Digital Commons Network^™

Bat Activity Across Urban Forest Plantings In Lexington, Kentucky, Grayson Marie Collier

Online Theses and Dissertations

Urbanization has led to major forest loss and negatively impacts ecosystem services. Urban reforestation efforts, such as Reforest the Bluegrass (RTB) in the Lexington-Fayette metropolitan area of Kentucky, have been implemented to address these negative effects, and to create habitat for forest-dependent wildlife such as bats. My research focused on assessing differences in bat activity across a 20-year chronosequence of RTB sites. Acoustic detectors were deployed across 10 different-aged plantings at 60 randomly-defined detector locations. Each planting was surveyed across 8 sampling periods from May – August 2023. Each recording session spanned ca. 7 consecutive nights, yielding a total of …

Gene-Environment Interactions In Non-Alcoholic Fatty Liver Disease: Insights From Mexican American Populations, Eron G. Manusov, Vincent P. Diego, Marcio Almeida, Jacob Galan, Auwal A. Bala, Marco Arriaga, Natasha Garcia-Rodriguez, Renee Hernandez, Satish Kumar, John Blangero, Sarah Williams-Blangero

School of Medicine Publications

Nonalcoholic Fatty Liver Disease (NAFLD) is a prevalent and complex condition influenced by both genetic and environmental factors. This chapter explores the genotype-by-environment interactions that contribute to the development and progression of NAFLD in the Mexican American population. Using advanced genetic epidemiology and bioinformatics approaches, we investigated how specific genetic variants interact with environmental factors such as depression, acculturation stress, and social determinants of health, to influence NAFLD risk and severity. Our findings reveal significant genotype-by-environment interactions for key NAFLD-related traits, including HbA1c, AST/ALT ratio, and steatosis-controlled attenuation parameter (CAP). We also discuss the application of cutting-edge proteomic and transcriptomic …

Comparing Multivalent Cross-Linked Sodium Alginate/ Montmorillonite Beads Containing Curcumin Or Cayenne Pepper As Drug Carriers And Their Antimicrobial Resistance, Shionainn Traynor, Shubham Sharma

SURE Journal: Science Undergraduate Research Experience Journal

The aim of the following work was to investigate and compare curcumin and cayenne pepper in microbeads composed of sodium alginate (SA) crosslinked with montmorillonite (MMT) to act as drug carriers and their antimicrobial resistance. The microbeads were prepared through ion-exchange in multivalent solutions of CaCl₂, MgCl₂ and AlCl₃. The microbeads were characterized by Scanning Electron Microscopy (SEM), Energy Dispersive X-ray analysis (EDX) and the time required for intercalation of curcumin and cayenne pepper with MMT. Simulated intestinal fluid (pH 7.3) and gastric fluid (pH 1.2) at 37°C were used for comparison in swelling studies. …

Mathematical Modelling Of Disease Outbreak, Favour Christian, Matthew Molloy

SURE Journal: Science Undergraduate Research Experience Journal

Establishing a model framework for more research necessitates a thorough understanding of the causes, distribution, prevalence, and evolution of infectious illnesses. The main mathematical concept used in this modelling simulation is ordinary differential equations (ODEs). The purpose of this study was to investigate the significance of the many criteria linked to a zombie virus spread. The zombie framework provides an accessible and relatively simple representation of the nature of infectious disease spread, allowing for tractable assumptions and the development of more complex situations.

The models are designed around a zombie outbreak in which the zombie virus is spread through a …

Editorial - Sure Journal Vol 6, Anne M. Friel, Eva Campion, Sinead Loughran

SURE Journal: Science Undergraduate Research Experience Journal

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Identification Of Conserved Eukaryotic Gene Products In Novel Mycobacteriophage, Brandon Mar, Jade Coxon, Lily Esterline, Sydney Clifford, Gabriella Burke, Mallory Motz, Alaina Gartner, Kioni Bush, James Lin, Lizzie Adams, Sophia Palant

