Life Sciences Commons^™

Heterotypic Interaction Of Α-Synuclein And Tdp-43 In Neurodegenerative Diseases, Shailendra Dhakal

Dissertations

Amyloid aggregates of specific proteins form important pathological hallmarks in many neurodegenerative diseases, defining neuronal degeneration and disease onset. Recently, increasing numbers of patients show co-morbidities and exhibit clinical and pathological overlaps between multiple neurodegenerative diseases including α-synucleinopathies and TDP-43 proteinopathies. These overlaps are often accompanied by co-localization of α-synuclein (αS) and TDP-43 enhancing the possibility of direct interactions to generate heterotypic amyloids with distinct cellular consequences. To understand this, we investigate the interaction of α-synuclein (αS) and prion-like domain of TDP-43 (TDP-43 PrLD) in both homogenous and inhomogeneous phases. Firstly, we show that monomeric TDP-43 PrLD and αS interact …

Structural Features Of Hiv-1 Integrase In The Late Stage Of Viral Replication, Tolga Catmakas

Dissertations

HIV-1 integrase (IN) is an essential enzyme for the viral life cycle as it integrates viral genomic material into the host cell genome. In addition to its’ essential catalytic function, IN has another important non-catalytic role where it binds the viral RNA to facilitate successful particle maturation during the viral life cycle. A significant number of IN mutants, addressed as class II IN mutants, show various defects, affecting different steps of the viral life cycle. Class II IN mutants exhibit aberrant morphology where viral ribonucleoprotein particles are mislocalized outside of the capsid core. This phenomenon can be observed in the …

Biophysical Factors Affecting Habitat Suitability For Crassostrea Virginica, Jason D. Tilley

Dissertations

Oyster reefs provide a variety of important ecosystem services. However, the mortality rate of eastern oyster, Crassostrea virginica, the dominant species that produces oyster reefs in the northern Gulf of Mexico, is increasing at an alarming rate due to a variety of abiotic and biological factors. I examined how biophysical factors, including the less-studied fatty acid profiles of the suspended particulate matter on which oysters feed, influenced morphometric condition of C. virginica.

I sampled suspended particulate matter (SPM) and oysters in-situ in the western Mississippi Sound, which historically supported the majority of oyster production in Mississippi waters. Sampling …

How Sewage Pollution Affects Distribution And Life History Traits Of The Southern House Mosquito, Culex Quinquefasciatus, Catherine Dean Bermond

Master's Theses

Eutrophication from wastewater can cause fluxes of nutrients like and carbon and nitrogen in urban waters. One source of nitrogen in freshwater is from untreated sewage discharging from septic tanks. This causes a variety of environmental issues including harmful algal blooms, harming natural predators, and increased production of mosquitoes. Culex quinquefasciatus is the vector of West Nile Virus in St. Tammany Parish, Louisiana. St. Tammany Parish has over 600 miles of septic ditches, which receive effluent directly from aerated treatment units. Culex quinquefasciatus oviposit in polluted waters, and larvae perform well in water with high levels of decomposing organic matter. …

Evaluating Habitat Use By Nekton In Widgeon Grass (Ruppia Maritima), Shoal Grass (Halodule Wrightii), And Unvegetated Bottom Habitats In The Grand Bay National Estuarine Research Reserve, Jessica Woodall

Master's Theses

Seagrass beds support high biodiversity and animal abundance, serve as feeding grounds for a variety of animals, offer shelter from predation, and act as a nursery habitat for juveniles. The species composition of seagrass beds can impact their use as habitat by animals. Two common species of seagrass in the Gulf of Mexico are Ruppia maritima (widgeon grass) and Halodule wrightii (shoal grass). The shallow coastal waters of the Grand Bay National Estuarine Research Reserve (NERR) support both species, but the use of each seagrass as habitat by nekton is poorly understood, which can limit management decision-making. Nekton communities were …

Bsc 345 Southern Miss Gulf Scholars Program Module, Southern Miss Gulf Scholars Program

Southern Miss Gulf Scholars

BSC 345 Southern Miss Gulf Scholars Program Curriculum

Throughout this course students will learn about important marine resources that drive the local seafood economy. On a field trip to the Maritime and Seafood Museum, students will learn about this historical seafood industry and industry practices. Student will also tour the USM Thad Cochran Marine Aquaculture Center to learn about modern aquaculture technologies and take an excursion at sea to observe the off-bottom aquaculture site next to Deer Island.

