Life Sciences Commons^™

Computational And Ai Frameworks For Identifying Key Regulatory Genes And Their Target Genes In Plants And Humans, Md Khairul Islam

Dissertations, Master's Theses and Master's Reports

This dissertation presents computational and AI-driven frameworks for identifying key regulatory genes and their downstream targets across plant and human biological systems. Three studies address distinct challenges in genomic regulation using advanced machine learning and bioinformatics approaches.

The first study introduces DyGAF (Dynamic Gene Attention Focus), a dual-attention transformer framework that identifies and ranks disease-relevant biomarker genes by simultaneously modeling independent molecular responses and interdependent regulatory network behavior. Two attention models provide complementary perspectives on gene importance and are fused through a novel combination metric. Applied to COVID-19 nasopharyngeal swab profiles, the attention-weighted representations achieved 94.23% classification accuracy, high sensitivity, …

Targeted And Screening Based Approaches To Analyze Drm Transcriptional Repressor Complex Activity In Caenorhabditis Elegans, Emily Washeleski

Dissertations, Master's Theses and Master's Reports

The molecular machinery that control the eukaryotic cell cycle, specifically the processes that mediate the switch between cellular division or quiescence, are essential for cellular and organismal viability. However, how the same machinery integrates with developmental or differentiation programs is less well understood. In Caenorhabditis elegans, the 8-subunit DRM complex (for Dp, Rb and MuvB), whose subunits belong to the Synthetic Mulitivulva (SynMuv) B class genes, is a central regulator of the cell cycle but also prevents inappropriate cell fate specification. The conserved mammalian DREAM complex (for Dp, Rb, E2F, And MuvB) is best known as a transcriptional repressor …

The Forensic Implications Of Hydrochloric Acid (Hcl) Exposure On Dna Preservation In Human Teeth, Shaelyn Lee Zimmerman

Graduate Student Theses, Dissertations, & Professional Papers

Identity is a human right, and forensic anthropological methods are often aimed at returning identity to decedents. Three main pathways are used for the identification of human remains: fingerprints, dental records, and DNA analysis. Identification efforts may be hindered when perpetrators attempt to obscure the victim’s identity. In cases where corrosive substances, such as hydrochloric acid (HCl) are used, dental comparison and fingerprinting often fail and genetic analysis becomes the best chance of achieving personal identification.

Previous studies have shown teeth are an excellent source of DNA. Large, multi-rooted teeth, such as molars, are often preferred because they contain the …

Metabolic Syndrome Beyond Diagnostic Criteria: Population-Scale Integrative Metabolomics Characterization, Marwa Talal

Theses and Dissertations

Background: Metabolic syndrome (MetS) is a complex cluster of interrelated metabolic abnormalities associated with elevated cardiometabolic risk. While diagnosis is based on well-established five clinical criteria, these may overlook early or atypical metabolic alterations. Large-scale metabolomic profiling offers an opportunity to identify biochemical signatures of MetS beyond diagnostic bias and to evaluate their relative importance across different presentations of the syndrome.

Methods: Data from 117,147 UK Biobank participants were analyzed in a cross-sectional design. High-throughput NMR quantified 75 circulating metabolites, for. Univariate analyses, MetS subtype stratification, and elastic net models with SHAP interpretation were applied to assess feature …

The Disruption Of Gastrointestinal Hormonal Control Of Digestion In Nile Tilapia By Omeprazole, Rema Abutaha

Theses and Dissertations (Comprehensive)

Stomach acidity is a critical feature of the digestive system, facilitating the breakdown of protein through the activation of the protease pepsin. Gastric acid is secreted by H⁺/K⁺ ATPase, the gastric proton pump. A previous study on Nile tilapia (Oreochromis niloticus) showed that inhibiting the production of stomach acid using the proton pump inhibitor omeprazole (omz), reduced growth that correlated with an acceleration of the rate of gastric emptying. This contrasts with omz exposure studies in mammals in which there is a delay in gastric emptying and no impact on growth. To understand the mechanism …

Acute Fatty Liver Of Pregnancy And Fetal Fatty Acid Oxidation Disorders: A Systematic Review, Dante Varotsis, Sarah Araji, Rebecca Horgan, Jennifer E. Powel, Rodney Mclaren Jr., Brian Kirmse, Mona Makhamreh, Huda B. Al-Kouatly

Department of Obstetrics & Gynecology Faculty Publications

OBJECTIVE:

To evaluate the association between maternal acute fatty liver of pregnancy (AFLP) and fetal fatty acid oxidation (FAO) disorders and to define the clinical and genetic characteristics of mothers with AFLP and their fetuses affected by FAO disorders, we performed a systematic literature review of all reported cases of AFLP that underwent genetic testing for FAO disorders.

