Genetics and Genomics Commons^™

Charge Modulation Of Peptide/Nucleic Acid Complexes: An Anionic Additive Enhances Gene Silencing And Crispr/Cas9 Editing By Promoting Intracellular Nucleic Acid Release, Abdulelah Alhazza, Sorour Khayyatnejad Shoushtari, Hasan Uludag, Keykavous Parang, Hamidreza Montazeri Aliabadi

Pharmacy Faculty Articles and Research

Introduction: Small interfering RNA (siRNA) and Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)/CRISPR-associated Protein 9 (Cas9) complexes are effective approaches to temporarily downregulate protein expression via post-transcription RNA interference or permanently altering protein expression via editing genomic DNA, respectively. However, the efficient delivery of these mediators to targeted cells has been challenging, largely due to their anionic and hydrophilic nature, which hinders their interaction with the cell membrane and cellular internalization. Cell-penetrating peptides (CPPs) exhibit dual characteristics as a carrier for nucleic acid delivery, where positively charged components bind to the negatively charged nucleic acid, and the hydrophobic components …

Effect Of Partial Ablation Of Skeletal Dynamin Related Protein 1 On Mitochondrial Health, Inflammation, And Fibrosis In A Mouse Model Of Duchenne Muscular Dystrophy, Tessa L. Duzz

Graduate Masters Theses

Duchenne muscular dystrophy (DMD) is a progressive neuromuscular disorder characterized by muscle weakness, degeneration, fibrosis, and impaired muscle regeneration. Mitochondrial dysfunction is an early pathological feature of DMD and has been linked to excessive mitochondrial fission. Dynamin-related protein 1 (Drp1) is a central regulator of mitochondrial fission, a key process in regulating mitochondrial quality and function. Inhibition of Drp1-mediated mitochondrial fission has shown promise as a potential therapeutic target for alleviating pathology and dysfunction in dystrophic muscle. The objective of this study was to determine whether partial skeletal muscle-specific ablation of Drp1 could improve muscle pathology and mitochondrial health in …

Mitochondrial Trna-Derived Fragments As Candidate Metastasis-Modifying Rna, Katy L. Swancutt, R. Mckinnon Walsh, Sydney Quijano, Emily Schueddig, Devin C. Koestler, Adam D. Scheid, Tony Vanden Bush, Yi Jing, Isidore Rigoutsos, Danny R. Welch

Computational Medicine Center Faculty Papers

UNLABELLED: How mitochondrial DNA (mtDNA) polymorphisms influence complex phenotypes remains poorly understood. Using mitochondrial-nuclear exchange mice, we previously showed that mtDNA single-nucleotide polymorphisms (SNP) modify metastasis, cardiovascular disease, and epigenetic marks independently of metabolic differences. The only mtDNA SNP correlating with these phenotypes resides in the gene encoding mitochondrial transfer RNA (tRNA)-arginine [mt-tRNAArg (UCG), mt-TR], suggesting a role for non-protein-coding loci. In this study, we identify and preliminarily characterize previously undescribed tRNA-derived fragments (tRF) generated from mt-TRs. Northern blotting revealed distinct tRF that are differentially expressed among mtDNA SNPs, between lung and liver, and between sexes. Surprisingly, small RNA sequencing …

Cells And Networks In Flux: Rethinking Ontogenesis And Pathogenesis, Mark L. Tykocinski

Department of Pathology, Anatomy, and Cell Biology Faculty Papers

Organ and tissue functions emerge from the coordinated activity of cell networks. Therapeutics that act on pathogenic cell networks, modulating their cellular interplay, follow naturally. Over several decades, our laboratory has developed a series of approaches for rewiring cell networks, culminating in a class of cell surface-directed signal converter proteins (SCPs) that do so by modulating juxtacrine and autocrine signaling in and among their nodal cells. A first such SCP has now produced encouraging clinical data for cancer immunotherapy. Yet, these early network-directed fusion proteins rest on a deliberately simplified picture: discrete end-cell types plugged into graphically tractable networks. That …

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 …

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 …

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) …

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

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% …

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?

