Genetics and Genomics Commons^™

Swarm Of One: Self-Organization In Multicellular Robots, Trevor Riley Smith

Graduate Theses, Dissertations, and Problem Reports (ETD)

Designing robots traditionally relies on centralized, top-down methods that constrain adaptability and resiliency, producing systems optimized for specific tasks. However, such systems often fail in complex environments, such as extraterrestrial, disaster, or natural settings, where designers cannot foresee every scenario a robot may encounter. Achieving autonomy in these contexts requires robots that are resilient and capable of adapting to the unknown. Multicellular organisms exhibit this adaptability through self-organization, where complex structures and behaviors emerge from local interactions among their cells. Such organisms can be viewed simultaneously as a single entity and a swarm of cooperating cells, i.e., a Swarm-of-One.

This …

Genetics Of Mycangial Development And Host Colonization Within The Ambrosia Symbiosis, Mckeon James Laws

Graduate Theses, Dissertations, and Problem Reports (ETD)

Ambrosia beetles, a polyphyletic group of weevils, utilize pouch-like structures at various locations on the body to transport for their sole food source, their fungal partner. Ambrosia fungi are known to originate from multiple unrelated fungal lineages with no consensus of traits required to become a fungal cultivar. While the biology and ecology of both partners is in many cases well understood, the genetic underpinnings of this fascinating mutualism remain a mystery. The aim of this dissertation is to add to the understanding of the ambrosia symbiosis by providing insights into its molecular and genetic underpinnings through RNA sequencing data, …

An Assessment Of Disease Risks, Population Genetics, And Spatial Ecology Of Appalachian Cottontails (Sylvilagus Obscurus) And Snowshoe Hares (Lepus Americanus) In West Virginia, Usa, Madison Leigh Miller

Graduate Theses, Dissertations, and Problem Reports (ETD)

Snowshoe hares (Lepus americanus) occupy a large range across the United States and Canada. While snowshoe hare populations are generally considered stable in the interior of their range, populations along range edges are experiencing declines, possibly driven by climate-related factors such as seasonal coat color mismatch. West Virginia represents one of the southernmost extents of the species’ range, yet little is known about the population genetic status or population sizes of snowshoe hares in the state. Appalachian cottontails (Sylvilagus obscurus) are another lagomorph species found in West Virginia. This species experienced a historical decline and currently …

Studying The Mechanism For Ricin-Induced Growth Suppression, Daniel Judge

Graduate Theses, Dissertations, and Problem Reports (ETD)

This study focuses on ribosome-inactivating proteins (RIPs), a class of potent toxins that includes ricin, α-sarcin, and shiga toxin, which irreversibly damage large subunit rRNA. Although the catalytic activity of ricin toxin A chain (RTA) is well characterized, the precise mechanisms linking ribosome damage to altered cellular morphology remain poorly understood. In this study, we engineered a tetracycline-regulatable expression system to express RTA in Saccharomyces cerevisiae. We characterized the effects of RTA expression on yeast growth, viability, and reproductive potential. We demonstrated that our expression system produced rapid and robust RTA expression and ribosome depurination within less than one …

35 Individuals With Huwe1-Related Neurodevelopmental Disorder And Suggested Clinical Evaluations, Mindy H. Li, Deziree L. Coleman, Kelsey Hogan, Danielle Luz, Lindsay Bhandari, Newell Belnap, Tiffany Busa, Charles Coutton, Klaus Dieterich, Svetlana Gorokhova, Clara Hildebrandt, Rachel Logan, Milena Mariani, Manuela Morleo, Vincenzo Nigro, John Pappas, Rachel Rabin, Kelly Schoch, Angelo Selicorni, Vandana Shashi, Rebecca Spillman, Jennifer Sullivan, Charlotte Tardy, Samantha A. Schrier Vergano, Brock Grill, Kristin Baranano

Department of Pediatrics Faculty Publications

HUWE1 (HECT, UBA, and WWE Domain Containing E3 Ubiquitin Protein Ligase1, OMIM 300697), located at Xp11.22, encodes a ubiquitin ligase that is highly conserved across species. Genetic variants in HUWE1 described in multiple independent studies cause X-linked intellectual disability, including in the patients identified by Juberg, Marsidi, and Brooks. This report describes 35 additional cases of individuals with variants in HUWE1 and suggested guidelines for clinical management. Our study includes several female cases, which have not been widely reported previously. Our findings confirm earlier reported clinical features including developmental delay, autism, hypotonia, short stature, and dysmorphic facial features as well …