DATA SOURCES:

We searched PubMed, Ovid MEDLINE, Cochrane Library, CINAHL (EBSCO), Scopus, and ClinicalTrials.gov. Terms included were related to AFLP and FAO testing.

METHODS OF STUDY SELECTION:

We conducted a systematic literature review from inception through May 18, 2025, to evaluate the …

Effects Of Volatile Organic Compounds Produced By Temperature-Adapted Microbes On Duckweed Growth, Phaedra Yael Stemp

Honors Theses and Capstones

As host-associated microbes adapt to their abiotic environment, these adaptations can affect their host species as well. Previous research showed that varying temperatures and volatile organic compound (VOC) production can affect microbial benefits to hosts. This experiment analyzed how 27 microbes pre-adapted to different temperature conditions affected growth of their host, common duckweed plants, comparing effects of direct contact with microbes, effects of microbe VOCs alone, or both. Each microbe was pre-adapted to one of three temperature regimes: “Northern” at 28 °C, “Southern” at 33 °C, and “Extreme” at 36 °C. We then grew duckweeds in I-plates with each microbe …

Mitochondrial Disorders Should Be Considered As A Differential Diagnosis Of Thiamine Deficiency, Josef Finsterer

HCA Healthcare Journal of Medicine

This letter to the editor addresses limitations to diagnosing thiamine deficiency for multisystem disorders and discusses the potential differential diagnoses that must be considered.

Esat-6 And Cfp-10 Reactive Igg In Patients With Tuberculosis Inhibits Intracellular Bacteria, Joshua R. Miles, Pei Lu, Shuangyi Bai, Genesis P. Aguillón-Durán, Javier E. Rodríguez-Herrera, Bronwyn M. Gunn, Blanca I. Restrepo, Lenette L. Lu

School of Medicine Publications

Perspectives beyond the CD4 T cell interferon (IFN)-γ paradigm are needed to understand immunity in tuberculosis (TB). Growing data in patients across a spectrum of TB highlight that changes in antibody Fc domain glycosylation and Fc effector functions correlate with disease and impact Mycobacterium tuberculosis (Mtb) infection. How antigen-specific antibodies within polyclonal responses affect bacteria is less clear. This study examines antibodies targeting ESAT-6 and CFP-10, Mtb virulence proteins essential for pathogenesis. Data from patients with TB show that polyclonal immunoglobulin (Ig)G reactive to ESAT-6 and CFP-10 diverges from other Mtb and non-Mtb antigens with enhanced sialylation, …

A Tissue Renewal-Based Mechanism Drives Colon Tumorigenesis, Ryan M. Boman, Gilberto Schleiniger, Christopher Raymond, Juan P. Palazzo, Anne Shehab, Bruce M. Boman

Department of Pathology, Anatomy, and Cell Biology Faculty Papers

Our Goal is to identify how colorectal cancer (CRC) arises in the single-layered cell epithelium (simple columnar epithelium) that lines the luminal surface of the large intestine. Background: We recently reported that the dynamic organization of cells in colonic epithelium is encoded by five biological rules and conjectured that colon tumorigenesis involves an autocatalytic tissue renewal reaction. Introduction Our objective was to define how altered crypt turnover explains tissue disorganization that leads to adenoma morphogenesis and CRC. Hypothesis: Changes in rate of tissue renewal-based cell polymerization leads to epithelial expansion and tissue disorganization during adenoma histogenesis. Methods: Accordingly, we created …

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.

A Genetic Interaction Between Ded1 And Hat1 In Saccharomyces Cerevisiae Reveals A Role For Hat1p In Cytoplasmic Rna Granule Accumulation, Audrey J. Panko, Aidan Winters, Nicholas R. Rothbard, Angela K. Hilliker

Biology Faculty Publications

Ded1p is an essential translation initiation factor that interacts with and is modulated by eIF4F. Ded1p also promotes the assembly and disassembly of stress granules, which contain nontranslating mRNAs and translation initiation factors. As Ded1p affects both mRNA storage and translation initiation, regulation of Ded1p's function may affect whether mRNAs are translated or localized to cytoplasmic RNA granules. To identify regulators of Ded1p in Saccharomyces cerevisiae, we screened for overexpression suppressors of the severe growth defect conferred by high levels of Ded1p. We found that overexpression of HAT1, a lysine acetyltransferase, can suppress the growth defect conferred by …

