Genetic Structures Commons^™

Terahertz Electromagnetic Effects And Chirality-Induced Spin Selectivity In Dna, F. Matthew Mihelic Md

Faculty Publications

The effects of terahertz electromagnetic stimulation of the DNA molecule can be understood through modeling of the quantum logical mechanics of the DNA molecule.  Coherent conduction of electron spin states along the aromatic nucleotide base pairs and chirality-induced spin selectivity are two characteristics of the DNA molecule that are involved in the precise separation of the double-stranded DNA molecule at a specific location.  Such modeling can inform predictions of DNA strand separation and has significant implications for understanding DNA transcription bubble formation.

Systematic Evaluation Of Batch Effects In The Cancer Genome Atlas Program Underscores The Need For Batch-Controlled Analysis, Zhongxuan Chen, Stepan Nersisyan, Isidore Rigoutsos, Eric Londin

Alpha Omega Alpha Research Symposium Posters

Purpose: To systematically assess the impact of batch effects on differential expression of isomiR, mRNA, and non-coding RNA (sncRNA) across 13 The Cancer Genome Atlas (TCGA) cancer types and develop a standardized, batch-controlled analysis protocol for TCGA datasets.

Methods: Data analysis and visualization were performed using Python v3.12. Plots were generated using matplotlib and seaborn. isomiR, mRNA, and sncRNA sequences across 13 TCGA cancer types were used. Principal Component Analysis (PCA) was performed using scikit-learn for dimensionality reduction. Differential expression was conducted using DESeq2 under the following protocols: 1) primary tumor samples vs matched normal samples processed in the same …

Using Genetically Diverse Mice To Examine The Effects Of Environmental Enrichment Of The Transcriptome, Michael Richard Leonardo

Theses, Dissertations and Capstones

Environmental impoverishment is a model of early life stress with direct consequences across a wide range of neurological and physiological conditions. Neuron morphology and density as well as anxiety disorders and addiction have shown to have significant relationships with environmental impoverishment models. Conversely, environmental enrichment confers therapeutic benefits that are protective across these conditions. There is an observed spectrum of resistance or vulnerability to the effects of housing conditions across populations, indicating genetics as an influential factor. Understanding this interaction is critical for deepening our knowledge of how genes and environment interact in ways that confer resistance or vulnerability, and …

Microarray Analysis Of Human Abdominal Aortic Aneurysm With Emphasis On Cardiovascular Genes Revealed Differentially Expressed Genes, Song Lu, Li Ping Li, John V. White, Xiaoying Zhang, Ifeyinwa Nwaneshiudu, Adaobi Nwaneshiudu, Nectaria Ntaoula, John Gaughan, Dimitri S. Monos, Wan-Lu Lin, Charalambos C. Solomides, Emilia L. Oleszak, Chris D. Platsoucas

Biological Sciences Faculty Publications

Background/Aim: We examined gene expression profiles in abdominal aortic aneurysm (AAA) lesions vs. normal aortas by cDNA microarray and real-time quantitative reverse-transcriptase polymerase chain reaction (qRT-PCR).

Materials and Methods: Phosphorus (32P)-labeled cDNA from AAA specimens (mean AAA size 6.65 cm) and normal aortas were hybridized with a 588-gene microarray primarily of the cardiovascular system. The results were validated by qRT-PCR.

Results: A total of 35 out of the 588 genes were differentially expressed, with either log2 ratio of AAAs/controls ≥1 (upregulated; 20 genes) or ≤−1 (downregulated; 15 genes) in AAA lesions vs. normal aorta, and 25 of these were significantly …

Methylation Of The Dat1 Dopamine Transporter Gene In Combat Sport Athletes: Associations With Impulsivity And Reward Sensitivity, Milena Lachowicz, Remigiusz Recław, Aleksandra Suchanecka, Krzysztof Chmielowiec, Elżbieta Grzywacz, Jolanta Chmielowiec, Kinga Łosińska, Anna Grzywacz

Baltic Journal of Health and Physical Activity

Epigenetic mechanisms, such as DNA methylation, modulate behavioral traits, including impulsivity and reward sensitivity. The dopamine transporter gene (DAT1) plays a key role in dopaminergic function and is associated with self-regulation, attention, and the trait of addiction. This study summarized the DAT1 methylation status in patients practicing combat sports and its association with impulsivity, ADHD symptoms, and consequence sensitivity. One hundred control subjects were recruited using the Barratt Impulsivity Scale (BIS), the ADHD scale, and the Opportunity Response Scale. DAT1 methylation was measured using the bisulfite ionization method. A correlation analysis was performed with the comparison group. Athletes …

Redesigning Beauty: Promoting Universal Design For Upper Extremity Deficits, Sierra Louise Forkey, Cynthia Haynes

Fall 2025 OTD Capstone Symposium

The purpose of this capstone project is to research and identify barriers individuals with upper extremity deficits face when participating in personal hygiene and grooming tasks and to use this information to advocate for individuals with upper extremity deficits by promoting inclusive design, educating consumers, and informing beauty manufacturers on the importance of implementing a universal design component to allow products to be more accessible.

