Genetics and Genomics Commons^™

Surveillance And Comparative Genomics Of Bacteria From Hospital And Human Reservoirs, Emily E. Benedict

WUSM Theses and Dissertations – All Programs

Bacteria are diverse and adaptable and, consequently, present in a wide variety of environments. They are capable of growing under intense pressures, including those brought on by the human immune system and disinfection strategies. To survive these pressures, bacteria develop resistances. Antimicrobial resistance, which occurs when a microbe is no longer responsive to the antibiotic intended to control it, is one such adaptation that presents an especially serious threat, as it limits treatment options for infections caused by antimicrobial resistant microbes. Similarly, the ability of bacteria to survive in environments subjected to heavy disinfection efforts, such as intensive care units …

Multiomic And Single-Cell Analysis Of Tumors And Their Immune Microenvironment For Personalized Cancer Therapy, Kartik Singhal

WUSM Theses and Dissertations – All Programs

Precision oncology aims to match cancer treatment to the biology of an individual patient’s tumor. However, tumors that share a diagnosis can differ in their molecular features, cellular composition, clinical course, and response to therapy, making it difficult to determine which treatment will benefit an individual patient. This dissertation integrates genomic, transcriptomic, and single-cell multiomic computational analysis to characterize tumors across their somatic alterations, transcriptional cell states, microenvironment, and the immune response they elicit.

The first study describes a rare case of donor-derived follicular lymphoma following kidney transplantation. Genomic profiling showed that the donor and recipient tumors shared 31 somatic …

Exploring Competitive Dynamics Between Pseudomonas Baetica And Salmonella In A Polymicrobial System, Braxton E.M. Stout

Electronic Theses and Dissertations

The global rise in antimicrobial resistance has catalyzed a greater focus on polymicrobial research aimed at characterizing microbial interactions and uncovering new therapeutic strategies. Though it has long been of interest, environmental soil-derived bacteria remain largely under-represented in research and thus uncharacterized in this field. This project aimed to identify soil microbes that display inhibitory mechanisms to potential nosocomial pathogens. Soil sample S1S3-2 displayed inhibitory phenotypes toward numerous bacteria and was identified as Pseudomonas baetica. In both planktonic and biofilm growth, P. baetica was able to inhibit Salmonella arizonae through a contact-dependent and temperature-dependent manner. Screening of a transposon insertion …

Association Of Vegf Gene Polymorphisms And Breast Cancer Susceptibility: An Updated Systemic Review And Meta-Analysis, Dr.Santhosh Kumar Y, Sushma Sree Kintali, Vignesh N

Chulalongkorn Medical Journal

Breast cancer is among the most common malignancies in women worldwide with genetic predispositions and environmental factors and identified low-penetrance genes such as BRCA1 and BRCA2 with implications in breast cancer susceptibility. Vascular endothelial growth factor polymorphisms of VEGF coding for VEGF protein that plays an important part in carcinogenesis through angiogenesis required for tumor growth, invasion, and metastasis. There are five polymorphisms associated with the VEGF gene; 936 C > T, 2578 C > A, 634 G > C, 460 T > C, and 405 C > G which have been linked to altered risks in cancer. Despite inconsistency in many results ascribed to …

Carpet Viper (Echis Romani) Envenoming In Nigeria: Ecology, Venom Pathophysiology, Clinical Burden And Health-System Determinants, Godpower Chinedu Michael, Auwal A. Bala

Human Genetics Publications

Purpose of review: The carpet viper (Echis romani, recently separated from E. ocellatus) accounts for at least 66% of confirmed snakebite envenomings in the Nigerian savanna. Despite this, continental hazard modeling ranks it second in Nigeria. It is smaller and not necessarily more venomous per bite than the puff adder (Bitis arietans) or the black-necked spitting cobra (Naja nigricollis). This review synthesizes evidence on the ecology, venom effects, clinical impact, and health-system factors of carpet viper envenoming in Nigeria, including its effects on livestock and One Health considerations.

