Digital Commons Network^™

Simple Improvements In Vector Design Afford Substantial Gains In Aav Delivery Of Aggregation-Slowing Aβ Variants, Ella Borgenheimer, Cameron Trueblood, Bryan L Nguyen, William R Lagor, Joanna L Jankowsky

Faculty, Staff and Students Publications

Adeno-associated virus (AAV) gene therapy for neurological disease has gained traction due to stunning advances in capsid evolution for CNS targeting. With AAV brain delivery now in focus, conventional improvements in viral expression vectors offer a complementary route for optimizing gene delivery. We previously introduced a novel AAV gene therapy to slow amyloid aggregation in the brain based on neuronal release of an Aβ sequence variant that inhibited fibrilization of wild-type Aβ. Here we explore three coding elements of the virally delivered DNA plasmid in an effort to maximize the production of therapeutic peptide in the brain. We demonstrate that …

Deciphering Immune Suppression Mechanisms Of Primary And Metastatic Breast Cancer, Seunghyun Lee

Arts & Sciences Graduate Student Theses and Dissertations

Immune checkpoint blockade (ICB) has revolutionized cancer treatment, receiving FDA approval for various previously incurable cancers. In breast cancer, the combination of pembrolizumab (an anti-PD-1 antibody) with chemotherapy has become the standard-of-care for early-stage (Keynote-522) and advance-stage (Keynote-355) triple-negative breast cancer (TNBC). Unfortunately, over 30% of TNBC patients fail to respond to the combined chemo-immune therapy treatment, and the causes are unknown. Furthermore, ICB has demonstrated poor results in hormone-receptor positive breast cancer. While it is well-established that breast cancer cells can evade immune responses, the specific mechanisms driving immune evasion remain unclear. Thus, deciphering the immune system's role in …

Transcription And 3d Chromatin Organization Interplay At Sub-Kilobase Scale, Hannah Harris

Theses & Dissertations

Nuclear compartments are prominent features of 3D chromatin organization, but sequencing depth limitations have impeded investigation at ultra fine-scale. CTCF loops are generally studied at a finer scale, but the impact of looping on proximal interactions remains enigmatic. Here, we critically examine nuclear compartments and CTCF loop-proximal interactions using a combination of in situ Hi-C at unparalleled depth, algorithm development, and biophysical modeling. Producing a large Hi-C map with 33 billion contacts in conjunction with an algorithm for performing principal component analysis on sparse, super massive matrices (POSSUMM), we resolve compartments to 500 bp. Our results demonstrate that essentially all …

Epigenetic Mechanisms And Senescence In Aging And Cancer, Alla Karpova

Arts & Sciences Graduate Student Theses and Dissertations

Aging is marked by the progressive decline of cellular and organ function. This process often manifests through DNA damage, epigenomic alterations, telomere shortening, and metabolic or mitochondrial dysfunction. As DNA damage and other stressors accumulate, cells take measures to prevent malignant transformation. One such measure is cellular senescence, a state of irreversible cell cycle arrest that halts the growth of pre-malignant cells. When cells are unable to enter senescence due to high levels of genomic alterations, they typically undergo apoptosis or necrosis. However, if mutations affect key driver genes, allowing cells to evade death, they may become malignant, continuing to …

Spatiotemporal Patterns In Orbicella Faveolata Wound Regeneration As An Indicator Of Colony Health, Alexander G. Wheeler

All HCAS Student Capstones, Theses, and Dissertations

Anthropogenic (e.g. damage from anchors, scuba divers, tissue sampling) and natural disturbances (e.g. predation, storm damage) can result in wounding of live tissue on coral colonies. Wounding has been shown to detract from a common resource pool, increasing disease susceptibility and impairing coral growth and reproductive activity. Regeneration not only varies between species, but also between conspecifics in the same location. A colony’s capacity to regenerate tissue can be an indicator of a colony’s condition and resilience. Understanding the physiological and environmental factors that affect tissue regeneration alongside the ultimate impact of sampling (disease and predation correlations) are needed for …

Black Grouper (Mycteroperca Bonaci) Neurocranium, Nicholas Burchett, Kelsee Rotering, Marissa Rosas, David Kerstetter, Derek Burkholder

All Scans: Kerstetter Fisheries and Avian Ecology 3D Scan Series

No abstract provided.

