Immunology and Infectious Disease Commons^™

Identification And Characterization Of Novel Immune Modulating Genes In Parkinson's Disease, Kathleen Chaundy Paul Murphy

Dartmouth College Ph.D Dissertations

Parkinson’s disease (PD) is a progressive age-related neurodegenerative disorder characterized by both motor and non-motor symptoms. The poorly understood prodromal period, decades-long progression, and disease-phenotype heterogeneity continue to impede the development of preventive and curative therapies. A growing appreciation of immune system changes during the progression of PD suggests that evaluating peripheral immune cells may help identify signatures relevant to disease etiology. We aimed to expand our understanding of the peripheral immune compartment in PD via two lines of investigation: (1) by employing single-cell RNA sequencing to profile the transcriptomes of peripheral blood mononuclear cells (PBMCs) from a cohort of …

Gene Therapy Strategies To Enhance Antifungal Immunity In Microgravity, Riley Dienna

Discovery Day - Daytona Beach

During spaceflight, the immune system of astronauts becomes impaired due to microgravity, resulting in increased susceptibility to infections caused by pathogens such as Candida albicans. One of the most common clinical treatments for aggressive candidiasis is amphotericin B, a polyene antimycotic that targeted ergosterol in the fungal cell membrane and compromised the stability of the membrane. However, due to the chemical similarities between ergosterol and cholesterol, this treatment also affects the somatic cells of patients it is administered to. A novel treatment is therefore required to combat the aggressive fungal infection while minimizing damage to the host’s cells. This project …

Bridging The Gap In Science Research: Preparing Students For College- Level Research In The Sciences, Victoria Helwig, Yaoguang Li

UConn Library Presentations

Many first-year students enter college unprepared to fully engage with scientific literature and academic library resources. Drawing on experiences from academic librarians working with STEM students, this session explores common gaps in science research skills, including navigating databases, identifying scholarly sources, and understanding the structure of scientific literature. Participants will be introduced to practical strategies and classroom-ready activities to better prepare students for college-level research. Discussion questions: What science research skills do students struggle with most when entering college? How can high school instruction better support these skills? Where can librarians and educators collaborate to support student success?

Biologically Informed Negative Samplingfor Antibody Chain Pairing Classification, Ishita Singh

Computer Science Senior Theses

Antibody heavy and light chain (H/L) pairing is fundamental to antigen recognition and stability. While single-cell sequencing preserves native pairing information, widely used bulk repertoire and spatial transcriptomics platforms do not, motivating the need for efficient ML methods to infer H/L pairing. Training a binary classifier for this task faces the methodological challenge of a lack of true biological negatives, since natural selection eliminates B cells with incompatible H/L pairs.

In this thesis, I introduce a biologically informed negative sampling strategy for H/L pairing classification, drawing on known V-gene biases in heavy and light chain pairing. Pseudo-negatives are constructed by …

From Cranes To Clinics: Genomic Epidemiology At The Human-Animal Interface, Sarah Shrum

Biology ETDs

Emerging infectious diseases represent a significant, increasing threat to human life, economic stability, and global security. The One Health framework, which promotes human health and wellness through the understanding that animal, environmental, and human health are interwoven, is critical to understanding pathogen emergence and transmission. This is underscored by the fact that roughly 60% of all human pathogens and 75% of emerging infectious disease are zoonotic, meaning they are transmitted from animals to humans.

The work presented in this dissertation integrates genomic epidemiology, ecological analysis, and One Health Surveillance approaches to characterize cross-species circulation of opportunistic yeast pathogens (Candida …

The Influence Of Prosthetic Obturators On Quality Of Life In Individuals With Maxillectomy Defects, Minseok Kim

Oral Health

Abstract

Introduction: In recent years, there has been a growing focus on understanding the impact of oral cancer on patients' quality of life. Prosthetic rehabilitation techniques, such as maxillary obturators, often in conjunction with reconstructive surgery, have emerged as interventions to address the challenges posed by post-maxillectomy abnormalities.

Objective: This study aims to systematically review and evaluate the effectiveness of maxillofacial prosthetic rehabilitation using obturators in enhancing the quality of life of patients following maxillectomy.