Recent findings: The risk of snakebite is influenced by multiple factors beyond …

Characterization Of The Genotypic And Phenotypic Spectrum Of Tcf7l2-Related Neurodevelopmental Disorder (Trnd), Sally Nijim, Mimi Kim, Melissa Denish, Michael V. Gonzalez, Joseph Zinski, Claudine Rieubland, Dominique Braun, Elsebet Ostergaard, Amelle Shillington, Laurence Faivre, Julien Maraval, Aurore Garde, Christophe Philippe, Fréderic Tran-Mau-Them, Amy Crunk, Robert Daber, Emily Westheimer, William O' Callaghan, Nirav Malni, Ingrid Chen, Kaylee Scozarro, Michelle Barbosa, Andrew Cohen, Arthur Ko, Emmanuele Delot, Georgia Pitsava, Seth Berger, Lightning Auriga, Ya Cui, Changrui Xiao, Charles Hadley King, Eric Vilian, Ivan De Dios, Jonathan Lotempio, Miguel Almalvez, Vincent Fusaro, Wei Li, Jamie Fraser, Meghan Delaney, Leandros Boukas, Bojan Losic, Esther (Yun-Ha) Hsiao, John Harting, Kriste Bluske, Rachid Karam, Sami Belhadj, Megan Hawley, Bert Callewaert, Maria Iascone, Anna Cereda, Cecilia Daolio, Tova Hershkovitz, Jean-Marc Good, Katharina Steindl, Tanja Frey, Anita Rauch, Alexandra Afenjar, Cyril Mignot, Jean-Madeleine De Sainte Agathe, Nicolette Den Hollander, Yvonne Hilhorst-Hofstee, Saskia Koene, Gijs Santen, Emilia K Bijlsma, Sara Berger, Lakshmi Mehta, Radka Stoeva, Clara Houdayer, Paul Gueguen, Helene Faust, Sabine Specht, Annick Klabunde-Cherwon, Melik Malek Khelifa, Anke Bergmann, Carol Saunders, Magdalena Krygier, Diana Carrasco, Kay Metcalfe, Stephan J. Sanders, David Y. Zhang, Renae Judy, Wes Nijim, David Exposito-Alonso, Christine X. Deng, Jusung Kim, Jozef Gecz, Corrado Romano, Cindy Skinner, Angie Lichty, Ellen Linebaugh, Steven A. Skinner, Maria Chahrour, Tianyun Wang, Kun Xia, Hui Guo, Sien Van Daele, Gert Van Goethem, Christina Fagerberg, Jesper Graakjaer, Susanne Anders, Heike Fink, Ward D. Isum, Dorothy K. Grange, Alanna Strong, Petra Zwijnenburg, Meghan Towne, René G. Feichtinger, Jennifer Morrison, Aditi Dagli, Jonathan Levy, Yline Capri, Rebecca C. Spillman, Sarah Hart, Vandana Shashi, Boris Keren, Tjitske Kleefstra, Rolph Pfundt, Christian Gilissen, Evan E. Eichler, Melanie Brugger, Michael Zech, Wendy K. Chung, Maria Fasolino, Holly C. Dow, Daniel J. Rader, Edward S. Brodkin, Maja Bucan, Eric D. Marsh, Caroline Dias, David C. Fajgenbaum

SKMC Student Presentations and Publications

PURPOSE: TCF7L2 (OMIM 602228; HGNC:11641) is a transcription factor and a critical effector of the Wnt/ β-Catenin pathway. In 2021, 11 pediatric patients with monoallelic predicted loss-of-function (pLOF) TCF7L2 variants and syndromic features were observed. Characterization of patients with pLOF TCF7L2 variants and neurodevelopmental features-herein referred to as TCF7L2-related neurodevelopmental disorder-is urgently needed.

METHODS: We leveraged multiple methods (eg, GeneMatcher, DECIPHER, literature review, and public/private repositories) to identify an international cohort of 76 patients with pLOF TCF7L2 variants and neurodevelopmental features and phenotypically characterized them. We also retrospectively searched for an independent cohort of adults with pLOF TCF7L2 variants (n …

Multi-Omic Characterization Of The Hispanic/Latino Blood Lipidome Reveals An Additional Locus And Attenuated Genetic Prediction, Wanying Zhu, Hung-Hsin Chen, Heather M. Highland, Corey Giles, Peter J. Meikle, Joanne Curran, Joseph B. Mccormick, Susan P. Fisher-Hoch, Kari E. North