Butterfly Peacock Bass (Cichla Ocellaris), Samuel K. Zellefrow, David Kerstetter, John Nichols

All Scans: Kerstetter Fisheries and Avian Ecology 3D Scan Series

No abstract provided.

Progerin Can Induce Dna Damage In The Absence Of Global Changes In Replication Or Cell Proliferation, Liza A. Joudeh, P. Logan Schuck, Nina M. Van, Alannah J. Dicintio, Jason A. Stewart, Alan S. Waldman

Faculty Publications

Hutchinson-Gilford Progeria Syndrome (HGPS) is a rare genetic condition characterized by features of accelerated aging, and individuals with HGPS seldom live beyond their mid-teens. The syndrome is commonly caused by a point mutation in the LMNA gene which codes for lamin A and its splice variant lamin C, components of the nuclear lamina. The mutation causing HGPS leads to production of a truncated, farnesylated form of lamin A referred to as "progerin." Progerin is also expressed at low levels in healthy individuals and appears to play a role in normal aging. HGPS is associated with an accumulation of genomic DNA …

Investigating The Relationship Between Population Density Surrounding An Airport And The Number Of Wildlife Strikes Per Operation., Alexandra E. Rowe, Daniel Alves, Evan Park, Brooke Wheeler, Vivek Sharma

Aeronautics Student Publications

This study compared the relationship between population density surrounding an airport and reported wildlife strikes per operation. A very weak correlation with no statistical significance was determined which emphasizes the need for future research on wildlife mitigation strategies and understanding wildlife patterns.

Consistency And Flexibility Of Character In Free-Ranging Male African Elephants Across Time, Age, And Social Contexts, Caitlin E. O’Connell-Rodwell, Jodie L. Berezin, Colleen Kinzley, Patrick T. Freeman, Monica N. Sandri, Dustin Kieschnick, Timothy C. Rodwell, Mariana Abarca, Virginia Hayssen

Biological Sciences: Faculty Publications

Post-dispersal male African elephants (Loxodonta africana) live within complex social networks. To quantify the consistency of male elephant character (or personality) within these networks, we employed behavioral repeatability analysis tools across social and environmental contexts. We collected behavioral data from thirty-four individually-identified male elephants at the same waterhole over five field seasons (2007–2011) in Etosha National Park, Namibia. Using repeatability models to assess ten behavioral categories, we found five behaviors (affiliation, aggression, dominance, self-directed anxious, and self-directed comfort) were consistent at the individual level. Some of these behaviors were also repeatable, depending on social context. In particular, the …

Glutamate Receptors At The Zebrafish Neuromuscular Junction, Trenton Randall

Honors College Theses

Glutamate is the main excitatory neurotransmitter in the CNS, but at the neuromuscular junction, that role is taken by acetylcholine. However, during embryonic development, non-cholinergic receptors, including those for glutamate, are also present at the NMJ, which are not maintained unless used. These receptors can still form functional circuits, as evidenced by a process called neurotransmitter respecification, in which a neuron changes which neurotransmitter it releases, and is accompanied by the upregulation of the corresponding receptor by the muscle. This process has been observed in frogs and in rats. We predict that zebrafish also exhibit this neurotransmitter plasticity. To assess …

The Challenges Of Diet Generalism In A Microbial Predator, Dictyostelium Discoideum, Shreenidhi Perukkaranai Madabhushi

Arts & Sciences Graduate Student Theses and Dissertations

Organisms vary widely in their diet breadth, ranging from specialists that feed on few resources to generalists that feed on many. Specialists have honed their ability to catch and process specific prey, but generalists must deal with prey that differ in nutritional quality and defensive mechanisms. Have generalist predators overcome costs associated with consuming multiple prey species or do they experience costly trade-offs when handling different prey? Generalist predators also live in environments that vary in the type and abundance of prey species. How do generalists navigate this variation in prey abundance and profitability and seek out their preferred prey? …

Trend And Awareness Of E-Cigarettes Among Students In A Private College In Sabah Malaysia, Vitalis Ronald Eden, Hazrina Hamid, Sreemoy Das, Regidor Iii Dioso

