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Examining The Restoration Potential Of Prescribed Fire And Tree Girdling Treatments On A Fire Dependent Ecosystem: Ecosystem Responses And Management Implications, Rebecca Daigle

Masters Theses

Oak savannas have greatly declined since the 1800s and management is needed to maintain these rare community types. A combination of prescribed burns and mechanical thinning are a common practice to increase forb abundance and biodiversity. This study examines the viability of another technique to thin the canopy called girdling, which was used in conjunction with low-intensity prescribed burns. Early summer prescribed burns were conducted in 2017, 2019, and 2021, while girdling treatments were implemented in 2017 and 2019. The study was conducted in Kent County, Michigan at two degraded former oak savanna communities. In 2022, we collected data to …

Cytokine Profiles In Peruvian Pinnipeds And Their Relationships With Environmental Stressors, Mykenzee L. Munaco

All HCAS Student Capstones, Theses, and Dissertations

Large colonies of two vulnerable, sympatric pinniped species, Peruvian fur seals (Arctocephalus australis Peruvian subpopulation; PFS) and South American sea lions (Otaria byronia; SASL), reside and reproduce in Punta San Juan, Peru (PSJ) where they are exposed to stressors such as environmental contaminants and El Niño-Southern Oscillation (ENSO) events. Cytokine concentrations can be indicative of an animal’s health and immune function by allowing for immunoresponse characterization as Th1 or Th2 dominant. Utilizing an archived pinniped plasma collection of samples from 2009-2019 (n=148), 13 cytokines were analyzed in PFS and SASL: GM-CSF, IFN-γ, KC-like, MCP-1, TNF-α, IL-2, IL-6, …

Characterizing Host-Pathogen Interactions Between Zostera Marina And Labyrinthula Zosterae, Yaamini R. Venkataraman, Amanda Shore, Sukanya Dayal, James Sanghyun Lee, Mahsa Alidoost Salimi, Grace Crandall, Malina M. Loeher, Mark Stoops, Megan Swanger, Morgan E. Eisenlord, Kathryn L. Van Alstyne, Mark D. Fast, Colleen A. Burge, Maya L. Groner

Biology

Introduction: Seagrass meadows serve as an integral component of coastal ecosystems but are declining rapidly due to numerous anthropogenic stressors including climate change. Eelgrass wasting disease, caused by opportunistic Labyrinthula spp., is an increasing concern with rising seawater temperature. To better understand the host-pathogen interaction, we paired whole organism physiological assays with dual transcriptomic analysis of the infected host and parasite.

Methods:: Eelgrass (Zostera marina) shoots were placed in one of two temperature treatments, 11° C or 18° C, acclimated for 10 days, and exposed to a waterborne inoculation containing infectious Labyrinthula zosterae (Lz) or sterile seawater. At two- and …

Regulation Of Stress Responses And Membrane Morphology By Dspa In Synechocystis Sp. Pcc 6803, Rebekah Kathryn White

Theses and Dissertations

In the world of microorganisms, cyanobacteria are a uniquely skilled powerhouse. They participate in global nutrient and carbon cycling. They have the ability to photosynthesize, which allows them to use sunlight and carbon dioxide to produce cellular energy. However, photosynthesis has a lot of points were environmental stresses can interfere, increasing the chances of oxidative stress and nutrient imbalances that can amplify deleterious effects. One regulator in particular will be the target of this study. DspA, also known as Hik33, is a histidine kinase that perceives and regulates multiple overlapping stress responses. In this project, abiotic stress effects will be …

The Role Of Phenylacetic Acid (Paa) Catabolism In Acinetobacter Physiology, Anna Josephine Hooppaw

Arts & Sciences Graduate Student Theses and Dissertations

Microorganisms are constantly challenged by stressful environments and have evolved mechanisms to adapt to or counteract these threats. The Gram-negative pathogen Acinetobacter baumannii is thought to rely on a “persist and resist” strategy that facilitates its remarkable ability to survive in a variety of harsh conditions, giving it the capacity to cause life-threatening infections. Currently, over 60% of the global A. baumannii clinical isolates are multidrug resistant (MDR), leading the World Health Organization and the Centers for Disease Control and Prevention to categorize this pathogen as a top priority for the research and development of new antimicrobial therapies. Understanding the …

