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Nuclear Aurka-Driven Early Dissemination Of Breast Cancer Uncovers Opposing Roles Of Hif-1a And Hif-1b In Metastasis, Abha Maskey

Graduate Theses, Dissertations, and Problem Reports (ETD)

Metastatic progression is the primary cause of mortality in the majority of solid tumors, including breast cancer (BC). The triple-negative breast cancer (TNBC) is the most aggressive BC subtype with the highest recurrence rates within 1-3 years post-diagnosis, and worst overall survival outcomes. Early distant recurrence of cancer is enabled by early disseminated tumor cells (eDTCs), yet the mechanisms of early dissemination remain poorly defined. Hypoxia-inducible factor 1 (HIF1) is a transcription factor normally induced under hypoxia to enable cell survival. It is the major cause of metastasis from hypoxic tumors. In our work, we demonstrated that the nuclear Aurora …

Mechanisms Of Glyphosate Toxicity: Uptake, Mitochondrial Function, And Metabolism, Dionysios Patriarcheas

Graduate Theses, Dissertations, and Problem Reports (ETD)

Glyphosate, the most widely used herbicide in the world, is an inhibitor of chorismate biosynthesis, the precursor of aromatic amino acids. The target of glyphosate is absent in animals, but findings reporting toxicity in model organisms without a known mechanism or target are increasing. Saccharomyces cerevisiae is a useful and versatile model for understanding molecular mechanisms of toxicity. In yeast, previous work has shown that the aspartate/glutamate permease Dip5 is the proposed transporter for glyphosate and that mitochondrial metabolism has been implicated in response to glyphosate toxicity. This dissertation aimed to identify the effects of glyphosate on mitochondrial function through …

Multi-Omic Characterization Of Immune And Metabolic Responses To Inflammatory Challenges In Sheep, Samanthia Raceine Johnson

Graduate Theses, Dissertations, and Problem Reports (ETD)

To meet the demands of the growing population, it is imperative to develop sustainable and applicable ways to improve animal health and productivity. The first step in doing so is understanding the mechanisms that govern health and immune response and find ways to appropriately modulate them to improve animal health and productivity. The objective of this study is to use multi-omic techniques to understand breed-specific immune responses in sheep that may contribute to their resistance and susceptibility to parasites and to a greater extent, immunocompetence. Known parasite-resistant breed, St. Croix (STC) were compared to parasite susceptible Suffolk (SUF) sheep for …

Genetics Of Mycangial Development And Host Colonization Within The Ambrosia Symbiosis, Mckeon James Laws

Graduate Theses, Dissertations, and Problem Reports (ETD)

Ambrosia beetles, a polyphyletic group of weevils, utilize pouch-like structures at various locations on the body to transport for their sole food source, their fungal partner. Ambrosia fungi are known to originate from multiple unrelated fungal lineages with no consensus of traits required to become a fungal cultivar. While the biology and ecology of both partners is in many cases well understood, the genetic underpinnings of this fascinating mutualism remain a mystery. The aim of this dissertation is to add to the understanding of the ambrosia symbiosis by providing insights into its molecular and genetic underpinnings through RNA sequencing data, …

New Fossil Mygalomorph Spiders (?Idiopidae, Pycnothelidae) From The Lower Cretaceous Crato Formation Of Brazil, Elis Maria Gomes Santana

Graduate Theses, Dissertations, and Problem Reports (ETD)

The infraorder Mygalomorphae represents one of the earliest-diverging lineages of spiders, but its fossil record remains sparse relative to the modern diversity of the group. This is a reflection of both ecological and preservational biases, such as the predominantly fossorial habits of many mygalomorphs and the strong bias of the spider fossil record toward amber deposits. Compression fossils from rock deposits are therefore especially important for documenting the evolutionary history of the group. Here, two new mygalomorph fossils from the Lower Cretaceous Crato Formation, Araripe Basin (Brazil) are described. The first specimen is tentatively referred to ?Idiopidae based on male …

The Role Of Small Extracellular Vesicles In Modulating Radiation Resistance In H3k27m-Pediatric Diffuse Midline Glioma, Viral Oza

Theses and Dissertations--Molecular and Cellular Biochemistry

Pediatric diffuse midline gliomas with H3K27M alteration (H3K27M-pDMG) are the leading cause of pediatric brain tumor-associated deaths. All H3K27M-pDMG are initially treated with fractionated radiotherapy, the standard of care, and most children succumb to their disease within two years of diagnosis. There are no universally effective chemotherapies and full resection is impossible due to the diffuse nature of the tumor and sensitive location. There has not been a significant clinical advancement in more than 40 years.

