Genetics Commons^™

Morphometric And Genetic Analyses Of The Sheat Catfish Genus Ompok And Kryptopterus (Siluriidae) From The Mahakam River, East Kalimantan, Indone-Sia, Jusmaldi Jusmaldi, Rudhy Gustiano, Haryono Haryono, Rusdianto Rusdianto, Gema Wahyudewantoro, Syahroma Husni Nasution, Yulianto Yulianto, Muhammad Hunaina Fariduddin Aththar, Safar Dody, Amran Ronny Syam, Irin Iriana Kusmini, Yosmaniar Yosmaniar

Makara Journal of Science

Anthropogenic impacts within the watershed threaten the survival of sheat catfish. Therefore, species of the genera Ompok and Kryptopterus should be conserved and domesticated to ensure their long-term persistence. Moreover, the accurate documentation of the existence and taxonomic validity of Ompok and Kryptopterus species is crucial. Accordingly, this study aims to assess the species diversity of the genera Ompok and Kryptopterus in the Mahakam River, East Kalimantan, Indonesia. The study was conducted between June and December 2014, with an update in August 2024. Fish samples were collected from the upstream and middle reaches of the Mahakam River. A total of …

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 …

Investigating The Role Of Centromere Deletion In Chromosome Segregation, Azait Imtiaz

ETDs from 2020-2029

Centromeres are critical genomic regions responsible for ensuring accurate chromosome segregation during cell division. Disruptions in the structural or functional integrity of centromeric DNA could impair kinetochore assembly, leading to chromosome missegregation and chromosomal instability (CIN), a hallmark of various human diseases, including systemic sclerosis (SSc). This study investigated the contribution of centromeric DNA damage and deletion to CIN and explored potential pathogenic mechanisms relevant to SSc. We utilized hTERT-immortalized fibroblast cell lines (CHON-002 and BJ-5ta) to implement two complementary approaches: (i) treatment with bleomycin, a chemotherapeutic agent known to induce DNA double-strand breaks (DSBs), and (ii) targeted deletion of …

Elucidating The Function Of Yedk In Response To Dna Damage, Hank Munro

University Honors Theses

Apurinic/Apyrimidinic (AP) sites are one of the most prevalent forms of DNA damage. These lesions arise spontaneously or during base excision repair of modified DNA bases and are potentially mutagenic in both mammalian and bacterial cells. 5-hydroxymethylcytosine binding, ES cell specific (HMCES), a protein found in eukaryotic cells, has been shown to form a stable DNA-protein crosslink with AP sites in single stranded DNA and to reduce the number of AP sites occurring either spontaneously or after alkylative DNA damage, resulting in increased genome stability. YedK, the Escherichia coli ortholog of HMCES exhibits some of the same biochemical properties as …

Polygenic Risk Scores, Sex, And Socioeconomic Factors As Predictors Of Age Of Onset For Major Depressive Disorder, Kaitlyn M. Nowak

USF Tampa Graduate Theses and Dissertations

Major Depressive Disorder (MDD) is a heterogeneous psychiatric condition influenced by genetic, sociodemographic, and environmental factors, yet the extent to which these factors jointly shape the timing of disease onset remains unclear. This study evaluated the effects of polygenic risk scores (PRS), sex, and socioeconomic status (SES) on age of onset for MDD across two independent cohorts: the Pharmacogenomics Research Network Antidepressant Medication Pharmacogenomics Study (PGRN-AMPS) (N = 486) and the All of Us Research Program (N = 8,014). Analyses were restricted to individuals of European genetic ancestry, and PRS were constructed using both European-ancestry (EA) and multi-ancestry (MA) genome-wide …

The Evolutionary Response Of HawaiʻI ʻAmakihi (Chlorodrepanis Virens) To The Introduction Of Avian Malaria (Plasmodium Relictum), Gabrielle Atkinson