Distinct Roles For Ltα3 And Ltα1Β2 Produced By B Cells Contribute To Their Multi-Faceted Impact On Ileitis, Emma Claire Erlich

Arts & Sciences Graduate Student Theses and Dissertations

Crohn’s disease, one of the most common forms of inflammatory bowel disease, is marked by local intestinal inflammation. However, pathology in CD patients is not strictly limited to the gastrointestinal system, and almost 50% of CD patients exhibit extraintestinal manifestations of disease. Many, though not all, of these systemic pathologies are linked to intestinal inflammation and, thus, resolution of local gastrointestinal disease also ameliorates systemic disease. How the connection between local and systemic inflammation is mediated is not well understand, nor is why only some patients exhibit these extraintestinal manifestations of disease. Blocking dissemination of inflammatory signals generated in the …

Effect Of Tamoxifen On Proteome Expression During In Vitro Myogenesis In Murine Skeletal Muscle C2C12 Cells, Emily A. Morris, Ahlenne Abreu, S. P. Scordilis

Biological Sciences: Faculty Publications

Tamoxifen (TMX), a selective estrogen receptor modulator, is commonly used in the treatment of hormone-responsive cancers. However, the effects of TMX in anabolic tissues harboring estrogen receptors, such as skeletal muscle, are poorly understood. We report a tandem mass-tag approach to TMX-treated myogenesis in C₂C₁₂ cells, a well-characterized model of in vitro murine skeletal muscle differentiation. A longitudinal analysis of >10,000 proteins identified in untreated C₂C₁₂ myogenesis revealed a novel subset of 1,062 myogenically regulated proteins. These proteins clustered into five distinct longitudinal expression trends which significantly overlap those obtained in similar analyses performed …

The Interaction Between Predation And Sound Pollution On The Internal And External Microbiome Of The Grasshoppers Melanopus Sanguinipes, Alanna Bond

Theses and Dissertations

Anthropogenic activities such as construction and agriculture directly affect its surrounding environments. Many studies have focused on how megafauna and flora are impacted by human activities, however, relatively little is known how new occupation of land affects smaller organisms such as insects and microbes. Additionally, other stressors such as predation can impact host physiology. The grasshopper species Melanopussanguinipes was chosen to be used in a study to measure how stress caused by artificial sound and predation can alter exoskeleton and gut microbiomes once exposed to these stressors.

Evaluation Of Occidiofungin Activity On Yeast-Hyphae Morphogenesis And Biofilm Formation By Candida Species, Rabina Kumpakha

Theses and Dissertations

Invasive fungal infections are a significant clinical challenge especially for hospitalized patients as traditional antifungal therapy often fails to resolve these infections. The ability of Candida to undergo yeast-to-hyphae morphological transition is central to this invasive behavior. Morphogenesis is also important for the formation of biofilms which are highly structured communities of microorganisms attached to one another or substratum and embedded within a protective extracellular matrix material. The refractory nature of cells within a biofilm to current antifungal therapies has created a need for alternative antifungal agents for the management of Candida biofilm-related infections. The novel antifungal occidiofungin is a …

Investigating The Role Of Plant Traits And Interactions In Emergent Wetland Nutrient Removal, Andrew Ryan Sample

Theses and Dissertations

Increasing wetland restoration in the Lower Mississippi Alluvial Valley has been identified as a method to reduce nutrient loading in the Gulf of Mexico. Wetlands have historically been used to treat water through processes facilitated by wetland plants, and relatively few species and plant traits have been identified as important in carrying out these processes. This study focuses on some of those species and traits and aims to identify species differences and plant traits that may be important for wetland nutrient mitigation. Chapter I provides background information on nutrient pollution, wetland biogeochemical mechanisms for nutrient sequestration, and the focal species …

Nanoscale Modeling Of Membrane Systems Under Mechanical Deformation In Traumatic Brain Injury Using Molecular Dynamics, Anh Thi Ngoc Vo

Theses and Dissertations

Neuronal membrane disruption and mechanoporation are nanoscale damage mechanisms that critically affect brain cell viability during traumatic brain injury (TBI). These nanoscale cellular impairments are elusive in experiments and necessitate in silico approaches such as molecular dynamics (MD) simulations. Implementing MD, this research aims to investigate the effects of different key factors related to membrane deformation and damage, including force field resolutions, lipid compositions, and loading conditions.