Methodology: Systematic review of identified literature spanning the timeframe from 2000 to 2020 was used. The comprehensive search encompassed widely recognized databases including PubMed, …

Understanding Epigenomic Landscapes In Cancer Progression And Immunotherapy Response, Jonathan Schulz

Dissertations and Theses (Open Access)

Nonmutational epigenomic reprogramming has emerged as a key hallmark of cancer that plays crucial roles in tumor evolution during its progression and response to therapy. However, the extent and nature of epigenomic reprogramming remains poorly understood. This dissertation examines how epigenetic regulation shapes cancer progression and response to immunotherapy. Working at the intersection of cancer biology and computational genomics, it develops analytical frameworks for characterizing chromatin structure and DNA methylation across diverse tumor contexts and uses these frameworks to address two complementary biological questions: how promoter-associated chromatin organization varies across cancer types, and how epigenetic perturbation modulates tumor immunogenicity in …

An Investigation Of Entamoeba Histolytica Chitin Synthases And Other Encystation Factors In Early Encystation, John N. Talledo

All Theses

Entamoeba histolytica is a food-and-water-borne human protozoan pathogen that relies on a two-stage life cycle for successful proliferation outside of the host. E. histolytica exists in its dormant cyst form while outside of its host and converts to the motile trophozoite (amoeba) form in the small intestine. The trophozoites colonize the large intestine to cause symptomatic disease in ~10% of infections, resulting in ~100 million cases of amoebic dysentery each year. Trophozoites can convert back to the cyst form, which is shed in feces to continue the infection cycle.

Currently, there is a lack of understanding of the exact molecular …

A Framework For Characterizing The Peripheral Immune Isonome Using Long-Read Single-Cell Rna Sequencing And Its Relevance To Neurological Disease, Patricia Hayes Doyle

Theses and Dissertations--Neuroscience

Long-read single-cell RNA sequencing provides an opportunity to understand human health and disease at isoform resolution, revealing cellular diversity and disease mechanisms difficult to resolve with bulk or short-read methodologies.

Using a modified PIPseq workflow and computational pipeline adapted for Oxford Nanopore (ONT) sequencing, we profiled isoform usage across immune cells, integrating marker expression and isoform discovery, generating the largest long-read single-cell dataset of human immune cells from a single individual to date. We identified non-canonical protein-coding variants of GZMB and CD3G enriched in unexpected cell types. We also discovered novel transcripts from CMC1 and LYAR with cell-type-specific signatures that …

Equid Major Histocompatibility Complex (Mhc) Evolution & Genome Organization, Lauren C. Johnson

Theses and Dissertations--Veterinary Science

The evolution of modern horses has a well-documented fossil record and has long been of interest to the genetics community. Although non-caballine equids (e.g. zebras, donkeys, and asses) can hybridize with horses, the resulting offspring are typically infertile. Despite these reproductive barriers, genomic analyses reveal regions of high sequence similarity among equid species. This dissertation investigates the role of historical introgression in the evolution of modern Equus species. The first chapter re-evaluates earlier findings derived from a limited horse population and a single reference genome. The variants of the identified regions were pushed through Ensembl’s Variant Effect Predictor to assess …

An Assessment Of Disease Risks, Population Genetics, And Spatial Ecology Of Appalachian Cottontails (Sylvilagus Obscurus) And Snowshoe Hares (Lepus Americanus) In West Virginia, Usa, Madison Leigh Miller

Graduate Theses, Dissertations, and Problem Reports (ETD)

Snowshoe hares (Lepus americanus) occupy a large range across the United States and Canada. While snowshoe hare populations are generally considered stable in the interior of their range, populations along range edges are experiencing declines, possibly driven by climate-related factors such as seasonal coat color mismatch. West Virginia represents one of the southernmost extents of the species’ range, yet little is known about the population genetic status or population sizes of snowshoe hares in the state. Appalachian cottontails (Sylvilagus obscurus) are another lagomorph species found in West Virginia. This species experienced a historical decline and currently …

Impact Of Prostate Cancer Tumor Microenvironment On Alternative Splicing Landscapes In Nk Cells: An Lncap-Based In Vitro Model, Pratham N. Modi

Honors Undergraduate Theses

NK cells play a significant role in anti-tumor activity, yet the transcriptomic mechanisms underlying NK cell dysfunction in the prostate cancer tumor microenvironment remain generally poorly characterized. While most transcriptomic studies focus on gene-level expression, alternative splicing and isoform-level analysis may reveal additional levels of regulation not identified in traditional analysis. The overall goal of this study was to characterize gene and isoform-level changes in NK cells exposed to in vitro prostate cancer conditions and to evaluate whether isoform-level analysis could provide additional depth and insights beyond gene-level analyses. NK92-MI cells were co-cultured with LNCaP prostate cancer cells using direct-contact …

Developing A Tool To Measure Resistance To Sustainable Food Choices: A Pilot Study In Ireland And The Netherlands, Kate Flanagan, Bart Sinteur, Patricia J. Bulsing, John M. Kearney

SURE Journal: Science Undergraduate Research Experience Journal

Consumer uptake of a sustainable diet is critical for addressing environmental challenges and promoting public health. Understanding why consumers resist adopting sustainable eating habits can inform targeted interventions and policies. This pilot study examines whether a newly developed scale can effectively detect consumer resistance to a sustainable diet. Currently, there is a lack of research on a tool to measure consumer resistance to a sustainable diet, highlighting the need for a reliable instrument.