Human Genetics Publications

While lipids have been extensively investigated, genetic regulation of the circulating lipidome in diverse populations remains poorly understood. We conducted a lipidome-wide genome-wide association study (GWAS) of 830 lipid species in 2,287 Hispanic/Latino participants and performed predictive modeling across omics layers. We identified 7,593 genome-wide significant SNPs mapping to 208 genes. Conditional analysis disentangled the long-range linkage disequilibrium artifacts from the pleiotropic FADS1/2/3 cluster. Separately, we discovered an association at the GPLD1 locus for a circulating ceramide. Colocalization revealed shared genetic architecture with conventional lipids alongside distinct, species-specific pathways. Incorporating Native/Indigenous American expression quantitative trait loci …

Building Genetic And Culturing Tools For The Understudied Soil Bacterium E. Flagellatus, Aaron Butler, Brenda Pratte, Lon Chubiz

Undergraduate Research Symposium

Soil bacteria play essential roles in nutrient cycling, yet many abundant groups remain poorly characterized due to challenges in cultivation and genetic manipulation. One such organism is Edaphobacter flagellatus, a member of the Acidobacteriota frequently detected in soil environments but lacking well-developed experimental tools. To address this limitation, our laboratory has generated a genome-wide mutant library using the Tn5 transposon, enabling random disruption of genes across the population.

This project aims to establish culture conditions necessary to support the use of this library for functional genomic studies. In particular, defined minimal media can impose selective pressures that reveal …

Bioinformatics-Driven Structural And Functional Characterization Of Caffeine Synthase (Ccs1), Asia Khalil, Muhammad Naveed, Raja Muhammad Ahmad, Sania Saeed, Ayesha Hameed, Ayman Iqbal, Fakhra Nazir

Journal of Bioresource Management

Caffeine synthase (CCS1; EC 2.1.1.160) is a S-adenosyl-L-methionine (SAM; S-adenosyl-L-methionine) dependent N-methyltransferase that executes the final methylation steps of caffeine biosynthesis in coffee, tea, and related plants. While paraxanthine can act as an efficient substrate, it contributes to a comparatively minor branch in the overall pathway. We conducted an integrated in silico analysis of CCS1, covering sequence retrieval, structure prediction, 3D modeling, and mutation assessment. Secondary structure was inferred using PSIPRED; physicochemical indices were computed via AA-PROP; 3D models were generated by I-TASSER and evaluated by Verify3D; and missense effects were prioritized using PolyPhen-2, PROVEAN, I-Mutant, and PhD-SNP. Taken together, …

Evaluation Of The Dhcr7/Nadsyn1 Rs4944946 Variant And Breast Cancer Susceptibility: A Case-Control Study In An Indonesian Cohort, Dian Tri Wahyudi, Rafika Indah Paramita, Sonar Soni Panigoro

Indonesian Journal of Medical Chemistry and Bioinformatics

Background: The rs4944946 variant, located in the 5’UTR of the DHCR7 gene and upstream of NADSYN1, is biologically implicated in vitamin D and cholesterol metabolism pathways closely linked to cancer pathogenesis. This study aimed to experimentally validate the association between the rs4944946 polymorphism and breast cancer susceptibility in an independent cohort of Indonesian women. Method: A case-control study was conducted involving 36 breast cancer patients and 39 healthy adult females. Genotyping of the rs4944946 variant was performed using Polymerase Chain Reaction-Restriction Fragment Length Polymorphism (PCR-RFLP). The genetic association was evaluated across codominant, dominant, and recessive models. Luminal B was the …

Hbb Gene Mutations And Their Impact On Phenotype And Protein Function In Β-Thalassemia Families From Dera Ismail Khan, Pakistan, Muhammad Ayaz, Muhammad Muzammal, Maria Shafiq, Nisar Ahmad, Dua Iman, Maria Faraz, Yaser Uddin Hoti, Sami Siraj, Muzammil Ahmad Khan, Jabbar Khan

