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Articles 1 - 17 of 17
Full-Text Articles in Genomics
A Toi Rna Editing In Three Members Of The Microbotryum Violaceum Fungal Complext And Characterization Of Adar Genes Of Microbotryum Superbum., Shikhi Baruri
Electronic Theses and Dissertations
A-to-I RNA editing is a process that occurs post-transcriptionally. Through this process, adenosine (A) is replaced by inosine (I) in RNAs by adenosine deaminase enzymes that act on the single-stranded RNA. These enzymes, also known as ADARs, act on RNA. The translation and splicing mechanisms subsequently interpret inosine as guanosine (G), which effectively alters genetic information. This kind of RNA alteration can cause both nonsynonymous and synonymous changes in codon, which may have an impact on protein function. A group of over 89 basidiomycete fungal species known as the Microbotryum violaceum complex infects a similarly large group of plant host …
Genes That Matter: Survival Modeling In Tcga-Brca With Treatment Interactions., David Pratt
Genes That Matter: Survival Modeling In Tcga-Brca With Treatment Interactions., David Pratt
Electronic Theses and Dissertations
High-dimensional genomic data offer both promise and challenges for identifying clinically relevant biomarkers. This study developed a parallelized survival modeling pipeline to identify genes associated with overall survival in breast cancer, with a focus on gene-by-treatment interactions and patient heterogeneity. RNA-Seq data from female patients in the TCGA-BRCA cohort were analyzed. Univariate Cox proportional hazards models were used to screen genes, adjusting for age, race/ethnicity, treatment status, and cancer stage. A LASSO-penalized Cox regression was fit across 2000 random seeds to assess feature stability. Genes were filtered by expression level, statistical significance, and hazard ratios (effect sizes) in either direction, …
Genetic Influence Of Allelic Variation On The Phenotypic Variability Of Cognitive Outcomes In Individuals With Williams Syndrome., Marinie P. Joseph
Genetic Influence Of Allelic Variation On The Phenotypic Variability Of Cognitive Outcomes In Individuals With Williams Syndrome., Marinie P. Joseph
Electronic Theses and Dissertations
Williams syndrome (WS) is caused by a rare microdeletion of 25 – 27 genes on chromosome 7q11.23, characterized by a distinctive cognitive profile with considerable phenotypic heterogeneity. However, the genetic factors underlying this phenotypic variability remain unclear. I explored two genetic mechanisms—parent-of-origin (PoO) effects and genome-wide polygenic variation, as measured by polygenic scores (PGSs)—to elucidate possible influences on cognitive variability in WS. The first study examined PoO effects on cognitive abilities in two overlapping samples of children with WS (N = 211, N = 251). PoO refers to which parental homolog of chromosome 7 contains the WS deletion. Despite …
Translation Of The Carcinogenic Dna Breakage-Repair Inhibition Mechanism For Hexavalent Chromium To Its Key Targets: Lung Epithelial Cells, Lung Tissue And Impacts On The Genome., Idoia Meaza Isusi
Electronic Theses and Dissertations
Lung cancer is the leading cause of cancer death worldwide. Hexavalent chromium [Cr(VI)] is a human lung carcinogen with widespread occupational and environmental exposure. Despite the known health risks, how Cr(VI) causes lung cancer remains unclear. This dissertation investigates the mechanisms of Cr(VI)-induced carcinogenesis. Cr(VI) causes DNA damage, specifically DNA double strand breaks, and inhibits homologous recombination repair, a high-fidelity repair pathway. Unrepaired DNA double strand breaks or those repaired through error-prone pathways, progress to chromosomal damage, and chromosome instability. The latter is a common characteristic of Cr(VI)-exposed cells, and a hallmark of lung cancer. Although the mechanism of Cr(VI)-induced …
Uncovering The Hidden Diversity Of Antibody Heavy Chains And Their Implications For Autoantibody Mediated Disease., Easton Earl Ford
Uncovering The Hidden Diversity Of Antibody Heavy Chains And Their Implications For Autoantibody Mediated Disease., Easton Earl Ford
Electronic Theses and Dissertations
Understanding the diversity of antibody (IG) molecules at the DNA and RNA level is imperative for understanding immunological processes and disease. Much of the work to uncover IG diversity has been focused on diversity in the variable region of the IG molecule which is crucial for antigen binding. However, the diversity of the constant region responsible for the functions of IG has largely been ignored in the field of immunogenetics. The work presented in this thesis challenges the dogma that the constant region is invariant in terms of genetic diversity. In this thesis we present the development of a long-read …
Characterization Of The Immunoglobulin Lambda Chain Across Diverse Human Populations., William Gibson
Characterization Of The Immunoglobulin Lambda Chain Across Diverse Human Populations., William Gibson
Electronic Theses and Dissertations
The adaptive immune system relies on a diverse set of over one hundred immunoglobulin (IG) genes across three genomic loci that are variably combined to form antibodies (Ab). The IG Lambda locus is one of two loci which encodes the IG light chain. The complexity of the IGL locus severely limits the effective use of standard short-read sequencing, limiting our knowledge of population diversity in these loci. We leveraged single molecule real-time (SMRT) long-read sequencing in conjunction with IGL-targeted DNA capture to develop the method IG-Cap for accurate and high-throughput sequencing of the IGL locus. We benchmarked this method using …