Predictive Gene Expression Signatures For Alzheimer's Disease Using Post-Mortem Brain Tissue, Ashley Duche, Oliver Tan, Andrius Baskys, Rachita K. Sumbria, Moom R. Roosan

Pharmacy Faculty Articles and Research

Background: Alzheimer’s Disease (AD) is a progressive neurodegenerative disorder characterized by amyloid-beta (Aβ) plaques and tau protein aggregates in the brain. These pathological features manifest in specific regions, but mechanisms rendering some areas more susceptible to early AD-related changes remain poorly understood. To address this, we developed predictive gene expression signatures to explore molecular mechanisms underlying regional vulnerability to AD pathology.

Methods: Post-mortem brain tissues from participants of the Religious Orders Study and Memory and Aging Project (ROSMAP), Mayo Clinic, and Mount Sinai Brain Bank (MSBB) were used to derive gene expression signatures from six brain regions affected at varying …

The Role Of Ceramides As Biomarkers And Therapeutic Targets For Cardiometabolic Disease And Its Intersection With Cellular Aging, Youssef Moustafa Shalaby

Thesis/ Dissertation Defenses

Ceramides (Cer), a subclass of sphingolipids with potent bioactive properties, have gained recognition as key players in the pathogenesis of cardiometabolic diseases (CMD). They modulate critical cellular functions such as apoptosis, inflammation, insulin signaling, and oxidative stress. This dissertation explores the dual role of Cer as both early diagnostic markers and therapeutic targets, bridging clinical insights with mechanistic understanding through a combination of human and experimental studies.

A highly sensitive liquid chromatography–tandem mass spectrometry (LC-MS/MS) method was developed and validated to quantify intracellular levels of specific Cer species, including CerC16:0, CerC18:0, CerC22:0, CerC24:0, and CerC24:1. This method was translated into …

Whole Genome Sequencing Identifies Monogenic Disease In 56.1% Of Families With Early-Onset Steroid-Resistant Nephrotic Syndrome, Eman Ramadan

Pharmacy

Genetic causes of steroid-resistant-nephrotic-syndrome (SRNS) represent a rapidly growing number of monogenic diseases. The reported diagnostic yield of various studies applying genetic panels and exome-sequencing to diagnose SRNS is usually < 30%. We performed genome-sequencing in a cohort of Egyptian SRNS patients. We recruited 47 SRNS patients belonging to 41 unrelated families [28 males/19 females; median (range): 6 (0.5-22 years)]. We established a pipeline for genome sequencing, bioinformatics analysis, variant curation and protein modeling at the Egypt Center for Research and Regenerative Medicine (ECRRM). Disease-causing variants were detected in 27/47 patients (57.4%) belonging to 23/41 families (56.1%), including nine novel variants in NPHS1, NPHS2, COL4A3, MYO1E, NUP93, PLCE1, PODXL, SMARCAL1 and WT1. Novel variants were confirmed by Sanger sequencing and were segregated in families of affected patients. NPHS2 was the most common causative gene in 8/23 (34.8%) of confirmed families, followed by NPHS1, WT1, and SMARCAL1 in 2/23 families (8.7%) each. All detected missense variants were evaluated through protein modeling and were predicted deleterious. Our study expanded the spectrum of SRNS disease-causing variants and revealed a monogenic cause in 56.1% of investigated families. In our cohort, no deep intronic or regulatory variants were detected by genome-sequencing. Pursuing genetic diagnosis in SRNS patients is crucial to inform clinical decision making, genetic counseling, transplantation strategy and prenatal diagnosis thus improving clinical outcome of affected patients.