Makara Journal of Science

The current genetic study aimed to screen out the genetic basis of ß-thalassemia in five unrelated consanguineous Pakistani families. Blood samples were collected, and targeted Sanger Sequencing of the HBB gene was done. Serum Interleukin-6 (IL-6) and quantitative measurements of T Helper and T Suppressor Lymphocytes were also carried out. Additionally, in silico analysis, including protein modeling, Protein-Protein docking, and Multiple sequence alignment, was also performed. Genetic analysis identified a homozygous mutation c.92+5G > C (IVS-I+5 G > C) in families 1, 2, and 3, which resulted in β⁺/ β⁺ Thalassemia Intermedia phenotype. While in the case of family …

Study Of Primer Efficiency And Relative Genetic Band Abundance In Different Genotypes, Mundher Kh. Jabbar

Karbala International Journal of Modern Science

This experiment was aimed to find some indicators related to primers and genetic variations. Six bread wheat genotypes were selected as the dataset. The RAPD marker technique was used with oligonucleotide primers as marker of study. The goal was to identify factors used for the relationship between primers and their ability to elicit DNA fragments through different genotypes, as well as the relative genetic band abundance among genotypes. After the designed factors, key findings emerged: in relative primer amplification rate, C1 genotype exhibited a higher relative primer amplification rate (RPAR) of fragments from OP-H01 but did not differ from OP-V19 …

Charge Modulation Of Peptide/Nucleic Acid Complexes: An Anionic Additive Enhances Gene Silencing And Crispr/Cas9 Editing By Promoting Intracellular Nucleic Acid Release, Abdulelah Alhazza, Sorour Khayyatnejad Shoushtari, Hasan Uludag, Keykavous Parang, Hamidreza Montazeri Aliabadi

Pharmacy Faculty Articles and Research

Introduction: Small interfering RNA (siRNA) and Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)/CRISPR-associated Protein 9 (Cas9) complexes are effective approaches to temporarily downregulate protein expression via post-transcription RNA interference or permanently altering protein expression via editing genomic DNA, respectively. However, the efficient delivery of these mediators to targeted cells has been challenging, largely due to their anionic and hydrophilic nature, which hinders their interaction with the cell membrane and cellular internalization. Cell-penetrating peptides (CPPs) exhibit dual characteristics as a carrier for nucleic acid delivery, where positively charged components bind to the negatively charged nucleic acid, and the hydrophobic components …

Individualized Bayesian Inference Identifies Novel Genetic Variants For Parkinson's Disease, Jin Ren, Yasaman J. Soofi, Md Asad Rahman, Qing Lu, Jinling Liu

Engineering Management and Systems Engineering Faculty Research & Creative Works

Parkinson's disease (PD) is a complex neurodegenerative disorder with a significant genetic component. While genome-wide association studies (GWAS) have been instrumental in identifying genetic variants associated with PD, the reliance on large sample sizes and population-level analyses may overlook variants with lower minor allele frequencies or individual-specific relevance. Individualized Bayesian Inference (IBI) offers a promising method to complement GWAS by identifying and prioritizing candidate genetic markers at both the individual and patients-like-me subgroup levels. This study evaluates the application of IBI to PD genetics, using GWAS as a baseline for comparison. We analyzed genetic data from the Fox Insight online …

Architects Of Mrna Fate: Molecular And Cellular Control Of P-Body Organization In The Drosophilia Melanogaster Female Germline, Samantha Milano

Dissertations, Theses, and Capstone Projects

Processing bodies (P-bodies) are cytoplasmic ribonucleoprotein condensates that regulate mRNA storage, translational repression, and decay. While the biochemical principles governing condensate assembly have been extensively studied in vitro, how P-body organization is established and dynamically regulated in vivo to control specific mRNA populations remains poorly understood. This dissertation investigated the molecular and cellular mechanisms that govern P-body architecture and function in the Drosophila melanogaster female germline. First, I identified the conserved LSm protein Trailer Hitch (Tral) as a central organizer of P-body architecture. Using quantitative confocal and super-resolution microscopy combined with chemical perturbations, I showed that Tral coordinates the …

Integration Of Lipidomic And Polygenic Risk Scores Within Contemporary Clinical Cardiovascular Risk Assessment Pathways: A Multi-Cohort Development And Validation Study, Aleksandar Dakic, Jingqin Wu, Tingting Wang, Thomas G. Meikle, Kevin Huynh, Changyu Yi, Habtamu B. Beyene, Agus Salim, Michelle Cinel, Nat Mellett, John Blangero

