Elucidating Mechanisms Of Enhanced Dsrna-Nanophytoglycogen Innate Immune Responses In Healthy Human Cells, Nicholas Jadaa

Theses and Dissertations (Comprehensive)

Immunostimulatory nucleic acids, such as long double-stranded RNA (ds)RNA, can stimulate innate immune responses in a non-sequence specific manner. These molecules are recognized by pattern-recognition receptors in the cytoplasm, endosome, and on the cell surface. Activation leads to the production of mediators of innate immune pathways, including type I interferon and proinflammatory cytokines. Although these receptors are present in all cells, their role in non-immune cells is often overlooked due to their lower level of responsiveness. Nanocarriers can enhance these nucleic acid-mediated responses, allowing for exploration of innate immune pathways in non-immune cells. Nanoparticles as carriers of nucleic acids can …

Plasmid-Borne Biosynthetic Gene Clusters Within A Permanently Stratified Marine Water Column, Paraskevi Mara, David Geller-Mcgrath, Elizabeth A. Suter, Gordon T. Taylor, Maria G. Pachiadaki, Virginia P. Edgcomb

BCES: Faculty Publications

Plasmids are mobile genetic elements known to carry secondary metabolic genes that affect the fitness and survival of microbes in the environment. Well-studied cases of plasmidencoded secondary metabolic genes in marine habitats include toxin/antitoxin and antibiotic biosynthesis/resistance genes. Here, we examine metagenome-assembled genomes (MAGs) from the permanently-stratified water column of the Cariaco Basin for integrated plasmids that encode biosynthetic gene clusters of secondary metabolites (smBGCs). We identify 16 plasmid-borne smBGCs in MAGs associated primarily with Planctomycetota and Pseudomonadota that encode terpenesynthesizing genes, and genes for production of ribosomal and non-ribosomal peptides. These identified genes encode for secondary metabolites that are …

A Molecular-Informed Species Inventory Of The Order Ceramiales (Rhodophyta) In The Narragansett Bay Area (Rhode Island And Massachusetts), Usa, Thomas Irvine, Brian Wysor, Alicia Beauvais

Arts & Sciences Faculty Publications

Narragansett Bay is an estuarine system in the western North Atlantic Ocean that harbors a diverse marine flora, providing structure, habitat, and food for native biodiversity. This area has been the center of numerous environmental, biological, ecological, and oceanographic studies; however, marine macroalgae have not been extensively examined using modern molecular methods. Here, we document the biodiversity of the red algal order Ceramiales based on DNA sequence comparisons of the 3′ end of the RuBisCo large subunit (rbcL-3P) and the universal plastid amplicon (UPA). Thirty-seven distinct species of this order were identified and validated with molecular data, including five new …

Four-Dimensional Ecology Education (4dee) For Everyone: Teaching Ecology To Non-Majors, Vikki L. Rodgers, Sara E. Scanga, Justin R St Juliana, Erica S. Tietjen, Jon M. Honea, Loren B. Byrne, Zakiya H. Leggett, George Middendorf

Arts & Sciences Faculty Publications

Originally developed for application to ecology courses for undergraduate majors, the Four-Dimensional Ecology Education (4DEE) Framework offers possibilities for adaptation to courses with ecology content for many other audiences. Recognizing the extraordinary range of classroom contexts and constraints, we developed some general, flexible recommendations and approaches to guide instructors in adapting the 4DEE Framework for an array of non-major audiences and classroom context needs. Our hope is that 4DEE-aligned courses for non-majors will provide these students with greater appreciation of ecology and inspire them to use their knowledge to address many critical environmental issues in their personal and professional lives. …

Application Of Environmental Dna Metabarcoding To Differentiate Algal Communities By Littoral Zonation And Detect Unreported Algal Species, Sergei Bombin, Andrei Bombin, Brian Wysor, Juan M. Lopez-Bautista

Arts & Sciences Faculty Publications

Coastal areas are the most biologically productive and undoubtedly among the most complex ecosystems. Algae are responsible for most of the gross primary production in these coastal regions. However, despite the critical importance of algae for the global ecosystem, the biodiversity of many algal groups is understudied, partially due to the high complexity of morphologically identifying algal species. The current study aimed to take advantage of the recently developed technology for biotic community assessment through the high-throughput sequencing (HTS) of environmental DNA (eDNA), known as the “eDNA metabarcoding”, to characterize littoral algal communities in the Northern Gulf of Mexico (NGoM). …

Forty Years Of Inferential Methods In The Journals Of The Society For Molecular Biology And Evolution, Claudia A.M. Russo, Adam Eyre-Walker, Laura A. Katz, Brandon S. Gaut

