Genetics and Genomics Commons^™

Data From: Complete Mitochondrial Genomes Of The Spring Pygmy Sunfish (Elassoma Alabamae), Kayla M. Fast, David Lee Pounders, Mayah P. Peterson, Michael W. Sandel

Research Data

The Spring Pygmy Sunfish, Elassoma alabamae (Mayden, 1993), is a small species of sunfish (Centrarchiformes) endemic to tributaries to the middle Tennessee River in north Alabama. Elassoma alabamae is the most geographically restricted member of Elassoma and the only species found above the fall line. This species was twice considered extinct and was listed under the Endangered Species Act (ESA) as threatened in 2013. To date, surveys for this species have been limited to traditional invasive methods using dipnets and seines. In order to reduce impacts on sensitive populations, we sequenced the mitochondrial genome with the intent of developing a …

Microbial Community Structure In Global Soils, Matthew Jabro

CMC Senior Theses

Soil harbors the most diverse microbial communities on Earth, yet whether predictable community types exist across biomes and whether taxonomic composition encodes habitat of origin remain open questions at global scale. This thesis addresses both questions by applying unsupervised clustering and supervised classification to transformed 16S ribosomal RNA (rRNA) amplicon profiles from two independent datasets: the global topsoil survey of Bahram et al. (193 samples) and the Earth Microbiome Project (EMP) soil subset of Thompson et al. (2,209 samples). Application of a sample clustering method based on a mixture of Gaussian Graphical Models (MixGGM) identified 19 clusters in the topsoil …

Genomic Signatures Of Decline And Recovery In An Endangered Bat, Myotis Grisescens, Marxe Altman-Orbach

Graduate Theses/Dissertations

Tremendous population declines may result in the loss of genetic diversity, which can, in turn, lead to reduced adaptive potential, overexpression of deleterious phenotypes, and further population declines. In this way, genetic drift from a severe demographic decline may ultimately lead to an extinction vortex. However, populations that avoid the loss of genetic diversity may remain viable, despite demographic crashes. Therefore, understanding genetic diversity is vital for assessing the conservation status of species that have undergone declines, and can even reflect the effectiveness of management actions. I investigated signatures of genetic bottlenecks in the gray bat (Myotis grisescens), …

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 …

Chromnet: A Multi-Task Learning Framework For Cross-Cell Type Prediction Of 3d Chromatin Interactions Using Epigenetic Signals, Bin Wang, Shaokai Wang, Liqing Ding, Hongdong Li, Yaohang Li, Jianxin Wang

Computer Science Faculty Publications

The 3D organization of chromatin plays a fundamental role in gene regulation, cellular function, and disease mechanisms. However, current experimental techniques, such as Hi-C, remain costly and labor-intensive, limiting their application in large-scale and disease-related studies. To address this challenge, ChromNet is presented, a multi-task learning framework that integrates epigenetic signals across diverse cell types to enable high-precision prediction of chromatin architecture. By incorporating noise perturbation and auxiliary classification tasks, ChromNet improves the identification of topologically associating domains (TADs) and cell-type-specific chromatin structures, demonstrating superior generalization performance. Notably, ChromNet accurately predicts chromatin interactions in acute myeloid leukemia (AML) samples by …

Attention-Based Multi-Omics Fusion For Drug Synergy Prediction, Kusal Debnath, Pratip Rana, Preetam Ghosh

Computer Science Faculty Publications

Drug combination therapy in disease management gained popularity in the last few decades. Computational modeling of such combinations is an active area of research in the drug discovery domain. While earlier approaches solely emphasized on the structural features of participating drugs for designing synergistic models, they lack other crucial factors directly linked with drug administration - omics expressions. As differential omics expression is a downstream consequence of the administered drug combinations, utilizing such expressions while designing synergistic models promises robust and dynamic modeling. In this work, we propose SynergyLM that fuses multi-omics features with drug embeddings to build an omics-aware …

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, …

Determining Genes Involved In Recovery From Chemotherapy In 4t1, Emt6, And Eo771 Breast Cancer Cells, Akash Jagdeesh, Joseph Landry Ph.D.