AUIQ Complementary Biological System

Objective: This study aims to investigate the trend and awareness of e-cigarette use among students in a private college located in Sabah, Malaysia. Research Methods: The cross-sectional study was conducted in a private college in Sabah. A self-administered questionnaire was adapted and distributed to 300 randomly selected students regardless of their e-cigarettes vaping status. IBM SPSS Statistic 27 was utilized to analysed accumulated data. Results: A-245 students participated in the study with a response rate of 81.6%. Majority of the respondent were female (69.8%), Bumiputera Sabah (72.2%), Diploma students (90%) aged 22-25 years’ old. The study revealed that almost all …

Survey And Comparative Analysis Of Pollinator Diversity, Abundance, And Foraging Activity Of Diptera And Hymenoptera In Selected Habitats Of South Texas, Melissa Villarreal

Theses and Dissertations

With the declining bee population, non-bee pollinators can serve as an alternative source for pollination. Diptera is a potential source of untapped pollinator resources based on their abundance and visitation rate, but they are understudied in the field of pollination ecology. This study aimed to characterize the pollinator community in selected areas of South Texas. It focused on the Diptera and Hymenoptera families to compare their diversity, relative abundance, foraging behaviors, environmental influences, and vegetation associations. Active sampling and line transect were used in the survey to sample the Hymenoptera and Diptera communities to their family taxonomic rank. Statistical analyses …

An In-Depth Investigation Into Yersinia Pestis Phages: Isolating A Yersinia Pestis Phage From Soil And Constructing A Comprehensive Phylogenetic Analysis Of Known Yersinia Pestis Phages, Jacqueline Chavez

All HCAS Student Capstones, Theses, and Dissertations

Yersinia pestis, the causative agent of the plague, has become increasingly resistant to many antibiotics; therefore, alternatives such as phage therapy are necessary. Phage therapy uses combinations of bacteriophages or phages, which are viruses that only infect bacteria. However, phages—especially Y. pestis phages —are severely understudied. Thus, this research has sought to specifically isolate a phage from soil that infects Y. pestis. There were 146 samples that were collected from across the US, focusing on those with reported cases of plague. These samples were enriched with Y. pestis to maximize the amount of potential phage that target Y. pestis. …

Red Grouper (Epinephelus Morio) Neurocranium, David Ferreiro

All Scans: Kerstetter Fisheries and Avian Ecology 3D Scan Series

No abstract provided.

Comparing Metabolism And Hypoxia Tolerance Of Native And Non-Native Florida Freshwater Fishes In Climate Change Scenarios, Benjamin A. Share

All HCAS Student Capstones, Theses, and Dissertations

As climate change brings rising water temperatures and lower dissolved oxygen (DO) concentrations to freshwater bodies, it has become increasingly important to understand how this will affect ecosystems with established non-native or invasive species. Fishes of the family Cichlidae are the most pervasive non-native fishes in the Everglades and may increase their range further north under a changing climate. To better understand potential invasibility and competition with native fishes, the metabolism and hypoxia tolerance of non-native Blue Tilapia Oreochromis aureus was compared to native Bluegill Lepomis macrochirus when acclimated across a range of seasonal and projected temperatures. Intermittent-flow respirometry was …

High-Severity Wildfires Alter Ant (Hymenoptera: Formicidae) Foraging Assemblage Structure In Montane Coniferous Forests And Grasslands In The Jemez Mountains, New Mexico, Usa, Jonathan Knudsen, Robert Parmenter, Theodore Sumnicht, Robin M. Verble

Biological Sciences Faculty Research & Creative Works

High-severity wildfires create heterogeneous patterns of vegetation across burned landscapes. While these spatial patterns are well-documented, less is known about the short- and long-term effects of large-scale high-severity wildfires on insect community assemblages and dynamics. Ants are bottom-up indicators of ecosystem health and function that are sensitive to disturbance and fill a variety of roles in their ecosystems, including altering soil chemistry, dispersing seeds, and serving as a key food resource for many species, including the federally endangered Jemez Mountain salamander (Plethodon neomexicanus). We examined the post-fire effects of the 2011 Las Conchas Wildfire on ant communities in the Valles …

