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The Sewage Microbiome Dynamics Of Different Serving Neighborhoods In Charleston, Illinois, Sandra Chiamaka Okoye

Masters Theses

The complex microbial ecosystem within sewage systems holds significant implications for environmental and public health. Unlike studies on wastewater treatment plant microbiomes, upstream sewage systems have not been studied widely. This research investigated the dynamic sewage microbiome across diverse serving neighborhoods in Charleston, Illinois, encompassing residential, hospital, industrial, and university areas. Drawing upon recent advancements in microbiome research, the study aimed to unravel the spatial and temporal variations in microbial structures. Three times between June to December 2023 sewage samples were collected from manholes in the areas mentioned above. Community DNA was extracted and sequenced for the V4-V5 region of …

Sediment Carbon Storage In Subtidal Beds Of The Invasive Seagrass Halophila Stipulacea Along An Extreme Water Depth Gradient, St. Thomas, U.S. Virgin Islands, Demian A. Willette, Kelsey M. Vaughn, Allie Durdall, Marilyn Brandt, Sophia Costa, Kristin Wilson Grimes

Biology Faculty Works

Blue carbon ecosystems such as mangroves, salt marshes, and seagrass beds are found globally and are fundamental to fisheries production, storm surge protection, and carbon sequestration. The contribution of seagrass ecosystems to global carbon stocks is still not well understood, including in the United States Virgin Islands (USVI). No study has been published to-date assessing the sediment carbon density (SCD) in seagrass beds in the USVI. This study focused on the carbon storage ability of the invasive species, Halophila stipulacea, which is compact in size compared to common native seagrasses and has spread rapidly to become a dominant seagrass in …

Drosophila Parasitoids Go To Space: Unexpected Effects Of Spaceflight On Hosts And Their Parasitoids, Jennifer Chou, Johnny R. Ramroop, Amanda M. Saravia-Butler, Brian Wey, Matthew P. Lera, Medaya L. Torres, Mary Ellen Heavner, Janani Iyer, Siddhita D. Mhatre, Sharmila Bhattacharya, Shubha Govind

Publications and Research

While fruit flies (Drosophila melanogaster) and humans exhibit immune system dysfunction in space, studies examining their immune systems’ interactions with natural parasites in space are lacking. Drosophila parasitoid wasps modify blood cell function to suppress host immunity. In this study, naive and parasitized ground and space flies from a tumor-free control and a blood tumor-bearing mutant strain were examined. Inflammation-related genes were activated in space in both fly strains. Whereas control flies did not develop tumors, tumor burden increased in the space-returned tumor-bearing mutants. Surprisingly, control flies were more sensitive to spaceflight than mutant flies; many of their …

Evaluation Of Alternative Methods For Dna Recovery Of Compromised Skeletal Remains, Ciara N. Rhodes

Theses and Dissertations

Skeletal remains frequently serve as the sole source of genetic material available for developing a profile in cases concerning unidentified human remains or mass casualties. Nevertheless, as unidentified skeletal remains age and are exposed to uncontrolled environmental conditions, the success rates of conventional methods of bone analysis diminish significantly. The physical and mechanical processing of skeletal remains into fine powder for DNA isolation and downstream analysis can substantially impact the quality and quantity of recoverable genetic information. This concern may be exacerbated when dealing with degraded forensic skeletal remains. Few studies have explored whether pulverization of bone samples contributes to …

Redesign, Evaluation, And Validation Of A Commercially Viable High-Resolution Melt Based Mixture Screening Tool, Chastyn Smith

Theses and Dissertations

Analysis of evidentiary samples containing DNA from multiple contributors (“mixtures”) is a time intensive process for a forensic analyst and one where the contributor nature of a sample is not revealed until the end of the traditional forensic workflow. Often, at this stage, retesting or additional testing of mixture samples may not be possible, particularly if the DNA collection device did not preserve the DNA well enough; consequently leaving only trace amounts of a contributor’s DNA present. Thus, a new collection device that would allow for the increased preservation/integrity of evidentiary samples as well as a method that would allow …

Facilitative And Competitive Interactions Among Dune Grass Species In Monoculture And Polyculture Communities, Anne M. Sciolino

Theses and Dissertations

Coastal dunes are natural barriers between land and sea and are imperative to the protection and preservation of inland ecosystems and human infrastructure. However, due to global warming, seal level rise, and coastal development, coastal dunes are under constant threat of destruction. Restoration efforts have been implemented to rebuild the protective function of dunes through the planting of dune building grasses. Dune grasses build and maintain these vital sand dunes. However, little is known about facilitative and competitive relationships among the grasses. In order to maximize restoration efforts, research is needed to better understand the biotic interactions among restorative grass …