The Journal of Purdue Undergraduate Research

Bacteriophage, a type of virus that infects bacteria, was discovered 100 years ago, initially isolated with a plaque assay in the 1940s. A mycobacteriophage is a subtype of bacteriophage that specifically infects mycobacteria. Since the introduction of DNA technologies and efforts to identify a plethora of bacteriophages, over 10,000 bacteriophages have been identified with 1,500 sequenced. Bacteriophage discovery has aided in genetic editing techniques, the development of synthetic biology tools, and disease treatment. However, to be able to expand on these capabilities, there is a need to identify more bacteriophages and sequence the genomes of these viruses, as they outnumber …

Next Generation Sequencing Based Profiling Of Genes In Patients With Syndromic Forms Of Retinitis Pigmentosa, Harshavardhini G

Theses and Dissertations

India is one of the largest populations in the world and is estimated to have a high prevalence of Retinitis Pigmentosa (RP). RP is clinically and genetically heterogenous, characterized initially as night blindness, leading to complete vision loss due to retinal degeneration. RP can occur in non-syndromic or syndromic forms, affecting other organs as observed in Bardet Biedl Syndrome (BBS) and Usher syndrome (USH).

BBS is characterized by RP, polydactyly, obesity, renal anomalies and learning difficulties. USH is characterized by RP and sensorineural hearing loss (SNHL), with variable presence of vestibular dysfunction. Nextgeneration sequencing (NGS) has become a cost-effective technology …

Tnf Prevents Establishment Of Anti-Tumor Immunity And Elucidates Toxicities Following Myxoma Virus Based Oncolytic Virotherapy, Miriam Beatriz Valenzuela Cardenas

Biomedical Sciences ETDs

Tumor Necrosis Factor Alpha (TNF) can lead to tumor regression through its direct cytolytic activity, yet it has also been implicated to facilitate tumor progression. This scenario complicates the efficacy and applicability of TNF based therapeutics as treatment for malignancies. In the context of oncolytic virotherapy (OV) which uses replicating viruses to treat tumors and acts by triggering production of pro-inflammatory cytokines, exploring such mechanisms is vital. Here we show that a Myxoma based oncolytic virus (vPD1/IL12) can induce large amounts TNF. The presence of TNF in the context of vPD1/IL12 plays a detrimental role both for tumor regression by …

Testing Vivo-Morpholino Mediated Gene Knockdown Of Stat6, Spi1b, And Hnf4Α In Adult Threespine Stickleback, Stella Dipippo

Honors Scholar Theses

The fibrotic immune response to the cestode parasite, Schistocephalus solidus, varies among threespine stickleback populations. Fibrosis suppresses parasite growth but has costly effects on the fish. Previous genomic studies in stickleback have suggested potential roles of Spi1b, STAT6, and HNF4α in modulating fibrosis severity, but there is presently no evidence for this in-vivo. We used antisense vivo-morpholino oligonucleotides (MOs) to attempt to knockdown the expression of each gene in the liver, spleen, and intestine of adult stickleback. Vivo-MOs have been proven effective in other species of teleost fish, as well as in mice and humans, but …

Early Host Defense Against Virus Infections, Søren R. Paludan, Thomas Pradeu, Andreas Pichlmair, K. Brad Wray, Jacob Giehm Mikkelsen, David Olagnier, Trine H. Mogensen

Presidential Fellows Articles and Research

Early host defense eliminates many viruses before infections are established while clearing others so they remain subclinical or cause only mild disease. The field of immunology has been shaped by broad concepts, including the pattern recognition theory that currently dominates innate immunology. Focusing on early host responses to virus infections, we analyze the literature to build a working hypothesis for the principles that govern the early line of cellular antiviral defense. Aiming to ultimately arrive at a criteria-based theory with strong explanatory power, we propose that both controlling infection and limiting inflammation are key drivers for the early cellular antiviral …