Unravelling Large-Scale Patterns And Drivers Of Biodiversity In Dry Rivers, Arnaud Foulquier, Thibault Datry, Roland Corti, Daniel Von Schiller, Klement Tockner, Rachel Stubbington, Mark O. Gessner, Frederic Boyer, Marc Ohlmann, Wilfried Thuiller, Delphine Rioux, Christian Miquel, Ricardo Albarino, Daniel C. Allen, Florian Altermatt, Maria Isabel Arce, Shai Arnon, Damien Banas, Andy Banegas-Medina, Erin Beller, Melanie L. Blanchette, Joanna Blessing, Iola Goncalves Boechat, Kate Boersma, Michael Bogan, Nuria Bonada, Nick Bond, Katherine Brintrup, Andreas Bruder, Ryan Burrows, Tommaso Cancellario, Cristina Canhoto, Stephanie Carlson, Nuria Cid, Julien Cornut, Michael Danger, Bianca De Freitas Terra, Anna Maria De Girolamo, Ruben Del Campo, Veronica Diaz Villanueva, Fiona Dyer, Arturo Elosegi, Catherine Febria, Ricardo Figueroa Jara, Brian Four, Sarig Gafny, Rosa Gomez, Lluis Gomez-Gener, Simone Guareschi, Bjorn Gucker, Jason Hwan, J. Iwan Jones, Patrick S. Kubheka, Alex Laini, Simone Daniela Langhans, Bertrand Launay, Guillaume Le Goff, Catherine Leigh, Chelsea Little, Stefan Lorenz, Jonathan Marshall, Eduardo J. Martin Sanz, Angus Mcintosh, Clara Mendoza-Lera, Elisabeth I. Meyer, Marko Milisa, Musa C. Mlambo, Manuela Morias, Nabor Moya, Peter Negus, Dev Niyogi, Iluminada Pagan, Athina Papatheodoulou, Giuseppe Pappagallo, Isabel Pardo, Petr Paril, Steffen U. Pauls, Marek Polasek, Pablo Rodriguez-Lozano, Robert J. Rolls, Maria Mar Sanchez-Montoya, Ana Savic, Oleksandra Shumilova, Kandikere R. Sridhar, Alisha Steward, Amina Taleb, Avi Uzan, Yefrin Valladares, Ross Vander Vorste, Nathan J. Waltham, Dominik H. Zak, Annamaria Zoppini

Biological Sciences Faculty Research & Creative Works

More than half of the world’s rivers dry up periodically, but our understanding of the biological communities in dry riverbeds remains limited. Specifically, the roles of dispersal, environmental filtering and biotic interactions in driving biodiversity in dry rivers are poorly understood. Here, we conduct a large-scale coordinated survey of patterns and drivers of biodiversity in dry riverbeds. We focus on eight major taxa, including microorganisms, invertebrates and plants: Algae, Archaea, Bacteria, Fungi, Protozoa, Arthropods, Nematodes and Streptophyta. We use environmental DNA metabarcoding to assess biodiversity in dry sediments collected over a 1-year period from 84 non-perennial rivers across 19 countries …

Relationship Between Capsule Production And Biofilm Formation By Mannheimia Haemolytica, And Establishment Of A Poly-Species Biofilm With Other Pasteurellaceae, Yue-Jia Lee, Dianjun Cao, Bindu Subhadra, Cristina De Castro, Immacolata Speciale, Thomas J. Inzana

Faculty Publications - Biological Sciences

Mannheimia haemolytica is one of the bacterial agents responsible for bovine respiratory disease (BRD). The capability of M. haemolytica to form a biofilm may contribute to the development of chronic BRD infection by making the bacteria more resistant to host innate immunity and antibiotics. To improve therapy and prevent BRD, a greater understanding of the association between M. haemolytica surface components and biofilm formation is needed. M. haemolytica strain 619 (wild-type) made a poorly adherent, low-biomass biofilm. To examine the relationship between capsule and biofilm formation, a capsule-deficient mutant of wild-type M. haemolytica was obtained following mutagenesis with ethyl methanesulfonate …

