Biology Commons^™

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 …

Bioinformatic Identification And Analysis Of Shared Splicing Errors In Myotonic Dystrophy Type (Dm1) And Fuchs' Endothelial Corneal Dystrophy (Fecd), Carter I. Wilkins

Electronic Theses & Dissertations (2024 - present)

Myotonic dystrophy type 1 (DM1) is an autosomal dominant form of muscular dystrophy, and it is the most common form of adult-onset muscular dystrophy. The disease is the result of CTG trinucleotide repeats (TNR) in the 3’UTR of the dystrophia myotonica protein kinase (DMPK) gene. This produces toxic RNA hairpin structures by CUG repeat expansions that sequester proteins–most relevantly muscleblind-like 1 (MBNL)–that regulate alternative RNA splicing. The missplicing of a wide variety of genes results in the symptoms such as myotonia (rigidity of the muscles), atrophy, and cardiac failure.

Fuchs’ Endothelial Corneal Dystrophy (FECD) is characterized by progressive loss and …

Functional And Microbial Consequences Of Experimental Evolution Under Starvation In Drosophila Melanogaster, Kristal Marie Aguilar-Conger

UNLV Theses, Dissertations, Professional Papers, and Capstones

Previous studies in the Gibbs lab have shown that starvation resistant Drosophila melanogaster flies have increased lipid content, lower metabolic rates, and poor physiological health. Historically, many evolutionary studies end at the phenotypic level, leaving the genomic basis largely unresolved. Using Evolve and Resequence (E&R) study, we can map genome-wide allele-frequency trajectories under selection, linking phenotypic shifts to their genomic underpinnings. This study utilized the E&R approach to identify enriched biological processes and pathways underlying starvation adaptation in Drosophila melanogaster. Five replicate restart populations (RS A–E) selected for starvation resistance, along with a control (RC), were resequenced at Generations 1, …

Microbial Guardians Of The Savannah: Unraveling The Gut Microbiome For African Carnivore Conservation, Laura E. Peirson

All NMU Master's Theses

Non-invasive fecal sampling is essential for wildlife gut microbiome (GMB) research, yet field conditions often limit preservation options. I compared gut bacterial communities in paired fecal samples preserved in stabilization tubes and air-dried in paper bags collected from anesthetized African lions (Panthera leo) and spotted hyenas (Crocuta crocuta) in Etosha National Park, Namibia. Additional opportunistic samples from carnivore kill sites were also analyzed. No significant differences in alpha or beta diversity were detected between preserved and dried samples, although bacterial beta diversity differed between preserved and opportunistic samples (PERMANOVA). Core bacterial communities remained consistent across sample …

Global Patterns Of Genetic Diversity And Species Delimitation In The Lichen-Forming Fungus Cladia Aggregata: A Restriction Site Associated Dna Sequencing (Rad-Seq) Analysis Across Neotropical, Australasian, And Asian Populations, John De Abreu

College of Science and Health Theses and Dissertations

Cladia aggregata is a group of lichen-forming fungi comprising multiple species which are difficult to differentiate. C. aggregata has a wide distribution on several different continents but is primarily found in the southern hemisphere. We aimed to further delimit the species complex while also investigating the relatedness of the different species, where they can be found geographically, and what phenotypic traits they possess. We used Restriction Site Associated DNA Sequencing (RAD-seq) to compare thousands of loci across 91 individuals from the Americas, Asia, and Australasia. All Asian samples formed a distinct clade in all phylogenetic trees. Asia, as a distinct …

Comparative Methylation Analyses Across Juglans Species To Investigate Epigenetic Contributions To Fungal Resistance, Keertana Chagari

Honors Scholar Theses

Juglans cinerea (butternut) is a critically threatened North American tree species experiencing severe declines due to the fungal pathogen Ophiognomonia clavigignentijuglandacearum. In contrast, its Asian relative, Juglans ailantifolia (Japanese walnut), shows natural resistance. To investigate the genomic and epigenetic factors underlying this difference, we constructed and analyzed high-quality, chromosome-level genome assemblies for both species from long-read sequencing data (J. ailantifolia: 527Mb; J. cinerea: 586Mb), focusing on transposable element (TE) content, DNA methylation patterns, and regulation of pathogen resistance genes (PRGs).

