Biology Commons^™

Developing Computational And Experimental Tools For Investigating Intrinsically Disordered Proteins And Biomolecular Condensates, Daniel Griffith

Arts & Sciences Graduate Student Theses and Dissertations

Intrinsically disordered proteins and protein regions (IDPs) compose a significant portion of eukaryotic proteomes yet remain relatively understudied. Unlike folded domains, IDPs lack a single fixed three-dimensional structure and instead are defined by a dynamic conformational ensemble. Despite this structural heterogeneity, IDPs carry out vital roles within the cell. IDPs are particularly important in cellular signaling and regulation, owing to their ability to mediate molecular interactions with a variety of affinities and specificities. Additionally, some IDPs drive the formation of higher-order non-stoichiometric assemblies called biomolecular condensates. This dissertation focuses on the development of a variety of computational and experimental tools …

Cellular And Molecular Basis Of Cd4+ T Cell Help At The Effector Phase During Immunotherapy Of Mhc-Ii Negative Tumors, Samuel Oche Ameh

Arts & Sciences Graduate Student Theses and Dissertations

Immune checkpoint therapies (ICT) have shown promise in treating solid tumors, providing cures and durable protection in some cases. However, only a subset of patients benefits from ICT, indicating a need for a deeper understanding of the requirements for successful therapy. In both mice and humans, αβ T cells are key mediators of spontaneous and ICT-induced anti-tumor responses. While the anti-tumor roles of CD8+ T cells are well-studied, the role of CD4+ T cells, particularly in ICT for MHC-II negative tumors, is less understood. New insights into how CD4+ T cells modulate CD8+ T cells during ICT may lead to …

Discovering And Characterizing Conserved Anthelmintic Targets In The Early Parasitic Stages Of Gastrointestinal Nematodes, Hyeim Jung

Arts & Sciences Graduate Student Theses and Dissertations

Gastrointestinal nematodes (GINs) collectively infect 1.5 billion people, leading to mortality and various forms of morbidity in humans and hindering normal development in children. GINs also diminish the productivity of food animals, which are crucial for economic and nutritional well-being, particularly in developing countries. Currently, the world still primarily relies on only a few drug classes for global de-worming of GINs in humans and animals. However, the high rate of reinfection, disappointing treatment success rates, and increasing drug resistance make GINs one of the most important contributors to promoting and maintaining global poverty. This highlights the urgent need for more …

Modern Building Structures Are A Landscape-Level Driver Of Bat–Human Exposure Risk In Kenya, Tamika Lunn, Reilly T. Jackson, Paul W. Webala, Joseph G. Ogola, Kristian M. Forbes

Biological Sciences Faculty Publications and Presentations

Identifying the locations and drivers of high-risk interfaces between humans and wildlife is crucial for managing zoonotic disease risk. We suggest that continent-wide improvements to residential housing in Africa are inadvertently creating artificial roosting habitat for synanthropic free-tailed bats (family Molossidae), and that improved buildings are a rapidly accelerating exposure interface that needs urgent research attention and investment. Along a residential gradient in rural southern Kenya, we mapped building use by free-tailed bats in 1109 buildings. We show that bats often roost in human-occupied buildings, with almost one-in-ten buildings exhibiting evidence of bat occupation (9.2%) and one-in-13 found to contain …

Immunological Feedback Loops Generate Parasite Persistence Thresholds That Explain Variation In Infection Duration, Clayton E. Cressler, Daniel C.G. Metz, David A. Chang Van Oordt, Andrea L. Graham

School of Biological Sciences: Faculty Publications

Infection duration affects individual host fitness and between-host transmission. Whether an infection is cleared or becomes chronic depends on the complex interaction between host immune responses and parasite growth. Empirical and theoretical studies have suggested that there are critical thresholds of parasite dose that can determine clearance versus chronicity, driven by the ability of the parasite to manipulate host immunity. However, the mammalian immune response is characterized by strong positive and negative feedback loops that could generate duration thresholds even in the absence of direct immunomodulation. Here, we derive and analyse a simple model for the interaction between T-cell subpopulations …