Development Of Self-Assembled Polymeric Polyplexes For Microrna Delivery: Toward Treatment Of Alcohol-Associated Liver Disease, Marjina Akter Kalpana

Theses & Dissertations

Self-assembled polymeric polyplexes have the potential to serve as an RNA interference (RNAi) delivery platform for the combined inhibition of CXCR4 and miR-155 in the treatment of alcohol-associated liver disease (AALD). A central challenge in RNA delivery is balancing the extracellular stability of polyplexes, cellular uptake, and intracellular release of RNA cargo. We developed polymeric polyplexes using the CXCR4-antagonist polymer PAMD, designed to target CXCR4 on activated hepatic stellate cells (HSCs) and deliver therapeutic miRNA to activated Kupffer cells (KCs) in fibrotic liver. We improved the polyplexes by cholesterol modification of PAMD and by PEGylation of PAMD-Ch. The cholesterol modification …

Mechanistic Insight Of Neuropilin-2 Expression During The Progression Of Prostate Cancer, Sanika Bodas

Theses & Dissertations

Advanced prostate cancer represents a particularly aggressive and challenging form of prostate cancer (PCa) that shows resistance to both traditional therapies, such as androgen deprivation therapy, and newer treatment modalities like hormone therapies and immunotherapies. For patients diagnosed with advanced stages of PCa, treatment options are limited, and chemotherapy is often the last line of defense. Unfortunately, chemotherapy can severely diminish the quality of life, particularly in older patients, due to its harsh side effects, including fatigue, immune suppression, and overall physical decline. Despite these challenges, researchers and clinicians remain focused on developing more effective and targeted treatments for patients …

Regulation Of Chromatin Remodeling By The Post-Hsa Domain Of Brg1, A Subunit The Baf Atp-Dependent Chromatin Remodeling Complex, Min Sze Ewe

Theses & Dissertations

The ATP-dependent chromatin remodeler BAF complex regulates nucleosome positioning, chromatin accessibility, and tissue specific gene expression. Its catalytic subunit, BRG1, contains several regulatory domains including the post-HSA region, proposed to modulate ATPase activity. Multiple cancer-associated mutations map to these regulatory regions underscoring their importance, yet the precise role of the post-HSA region in chromatin remodeling remains poorly understood.

To investigate the function of the post-HSA domain, we ectopically expressed FLAG-tagged BRG1 with post-HSA deletion (Δpost-HSA BRG1) in mouse embryonic stem cells. Western blot analysis confirmed expression of the mutant protein. To determine the effects of mutant protein expression on chromatin …

Function Of Drosophila Melanogaster Domesticated Transposable Element Protein Dplg3 In Oogenesis And Total Fitness, Aron Herrera

2025 Fall Honors Capstones Projects - Archive

Transposable elements (TEs) are selfish DNA segments capable of self-replication and reinsertion within genomes, often harming hosts. Rarely, host genomes can adopt TEs and use their proteins for new cellular functions through molecular domestication. One example primarily expressed in Drosophila melanogaster ovaries is DPLG3. Previous Betrán Lab students generated DPLG3 loss-of-function flies and found that their ovaries misregulated one primordial and 14 testis-specific genes, leading to variable ovarian malformations. However, it is unclear when during oogenesis these misexpressions occur. We will extract RNA from non-rudimentary ovaries at early and late stages to generate cDNA for qRT-PCR analysis of three …

Capillary Electrophoresis Vs Massively Parallel Sequencing: A Cost-Benefit Analysis, Samia Williams

Honors Projects

Massively Parallel Sequencing (MPS) is a new Forensic Science field allowing multiple samples to be sequenced simultaneously. In contrast to CE, multiple types of genetic markers including those from different nucleic acids can be used in the same assay. Additionally, MPS has opened the doors to certain fields of Forensic DNA Analysis like Forensic Investigative Genetic Genealogy and Forensic Phenotyping assays containing upwards of 100 SNPs. While quite expensive and requiring a high cost for initiating, MPS has the potential to save time and greatly increase the throughput of Forensic DNA Analysis in crime labs.