To examine the impact of force field resolution, MD deformation simulations were conducted on 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphatidylcholine (POPC) lipid bilayer membranes, using all-atom (AA), united-atom (UA), and coarse-grained Martini (CG-M) force fields. The mechanical responses …

Evaluating The Immunogenicity Of Colonization Proteins Of S. Pneumoniae For Identification Of Vaccine Candidates, Isidora Fereday

Theses and Dissertations

Streptococcus pneumoniae is typically an asymptomatic colonizer of the upper respiratory tract but can cause invasive disease in susceptible populations. Pneumococcal vaccines which are currently in use have failed to significantly reduce colonization by S. pneumoniae. To control invasive pneumococcal disease, novel strategies must be utilized. One such strategy is to reduce or eradicate colonization by pneumococcus. Supplementary vaccination with pneumococcal proteins important for colonization could serve to prime the immune system against these targets. This study serves as an initial step towards identification of crucial pneumococcal colonization proteins which may previously have been uncharacterized. Assessing the immune reactivity …

Roles Of Type I Interferon Signaling In Drug Resistant Mycobacterium Tuberculosis Infection, Suhas Bobba

Arts & Sciences Graduate Student Theses and Dissertations

Tuberculosis (TB) is a global health threat, with 10 million people developing active TB disease and a million deaths attributed to TB annually. Emergence of drug resistance in Mycobacterium tuberculosis (Mtb), the causative agent of TB, has led to half a million cases of drug resistant (DR) TB annually. Further, clinical reports suggest dysregulation and suppression of immune responses in DR TB patients as compared with DS TB patients. However, we do not understand how acquisition of drug resistance-conferring mutations can drive broad and systemic differences in immune responses of DR TB patients. We found that rpoB-H445Y a specific DR …

Representing Quantum Spins In Different Coordinate Systems For Modelling Rigid Body Orientation, Nadjet Zioui, Aicha Mahmoudi, Mohamed Tadjine

Karbala International Journal of Modern Science

Various methods for representing the spatial orientation and rotation of objects are presented and compared with the quantum bit state representation. By contrasting spherical, Euler angle, quaternion, and quantum spin coordinate systems, this work highlights important concepts regarding the rotation axis of the X gate. Several ambiguities and incomplete definitions associated with the qubit state representation are discussed, such as the spin around the qubit itself and the explanation of the considered rotation angles and signs. A mathematical analysis of the physical meaning of each eigenstate is provided along with a new comprehensive and meaningful YPR-based 3D representation of a …

Improving The Burt’S Sensitivity Using Noise Calibration Unit Via Crab Nebula Observations, Uday E. Jallod, Lana T. Ali, Hareth S. Mahdi, Kamal M. Abood

Karbala International Journal of Modern Science

Radio observations from astronomical sources like supernovae became one the most important sources of information about the physical properties of those objects. However, such radio observations are affected by various types of noise such as those from sky, background, receiver, and the system itself. Therefore, it is essential to eliminate or reduce these undesired noise from the signals in order to ensure accurate measurements and analysis of radio observations. One of the most commonly used methods for reducing the noise is to use a noise calibrator. In this study, the 3-m Baghdad University Radio Telescope (BURT) has been used to …

Analyzing Pseudomonas Aeruginosa With Bacteriophage Tags Using Photoacoustic Flow Cytometry, Jennifer C. Schinke