Repeat analysis revealed that J. cinerea has a slightly higher overall transposable element (TE) content, with …

How Soil Fungal Communities Respond To Invasive Plant Species Treatments In Soil From Banksia Woodland, South-Western Australia, Aaron J. Brace, Katinka X. Ruthrof, Joseph B. Fontaine, Ben P. Miller, Anna J.M. Hopkins

Research outputs 2022 to 2026

Context. Invasive plants are one of the most significant threats to woodlands globally. Methods of invasive plant control include manual removal and herbicide application. While the impacts of control methods on invasive and off-target native plant species are often explored, the impacts on below-ground organisms, such as fungi, are less well understood. Aims. We conducted a glasshouse trial to investigate the responses of soil fungal communities to herbicides and manual removal that are used to control common invasive plant species in Banksia woodland in south-western Australia. Methods. Broad spectrum (glyphosate and pelargonic acid) and grass-specific (fluazifop-p-butyl) herbicides were separately applied …

Pan-Cancer Universal Targets For Immunotherapy Resulted From Transposable Elements Activation, Yonghao Liang

Arts & Sciences Graduate Student Theses and Dissertations

Transposable elements (TEs) contribute to nearly half of the human genome yet have been overlooked in genomic medicines due to the stereotypic impression as “junk DNA” and technical challenges. However, studies in the last two decades demonstrated that dysregulation of the epigenome in cancer cells resurrects the cis-regulatory functions of TEs, including the promoter activities. The tumor-specific TE activation events along with the resulting tumor-specific RNA and protein molecules, provide a potential “gold mine” for identifying tumor-specific therapeutic targets for cancer treatments, including immunotherapy. Here, I present a series of works to investigate the potential of providing actionable, pan-cancer, and …

Analyzing Microalgae-Bacteria Population Changes In Response To Environmental Parameters For Improved Wastewater Treatment, Amanda M. Moravek

All Graduate Theses and Dissertations, Fall 2023 to Present

Microalgae are incredible organisms that have a variety of uses such as wastewater treatment, fertilizer, livestock feed, and bio-compound production. Microalgae require a light source and minimal nutrients space to proliferate, making them an environmentally friendly and sustainable option for such processes. The Sustainable Wastes-to-Bioproducts Engineering Center at Utah State University is developing and implementing a Rotating Algae Biofilm Reactor (RABR) to remove total nitrogen and phosphorous from the Central Valley Wastewater Reclamation Facility wastewater effluent. Harmful compounds such as nitrates and phosphates are metabolized by the microalgae and converted into useful bioproducts, resulting in a circular economy. These RABRs …

Aligning Exons, Introns, And Flanking Regions Of Cyc And Cuc Genes In Lonicera (Caprifoliaceae), Mark Mordukhay

Theses and Dissertations

The genus Lonicera (Caprifoliaceae) exhibits great diversity in floral symmetry, petal fusion, and organ arrangement, making it an ideal system for exploring the genetic basis of morphological evolution. We focus here on the roles of CYC and CUC gene families, (CYC2A, CYC2B, CYC3A, CYC3B, CUC2A, and CUC2B) and their potential contributions in shaping floral symmetry and organ fusion. The data set included nucleotide sequences from over 90 Lonicera species, extracted from samples collected from natural habitats or herbaria and then sequenced. A custom bioinformatics pipeline was developed in R using Bioconductor packages to automate BLAST searches, filter results, scan for …

Enabling Better Interoperability And Reusability For Down Syndrome Transcriptomic Datasets, Harrison Oaks, Garrett L. Wride, Stephen Piccolo

Library/Life Sciences Undergraduate Poster Competition 2025

Introduction: Gene expression profiling has become a cornerstone of biomedical research, offering relevant insights into the molecular mechanisms that underlie complex conditions such as Down syndrome (DS), a condition caused by trisomy 21. RNA expression data from individuals with DS have highlighted critical pathways involved in development, immune function, and disease susceptibility. Despite the availability of over 100 publicly shared RNA expression datasets, their potential remains underutilized due to inconsistent metadata, diverse normalization protocols, and varying data quality. Addressing these barriers is vital to enabling researchers to standardize, integrate, and analyze datasets effectively. We do this by creating a data …

Epigenetic Reprogramming In Pediatric Tumors Predicts Active Pathways In The Tumor Microenvironments, Noah Moffat, Clark Tolbert, Colin Wessman, Matthew H. Bailey

Library/Life Sciences Undergraduate Poster Competition 2025

Figure 1: We collected samples from five different studies that analyzed and generated spatial transcriptomic data from adult and pediatric brain tumors1-4.