Tumors become completely resistant to radiation within the first six months of treatment. The mechanism of radiation resistance is unknown but is thought to …

Scientific Kenyon: Neuroscience Edition (Full Issue)

Scientific Kenyon: The Neuroscience Edition

No abstract provided.

Ctrl + Alt + Neuron, Stuart Hilton

Scientific Kenyon: The Neuroscience Edition

No abstract provided.

Cogram: A Computational Pipeline For Genome Assembly And Reconstruction Using Graph Neural Networks, William Coggins

College of Graduate Studies: Theses & Dissertations

Genome assembly — the reconstruction of a complete DNA sequence from short, overlapping reads — remains a fundamental challenge in computational biology. A central difficulty is distinguishing true genomic overlaps from spurious connections arising from repetitive sequences, a task that traditional assemblers address through hand-tuned heuristic rules applied to de Bruijn or overlap graphs. This thesis introduces COGRAM (Coggins–Ramasamy Assembly Method), a genome assembly pipeline that reframes sequence reconstruction as an edge classification task on a k-mer overlap graph, replacing heuristic graph cleaning with a learned model.

COGRAM constructs a directed overlap graph from raw sequencing reads using a k-mer …

Integrated Crop Management For Hemp (Cannabis Sativa L.) Grain Production In Kentucky, Maria M. Ricciardi

Theses and Dissertations--Plant and Soil Sciences

Cannabis sativa L. is legally defined (U.S.) as hemp if the total tetrahydrocannabinol (THC) concentration remains less than 0.3% on a dry weight basis. Hemp can be produced for cannabinoid extraction, fiber, or grain. Hempseed meal and hempseed oil were approved as feed ingredients for chickens and performance horses in Kentucky. To leverage this opportunity, production requires improvement through an integrated crop management approach. This dissertation (1) reports the main arthropod and disease pests impacting hemp grain; (2) identifies grain yield components and their relationship with corn earworm, Helicoverpa zea (Boddie) (CEW); (3) evaluates Fusarium head blight (FHB) development across …

The Biology Of Soulmates: Are We Wired For Connection?, Christiane Betfarhad

Scientific Kenyon: The Neuroscience Edition

No abstract provided.

Dna Barcoding Complements Citizen Science Identifications In An Arthropod Survey At Governors Island, New York, Malky Gestetner

Dissertations and Theses

Arthropods are declining worldwide, threatened by habitat loss, climate change, and growing urbanization. Efforts to monitor arthropod biodiversity are crucial for conservation policies and for maintaining the ecosystem services provided by these animals in urban environments. Surveys of arthropods have been attempted in many New York neighborhoods, but no formal assessment has been conducted on Governors Island, which harbors 72-acres of parkland within a short boat ride away from Manhattan. This is a deficiency which this study helps to address. Following student-led collection efforts within four Governors Island sites, DNA barcoding was employed to complement specimen identification based on morphology …

Signs Of Life: Interkingdom Communication And The Sympoietic Organism, Scott F. Gilbert

Biology Faculty Works

No abstract provided.

Complexity Theory And Environmental Conservation Management: A Case Study With Coyote And Red Wolf Hybridization, Gretchen E. Mahalic

Honors Undergraduate Theses

Conservation biology and invasion biology are value-led scientific disciplines founded on environmental advocacy, operating at the intersection of research and action. Though these disciplines are known for their scientific veracity, unexamined values are often promulgated without scrutiny and drive decisions that work against good ecological outcomes. A case in point is that coyotes migrating into southeastern territory are framed as the greatest threat to the conservation of the endangered red wolf because hybridization is seen as diminishing their species integrity. Applying Val Plumwood’s ecofeminist account of dualistic frameworks, I will use this case to show how the vilification of the …

Investigating The Role Of Traditional Chinese Herbal Medicine For Cancer Symptom Management In Older Adults: A Rapid Review, Isabelle C. Karshner

Honors Undergraduate Theses

Background: Patients with cancer often experience symptoms related to disease, complications, and treatment. One potential method of alleviating these symptoms is traditional Chinese herbal medications (TCHM). This rapid review explores the role of traditional Chinese herbal medications in treating cancer-related symptoms in older adults.