Electronic Theses and Dissertations

The number of daily bacterial infections is climbing and the CDC explains that this is due to the antibiotic-resistant threat in the United States. Finding a faster way of bacterial identification is necessary as it currently takes 1-4 days for a medical lab to culture and identify bacteria. Photoacoustic flow cytometry (PAFC) can be used as an alternative method resulting in swift identification within an hour (Edgar, 2019). Pseudomonas aeruginosa, cell line PA01, will be coated in up to a few hundred red dyed phages making it detectible by the photoacoustic flow cytometry system. Bacteriophages (phages) are viruses that …

Molecular Detection And Characterization Of Rickettsia Sp. In Hard Ticks Collected In Nacogdoches, Texas, Haley Nicole Standifird

Electronic Theses and Dissertations

The number of cases of tick-borne diseases is increasing in the United States. Many efforts to control ticks have been made and are continuously being developed. These methods include surveillance of ticks and detection of the tick-borne pathogens.This study examined hard ticks in Nacogdoches, Texas, to test for the presence of Rickettsia sp. 47 ticks were collected from vegetation by flagging and their species, sex, and developmental stage were determined using available keys. Individual ticks were processed for nucleic acid extraction and molecular detection of Rickettsia sp. using PCR-based methods. The citrate cynthease gene, 17kDa gene, and outer membrane protein …

Glycerophosphocholine Is Used For Lipid And Phosphate Metabolism By Candida Albicans, Will King

Electronic Theses and Dissertations

The metabolism of phosphatidylcholine (PC), a major eukaryotic membrane lipid, has been shown to be an important aspect of pathogenesis in Candida albicans. Of note, PC turnover product, glycerophosphocholine (GPC), is abundant renal metabolite available within the host. GPC is readily imported by C. albicans, and deletion of the major GPC transporter, Git3, leads to decreased virulence in a bloodstream infection model. Here I have characterized two potential metabolic fates of internalized GPC. The first metabolic fate explored is internalized GPC can be hydrolyzed to release P_i. To determine if GPC import and subsequent metabolism impact phosphate …

Investigating How Sterol Transport Affects Survival Of The Pathogenic Fungus Cryptococcus Neoformans In Host-Like Conditions, Hau Lam Choy

Arts & Sciences Graduate Student Theses and Dissertations

Cryptococcus neoformans is an opportunistic fungal pathogen that has an enormous impact on global health and is the most common cause of meningitis in adults living with HIV in sub-Saharan Africa. With a mortality rate of 10-75%, cryptococcal meningitis results in over 100,000 deaths per year, comprising 18% of all AIDS-related deaths worldwide. These numbers emphasize the need to understand the basic biology and pathogenesis of this fungus. During infection, spores or desiccated yeast cells are inhaled, resulting in primary pulmonary infection. In immunocompetent hosts, these infections are asymptomatic and are either quickly cleared or remain latent. In immunocompromised patients, …

Mechanisms Of Immunopathology And Protection In Genital Herpes Simplex Virus 2 Infection, Ying Shiang Lim

Arts & Sciences Graduate Student Theses and Dissertations

Genital Herpes Simplex Virus-2 (HSV-2) infections is a highly prevalent and incurable sexually transmitted disease. Upon infection at the primary genital mucosa, HSV-2 localizes to the sensory ganglia to establish chronic latency. Symptomatic and asymptomatic recurrences can then occur episodically to promote viral transmissions. Painful genital and peri-genital lesions can be formed, increasing the risk for secondary HIV-1 acquisition by three times. Despite being a serious public health risk with severe physiological and psycho-sociological impacts, there are currently no cures or FDA-approved vaccines for this chronic infection. Thus, it is imperative to understand how the immune system interacts with HSV-2 …

Ca2+ Dynamics And Genome Protection, Lingzhen Kong

Arts & Sciences Graduate Student Theses and Dissertations

DNA replication is a fundamental process and defects in replication can cause genetic mutations and instability and various human diseases including cancer. The progression of replication forks can be challenged by both intrinsic and environmental factors, such as DNA lesions, secondary structure, insufficient nucleotides, collision with the transcription apparatus, radiation, or cancer drugs. These challenges necessitate robust mechanisms to protect the fork structure in the event of replication stress. Tumor suppressors like BRCA1, BRCA2, and FANC can protect fork structure by controlling nucleases that can attack stalled replication forks, which otherwise can cause fork collapse and DNA damage. In addition …