Inhaling The Unseen: Exploring The Presence Of Microplastics In The Human Respiratory Tract, Kara Coffman-Rea

Graduate Research Theses & Dissertations

Microplastics (plastic pieces less than 5 mm) have emerged as a pervasive form of pollution acknowledged as a universal threat to both environmental and human health. Their small size and widespread distribution pose significant risks to marine life, terrestrial ecosystems, and ultimately human health. Microplastics have been reported in food and drink items designated for human consumption, in cosmetics and consumer goods designed for human use, and within the air we breathe, each providing an entry route for microplastics to enter the human body. Recently, microplastic particles have been detected in a variety of human tissue samples (e.g., lung tissue). …

Longevity,Feeding Behavior, And Egg Production Of Adult House Flies (Musca Domestica) Provided With Potential Farm Foods, Anna Elise Grimenstein

Graduate Research Theses & Dissertations

House flies (Musca domestica) are cosmopolitan pests to both humans and livestock, and they can vector many diseases. House flies are especially associated with livestock facilities, as adult flies lay eggs in rotting organic matter such as manure. While it is understood that the diet an adult fly receives can affect biological parameters such as longevity and egg production, not much research has been done to address foods that are accessible to house flies in their natural habitat. The present study examined the longevity, feeding behavior, and egg production rates of adult house flies given different foods they would have …

A Wasteside Story: Establishment And Evolution Of A Wastewater Surveillance Lab, Through The Pandemic And Beyond, Syed Shahrukh Hyder

Graduate Research Theses & Dissertations

Wastewater based epidemiology is a fast growing and practical solution to monitor the spread of disease within a population. As the COVID-19 pandemic grounded the world to a standstill, methods to monitor its spread and prepare appropriate responses became vital to begin the return to normalcy. Such was the case in universities around the world where the campus and surrounding community were vital in fulfilling the educational mission in the face of a generational health crisis. The population in a midsize higher educational institute such as Northern Illinois University (NIU) is a broad mix of on-campus and off campus students, …

The Energetics Of Seasonality In Wild Diademed Sifaka (Propithecus Diadema): A Technical And Biological Validation Of Fecal Triiodothyronine Radioimmunassay, Casey Farmer

Graduate Research Theses & Dissertations

The energetic state of an animal has vital consequences for its fitness, but it can be difficult to detect through behavioral observations. The development of techniques to determine an animals’ energetic state non-invasively would allow conservation planners to rapidly assess the energy balance and conservation potential of individuals, groups, and populations. Thyroid hormones like triiodothyronine (T3) regulate and reflect metabolic state in mammals. T3 is a non-invasive biomarker that can be detected in feces and could potentially be used for this purpose. I perform the first validation of a commercially available T3 radioimmunoassay designed for humans on a wild strepsirrhine …

Evaluation Of Conservation Strategies For Blanding’S Turtles (Emydoidea Blandingii), Callie Klatt Golba

Graduate Research Theses & Dissertations

Across the globe, biodiversity is threatened due to anthropogenic changes to the environment and large numbers of freshwater species, especially turtles, are facing population declines. Resources for conservation are limited, making empirically based conservation planning of utmost importance. Effective management strategies incorporate relevant biological information to outline specific and feasible actions that will mitigate the greatest threats to a species. Blanding’s Turtles (Emydoidea blandingii) are a long-lived, semi-aquatic, freshwater species that are classified as endangered in Illinois and internationally. As with other species of concern, Blanding’s Turtles are threatened by habitat loss, fragmentation, and degradation. They are also threatened by …

Ascertaining A Biochemical Approach To Chlorophyll D Biosynthesis In Acaryochloris Spp., Rashmi Shivni

Graduate Research Theses & Dissertations

Photosynthesis is one of the most abundant metabolic systems on Earth, and specifically, oxygenic photosynthesis primed the planet for complex, multicellular life. The hallmark of modern oxygenic photosynthesis is the photopigment chlorophyll a found in nearly all oxygenic phototrophs as their primary photopigment in their photosynthesis pathways. There are also many organisms that tap into a variety of chlorophylls to extend the energetic limits of photosynthesis, which are largely found as accessory pigments. One genus of cyanobacteria, Acaryochloris, has garnered attention for the ability to undergo photosynthesis by harnessing the far-red part of the visible light spectrum using chlorophyll d …