Edna Surveys For The Critically Endangered Caribbean Staghorn Coral, Acropora Cervicornis (Lamarck, 1816), Pari Elaine Cribbins

All HCAS Student Capstones, Theses, and Dissertations

Historically, Acropora cervicornis was a dominant coral on Caribbean reef systems, but an outbreak of white band disease in the late 1970s marked the beginning of devastating, multi-decadal population declines that led to the coral being listed as “critically endangered” on the IUCN Red List in 2022. Today, after a record-setting marine heat wave in 2023 triggered a mass bleaching event on Florida’s Coral Reef (FCR), A. cervicornis is considered functionally extinct on the FCR. While individuals of A. cervicornis do remain on the FCR, the small population size of the coral makes in situ surveys difficult. However, surveys using …

A Persistent Homology Framework For Scrna-Seq: Assessing Clustering Robustness And Quantifying Preprocessing And Integration Effects On Topological Features., Jonah Daneshmand

Electronic Theses and Dissertations

As single-cell RNA sequencing (scRNA-seq) data expands, robust methods for integrating diverse datasets are critical. This dissertation applies Persistent Homology (PH), a technique from Topological Data Analysis (TDA), to a collection of scRNA-seq datasets spanning eight tissue types to quantify how data integration affects topological features and biological interpretability. We assessed global topological structure using Betti curves, Euler characteristics, and persistence landscapes across raw, normalized, and integrated data representations. Our analysis revealed a performance inversion: while conventional methods excelled on unintegrated data, high-granularity topological methods, particularly those sensitive to global data structure, became superior after integration. This suggests a synergy …

Neural Rrp6 Depletion Drives Circrna Accumulation And Motor Impairment In Drosophila Melanogaster Neurons, Joseph Serio

Honors Theses

Circular RNAs (circRNAs) are a class of ubiquitous eukaryotic RNAs created by back splicing. These noncoding RNAs can modulate gene expression and are implicated in aging and neurodegenerative diseases. To limit the contribution of circRNAs to aging and pathobiology, it is essential to understand how turnover of these molecules is regulated, as it is not clear which enzymes are chiefly responsible for degrading circRNAs in neurons. This study evaluates the roles of ribonucleases potentially involved in neural circRNA turnover using the model fly Drosophila melanogaster. A mifepristone-activated GAL4/UAS GeneSwitch expressed RNAi transgenes and inactivated the ribonucleases. Flies were evaluated on …

Striatal Compartment And White Matter Alterations In Focal Dystonia Subtypes: An Mri Study, Artur José Marques Paulo, Jeff L. Waugh, Anderson M. Winkler, Joselisa Peres Queiroz De Paiva, Danilo Donizete De Faria, Vanderci Borges, Sonia De Azevedo Silva, Henrique Ballalai De Ferraz, Patricia De Carvalho Aguiar

Human Genetics Publications

Introduction: Dystonia is a movement disorder marked by involuntary muscle contractions that cause abnormal postures or repetitive movements. The striatum plays a key role in motor control and is central to dystonia pathophysiology. Recent advances in diffusion MRI enable in vivo parcellation of the striatum into matrix- and striosome-like compartments, associated with sensorimotor and limbic functions. We aimed to assess structural brain differences between focal dystonia patients and healthy controls (HC) using T1-weighted and diffusion MRI, and to explore subtype-specific alterations in striatal compartments.

Methods: We analyzed 3T MRI data from 91 participants: 29 with upper limb dystonia (ULD), 25 …

The Genetic And Environmental Determinants Of Stress Resilience Across Model Systems, Carson Len Stacy

Graduate Theses and Dissertations

Survival in fluctuating environments demands that organisms effectively anticipate and respond to future challenges. This capacity is shaped by both genetic background and environmental context. In this dissertation, I apply a population aware lens to explore how genetic diversity and environmental conditions intersect to shape stress survival. Integrating functional genomics and transcriptomics in Saccharomyces cerevisiae (brewer’s yeast) and a vertebrate (common canary) system, I dissect gene-by-environment (GE) interactions that underpin resilience. First, I move beyond a single reference genome by using a pan-genomic CRISPR knockout screen to assess osmotic stress survival across diverse S. cerevisiae isolates. This analysis reveals a …

Structure And Function Studies On Trna Splicing Endonuclease, Justin G. Underwood

Dissertations and Theses (Open Access)

A subset of eukaryotic pre-tRNAs have introns that must be spliced out to become mature molecules capable of functioning in translation. This essential processing step is performed by tRNA splicing endonuclease (TSEN), a highly conserved heterotetramer with two catalytic and two structural subunits. In addition to this conserved function, archaeal TSEN also processes pre-rRNA and yeast TSEN cleaves some mRNAs that encode mitochondrial proteins to initiate mRNA degradation. Interestingly, single amino acid mutations in TSEN cause the human Mendelian disease pontocerebellar hypoplasia (PCH) by an unknown mechanism. Recently, several groups have determined the structure of human TSEN, revealing similarities and …