Sensing The Rhizosphere: Microbial Transcriptome Responses To Root Exudates And Redox-Active Metabolites, Ankita Bhattacharyya

Dissertations

The term “rhizosphere” describes the dynamic interface between plant roots and soil influenced by root exudates. It is a hotspot of microbial activity, plant-microbe, and microbe-microbe interactions. Distinct variations in bacterial diversity are thought to be driven by plant root exudates. However, the molecular details of these processes still remain unclear.

I addressed this gap by focusing on two strains, Pseudomonas synxantha 2-79 and Burkholderia lata 383, representing diverse groups of Gammaproteobacteria comprised of species with environmental, agricultural, and medical significance. In the first part of this project, we used a combination of metabolomics and RNA-seq to characterize transcriptome responses …

Genetic Parameters For Heat And Salinity Stress Tolerance In Northern Gulf Of Mexico Eastern Oyster, Crassostrea Virginica, Paul Mcdonald

Master's Theses

Summer mortalities in Gulf of Mexico eastern oysters have been linked to excessively high temperatures, and chronic exposure to low salinity. In this study, the feasibility of improving tolerance to these two stresses by selection was evaluated in common garden experiments employing a pool of 160 families. Heat stress tolerance was evaluated in seed (3.5 months) and adults (14 months) by applying a sustained temperature of 38-39 °C until all oysters expired. Low salinity challenges on juveniles (9 months) and adults (15 months) applied a salinity of 2.5 psu. Survival duration of individual oysters during challenges was recorded and tissue …

Missing Value Imputation For Single Omics And Multi-Omics Data, Meng Song

Dissertations

The integration analyses of multi-omics data have the advantages of extending our understanding of biological system across multiple omics layers, unraveling the functional mechanism of complex disease development, and refining the discovery of novel drug targets. However, multi-omics studies often face challenges such as data heterogeneity, missing values problem, interpretability, and imbalance classes. Among these challenges, the missing values problem is a critical issue for large cohort studies as not all samples will get a complete measurement for all the omics layers. To address the problem of missing values in multi-omics data, I focused on the imputation of completely missing …

Annotation Of Non-Model Species’ Genomes, Taiya Jarva

Master's Theses

The innovations in high throughput sequencing technologies in recent decades has allowed unprecedented examination and characterization of the genetic make-up of both model and non-model species, which has led to a surge in the use of genomics in fields which were previously considered unfeasible. These advances have greatly expanded the realm of possibilities in the fields of ecology and conservation. It is now possible to the identification of large cohorts of genetic markers, including single nucleotide polymorphisms (SNPs) and larger structural variants, as well as signatures of selection and local adaptation. Markers can be used to identify species, define population …

Characterization And Estimation Of Musculoskeletal Pain Using Machine Learning, Boluwatife Faremi

Master's Theses

Traditional scales utilized for recording pain are known to be highly subjective and biased due to inaccuracies in recollecting actual pain intensities. As a result, machine learning (ML) models that are trained using these scores as ground truth are reported to have low performance for objective pain classification because of the huge disparity between what was felt in moments of pain and the scores recorded afterward.

In the present study, two devices were designed for gathering real-time, continuous in-session subjective pain scores and the recording of the autonomic nervous system (ANS) altered endodermal (EDA) activity. 24 participants were recruited to …

Predictive Ability Of A 3d Body Scanning Mobile Application For Metabolic Health Risk, Caleb Brandner

Master's Theses

There is an increasing prevalence of obesity within the US and rising rates of metabolic syndrome among those aged 20-39 concurrent with a decrease in the reception of primary care. Limitations to healthcare including access, cost, and availability, highlighting the need for simple, efficient, and accessible cardiometabolic health risk screening. Given the surge in smartphone ownership over the last decade, this study sought to determine the predictive ability of a mobile 3D-optical (3DO) body composition assessment application in determining metabolic health risk. A total of 62 participants (female: 36) underwent traditional anthropometric measurements, 3DO body scanning using a smartphone application, …

