Digital Commons Network^™

Single-Nuclei Resolution Kidney Profiling In Physiological And Disease Settings, Ruiyang Liu

Arts & Sciences Graduate Student Theses and Dissertations

The kidney is a critical organ responsible for the maintenance of fluid, electrolyte and metabolites in the body. Recent advancements in kidney research, including the use of single-nuclei RNA Sequencing (snRNA-Seq), have uncovered a complex landscape that encompasses both physiological and pathological conditions. The scope of my thesis covers two important aspects: (1) the exploration of kidney sexual dimorphism, (2) a detailed investigation of polycystic kidney disease (PKD). To obtain a comprehensive understanding of the molecular regulation of kidney sexual dimorphism, we integrated single nucleus RNA and ATAC sequencing (snRNA-Seq and snATAC-Seq) and Visium spatial transcriptomics (ST) data to build …

The Mayfly Newsletter, Donna Giberson

The Mayfly Newsletter

The Mayfly Newsletter is the official newsletter of the Permanent Committee of the International Conferences on Ephemeroptera.

Investigating Telomere Lengths In Chestnut-Crowned Babblers, Gabriella Rose Beberg

Honors Thesis

Telomeres are chromosomal elements that protect and maintain genes as DNA replicates in many organisms. As individuals age and DNA replicates, telomeres often shorten; thus, telomere length often corresponds with an individual’s lifespan, and early-life decreases in telomere length can be predictive of longevity. Here, I investigated the relationship between telomere length and developmental environment in a cooperatively breeding species, the chestnut-crowned babbler (Pomatostomus ruficeps; CCB). Cooperative species are unique, as some individuals give up their own breeding opportunities to help rear the offspring of others; further, cooperative breeding systems generate considerably more variation in adult carers, which …

Acid Attack: How Escherichia Coli Strains Resist Acid Stress, Lindsey Miller

Honors Theses

The systems used by Escherichia coli to combat heightened levels of acidity within their environment are varied and complex. Four distinct systems used by E. coli to resist acid-induced stress were identified in 2004 by Foster (1), though six now are known today. These systems include the glucose-repressed, glutamate-dependent, arginine-dependent, lysine-dependent, ornithine-dependent, and serine-dependent acid resistance systems. Each system is also known by its corresponding abbreviation, AR1-AR6. What is known about each system varies due to identification date, complexity of the pathway, and amount of research completed. Within this paper, each system will be identified and the pathway defined, combining …

Embracing Digital Mindsets To Ensure A Sustainable Future, Chengjun Li, Riqing Yu, Wenjing Ning, Huan Zhong, Christian Sonne

Biology Faculty Publications and Presentations

The 19th Asian Games astounded global audiences with an opening spectacle that showcased stunning digital fireworks (International Olympic Committee, 2021; Zhe, 2023). The groundbreaking display was brought to life through virtual reality (VR) and augmented reality (AR) technologies. It sets a pioneering example to replace conventional fireworks in major international events as well as in other large-scale entertainment activities, marking a historic milestone in the pursuit of a sustainable and healthy future.

The Potential Of Endophytic Bacteria As The Biocontrol Agents Of Fusarium Proliferatum, Rima Ernia, Nisa Rachmania Mubarik, Lisdar Idwan Sudirman

Makara Journal of Science

Fusarium proliferatum decreases the productivity of shallot (Allium cepa L.). Endophytic bacteria are potential biocontrol agents in controlling the growth of F. proliferatum. This study aimed to select and characterize endophytic bacteria producing bioactive compounds that inhibit the growth of F. proliferatum. The endophytic bacteria used were isolated from the roots, stems, leaves, and soil of shallot plants from healthy and diseased shallot farming fields. The endophytic bacteria were selected using the dual culture method and extracted using ethyl acetate solvent. The results of the 16S rRNA identification suggested that isolate ABP5.2 is similar to Pseudomonas …

Catfish Neurocranium 3-D Scan, Pamela Gonzalez, Jarod Johnson, David Kerstetter

All Scans: Kerstetter Fisheries and Avian Ecology 3D Scan Series

No abstract provided.