Biological Sciences: Faculty Publications

We are launching a series to celebrate the 40th anniversary of the first issue of Molecular Biology and Evolution. In 2024, we will publish virtual issues containing selected papers published in the Society for Molecular Biology and Evolution journals, Molecular Biology and Evolution and Genome Biology and Evolution. Each virtual issue will be accompanied by a perspective that highlights the historic and contemporary contributions of our journals to a specific topic in molecular evolution. This perspective, the first in the series, presents an account of the broad array of methods that have been published in the Society for Molecular Biology …

Mammalian Biodiversity On Greenways Across An Urban-To-Rural Gradient, Brooklyn C. Zwinklis

College of Graduate Studies: Theses & Dissertations

Large-scale urbanization is one of the leading causes of biodiversity loss on a global scale due to habitat loss and fragmentation. This has created a need to investigate ways to mitigate the damage caused by urban development, such as studying whether green spaces in urban areas can serve as means of preserving mammalian biodiversity in cities. This study specifically focused on greenways as they are understudied when compared to other green spaces, such as parks and cemeteries. Greenways are linear tracts of paved land, usually designed for human recreational activities. However, their benefits to wildlife have not been well researched. …

Evaluating Reactive Gliosis In The Brain Of Adult Zebrafish Following The Ingestion Of Nanopolystyrene., Hannah A. Kelehear

College of Graduate Studies: Theses & Dissertations

Polystyrene nanoplastics are one of the most pervasive environmental contaminants and have been shown to infiltrate multiple organ systems following ingestion. Studies in several animal models and humans have demonstrated that nanoplastics can cross the blood-brain barrier. Additionally, there is evidence that plastics will induce an inflammatory response in the brain involving reactive gliosis of microglia and astrocytes. This process has yet to be thoroughly investigated in the zebrafish model system in the context of micro-/nanoplastic ingestion. In the current study, we examined microglial and astrocytic phenotypes in the adult zebrafish telencephalon after consuming food contaminated with 44 nm polystyrene …

Ribosome Hibernation Factor Induces Antibiotic Persisters Of Mycobacterium Tuberculosis In Neutrophil-Rich Lung Lesions, Jamie Corro

Electronic Theses & Dissertations (2024 - present)

Mycobacterium tuberculosis (Mtb), the etiological agent of tuberculosis, is a prescient global health threat and the leading cause of death by an infectious agent. Treatment of Mtb infection involves administering 2-4 antibiotics for a minimum of 6 months. This extended drug regimen is required to target a subpopulation of persistent bacilli. As their name implies, these bacteria can “persist” by acquiring nonhereditary and transient antibiotic tolerance. Although the precise mechanism is unknown, it’s often attributed to slowing cellular growth and metabolic processes. During zinc deprivation, bacteria can remodel their ribosomes by replacing their zinc-binding paralogues containing the CXXC motif (C+) …

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 …

Female Titin Mutant Mice Outperform Young And Old Males, Reese Ger

Scripps Senior Theses

Exercise performance is widely believed to generally be maximal among young males. However, little research has been conducted to investigate the impact of sex or age on muscle performance. This study investigated the effects of sex and age on forelimb and all limb grip strength performance in wildtype and titin mutant mice. Titin is the largest known protein, with known involvement in muscle function. The mice in this study were Ttn∆112-158 with a 75% deletion to the PEVK region of titin. Based on limited existing research, we hypothesized that wildtype mice would outperform all Ttn∆112-158 mice, males would outperform females …

Effect Of Bioactive Borate Glass On Printability And Physical Properties Of Hydrogels, Fateme Fayyazbakhsh, Mehedi H. Tusar, Yue-Wern Huang, Ming C. Leu

Mechanical and Aerospace Engineering Faculty Research & Creative Works

Hydrogels are a key component in bioinks and biomaterial inks for bioprinting due to their biocompatibility and printability at room temperature. The research described in the present paper contributes to the advancement of bioprinting by studying the effect of bioactive borate glass (BBG) incorporated into hydrogels on printability and physical properties. In this study, we fabricated 3D-printed hydrogel scaffolds using gelatin and alginate hydrogel mixture incorporated with various amounts of BBG, a bio ceramic rich in therapeutic ions including boron, calcium, copper, and zinc. We investigated the effect of incorporating BBG on the density, viscosity, physical interactions, chemical structure, and …

Development Of A Novel Bioink For Human Vascularized Organoids, Bradley Allen Bromet

Masters Theses

"There is a need for a model to better mimic human physiology in the clinic, so the objective was to develop a novel bioink for a 3D tissue model to study human disease and development in a dynamic 3D environment. The results from each corresponding study helped in developing a novel bioink for use in a bio printed human vascularized organoid. The bioink composed of alginate with other natural hydrogels to function as extracellular matrix and with the addition of borophosphate bioactive glasses (BPBGs) to replace growth factors, can be used with multiple cell types to bio print the proposed …