Solving The Cable Equation, A Second-Order Time Dependent Pde For Non-Ideal Cables With Action Potentials In The Mammalian Brain Using Kss Methods, Nirmohi Charbe

Master's Theses

In this thesis we shall perform the comparisons of a Krylov Subspace Spectral method with Forward Euler, Backward Euler and Crank-Nicolson to solve the Cable Equation. The Cable Equation measures action potentials in axons in a mammalian brain treated as an ideal cable in the first part of the study. We shall subject this problem to the further assumption of a non-ideal cable. Assume a non-uniform cross section area along the longitudinal axis. At the present time, the effects of torsion, curvature and material capacitance are ignored. There is particular interest to generalize the application of the PDEs including and …

Genetic Population Structure And Effective Number Of Breeders In Systems Across The Range Of The Gulf Sturgeon, Jacob Zona

Master's Theses

Gulf sturgeon (Acipenser oxyicnhus desotoi) are a large, anadromous fish belonging to an ancient lineage that diverged as early as 400 MYA. Overfishing for meat and caviar during the early 1900’s reduced their range and abundance and continued habitat destruction and mortality have limited their ability to recover, leading to their listing under the Endangered Species Act. This study uses genetic techniques to determine the effective number of breeders for multiple spawning groups of Gulf sturgeon in river systems across their range to set a baseline for tracking reproductive success of the species. Accompanying genetic information relevant to …

Effects Of Membrane Components On The Oligomerization Of Amyloid-Β (Aβ) In Alzheimer Disease, Jhinuk Saha

Dissertations

Deposition of extracellular proteinaceous plaques of amyloid-β (Aβ) is one of the major hallmarks of Alzheimer disease (AD). Although, insoluble high molecular fibrils of Aβ are the main constituents of the senile plaques in AD, low molecular weight soluble Aβ oligomers have emerged as the key toxic species involved in memory impairment and neuronal cell death in AD. The process for generation of oligomers can be highly diverse and can involve homotypic interactions of Aβ as well as heterotypic interaction of Aβ with other macromolecules. Previously, the generation of Aβ oligomers with distinct biochemical and biophysical characteristics catalyzed non-esterified fatty …

Connecting Social And Ecological Systems In Small-Scale Fisheries In The Philippines, Sara Eisler Marriott

Dissertations

Nearly 50% of all marine fish capture in the Philippines is from artisanal fisheries, most of which is un- or under-reported. As in many emerging nations around the world, the Philippines cannot fully address overfishing by managing only half of the catch that comes from commercial fisheries. Marine reserves are a popular governance strategy for conservation and of growing interest for fisheries management. Many marine reserves in the Philippines, however, are not considered effective. In 2014, Rare, an international NGO, implemented a community-based management program to increase the effectiveness of the marine reserves, and while it found biomass increased, there …

Effects Of Increased Shoe Collar Height And Limb Dominance On Landing Knee Biomechanics In Collegiate Volleyball Players, Lindsey Legg

Master's Theses

Athletic footwear with higher collar heights are worn to restrict ankle motion. Reduced ankle dorsiflexion has been associated with increased frontal plane knee motion. Volleyball players wear mid-cut shoes (MC) that have an increased collar height rising slightly superior to the talocrural joint and malleoli. The purpose of this study was to determine the effect of MC and limb dominance on knee landing mechanics. It was hypothesized that participants would land with greater initial contact (IC) and peak frontal joint plane angles and moments and smaller IC and peak sagittal plane joint angles and moments at the knee in MC …

Comparative Analysis Of Rhizosphere And Endosphere Microbiome Of Different Blueberry Species (Vaccinium Sp.), Niladri Bhowmik

Master's Theses

Blueberries are an important agricultural commodity in all over the United States. Due to its health benefits, there is a huge demand globally, thus expanding the industry. Breeding programs are essential to maintain such industries. Challenges that play a role in contemporary breeding programs are various biotic and abiotic stress factors. Studies have shown that microorganisms are recruited by plants to alleviate them during stressful conditions. Though blueberries have been cultivated for about 100 years, how the microbiome has been affected due to this is poorly understood. We hypothesized that interspecific crosses and artificial selection have significantly changed the microbiome …