The aim of this study is to develop a scale, based on existing literature, to measure consumer resistance to a sustainable diet. Additionally, the study aims to …

Editorial-Sure Journal Volume 7, Issue 2, Geraldine M. Dowling, Eva Campion, Sinead Loughran, Ariane Perez-Gavilan, Josephine Treacy

SURE Journal: Science Undergraduate Research Experience Journal

No abstract provided.

Losing Focus In The Age Of Tik Tok: Clinical Evidence For Policy Action On Social Media Use, Megan Conefrey, Robert Griffin

SURE Journal: Science Undergraduate Research Experience Journal

No abstract provided.

Tracking Livestock Heart Rate & Location Using Long-Range Radio Networks. An Immediate Solution For Farms Without Reliable Wi-Fi, Dermott Harkin, Martin Bradley

SURE Journal: Science Undergraduate Research Experience Journal

No abstract provided.

Voices Matter: Tackling Accentism In Ireland. A Study Addressing Accent-Based Discrimination Awareness In Education, Sadhbh Reddington, Victoria Graham, Holly Jordan, Mairead Moriarty

SURE Journal: Science Undergraduate Research Experience Journal

No abstract provided.

Supporting Single Parents: How Loneliness And Self-Stigma Can Impact Single Parents And Their Quality Of Life, Alana Powell, David Mothersill

SURE Journal: Science Undergraduate Research Experience Journal

No abstract provided.

Income Inequality And Attitudes Towards Immigrants – How Increased Inequality Drives Division, Niamh Anderson, Vincent O'Sullivan

SURE Journal: Science Undergraduate Research Experience Journal

No abstract provided.

Ireland Blossoms Through Multiculturalism - Designing For Community Connection, Julia Kuczera, Shirley Casey, Hilary Kenna

SURE Journal: Science Undergraduate Research Experience Journal

No abstract provided.

Unheard And Underserved: Exploring Support For Male Victims Of Partner Abuse, Michael Keenan, Colletta Dalikeni

SURE Journal: Science Undergraduate Research Experience Journal

No abstract provided.

Assessing Demand And Simulating Feasibility For Commuter Rail In Lagging Regional Areas. Case Study: Sligo, Holly Briere-Edney, Brian Mccann

SURE Journal: Science Undergraduate Research Experience Journal

No abstract provided.

Ireland's Infrastructure: From Delays To Deliveries!, Conor Barnett, Keren Goodman

SURE Journal: Science Undergraduate Research Experience Journal

No abstract provided.

A Fast-Track Way To Identify Derelict And Vacant Homes For Refurbishment, Dylan O'Donnell, Enda Dunican

SURE Journal: Science Undergraduate Research Experience Journal

No abstract provided.

Making Buildings Smarter And More Sustainable With Ai, Anthony Lowe, Martin Klepal

SURE Journal: Science Undergraduate Research Experience Journal

No abstract provided.

Solving The Bed Crisis - Predicting 30-Day Hospital Readmissions In Elderly Patients Using Ai, Mark Mckeon, Thoa Pham

SURE Journal: Science Undergraduate Research Experience Journal

No abstract provided.

The Impact Of Chronic Pain On Income And Employment, Jordan Vaarsi, Amber Jolly, Karim S. Ladha

SURE Journal: Science Undergraduate Research Experience Journal

No abstract provided.

Living The Life: A Community Approach To Men’S Health And Longevity, Paul Anders, Aisling Mcgrath

SURE Journal: Science Undergraduate Research Experience Journal

No abstract provided.

When Care Can’T Move Forward – The Human And Social Cost Of Freezing Of Gait In Parkinson’S Disease, Padraig Cronin, Lucy M. Collins, Aideen M. Sullivan

SURE Journal: Science Undergraduate Research Experience Journal

No abstract provided.

Life Under Pressure: How Doubling The Genome Affects The Memory Of Environmental Stress In Worms, Aisling Phelan, Emma Bazzani, Clément Verdier, Laetitia Chauve, Aoife Mclysaght

SURE Journal: Science Undergraduate Research Experience Journal

No abstract provided.