Purpose: The purpose of this rapid review is to gain and provide a better understanding of the effects of TCHM on cancer-symptom management in the older adult population. This review explores the association between TCHM and effects on cancer symptoms in older adults, including interactions, toxicity, and signs/symptoms of TCHM use that may be useful information …

Comorbid Psychosis In The General Population, Mariam Sankoh

Theses and Dissertations

Psychosis is a complex psychiatric phenotype characterized by substantial heterogeneity in symptom presentation, psychosis diagnosis, comorbidity patterns, and genetic architecture across diverse populations in the general population. Despite advances in psychiatric epidemiology and genomics, important gaps remain in understanding how psychosis symptoms and psychosis-related diagnoses manifest across racial and ethnic groups and how evolutionary genomic factors may contribute to disease risk and cross-ancestry genetic prediction. This dissertation, Characterizing Comorbidity in Psychosis in the General Population, integrates epidemiological, psychometric, and evolutionary genetic approaches to examine psychosis across diverse populations.

Aim 1 examined racial and ethnic differences in psychosis comorbidity patterns …

Nutritional Niche Separation Amongst Sympatric Threatened Lemurs: The Role Of Micronutrients In Food Selection And Implications For Physiological Health, Maire K. O'Malley

Graduate Research Theses & Dissertations

Madagascar’s biodiversity is heavily affected by anthropogenic change and consequently, conservation management plans need to reflect current research to protect biodiversity. Primate nutritional ecology offers valuable insights into ecology, evolution, health, habitat requirements, social behavior, and conservation management strategies. Macronutrients (fat, carbohydrates, and protein) provide consumers with energy whereas micronutrients (vitamins and minerals) are essential to metabolic processes but are frequently overlooked. This study provides a novel examination of dietary niche separation by comparing mineral consumption between three sympatric species differing in feeding strategies: 1) Grey Bamboo lemur (Hapalemur griseus), a bamboo specialist, 2) Diadema sifaka (Propithecus diadema), a folivore, …

Feasibility Of Corn Stover For Biogas Production In Northwestern Illinois: A Case Study Of Jo Daviess And Carroll Counties, Anthony Amotoe-Bondzie

Masters Theses

The growing demand for renewable energy and sustainable waste management has intensified interest in agricultural residues such as bioenergy feedstocks. This study evaluated the feasibility of converting corn stover into biogas through anaerobic digestion (AD) in Jo Daviess and Carroll Counties, Illinois, with consideration of the Savanna Industrial Park as a potential centralized processing hub. Although corn stover represents one of the largest biomass resources in the United States, this research identifies a critical gap between theoretical availability and practically recoverable feedstock. Using a mixed-methods framework, the study integrates biomass quantification, methane yield modeling, economic analysis, and policy assessment. Results …

A Marine Science Career In The Eastern Caribbean: Witnessing Four Decades Of Change, Hazel A. Oxenford

Gulf and Caribbean Research

Reflecting back on a long and rewarding career from 1980—2023 at the University of the West Indies, based on the small island of Barbados, this paper tracks the many and often remarkable changes in the marine environment, in attitudes and policies, and available opportunities that have influenced my journey as a marine scientist in an ever—changing but resilient Caribbean. From free—access fisheries to degraded stocks, from coral to algal dominated reefs, from flyingfish to Almaco Jacks, from sandy beaches and clear water to a Sargassum crisis — these are just some of the fundamental changes in the marine environment that …

Daily Rhythms In Psychosocial Stress, Sleep, And Mood: A Multimethod Approach To Transdiagnostic Psychopathology Risk And Intervention, Gabriel Gilmore

Theses and Dissertations--Psychology

Rhythms are central to nearly every core physiological and psychological process and have profound influences on overall health and well-being, particularly in the context of mood disorders. This dissertation emphasizes a rhythm-centered framework for understanding transdiagnostic psychopathology, proposing that the temporal organization of psychosocial stress, sleep, and mood provides crucial information for the development and treatment of mood disorder symptomology. Current literature relies primarily on mean symptom levels, overlooking day-to-day patterns in psychosocial experiences. To address this key methodological gap, three studies are examined. Study 1 develops and validates the Psychosocial Stress Regularity Measure (PSRM), a brief single-item measure of …

South Asian Nutrition Guide For Heart Health: A Practical Guide To Sodium, Saturated Fat, Packaged Foods, Recipes And Meal Planning, Ashwini Wagle

Open Educational Resources

South Asians, including people with ancestry from India, Pakistan, Bangladesh, Sri Lanka, Nepal, Bhutan, and the Maldives, have a higher risk of cardiovascular disease and diabetes than many other populations. They often develop heart disease at younger ages and sometimes at lower body weights. (Jose, 2024; Patel et al., 2021; Volgman et al., 2018).