The Sperm-Specific K+ Channel Slo3, A Regulator Of Human Fertility And New Target For Contraception, Maximilian Daniel Lyon

Arts & Sciences Graduate Student Theses and Dissertations

Sperm from mammalian species are incapable of fertilization at the point of ejaculation. Several maturation steps must take place in the female genital tract that give the sperm the capacity to fertilize, which are collectively called capacitation. The mechanisms behind and interactions between these steps appear to rapidly evolve between species. One of these steps is a hyperpolarization of the membrane to a more negative potential. Human sperm hyperpolarize during capacitation, however the processes that regulate and are regulated by this hyperpolarization remain unclear. This is due in part to discrepancies between what is known about hyperpolarization in other species, …

Dna-Encoded Chemical Libraries Yield Non-Covalent And Non-Peptidic Sars-Cov-2 Main Protease Inhibitors, Ravikumar Jimmidi, Srinivas Chamakuri, Shuo Lu, Melek Nihan Ucisik, Peng-Jen Chen, Kurt M Bohren, Seyed Arad Moghadasi, Leroy Versteeg, Christina Nnabuife, Jian-Yuan Li, Xuan Qin, Ying-Chu Chen, John C Faver, Pranavanand Nyshadham, Kiran L Sharma, Banumathi Sankaran, Allison Judge, Zhifeng Yu, Feng Li, Jeroen Pollet, Reuben S Harris, Martin M Matzuk, Timothy Palzkill, Damian W Young

Faculty, Staff and Students Publications

The development of SARS-CoV-2 main protease (Mpro) inhibitors for the treatment of COVID-19 has mostly benefitted from X-ray structures and preexisting knowledge of inhibitors; however, an efficient method to generate Mpro inhibitors, which circumvents such information would be advantageous. As an alternative approach, we show here that DNA-encoded chemistry technology (DEC-Tec) can be used to discover inhibitors of Mpro. An affinity selection of a 4-billion-membered DNA-encoded chemical library (DECL) using Mpro as bait produces novel non-covalent and non-peptide-based small molecule inhibitors of Mpro with low nanomolar Ki values. Furthermore, these compounds demonstrate efficacy against mutant forms of Mpro that …

Biophysically-Informed Models Of Heterogeneity In Transcription Factor Activity, Kaiser Loell

Arts & Sciences Graduate Student Theses and Dissertations

The activity of a transcription factor (TF) can be remarkably heterogeneous, both within andbetween cells. Between cells, molecular fluctuations drive stochastic differences in the activitiesof TFs. I will describe a project in which we have quantified how the different components of aTF (its activation domain, affinity for DNA, concentration, and cooperative interactions) influencestochastic fluctuations in TF activity. In addition to stochastic fluctuations between cells, withincells TFs can switch between activating and repressing activities depending on the cis-regulatorycontent of their target genes. I will describe a second project in which we have modelled howthe balance between homo- and heterotypic interactions determines …

Two Structurally Defined Aβ Polymorphs Promote Different Pathological Changes In Susceptible Mice, Ruben Gomez-Gutierrez, Ujjayini Ghosh, Wai-Ming Yau, Nazaret Gamez, Katherine Do, Carlos Kramm, Hamid Shirani, Laura Vegas-Gomez, Jonathan Schulz, Ines Moreno-Gonzalez, Antonia Gutierrez, K Peter R Nilsson, Robert Tycko, Claudio Soto, Rodrigo Morales

Faculty, Staff and Student Publications

Misfolded Aβ is involved in the progression of Alzheimer's disease (AD). However, the role of its polymorphic variants or conformational strains in AD pathogenesis is not fully understood. Here, we study the seeding properties of two structurally defined synthetic misfolded Aβ strains (termed 2F and 3F) using in vitro and in vivo assays. We show that 2F and 3F strains differ in their biochemical properties, including resistance to proteolysis, binding to strain-specific dyes, and in vitro seeding. Injection of these strains into a transgenic mouse model produces different pathological features, namely different rates of aggregation, formation of different plaque types, …