Balancing Ecology And Practicality To Rank Waterbodies For Preventative Invasive Species Management, Caleb P. Roberts, William E. Grant, Matthew L. Horton, Lindsey A.P. Labrie, Miranda R. Peterson, Jane S. Rogosh, Hsiao-Hsuan Wang

Biological Sciences Faculty Publications and Presentations

• ‘Early detection and rapid response’ (EDRR) is the most successful framework for preventative invasive species management, but prioritizing localized EDRR actions with limited resources is challenging. An approach that ranks individual locations, such as waterbodies, for EDRR by combining an invasive species' establishment risk with the practicality of managing it could help set reasonable priorities.
• Here, we worked with regional practitioners in Arkansas, USA, and the broader Southeastern USA to co-produce a workflow for preventative aquatic invasive species management that (1) estimates establishment risk under current and future climates with a species distribution model, (2) scores waterbodies according to difficulty …

The Effects Of People, Time Of Day, And Season On Affiliative And Stereotypic Behaviors In Captive Rhinoptera Bonasus And Other Rays Across Two Human-Interactive Enclosures, Wren C. A. Newman

Theses and Dissertations

Cownose rays (Rhinoptera bonasus) are among the most common species found in aquaria, yet the impact of touch enclosures on their welfare remains largely unknown. While research on animal-visitor interactions has produced mixed results for other species, the lack of studies focusing on fish welfare poses a risk of overlooking potential welfare concerns. Therefore, we aimed to establish a baseline for cownose rays regarding stereotypic behaviors, sociality, and activity in captivity, and to examine the influence of human interaction on these behaviors. We collected over 700 hours of footage from two enclosures at Adventure Aquarium in Camden, NJ …

Sex Differences In The Diets Of Forest-Dwelling Baboons (Papio Anubis), Kara Hartunian

Theses and Dissertations

The ability to eat and switch between many food sources is an adaptative feeding strategy utilized for meeting nutritional needs across different environments, seasons, and physiological conditions. Baboons (genus Papio) excel at both dietary flexibility and foraging selectively, and consequently have one of the most widespread geographic distributions in the Order. To further expand to our understanding of baboon feeding ecology, I analyzed foraging activity and the nutritional characteristics of the diets of the relatively understudied rainforest baboons (Papio anubis) living in Kibale National Park, Uganda. I also investigated if there are differences in food type choice …

The Role Of Southern Red-Backed Voles, Myodes Gapperi, And Peromyscus Mice In The Enzootic Maintenance Of Lyme Disease Spirochetes In North Dakota, Usa, Michael W. Dougherty, Nathan M. Russart, Robert A. Gaultney, Emily Marie Gisi, Haley M. Cooper, Lindsey R. Kallis, Catherine A. Brissette, Jefferson A. Vaughan

Biology Faculty Publications

Lyme disease has expanded into the Great Plains of the USA. To investigate local enzootic transmission, small mammals were trapped in two forested tracts in northeastern North Dakota during 2012 and 2013. Peromyscus mice and southern red-backed voles, Myodes gapperi, comprised over 90% of all mammals captured. One site was dominated by Peromyscus (79% of 100 mammals captured). At the other site, M. gapperi (59% of 107 mammals captured) was more abundant than Peromyscus (36%). Immature stages of two tick species parasitized small mammals: Dermacentor variabilis and Ixodes scapularis. Larval I. scapularis ectoparasitism was significantly higher on Peromyscus (81% …

Activated Carbon Derived From Rice Husk Biomass Using Pyrolysis-Assisted Tartaric Acid Activation For Removal Of Reactive Orange 16 Dye: Adsorption Modeling Using Response Surface Methodology, Ahmed Saud Abdulhameed, Ruihong Wu, Abdallah Reghioua, Harun M. Mbuvi, Zaher Mundher Yaseen, Zaharaddeen N. Garba