This increased risk is not caused by a single factor. Evidence points to a combination of inherited, metabolic, lifestyle, and social influences. Common contributors include insulin resistance, abdominal or visceral fat, type 2 diabetes, high triglycerides, low HDL cholesterol, elevated lipoprotein(a), family history, stress, migration-related changes …

Activity-Dependent Remodeling Of Muscle Architecture During Distinct Locomotor Behaviors In Caenorhabditis Elegans, Adina Fazyl, Akash Anbu, Sabrina Kollbaum, Andres G. Vidal-Gadea

Faculty Publications – Biological Sciences

Muscle structure is dynamically shaped by mechanical use, yet how distinct locomotor behaviors influence sarcomere organization remains poorly understood. In Caenorhabditis elegans, crawling and swimming constitute discrete gaits that differ in curvature, frequency, and mechanical load, providing a tractable model for studying activity-dependent remodeling. Using confocal imaging of phalloidin-stained body-wall myocytes, we quantified myocyte geometry, sarcomere length, and sarcomere number across anterior, mid-body, and posterior regions in animals reared exclusively under crawling or swimming conditions. Quantification and hypothesis testing used linear mixed models that accounted for repeated myocyte measurements within animals, with interaction terms testing region-specific effects of locomotor …

Serum Protein Signatures For Breast Cancer Detection In Treatment-Naïve African American Women Using Integrated Proteomics And Pattern Analysis, Padma Tadi Uppala, Elmer Rivera, Hyun J. Kwon, Sharon S. Lum

Faculty Publications

Breast cancer is the leading cause of cancer-related mortality in African American (AA) women. In this study we evaluated the serum proteomic profile of AA women with breast cancer using an integrated proteomic framework with multivariate pattern analysis. Using 2D-DIGE, thousands of serum protein spots were detected across 33 gels; 46 spots met criteria for presence, statistical significance, and differential expression. Proteins from the spots were identified by MALDI-TOF/TOF and matched in curated databases, highlighting serum biomarkers including ceruloplasmin, alpha-2-macroglobulin, complement component C3 and C6, alpha-1-antitrypsin, alpha-1B-glycoprotein, alpha-2-HS-glycoprotein and haptoglobin-related protein. LC-MS/MS analysis revealed 163 differentiating peptides after imputing and …

Taxonomy, Distribution And Ecology, Biology, Nutritional Composition, And Conservation Status Of Critically Endangered Lake Chala Tilapia Oreochromis Hunteri (Günther, 1889): Implications For Aquaculture Development, Jonathan Munguti, Mavindu Muthoka, Domitila Kyule, Esther Magondu, Jacob O. Iteba, Kevin Obiero, Paul Orina, Menaga Meenakshisundaram, Tanga M. Chrysantus

All Peer-Reviewed Publications

Oreochromis hunteri Günther, 1889, commonly known as Lake Chala tilapia, is an endemic cichlid restricted to the small crater lake, Lake Chala, on the border of Kenya and Tanzania. This review synthesizes existing knowledge on the taxonomy, and phylogenetic placement, distribution and ecology, and biology including nutritional composition, and conservation status of O. hunteri and identifies knowledge gaps to assess its potential for aquaculture development. The knowledge gaps include its reproductive biology, population structure, and adaptive capacity to environmental and climatic variability. As the type species of the genus Oreochromis, O. hunteri is a unique, genetically isolated lineage within a …

From Theory To Ecosystems: Exploring Biodiversity And Ecosystem-Function In Pitcher Plant (Darlingtonia Californica) Microbial Communities, Gavin Sutter