Interactions Of The Sars-Cov-2 Viral Genome 3’-Untranslated Region With Viral And Host Rnas, Caleb Frye, Mihaela Rita Mihailescu

Electronic Theses and Dissertations

This dissertation focuses on the characterization of RNA-RNA interactions within the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) genome and with host microRNAs. As the causative agent of coronavirus disease 2019 (COVID-19), SARS-CoV-2 has evolved rapidly since its appearance. This has warranted prompt characterization of the virus particularly of its single stranded RNA (ssRNA) genome. By using a combination of bioinformatics, biophysics, and/or biological assays, we analyzed the SARS-CoV-2 viral genomic RNA and uncovered interactions of genomic RNA with host RNAs, highlighting an underutilized method of targeting RNA viruses. We showed here that the conserved elements in the viral genomic …

Multi-Omic Analysis Of Phototrophic Extracellular Electron Uptake In Novel Rhodovulum Spp. Isolated From A Marine Estuary, Emily J. Davenport

Arts & Sciences Graduate Student Theses and Dissertations

Microbial metabolisms are incredibly versatile and dynamic, allowing adaptive strategies for growth in even the most limiting environments. For an ever-increasing number of microbes, this includes utilizing soluble or insoluble inorganic mineral species as electron donors, driving geochemical cycles and microbial metabolisms. This metabolic function of transporting electrons derived from the extracellular environment across cell membranes is called extracellular electron uptake (EEU). Within (photo)autotrophs, (p)EEU also sustains CO2 fixation to cell biomass, implicating a potentially fundamental role of microbial carbon cycling in aquatic and soil ecosystems. A model metabolic scheme of pEEU occurring in natural environments is photoferrotrophy, which pairs …

Studies Of Media To Maximize The Expression Of Bacterial Metalloprotease Genes As Potential Therapeutics For Human Alzheimer’S Disease, Uday Kiran Chigurupati

Honors Capstones

This study investigates the potential of bacterial metalloprotease genes as therapeutic agents for Alzheimer's Disease (AD). The research focuses on Pseudomonas 20ei1 (P. 20ei1), a bacterial species isolated from lagoon water, which contains pitrilysin genes that share similarities with human insulysin. Six pqqL-related genes were identified in P. 20ei1 for this study. The research methodology involved bioinformatic studies, bacterial cell culture in various media, RNA extraction, purification, and cDNA synthesis. Quantitative PCR analysis was performed to analyze gene expression levels in different cDNA samples. The bacteria grown in the medium with insoluble phosphate has shown higher expression of selected genes …

What Drives Gut Microbial Diversity And Community Structure Among Closely-Related Host Species?, Rylee Jensen

All NMU Master's Theses

The gut microbiome (GMB) of mammals hosts an important community of microbes that perform countless micro-ecosystem services for the host and are influenced by numerous factors including host physiology, environment, and phylogeny. Phylogeny may have a unique effect on GMB diversity and community structure (i.e., a GMB profile) via phylosymbiosis, a theory in which the evolution of hosts matches the evolution of their associated microbiota. Elucidating phylosymbiosis in mammals is difficult because multiple intrinsic and extrinsic factors collectively drive individual GMB variation. Thus, there is a need to simultaneously analyze the role of physiology, environment, and phylogeny on shaping host …

Early Onset Alzheimer’S Disease Markers In Mouse Hippocampus Unveiled By Single-Cell Transcriptomic Analysis Following Cranial Radiotherapy, Tuba Aksoy

Dissertations and Theses (Open Access)

Cranial radiation therapy plays an integral role in the treatment of brain tumors but can lead to progressive cognitive deficits in survivors by mechanisms that are poorly understood. To develop preventive or mitigative strategies, it is crucial to better understand the underlying pathogenesis of radiation-induced cognitive impairments. The study investigated single-cell transcriptomics and DNA methylation changes as potential drivers of persistent cellular dysfunction after radiation exposure, specifically concentrating on the CA1-3 regions of the hippocampus and the prefrontal cortex due to their role in cognitive functions. Thirteen-week-old mice underwent whole-brain radiation at clinically relevant doses. Following whole-brain radiation, an assessment …

Understanding The Relationship Between Genetic And Epigenetic Variation At A Species And Individual Level, Kara Quaid

Arts & Sciences Graduate Student Theses and Dissertations

Genetic sequences and epigenetic features work together to regulate gene expression, which can vary across species, individuals, and cell-types. Understanding this relationship between genetics and epigenetics is a key step to revealing the connection between genotype and phenotype on a systematic, genome-wide level. The first chapter of my thesis outlines the ways genetic variation and epigenetic variation may interact to shape gene regulation across scales, as well as how we can question it further. One of the most studied mechanisms is genetic variation that has a direct impact on epigenetic variation. At the species level, it is documented that species-specific …

Feather Mites Through Genomic And Ecological Lenses: Host Specificity And Symbiosis At Multiple Levels Of Organization, Alix Elizabeth Matthews