Developmental Stability Of Task-Rest Neural Efficiency In Youth Using A Threat And Cognitive Control Task, Parmis Khosravi, Julia O. Linke, Anjali D. Poe, Chase Antonacci, Reut Naim, Elise M. Cardinale, Katharina Kircanski, Anderson M. Winkler, Nathan A. Fox, Daniel Samuel Pine, Simona P. Haller

School of Medicine Publications

Behaviors arise from coordinated neural activity across diverse spatial and temporal scales. Prior work has linked better task performance and cognitive functioning to patterns of global network connectivity requiring minimal reconfiguration when switching between task demands. This metric indexing similarity in functional connectivity across task and rest has been termed “neural efficiency.” Here we assess stability of neural efficiency over approximately 3 years in adolescence, specificity across two task-rest combinations and associations with anxiety. At approximately age 16 and/or 19, 95 participants completed a resting state scan alongside a cognitive control and/or threat task. Neural efficiency was quantified as partial …

Pearson Syndrome: Expanding The Clinical Spectrum Of A Mitochondrial Cytopathy-A Case Report, Alizah Faisal, Hooria Waqas, Hania Masood, Armeen Butt, Saad Rahman, Muhammad Sheraz Hameed, Syed Rafay Hussain Zaidi, Ali Iqbal, Muhammad Usama Naveed

Department of Medicine Faculty Papers

BACKGROUND: Pearson syndrome (PS) is a rare multisystem mitochondrial disorder characterized by single large-scale mitochondrial DNA deletions (SLSMDs). It typically presents in infancy with refractory sideroblastic anemia, exocrine pancreatic insufficiency, and failure to thrive. Due to its heterogeneous manifestations and resemblance to other hematological conditions, early diagnosis remains a clinical challenge.

CASE PRESENTATION: A south asian male infant presented with persistent pancytopenia, severe anemia unresponsive to intravenous and oral iron and multivitamin supplements, exocrine pancreatic insufficiency, failure to thrive, and metabolic acidosis. Born to consanguineous parents, the child had a significant family history of early infant deaths and hematological abnormalities. …

Proteogenomics Of Hypertrophic Cardiomyopathy Reveals Subtype-Specific Therapy, Ke Ma, Jie Yang, Hongchang Guo, Ping Li, Xiaowei Li, Zhujun Dong, Jing Zhang, Congcong Zhang, Pengli Yang, Chongpei Hua, Shuolin Zhu, Guoqing Li, Jianchao Zhang, Ningyu Ding, Jizheng Wang, Xin-Liang Ma, Zhuofeng Lin, Jianzeng Dong, Yang Li, Yulin Li

Department of Emergency Medicine Faculty Papers

BACKGROUND: Hypertrophic cardiomyopathy (HCM) is a heterogeneous disease with diverse prognosis. The underlying mechanisms remain unknown, resulting in limited risk stratification and therapeutic strategies. This study aimed to elucidate molecular subtypes of HCM through integrated proteogenomic analysis and explore subtype-specific therapeutic strategies.

METHODS: We conducted an integrated proteogenomic analysis of 132 patients with HCM using myocardial samples, incorporating whole-exome sequencing, RNA sequencing, and proteomics. Unsupervised clustering was used to identify HCM subtypes, which were validated in heart tissues and human induced pluripotent stem cell-derived cardiomyocytes from 2 independent HCM subsets. Subtype-specific signatures and pathways were explored, and their causal link …

Crispr/Cas9-Based Genome Editing: Understanding Differences In Dna Repair Pathways, Profiles, And Outcomes, Samuel Effah, Shirley Barrera, Nahia Urturi Ortiz, Will Dampier, Michael Nonnemacher, Brian Wigdahl