AUIQ Complementary Biological System

In the current work, rice husk (RH) biomass was pyrolyzed using tartaric acid as an activating agent to produce activated carbon (AC). For 60 min, the procedure was run at 700 °C and 5 L/min of nitrogen (N₂) flow rate. The study used response surface methodology (RSM) and a 3-level Box-Behnken design (BBD) to optimize the extraction efficiency of rice husk activated carbon (RHAC) in eliminating reactive orange 16 (RO16) dye from an aqueous solution. Different process parameters, such as pH (2–12), RHAC dose (0.04 – 0.14 g), and time (60-240 min), were chosen as part of the …

Oil Palm Fronds Activated Carbon Via Microwave-Assisted H3po4 Activation: Box-Behnken Optimization For Crystal Violet Dye Removal, Nur Atirah Shamsudin, Qistina Omar, Ismaniza Ismail, Noor Artika Hassan, Syarifah Abd Rahim, Nur Fazreen Dzulkafli, Ruihong Wu, Soon Kong Yong

AUIQ Complementary Biological System

The extensive use of crystal violet (CV) dyes may cause water pollution. A highly porous and functionalized activated carbon can be used for adsorption of CV dyes. Activated carbon was prepared from oil palm fronds through microwave-assisted pyrolysis and activation with phosphoric acid (H₃PO₄) for removal of CV dye from wastewater. The physico-chemical characteristics of oil palm fronds activated carbon (OPFAC) was employed by Brunauer-Emmett-Teller (BET) surface area analysis, Fourier transform infrared (FT-IR) analysis, Scanning Electron Methodology-Energy Dispersive X-Ray (SEM-EDX) analysis, thermogravimetric analysis (TGA), and point of zero charges (pH_pzc). The adsorption parameters such …

Impact Of Some Parameters On The Survival And Proliferation Of Foodborne Pathogens: Escherichia Coli, Bacillus Subtilis, Staphylococcus Aureus, And Streptococcus Pyogenes, Hassan Agha, Ahmed Bashir Sanaalla, Muhanad Abdullah Salim Abdulsamad, Maroua Abderrahmane Salhi, Ghada Abdu-Razzaq Mohammad, Abdulmutalib Alabeed Alkamil Allaq

AUIQ Complementary Biological System

Food poisoning caused by foodborne microorganisms is a significant public health concern. This study aims to investigate the impact of several nutritional and environmental parameters on the growth of Escherichia coli, Bacillus subtilis, Staphylococcus aureus, and Streptococc pyogenes in both model systems and food. The specific impact of temperature, pH, and UV light stress on pathogens.Applying physical stress on microorganisms is a standard method to induce cell inactivation and promote food stability.This study found that the optimal temperature for the growth of these pathogens is between 30°C and 50°C. No growth was observed beyond 50°C, indicating temperature sensitivity; low temperatures …

Biodiversity Assessment Of A Mississippi River Backwater Complex Using Edna Metabarcoding, Eric J. Ludwig, Veronica M. Lee, Leah K. Berkman, Aaron D. Geheber, David D. Duvernell

Biological Sciences Faculty Research & Creative Works

The backwater lowland habitats of large rivers, like the Mississippi River in North America, present complex and often inaccessible environments for traditional capture-based fish biodiversity sampling. Our knowledge of the assemblages of the fishes that occupy such habitats is often incomplete, and this can compromise management efforts. We employed environmental DNA (eDNA) metabarcoding methods to sample a Mississippi River bottom wetland system to assess the ichthyofaunal diversity and the assemblage structure across habitat types, and we compared our results with capture-based survey records for the same habitats. We collected water samples in the spring and fall of 2022 from slough, …

Effect Of Glucocorticoid Blockade On Inflammatory Responses To Acute Sleep Fragmentation In Male Mice, Zim Hasan

Masters Theses & Specialist Projects

The association between sleep and the immune-endocrine system is well recognized, but the nature of that relationship is not well understood. Sleep fragmentation induces a pro-inflammatory response in peripheral tissues and brain, but it also activates the hypothalamic-pituitary-adrenal (HPA) axis, releasing glucocorticoids (GCs) (cortisol in humans and corticosterone in mice). It is unclear whether this rapid release of glucocorticoids acts to potentiate or dampen the inflammatory response in the short term. The purpose of this study was to determine whether blocking or suppressing glucocorticoid activity will affect the inflammatory response from acute sleep fragmentation (ASF). Male C57BL/6J mice were injected …