An Environmental Isolate Of Pseudomonas, 20ei1, Reduces Aspergillus Flavus Growth In An Iron-Dependent Manner Affecting The Expression Of Numerous Genes, Elizabeth Marion Wyman

Graduate Research Theses & Dissertations

Aspergillus flavus is an opportunistic pathogenic fungus that infects oilseed crops worldwide. When colonizing the plants, it produces mycotoxins, including carcinogenic compounds such as aflatoxins. Mycotoxin contamination results in an important economic and health impact. The design of new strategies to control A. flavus colonization and mycotoxin contamination is paramount. In this study, we identified a promising new isolate of Pseudomonas spp., 20EI1, and observed that it is able to reduce the growth of A. flavus AF70. Furthermore, we determined that this growth inhibition is iron-dependent. To further elucidate the nature of this bacterial-fungus interaction, we performed metabolomics and transcriptomics …

Bidirectional In-Situ Analysis And Visualization Of Fluid Structure Interactions With Applications In Blood Flow, Nazariy Tishchenko

Graduate Research Theses & Dissertations

Interactive blood flow simulation has applications in the understanding of complex fluids,training medical professionals, diagnostics, and surgical procedure planning. Bidirectional in situ visualization and analysis are much needed to streamline the analysis of large-scale patient-specific blood flow simulations. The in situ component ensures the live visualization of the simulation results while the simulation is running, and the bidirectional component allows for real-time control and configuration of the simulation parameters (i.e., setting and retrieving the simulation parameters and data based on need). In this project, a highly accurate multiphysics simulation was instrumented to work with an existing bidirectional in situ framework. …

The Glutamine-Asparagine Interplay: Exploring The Role Of Asparagine Synthetase In Hepatocellular Cancer Cells, Babatunde George Olawuni

Graduate Research Theses & Dissertations

Hepatocellular Carcinoma (HCC) is a liver cancer that accounts for a significant proportion of cancer-related deaths globally; likewise, as the primary metabolic regulatory center in the body, the liver undergoes profound metabolic shifts in carcinogenesis, with net glucose and glutamine consumption. Much attention has been focused on the myriad roles of glutamine in supporting cellular growth over the past several decades, but more recently, the relationship between glutamine and the other amide-bearing amino acid, asparagine, has garnered attention. Asparagine is synthesized from glutamine, aspartic acid, and ATP via the enzyme Asparagine Synthetase (ASNS). Extracellular asparagine reliance has been targeted in …

Effects Of Isoacids Supplementation In Lactating Cows’ Diet Varying In Forage Fiber Level On Performances, Feed Efficiency, And Milk Fatty Acids Profile, Sumon Ahmed

Electronic Theses and Dissertations

No abstract provided.

Csn-5: A Tumor's Friend Or Foe In The C. Elegans Germline?, Kellie C. Kuch

Graduate Student Theses, Dissertations, & Professional Papers

The COP9 signalosome is a highly conserved eukaryotic complex regulating protein degradation via deneddylation of Cullin-RING E3 ligases. CSN5, the COP9’s fifth component, contains the catalytically active domain for CSN deneddylation. The complex is inactive without CSN5; however, CSN5 engages in COP9-independent binding with several other proteins, typically promoting either destruction or stabilization of its partners. Many of its confirmed interaction partners are also implicated in tumorigenesis (prominent examples being p27 and p53) and a complex cancer interactome has been established for CSN5. Additionally, CSN5 overexpression has been documented in a staggering array of cancers of diverse origins. This discovery …

The Blackfeet Nation’S Bison Conservation Herd Management Plan, Brandon Kittson

Graduate Student Theses, Dissertations, & Professional Papers

This document is meant to act as a guide to understanding Bison reintroduction on the Blackfeet reservation and serve as a resource for bison management. This report and plan will: 1) review bison ecology and the history of reintroduction efforts on the reservation; 2) identify potential issues and barriers to successful reintroduction; 3) present a summary of current land policies and patterns of land use on the reservation; and 4) provide recommendations for dealing with those potential issues. Recommendations will be based on analyses of previous knowledge of bison and bison behavior.