The Rna-Binding Protein Hur Modulates The Expression Of The Disease-Linked Ccl2 Rs1024611g-Rs13900t Haplotype, Feroz Akhtar, Joselin Hernandez-Ruiz, Ya-Guang Liu, Roy G. Resendez, Denis Feliers, Liza D. Morales, Alvaro Diaz-Badillo, Donna M. Lehman, Rector Arya, Juan Carlos Lopez-Alvarenga, John Blangero, Ravi Duggirala, Srinivas Mummidi

School of Medicine Publications

CC-chemokine ligand 2 (CCL2) is involved in the pathogenesis of several diseases associated with monocyte/macrophage recruitment, such as HIV-associated neurocognitive disorder (HAND), tuberculosis, and atherosclerosis. The rs1024611 (alleles: A>G; G is the risk allele) polymorphism in the CCL2 cis-regulatory region is associated with increased CCL2 expression in vitro and ex vivo, leukocyte mobilization in vivo, and deleterious disease outcomes. However, the molecular basis for the rs1024611-associated differential CCL2 expression remains poorly characterized. It is conceivable that genetic variant(s) in linkage disequilibrium (LD) with rs1024611 could mediate such effects. Previously, we used rs13900 (alleles: C>T) in the CCL2 …

Dosage Sensitivity And The Evolution Of Dosage Compensation: Tests Of The Insensitive Sex Chromosome Hypothesis In Flour Beetles, Shana Pau

Biology Dissertations

Sex chromosome evolution generates imbalances in gene dosage that can disrupt gene expression and organismal function. These imbalances are often resolved through dosage compensation mechanisms, yet the factors that drive the emergence and diversity of these systems remain poorly understood. This dissertation addresses a central question in evolutionary genomics: what governs the evolution of dosage compensation?

Focusing on dosage sensitivity as a potential driver, I evaluate the Insensitive Sex Chromosome Hypothesis (ISCH), which predicts that chromosome-wide compensation is more likely to evolve in genomic contexts that are not depleted of dosage-sensitive genes. Using flour beetles (Tribolium spp.) as a …

Coordinating The Layers: Regulation Of Peptidoglycan Synthesis And Cell Wall Assembly In Mycobacterium Smegmatis By Murj And Pgfa, Karen Emmanuella Samaga-De-Tembiwa

Biology Dissertations

The mycobacterial cell envelope consists of three covalently linked layers whose synthesis must be coordinated to maintain structural integrity during polar growth. While the biosynthetic enzymes for each layer are well characterized, the molecular mechanisms that coordinate synthesis across layers have remained poorly understood. This thesis investigates two essential transmembrane proteins, PgfA and MurJ, that regulate peptidoglycan metabolism in Mycobacterium smegmatis and provide new insight into how mycobacteria synchronize cell wall assembly.

We present evidence that PgfA functions as a bifunctional regulator that links peptidoglycan metabolism to the availability of trehalose monomycolate (TMM), a key mycolic acid precursor. Through epistasis …

Generating Genomic Resources For The Pink Sundew And Its Specialist Herbivore Moth From A Single Gene To Entire Genomes, Kerissa F. Tarpley

Honors Undergraduate Theses

Genomic resources are critical for the conservation of threatened species, providing valuable insights into genetic diversity, population structure, and adaptive potential. This thesis focuses on two ecologically interconnected species: the carnivorous plant pink sundew (Drosera capillaris) and its specialist herbivore the sundew plume moth (Buckleria parvulus). The sundew and plume moth face an uncertain future as their vital bog habitats continue to disappear. The sundew plays a crucial role in the life cycle of the plume moth, which relies on the sundew during its larval stages for survival. To aid in species detections, I first generated …

Assessing The Impact Of Storing Water Samples At Ambient Temperature On Plankton Metabarcoding, Stephanie N. Lievano

Honors Undergraduate Theses

Increasing incidence of Harmful Algal Blooms (HABs) has led to fish kills, air quality hazards, and economic impacts. One economic impact is on tourism, one of the main sources of Florida’s income, where billions of dollars are lost to such events. The Florida Fish and Wildlife Conservation Commission Fish and Wildlife Research Institute (FWC-FWRI), with the help of collaborators, collects water samples from across the state for HAB monitoring. These samples are stored at ambient temperature for up to 24 hours which could directly affect data analyses. Here, in collaboration with FWRI-FWC, I investigated whether this storage technique affects plankton …