Human Genetics Publications

Background: Guideline-recommended clinical risk scores such as AusCVDRisk underestimate cardiovascular disease (CVD) risk in a substantial proportion of individuals who later experience events, with up to 65% initially classified as low or intermediate risk. This limitation is most consequential in the intermediate-risk group, where treatment decisions are uncertain and additional risk refinement could alter management. Circulating lipid species and inherited genetic variation capture complementary molecular aspects of atherosclerotic risk that are not fully reflected by conventional clinical variables, but are not routinely incorporated into primary-care risk assessment. We investigated whether selective integration of lipidomic and genomic risk signals into AusCVDRisk …

A Cell-Type-Resolved Meta-Analysis Reveals Glial Dna Methylation Changes Associated With Aging And Alzheimer's Disease, Uchit Bhaskar, Mark Z. Kos, Melanie A. Carless

Human Genetics Publications

INTRODUCTION: Epigenome-wide association studies implicate DNA methylation in Alzheimer's disease (AD) pathology. Although recent studies identified epigenetic signatures within non-neuronal cell types in disease risk, the role of the methylome in glial cell types (i.e., astrocytes, oligodendrocytes) in biological aging and AD pathogenesis is unclear.

METHODS: In this study, we examined archived DNA methylation data across 13 cohorts and performed cell type deconvolution in silico to identify novel epigenetic signatures associated with aging and AD in glial cells.

RESULTS: We observed pronounced age-associated methylation signatures in astrocytes within the prefrontal cortex (PFC) and AD-associated methylation signatures in oligodendrocytes of the …

Effect Of Partial Ablation Of Skeletal Dynamin Related Protein 1 On Mitochondrial Health, Inflammation, And Fibrosis In A Mouse Model Of Duchenne Muscular Dystrophy, Tessa L. Duzz

Graduate Masters Theses

Duchenne muscular dystrophy (DMD) is a progressive neuromuscular disorder characterized by muscle weakness, degeneration, fibrosis, and impaired muscle regeneration. Mitochondrial dysfunction is an early pathological feature of DMD and has been linked to excessive mitochondrial fission. Dynamin-related protein 1 (Drp1) is a central regulator of mitochondrial fission, a key process in regulating mitochondrial quality and function. Inhibition of Drp1-mediated mitochondrial fission has shown promise as a potential therapeutic target for alleviating pathology and dysfunction in dystrophic muscle. The objective of this study was to determine whether partial skeletal muscle-specific ablation of Drp1 could improve muscle pathology and mitochondrial health in …

Transcriptomic Architecture Of Metabolic Dysfunction-Associated Steatotic Liver Disease (Masld) Risk In Mexican Americans, Satish Kumar, Miriam Aceves, Lorena Guerra, Jose C. Granados, Earl Novilla, Felicia Juarez, Tolulope Oluwadairo, Ana C. Leandro, Marcelo Leandro, Juan M. Peralta, Sarah Williams-Blangero, John Blangero, Joanne E. Curran

Human Genetics Publications

Hispanics of Mexican American descent in South Texas show a very high prevalence of MASLD, with some studies reporting rates as high as 50% in adults. However, assessment of genetic risk factors underlying this prevalence is complicated by a high co-occurrence of other metabolic disorders and variable endogenous and exogenous environmental risk factors. To map the transcriptomic architecture of MASLD hepatic steatosis risk, we conducted an epidemiological-scale investigation using human induced pluripotent stem cell (iPSC)-derived hepatocyte cultures from 193 participants in our longitudinal South Texas Family Study (STFS). iPSC-based models offer greater power to map genetic risk factors by experimentally …

Data Curation And Integration For Cancer Cell Line Pharmacogenomics Analysis, Meric Kinali

Graduate Masters Theses

Cancer cell lines are essential resources for connecting genomic and molecular features with drug response and identifying biomarkers. Therefore, large-scale cancer cell line resources have been growing, but this introduces challenges such as data standardization, consistent annotation, matching identifiers, cross-database integration, and a reproducible computational framework. CellMiner Cross Database (CellMinerCDB) integrates pharmacogenomic datasets from multiple resources and provides a standardized analysis of cell lines across datasets. This thesis examines cancer cell line cross-databases and their importance in pharmacogenomics, with a particular focus on CellMinerCDB. As part of this work, I developed an R package for the gCSI (Genentech Cell Line …