Modeling X-Linked Dystonia Parkinsonism (Xdp) In Patient-Derived Medium Spiny Neurons, Shivani Aryal

Arts & Sciences Graduate Student Theses and Dissertations

X-linked dystonia-parkinsonism (XDP) is an adult-onset neurodegenerative disorder that results in the loss of striatal medium spiny neurons (MSNs). XDP is an X-linked disorder caused by disease-specific mutations around the TAF1 gene. This thesis highlights the utility of directly reprogrammed MSNs from fibroblasts of affected XDP as a platform that captures cellular and epigenetic phenotypes associated with XDP neurodegeneration. In addition, this thesis demonstrates the neuroprotective effect of SAK3 currently tested in other neurodegenerative diseases. XDP fibroblasts from three independent patients as well as age- and sex-matched control fibroblasts were used to generate MSNs using miRNA-9/9*-124 and the transcription factors …

Oliver Agee Catfish Neurocranium, Charlotte R. Oliver, Kristina Agee, David Kerstetter

All Scans: Kerstetter Fisheries and Avian Ecology 3D Scan Series

Neurocranium from 10.7 cm total length, [Catfish], collected by [Kerstetter].

Pathogenicity Of Acinetobacter Calcoaceticus, Kaitlan A. Sullivan

MUSC Theses and Dissertations

Acinetobacter is a genus of gram-negative bacteria that have been appearing frequently in hospitals contributing to infections in the blood, lungs, urinary tract, and other parts of the body. It infects patients with weakened immune systems that are placed on ventilators, after the use of catheters, or have any other open wounds produced by prolonged hospital stays. This genus of bacteria is problematic due to its high probability of becoming resistant to multiple classes of antibiotics. Thus, we are determining the pathogenicity of clinical isolates of Acinetobacter calcoaceticus using the organism Caenorhabditis elegans as a model.

We are testing …

Hazards And Perceptions Of Cigarette And E-Cigarette Waste, Jossalyn Rogalski

Honors Theses

No abstract provided.

Human Motion Detection Evaluated Through An Evoked Cortical Potential Frequency Spectrum, Howard E. Painter

USF Tampa Graduate Theses and Dissertations

Electrical potentials were recorded from scalp of normal male subjects while they were viewing continuously moving sinusoidal gratings. Responses from the occipital cortex were amplified, digitized, stored and then transformed from the time domain to the frequency domain using a microcomputer based Fast Fourier Transform algorithm. High frequency components (Beta Activity) of the resulting power spectrum were analyzed for evidence on neural generators (electrical sources) in the striate cortex driven presumably by transient-cells (Y-cells or Magnocellular) responding to the continuously moving grating. Several stimulus parameters were examined: angular velocity, spatial frequency, direction (orientation), color, and intensity. A16 Hz component of …

Development Of Computational And Experimental Approaches For Rna Virus Serology, Brittany Kaye Smith

Arts & Sciences Graduate Student Theses and Dissertations

Neutralization assays like the plaque reduction neutralization test (PRNT) and focus reduction neutralization test (FRNT) are the most specific ways to measure neutralizing antibodies, which provide a good estimate of protection for RNA viruses. However, these assays are time-consuming, labor-intensive, and low-throughput. Alternative methods that are faster and convenient are necessary to quantify antibody responses in large-scale studies. In this dissertation, I develop a mix of computational and experimental methods to quantify antibody responses to dengue viruses (DENV) and SARS-CoV-2. DENV is the most significant mosquito-borne viral infection in humans. Four serotypes of DENV exist. Traditionally, infection with one serotype …

Common Snook (Centropomus Undecimalis) Neurocranium, Ryan Robison, Lesley Wallace, David Kerstetter

All Scans: Kerstetter Fisheries and Avian Ecology 3D Scan Series

Neurocranium length of 16.5 cm Common Snook (Centropomus undecimalis), collected from Dr. Kerstetter's Lab on 10/23 by Ryan Robison and Lesley Wallace.

Yellow Grouper (Epinephelus Awoara), Tyler Jurain, David Kerstetter

All Scans: Kerstetter Fisheries and Avian Ecology 3D Scan Series

No abstract provided.

Jack Crevalle Neurocranium, Rodolfo A. Heredia, David Kerstetter

All Scans: Kerstetter Fisheries and Avian Ecology 3D Scan Series

No abstract provided.