Interacting With Ideas: How To Engage Stem Students In Active Learning Of Theory Using Technology, Jessica Elizabeth Whitney, Keith Brian Morris

2026 Scholarly Teaching Conference: Concurrent Session Papers

STEM education in the modern age has been subject to much reform – from the integration of technology to an emphasis on student-centered teaching strategies, such as active learning. However, in the wake of virtual and blended-learning environments, student engagement and teacher assessment of student success have been challenged. Tools such as KAHOOT! and iClicker have been promoted to foster an active learning environment while sometimes falling short in regards to student retention of course material. In light of this technological educational revolution, instructors need to be able to determine the most effective tools for their discipline to aid in …

Searching For Cause Of Unexplained Protein Interaction With Multiple Assembly Methods, Gavin Anderson

Master's Projects

Research into colistin adjuvants has identified interactions between a host of proteins and proteins found within certain strains of bacteria. BLAST, a widely adopted local sequence alignment tool, was used to create a database containing the genomes of relevant bacterial strains, which would then be used to query against the previously identified proteins. Many of these strains do not have publicly available assemblies, which makes database construction difficult. CATwalk, a new naïve fragment extender, is first described in this paper and used to extend fragments of interest. BLAST results first identified short fragments with sufficient similarity, which can then be …

Rapid Urbanization Reduces Genetic Diversity And Increases Genetic Differentiation Of A Lynx Spider Oxyopes Sertatus In Central Taiwan, Ying-Yuan Lo, Chi Wei, Wan-Jyun Chen, Chung-Ping Lin

Biological Sciences Faculty Publications

Urbanization is a dominant force driving destructive and irreversible changes of natural habitats in modern times. While the effects of urbanization on community composition and phenotypic responses are well-documented, its influence on genetic diversity and population structure remains understudied, particularly for invertebrates in subtropical regions. This study tested the hypothesis that urbanization reduces genetic diversity and increases population differentiation in the lynx spider Oxyopes sertatus, a common foliage-dwelling spider in Taiwan. We sampled 245 individuals from 17 sites distributed along an urban-rural gradient and quantified urbanization intensity using land-use composition at both landscape (4 km²) and local (0.25 km²) …

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 …

Characterization Of Microrna Expression In Neuron-Enriched Extracellular Vesicles During Early Life, Allison Molen

Theses and Dissertations

Extracellular vesicles (EVs) are membrane-bound sacs released by cells that carry molecular cargo reflective of their cell of origin. EVs enriched using L1 cell adhesion molecule (L1CAM) as a marker of putative neuronal origin can cross the blood–brain barrier and provide a minimally invasive window into brain-related processes. Exosomal microRNA (miRNA) regulate gene expression and have been implicated in psychiatric disorders, including major depressive disorder (MDD). However, measuring and analyzing miRNA from L1CAM-positive EVs presents substantial analytical challenges due to low abundance and sparse detection across samples.

Plasma samples from participants recruited through the Mid-Atlantic Twin Registry (MATR) were used …

Sex In Plants: Birth, Death, And Trying To Survive In Changing Climates, Elena M. Meyer

Theses and Dissertations

Plant mating systems are key determinants of fitness. Angiosperms exhibit a wide variety of reproductive strategies, including self-fertilization (or selfing), outcrossing, and mixed mating. It has been estimated that up to 43% of plant species are capable of selfing, and selfing has been hypothesized to provide reproductive assurance where opportunities for mating may be limited, such as in marginal environments. However, questions regarding the overall distribution of selfing rates across angiosperms, the maintenance of mixed mating in the face of inbreeding depression, and the impact of self-fertilization on diversification rates remain incompletely resolved. Here, we explore the dynamics of self-fertilization …

Epigenetic Modifications In Dedifferentiated Liver Cells To Restore Lost Liver Function, Shreya Sharma