Kimmel Cancer Center Faculty Papers

Over a decade of advances in Clustered Regularly Interspersed Short Palindromic Repeats (CRISPR) and CRISPR-associated protein 9 (Cas9)-based technologies have culminated in the first-ever FDA-approved CRISPR/Cas-based therapy. Aside from this approved therapy for sickle cell anemia, several CRISPR/Cas-based therapies are currently under development or testing for a range of chronic diseases, including viral diseases like human immunodeficiency virus type 1 (HIV-1) infection, genetic diseases like familial hypercholesterolemia, and cancer. The success of these therapies hinges on the effective delivery of CRISPR/Cas9 components to target regions, efficient Cas endonuclease editing, repair profiles generated, and their resulting outcomes. Here, we discuss the …

Advocating For A Care-Based Ethic: Stories Of Pregnancy And Birth From Caregivers Of Children With Down Syndrome, Lydia Ocasio-Stoutenburg, Nayma Sultana Mim

Developmental Disabilities Network Journal

Down syndrome (DS) impacts about 1 in every 640 childbirths in the United States. While quality of life has improved for people with DS, systemic inequities and deficit-based perceptions have persisted throughout history, with material impacts on people with DS and their caregivers. Researchers have documented how caregivers of children with DS have had negative experiences with healthcare providers and genetic counselors, whose biased views about DS translate into subtle and overt pressures. Few studies explicitly focus on the experiences of Caregivers of Color, multilingual families, as well as families with varying economic experiences who have children with DS. This …

Gene × Sex Interactions On Cognition In The Philadelphia Neurodevelopmental Cohort, Josephine Mollon, Emma M. Knowles, Samuel R. Mathias, Amanda Rodrigue, Ruben C. Gur, Juan M. Peralta, Daniel J. Weiner, Elise B. Robinson, Armin Raznahan, Raquel E. Gur, John Blangero, Laura Almasy, David C. Glahn

School of Medicine Publications

Background: Small differences between females and males in cognitive abilities have been consistently reported, but the factors underlying these sex differences remain unclear. Social and cultural factors are thought to play a key role, but studies on this topic have been inconclusive. Examination of genetic factors may shed some light on the mechanisms underlying cognitive sex differences.

Methods: Using data from the Philadelphia Neurodevelopmental Cohort, a large, general population sample of individuals aged 8 to 21 years old (N = 4,694), we tested for sex differences in the genetic factors (i.e., Gene × Sex interactions) underlying cognitive ability. Participants completed …

Disease-Causing Mfn2 Mutants Impair Mitochondrial Fission Dynamics By Distinct Drp1 Dysregulation, Daniel Lagos, Pamela R. De Santiago, Nicolás Pérez-Bravo, Benjamín Cartes-Saavedra, Josefa Vial-Brizzi, Diego Troncoso-Chandía, Oliver Podmanicky, Rita Horvath, Verónica Eisner

Department of Pathology, Anatomy, and Cell Biology Faculty Papers

Mitochondria undergo fusion and fission. While DRP1 regulates fission, fusion is controlled by OPA1, MFN1, and MFN2. The balance between these processes and the crosstalk between machineries remains poorly understood. MFN2 mutations cause Charcot-Marie-Tooth disease type 2 A (CMT2A), affecting mitochondrial fusion and morphology. However, their role in fission is unclear. Using skin fibroblasts from CMT2A patients (L248H and M376V MFN2 mutations) and wild-type mouse embryonic fibroblasts expressing these variants, we studied how MFN2 mutations impact mitochondrial dynamics beyond fusion. We analyzed mitochondrial morphology and dynamics by live-cell confocal microscopy and tested fusion/fission protein levels, oxygen consumption rate (OCR), extracellular …

Decentralizing Dementia Research To The Us–Mexico Border: The Rio Grande Valley Ad-Rcmar As A Model For Translational Equity, Gladys E. Maestre, John Blangero, Eron Manusov, Gabriel A. De Erausquin, Francisco Fernandez, Silvia Mejia-Arango, Vincent P. Diego, Juan C. Lopez-Alvarenga, Claudia Alaniz, Neyra García, Rosa V. Pirela, Andrew Tsin, Michael Mahaney