The Unexpected Significance Of Myosin A In Organization Of M-Line Protein Unc-89/Obscurin Within Striated Muscle Cells Of Caenorhabditis Elegans, Kar Men Lee

Honors Theses

This research investigates the unexpected significance of Myosin A in the organization of M-line protein UNC-89/obscurin within striated muscle cells of the nematode Caenorhabditis elegans (C. elegans). The study employs immunofluorescence techniques to examine the spatial and temporal dynamics of UNC-89/obscurin and Myosin A during embryonic development. The sarcomere, a fundamental unit in muscle cells, is governed by the 'sliding filament model,' where the M-line serves as a crucial anchor for Myosin A. This research seeks to understand the relationship between muscle function in humans and C. elegans, utilizing the latter's simple anatomy and genetic tractability. The …

Brown Bullhead Catfish (Ameiurus Nebulosus) Neurocranium, Reginald Leon Kempson Iii, David Kerstetter

All Scans: Kerstetter Fisheries and Avian Ecology 3D Scan Series

Neurocranium from [6.3] cm total length (30 cm) [Brown Bullhead Catfish (Ameiurus nebulosus)], collected from [Dr.Kerstetters lab] on [6/December/2023] by [Reginald Kempson III]

We Are The Reason We Stand Still In The Face Of Climate Change., Sydney Hemp

Honors Theses

Many different factors can impact the way any information is received but it is especially important to see how scientific information is received because it is often backed up by a great deal of evidence, especially in the case of global climate change. Many of these factors have nothing to do with science and everything to do with social influences, political parties, and other demographic measures. Discussion of these relationships is important when discussing communication in a broad sense, but it can be even more important when bringing up things like global climate change, which has become a political topic …

Gag Grouper (Mycteroperca Microlepis) Neurocranium, Sierra Potts, David Kerstetter

All Scans: Kerstetter Fisheries and Avian Ecology 3D Scan Series

10 cm neurocranium from Gag Grouper, Mycteroperca microlepis, collected from Snapper Mike's on 05/11/2023 by Sierra Potts

Microplastics, Macro-Problems: Abundance Of Man-Made Materials In The Waters And Sediments Of Florida State Parks, Luciana M. Banquero, Kate Mclendon, Andres Alatorre, Mackenzie Daniels, Savanna Freeman, Cassidy Starke, Katherine Harris, Sidney J. Busch

The Pegasus Review: UCF Undergraduate Research Journal

Man-made materials (MMM) are pollutants introduced to the environment by human activity. Microplastics (MP) are a type of MMM that threaten living organisms through bioaccumulation. The term MMM also encompasses pollutants produced from natural materials, such as rayon and microfibrillated cellulose, which are used in food packaging. This study aims to determine the extent of MMM pollution within estuaries in two of Florida’s state parks, as well as the effectiveness of using restored vegetation on shorelines to reduce MMM pollution. Tomoka State Park and Gamble Rogers State Park were selected at the request of the Florida Department of Environmental Protection. …

Determining The Extent Of Pioneer Mangrove Acidification On Intertidal Oyster Reefs, Cindy Whitten, Andres Alatorre, Nicole Campbell, Savanna Freeman, Sydney Henderson, Kate Mclendon, Connor Wright, June Davison, Madison Ganci, Katherine Harris

The Pegasus Review: UCF Undergraduate Research Journal

The Indian River Lagoon (IRL) stretches 251 kilometers along Florida’s east coast and is one of the most biodiverse estuaries in North America. Mosquito Lagoon, the northernmost portion of the IRL, is home to mangroves and intertidal oyster reefs that provide numerous ecosystem services. These two habitats are overlapping as climate change drives mangroves poleward. Scientists have documented mangrove expansion and the transition of oyster reef habitat to mangrove islands. Past studies have shown large, adult mangrove stands drive soil acidification. The goal of this study was to understand if stand-alone, or pioneer, Rhizophora mangle (red mangroves) and Avicennia germinans …

Hypothesis And Theory: Do Trees "Release The Tension" In Rainwater? Surface Tension Reduction In Throughfall And Stemflow From Urban Trees, Benjamin J. Noren, Nicholas R. Lewis, Kelly Cristina Tonello, Anna Ilek, John T. Van Stan Ii

Biological, Geological, and Environmental Faculty Publications

Knowledge of the processes and impacts associated with the canopy's partitioning of rainfall into stemflow (water that drains to the base of tree stems) and throughfall (water that drips through gaps and from canopy surfaces) has expanded in recent years. However, the effect of canopy interactions on the fundamental physical properties of rainwater as it travels through the canopy to the soil, particularly surface tension, remains understudied. To discuss specific hypotheses within this context and their relevance to ecohydrological theory, the surface tension of rainwater samples was examined directly. Over a period of 9 months, open rainwater, throughfall and stemflow …