A Multi-Level Gene-Diet Interaction Analysis Of Fish Oil And 14 Polyunsaturated Fatty Acid Traits Identifies The Fads And Gpr12 Loci, Susan Adanna Ihejirika, Alexandra Huong Chiang, Aryaman Singh, Eunice Stephen, Han Chen, Kaixiong Ye

Faculty, Staff and Student Publications

Fish oil supplements (FOS) are known to alter circulating levels of polyunsaturated fatty acids (PUFAs) but in a heterogeneous manner across individuals. These varied responses may result from unidentified gene-FOS interactions. To identify genetic factors that interact with FOS to alter the circulating levels of PUFAs, we performed a multi-level genome-wide interaction study (GWIS) of FOS on 14 plasma measurements in 200,060 unrelated European-ancestry individuals from the UK Biobank. From our single-variant tests, we identified genome-wide significant interacting SNPs (p < 5 × 10-8) in the FADS1-FADS2 gene cluster for total omega-3, omega-3%, docosapentaenoic acid (DHA), DHA%, and the omega-6 to omega-3 ratio. Among the interaction signals for omega-3%, the lead SNP, rs35473591 (C>CT, CT allele frequency = 0.34), had a lower association effect size in the FOS-taking group (β = 0.35 for …

Role Of Evolutionarily Conserved G4 Structures In Enhancer-Promotor Interactions, Shahem Alqudah

Honors Theses

Gene regulation is governed by complex networks of interactions between enhancers and promoters, regions of the genome that are typically distant from one another yet functionally linked through chromatin looping. Recent research has revealed the significant role of Gquadruplexes (G4s) in facilitating these interactions. This thesis explores the role of long Gquadruplex regions (LG4s) in enhancer–promoter communication, proposing that these regions mediate physical interactions between enhancers and their target promoters through direct G4:G4 interactions. Using a chromatin conformation capture (EQuIP-seq), electrophoretic mobility shift assays (EMSA), and luciferase reporter assays, the study demonstrates that LG4s may drive gene expression by promoting …

A Long Non-Coding Erna Forms R-Loops To Shape Emotional Experience-Induced Behavioral Adaptations, Rose Marie Akiki

MUSC Theses and Dissertations

Emotional experiences often evoke neural plasticity that supports adaptive changes in behavior, including maladaptive plasticity associated with mood and substance use disorders. These adaptations are supported in part by experience-dependent activation of immediate-early response genes, such as Npas4. We discovered that a conserved, long non-coding enhancer RNA (lnc-eRNA) transcribed from an activity-sensitive enhancer produces DNA-RNA hybrid R-loop structures that support 3D chromatin-looping of the enhancer and proximal promoter and stimulus-induced, rapid Npas4 gene induction. We also show that this Npas4 lnceRNA and its R-loops are required for the development of behavioral adaptations produced by chronic psychosocial stress or cocaine exposure, …

Investigating The Drug Response Of Pdac Cells To Pan-Kras Inhibitor, Jalyn De La Fuente, Yi Xu, Jun Liu, Angel Dominquez, Ava Sanchez, Pei Wang

Posters - 2025

Pancreatic ductal adenocarcinoma (PDAC) is an exocrine pancreatic cancer. It is one of the most lethal types of cancer and is projected to become the second leading cause of cancer-related deaths by 20401 . One major challenge in treating PDAC is drug resistance and the lack of effective treatments. Oncogenic KRAS mutation and loss of function mutation in tumor suppressor genes including P16, TP53, and SMAD4 are found in most PDAC patients. It is unclear whether the different driver mutations can affect the tumor responses to chemo- and targeted therapy. Gemcitabine, a chemotherapy drug, is a cytotoxic agent that has …

Characterization Of The Overexpression Of Reca Homologs Rad51 And Dmc1 In Tetrahymena Thermophila, Jianna M. Cox

Graduate Theses/Dissertations

RecA homologs, Dmc1 and Rad51, work to repair DNA double-strand breaks (DSBs) within the cell through the recombination of homologous sections of DNA. Dmc1 works to repair programmed DSBs through meiotic recombination, while Rad51 functions to repair both meiotic and non-meiotic DSBs, the latter repaired through the process of homologous recombination repair (HHR). Chemotherapeutics, exogenous agents, work to form DSBs in cancer cells, attempting to inhibit the cell’s growth. A hyper recombinant phenotype is often seen in cancer cells due to the overexpression of RAD51, leading to drug resistance, the persistence of cancers, and an overall poor patient outcome. …

Unraveling Dilated Cardiomyopathy Linked To An Enigmatic Mybpc3 Variant, Khiem D. Ngo, Carlos Alejos, Jennifer Rojas, Sobia Memon, James Stone

Research Colloquium

Background: Non-ischemic cardiomyopathy (NICM), can arise from various causes, including hemodynamic pathology, infections, immunologic abnormalities, toxic injuries, and genetic factors. Determining the prevalence of NICM is challenging due to varying definitions and diagnostic criteria, selection bias, and geographic variation. MYBPC3 is the primary gene known to cause restrictive cardiomyopathy, dilated cardiomyopathy, and left ventricular non-compaction. This gene encodes cMyBP-C, a structural protein of the heart muscle that interacts with actin, myosin, and titin to maintain sarcomeric integrity. While loss-of-function mutations are common, MYBPC3 missense variants of uncertain significance (VUS) are also prevalent. Individuals with MYBPC3 missense VUS predicted to disrupt …

