Genomics Commons^™

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 …

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 …

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 …

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 …

The Past, Present, And Future Of Climate Adaptation In A Widespread Lizard Species, Matthew R. Mcternan

All Dissertations

Climate, as a selective force, shapes patterns of biodiversity globally. However, how species adapt to climate remains a central question of biology. The need to understand climate adaptation is paramount, as global climate change threatens a large portion of global diversity. Climate can impose selection on life by either controlling rates of energy intake and expenditure through effects on body temperature and activity, or by exposing organisms to conditions beyond their physiological limits. Studies of climate adaptation have identified a wide-range of putatively adaptive phenotypic patterns, but genomic evidence is increasingly being used to investigate these patterns and better understand …

Prenatal Acoustic Programming Of The Developing Hypothalamus: A Multi-Omic Analysis Of Heat Call Exposure In Zebra Finch Embryos, Prakrit Subba

All Dissertations

Climate change is intensifying thermal stress on wildlife globally, yet the developmental mechanisms by which embryos use prenatal cues to adjust to predicted environments remain unclear. In Australian zebra finches (Taeniopygia guttata), incubating parents produce distinctive heat call vocalizations at high ambient temperatures, and embryos exposed to these calls during late incubation develop altered growth trajectories, thermoregulatory capacity, and reproductive outcomes, suggesting a form of anticipatory developmental programming triggered by sound alone. To investigate the molecular basis of this response, I initially hypothesized that prenatal heat call exposure would act primarily through hypothalamic neuroendocrine reprogramming, given the central …

Summer Research Internships In Agricultural Biotechnology For Off-Campus Undergraduate Students, Aaron J. Thomas

Funded Research Records

No abstract provided.

Proteogenomics Of Hypertrophic Cardiomyopathy Reveals Subtype-Specific Therapy, Ke Ma, Jie Yang, Hongchang Guo, Ping Li, Xiaowei Li, Zhujun Dong, Jing Zhang, Congcong Zhang, Pengli Yang, Chongpei Hua, Shuolin Zhu, Guoqing Li, Jianchao Zhang, Ningyu Ding, Jizheng Wang, Xin-Liang Ma, Zhuofeng Lin, Jianzeng Dong, Yang Li, Yulin Li

Department of Emergency Medicine Faculty Papers

BACKGROUND: Hypertrophic cardiomyopathy (HCM) is a heterogeneous disease with diverse prognosis. The underlying mechanisms remain unknown, resulting in limited risk stratification and therapeutic strategies. This study aimed to elucidate molecular subtypes of HCM through integrated proteogenomic analysis and explore subtype-specific therapeutic strategies.

METHODS: We conducted an integrated proteogenomic analysis of 132 patients with HCM using myocardial samples, incorporating whole-exome sequencing, RNA sequencing, and proteomics. Unsupervised clustering was used to identify HCM subtypes, which were validated in heart tissues and human induced pluripotent stem cell-derived cardiomyocytes from 2 independent HCM subsets. Subtype-specific signatures and pathways were explored, and their causal link …

Disease-Causing Mfn2 Mutants Impair Mitochondrial Fission Dynamics By Distinct Drp1 Dysregulation, Daniel Lagos, Pamela R. De Santiago, Nicolás Pérez-Bravo, Benjamín Cartes-Saavedra, Josefa Vial-Brizzi, Diego Troncoso-Chandía, Oliver Podmanicky, Rita Horvath, Verónica Eisner

Department of Pathology, Anatomy, and Cell Biology Faculty Papers

Mitochondria undergo fusion and fission. While DRP1 regulates fission, fusion is controlled by OPA1, MFN1, and MFN2. The balance between these processes and the crosstalk between machineries remains poorly understood. MFN2 mutations cause Charcot-Marie-Tooth disease type 2 A (CMT2A), affecting mitochondrial fusion and morphology. However, their role in fission is unclear. Using skin fibroblasts from CMT2A patients (L248H and M376V MFN2 mutations) and wild-type mouse embryonic fibroblasts expressing these variants, we studied how MFN2 mutations impact mitochondrial dynamics beyond fusion. We analyzed mitochondrial morphology and dynamics by live-cell confocal microscopy and tested fusion/fission protein levels, oxygen consumption rate (OCR), extracellular …

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 …

Adapting Population Genetics, Practice, And Policy For Plant Conservation In A Changing World, Cooper M. Kimball-Rhines

Graduate Doctoral Dissertations

Biodiversity conservation is an inherently interdisciplinary goal that requires effective collaboration among academics, ecosystem managers, policymakers, and other stakeholders. Codesigning research with these groups ensures experiments are useful and improves adoption of policy and practice recommendations while advancing our understanding of basic science. This dissertation explores the power of codesigned research in shaping plant conservation strategies using stakeholder engagement, causal inference, demographic modeling, and multi-omic sequencing techniques. In chapter 1 I discuss the history of New England ecosystems and the need for research-driven changes to plant conservation policy and practice in the face of global change. In chapter 2, I …

Investigating Cryptic Diversity In The Hawaiian Endemic Plant, Psychotria Mariniana (Rubiaceae), Uyen Thi Hoang Nguyen

Master's Theses

Islands, with their isolation and steep environmental gradients, serve as natural laboratories for studying speciation. Molecular phylogenetic and population genetic methods utilizing Next-Generation Sequencing (NGS) have revolutionized our ability to document patterns of genetic divergence and diversity. Cryptic diversity, genetically distinct populations that were previously unrecognized as unique, and cryptic speciation, where divergent genetic populations may be deserving of status as unique species, have been observed in many taxa. The Hawaiian Islands provide an ideal setting for studying divergence and speciation due to their extreme isolation, known ages, and volcanic origin. Previous work has investigated the evolutionary relationships of the …

Denisovan Introgression And Selection At Cntnap2 In Ancient And Modern American Populations, Matthew Barker

All Theses

The peopling of the Americas created new opportunities for genetic adaptation as ancient populations encountered novel environments across North and South America. Previous research has shown that segments of Indigenous American ancestry contain elevated proportions of Denisovan alleles. The gene CNTNAP2, which is involved in brain development and neuronal function, contains a Denisovan-derived haplotype that represents a candidate locus for adaptive introgression in admixed American populations. A Denisovan-derived core haplotype approximately 55 kb in length was identified within intron 13 of CNTNAP2. This haplotype is primarily found in admixed American populations and occurs rarely outside the Americas, and …

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 …

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 …

Improving Genomic Prediction For Feed Efficiency Traits In Beef Cattle Using Microbiome As An Intermediate Omics, Egodage Bhagya Sewwandi Samarakoon

Department of Animal Science: Dissertations, Theses, and Student Research

Feed efficiency traits, including feed conversion ratio (FCR), average daily gain (ADG), and average daily dry matter intake (ADDMI), are economically important in beef cattle production. Emerging evidence suggests that host genetics influences feed efficiency traits through the microbiome. This study evaluates the integration of microbiome data as an intermediate layer in the Neural Network Mixed Model (NNMM), which hierarchically models genotype–microbiome–phenotype relationships as a unified regulatory network to improve genomic prediction accuracy. To reduce the computational burden of NNMM, microbiome features dimension were reduced using principal component analysis (PCA) and direct feature selection of top-ranked open reading frames (ORFs) …