Clustering And Analysis Of G Quadruplex Sequences., Aryan Neupane
Clustering And Analysis Of G Quadruplex Sequences., Aryan Neupane
Electronic Theses and Dissertations
G quadruplex structures are secondary structures located throughout the genome of various organisms with involvement in regulatory functions in different transcription, translation, genome stability, epigenetic regulation as well as cell division. Even with the diverse acknowledgement of G4 structure in vivo, there are no current search tools for G quadruplexes based on already identified G quadruplexes and identified families across different genomes based on sequence diversity. Construction of families of G4 sequences and identifying their polymorphisms within disease and disorders will lead to a better understanding of their functional roles and will further research into the biophysical modeling of interactions …
Anomalies In The Mitochondrial Genomes Of Members Of Aliciidae, Boloceroididae, And Gonactiniidae (Actiniaria:Metridioidea), Isabel Pen
2023 Midwest Ecology & Evolution Conference
Analysis of gene sequences from three mitochondrial and two nuclear genes for a broad sampling of actiniarian taxa proposed a novel grouping of the families Aliciidae, Boloceroididae, and Gonactiniidae. (Rodríguez et al., 2014). Although previously unlinked, the association of these taxa was credible given the consistency of the genetic data and the shared occurrence of anatomical traits, including complex column structures (Aliciidae and Boloceroididae), tentacular sphincters (Boloceroididae and Gonactiniidae), and retention of juvenile musculature in adults (Boloceroididae and Gonactiniidae). Although the mitochondrial genome structure of actiniarians is generally conserved, complete mitochondrial genomes identify unusual gene orders (Alicia sansibarensis: …
Everything But The Lab Sink: Using 1,000 Phylogenomically Informative Markers To Resolve Historically Messy Species Groups In Anastrepha Fruit Flies (Diptera: Tephritidae), Kristie J. Schmidt
Everything But The Lab Sink: Using 1,000 Phylogenomically Informative Markers To Resolve Historically Messy Species Groups In Anastrepha Fruit Flies (Diptera: Tephritidae), Kristie J. Schmidt
2023 Midwest Ecology & Evolution Conference
The genus Anastrepha (Diptera: Tephritidae) is long overdue for a major taxonomic revision. Of the 22 recognized species groups within Anastrepha, only ~5 are well supported clades. Molecular methods, such as traditionally used mitochondrial DNA markers, have been unsuccessful at elucidating relationships amongst Anastrepha species; therefore, a more robust phylogenomic tool is likely necessary. To accomplish this, we used Highly Multiplexed Amplicon-based Phylogenomics (HiMAP) to identify 1,000 phylogenomically informative nuclear markers. Post sequencing, we obtained data for 500+ amplicons for 90 Anastrepha spp. belonging to 18 Anastrepha species groups. Our findings agree with some aspects of the most recently …
Convergent Evolution Of Antifreeze Proteins In Two Insect Families Supported By Whole Genome And Gene Family Loci Analyses, Shaw Kagawa
2023 Midwest Ecology & Evolution Conference
Various Coleoptera (beetles) and Lepidoptera (moths) insects are known to produce highly active antifreeze peptides (AFPs), an adaptive trait that enabled them to avoid freezing and survive severe winters. These include the grain pest Tenebrio molitor (yellow mealworm), pine-boring Rhagium beetles, the fire-colored Dendroides beetles, a stag beetle, and the Choristoneura spruce budworms (moths). Insect AFPs are small peptides of ~8 to 15 kDa, consisting of several tandem 13-amino acid repeats of similar sequences, each ending with a conserved tripeptide Thr-Cys/aa-Thr motif, found to be important for ice binding. Except for the eastern spruce budworm, the evolutionary origin/s and process/es …
Novel Model For Tau Protein Expression And Function: The Honeybee Brain, Abdallah F. Sher
Novel Model For Tau Protein Expression And Function: The Honeybee Brain, Abdallah F. Sher
2023 Midwest Ecology & Evolution Conference
Scientists have long attempted to understand the mechanisms by which senescence occurs. Leading theories suggest that aging is an emergent property of natural selection’s prioritization of reproductive ability. Social insects, such as the honeybee (Apis mellifera) challenge this idea, separating colonies into reproductive and non-reproductive castes. Worker honeybees do not reproduce, suggesting that selection prioritizes tasks other than reproduction. Forager honeybees, for example, display improved cognitive and immune function compared to other behavioral phenotypes of bees, likely to support their ability to perform tasks such as navigating complex environments or making context-dependent decisions while foraging. Foragers are normally older honeybees, …
Geographic Analysis Of Sex Chromosome Polymorphism In The Virginian Wild Strawberry, Trezalka A. Budinsky
Geographic Analysis Of Sex Chromosome Polymorphism In The Virginian Wild Strawberry, Trezalka A. Budinsky
2023 Midwest Ecology & Evolution Conference