A Kid's Guide To Infectious Disease, Abby Carroll

Honors Theses

A Kid’s Guide to Infectious Disease is an educational illustrated book intended for young pediatric patients, ages three to five. This project was inspired by my personal interests, involvement at the University of Mississippi, and experience as a medical assistant. Over the past couple of years, I have had the opportunity to work as a medical assistant, interacting with many pediatric patients and their families at HealthPointe Primary Care. As a pre-physician assistant student studying biology, I was inspired to create a resource for these kids by both my classes at the University of Mississippi and my passion for pediatric …

Evaluation Of Current Management Strategies For The Tarnished Plant Bug And Tobacco Thrips In Midsouthern Cotton, Hunter Lane Lipsey

Theses and Dissertations

The tarnished plant bug, Lygus lineolaris (Palisot de Beauvois), is an important economic pest of cotton, Gossypium hirsutum (L.), in the Midsouth region of the United States. An experiment was conducted to determine the impact of insecticide class loss on yield and Lygus populations in the recently commercialized ThryvOn cotton technology. Data indicated no significant yield loss when excluding any currently utilized insecticide class for tarnished plant bug management. An additional objective was to reevaluate the sampling interval necessary to scout ThryvOn cotton for Lygus. No significant differences were observed between a 3 or 7-day sample interval compared to plots …

Safety, Immunogenicity, And Efficacy Of A Recombinant Vesicular Stomatitis Virus Vectored Vaccine Against Severe Fever With Thrombocytopenia Syndrome Virus And Heartland Bandavirus, Philip Hicks, Tomaz B. Manzoni, Jonna B. Westover, Raegan J. Petch, Brianne Roper, Brian B. Gowen, Paul Bates

Animal, Dairy, and Veterinary Science Faculty Publications

Background: Severe fever with thrombocytopenia syndrome virus (STSV) is a recently emerged tickborne virus in east Asia with over 18,000 confirmed cases. With a high case fatality ratio, SFTSV has been designated a high priority pathogen by the WHO and the NIAID. Despite this, there are currently no approved therapies or vaccines to treat or prevent SFTS. Vesicular stomatitis virus (VSV) represents an FDA-approved vaccine platform that has been considered for numerous viruses due to its low sero-prevalence in humans, ease in genetic manipulation, and promiscuity in incorporating foreign glycoproteins into its virions. Methods: In this study, we developed a …

Design, Synthesis, And Nmr-Guided Characterization Of A Targeted Covalent Inhibitor-Like Molecule Against Ivyp1 From P. Aeruginosa, Samuel Taylor Moore

Master's Theses

Multi-drug resistance poses a serious threat to future generations and historical antibiotic pipelines; consequently, the medical and economic burdens associated with treating multidrug-resistant bacteria are substantiated. In this context, P. aeruginosa (PA) emerges as one of the most significant healthcare challenges, being a leading cause of resistance-associated mortality worldwide. Despite modern efforts to combat these poor outcomes, drug-resistant cases continue to rise, and the need for novel antibiotic treatment is apparent. To this end, we investigated relevant resistance mechanisms and past antibiotic targets within PA, and in doing so, we identified relationships between peptidoglycan biology and a periplasmic protein, Inhibitor …

Staphylococcus Epidermidis St2 Strains Associated With Bloodstream Infections Contain A Unique Mobile Genetic Element Encoding A Plasmin Inhibitor, Amy A Gomez, Clara Kjerfve, Minseo Choi, Wen Liu, Kelly Churion, Sheila Thomas, Holger Rohde, Sam Shelburne, Jon T Skare, Magnus Hook, Srishtee Arora

Faculty, Staff and Student Publications

Staphylococcus epidermidis, a common commensal bacterium, is a leading cause of nosocomial catheter-associated bloodstream infections. S. epidermidis sequence type 2 (ST2) is specifically recognized globally for causing invasive disease. In this study, we identified a novel putative integrated conjugative element, pICE-Sepi-ST2, unique to the genomes of S. epidermidis ST2. Our investigation identified pICE-Sepi-ST2 in all ST2 isolates from bloodstream infections. Meanwhile, ST2 isolates from other infection sources, such as catheters, prosthetic joints, and fracture fixations, showed variable pICE-Sepi-ST2 prevalence. pICE-Sepi-ST2 encodes two putative cell wall anchored proteins that we have designated SesX and SesY. Biochemical characterization of SesY revealed …

