Genetics and Genomics Commons^™

Integrative Rna-Seq Analysis Reveals Stress Type-Dependent Lncrna-Centered Co-Expression Networks Across Human Cellular Stress Contexts, Christina Anastasiadi, Aggeliki Kasapi, Ioannis Sentementes, Vasileios Gouzouasis, Margaritis Tsifintaris, Antonis Giannakakis

Computational Medicine Center Faculty Papers

Long non-coding RNAs (lncRNAs) are emerging as important regulators of cellular adaptation to environmental and molecular stress, but the extent to which their responses remain reproducible and stress-type-dependent across human stress conditions remains unclear. Here, we performed an integrative transcriptomic meta-analysis of human stress-response datasets from ASTRA and GEO, focusing on normal, non-cancerous, wild-type human cell lines exposed to oxidative stress (H2O2), hypoxia, heat stress, or UV-induced DNA damage. Gene Ontology (GO) enrichment analysis of differentially expressed (DE) protein-coding mRNAs confirmed that the resulting stress-stratified comparison captured biologically coherent transcriptional programmes to oxidative stress signaling, hypoxic and metabolic adaptation, heat-induced …

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 …

Transcriptomic Profiling Of The Donkey Endometrium Reveals Dynamic Molecular Transitions Across The Estrous Cycle, Limeng Shi, Shuaishuai Wu, Mingyue Zhao, Wenhao Zhou, Abd Ullah, Muhammmad F. Akhtar, Changfa Wang, Muhammad Z. Khan, Ying Han

The Thai Journal of Veterinary Medicine

The endometrium undergoes extensive cyclical remodeling essential for reproductive success; however, the molecular mechanisms governing these processes in donkeys (Equus asinus) remain poorly characterized. To address this gap, we performed high-throughput RNA sequencing on endometrial tissues collected from Dezhou donkeys (n = 16) at four post-ovulation stages: Day 0 (ovulation), Day 3 (early luteal), Day 7 (mid-luteal), and Day 18 (late luteal/pre-luteolysis). Differential gene expression analysis, Gene Ontology enrichment, and KEGG pathway mapping were conducted to characterize temporal transcriptomic dynamics. We identified 2,474, 6,548, and 1,288 differentially expressed genes in Day 0 versus Day 3, Day 0 versus …

Fraction-Seq: An Integrated Experimental And Computational Workflow For Determining The Localization And Abundance Of Small Non-Coding Rnas In Subcellular Compartments, Siddhartha Shah, Tess Cherlin, Yi Jing, Stepan Nersisyan, Benjamin E. Leiby, Isidore Rigoutsos

Computational Medicine Center Faculty Papers

Small non-coding RNAs (sncRNAs) have garnered considerable attention in recent years, following accumulating evidence of their critical roles in many cellular processes. Among sncRNAs, microRNAs (miRNAs) and their isoforms (isomiRs), tRNA-derived fragments (tRFs), rRNA-derived fragments (rRFs), and Y RNA-derived fragments (yRFs) account for more than 95% of all sncRNAs found in cells. Despite their critical regulatory roles, most sncRNAs remain uncharacterized because their functionalization is a lengthy and challenging undertaking. Knowing an sncRNA's abundance helps prioritize among the various choices, while knowing where it localizes in the cell greatly limits the number and identity of its potential targets and helps …

Assessing Gene Expression Changes In The Octocoral Briareum Asbestinum Due To Vibrio Coralliilyticus Exposure, Hailey Poignant

All HCAS Student Capstones, Theses, and Dissertations

Coral reefs are an essential ecosystem home to tons of marine diversity that humans have also  learned to rely on, but they are harmed by climate change and the increasing prevalence of disease. While most studies focus on reef-building coral, octocorals also warrant attention to reveal how they respond to similar stressors. Octocorals share distant ancestry with reef-building corals, so there may be overlap in their immune responses which could provide insight into future restoration projects. To understand how octocorals respond to disease, the octocoral Briareum asbestinum was used as a model to examine gene expression changes caused by the …

From Genes To Streams: Mitochondrial Approaches To Population Monitoring Of The Santa Ana Sucker Catostomus Santaanae, Mariana Antonio