An Open Letter To Leslie, Anne G. Kinne Phd

Journal of Conscious Evolution

This article celebrates the life and work of dear friend and mentor, Allan Leslie Combs, acknowledging his continued presence in my life. Interweaving stories of our relationship with his insights on integral consciousness, Bateson’s concept of aphanipoiesis, Varela et al.’s notion of autopoiesis, and using narrative, storytelling, and autoethnographic methodologies, I tell a tale of becoming that troubles and haunts my past. The sticky tendrils of Ancestral trauma and its transhistorical epigenetic inheritance, once acutely troublesome, are shifting due in large part to the contents of this letter. Woven together, these conscious, intersecting, and interactive lenses show how Leslie has …

Characterization Of Mitochondrial Dna Repair Components And Repair Choices At Targeted Double-Strand Breaks In Arabidopsis Thaliana, Moira Rodriguez

Dissertations and Doctoral Documents, University of Nebraska-Lincoln, 2023–

Plant mitochondrial genomes are complex when compared to most other eukaryotic mitochondrial genomes. They are large and variable in size, expand and rearrange frequently, abundant in non-tandem repeats, but maintain a very low synonymous substitution rate in the remaining coding regions. Many of these complexities can be explained by the increased use of double-strand break repair for DNA damage. To advance the understanding of mitochondrial genome dynamics as it relates to double-strand break repair, we performed a forward genetics screen to identify proteins involved in DNA repair in plant mitochondrial genomes. Through this screen, we identified an RNA/DNA helicase, Suv3, …

Citrullus Amarus Drought Tolerance: An Above And Below Ground Analysis, Ben A. Hyland

All Theses

Ever rising environmental temperatures threaten global food security by worsening severity and increasing the occurrence of drought. Commercially cultivated watermelon (Citrullus lanatus), have reduced drought tolerance due to a narrow genetic base caused by breeding for desirable traits such as sweetness, size, and flesh/rind color. Comparatively, the crop wild relative desert watermelon variety (Citrullus amarus), while more drought tolerant than their commercially cultivated relatives (C. lanatus), still require large amounts of water to grow and produce reliable fruit yields. Watermelon root morphology plays a key role in their ability to tolerate drought, with more …

Context Dependent Regulation Of Dicer Function During Oocyte-To-Embryo Transition, Nick A. Newkirk

Dissertations and Theses (Open Access)

Over two decades ago, Dicer was discovered as the primary enzyme responsible for the generation of small RNAs known as the microRNAs (miRNAs) and short interfering RNAs (siRNAs). Spatiotemporal regulation of Dicer-dependent small-RNA biogenesis affects many aspects of biology, including aging, disease progression, fertility, and cancer. Interestingly, a distinct population of Dicer-dependent small RNAs, known as the endogenous siRNAs (endo-siRNAs), are uniquely abundant in the germ cells and gametes, and are critical for normal fertility. Despite their function regulating new life, the mechanisms controlling their biogenesis and subsequent germ cell functions remain poorly defined. Work to parse these mechanisms in …

Orthogonal Comparison Of Nuclear And Mitochondrial Clonal Architectures In Hematologic Malignancies, Nehali Shah

Dissertations and Theses (Open Access)

Acute myeloid leukemia (AML) is a hematologic malignancy characterized by accumulation of mutations that disrupt hematopoietic differentiation and promote clonal expansion. Understanding how these mutations arise and evolve is essential for improving diagnosis, prognosis, and treatment stratification. Current methods are limited by either restricted genomic coverage (targeted panels) or low throughput and high cost (in single-cell whole genome sequencing, scWGS). An emerging alternative is the use of mitochondrial DNA (mtDNA) mutations as clonal markers.

This study aims to determine whether mitochondrial-derived clonal architectures correlate with nuclear-derived clonal architectures in AML, thereby evaluating mtDNA as a scalable orthogonal tool for lineage …

Improved Model For Neurodegeneration In C. Elegans, Jean-Pierre Arditi

Graduate Theses and Dissertations (2019 - present)

During Alzheimer's disease (AD), insoluble amyloid beta (AP) peptides accumulate to form extracellular aggregates (plaques). The direct cause of neuronal dysfunction observed in AD has been broadly investigated. The amyloid hypothesis states that AP plaques are neurotoxic, but recent studies support the AP oligomer hypothesis, which states that intracellular AP (iAP) is neurotoxic. To test this hypothesis, I used CRISPR-Cas9 gene editing to generate two transgenic Caenorhabditis elegans (C. elegans) strains. I generated a strain (RSLl 11) using the rab-3 promoter to co-express GFP in neurons, which showed no gross behavioral changes but had a 50% reduced egglaying rate. RSLl …