The evolution of sex chromosomes is a ubiquitous and essential diversifying mechanism in eukaryotes. Yet early stages of sex-chromosome differentiation are poorly understood. The subdioecious octoploid, Fragaria virginiana, provides a rare opportunity to study the beginnings of sex chromosome evolution due to its young, polymorphic ZW sex system. Females are ZW and males/hermaphrodites are ZZ. F. virginiana has a small sex-determining region (SDR) located on the female W chromosome that has undergone three transposition events between the strawberry's four subgenomes, resulting in three SDR haplotypes: alpha (the result of a first transposition and closest to a pre-sex chromosome ancestral …
Potential Loss Of Pheromone Receptors In The Red Milkweed Beetle, Tetraopes Tetrophthalmus (Coleoptera: Cerambycidae), Mathew A. Price
Potential Loss Of Pheromone Receptors In The Red Milkweed Beetle, Tetraopes Tetrophthalmus (Coleoptera: Cerambycidae), Mathew A. Price
2023 Midwest Ecology & Evolution Conference
The family of longhorn beetles (Coleoptera: Cerambycidae) are characterized by their elongate antennae, which are well adapted for detecting volatile compounds. This makes them an ideal family to study odorant receptor genes (ORs), which are the rapidly evolving family of proteins that are used by insects to detect odors at the molecular level. Here, we present data on 48 ORs we have sequenced and annotated from an antennal transcriptome of a male red milkweed beetle, Tetraopes tetrophthalmus. In contrast to most cerambycids, T. tetrophthalmus is not known to produce long-range sex pheromones to attract or select mates; correspondingly, …
Functional Role Of Ppal And Potential For Moss In Industrial Applications., Susana Perez Martinez
Functional Role Of Ppal And Potential For Moss In Industrial Applications., Susana Perez Martinez
Electronic Theses and Dissertations
This dissertation is an examination and characterization of the functional roles of PPAL. PROTEIN PRENYLTRANSFERASE ALPHA SUBUNIT-LIKE (PPAL) is a recently discovered gene. PPAL homologs are present in all plants and many animals, where its function is largely unknown. It is possible that PPAL could participate in prenylation processes since it shares similarity to the α subunits of known prenylation enzymes. Prenylation is a post-translational modification of proteins that involves the addition of a lipid moiety to proteins to facilitate membrane targeting and association and promote protein-protein interactions. Prenylation has important roles in plant growth and development, including …
Genomic Tools And Models For Investigating The Role Of Germline Diversity In Mouse Antibody Repertoire Development., Justin T. Kos
Genomic Tools And Models For Investigating The Role Of Germline Diversity In Mouse Antibody Repertoire Development., Justin T. Kos
Electronic Theses and Dissertations
Given the diversity and complexity within immunoglobulin (IG) loci, effective mouse models first require characterization of intra-strain differences and construction of high-quality reference assemblies for IG loci in several representative strains. To understand light chain germline diversity across biomedically significant mouse strains, we profiled the expressed IGK and IGL repertoires of 18 commonly used laboratory mouse strains using AIRR-seq. Across strains, we observed germline IGKV sequences shared by three different IGK haplotypes and a more conserved IGLV germline repertoire among common laboratory strains. Pacific Biosciences (PacBio) Single-Molecule Real-Time (SMRT) sequencing was used to sequence and assemble bacterial artificial chromosomes (BAC) …
Statistical Approaches Of Gene Set Analysis With Quantitative Trait Loci For High-Throughput Genomic Studies., Samarendra Das
Statistical Approaches Of Gene Set Analysis With Quantitative Trait Loci For High-Throughput Genomic Studies., Samarendra Das
Electronic Theses and Dissertations
Recently, gene set analysis has become the first choice for gaining insights into the underlying complex biology of diseases through high-throughput genomic studies, such as Microarrays, bulk RNA-Sequencing, single cell RNA-Sequencing, etc. It also reduces the complexity of statistical analysis and enhances the explanatory power of the obtained results. Further, the statistical structure and steps common to these approaches have not yet been comprehensively discussed, which limits their utility. Hence, a comprehensive overview of the available gene set analysis approaches used for different high-throughput genomic studies is provided. The analysis of gene sets is usually carried out based on …
Comparative Secretomics And Functional Analysis Of Effectors Utilized By The Microbotryum Genus Of Anther-Smut Fungal Pathogens, And Their Role In Host-Specificity., William Christopher Beckerson
Comparative Secretomics And Functional Analysis Of Effectors Utilized By The Microbotryum Genus Of Anther-Smut Fungal Pathogens, And Their Role In Host-Specificity., William Christopher Beckerson
Electronic Theses and Dissertations
Understanding how pathogens evolve in response to changes in their host is paramount to combating the spread of emergent strains of disease. This is particularly true for plant pathogens that cause billions of dollars of damages to crops globally, every year. Understanding the molecular interactions between pathogens and their hosts therefore sheds light on the coevolutionary arms race that can result in host-specificity and host-shifts in plant pathogens. This research approaches the question of how fungal pathogens interact with their plant hosts utilizing both unique and shared arsenals of secreted proteins (SPs) during infection, and addresses the question of whether …