Doctoral Dissertations

The emergence of novel pathogens can impose intense selective pressures on natural populations, driving rapid evolutionary change or precipitating population collapse. In Hawaiʻi, the introduction of avian malaria (Plasmodium relictum) and its mosquito vector (Culex quinquefasciatus) have caused severe declines and extinctions among native forest birds. Yet some populations of Hawaiʻi ʻamakihi (Chlorodrepanis virens) persist across a broad elevational and disease gradient, providing a powerful natural system for examining the genomic basis of rapid adaptation, the role of gene flow in adaptive response, and the potential for parallel evolutionary responses. This dissertation integrates genomic, population genetic, and transcriptomic approaches to …

Marine Heatwaves And Fish Reproduction: Endocrine Responses In The Eurythermal Sheepshead Minnow (Cyprinodon Variegatus), Isabel Villafuerte

Master's Theses

Marine heatwaves associated with climate change are increasing in frequency and severity, posing significant threats to fish populations in shallow habitats such as estuaries and salt marshes. Because temperature is a primary regulator of fish reproduction, understanding how heatwaves affect reproductive physiology is critical for anticipating the biological consequences of ongoing climate change for coastal fishes. Here we examined how simulated heatwave conditions affect the reproductive hypothalamic-pituitary-gonadal (HPG) endocrine axis in the estuarine sheepshead minnow (Cyprinodon variegatus), a eurythermal fish well suited to studying thermal stress responses in estuarine environments. Adult sheepshead minnows acclimated to a daily oscillating …

Filtered Genome Of Commercial Philippine Varieties Of Sugarcane (Saccharum Officinarum L.) For The Characterization And Identification Of Ssrs Associated With Resistance To Philippine Downy Mildew (Peronosclerospora Philippinensis), Antonio G. Lalusin, Jhun Lawrence S. Rasco

The Philippine Agricultural Scientist

Sugarcane is a major global source of sugar, with total production reaching 1.89 billion t. Although the Philippines produces about 1.85 million t of sugarcane annually, yields are limited by downy mildew and smut. Developing varieties resistant to these pathogens is the most economical and practical approach to mitigating losses from these biotic stresses. In this study, SSRs related to disease resistance were developed through Next-Generation Sequencing (NGS) of the filtered genomes of sugarcane varieties with known phenotypic responses to downy mildew. Two assemblies based on minimum contig lengths (450 and 900 bp) were performed using SoapDeNovo2. The 900-bp assembly …