Insects Are Attracted To White Wind Turbine Bases: Evidence From Turbine Mimics, Madison S. Crawford, Delina E. Dority, Michael E. Dillon, Lusha M. Tronstad

Western North American Naturalist

Wind power is one of the fastest growing forms of renewable energy, but the interactions between wind turbines and insects are largely unknown beyond the observation that the accumulation of dead insects on turbine blades drastically reduces the power produced. Insects may be attracted to wind energy facilities because of topography, the heat that turbines produce, the lighting, or the visual cue of the turbine itself. Turbines can present a striking visual contrast relative to the surrounding landscape, particularly when they are painted bright white and reflect ultraviolet wavelengths. To test the hypothesis that wind turbine color attracts insects, we …

The Impact Of Soil Disturbance On Soil Bacterial Community Composition, Marie A. Rodriguez, Mark Peach, Timothy D. Trott

Research in Biology

Soil bacterial communities are an important part of terrestrial ecosystems due to their roles in biogeochemical cycling processes. Consequently, understanding how soil disturbance affects the soil bacterial diversity is vital to understanding the entire ecosystem. In this study we examined the effects of soil disturbance (by mining) on the soil bacterial community composition from three sites on Bauxite Ridge in Southeast Tennessee compared to three undisturbed sites in a nearby location. The soil bacterial community was analyzed by 16S rDNA amplicon sequencing of total DNA extracted from the soil samples collected from each of the six sites. Characterization of the …

Examining The Different Soil Horizons Of White Oak Mountain, Tn And Their Effect On The Soil Microbial Community, Ji Won Moon, Timothy D. Trott

Research in Biology

Soil microorganisms participate in the diverse interaction within virtually all ecosystems, consequently affecting the associated human and animal population. Identifying how edaphic variables alter the functional and taxonomic diversity of the soil microbial community requires an examination of total microbial soil diversity and abundance. This research study examined the effect of soil depth and horizon on the soil microbial community composition of White Oak Mountain. The soil microbial community was characterized by 16S/18S/ITS rDNA amplicon sequencing of the DNA extract of six samples from the three major soil types identified: HcE, MoE, and uMvC. OTU clustering analysis and both alpha …

Variable Rates Of Hybridization Among Contact Zones Between A Pair Of Topminnow Species, Fundulus Notatus And F. Olivaceus, David D. Duvernell, Naznin S. Remex, Jeffrey T. Miller, Jacob F. Schaefer

Biological Sciences Faculty Research & Creative Works

Pairs of species that exhibit broadly overlapping distributions, and multiple geographically isolated contact zones, provide opportunities to investigate the mechanisms of reproductive isolation. Such naturally replicated systems have demonstrated that hybridization rates can vary substantially among populations, raising important questions about the genetic basis of reproductive isolation. The topminnows, Fundulus notatus and F. olivaceus, are reciprocally monophyletic, and co-occur in drainages throughout much of the central and southern United States. Hybridization rates vary substantially among populations in isolated drainage systems. We employed genome-wide sampling to investigate geographic variation in hybridization, and to assess the possible importance of chromosome fusions to …

The Importance Of Contrast Sensitivity, Color Vision, And Electrophysiological Testing In Clinical And Occupational Settings, Frances Silva

Theses & Dissertations

Visual acuity (VA) is universally accepted as the gold standard metric for ocular vision and function. Contrast sensitivity (CS), color vision, and electrophysiological testing for clinical and occupational settings are warranted despite being deemed ancillary and minimally utilized by clinicians. These assessments provide essential information to subjectively and objectively quantify and obtain optimal functional vision. They are useful for baseline data and monitoring hereditary and progressive ocular conditions and cognitive function. The studies in this dissertation highlight the value of contrast sensitivity, color vision, and cone specific electrophysiological testing, as well as the novel metrics obtained with potential practical clinical …