Student Theses and Dissertations

Symbionts, or organisms that form close and persistent associations with hosts, are ubiquitous across the tree of life, and symbioses are among the most common interspecific interactions in the natural world. Symbionts play a fundamental ecological and evolutionary role across multiple levels of biological organization – from individuals to ecosystems – and can have strong effects on global biodiversity. However, many aspects of these relationships are poorly understood including symbiont genetic diversity (inter- and intraspecific), host specificity, and the mechanisms underlying their functional nature or any context-dependent patterns. This dissertation uses a model symbiosis between permanent, obligate, ectosymbiotic vane-dwelling feather …

Investigating A Family Of Fungal Pseudopeptidases With Bioinformatics Tools, Andy Zhao

Honors Theses

Enzymes catalyze chemical reactions; however, some proteins related to enzymes lack enzyme activity. To investigate changes that occur as enzymes becomes pseudoenzymes, I studied a unique family of fungal carboxypeptidases. I identified all fungal carboxypeptidase protein sequences in the NCBI database, constructed an alignment and phylogenetic tree for sequence comparison, and used Alphafold2 for 3D modeling of representative proteins. Fourteen unique groups were identified. All fungal proteins selected are separated into 3 categories, predicted to be active, intermediate, and inactive, respectively. Proteins predicted to be pseudoenzymes contained additional loops in mutation hotspots not found in predicted active enzymes. This research …

Investigating The Role Of Circular Rnas In Metastatic Colorectal Cancer Progression, Sidi Zhao

Arts & Sciences Graduate Student Theses and Dissertations

Colorectal cancer (CRC) is the most common gastrointestinal malignancy and a leading cause of cancer deaths in the U.S.A. More than half of CRC patients develop metastatic disease (mCRC) with a 13% average 5-year survival rate. Despite advances in our understanding of primary CRC oncogenesis and biology, the mechanisms of tumor metastasis remain poorly characterized. To date, CRC research has primarily focused on the dysregulation of protein-coding genes to identify oncogenes and tumor suppressors as potential diagnostic and therapeutic targets, thereby under-representing the critical role of many classes of non-coding RNAs (ncRNAs). One emerging class of ncRNAs, circular RNAs (circRNAs), …

Advances In Methods For Trna Sequencing And Quantification, Nigam H. Padhiar, Upendra Katneni, Anton A. Komar, Yuri Motorin, Chava Kimchi-Sarfaty

Biological, Geological, and Environmental Faculty Publications

In the past decade tRNA sequencing (tRNA-seq) has attracted considerable attention as an important tool for the development of novel approaches to quantify highly modified tRNA species and to propel tRNA research aimed at understanding the cellular physiology and disease and development of tRNA-based therapeutics. Many methods are available to quantify tRNA abundance while accounting for modifications and tRNA charging/acylation. Advances in both library preparation methods and bioinformatic workflows have enabled developments in next-generation sequencing (NGS) workflows. Other approaches forgo NGS applications in favor of hybridization-based approaches. In this review we provide a brief comparative overview of various tRNA quantification …

Shifting Soil Fungal Communities In Response To Fire And Weed Management In Urban Banksia Woodlands, Aaron Justin Brace

Theses: Doctorates and Masters

This research aims to fill the knowledge gap in soil fungi in the Banksia woodland and emphasizes considering holistic ecosystem dynamics in invasive species management strategies. This is accomplished by surveying soil fungi under different fire regime across the Swan Coastal Plain, and within both in and ex situ herbicide application trials. This is the first such study to investigate the fungal component of the Banksia woodland so thoroughly. Chapter 2 quantified and analysed changes in soil fungal community composition and functional groups over a 50-year fire chronosequence in fire-prone Banksia woodland in southwestern Australia. Effects were variable, but fungal …

Deep Learning In Bioinformatics, Malik Yousef, Jens Allmer

Turkish Journal of Biology

Deep learning is a powerful machine learning technique that can learn from large amounts of data using multiple layers of artificial neural networks. This paper reviews some applications of deep learning in bioinformatics, a field that deals with analyzing and interpreting biological data. We first introduce the basic concepts of deep learning and then survey the recent advances and challenges of applying deep learning to various bioinformatics problems, such as genome sequencing, gene expression analysis, protein structure prediction, drug discovery, and disease diagnosis. We also discuss future directions and opportunities for deep learning in bioinformatics. We aim to provide an …

Engaging Students In A Genetics Course-Based Undergraduate Research Experience Utilizing Caenorhabditis Elegans In Hybrid Learning To Explore Human Disease Gene Variants, Natalie Forte, Virginia Veasey, Bethany Christie, Amira Carter, Marli Hanks, Alan Holderfield, Taylor Houston, Anil Challa, Ashley Turner