Du Undergraduate Showcase Abstracts: Research, Scholarship, And Creative Works, Sophia Wismar, Henry Staats, Allison Metzler, Chloe Puckett, Rachel Levine, Christa Kilpatrick, Scott Wolf, Joe Walsh, Grace Doolittle, John Engebreston, Zoe Lopez, Christopher Aaby, Audrey Duff, Timothy Sisk, Katelyn Lamberton, Angela Narayan, Gilkah Argueta, Habiba Samir, Girena Tesfazghi, Genet Kenore, Sinit Tesfamariam, Effley Brooks, Abi Newell, Megan Doherty, Natalie Baer, Lexi Blood, Talya Riciputi, Jessica Jimenez, Devin Hernandez, Lynn Clark, Taj Kumar, Sunil Kumar, Allen Rutman, Mira Pronobis, Tess Carson, Anna Sher, Frankie Stroud, Tamra Pearson D'Estree, Alyssa Wilson, Emily Melnick, Jenalee Doom, Yihang Gao, Gwendolyn Geiger, Noah Gettle, Scott Nichols, Clare Ayoub, Cara Dienno, Sunny Walker, Zoe Hansen, Maya Wheeler, Addison Rice, Patrick Martin, Sanjana Acharya, Daniel Mcintosh, Amanda Mckellips, Calli Cain, Justin Blake, Peter Sokol-Hessner, Natalie Miller, Max Weisbuch, Sophia Dellota, John Macikas, Charlotte Snow, Mark Siemens, Zoe Lynch, Alex Huffman, Prachi Shah, Jason Roney, Halcyon Levi, Nicole Herzog, Andrea Koly, Daniel Linseman, Annie London, Xi Yang, Avery Zwisler, Jane Smith, Chaz Contag, Michael Kerwin, Lucy Rand, Grace Schroeder, Michelle Rozenman, Nissa Tapper, Guiming Zhang, Mateo Mazariego-Halpern, Keith Meyer, Julie Do, Dakota Park-Ozee, Travis Herink, Kara Neu, Jonathan Plomin, Eve-Odine Duchaufour, Debbie Gale Mitchell, Tennyson Anderson-Stricklin, Lily Treitz, Samantha Rosenberger, Sierra Griffith, Finley Joseph, Daniel Sampson, Emmy Davis, Skyler Kasnoff, Evon Lopez, Vivian Nguyen, Cassy Young, Franklin Sellner, Martin Tobon, Ila Graham, Zach Billings, Holden Hedit, Decatur Boland, Paul Kosempel, Cory Chandler, Jay Mahoney, Sam Dragan, Susan Dagget, Yarrow Ator, Heidi Vuletich, Owen Weber, Andrew Kloeppel, Petersen Gray, Mandi Schaeffer-Fry, Razleen Bassra, Bryanna Rodriguez, Christina Blue, Taubie Sanders, Rachel Epstein, Luke Milburn, Camryn Evans, Ezra Martinez, Mary Westwood, Gabri Notov, Robin Tinghitella, Lilou Cabrol, Eli Barbour, Juliet Mendik, Selma Myers, Zac Wise, Noah Fahlin, Michelle Knowles, Abigail Hopper, Michael Greenberger, Romi Laclair, Sarah Watamura, Sabrina Efroymson, Casey Barker, Sydney Seltzer, Bryn Yehle, Jennifer Hoffman, Sara Garcia, Ryuka Nagamine, Trevor Briggs, Remy Le Boeuf, Elena Krone, Eileen Farrell, Regan O'Rourke, Elena Roel, Greg Mortimer, Ali Ayoub, Stefani Langehennig, Caitlin Turk, Logan Scmid, Stefan Chavez-Norgaard, Karen Kim, Tatiana Peccedi, Courtney Cassidy, John Sebesta, Rhianna Lewis, Janice Bening-Lacek, Vivian Lawless, Mckenna Hanson, Jeffrey Amidon, Riya Joshi, Ram Ambre, Brady Worrell, Perrin Schneider, Ali Azadani, Brooke Agulnek, Lyndsie Salvagio, Elise Siemanowki, Yan Qin, Andre Allen, Melodie Nguyen, Megan Livengood, Abby Reams, Saffron Hartreeve, Bri Wylie, Sarah Brookman, Mariah Loiacono, Green Russo, Abhia Lodhi, Gabrielle Welsh, Nika Spehar, Shahked Levin, Evrim Baykal, Kimberly Chiew, Jocelyn Torres, Kailey Hicks, Mykaela Tanino-Springsteen, Audrey Bellows, Akam Chahal, Madeline Tepper, Shannon Murphy, Alexa Fonseca, Deborah Han, Cassandra Perez, Oluwatoyin Alaba, Julia Roncoroni, Vy Nguyen, Nana Burn, Sarah Sasse, Rubin Tuder, Anthony Gerber, Nancy Lorenzon, Christine Vohwinkel, Camryn Gunter, Tristan Weber, Sam Rommel, Brian Michel, Muskan Fatima, Alannah Oleson, Kira Frey, Edward Garrido, Beckett Morris, Kerstin Haring, Drew Middleton, Abigail Walpert, Liam Dee, Gabby Ishaw, Cole Carnes, Maddie Weiser, Claire Fox, Valeriia Vlasenko, Kateri Mcrae, Riley Smith, Abigail Templin, Kushani Rajapaksha

DU Undergraduate Research Journal Archive

Abstracts from the DU Undergraduate Research Showcase.