The Impacts Of Seasonality And Nutrient Loading On Microcystis Bloom Development In Wall Pond, Alyssa Antolak

Bridges: A Journal of Student Research

The harmful cyanobacteria Microcystis dominates eutrophic freshwater systems globally. Eutrophication leading to nitrogen and phosphorus loading into aquatic systems is increasing bloom propagation and shifting diatom/dinoflagellate dominated systems to cyanobacteria dominated systems. Understanding seasonal variability and environmental parameters combined with nutrient loading will allow for better understanding of what factors are influencing Microcystis blooms. Biweekly plankton samples and environmental parameters were collected from Wall Pond on campus from spring 2022-spring 2023. Results show that yearly plankton samples shifted from Microcystis dominated in the early summer to diatom dominated in the late summer-early fall, then back to Microcystis dominated in late …

Are Rising Seas Pushing Ghost Crabs Out Of Their Comfort Zone?, Finn Gillette

Bridges: A Journal of Student Research

Ghost crabs (Ocypode quadrata) can be found on sandy beaches bordering the western Atlantic Ocean. These semiterrestrial crustaceans are often found between the swash zone and the dunes on beaches. Dunes are critical refuges for ghost crabs during storms and extreme tide events. This makes them a useful indicator species for monitoring the effects of global warming-induced sea level rise on beach biota, as their distribution patterns among beach zones may correlate with shifts found in other species. Beach surveys conducted from 2015 onward assessed the population density of ghost crabs on beaches of Horry and Georgetown counties in South …

Environmental Health Of Wildland Firefighters: A Scoping Review, M. Bryan Held, Miranda Rose Ragland, Sage Wood, Amelia Pearson, Seth Wayne Pearson, Olivia Chenevert, Rachel Marie Granberg, Robin M. Verble

Biological Sciences Faculty Research & Creative Works

Background: Wildland firefighters are likely to experience heightened risks to safety, health, and overall well-being as changing climates increase the frequency and intensity of exposure to natural hazards. Working at the intersection of natural resource management and emergency response, wildland firefighters have multidimensional careers that often incorporate elements from disparate fields to accomplish the tasks of suppressing and preventing wildfires. Thus, they have distinctly different job duties than other firefighters (e.g., structural firefighters) and experience environmental health risks that are unique to their work. We conducted a systematic scoping review of scientific literature that addresses wildland firefighter environmental health. Our …

(R2108) Global Asymptotic Stability Analysis Of Discrete Time Population Model With Allee Effect Through Lyapunov Function, Govind Jha, Neeraj Kumar, Sarita Jha

Applications and Applied Mathematics: An International Journal (AAM)

This study explores the idea of stability analysis by using Lyapunov functions in discrete time population models; this work focuses on the nth generation. Further, this investigation aims to extend global stability concepts to discrete-time models and considers the influence of the Allee effect on population dynamics. Mathematical formulations and specific modelling approaches are utilized to investigate the behavior of the population system. The results reveal a larger range of stability in comparison to previous findings, emphasizing the effectiveness of the Lyapunov function approach. Specifically highlighted here are the extension of global stability concepts to the nth generation providing insights …

Neuronal And Glial Cell Alterations Involved In The Retinal Degeneration Of The Familial Dysautonomia Optic Neuropathy, Anastasia Schultz, Henar Albertos-Arranz, Xavier Sánchez Sáez, Jamie Morgan, Diane Darland, Alejandra Gonzalez-Duarte, Horacio Kaufmann, Carlos E. Mendoza-Santiesteban, Nicolás Cuenca, Frances Lefcort

Biology Faculty Publications

Familial dysautonomia (FD) is a rare genetic neurodevelopmental and neurodegenerative disorder. In addition to the autonomic and peripheral sensory neuropathies that challenge patient survival, one of the most debilitating symptoms affecting patients' quality of life is progressive blindness resulting from the steady loss of retinal ganglion cells (RGCs).Within the FD community, there is a concerted effort to develop treatments to prevent the loss of RGCs. However, the mechanisms underlying the death of RGCs are not well understood. To study the mechanisms underlying RGC death, Pax6-cre;Elp1loxp/loxp male and female mice and postmortem retinal tissue from an FD patient were used to …