Exploring The Utility Of The Septicyte In Clinical Decision-Making In The Emergency Department, Sylvia Lowery-Taylor

Doctoral Dissertations and Projects

Know thy enemy. A significant obstacle in treating and managing sepsis is the absence of a test or method to diagnose the disease rapidly. Sepsis is defined as a life-threatening organ dysfunction caused by a dysregulated host response to infection (Sinha & Ray, 2018). Despite improvements to sepsis-related care and sepsis outcomes, it remains a worldwide concern and a leading cause of mortality. Early recognition and management of sepsis is critical to provide rapid treatment and to prevent deaths associated with sepsis and septic shock. Since most patients with sepsis receive their initial care in the emergency department, it is …

The Long Shadow Of Infection: The Long-Term Implications Of Herpes Simplex Virus And M. Tuberculosis Infection, Lydia Howell

Theses and Dissertations

Infectious diseases and autoimmune diseases, such as multiple sclerosis (MS) and type 1 diabetes (T1D), have traditionally been seen as distinct, with separate etiologies and courses of disease. Recent research has shown that infection and autoimmune disease are more closely woven together than previously thought; certain pathogens like Epstein-Barr virus and M. tuberculosis have been shown to cause long-term disruption to the immune system, for example (Bordignon et al 2011, #1) (Zhang et al 2023, #2) (Bjornevik et al 2023, #3). Conversely, a distinct pattern has emerged in developed countries where as rates of infection fall, rates of autoimmune disease …

Phenotypic And Molecular Characterization And Antimicrobial Susceptibility Pattern Of Pasteurella And Mannheimia Species Obtained From Cattle And Sheep With Pneumonia, Eli̇f Karadeni̇z Pütür, Fati̇h Büyük, Yaren Ersoy

Turkish Journal of Veterinary & Animal Sciences

Among the heterogeneous Pasteurellaceae family, Pasteurella multocida and Mannheimia haemolytica are the pathogenic species that cause enzootic pneumonia in cattle and sheep. This study aimed to characterise Pasteurella and Mannheimia species obtained from pneumonia cases in cattle and sheep. 100 cattle and 100 sheep lungs diagnosed with infectious pneumonia as a result of histopathological examination were analyzed for Pasteurellaceae members by phenotypic methods, VITEK 2 Compact system and PCR. Antibiotic susceptibilities and phylogenetic analysis of the isolates were done by VITEK 2 Compact System and 16S rRNA-PCR, respectively. Seven Pasteurella multocida and 9 Mannheimia haemolytica were identified. All strains were …

An In-Depth Investigation Into Yersinia Pestis Phages: Isolating A Yersinia Pestis Phage From Soil And Constructing A Comprehensive Phylogenetic Analysis Of Known Yersinia Pestis Phages, Jacqueline Chavez

All HCAS Student Capstones, Theses, and Dissertations

Yersinia pestis, the causative agent of the plague, has become increasingly resistant to many antibiotics; therefore, alternatives such as phage therapy are necessary. Phage therapy uses combinations of bacteriophages or phages, which are viruses that only infect bacteria. However, phages—especially Y. pestis phages —are severely understudied. Thus, this research has sought to specifically isolate a phage from soil that infects Y. pestis. There were 146 samples that were collected from across the US, focusing on those with reported cases of plague. These samples were enriched with Y. pestis to maximize the amount of potential phage that target Y. pestis. …

Dissecting Metabolic Landscape Of Alveolar Macrophage, Sunayana Malla

Department of Chemical and Biomolecular Engineering: Dissertations, Theses, and Student Research