Mesenchymal Stem Cells In Autoimmune Disease: A Systematic Review And Meta-Analysis Of Pre-Clinical Studies, Hailey N. Swain, Parker D. Boyce, Bradley A. Bromet, Kaiden Barozinksy, Lacy Hance, Dakota Shields, Gayla R. Olbricht, Julie A. Semon

Mathematics and Statistics Faculty Research & Creative Works

Mesenchymal Stem Cells (MSCs) Are of Interest in the Clinic Because of their Immunomodulation Capabilities, Capacity to Act Upstream of Inflammation, and Ability to Sense Metabolic Environments. in Standard Physiologic Conditions, They Play a Role in Maintaining the Homeostasis of Tissues and Organs; However, there is Evidence that They Can Contribute to Some Autoimmune Diseases. Gaining a Deeper Understanding of the Factors that Transition MSCs from their Physiological Function to a Pathological Role in their Native Environment, and Elucidating Mechanisms that Reduce their Therapeutic Relevance in Regenerative Medicine, is Essential. We Conducted a Systematic Review and Meta-Analysis of Human MSCs …

Contaminant Transport Mechanisms And Source Tracking In Karst Groundwater Systems Under Agricultural Land Use, Shreya Pandey

Masters Theses & Specialist Projects

Karst areas in general face severe groundwater contamination problems that can degrade their water quality. In comparison to other landscapes, groundwater within karst regions is more susceptible to contamination. The situation gets worse when agriculture is practiced in these karst regions, because the nutrients and bacteria like nitrates and E. coli (Escherichia coli) are released into the groundwater systems which contaminate the water quality of those karst groundwater systems. This research aims to study the impacts of these contaminants, specifically nitrates and E. coli., by identifying the contaminant transport mechanisms and source tracking of these contaminants in the groundwater under …

Climate-Smart Agriculture In Southern Kenya: An Assessment Of Factors Influencing Crop Development And Productivity, Matthew Bowers

Masters Theses & Specialist Projects

Globally, the adverse effects of climate change are forcing farmers to adapt their practices or risk crop failures. Throughout Sub-Saharan Africa, agriculture is the largest source of food, income, and employment, so threats such as climate change can put millions of lives and livelihoods in peril if modifications are not made to the existing system. Climate-Smart Agriculture (CSA) is a potential solution, as CSA techniques aim to increase the productivity and resilience of land affected by climate change. While CSA is a relatively new conceptual approach, many traditional and Indigenous techniques can be considered “climate-smart”. Understanding what biotic and abiotic …

The Evolution Of A Response To Smoke Within The Arthropoda, Adam Miles

Masters Theses & Specialist Projects

Many animals have a survival instinct to flee in response to fire, but do they respond to smoke alone? Many arthropods respond to fire or smoke by moving in the opposite direction (a negative taxis) to obtain shelter. At the species level, taxa that have adapted a behavioral response to fire increase their fitness. This response behavior has been observed in many terrestrial arthropods. Still, the behavior is currently unknown for marine, aquatic, or cave arthropods, which are atypically exposed to smoke or fire. This project assesses how often behavioral adaptation to smoke avoidance may have evolved within Arthropoda. Twenty-two …

Proceedings Of The 2024 Berry Summer Thesis Institute, University Of Dayton. University Honors Program, Magdelyn Stewart, Noah Clemens, Sarah Theewis, Henry Salisbury, Kevin Johnston, Adin Stoller, Meggie Bailey, Erin T. Flaherty, Adelyn Hughes, Marc Nya

Proceedings of the Berry Summer Thesis Institute (2013-Present)

Thanks to a gift from the Berry Family Foundation and the Berry family, the University Honors Program launched the Berry Summer Thesis Institute in 2012. The institute introduces students in the University Honors Program to intensive research, scholarship opportunities and professional development. Each student pursues a 12-week summer thesis research project under the guidance of a UD faculty mentor. This contains the product of the students' research.