Masters Theses

The goal of the study is to investigate whether the epigenetic modifications can enhance the restoration of liver gene expression in dedifferentiated hepatoma cells or not. For the study, we used dedifferentiated H11 hepatoma cell lines which overexpress one of a panel of introduced candidate liver-enriched transcription factors H11-HNF1a, H11-CREB3L3, H11-CREG1, H11- HHEX, H11-HNF6, and H11-IGFBP1. The cells were treated with the DNA methyltransferase inhibitor 5-azacytidine and the histone deacetylase inhibitor sodium butyrate, both individually and in combination. Gene expression analysis was determined by RT-qPCR, which revealed that while transcription factor overexpression alone produced limited activation, epigenetic modulation, particularly Histone …

A Complete Diploid Human Genome Benchmark For Personalized Genomics, Nancy F. Hansen, Nathan Dwarshuis, Hyun Joo Ji, Arang Rhie, Hailey Loucks, Glennis A. Logsdon, Mitchell R. Vallger, Jessica M. Storer, Juhyun Kim, Eleni Adam, Nicolas Alternose, Dmitry Antipov, Mobin Asri, Sofia Barreira, Stephanie C. Bohaczuk, Andrey V. Bzikadze, Sara A. Carioscia, Andrew Carroll, Kuan-Hao Chao, Yanan Chu, Arun Das, Peter Ebert, Adam English, Mark Fleharty, Laura E. Fleming, Giulio Formenti, Andrea Guarracino, Gabrielle A. Hartley, Katharine Jenike, Jenna Kalleberg, Yu Kang, Robert King, Josipa Lipovac, Mira Mastoras, Matthew W. Mitchell, Shloka Negi, Nathan D. Olson, Keisuke K. Oshima, Luis F. Paulin, Brandon D. Pickett, David Porubsky, Jane Ranchalis, Desh Ranjan, Mikko Rautiainen, Harold Riethman, Robert D. Schnabel, Fritz J. Sedlazeck, Kishwar Shafin, Mile Sikic, Steven J. Solar, Alexander P. Sweeten, Winston Timp, Justin Wagner, Dongahn Yoo, Ying Zhou, Erik Garrison, Evan E. Eichler, Michaeel C. Schatz, Andrew B. Stergachis, Rachel J. O'Neill, Karen H. Miga, Steven L. Salzberg, Sergey Koren, Justin M. Zook, Adam M. Phillippy

School of Medical Diagnostics & Translational Sciences Publications

Human genome sequencing typically relies on mapping reads to a reference genome to call variants, but this approach introduces technical biases, excluding duplicated and structurally polymorphic regions of the genome. To overcome this, we present a telomere-to-telomere genome benchmark with near-perfect accuracy across 99.4% of the diploid HG002 genome. This benchmark adds 701.4 Mb of autosomal sequence and both sex chromosomes (216.8 Mb), which were absent from prior benchmarks. We annotated genes and repeats on both haplotypes, including 19,956 protein-coding genes on the maternal haplotype and 19,190 on the paternal haplotype, and developed new methods to measure the accuracy of …

Identifying Rna Splicing Changes During Alcohol Withdrawal Using An Optimized Rna-Seq Analysis Pipeline, Yasaswi Veera, Luana Martins De Carvalho, Amy Lasek

UROP Posters

Alcohol use disorder (AUD) causes long-lasting changes in brain gene expression and RNA splicing, particularly in the ventral hippocampus. This study analyzes RNA-Seq data from rats exposed to chronic alcohol and withdrawal to identify transcript-level and splicing alterations. An optimized RNA-Seq pipeline using STAR, FeatureCounts, edgeR, and WGCNA improved efficiency by 25-40% while maintaining consistency across 25 datasets. Results reveal changes in neural signaling and stress-response pathways associated with withdrawal. This work provides both biological insight into AUD and a reproducible computational framework for transcriptomic analysis.

A Novel 3d Imaging Approach To Study Evolutionary Innovations In Solanaceae Inflorescences, Devin L. Jackson, Joonseog Kim, Wenheng Zhang Dr.

UROP Posters

Understanding the relatedness of angiosperms and the evolution of their inflorescence remains challenging, as these structures are highly modified and prone to convergent evolution. The current research describing inflorescence architecture, whether genetically or morphologically focused, typically relies on text based explanations, 2D images, or 3D based models created with CAD modeling software. This creates a disparity in the reader's understanding of these models since descriptions rely heavily on the author's interpretation of the inflorescence. The goal of our study is to bridge this disconnection by producing anatomically and color-correct 3D inflorescence models using Solanaceae flowers that readers can explore directly, …