Pirna Expression In The Tube Feet Of Lytechinus Variegatus, Reagan Milliet

Honors Theses

Tissue regeneration is an area of research with implications for medicine and animal health. While nearly all living multi-cellular organisms are capable of regeneration, there are major differences in the animal kingdom. Some organisms are capable of regenerating virtually every cell in their bodies. In hopes of engineering tissue regeneration for medical applications, the mechanisms by which organisms regenerate are being widely investigated. To better understand regeneration, the role of P-element Induced WImpy testis (PIWI) proteins are being evaluated. In collaboration with PIWIinteracting RNAs (piRNAs), PIWI proteins have been proven instrumental to transposon silencing and maintenance of the genome in …

Validity Of The Loadsol Pro Insole For Pedal Reaction Force Measurements During Stationary Cycling, Anabelle Vallecillo Bustos

Honors Theses

Advancements in wearable technology have allowed clinicians, coaches, and researchers the ability to observe and quantify human movement outside the laboratory. Instrumented insoles are an example of novel technology that can be worn in the shoes and measure vertical reaction force wirelessly. The use of such insoles will prove to be beneficial for athletes as they train, patients as they progress through rehabilitation, and researchers as they experiment in their respective fields. The Loadsol Pro (Novel Inc., St Paul., MN, USA) has been shown to produce accurate and reliable measures of ground reaction forces (GRF) in various dynamic activities including …

Uptake And Localization Of Poly(2-Vinyl-4,4-Dimethyl Azlactone) Modified With Rhodamine- And Coumarin-Based Molecules In Human Embryonic Kidney (Hek293) Cells, Garrett Tassin

Honors Theses

Fluorescence microscopy is a bioimaging technology that utilizes the excitation and emission of fluorophores to identify cellular structures, processes, and interactive events. Natural and synthetic organic dyes are frequently used in fluorescence microscopy techniques for imaging, therapeutic, and biomedical applications. It is also employed in the development of novel organic dyes for innovative methods of drug delivery and labelling. In this study, we investigate the behavior of an organic dye consisting of the post-polymerization modification of poly(2-vinyl-4,4-dimethyl azlactone) (PVDMA) with tetramethyl rhodamine cadaverine (TMR) and a coumarin-based molecule (DBAC). Using cultured HEK293 cells and fluorescence confocal microscopy, we show the …

Development Of A Novel Environmental Dna (Edna) Tool For Monitoring Vulnerable Freckled Guitarfish, Pseudobatos Lentiginosus, In The Western Central Atlantic, Sarah Toepfer

Honors Theses

Rhino-rays are the most threatened group of elasmobranchs, having experienced widespread declines due to mortalities in fisheries and habitat degradation. Within the Western Central Atlantic, there are two extant species of Rhino-rays, the Critically Endangered Smalltooth Sawfish, Pristis pectinata, and the Vulnerable Freckled Guitarfish, Pseudobatos lentiginosus. Although there is research committed to P. pectinata in this region, less is known about the distribution status of P. lentiginosus. Over the past 50 years, P. lentiginosus have undergone a presumed range contraction in U.S. waters; once found from North Carolina to Texas, and historically common in the north central …

Variations In Thermoregulation Strategies Of Northern And Southern Populations Of Mischocyttarus Mexicanus, Taylor Guild

Honors Theses

Mischocyttarus mexicanus is a species of eusocial paper wasp that is found across much of the Southeastern coastal region of the United States. Contrasting wintering strategies have been seen in northern versus southern populations. Anecdotally, northern populations overwinter by clustering on top of palmetto fronds, their preferred nesting substrate, in a sort of "taco" shape, while southern populations stand on their nests that hang on the underside of the palmetto frond throughout the year. I tested three hypotheses related to the adaptive value of northern over-frond clustering behavior: 1) Over-frond clustering is thermoregulation related, meaning it would be temperature driven. …

Morphological And Functional Classification Of The Amblyomma Americanum (Lone Star Tick) Hemocytes, Julia Hanson

Honors Theses

Ticks are a diverse group of obligate blood-feeding (hematophagous) arthropods that transmit a wide array of human and animal pathogens. These pathogens have caused an increase in tick-borne diseases that pose a significant threat to public health without preventative measures. These pathogens interact with the tick immune system upon uptake, which is primarily divided into humoral and cellular components. Cellular immunity in ticks encompasses several pathogen-eliminating mechanisms including phagocytosis. These mechanisms are mediated by the action of immune cells, commonly referred to as hemocytes, which are analogous to mammalian white blood cells. This study utilized a combination of morphological, functional, …

