Genetics and Genomics Commons^™

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 …

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 …

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) …

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% …

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 …

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?

From Chromosomes To Precision Therapy: Clinical Cytogenetics And Cytogenomics In The Era Of Genomic Medicine, Jinglan Liu

Department of Pathology, Anatomy, and Cell Biology Faculty Papers

No abstract provided.

Epigenetic Regulators Mll3 And Mll4 Sustain Hematopoietic Stem Cell Multipotency, Helen Chenwei Wang

Arts & Sciences Graduate Student Theses and Dissertations

Hematopoietic stem cells (HSCs) maintain lifelong blood production by balancing self-renewal and multilineage differentiation. They are sustained by networks of transcription factors and epigenetic regulators that prime lineage-specific programs while simultaneously preventing activation of any one program up until the moment of lineage commitment. Despite extensive study, it remains unclear how these complex transcriptional programs are coordinated and how specific epigenetic regulators are deployed to reinforce specific cell fate decisions. Epigenetic regulators, MLL3 and MLL4, play a central role in pluripotent embryonic stem cell fate transitions, but their functions in multipotent somatic stem cells are less well characterized. MLL3 (also …

Summer Research Internships In Agricultural Biotechnology For Off-Campus Undergraduate Students, Aaron J. Thomas

Funded Research Records

No abstract provided.

Homocysteine Thiolactone From Translation Proofreading Is An Endogenous Ligand For Cell-Cell Signaling By The Receptor Sdia, Lorenzo Eugenio Leiva, Roberto A. Zúñiga, Gregory J. Phillips, Michael Ibba

Biology, Chemistry, and Environmental Sciences Faculty Articles and Research

Several widespread mechanisms enable cellular communication and coordinate the behavior of bacterial populations. The modules responsible for cellular communication are often found in matching pairs: an enzyme that synthesizes a signal molecule and a specific receptor that decodes it. A notable exception is Escherichia coli SdiA, a homolog of known N-acyl-homoserine lactone (AHL) receptors, for which no corresponding AHL synthase exists. SdiA is an orphan receptor that enables cross-talk by sensing AHLs from other bacterial species. In this work, we investigated whether homocysteine thiolactone (HTL), an AHL-like molecule arising from a proofreading reaction of methionyl tRNA synthetase (MetRS) to correct …

Vertebrate Diversity In Cave Systems Of Colombia: An Approach Based On Environmental Dna Metabarcoding Analysis, Rita Daniela Martinelli Marín, Carlos Andres Lasso, Francesco Sauro, Susana Josefina Caballero

International Journal of Speleology

There is currently limited knowledge of the biological communities inhabiting cave ecosystems in South America. This study examines the vertebrate community composition of 21 caves across diverse subterranean ecosystems in Colombia using environmental DNA (eDNA) analysis. Water was collected from water bodies inside caves and subterranean systems in six of the eight speleological regions of Colombia in eight departments. Water was filtered manually through a 0.8 m pore size filter and preserved with Longmire solution. A 170-base pair (bp) fragment of the 12s mitochondrial gene specific for vertebrate identification was amplified by PCR and sequenced by Illumina (metabarcoding). Data corresponding …

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. …

Birds Of A Tether Flock Together: Examining Centromere Tethering And Chromosome Segregation In Caulobacter Crescentus, Jake Dwyer, Simon Kruczak, Rodrigo Arana-Garrido, Paola Mera

MICRO-CCS student projects

Introduction:

Chromosome segregation is essential for all domains of life. Caulobacter crescentus is a key model for studying this process. It divides asymmetrically into two morphologically distinct cells. Proteins can be seen directly with fluorescent tags.

Research done on Caulobacter can apply to many different bacteria. The ParABS system is integral to chromosome segregation in Caulobacter.

ParS – DNA sequence on the chromosome

ParB – CTP-binding protein that specifically recognizes parS

ParA – ATP-binding protein that non-specifically binds DNA and provides the force for segregation.

PopZ – Polar tethering protein via interactions with ParB.

TipN - Polar protein that …

Association Of Ultra-Processed Food Intake With Insulin Secretion And Sensitivity In Mexican American Children: Results From The Safari Study, Hemant Kulkarni, Rector Arya, Srinivas Mummidi, Sharon P. Fowler, Roy G. Resendez, Juan C. Lopez-Alvarenga, Vidya Farook, John Blangero

Human Genetics Publications

Background/Objectives: There is increasing interest in and evidence for the role of ultra-processed foods (UPFs) in cardiometabolic risk. We tested the hypothesis that UPF intake score derived from dietary history is associated with measures of insulin secretion and sensitivity in a family setting even when the process of type 2 diabetes is still to ensue. Methods: We used data from our well-characterized San Antonio Family Assessment of Metabolic Risk Indicators in Youth (SAFARI) study cohort of nondiabetic children (aged 6–17 years). Dietary history was assessed using the Block Food Frequency Questionnaire. Outcomes of interest were 19 clinically useful indexes of …

Mosaic Loss Of Y Chromosome Associates With Lung Function, Emphysema, And Epigenetic Aging, Woei Yuh Saw, Kangjin Kim, Yichen Huang, Jeong H. Yun, Xiaolong Ma, Jason Bacon, Yash Pershad, Daniel Levy, George T. O’Connor, John Blangero

Human Genetics Publications

Rationale: As the global population ages, identifying risk factors for age-related diseases, such as COPD, is crucial for public health. Mosaic loss of Y chromosome (mLOY) in blood cells is an age-related somatic mosaicism event, but its relationship with pulmonary health remains undercharacterized. Objectives: To examine the association between mLOY and pulmonary outcomes in men. Methods: Leveraging mLOY assessment (cell fraction ≥ 5%) in over 12 000 men, including 5097 from the COPDGene Study and 7235 from six additional cohorts in the Trans-Omics for Precision Medicine program, we investigated mLOY associations with respiratory outcomes and epigenetic aging using multivariable cross-sectional, …

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 …