The highly plastic nature of alveolar macrophage (AM) plays a crucial role in the defense against inhaled particulates and pathogens in the lungs. Depending on the signal, AM acquires either the classically activated M1 phenotype or the alternatively activated M2 phenotype. In this study, we investigate the metabolic shift in the activated phases of AM (M1 and M2 phases) by reconstructing context specific genome-scale metabolic (GSM) models. Metabolic pathways such as pyruvate metabolism, arachidonic acid metabolism, chondroitin/heparan sulfate biosynthesis, and heparan sulfate degradation are found to be important driving forces in the development of the M1/M2 phenotypes. Additionally, we formulated …

Proteolytic Manipulation Of Neutrophil Responses And The Efferocytic Synapse By Porphyromonas Gingivalis., Kelley N. Cooper

Electronic Theses and Dissertations

Porphyromonas gingivalis (Pg) is etiologically associated with chronic periodontitis, a highly prevalent chronic inflammatory disease characterized by the destruction of hard and soft tissues of the periodontium. Pg is adapted to live in the human oral subgingival niche, a hostile environment dominated by excessive numbers of activated neutrophils and antimicrobial mediators. Its survival is contingent upon prompt and effective inactivation of neutrophil effector functions. In this dissertation, I uncover a novel pathogenic mechanism employed by Pg that disarms the antimicrobial capacity of live neutrophils and simultaneously sequesters them within macrophages. Mechanistically, RgpB, a cysteine protease produced by Pg …

Differential Responses Of Human Neutrophils To Legionella Species., Hannah E. Hanford

Electronic Theses and Dissertations

Legionella species are Gram-negative facultative intracellular bacterial pathogens commonly found in freshwater or soil environments where they survive and replicate within their natural protozoan hosts. Humans serve as an accidental host for Legionella species after inhalation of contaminated aerosolized water droplets or soil particles enabling the bacteria to enter the lungs, infect alveolar macrophages, and result in severe pneumonia. Evasion of degradation and proliferation within alveolar macrophages by Legionella species and manifestation of “Legionnaires’ disease” is dependent on the Dot/Icm type IV secretion system (T4SS). The T4SS apparatus is a needle-like channel for translocation of over ~350 effector proteins, depending …

Evaluation Of Commercially Available Sanitizers Efficacy To Control Salmonella (Sessile And Biofilm Forms) On Harvesting Bins And Picking Bags, Colton Ivers, Samhitha Chalamalasetti, Blanca-Ruiz Llacsahuanga, Faith Critzer, Manreet Bhullar, Londa Nwadike, Umut Yucel, Valentina Trinetta

Dairy Science and Food Science Faculty Publications: 2022 to Present

This study evaluated the efficacy of five commercially available sanitizers to reduce Salmonella (sessile and biofilm forms) count on experimentally inoculated materials representative of harvesting bins and picking bags in the fresh produce industry. Sessile Salmonella cells were grown onto tryptic soy agar to create a bacterial lawn, while multistrain Salmonella biofilms were grown in a Centers for Disease Control and Prevention (CDC) reactor at 22 ± 2 °C for 96 h. Samples were exposed to 500 ppm free chlorine, 500 ppm peroxyacetic acid (PAA), 75 psi steam, and 5% silver dihydrogen citrate (SDC) for 30 sec, 1, or 2 …

On Humans, Hogs, And Habitat: How Landscape Features And Vegetation Influence Wild Hog (Sus Scrofa) Detection On Private Lands And Using Existing Wild Hog Outreach Websites To Create An Effective Website For South Carolina, Andrew Jamison

All Theses

Invasive species are a source of human conflict with wildlife on a global scale and exist to the detriment of native wildlife species. Invasive species often possess the ability to respond rapidly to change and they often exist alongside humans. Wild hogs (Sus scrofa) are perhaps one of the most infamous examples of an invasive species. The spread of wild hogs necessitates effective communication with the public being impacted by them, as well as a continuation of research to learn more about wild hog behavior to promote effective management. Chapter 1 focuses on how we created a website …

Synthesis Of Novel Chromenone Esters For Biochemical Assays, Andrew Dean Helmerich