Cal Poly Humboldt theses and projects

The relationship between biodiversity and ecosystem-function (BEF) has been a central focus of ecological research for the last three decades, yet the role of space in shaping BEF relationships remains relatively unknown. Research has shown that community diversity and composition can strongly influence productivity, nutrient cycling, and decomposition, but much of this work treats communities as spatially isolated, leaving open how dispersal and other spatial processes shape BEF at broader scales. To begin addressing this gap, I used microbial communities inhabiting Darlingtonia californica pitcher plant leaves to evaluate how spatial organization and successional change shape biodiversity and ecosystem-functioning. I quantified …

A Multi-Omic Approach For Understanding The Individual Roles Of Atf4 And Atf3 Upon Induction Of Different Branches Of The Integrated Stress Response, Elianna T. Cruz González

Electronic Theses & Dissertations (2024 - present)

The integrated stress response (ISR) is a critical cellular pathway that coordinates adaptation to various stressors, including endoplasmic reticulum (ER) stress, amino acid (AA) starvation, heme deficiency, and viral infection. Central to this pathway are the transcription factors ATF4 and its downstream target ATF3, which regulate gene expression programs that influence cell survival, metabolism, and immune responses. While previous studies have identified ATF3 as an antiviral factor during Zika virus (ZIKV) infection, the broader relationship between ATF3 and ATF4 across multiple branches of the ISR remains incompletely understood.

In this study, I employed multi-omic approaches to characterize the roles of …

The Importance Of The Proline Residue In The Ldiapa Motif Of Cholera Toxin, Akash Bharathan

Honors Undergraduate Theses

Cholera is currently on its seventh global pandemic, disproportionately affecting developing countries. Vibrio cholerae, the bacterial etiologic agent, is able to cause infection by adhering to intestinal epithelial cells and secreting cholera toxin (CT), an AB-type exotoxin that dysregulates signaling pathways. Previous research by the Teter lab has shown that Hsp90, a host cytosolic chaperone, is required for CT to enter the cytosol where it produces toxic effects. Hsp90 binds to CT at two specific motifs, RPPDEI and LDIAPA. The prolines in the RPPDEI motif are essential for binding, but the proline in the LDIAPA has yet to be …

Combating Antibiotic Resistance With Plasmid-Dependent Phages, Rhiannon T. Mariano

Electronic Theses & Dissertations (2024 - present)

The alarming rise of carbapenem-resistant bacteria poses an urgent global health threat, driven in large part by the horizontal spread of carbapenemase-encoding plasmids (Ma et al., 2023). These plasmids are often highly mobile and transmissible, enabling rapid dissemination of resistance genes across diverse bacterial populations. Their mobility is largely mediated by conjugation, a process dependent on the formation of pili, which serve as physical bridges for plasmid transfer between cells (Murray et al. 2022; San Millan and MacLean 2017; Virolle et al. 2020). Beyond their role in gene exchange, these pili also act as entry points for a unique class …

Enhancing The Recovery Of Threatened And Endangered Shorebird And Plant Species In Southampton, New York: A Structured Policy Analysis Approach, Joann Smith

Electronic Theses & Dissertations (2024 - present)

Settled on the eastern end of the most human populated island in North America, Long Island, New York, is the Town of Southampton. The Towns’ Board of Trustees are responsible for the management of federal or state listed species, which they carry out through their Threatened and Endangered Species Program (T&E program). Currently the program manages two listed shorebirds and two listed seabeach plants; the Piping plover (Charadrius melodus), a federally threatened species, and the Least Tern (Sternula antillarum), a New York State threatened species, Seabeach amaranth (Amaranthus pumilus), both federal and state threatened, and …

Bio-Orthogonal Chemistry-Based Strategy To Turn-On And Turn-Off Crispr-Cas9 Gene Editing In Solution And In Live Cells, Bhoomika Pandit

Electronic Theses & Dissertations (2024 - present)

The CRISPR–Cas9 system is a widely popular tool for genome engineering. There is a strong interest in developing tools for temporal control of CRISPR-Cas9 activity to address some of the challenges and to broaden the scope of potential applications. In this thesis I describe two biorthogonal based approaches to either Turn-ON and Turn-OFF CRISPR-Cas9 gene editing.

In first project work I describe a bio-orthogonal chemistry-based approach to Turn-ON Cas9 nuclease activity with temporal precision. We report a TCO-acylimidazole reagent that acylates 2′-OH groups of RNA. Poly-acylation (“cloaking”) of RNA was optimized in vitro using a model 18-nt oligonucleotide, as well …