Stem-Loop And Circle-Loop Tads Generated By Directional Pairing Of Boundary Elements Have Distinct Physical And Regulatory Properties, Wenfan Ke, Miki Fujioka, Paul Schedl, James Jaynes

Department of Biochemistry and Molecular Biology Faculty Papers

The chromosomes in multicellular eukaryotes are organized into a series of topologically independent loops called TADs. In flies, TADs are formed by physical interactions between neighboring boundaries. Fly boundaries exhibit distinct partner preferences, and pairing interactions between boundaries are typically orientation-dependent. Pairing can be head-to-tail or head-to-head. The former generates a stem-loop TAD, while the latter gives a circle-loop TAD. The TAD that encompasses the Drosophila even skipped (eve) gene is formed by the head-to-tail pairing of the nhomie and homie boundaries. To explore the relationship between loop topology and the physical and regulatory landscape, we flanked the nhomie boundary …

Long G4-Rich Enhancers Physically Interacts With Promoters Via A G4:G4 Dna-Based Mechanism, Jeffrey David Demeis

Graduate Theses and Dissertations (2019 - present)

Enhancers are genomic sequences that function as regulatory elements capable of increasing the transcription of a given gene often located at a considerable distance. The broadly accepted model of enhancer activation involves bringing an enhancer-bound activator protein complex into close spatial proximity to its target promoter through chromatin looping. Equally relevant to the work described herein, roles for guanine (G) rich sequences in transcriptional regulation are now widely accepted. Non-coding G-rich sequences are commonly found in gene promoters and enhancers, and various studies have described specific instances where G-rich sequences regulate gene expression via their capacity to form G-quadruplex (G4) …

Rna 2′-O-Methylation Promotes Persistent R-Loop Formation And Aid-Mediated Igh Class Switch Recombination, Muzaffer Ahmad Kassab, Yibin Chen, Xin Wang, Bo He, Eric J Brown, Xiaochun Yu

Faculty, Staff and Student Publications

BACKGROUND: RNA-DNA hybrids or R-loops are associated with deleterious genomic instability and protective immunoglobulin class switch recombination (CSR). However, the underlying phenomenon regulating the two contrasting functions of R-loops is unknown. Notably, the underlying mechanism that protects R-loops from classic RNase H-mediated digestion thereby promoting persistence of CSR-associated R-loops during CSR remains elusive.

RESULTS: Here, we report that during CSR, R-loops formed at the immunoglobulin heavy (IgH) chain are modified by ribose 2'-O-methylation (2'-OMe). Moreover, we find that 2'-O-methyltransferase fibrillarin (FBL) interacts with activation-induced cytidine deaminase (AID) associated snoRNA aSNORD1C to facilitate the 2'-OMe. Moreover, deleting AID C-terminal tail impairs …

Maldi Imaging Mass Spectrometry Visualizes The Distribution Of Antidepressant Duloxetine And Its Major Metabolites In Mouse Brain, Liver, Kidney, And Spleen Tissues, Saleh M Khalil, Xuan Qin, John M Hakenjos, Jian Wang, Zhaoyong Hu, Xinli Liu, Jin Wang, Mirjana Maletic-Savatic, Kevin R Mackenzie, Martin M Matzuk, Feng Li

Faculty, Staff and Student Publications

Imaging mass spectrometry (IMS) is a powerful tool for mapping the spatial distribution of unlabeled drugs and metabolites that may find application in assessing drug delivery, explaining drug efficacy, and identifying potential toxicity. This study focuses on determining the spatial distribution of the antidepressant duloxetine, which is widely prescribed despite common adverse effects (liver injury, constant headaches) whose mechanisms are not fully understood. We used high-resolution IMS with matrix-assisted laser desorption/ionization to examine the distribution of duloxetine and its major metabolites in four mouse organs where it may contribute to efficacy or toxicity: brain, liver, kidney, and spleen. In none …

A Trna Modification Pattern That Facilitates Interpretation Of The Genetic Code, Isao Masuda, Ya-Ming Hou

Department of Biochemistry and Molecular Biology Faculty Papers

Interpretation of the genetic code from triplets of nucleotides to amino acids is fundamental to life. This interpretation is achieved by cellular tRNAs, each reading a triplet codon through its complementary anticodon (positions 34–36) while delivering the amino acid charged to its 3′-end. This amino acid is then incorporated into the growing polypeptide chain during protein synthesis on the ribosome. The quality and versatility of the interpretation is ensured not only by the codon-anticodon pairing, but also by the post-transcriptional modifications at positions 34 and 37 of each tRNA, corresponding to the wobble nucleotide at the first position of the …