Developing A Continuous Cell Line Derived From The Gulf-Coast Tick (Amblyomma Maculatum) Embryos, Sabrina Walia

Honors Theses

Tick cell lines provide an affordable, reproducible, and efficient in vitro experimental system to study tick-pathogen interactions at the cellular level. Before the first tick cell lines were developed, there was no established method to perform in vitro studies with ticks. Tick research at the organismal level is full of difficulties and challenges. An increase in tick-borne infections and the availability of cutting-edge molecular tools have stimulated the research community's interest in using tick cell lines to answer important biological questions related to new and emerging tick-borne diseases. Unfortunately, not all medically relevant tick species have a cell line available. …

A Proof Of Concept For Detection Of Palato-Lingual Contact Without Intraoral Electrodes In A Human Participant, Amitava Biswas

Master's Theses

The author of this thesis conceived and investigated an unexpected electrical signal that may not be noticed during regular electroglottography (EGG) when electrodes are conventionally placed on the anterior surface of the throat. It appears that there is a measurable electrical signal from the EGG equipment when electrodes are placed over the frontal cheek (belly of zygomatic muscle), and the tongue is elevated to contact the hard palate, or the tongue is lowered to break the contact. Therefore, this phenomenon is designated as unconventional electroglottography (UEGG, Dr. Steven Cloud, private communication, July 17, 2022).

Two distinctive patterns of waveforms were …

Estimation Of Mortality Rates For The Gulf Menhaden Stock And Reference Point Implementation For The Fishery, Catherine Wilhelm

Master's Theses

The Gulf menhaden stock is the target of a large commercial fishery in the Gulf of Mexico. To address the needs of both the stock and fishery, I performed two studies. I first addressed the natural mortality rates currently used in the Gulf menhaden stock assessment. To update these rates, I used data from a tagging study conducted from 1970 to 1988. Adult and juvenile menhaden were tagged, released, and recovered in fish processing plants. To evaluate the data, I built a Bayesian model using the negative binomial distribution to estimate natural mortality, catchability, and the overdispersion factor parameters. I …

Assessing Athletes’ Risk For Developing The Female Athlete Triad At Two Mississippi Universities, Laura G. Warren

Honors Theses

Despite the health benefits associated with regular exercise, some female athletes experience menstrual dysfunction and low bone mineral density associated with low energy availability as a result of a high volume of exercise and inadequate caloric intake; these three components characterize the female athlete triad (FAT). Prior research explored the severity of the FAT, pre-season screenings, and nutrition intervention methods; however, current research regarding the relationship between the risk for developing the FAT and access to nutrition resources is lacking. The purpose of this study was to assess the risk of female athletes at two Mississippi universities for developing the …

Pirna Expression In Regenerative Tissue Of Octopus Bimaculoides, Bailey Ervin

Honors Theses

Tissue regeneration is present in varying capacities across the animal kingdom. Animals such as Hydra and planarians have the capacity to regenerate entire bodies from extremely small sections of amputated tissue. Others, such as humans, have restricted capacities of regeneration, especially in terms of full appendages and specialized tissues such as cardiac and nervous tissue. One of the primary goals of studying regeneration in other organisms is to achieve the development of regenerative medicine. Interaction of P-element induced WImpy testis (PIWI) proteins and PIWI-interacting RNAs (piRNAs) have been implicated in germline genome maintenance, as well as transposable element silencing. Research …

Impact Of Training Volume On Female Athlete Triad Risk For Female Collegiate D1 Track And Field Athletes, Sarah Parnell

Honors Theses

iv ABSTRACT The Female Athlete Triad is the joint-presentation of three intertwined conditions (i.e., low energy availability (LEA), low bone mineral density (BMD), and menstrual dysfunction) that range in severity across affected individuals and have been known to affect the mental, emotional, and physical health of female athletes in a number of sports, especially those that are leanness-orientated and feature a high prevalence of disordered eating. The purpose of this study is to assess the potential relationship between increasing amounts of training volume and individual Triad risk factors in women’s collegiate track and field. Online Qualtrics surveys were administered to …