Contents:

Testing the Influence of Lithology and Ice Sheet Dynamics on Waterfall Formation in Hocking Hills State Park // Magdelyn Stewart

Step-Rate Manipulation for Improved Performance: A Review// Noah Clemens

Alfred Rosenberg: An …

Ecosystem Effects Of Targeted Grazing With Sheep To Manage Cheatgrass, Madelyn Sorrentino

Boise State University Theses and Dissertations

Cheatgrass (Bromus tectorum) invasion is widespread across the Great Basin region of the United States and is expected to continue. Cheatgrass degrades ecosystem functioning, increases the risk of wildfire, and negatively affects rangeland-based agriculture and other land uses. Targeted grazing—the use of livestock to accomplish a vegetation management objective—has been suggested as a management practice that could combat cheatgrass invasion at the landscape level. However, knowledge of targeted grazing at a management-relevant scale and its effects on other vital ecosystem components, such as non-target plant species and soil properties, remains limited. To test the efficacy of sheep targeted …

From Inbreeding To Admixture: How The Diverse Consequences Of Gene Flow Shape Evolutionary Dynamics And Population Viability, Amy L. Springer

All Graduate Theses and Dissertations, Fall 2023 to Present

When Homo sapiens traveled out of Africa and interbred with the Neanderthals of Europe, human genes spread into the Neanderthal population. Likewise, genes from Neanderthals spread into the human genome—genes humans still carry to this day. The process whereby genetic material from one population is spread to another is known as gene flow. Gene flow—or the absence thereof—can have critical consequences for a population’s health and survival. On one hand, if no gene flow occurs, mating among close relatives can lead to high levels of inbreeding. Inbreeding can have devastating consequences for the health of populations, in some cases even …

Shifting Paradigms In Recreation Management: Applying Social-Ecological System Frameworks To Parks And Protected Areas, Noah Creany

All Graduate Theses and Dissertations, Fall 2023 to Present

Park and protected area (PPA) recreation management is often characterized by social, ecological, and managerial dimensions. These dimensions have increasingly been conceptualized as social-ecological systems (SESs) to understand the complex interrelationships between them. Contemporary trends of increased visitation on public lands in the United States, including US National Parks, have accentuated the complex interactions between the amount of recreation use, the capacity of the setting, the quality of the visitor experience, and ecological resource conditions. These challenges of managing recreation use and understanding these interactions will be further compounded by climate change and its effects on ecosystem composition and dynamics. …

Characterizing Oxylipins In Human Milk Extracellular Vesicles, Priscila Herrera

Food Science (MS) Theses

Extracellular vesicles (EVs) are non-replicating lipid bilayer membrane-bound particle formed by a parent cell and secreted into the extracellular environment. EVs in human milk are bioavailable and influence physiologic pathways that may contribute to newborn growth and development. There is interest in the oxylipin content of EVs that may contribute to the bioavailability of EVs. This research aims to characterize the oxylipin content of human milk EVs. Centrifugation and precipitation were used to isolate EVs from human milk (n = 20). The Folch method was used to extract lipids, and liquid chromatography-mass spectrometry (LC– MS) was used to qualify and …

Signatures Of Selection, Gene Flow, And Genetic Drift On The Genomes Of A Recent Avian Radiation, Flor Brigitte Hernandez Camacho

Open Access Theses & Dissertations

Speciation is not a discrete event but rather a gradual process that occurs along a continuum. Initially, populations remain genetically and reproductively connected, but they become reproductively isolated as the process of speciation progresses. Advances in DNA sequencing technology has helped our understanding of the processes that contribute to changes in the genetic composition of populations over the progression of speciation, also known as drivers of evolution (i.e. genetic drift, mutation, selection, and gene flow). Among them, hybridization, or the interbreeding between distinct lineages, is increasingly recognized as a natural process that can have significant consequences to the speciation process. …

Unraveling The Behavioral Ecology Of The Western Diamond-Backed Rattlesnake (Crotalus Atrox) Through The Lenses Of Personality, Predator-Prey Interactions, And Crypsis, Oceane Da Cunha