Electronic Theses, Projects, and Dissertations

This study was developed to use aquatic environmental DNA (eDNA) as a tool to detect the presence of the Santa Ana sucker (Catostomus santaanae), a federally threatened fish species, across the Santa Ana River in Southern California. Environmental DNA is any genetic material that an organism sheds into the environment. We can get an idea of what aquatic species are present when sampling water at a given site. We sequenced the complete mitochondrial genome (mitogenome) of the Santa Ana sucker and designed custom DNA primers to improve eDNA detection accuracy. These primers were selected based on high genetic …

Engagement Of Understudied Populations As Community Change: The South Texas Adrc Model, Gladys E. Maestre, Neela K. Patel, Rosa V. Pirela, Robin C. Hilsabeck, Kendra Stine, Neyra García, Roberto Reyes, Omar Oropeza, Cristian Maestre, Jesus D. Melgarejo, Sarah Williams-Blangero, Ney Alliey Rodriguez, Sylvia A. Robles

School of Medicine Publications

Many populations experiencing the highest burdens of Alzheimer's disease and related dementias remain understudied, in part because traditional recruitment and retention models are insufficient to support sustained engagement. The Outreach, Recruitment, and Engagement Core (OREC) of the South Texas Alzheimer's Disease Research Center reconceptualized participant recruitment as a long-term system change in a Hispanic-majority, urban–rural region. OREC institutionalizes shared power through community advisory governance, aligns research protocols with local lived realities (through patient navigators, community health workers/promotores, and decentralized access points), and employs a data-driven feedback loop for continuous improvement. In 1 year, 46 outreach events touched 10,134 individuals (71% …

A Genetic Analysis Of The Rare Endemic Astragalus Ripleyi Barneby, Juan Antonio Jaramillo-Chico

Master's Theses

Astragalus ripleyi Barneby is a rare endemic species found in the San Luis Valley of the southern portions of the Rocky Mountains in Colorado and New Mexico. Though not federally listed as endangered, the species is on the Bureau of Land Management’s Sensitive Species List, warranting protection and continued management. This study aims to provide information about the genetic health of the species to inform conservation efforts and provide updated management recommendations. A genetic health analysis was conducted investigating the levels of diversity present in the species, how genetic diversity is structured across the known range of the species and …

Towards Improved Stress Resilience, Optimal Growth And Enhanced Biosafety In Transgenic Plants, Xiaotong Chen

All Dissertations

This dissertation investigates biotechnology strategies to improve plant stress resilience, growth, and biosafety in transgenic perennial grasses using creeping bentgrass as a model system. Functional analyses of non-coding RNAs such as miR164 and miR169 showed that regulatory non-coding RNAs influence plant architecture and abiotic stress responses through broad developmental and transcriptional networks, supporting them as valuable engineering targets for complex trait improvement. The dissertation also developed a dual recombinase platform for transgene containment and removal, linking trait engineering with biosafety control. Additionally, the recombinases themselves were examined for their potential impact on heterologous host and were found to reshape plant …

The Past, Present, And Future Of Climate Adaptation In A Widespread Lizard Species, Matthew R. Mcternan

All Dissertations

Climate, as a selective force, shapes patterns of biodiversity globally. However, how species adapt to climate remains a central question of biology. The need to understand climate adaptation is paramount, as global climate change threatens a large portion of global diversity. Climate can impose selection on life by either controlling rates of energy intake and expenditure through effects on body temperature and activity, or by exposing organisms to conditions beyond their physiological limits. Studies of climate adaptation have identified a wide-range of putatively adaptive phenotypic patterns, but genomic evidence is increasingly being used to investigate these patterns and better understand …

Prenatal Acoustic Programming Of The Developing Hypothalamus: A Multi-Omic Analysis Of Heat Call Exposure In Zebra Finch Embryos, Prakrit Subba