Bioindicators Of Mercury In Riverine Systems, Kathryn Mudica

All-Inclusive List of Electronic Theses and Dissertations

This study focuses on the bioaccumulation and biomagnification of mercury in freshwater food webs, with emphasis on bioindicators, such as macroinvertebrates, crayfish, and river otters. Despite regulatory efforts and advancements in monitoring, significant gaps remain in understanding mercury dynamics in freshwater systems—especially regarding its transport, methylation, and bioavailability across different ecosystems. To address these knowledge gaps, this study adopts a biocentric approach, emphasizing the role of living organisms in their environment. By utilizing macroinvertebrates, crayfish, and river otters as bioindicators, we aim to assess mercury bioavailability and distribution. These organisms provide varying temporal and spatial scales of mercury accumulation, offering …

Elucidating The Mechanism Of Interleukin-17a Signaling In The Pathogenesis Of West Nile Virus, Farzana Nazneen

Dissertations

West Nile Virus (WNV), a neurotropic flavivirus transmitted by mosquitoes, is a leading cause of viral encephalitis in the United States and remains a significant public health concern. Unfortunately, no vaccine or therapeutic intervention is available against WNV infection. Previous studies, including ours, demonstrated that interleukin-17A (IL-17A) signaling increases the cytotoxic potential of CD8⁺ T cells to facilitate WNV and parasite clearance; however, the molecular mechanism is not understood. IL-17 receptor C (IL-17RC) is an obligatory co-receptor with IL-17 receptor A (IL-17RA) for signaling induced by IL-17A, IL-17A/F, and IL-17F. In this study, we found that IL-17RC deficient ( …

Dissecting Metabolic Landscape Of Alveolar Macrophage, Sunayana Malla

Department of Chemical and Biomolecular Engineering: Dissertations, Theses, and Student Research

The highly plastic nature of alveolar macrophage (AM) plays a crucial role in the defense against inhaled particulates and pathogens in the lungs. Depending on the signal, AM acquires either the classically activated M1 phenotype or the alternatively activated M2 phenotype. In this study, we investigate the metabolic shift in the activated phases of AM (M1 and M2 phases) by reconstructing context specific genome-scale metabolic (GSM) models. Metabolic pathways such as pyruvate metabolism, arachidonic acid metabolism, chondroitin/heparan sulfate biosynthesis, and heparan sulfate degradation are found to be important driving forces in the development of the M1/M2 phenotypes. Additionally, we formulated …

Minimizing Take Of Threatened Rattlesnakes And Optimizing Project Review In Se Nebraska, Shaun Dunn, Dan Fogell, Colleen Rothe-Groleau

Nebraska Department of Transportation: Research Reports

The western massasauga (Sistrurus tergeminus) and the timber rattlesnake (Crotalus horridus) are protected under Nebraska Statute 37-801-811 and listed as threatened species. These species occur in the right-of-way (ROW) along several roads in Jefferson, Gage, Pawnee, and Richardson Counties which necessitates the need for added Environmental Review (ER) from Nebraska Department of Transportation (NDOT) staff and onsite surveys prior and during maintenance and construction to roadways. This project sought to minimize ER time, staff time, and increase the knowledge of these species in southeast Nebraska by:

1. Identifying precise locations of western massasauga brumation sites;
2. Mapping travel …

Effect Of Hyperbaric Oxygen Therapy (Hbot) On The Proportion Of Splenic Leukocytes During Skeletal Muscle Regeneration, Hetvi Patel

2024 Fall Honors Capstone Projects - Archive

Hyperbaric oxygen therapy (HBOT) can accelerate the regeneration of skeletal muscle after injury and improve overall recovery. Certain cells of the spleen are increased during muscle regeneration; however, the effect of HBOT on splenic cells during muscle regeneration is not well understood. In other experimental models, HBOT proliferates the proportion of splenic cells. In this study, eight male and nine female mice sustaining crush muscle injuries underwent HBOT at 1.5 atmospheres absolute for 60 min or normobaric hyperoxia (100% O₂) for 60 min within 2-6 hours of injury for 4 days. The mice were then euthanized at 4- …