School of Medicine Publications

Translational equity means ensuring that diagnostics, treatments, care models, and prevention strategies are developed and implemented so they work for populations with the greatest burden and least access to care. In Alzheimer's disease and related dementias (ADRD), where most evidence derives from highly educated, non-Hispanic White participants at large academic centers, translational equity is critical to prevent misclassification, limited access, and widening disparities and to ensure that underrepresented communities shape how new knowledge moves into practice. Hispanic and other populations in the United States are disproportionately affected by ADRD yet remain underrepresented in research, with gaps especially pronounced in high-poverty …

Computational Insights Into Nucleosome Dynamics In Epigenetics Using Molecular Dynamics Simulations, Rutika Patel

Dissertations, Theses, and Capstone Projects

Nucleosome core particles (NCP) are the building blocks that form a highly organized and compact chromatin structure. Nucleosomes package DNA in the nucleus of eukaryotic cells. The NCP consists of about 147 base pairs of DNA wrapped around the histone octamer, with 1.65 superhelical turns in a left-handed manner. The histone octamer is composed of two copies of H3, H4, H2A, and H2B. Together with histone H1 and linker DNA, they further assemble into a higher-order chromatin structure. The nucleosome complex is stabilized by electrostatic interactions between positively charged histone residues and the negatively charged DNA backbone. To effectively access …

A Disorder-Aware Computational Framework To Identify Structurally Tractable Targets In Proliferative Vitreoretinopathy, Mak B. Djulbegovic, Nedym Hadzijahic, David J. Taylor Gonzalez, Michael Antonietti, Sidra Zafar, Ajay E. Kuriyan

Wills Eye Hospital Papers

OBJECTIVE: Proliferative vitreoretinopathy (PVR) remains a major cause of failure after rhegmatogenous retinal detachment repair and lacks effective pharmacologic therapies. Although epithelial-mesenchymal transition (EMT) is central to PVR pathogenesis, the structural determinants governing the tractability of EMT regulators, particularly those involving intrinsic disorder, remain poorly defined. We developed a disorder-aware, artificial intelligence-enabled computational framework to evaluate EMT-associated proteins in PVR and prioritize structurally tractable regulators for structure-based targeting.

DESIGN: A computational, hypothesis-generating study employing an in silico screening and structural modeling pipeline.

SUBJECTS: No human subjects or biological specimens were included. The dataset comprised 25 EMT-associated proteins implicated in PVR, …

Brain Age Prediction In Generalized Anxiety Disorder Using A Convolutional Neural Network, Corey Richier, André Zugman, Anita Harrewijn, Elise M. Cardinale, Parmis Khosravi, Moji Aghajani, Willem B. Bruin, Kevin Hilbert, Narcis Cardoner, Anderson M. Winkler

Human Genetics Publications

Higher predicted brain age difference has been associated with several psychiatric disorders. Generalized anxiety disorder (GAD) is associated with markers of accelerated aging. In this study, we determined brain predicted age difference (PAD) in individuals with GAD and healthy controls (HC) as well as group differences in PAD variability using voxel-wise structural MRI. The training dataset included 3511 controls, and the testing dataset included 1595 individuals with GAD and 4552 HC from the ENIGMA-Anxiety GAD Working Group. A convolutional neural network model using four input modalities per subject and a model ensemble approach was used to predict brain age. The …

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 …

Associations Between Father–Mother Food Parenting Practices And Children’S Dietary Intake, Brian K. Lo, Natalie Grafft, Mariane Helen De Oliveira, Sebastien Haneuse, In Young Park, Alejandra Cantu-Aldana, Katherine W. Bauer, Rebekah Levine Coley, Jorge E. Chavarro, Kirsten K. Davison, Jess Haines

Human Genetics Publications

Objective: To examine whether the number of parents using high levels of structure or coercive control food parenting practices is associated with children’s dietary intake.

Design: Cross-sectional analysis of father–mother dyads from the Fathers & Families cohort study. Fathers and mothers independently reported their food parenting practices and child’s dietary intake. Multivariate logistic regression models estimated associations between the number of parents (0, 1 or 2) using high structure or coercive control practices and children’s intake of fruit, vegetables, fast food and sugar-sweetened beverages (SSB), adjusting for demographics and recruitment site.