All Dissertations

Climate change is intensifying thermal stress on wildlife globally, yet the developmental mechanisms by which embryos use prenatal cues to adjust to predicted environments remain unclear. In Australian zebra finches (Taeniopygia guttata), incubating parents produce distinctive heat call vocalizations at high ambient temperatures, and embryos exposed to these calls during late incubation develop altered growth trajectories, thermoregulatory capacity, and reproductive outcomes, suggesting a form of anticipatory developmental programming triggered by sound alone. To investigate the molecular basis of this response, I initially hypothesized that prenatal heat call exposure would act primarily through hypothalamic neuroendocrine reprogramming, given the central …

Transcriptional Regulation In The Uterine Luminal Epithelium, Evelyn A. Carrion

Dissertations and Theses (Open Access)

Transcriptional Regulation in the Uterine Luminal Epithelium

Evelyn A. Carrion

Advisor: Richard R. Behringer, PhD

Abstract

The uterus is an organ comprised of multiple tissues that are essential for women’s health and reproduction. The uterus is composed of multiple tissue layers, including the perimetrium, myometrium, and the endometrium. The endometrium is the inner lining of the uterus, and contains the luminal epithelium, glandular epithelium, and stroma. The luminal epithelium is a simple columnar layer of cells that is necessary for embryo implantation. The uterus is derived in part from the embryonic precursor tissue called the Müllerian duct. There are no …

Regulation Of Müllerian Duct Mesenchyme Transcription During Mammalian Sex Differentiation, Haowen Li, Richard R Behringer, Rachel D Mullen

Dissertations and Theses (Open Access)

Sp7/Osterix (Osx) encodes a zinc-finger transcription factor of the Specificity-protein family discovered by Nakashima et al. at the MD Anderson Cancer Center. While primarily recognized for its role in osteogenesis, Osx has also been implicated in mammalian reproductive development, particularly in male sex differentiation, where Müllerian Duct (MD) regression occurs, mediated by anti-Müllerian hormone (AMH) signaling. AMH-induced regression signals are transduced by the mesenchymal tissue surrounding the ductal structure, known as the Müllerian Duct mesenchyme (MDM). It was discovered that AMH signaling is necessary and sufficient for driving Osx expression in MDM. A previous transgenic mouse reporter …

Mutational Analysis Of Domain Functions In The Yeast Decapping Enzyme Dcp2, Jellisa Ewan, Ambro Van Hoof

Dissertations and Theses (Open Access)

In yeast, the major mRNA decay pathway involves deadenylation of the 3’ poly-A tail, followed by decapping of the 5’ m7Gppp cap and subsequent 5’ to 3’ degradation or 3’ to 5’ degradation. This is carried out by Pan2/Pan3 and Ccr4/Not deadenylases, the decapping enzyme Dcp2, and Xrn1 and  RNA exosome exoribonucleases, respectively. The eukaryotic mRNA decapping enzyme complex, Dcp1/Dcp2, is essential in yeast, and deletion of either gene is lethal. However, the deadenylases that act upstream and the 5’ exoribonuclease that act downstream of the decapping step are not, even though they are all highly conserved with no known …

Shared And Distinct Alterations In Brain Structure Of Youth With Internalizing Or Externalizing Disorders: Findings From The Enigma Antisocial Behavior, Adhd, Major Depressive Disorder, And Anxiety Working Groups, Sophie Townend, Marlene Staginnus, Yidian Gao, Nina Alexander, Volker Arolt, Tobias Banaschewski, Katja Beesdo-Baum, Mark A. Bellgrove, Vivek Benegal, Anderson M. Winkler

Human Genetics Publications

Background: Externalizing and internalizing disorders are common in youth but are often studied separately, preventing researchers from identifying shared (i.e., transdiagnostic) alterations in brain structure. Using data from the ENIGMA (Enhancing NeuroImaging Genetics through Meta-Analysis) Consortium, we conducted a mega-analysis to identify shared and distinct cortical and subcortical brain alterations across internalizing (anxiety disorders and depression) and externalizing (attention-deficit/hyperactivity disorder [ADHD] and conduct disorder [CD]) disorders in youth.