UROP Posters

Breast cancer is one of the most common types of cancer, and often has poor prognosis. Traditional treatments for breast cancer include chemotherapy, which involves a chemical attack on all growing cells within the body. However, these treatments are not 100% effective, and patients might experience recurrence in their cancer months or years after achieving remission. Cancer cells can evade chemotherapy through five mechanisms: senescence, quiescence, cytoprotective autophagy, and apoptosis/necroptosis suppression. Prior studies have conducted CRISPR screens and experiments involving inhibition of epigenetic regulators, to alter the regulation of genes that can contribute to breast cancer chemotherapy resistance. This study …

Fluorescent Protein Imaging Approaches Uncover Dynamic Subcellular Distribution Of Core Clock Proteins In Neurospora Crassa, Ziyan Wang

Dartmouth College Ph.D Dissertations

Circadian clocks are endogenous self-sustained timekeeping systems that allow organisms to anticipate and adapt to daily environmental cycles. Found in diverse forms of life, these molecular clocks regulate the expression of ~ 40% of the genome in animals, fungi, and plants. In animals and fungi, circadian oscillators are built on transcription-translation feedback loops (TTFLs), in which positive regulators drive the expression of negative regulators which, once synthesized and imported into the nucleus, inhibit their own activators. This precisely regulated negative feedback incorporates multiple steps of delays that are essential for generating ~24-hour rhythms. Through these mechanisms, circadian clocks temporally coordinate …

Genomic Determinants Of Appetite Regulation And Their Role In Obesity Risk, Timothy J. Renier

Dartmouth College Ph.D Dissertations

Over 40% of US adults and 20% of children live with obesity. It is related to increased risks of diseases including type II diabetes and cancer, is a source of harmful stigma, and impairs child development. Appetitive traits describing patterns of food approach and avoidance behaviors may serve as windows into the underlying pathophysiology of obesity. As both obesity and appetitive traits are heritable, common genetic drivers of obesity may lead to phenotypic obesity through appetitive traits as a disease mechanism. Additionally, GLP-1 receptor agonists (GLP-1RAs) have been shown to exert their profound clinical effects in part by modulating appetite. …

From Molecules To Minds: Integrative Multi-Omics In Psychiatry, Hossein Abbasi, Sage E. Hawn, Arash Javanbakht, Soraya Seedat, Kyle Bourassa, Sinead M. Sinnott, Antonia V. Seligowski, Sian Hemmings, Nathan A. Kimbrel, Alicia K. Smith, Leslie Brick, Divya Mehta

Psychology Faculty Publications

Psychiatric disorders are biologically complex conditions arising from interactions across genomic, epigenomic, transcriptomic, proteomic, metabolomic, and metagenomic layers. Single-omics approaches rarely capture more than a fraction of the variance in complex conditions, underscoring the importance of integrative multi-omics frameworks. This mini-review summarizes key methodologies and their application in psychiatric research, with a focus on systems-level integration of genomic risk scores, transcriptomic networks, and neuroimaging data to advance biological understanding of disorders such as depression, schizophrenia, and Alzheimer’s disease. We also outline the infrastructural requirements for effective multi-omics research, including standardized biobanking, Laboratory Information Management Systems, adherence to FAIR data principles, …

Regulation And Localization Of Urease In Sporosarcina Pasteurii: Implications For Coastal Protection, Amar Kosovac

UNF Graduate Theses and Dissertations

Coastal erosion is a persistent problem exacerbated by global warming. As the climate changes, the southeastern coast is likely to experience an increased frequency and intensity of storms, which can significantly damage the coastline. The coast is crucial as it serves as a habitat for numerous animals, supports tourism, and underpins infrastructure. Microbially induced calcite precipitation (MICP) is a novel method to enhance erosion resistance in sandy soils using the non-pathogenic bacterium Sporosarcina pasteurii. S. pasteurii produces urease to catalyze urea into bicarbonate, which drives the precipitation of calcium carbonate. Maximal expression of urease is a limiting factor for …

Comparative Analysis Of Six New Chloroplast Genomes In Platanthera (Orchidaceae) Enhances Understanding Of Its Diversification, Lisa E. Wallace, Martin I. Batalla, Matthew Maisonave

Biological Sciences Faculty Publications

Platanthera is among the most diverse genera of orchids in north temperate regions, with high species diversity in Asia and North America. Despite many ecological studies in this group, little is known about its genomic diversity. Here, we report the newly annotated chloroplast genomes from six species in subgenus Limnorchis from North America and compare them with plastomes published for Platanthera species from Asia and Europe. We found that the plastomes of species in subg. Limnorchis are among the smallest reported for Platanthera thus far. While major structural differences were not detected in the newly sequenced species, ndh genes were …

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 …

Building A Cell Specific System For In Vivo Rna Imaging Of The Endogenous Actin Gene In C. Elegans, Jasmine A. Huerta Canete

Theses and Dissertations

Messenger RNA (mRNA) plays a crucial role in protein synthesis and cellular processes, important for the development of cells such as neurons. When dysregulation occurs, it can lead to outcomes such as aberrant translation, causing neurodegenerative conditions to arise. Unfortunately, the localization of mRNA in an in vivo cell specific manner is still not understood. To address this, we decided to develop a cell-specific system to image RNA in vivo, within the organism known as C. elegans with a focus on the actin gene. The Actin gene encodes for an important cytoskeleton protein expressed ubiquitously, vital for the cell …

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 …

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) …