Setting: United States

Participants: 474 father–mother dyads with a …

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, …

Isolation And Quantification Of Rna From Extracellular Vesicles Derived From A549 Human Non-Small Cell Lung Cancer Cells Using Ultracentrifugation, Yousef Dimian, Vanessa Pizutelli, Dimitri Pestov

Rowan-Virtua Research Day

Extracellular vesicles (EVs) have gained attention as potential diagnostic tools due to their presence in body fluids and their ability to carry nucleic acids, including RNA. EV-derived RNA, particularly ribosomal RNA (rRNA), may reflect cellular stress and disease states, making it a promising biomarker1, 2. This project focuses on optimizing methods to isolate EVs and quantify their RNA content using human cell culture models. Differential ultracentrifugation was used to separate vesicle populations based on size, followed by RNA extraction and quantification using a high-sensitivity assay. Initial experiments using media from three 150 mm culture dishes yielded no detectable RNA, whereas …

Identification Of Genes Regulating The Gli Protein Tra-1 In ​Caenorhabditis Briggsae Through A Genetic Suppressor Screen​, Alexander Glenn Cabrera, Sanese Brown-White, Ronald Ellis

Rowan-Virtua Research Day

BACKGROUND:
Gli proteins are conserved transcription factors that regulate cell fate, proliferation, and patterning. In Caenorhabditis briggsae, the Gli protein TRA-1 functions as the terminal regulator of the sex-determination pathway to control sexual development. These nematodes lack Hedgehog signaling, so TRA-1 is regulated by other factors. The missense mutation tra-1(v48) disrupts TRA-1 activator function, resulting in complete feminization of XX animals, which would otherwise be hermaphrodites.

HYPOTHESIS:
Suppressor screens using tra-1(v48) mutants will identify novel cofactors required for TRA-1–mediated Gli activation and spermatogenesis.

METHODS:
Ethyl methanesulfonate (EMS) mutagenesis was performed on tra-1(v48) strains to induce random mutations. Dominant suppressors were …

Validation Of A Real-Time Pcr Laboratory Developed Test For The Detection Of Pneumocystis Jirovecii In Bronchoalveolar Lavage Samples, Caitlyn Moon

Honors Scholar Theses

Pneumocystis jirovecii is an opportunistic, host-obligate fungal pathogen responsible for causing P. jirovecii pneumonia (PJP) in humans. PJP is treated with trimethoprim-sulfamethoxazole (TMP-SMX), a strong broad-spectrum antibiotic that carries risk of renal and hepatotoxicity. Therefore, rapid diagnosis or exclusion of PJP is crucial to ensure PJP-positive patients receive effective treatment and PJP-negative patients avoid unnecessary antibiotics. Unlike most microorganisms, P. jirovecii cannot be cultured, presenting complications for the typical methods of diagnosing fungal pathogens. Historically, the gold standard for diagnosis was direct microscopic examination with stains such as methenamine silver and calcofluor white, but this diagnostic technique requires highly skilled …

Abnormal Trafficking And Processing Of Multiple Matrix Metalloproteinases Drive Cartilage Defects In Congenital Disorders Of Glycosylation, Chia-Lun Wu

All Dissertations

Congenital Disorders of Glycosylation (CDG) are rare metabolic diseases caused by defects in glycosylation. Despite identification of over 200 CDG types, the mechanisms linking glycosylation defects to diverse clinical phenotypes remain unclear. This dissertation uses zebrafish models of PMM2-CDG and STT3-CDG to redefine CDG pathogenesis, shifting from a simple glycan deficiency model to one involving disrupted cellular spatial organization.

We identify a protease-dependent pathway underlying craniofacial cartilage defects. Specifically, defective proteolytic processing of N-cadherin, a key adhesion molecule in chondrogenesis, is a central driver of pathology. We further uncover an unconventional trafficking mechanism in which ER stress and altered secretory …