Mitochondrial Trna-Derived Fragments As Candidate Metastasis-Modifying Rna, Katy L. Swancutt, R. Mckinnon Walsh, Sydney Quijano, Emily Schueddig, Devin C. Koestler, Adam D. Scheid, Tony Vanden Bush, Yi Jing, Isidore Rigoutsos, Danny R. Welch

Computational Medicine Center Faculty Papers

UNLABELLED: How mitochondrial DNA (mtDNA) polymorphisms influence complex phenotypes remains poorly understood. Using mitochondrial-nuclear exchange mice, we previously showed that mtDNA single-nucleotide polymorphisms (SNP) modify metastasis, cardiovascular disease, and epigenetic marks independently of metabolic differences. The only mtDNA SNP correlating with these phenotypes resides in the gene encoding mitochondrial transfer RNA (tRNA)-arginine [mt-tRNAArg (UCG), mt-TR], suggesting a role for non-protein-coding loci. In this study, we identify and preliminarily characterize previously undescribed tRNA-derived fragments (tRF) generated from mt-TRs. Northern blotting revealed distinct tRF that are differentially expressed among mtDNA SNPs, between lung and liver, and between sexes. Surprisingly, small RNA sequencing …

The Role Of Seed Mix Characteristics And Soil Amendments During Post-Agricultural Prairie Restoration, Valerie N. Thurston, Michaela J. Woods, Madelaine Gregory, Mary C. Lloyd, Ryan W. Mcewan

Biology Faculty Publications

Introduction: Prairie restoration on degraded lands may be influenced by seed mix characteristics, including species richness and legume establishment. Soil amendments may facilitate restoration; however, the practical usefulness of techniques such as applications of whole soil and leaf mulch remains relatively unclear.

Objectives: We assessed whether increasing species richness and legume content in seed mixes enhances prairie restoration success and examined how soil amendments interact with seed mix composition to influence cover, species richness, diversity, and legume establishment.

Methods: We conducted a field experiment on a 12-ha post-agricultural site in Ohio, U.S.A. Twenty 50 × 50 m plots received one …

Identification And Characterization Of Novel Immune Modulating Genes In Parkinson's Disease, Kathleen Chaundy Paul Murphy

Dartmouth College Ph.D Dissertations

Parkinson’s disease (PD) is a progressive age-related neurodegenerative disorder characterized by both motor and non-motor symptoms. The poorly understood prodromal period, decades-long progression, and disease-phenotype heterogeneity continue to impede the development of preventive and curative therapies. A growing appreciation of immune system changes during the progression of PD suggests that evaluating peripheral immune cells may help identify signatures relevant to disease etiology. We aimed to expand our understanding of the peripheral immune compartment in PD via two lines of investigation: (1) by employing single-cell RNA sequencing to profile the transcriptomes of peripheral blood mononuclear cells (PBMCs) from a cohort of …

Cells And Networks In Flux: Rethinking Ontogenesis And Pathogenesis, Mark L. Tykocinski

Department of Pathology, Anatomy, and Cell Biology Faculty Papers

Organ and tissue functions emerge from the coordinated activity of cell networks. Therapeutics that act on pathogenic cell networks, modulating their cellular interplay, follow naturally. Over several decades, our laboratory has developed a series of approaches for rewiring cell networks, culminating in a class of cell surface-directed signal converter proteins (SCPs) that do so by modulating juxtacrine and autocrine signaling in and among their nodal cells. A first such SCP has now produced encouraging clinical data for cancer immunotherapy. Yet, these early network-directed fusion proteins rest on a deliberately simplified picture: discrete end-cell types plugged into graphically tractable networks. That …

Integrative Rna-Seq Analysis Reveals Stress Type-Dependent Lncrna-Centered Co-Expression Networks Across Human Cellular Stress Contexts, Christina Anastasiadi, Aggeliki Kasapi, Ioannis Sentementes, Vasileios Gouzouasis, Margaritis Tsifintaris, Antonis Giannakakis