Research, Publications & Creative Work

Genetic analysis in model systems using bioinformatic approaches provides a rich context for a concrete and conceptual understanding of gene structure and function. With the intent to engage students in research and explore disease biology utilizing the nematode Caenorhabditis elegans model, we developed a semester-long course-based undergraduate research experience (CURE) in a hybrid (online/in-person) learning environment—the gene-editing and evolutionary nematode exploration CURE (GENE-CURE). Using a combination of bioinformatic and molecular genetic tools, students performed structure-function analysis of disease-associated variants of uncertain significance (VUS) in human orthologs. With the aid of a series of workshop-style research sessions, students worked in teams …

An Evolutionary Comparative Study Of Congenital Stationary Night Blindness-Associated Trpm1 Genetic Variants Of Uncertain Significance In Horses And Humans Utilizing Caenorhabditis Elegans, Gabrielle Davis

Theses

Congenital stationary night blindness (CSNB) is a heterogeneous collection of genetic diseases affecting the eyes and vision in horses and humans. Current research has implicated several genetic mutations impacting different genes involved in phototransduction and signal transmission, including TRPM1. In horses, genetic mutations in TRPM1 also result in a leopard spotting pattern or leopard complex. The goal of this study is to examine the potential impact of CSNB associated TRPM1 missense variants of uncertain significance (VUS). Previous research in Caenorhabditis elegans have revealed an orthologous TRPM1 gene known as gon-2 that allows for comparative studies. The evolutionary relationship of …

Targeted Mapping Of Oryza Sativa Chilling Tolerance Candidate Genes Using Multiple Stress-Relevant Quantitative Traits, Naoki Simon Shimoyama

Dissertations (1934 -)

Developing chilling tolerant accessions of domesticated Asian rice is a potential source of significant crop improvement to address the needs of a growing global population. The uniquely chilling sensitive nature of the tropically originating Oryza sativa make it the most important staple crop that could gain the maximum benefit from improved tolerance to low temperature stress. However, mechanisms underlying this complex trait are not fully understood. Oryza sativa has two major varietal groups with different levels of chilling tolerance, JAPONICA and INDICA, providing an ideal tool to investigate mechanistic differences in the chilling stress tolerance responses within this important crop …

Vircy-Seq : A Protocol For Characterizing Viral Activity, Tyler James Dion

Legacy Theses & Dissertations (2009 - 2024)

The main purpose of pharmaceutical production is to produce safe effective medicine for patient use. In an effort to ensure patient safety constant surveillance for viruses takes place. The detection of a viral nucleic acid in a pharmaceutical production setting results in investigations to assess its infectious potential. This is an intensive, expensive process that entails many tests such as the observation of hemadsorption, cytopathic effects (CPE), and more. These tests are typically specific and only capture certain viruses, as factors like CPE can only be observed in some viral species. A new investigational method that is effective on all …

Ngly1 Deficiency Affects Glycosaminoglycan Biosynthesis And Wnt Signaling Pathway In Mice, Amy Batten

PANDION: The Osprey Journal of Research and Ideas

Individuals affected by NGLY1 Deficiency cannot properly deglycosylate and recycle certain proteins. Even though less than 100 people worldwide have been diagnosed with this rare autosomal recessive condition, thousands are affected by similar glycosylation disorders. Common phenotypic manifestations of NGLY1 Deficiency include severe neural and intellectual delay, impaired muscle and liver function, and seizures that may become intractable. Very little is currently known about the various mechanisms through which NGLY1 deficiency affects the body and this has led to a lack of viable treatment options for those afflicted. This experiment uses a loss-of-function (LOF) mouse model of NGLY1 Deficiency homologous …

Genome-Wide Identification And Salt Stress Response Analysis Of The Bzip Transcription Factor Family In Sugar Beet, Yongyong Gong, Xin Liu, Sixue Chen, Hongli Li, Huizi Duanmu

Faculty and Student Publications

As one of the largest transcription factor families in plants, bZIP transcription factors play important regulatory roles in different biological processes, especially in the process of stress response. Salt stress inhibits the growth and yield of sugar beet. However, bZIP-related studies in sugar beet (Beta vulgaris L.) have not been reported. This study aimed to identify the bZIP transcription factors in sugar beet and analyze their biological functions and response patterns to salt stress. Using bioinformatics, 48 BvbZIP genes were identified in the genome of sugar beet, encoding 77 proteins with large structural differences. Collinearity analysis showed that three pairs …