Undergraduate Honors Thesis Collection

This project details the synthesis of a variety of novel chromenone esters to be used as enzymatic probes. A robust, initial library of 22 chromenone esters was successfully synthesized with differences in chain length, branching, and the incorporation of cyclic and heteroatomic moieties. These new chromenones were fully characterized by 1HNMR, 13CNMR, DEPT HRMS, 19FNMR, and HSQC. The utility of these compounds comes from the fact that they will fluoresce upon cleavage of the ester; thus, this property makes them ideal candidates to be used in the monitoring of enzymatic activity of esterases. Elucidating the enzyme-substrate structure activity relationship (SAR) …

Metagenomic Sequencing For Early Detection Of Future Engineered Pandemics: Foreshadowing The Privacy Challenge, Nir Eyal, Bridget Williams, Kevin M. Esvelt, Jane R. Bambauer

UF Law Faculty Publications

In this commentary, we imagine how a global system of metagenomic sequencing could be governed in order to reap the benefits and manage the risks. Global institutional engineers and their academic partners would need to develop a new governance model to ensure that all partners involved in a global metagenomic surveillance system cooperate as needed.

The Impact Of Wild Pigs (Sus Scrofa) On Avian Occupancy And Vegetation Structure, Kenneth Wilson

Graduate Theses and Dissertations

Invasive species, particularly wild pigs (Sus scrofa), pose a significant threat to native ecosystems through both direct and indirect impacts. Wild pigs are large-bodied omnivorous species that can consume a wide variety of plants and animals and are known for destructive foraging behaviors, which likely threatens avian communities through habitat alteration and can impact the long term structure of ecosystems where they are present.

In chapter 1, we used a combination of avian point count surveys, vegetation assessments, and camera trap surveillance to quantify how the occupancy of breeding birds in bottomland hardwood forests changed in relation to …

Soybean Cyst Nematode (Heterodera Glycines Ichinohe) Virulence Assay Against Resistance Sources In Nebraska, Pratibha Karki

Department of Plant Pathology: Dissertations, Theses, and Student Research

Soybean cyst nematode (SCN, Heterodera glycines Ichinohe), one of the major yield-limiting pathogens of soybean, is currently found in 60 counties of Nebraska that produce more than 90% of the state’s soybean. Often, yield loss occurs without any above-ground symptoms, which makes it difficult to manage. The primary management option is the use of SCN-resistant varieties. Several soybean plant introductions serve as resistance sources against SCN. Unfortunately, the single source, PI 88788, is used in approximately 90% of resistant varieties and its prolonged use has increased the virulence status of SCN in the U.S. A study was conducted to assess …

An Extensive Exploration Of Generalist Microbotryum Species Through Host Interactions., Emilee Walters

College of Arts & Sciences Senior Theses

The Microbotryum species complex is a group of fungi, commonly known as anther smuts. Anther smuts are plant parasites that must invade a host plant in order to fulfill their life cycle. As the Microbotryum fungus grows, it sterilizes the host plant, such that infected plants produce fungal teliospores instead of pollen on the male reproductive organs and female reproductive structures do not mature. Microbotryum usually exists as a specialist species, however, there is evidence that several species of anther smuts can exist as generalist species. Comparisons of the infection process and the resulting response of both parasite and host …

Delineating Genetic Influences On Neurodegenerative Disorders And Infectious Diseases Through Advanced Computational Methods, Xiaowei Zhuang

UNLV Theses, Dissertations, Professional Papers, and Capstones

Genetics plays a critical role in understanding the molecular mechanisms underlying neurodegenerative disorders and pathogen evolution in infectious diseases. For example, identifying genetic variants associated with a disease phenotype uncovers functional pathways that could lead to potential drug targets and therapeutic interventions. In addition, tracking the genetic evolution of pathogens enables early detection and warning of infectious disease outbreaks. In both applications, given the large amount of genetic data, advanced computational methods, including longitudinal and multivariate models, could significantly boost the statistical power and capture interrelationships among traits, environmental factors and genetic influences. This dissertation focuses on four applications of …