Preliminary New Study Indicates Possible Dramatic Decline In The Diversity Of Insects Visiting Flowers Of Jarrah (Eucalyptus Marginata) In Kings Park Over 26 Years, Ashley R. Jenkin, Siegfried L. Krauss, Eddie Van Etten

Research outputs 2022 to 2026

The recent decline of terrestrial insects in many parts of the world is of growing concern due to the fundamental ecosystem services they perform. Pollination is a vital ecosystem service predominantly performed by insects, with inestimable environmental and economic benefits. Accurate assessment and management of insect pollinator declines, and of other ecosystem impacts are hindered by a lack of long-term monitoring data and notably an absence of Southern Hemisphere studies. This preliminary study aims to address some of these gaps by determining if the diversity of insect floral visitors and potential pollinators of the canopy tree species Jarrah (Eucalyptus marginata) …

Trends In Monitoring Of Australia’S Threatened Birds (1990–2020): Much Improved But Still Inadequate, Simon J. Verdon, Robert A. Davis, Ayesha Tulloch, Sarah M. Legge, David M. Watson, John C. Z. Woinarski, G. Barry Baker, Joris Driessen, Hayley M. Geyle, Hugh Possingham, Stephen T. Garnett

Research outputs 2022 to 2026

Monitoring is vital to conservation, enabling conservation scientists to detect population declines, identify threats and measure the effectiveness of interventions. However, not all threatened taxa are monitored, monitoring quality is variable, and the various components of monitoring are likely to differ in their rates of improvement over time. We assessed the presence of monitoring and monitoring quality, using a range of metrics, for all Australia’s threatened bird taxa from 1990 to 2020 (four assessments spanning 30 years). We used our assessments to understand decadal trends in the number of taxa monitored; monitoring quality; and the groups that conduct monitoring. The …

Long-Term Climatic Stability Drives Accumulation And Maintenance Of Divergent Freshwater Fish Lineages In A Temperate Biodiversity Hotspot, Sean James Buckley, Chris J. Brauer, Peter J. Unmack, Michael P. Hammer, Mark Adams, Stephen J. Beatty, David L. Morgan, Luciano B. Beheregaray

Research outputs 2022 to 2026

Anthropogenic climate change is forecast to drive regional climate disruption and instability across the globe. These impacts are likely to be exacerbated within biodiversity hotspots, both due to the greater potential for species loss but also to the possibility that endemic lineages might not have experienced significant climatic variation in the past, limiting their evolutionary potential to respond to rapid climate change. We assessed the role of climatic stability on the accumulation and persistence of lineages in an obligate freshwater fish group endemic to the southwest Western Australia (SWWA) biodiversity hotspot. Using 19,426 genomic (ddRAD-seq) markers and species distribution modelling, …

Characterization Of Tonneau1 Recruiting Motif Proteins And Ton2 Signaling Functions, Tyler Falk

Theses and Dissertations

Plants cells are fixed in place. As a result they have to carefully divide in order to function properly. Plants use a number of complex microtubule arrays to ensure proper division and orientation including the preprophase band (PPB) and the phragmoplast. The PPB orients the cell prior to division and marks the cortical division site, which is where the phragmoplast is guided to. The phragmoplast is a dynamic microtubule array that builds the cell plate which later becomes the cell wall that divides daughter cells. Proteins involved with PPB formation include Tonneau1 (TON1) and Tonneau2 (TON2) which localize to and …

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 …

Aberrant Lipid Accumulation And Retinal Pigment Epithelium Dysfunction In Prcd-Deficient Mice, Sree Indrani Motipally

Graduate Theses, Dissertations, and Problem Reports (ETD)

Progressive Rod-Cone Degeneration (PRCD) is a peripheral membrane protein predominantly expressed in photoreceptor outer segment (OS) disc membranes with an unknown function. Several mutations in Prcd are implicated in Retinitis pigmentosa (RP) in humans. The most common “cysteine to tyrosine” (C2Y) mutation in Prcd leads to progressive retinal atrophy in multiple dog breeds and RP in humans. Canine models harboring the C2Y mutation in Prcd show disorganized OS structure with greatly attenuated photoreceptor OS renewal rates. Recent studies show defects in the photoreceptor nascent disc flattening in the absence of Prcd. However, it is unclear how OS discs eventually …

Mortality Index Of Drosophila Melanogaster, Following Traumatic Brain Injury, Megan N. Ashworth

Graduate Student Dissertations, Theses, Capstones, and Portfolios

Traumatic brain injuries (TBI) are associated with immediate and long-term consequences that can be divided into primary and secondary injuries. A primary injury results due to the direct damage inflicted on the brain by the hit, whereas a secondary injury takes more time to manifest due to the cascade of molecular events that lead to cellular damage and death within the brain. This study analyzes mortality as a secondary injury following traumatic brain injury in the presence of a human neurodegenerative genetic risk factor, APOE ε4. The High Impact Trauma (HIT) device developed by Katzenberger et al. (2013) was utilized …