Structural Basis Of Gating In Msl Channels, Jingying Zhang

Arts & Sciences Graduate Student Theses and Dissertations

All living organisms experience exogenous and endogenous mechanical stress that are fundamental to their growth, survival, and development. A prominent strategy to manage these stresses and ensure efficient physiological responses is through mechanosensitive (MS) ion channels by transforming mechanical forces into electrochemical signaling. However, given their structural diversity and the inherent challenges of applying membrane tension during structural study, how MS channels sense mechanical force and transit into different functional states remain unclear. MSL channels in plants, members of the mechanosensitive ion channel of small conductance (MscS) superfamily, provide a compelling avenue for studying the structural basis for gating of …

Modeling A Parkinson’S Disease Like State In Zebrafish Larvae Utilizing 6-Hydroxydopamine, Adrian Romero

Biology Theses

Parkinson's’ disease (PD) is a neurodegenerative disorder characterized by the loss of midbrain dopaminergic (mDA) neurons that currently has no cure. It is primarily characterized in patients by motor symptoms that include but are not limited to: tremor at rest, rigidity, akinesia, and postural instability affecting the quality of life for over 8.5 million people worldwide. The neurotoxin 6-hydroxydopamine (6-OHDA) has been used to induce a Parkinson’s disease-like state in several animal models; however, assessment of 6-OHDA use in zebrafish demonstrated a lack of consensus on method and utility. We determined an optimized protocol utilizing 6-OHDA to produce a PD-like …

+Protective Roles For Interferon-Gamma In Astrocytes During Chronic Autoimmunity, Brandon C. Smith

ETD Archive

Multiple sclerosis (MS) is an inflammatory and neurodegenerative disease of the central nervous system (CNS). Infiltrating inflammatory immune cells perpetuate demyelination and axonal damage in the CNS and significantly contribute to pathology and clinical deficits. Interferon (IFN)γ is classically described as deleterious in acute CNS autoimmunity, we and others have shown astrocytic IFNγ signaling also has a neuroprotective role. We found IFNγ signaling on astrocytes upregulates subunits of the immunoproteasome (iP) and programmed death ligand 1 (PD-L1), both of which serve protective roles during autoimmunity. Astrocyte-specific knockouts of Ifngr1 resulted in increased clinical severity in the MS murine model, experimental …

First Genomic Resource For An Endangered Neotropical Mega-Herbivore: The Complete Mitochondrial Genome Of The Forest-Dweller (Baird's) Tapir (Tapirus Bairdii), Caroline C. Ennis

Honors College Theses

Baird's tapir, or the Central American Tapir Tapirus bairdii (family Tapiridae), is one of the largest mammals native to the forests and wetlands of southern North America and Central America and is categorized as `endangered' on the 2014 IUCN Red List of Threatened Species. This study reports, for the first time, the complete mitochondrial genome of T. bairdii and examines the phylogenetic position of T. bairdii amongst closely related species in the same family and order to which it belongs using mitochondrial protein-coding genes (PCG's). The circular, double-stranded, A-T rich mitochondrial genome of T. bairdii is 16,697 bp in length …

The Influence Of Rusty Crayfish And Zebra Mussel Invasion On Yellow Perch Population Dynamics In North-Central Minnesota Lakes, Kendra Fink

Biology Graduate Theses

Over the last 50 years, Minnesota Department of Natural Resources standard fisheries survey catch rates of Yellow Perch have declined. Yellow Perch Perca flavescens are an important, widespread game fish, are essential prey species for Walleye Sander vitreus and other piscivorous fish and rely greatly on benthic resources through many life stages. Aquatic invasive species (AIS) like rusty crayfish Faxonius rusticus and zebra mussels Dreissena polymorpha have the potential to change water quality, vegetation and prey assemblages in aquatic systems and could cause shifts in energy flow, subsequently altering growth, condition, and maturity of native fish species. In this study, …

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 …

Parrotfish Skull, Grace Mikus, David Kerstetter

All Scans: Kerstetter Fisheries and Avian Ecology 3D Scan Series

No abstract provided.