Open Access Theses & Dissertations

To thrive in an environment, individuals need to be able to forage efficiently and acquire mates. These resources are limited, and their acquisition depends upon the energy and time an individual chooses to allocate to each activity and the environmental conditions, leading to behavioral trade-offs. Different species, or even different individuals within the same population, respond to these trade-offs by employing contrasting strategies, leading to differential life-history outcomes. The overarching goal of this dissertation is to gain a better understanding of the trade-offs cryptic ambush mesopredators are facing using the western diamond-backed rattlesnake (Crotalus atrox) as a model species. Each …

The Role Of Elevation In The Migration, Physiology, And Genomic Diversification Of Birds, Jessie L. Williamson

Biology ETDs

Elevational gradients cause profound eco-climatic variation across short distances. Partial pressure of oxygen (PO₂) is a severe challenge that organisms face at high elevations; due partly to specialization on PO₂, most Neotropical bird species have narrow elevational ranges. However, a small fraction are elevational generalists that span sea level to high elevations, and a subset undertake extreme migratory journeys from low to high elevations biannually. My dissertation combines diverse approaches across levels of biological organization to understand how elevation impacts the ecology, evolution, physiology, and migration of montane birds. I examined ‘extreme’ elevational …

Application Of Criminology In Urban Ecology And Evolution: Routine Activity Theory And Field Equipment Disappearance Dynamics, Ignacy Stadnicki, Michela Corsini, Marta Szulkin

Biology Faculty Publications and Presentations

Research in urban ecology and evolution relies on the use of deployable scientific equipment. If left unattended in the field, scientific equipment may be prone to vandalism and theft, especially in the urban space. Here, we empirically applied a theory derived from the field of criminology, specifically the Routine Activity Theory (RAT) framework, to predict disappearance rates of scientific equipment in an ongoing urban ecology research project. First, we tested a routinely applied method of equipment protection – labelling – and investigated whether equipment disappearance varied with label information content and message tone. Second, we examined whether equipment attributes (price, …

Using Wasp Specimens In Taxonomic, Biogeographic, Evolution, And Informal Education Studies, Brenna Lynn Decker

All Graduate Theses and Dissertations, Fall 2023 to Present

Entomology collections hold an untapped wealth of information, from insect morphology, genetics, locality and association data, and potential for use in education. Especially with insects that generate initial fears, such as wasps, seeing insect specimens provides a safe environment to learn about their behaviors. Wasps are insects in the order Hymenoptera, along with ants and bees. The public may hold fears against wasps, due to their negative portrayal in various media, but they serve as integral components of a functional ecosystem. Even with their importance, many groups of wasps are still highly understudies. This dissertation aims to tackle this fear …

Evidence For Partitioning? A Comparison Of Thermal Niche In Three Species Of Sympatric Lizards In Northeastern Utah, Kristopher B. Pedersen

All Graduate Theses and Dissertations, Fall 2023 to Present

Lizards actively maintain a narrow range of body temperatures through behavioral thermoregulation and microhabitat selection. Body temperature plays a critical role in many physiological processes. As a result, there is a range of body temperatures at which a lizard’s reproductive success (fitness) is maximized, known as the lizard’s thermal niche. There is strong evidence linking the available temperatures, or thermal properties of a microhabitat, to success in maintaining body temperatures within a preferred set range. Microhabitats have differing thermal properties, and so have different relative quality. Because thermal properties are limited in space and time, competition for high quality microhabitat …

Impacts Of Anthropogenic Disturbances And Urbanization On The Behavior And Morphology Of Two Free-Living Lizard Species (Uta Stansburiana And Aspidoscelis Neotesselatus), Layne O. Sermersheim

All Graduate Theses and Dissertations, Fall 2023 to Present

Urbanization can alter wildlife, requiring species to adjust to anthropogenic changes via life history strategies. Reptiles are particularly vulnerable to these changes, as ectotherms directly rely on their environment to maintain their optimal homeostatic state. As urbanization changes the landscape, reptiles will have to adapt to anthropogenic change, but it is unclear what behaviors may be aiding in this adaptation and whether there are morphological tradeoffs existing to support this change. To analyze the impact of urbanization and anthropogenic disturbances on reptile behavior and morphology, I conducted three research studies on two different species – the common side-blotched lizard and …