Do Duckweeds Adapt To Water And Microbes?, Ava M. Rose

Honors Theses and Capstones

Organisms in their home environment sometimes outperform transplanted individuals native to other areas, in a phenomenon termed local adaptation. While local adaptation is traditionally considered to be driven by the abiotic factors of an environment, scientists have recently increased consideration of biotic factors. Specifically, of interest to many is host-associated microbiomes, which can alter host trait expression. As the desire to commercialize microbiome treatments for agriculture and medicine grows, it is important to analyze the potential value of local microbiomes, which may be adapted to their hosts, or to which local hosts may have adapted. Using Lemna minor (duckweed) as …

An Updated Outline For Clearing And Staining Of Preserved Specimens, Sadie E. Smith

Honors Theses and Capstones

This protocol outlines a enhanced clearing and staining procedure for persevered specimens, focusing on the visualization of cartilage and bone in small taxa. With origins from O. Shultze's diaphonization methodology in 1897, the process of clearing and staining improves the clarity and contrast of intricate tissues. It is essential for studies in developmental biology, histology and anatomy. This protocol covers the key steps of the process while detailing the materials, solutions and estimated timeline for each step pertaining to specific taxa. The aim of the protocol is to standardize and provide guidance for procedures in the Biological Sciences department at …

Examining Genome Size And Nutrient Influence On Damage Patterns, And Plant-Invertebrate Community Dynamics, Hailee B. Petosky

Dissertations, Master's Theses and Master's Reports

Genome size (GS) varies widely among angiosperms and has been shown to mediate plant responses to nutrients. Variations of GS drastically impact plant growth, fitness, and competitive responses, influencing plant functioning, nutrient requirements, and potentially, consumptive interactions. Specifically, plants with larger genomes vary in their cellular nutrient requirements, affecting tissue quality, nutrient constraints, and invertebrate interactions. Furthermore, environmental nutrient enrichments are a key driver affecting ecosystem functioning and species interactions. Plant communities are impacted by both top-down and bottom-up controls of herbivores and nutrients, respectively, and alterations to these interactions may cause cascading trophic level effects to influence damage patterns …

The Effects Of Early Exposure To Prescription/Illicit Drugs And Drug Metabolites On Larval Zebrafish Behavioral And Motor Function Development, Jacob Thomas, Dena Weinberger, Bikram Subedi, Brandon Capps

Murray State Theses and Dissertations

THE EFFECTS OF EARLY EXPOSURE TO PRESCRIPTION/ILLICIT DRUGS AND DRUG METABOLITES ON LARVAL ZEBRAFISH BEHAVIORAL AND MOTOR FUNCTION DEVELOPMENT

A Thesis Presented to the Faculty of the Department of Biology

Murray State University

Murray, Kentucky

In Partial Fulfillment of the Requirements for the Degree of Masters In Science

By Jacob Thomas, B.S., Murray State University

December 2024

Acknowledgements

Brandon Capps, who pretty much did a whole third of the legwork on this project and saved me lots of headaches;

Chandler Maddox, one of the University of Kentucky’s finest undergrads who came in from the top rope with a folding chair …

Optimization Of An Immune Assay To Detect Binding Of Nod2 To Staphylococcus Aureus, Precious Mckenzie

All Student Theses and Dissertations

Staphylococcus aureus, a gram-positive, commensal bacterium, is the cause of a multitude of opportunistic diseases and infections. While S. aureus has evolved ways to escape innate immune responses in the host, the mechanisms are not fully understood. One area of active research involves mechanisms by which S. aureus avoids detection by Pattern Recognition Receptors (PRRs), such as Nuclear Oligomerization Domain 2 (NOD2), present on the surface of and inside innate immune cells. This study aimed to design and optimize an assay that can be utilized to investigate S. aureus components that contribute to the activation of NOD2 receptors. The …

Pseudomonas Mosselii Improves Cold Tolerance Of Asian Rice (Oryza Sativa L.) In A Genotype-Dependent Manner By Increasing Proline In Japonica And Reduced Glutathione In Indica Varieties, Nasim Maghboli Balasjin, James Maki, Michael Schläppi

Biological Sciences Faculty Research and Publications

Cold stress is an important factor limiting rice production and distribution. Identifying factors that contribute to cold tolerance in rice is of primary importance. While some plant specific genetic factors involved in cold tolerance have been identified, the role of the rice microbiome remains unexplored. In this study, we evaluated the influence of plant growth promoting bacteria (PGPB) with the ability of phosphate solubilization on rice cold tolerance and survival. To reach this goal, inoculated and uninoculated 2-week-old seedlings were cold stressed and evaluated for survival and other phenotypes such as electrolyte leakage (EL) and necessary elements for cold tolerance. …