The Competition Between Splicing And 3′ Processing Shapes The Human Transcriptome, Lindsey V. Soles, Shuangyu Li, Liang Liu, Kristianna S.K. Sarkan, Erik G. Alvstad, Lusong Tian, Yoseop Yoon, Marielle Valdez, Ivan Marazzi, Yongsheng Shi

Biology, Chemistry, and Environmental Sciences Faculty Articles and Research

Eukaryotic pre-mRNA processing steps, including splicing and 3′ processing, are tightly coordinated, yet the underlying mechanisms remain incompletely understood. U1 snRNP has been proposed to inhibit 3′ processing at intronic polyadenylation (IPA) sites through a splicing-independent mechanism termed telescripting. In contrast, we discovered that disrupting splicing by using six different methods—targeting various key components such as U1 snRNP, U2 snRNP, U2AF, and SF3b—activates 3′ processing at thousands of IPA sites. Notably, splicing inhibition, especially of U1 snRNP, induced widespread premature transcription termination within gene bodies through both IPA-coupled and IPA-independent mechanisms. Inhibition of different splicing factors activated overlapping and distinct …

Quantifying Genetic Diversity In Nematode Feeding Rate, Jacob King

Honors Theses

Understanding how populations persist under changing environmental conditions is a central question in ecology and evolutionary biology. Variation in traits related to resource acquisition may play a key role in determining population survival when resources are limited or fluctuate over time. In this study, I investigated how variation in feeding-related traits influences population persistence using a combination of computational modeling and laboratory experiments. I developed a stochastic, individual-based consumer–resource model to simulate population dynamics across varying levels of trait variance and resource regimes. Across 60,000 simulated populations, increased trait variation consistently reduced extinction risk and extended persistence time, although the …

Navigating The Genetic Frontier: Clinical And Ethical Implications Of Free Genetic Testing In India, Preetha Vijayalakshmi

Journal Of Indian Physician Associates

The expansion of free genetic testing services in India, resulting from government policies like the Ayushman Bharat Digital Mission, corporate-sponsored initiatives, and international collaborations, makes it easier to access genomic services for early identification of inherited disorders such as thalassemia, sickle cell anemia, and certain genetic kidney diseases, particularly in tribal populations. However, this review reveals significant clinical and ethical challenges. Clinically, Western-based genotyping platforms, not tailored to India’s genetic diversity, risk inaccurate results, including false positives and negatives, complicating clinical decision-making. A shortage of genetic counsellors and inadequate post-test care leaves patients, especially in rural areas, struggling within fragmented …

Using The Flexon Approach To Rnai For Analysis Of Gene Function In Gonadal Development In C. Elegans, Andrew D. Spalding

Undergraduate Theses

C. elegans, a nematode worm, was used as a model organism to analyze the developmental effects of knocking down the expression of genes that are both essential to worm viability and highly enriched in reproductive tissues. In earlier research, approximately 70 C. elegans genes were identified that are both gonad-enriched and essential. To prioritize which genes should be the focus of future studies, a new strain of C. elegans was produced with three specific genetic variations that: 1) silence essential, somatic gonad-enriched gene expression, 2) limit the effects of this gene silencing to the gonad, and 3) yield a …

Investigating The Taxonomic Uncertainties Of Potentilla Rupincola, Natalie Elizabeth Hieber

Master's Theses

Landscape stewardship is an integral role for land managers that becomes more important when rare or endangered species occur within managed areas. Conservation across the landscape is a primary concern for land managers, but resources allocated for conservation can be limited due to many competing goals. Taxonomic uncertainty surrounding rare and endangered taxa, particularly plant taxa, that have historically been classified solely using morphological features further complicates conservation planning. One such taxon is Potentilla rupincola, a rare plant endemic to the eastern Rocky Mountains in Colorado. For over a century, botanists have debated whether P. rupincola is a distinct species …

