative gravitropism. In the model dicotyledonous plant Arabidopsis thaliana, gravity is sensed by starch-filled amyloplasts, which trigger the shoot gravitropic response through the action of a growth hormone called auxin. In the darkness, a group of transcription factors named PHYTOCHROME-INTERACTING FACTORS (PIFs) promote stem negative gravitropism by inhibiting the starch metabolism in the endodermal amyloplasts. Red light promotes starch metabolism and converts amyloplasts into other types of plastids (e.g., chloroplasts) through the red/far-red light photoreceptors—phytochromes. Consequently, red-light-grown seedlings lose starch granules in amyloplasts and exhibit agravitropic growth. However, the …

Ontogenetic Niche Shift As A Driver Of Community Structure And Diversity In Non-Avian Dinosaurs, Katlin M. Schroeder

Biology ETDs

As some of the most charismatic megafauna to ever walk the earth, the physiology, morphology, growth and evolution of non-avian theropods has been studied exhaustively, yet little is understood about their roles in ecosystems as juveniles. For carnivorous megatheropods, which exceed 1,000kg in mass yet hatched from eggs of limited size, the likelihood of utilizing different prey through ontogeny was high, simply by proxy of the immense difference in size between adults and juveniles. We found these ontogenetic niche shifts, evidenced by significantly different dental microwear in Tyrannosaurids, to have excluded dinosaurian mesocarnivores from Mesozoic communities. The few dinosaurian mesocarnivores …

Cache Like A Squirrel: Effects Of Long Term Storage On Crude Fat Content Of Q. Palustris And Q. Alba Acorns, Cheyenne T. Villarosa, Sabrina Volponi, Timothy A. Kreps, Tamara L. Johnstone-Yellin

Honors Projects

Quercus palustris and Quercus alba acorns are a primary component in many wild animal diets, particularly during preparation for winter. As such, they provide a natural, easily gathered food staple for wildlife recovering in rehabilitation facilities. We examined whether collection and temperature-controlled storage methods differentially affect the nutritional deterioration of crude fat in acorns to assess both caching by wildlife and to provide recommendations to rehabilitators. We collected acorns from Q. palustris in 2020 (N=8) and Q. alba in 2017 (N=11) in Bridgewater, VA, USA. Acorns were dried for 7 days using a fan or for 30 minutes in an …

Determining The Distribution Of Elemental Compounds And Oxidative Potential Across Fine Particulate Matter (Pm2.5) Filters, Allie Michelle Sidwell

Honors Theses

Fine particulate matter (PM_2.5) is a complex mixture of particles and sorbed chemicals that poses serious, adverse effects on human health such as increasing cardiovascular and respiratory morbidity and mortality. There is ongoing research into the impacts of PM_2.5 of differing chemical compositions, sampling location, and the mechanisms for the observed health effects. To conduct these analytical and toxicology studies of PM_2.5, researchers often split filters into sections. This process allows multiple, often destructive, assays to be performed. Our previous research showed chemical composition differences across PM_2.5 filters. The goal of our study was …

Detection And Occurrence Of Nerodia Harteri (Serpentes: Colubridae) In An Upper Portion Of The Brazos River Watershed, Jessica Yates

Electronic Theses and Dissertations

Semiaquatic snakes are disproportionately impacted by habitat alteration adjacent to wetlands because of their reliance on both terrestrial and aquatic habitats. Brazos River Watersnakes, Nerodia harteri, are endemic natricines with one of the most restricted geographic ranges in North America. I quantified detection and site occupancy probabilities of N. harteri and its sympatric congeners (N. erythrogaster and N. rhombifer), as well as microhabitat selection within the Nerodia community. Within occupied transects, search effort was positively correlated with detecting N. harteri, whereas environmental and/or habitat variables were better predictors for detecting the sympatric congeners. Microhabitat selection between …

Isolation Of Arabidopsis Thaliana Plants Homozygous For An Insertional Inactivation Mutation Within Atprp4., Sydney Raitz, Timothy D. Trott

Faculty Works

The AtPRP4 gene in Arabidopsis thaliana has been shown to function in several specific parts of the plant’s cell wall. It is shown to be expressed in the seeds, radicles, roots, leaves, inflorescences, and embryos of Arabidopsis thaliana. These patterns have suggested unique functions for ATPRP4 in determining cell-type-specific wall structure during the development of a plant as well as contributing to defense reactions against physical damage to the plant and pathogen infection within the plant. In this study, a simple DNA prep was performed on the true leaves of Arabidopsis thaliana. Subsequent PCR reactions were performed using …