Methods: 3D T1-weighted magnetic resonance imaging data from youths (age range 4-21 years) with anxiety disorders (n = 1044), depression (n = 504), ADHD (n = 1317), and CD (n = 1172) …

Associations Of Polygenic Risk Scores For Type 2 Diabetes With Metabolic Measures In Pacific Islanders From Guam And Saipan, Maria J. Ramirez-Luzuriaga, Saied Safabakhsh, Rasol Salehi, Sayuko Kobes, Tanisha F. Aflague, Jenny Duenas Sarmiento, Joanne Curran, Robert G. Nelson, Jeffrey M. Curtis, Carol D. Moffett

Human Genetics Publications

Several polygenic risk scores (PRSs) for type 2 diabetes (T2D) have been derived from genome-wide association studies (GWASs), but Pacific populations have generally not been represented in these GWASs. The aim of this study was to examine the association of PRS for T2D with diabetes and clinical measures in Pacific Islander populations from Guam and Saipan. We analyzed seven constructions of PRSs in 1990 participants in a GWAS from a community-based cross-sectional study of diabetes. Associations of T2D PRS with diabetes, maximum body mass index (BMI), fasting glucose, and HbA1c were examined with adjustment for age, sex, and the first …

Computational And Ai Tools For Understanding Telomere-Associated Cancer Mechanisms, Eleni Adam

Computer Science Theses & Dissertations

Telomeres are the protective caps of the human chromosomes and are critical for genome stability. Dysfunctional telomeres caused by their erosion with age and cell proliferation as well as by defects in their maintenance is a major early event leading to genome changes and cancer. Subtelomeres possess the critical role of regulating adjacent telomeres. Due to their complex repeat structure and high variance from one person to another, these areas have not been analyzed in detail. We present a set of computational and machine learning tools to aid in the understanding of subtelomere structure and its rearrangements in cancer.

Initially, …

Validating The Expression Of Genes Potentially Involved In The Development Of Aggressive Melanoma Tumor In The Zebrafish Melanoma Model, Mayra Matos Diaz

Theses, Dissertations and Culminating Projects

Melanoma is an aggressive form of skin cancer characterized by rapid progression, metastatic potential, and the frequent development of resistance to targeted therapies. Although the Inducible cAMP Early Repressor (ICER) has been identified as a potential tumor suppressor in melanoma, the molecular mechanisms underlying its role in tumor progression remain poorly understood. Building upon the transcriptomic findings of Wheelan et al. (2025), this study investigates the relationship between ICER and ten candidate genes (gdf6a, pdgfra, col4a4, fgfr2, pdgfrb, cdkn1a, fgf5, akt1, met, and notch3) associated with BMP signaling. Quantitative polymerase chain reaction (qPCR) was used to compare gene expression between …

Long-Term Spatiotemporal Change In Coral Reef Fish Populations And Communities In The Philippines, John Christopher Whalen

Biological Sciences Theses & Dissertations

The Visayas Region of the Philippines is a global epicenter of marine fish biodiversity. Hypotheses attribute this peak of species richness within the Coral Triangle to processes that occur at geological time scales. However, changes in biodiversity may occur on ecological time scales, allowing for the assessment of the potential impact of anthropogenic activities. Recent declines in genetic, species, and ecosystem diversity have been observed in the tropics, including the Philippines. Within the Philippines the Visayas Region is considered the epicenter of species adversity due to anthropogenic stressors such as habitat degradation, overfishing, and harvesting individuals for the aquarium trade. …

The Impact Of Hypoxia And Androgen Inhibition On Prostate Cancer Cell Dedifferentiation And The Dna Damage Repair Response At Telomeres, Arooba Ayaz

Biomedical Sciences Theses & Dissertations

Long-term Androgen deprivation therapy (ADT) is used to treat Prostate cancer (PCa) but is often met with resistance & the development of Neuroendocrine (NE) PCa which is rarer but more aggressive. Antiandrogens are a part of ADT that work to inhibit androgen receptor in PCa cells. In vitro, PCa cells under long-term antiandrogen treatment become NE-like and adopt stem-like characteristics. The disruption of androgen signaling though the use of antiandrogens impacts many cellular processes that play a major role in cancer cell proliferation such as the DNA damage repair response (DDR) and telomere dysfunction. In vivo, PCa tumors have disorganized …