Sorghum Grain Secondary Metabolites And Underlying Genetics To Reduce Foodborne Pathogens In Poultry, Maria A. Conti

All Dissertations

The rise in antibiotic-resistant pathogens poses a threat to the poultry industry's ability to maintain animal health, prompting growing interest in alternatives to synthetic antibiotics. The use of non-tannin sorghum [Sorghum bicolor (L.) Moench] in poultry rations offers a valuable alternative, as this cereal grain has a high bioactive profile that can provide health benefits, including antimicrobial (AM) activity. The scope of this study was to examine the AM potential of non-tannin sorghum grain against Clostridium perfringens, a major foodborne pathogen that negatively impacts poultry health and production. To that end, the inhibitory effects of a non-tannin sorghum …

Morphological And Dietary Consequences Of Hybridization Between Mexican Ducks And Western Gulf Coast Mottled Ducks In A Human-Altered Landscape, Vergie Miranda Musni

Open Access Theses & Dissertations

Hybrid zones provide unique opportunities to study morphological and ecological consequences of hybridization. While landscape genetic studies confirm a newly established contact zone between Mexican Ducks (Anas diazi) and Western Gulf Coast Mottled Ducks (Anas fulvigula maculatus), I provide the first quantitative morphological comparisons of the two taxa and their hybrids in Chapter 1. First, I report significant differences among parental species in lamellar density, body mass, tarsus length, and wing chord lengths, with hybrids exhibiting intermediate or backcross-aligned phenotypes. In contrast, measured bill dimensions did not differ significantly between parental taxa. Despite substantial overlap in bill morphology between Mexican …

The Genetic Basis Of High Transformation Efficiency In The Model Yeast Saccharomyces Cerevisiae, Mary Kathryn E. Cheek

Biological Sciences Undergraduate Honors Theses

Transformation, a type of horizontal gene transfer, describes the uptake, maintenance, and integration of environmental DNA by cells. Despite the known effects of transformation on evolutionary processes, little is known about the genetic basis of this phenomenon. Saccharomyces cerevisiae is a eukaryote able to transform at quantifiable rates when made chemically competent and treated with a heat shock. S. cerevisiae also has variation in transformation efficiencies between various strains, and high recombination rates allow for sufficient allele “shuffling” in intercross populations. This project utilizes a bulk segregant analysis approach to compare sequencing data between transformant pools and non-transformant pools of …

Precursor Rna Properties Driving Cryptic 3’ Splice Site Selection In Sf3b1 Mutant Malignancies, Austin A. Herbert

All Dissertations

SF3B1 is a core component of the spliceosome involved in branch point recognition and 3’ splice site selection. SF3B1 is commonly mutated in myelodysplastic syndromes and other blood cancers with the K700E mutation being the most frequent. This mutation of SF3B1 induces cryptic 3’ splice site activation in hundreds of genes. Introduction of such cryptic 3’ splice sites can shift the reading frame of protein coding transcripts, causing the transcript to be tagged for nonsense-mediated decay or resulting in the production of a truncated protein. Both these scenarios can lead to down-regulated protein expression. Sequence and structural properties of precursor …

Genetic Screen For Regulators Of Pol4, A Dna Repair Polymerase In Saccharomyces Cerevisiae, Pasang Dolma Sherpa

Theses and Dissertations

In Saccharomyces cerevisiae, DNA polymerase 4 (POL4) is the beta repair polymerase, the product of the POL4 gene, and is involved in base excision repair (BER) and microhomology-mediated end joining (MMEJ). Despite its involvement in these repair pathways and its conservation across eukaryotes, deletion of POL4 shows no detectable phenotype under standard laboratory conditions. I hypothesized that unknown genes act as backup systems, providing redundant activities that allow pol4Δ cells to survive. To test this, a genetic screen for mutants showing synthetic lethality with pol4Δ was implemented. I constructed a strain lacking the POL4 gene and carrying …

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 …