Computational Medicine Center Faculty Papers

Long non-coding RNAs (lncRNAs) are emerging as important regulators of cellular adaptation to environmental and molecular stress, but the extent to which their responses remain reproducible and stress-type-dependent across human stress conditions remains unclear. Here, we performed an integrative transcriptomic meta-analysis of human stress-response datasets from ASTRA and GEO, focusing on normal, non-cancerous, wild-type human cell lines exposed to oxidative stress (H2O2), hypoxia, heat stress, or UV-induced DNA damage. Gene Ontology (GO) enrichment analysis of differentially expressed (DE) protein-coding mRNAs confirmed that the resulting stress-stratified comparison captured biologically coherent transcriptional programmes to oxidative stress signaling, hypoxic and metabolic adaptation, heat-induced …

Gene Therapy Strategies To Enhance Antifungal Immunity In Microgravity, Riley Dienna

Discovery Day - Daytona Beach

During spaceflight, the immune system of astronauts becomes impaired due to microgravity, resulting in increased susceptibility to infections caused by pathogens such as Candida albicans. One of the most common clinical treatments for aggressive candidiasis is amphotericin B, a polyene antimycotic that targeted ergosterol in the fungal cell membrane and compromised the stability of the membrane. However, due to the chemical similarities between ergosterol and cholesterol, this treatment also affects the somatic cells of patients it is administered to. A novel treatment is therefore required to combat the aggressive fungal infection while minimizing damage to the host’s cells. This project …

Transcriptomic Profiling Of The Donkey Endometrium Reveals Dynamic Molecular Transitions Across The Estrous Cycle, Limeng Shi, Shuaishuai Wu, Mingyue Zhao, Wenhao Zhou, Abd Ullah, Muhammmad F. Akhtar, Changfa Wang, Muhammad Z. Khan, Ying Han

The Thai Journal of Veterinary Medicine

The endometrium undergoes extensive cyclical remodeling essential for reproductive success; however, the molecular mechanisms governing these processes in donkeys (Equus asinus) remain poorly characterized. To address this gap, we performed high-throughput RNA sequencing on endometrial tissues collected from Dezhou donkeys (n = 16) at four post-ovulation stages: Day 0 (ovulation), Day 3 (early luteal), Day 7 (mid-luteal), and Day 18 (late luteal/pre-luteolysis). Differential gene expression analysis, Gene Ontology enrichment, and KEGG pathway mapping were conducted to characterize temporal transcriptomic dynamics. We identified 2,474, 6,548, and 1,288 differentially expressed genes in Day 0 versus Day 3, Day 0 versus …

Fraction-Seq: An Integrated Experimental And Computational Workflow For Determining The Localization And Abundance Of Small Non-Coding Rnas In Subcellular Compartments, Siddhartha Shah, Tess Cherlin, Yi Jing, Stepan Nersisyan, Benjamin E. Leiby, Isidore Rigoutsos

Computational Medicine Center Faculty Papers

Small non-coding RNAs (sncRNAs) have garnered considerable attention in recent years, following accumulating evidence of their critical roles in many cellular processes. Among sncRNAs, microRNAs (miRNAs) and their isoforms (isomiRs), tRNA-derived fragments (tRFs), rRNA-derived fragments (rRFs), and Y RNA-derived fragments (yRFs) account for more than 95% of all sncRNAs found in cells. Despite their critical regulatory roles, most sncRNAs remain uncharacterized because their functionalization is a lengthy and challenging undertaking. Knowing an sncRNA's abundance helps prioritize among the various choices, while knowing where it localizes in the cell greatly limits the number and identity of its potential targets and helps …

Assessing Gene Expression Changes In The Octocoral Briareum Asbestinum Due To Vibrio Coralliilyticus Exposure, Hailey Poignant

All HCAS Student Capstones, Theses, and Dissertations

Coral reefs are an essential ecosystem home to tons of marine diversity that humans have also  learned to rely on, but they are harmed by climate change and the increasing prevalence of disease. While most studies focus on reef-building coral, octocorals also warrant attention to reveal how they respond to similar stressors. Octocorals share distant ancestry with reef-building corals, so there may be overlap in their immune responses which could provide insight into future restoration projects. To understand how octocorals respond to disease, the octocoral Briareum asbestinum was used as a model to examine gene expression changes caused by the …

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 …