Better Understanding The Barred Owl, Adam Lee Potts

Graduate Student Theses, Dissertations, & Professional Papers

This thesis research presents an analysis of barred owl nest site selection in an understudied region of their expanded range. The barred owl has dramatically expanded its range westwards over the last 150 years, prompting multiple conflicting reinterpretations of their species account. Hypotheses of range expansion are reviewed to provide context for this study’s research. This study gathers empirical data on nest site selection in the mixed conifer forests of Montana’s Seeley-Swan and Mission Valleys. Eight barred owl nests were located following extensive territory surveys. Field measurements of tree height and diameter using USFS Forest Inventory and Analysis (FIA) plot …

Repatriation And A Biological Profile Of Indigenous Remains Of West Texas, Haley P. Rebardi

Graduate Student Theses, Dissertations, & Professional Papers

The Native American Graves Protection and Repatriation Act (NAGPRA) was created in response to the injustice, mishandling, looting, and trafficking of Native American remains and cultural artifacts. However, even with the latest amendment in December of 2023, there are still gray areas in the context and language. Notably, an issue with NAGPRA is the act only includes institutions and organizations that receive and are supported by Federal funding. Consequently, the act does not cover private collections. The main concern in these contexts is the lack of communication, awareness, and/or permission with and from descendant tribes or potential descendants when it …

Exploring The Relative Contribution Of Humans On Genetic Differentiation Among Speyeria Callippe Populations In The California Coast Ranges, Laura K. Heller

University of the Pacific Theses and Dissertations

The distinction between populations due to environmental factors like climate and geography are well-known and expected, therefore it is not illogical to believe more disjunct habitats would also impact genetic structure. Through Restriction Site Associated DNA Sequencing (RADseq) and Mitochondrial DNA (mtDNA) analysis the genetic structure and differentiation (fixation index, Fst) of Speyeria callippe across four regions in California: the North Coast Ranges, Bay Area, Diablo Range, and South Coast Ranges were analyzed. The influence of geographic distance, human population density, and forest cover were explored as factors influencing the genetics of these populations. The combination of mtDNA and RADseq …

Quantitative Shotgun Proteomic Analysis Of Bacteria After Overexpression Of Recombinant Spider Miniature Spidrion, Masp1, Kathryn P. Randene

University of the Pacific Theses and Dissertations

Spider silk has extraordinary mechanical properties, displaying high tensile strength, elasticity, and toughness. Given the high performance of natural fibers, one of the long-term goals of the silk community is to manufacture large-scale synthetic spider silk. This process requires vast quantities of recombinant proteins for wet-spinning applications. Attempts to synthesize large amounts of native size recombinant spidroins in diverse cell types have been unsuccessful. In these studies, we design and express recombinant miniature black widow (Latrodectus hesperus) MaSp1 spidroins in bacteria that incorporate the NTD and CTD, along with varying numbers of codon-optimized internal block repeats. Following spidroin overexpression, we …

Effects Of Glyphosate-Based Herbicide Exposure On Life History, Stress Tolerance, And Microbiome—From Plasticity To Evolution, Jacob R. Whitlock

University of the Pacific Theses and Dissertations

Glyphosate (GLY) is the most used pesticide worldwide, and GLY-based herbicides (GBHs) can affect animals’ microbiomes and, in turn, their physiology and morphology. Environmental stressors can be mitigated by flexibility in life-history strategies, which can also dictate animal physiology and morphology. However, we lack an understanding of how GBH influences life-history strategies and stress tolerance, in addition to its effects across generations. Thus, I exposed the variable field cricket, Gryllus lineaticeps, to GBH within- and across-generations to examine the role of GBH in developmental plasticity and evolution. Specifically, I measured its effects on life-history traits (e.g., developmental duration and a …

Effects Of Fetal Bovine Serum On The Proteome And Secretome Of Pichia Pastoris, Kenneth L. Nguyen

University of the Pacific Theses and Dissertations

Komagataella pastoris, formerly known as Pichia pastoris, and hereafter referred to as Pichia, is a methylotrophic yeast widely employed as a recombinant protein factory for biotechnical and industrial purposes. P. pastoris boasts the ability to thrive at high cell densities, executes numerous post-translational modifications, and exhibits minimal secretion of endogenous proteins, thus greatly facilitating the expression and purification of recombinant proteins. Despite these advantages, Pichia still presents certain challenges as an expression system. Occasionally, recombinant proteins are retained within the cell and subject to degradation. Furthermore, Pichia falls short in matching the production capabilities of more widely used systems like …

The Role Of The Unfolded Protein Response In Fatty Liver Disease, Anusha L. Murshed

University of the Pacific Theses and Dissertations

The unfolded protein response (UPR) is composed of three highly conserved pathways (ATF6, IRE1, PERK). Cellular stressors induce protein misfolding and aggregation in the endoplasmic reticulum (ER). This signaling pathway maintains protein homeostasis when there is stress in the ER. When the UPR is activated, the eukaryotic initiation factor 2 alpha (eIF2α) becomes phosphorylated, which inhibits global mRNA translation. If ER stress remains chronically unmitigated, the UPR induces apoptosis. GADD34 and CReP shift in expression when the UPR is activated and work as phosphatases and dephosphorylate eIF2α in a feedback loop, allowing protein synthesis to resume. Several human diseases, including …

Insight Into A Sexually Dimorphic Ostracod Crustacean By Mass Spectrometry And Microtomography, Cindy D. Davis

University of the Pacific Theses and Dissertations

The importance of the central nervous system cannot be understated. An array ofmolecules associated with the brain regulate basic behaviors as well as sex specific behaviors. Describing the molecular background is not the only way that I can learn more of the central nervous system. Describing the anatomy of the central nervous system can be crucial in understanding what regions of the brain is particularly key to the animal. Euphilomedes carcharodonta is a small marine crustacean native to the subtidal zone of the California coast. This ostracod makes for a compelling candidate to explore these research interests as this organism …

Plasticity In Response To Temperature Magnitude And Variation---From Life History To Thermal Tolerance And Coloration, Austin Rex Hoffman

University of the Pacific Theses and Dissertations

Warming associated with climate change has many direct and downstream effects on animals. For example, warmer developmental temperatures can improve heat tolerance and reduce insect melanization, which is related to coloration, thermoregulation, immunity, desiccation resistance, and potentially life-history traits, such as investment into reproduction and dispersal. Increased temperature variation is also a feature of climate change, and it may have a larger impact on animals than warming. However, I lack insight into the combined effects of temperature magnitude and variability on important traits of life history, thermal tolerance, and coloration. Thus, I integrated temperature variation into thermal performance using a …

Transgenerational Effects Of Stress On The Plasma Proteome Of A Marine Mammal, Emily Voelkner

University of the Pacific Theses and Dissertations

The physiological stress response enables animals to respond to changes in their environment, and is mediated by the hypothalamic-pituitary-adrenal (HPA) axis in mammals. Increased activation of the HPA axis by repeated stress during critical life stages like reproduction could affect fitness. Information about a stressor can be communicated to offspring via hormone signals prenatally, or postnatally via milk, and affect offspring development and stress reactivity. Experimentally activating the HPA axis by adrenocorticotropic hormone (ACTH) administration results in the synthesis of the major glucocorticoid hormone cortisol, which has well-studied far-reaching effects on growth, metabolism, and immunity. Beyond cortisol levels alone, biomarkers …

Developing Cellular Systems To Elucidate Rna Structural Dynamics Of Cag Expansion Transcripts In Spinocerebellar Ataxias, Victoria Demeo

Electronic Theses & Dissertations (2024 - present)

Spinocerebellar ataxias (SCAs) are a diverse group of over 40 genetically heterogeneous neurodegenerative disorders, many of which are caused by a trinucleotide CAG repeat expansion in the coding region of specific genes. These expansions lead to the production of polyglutamine (polyQ) tracts that interfere with normal protein function, triggering cellular dysfunction and contributing to disease pathogenesis. The most well-known of these SCAs, such as SCA1, SCA2, and SCA3, exhibit progressive neurodegeneration, yet the precise mechanisms through which these mutations cause disease remain poorly understood.

A significant challenge in studying CAG repeat expansion disorders lies in the complexity of the disease …

Investigation Of L-Serine Synthesis And Transport As Stabilizing Feedback Mechanisms Within The Tsetse-Wigglesworthia Symbiosis, Ryan Phillips

Graduate Theses, Dissertations, and Problem Reports (ETD)

Tsetse flies (Glossina morsitans), which are the obligate vectors of Old-World trypanosomes (Trypanosoma spp.) that cause African trypanosomiasis, have a bacteriome that houses the intracellular endosymbiont Wigglesworthia glossinidia. The ancient coevolution of these species has led to the integration of Wigglesworthia metabolism into tsetse physiology and a subsequent reliance on nutrient exchange for maintaining the fitness of both partners. The establishment of this obligate mutualism has facilitated the emergence of feedback mechanisms that stabilize the symbiosis, such as that which involves the exchange of L-serine and B vitamins. The Gammaproteobacteria Wigglesworthia supplement B vitamins lacking …