Genetics Commons^™

Analysis Of Symptom Expressions And Transmission Rates Caused By The Plant Pathogen Phytophthora Ramorum On Native Chaparral Plants From The Genus Arctostaphylos, Bharati Gaonker

Natural Sciences and Mathematics | Biological Sciences Master's Theses

Phytophthora ramorum is the causal agent of Sudden Oak death (SOD), ramorum dieback and ramorum leaf blight which affect both forest environments and nurseries. This oomycete pathogen has had a huge economic impact on the nursery and lumber industry. Forests in California have experienced substantial mortality of oaks affecting the forest dynamics and diversity. Our research investigates four native species and two ornamental cultivars of plants, which belong to the genus Arctostaphylos (manzanita) and are considered to be new hosts for P. ramorum in the chaparral ecosystem of California. Symptom expression and transmission rates were analyzed on Arctostaphylos glauca, …

Identifying The Cell Composition And Clonal Diversity Of Supratentorial Ependymoma Using Single Cell Rna-Sequencing, James He

University Scholar Projects

Ependymoma is a primary solid tumor of the central nervous system. Supratentorial ependymoma (ST-EPN), a subtype of ependymomas, is driven by an oncogenic fusion between the ZFTA and RELA genes in 70% of cases. We introduced this fusion into neural progenitor cells of mice embryos via in utero electroporation of a non-viral binary piggyBac transposon system containing ZFTA-RELA. From preliminary data in the LoTurco lab, inducing the expression of ZFTA-RELA into different neural progenitor cells produces tumors of varying lethality and cellular composition. To define the cellular composition and subclonal diversity of ST-EPN tumors, we used single cell RNA-sequencing to …

The Effects Of Mapk Signaling On The Development Of Cerebellar Granule Cells, Kerry Morgan

University Scholar Projects

The granule cells are the most abundant neuronal type in the human brain. Rapid proliferation of granule cell progenitors results in dramatic expansion and folding of the cerebellar cortex during postnatal development. Mis-regulation of this proliferation process causes medulloblastoma, the most prevalent childhood brain tumor. In the developing cerebellum, granule cells are derived from Atoh1-expressing cells, which arise from the upper rhombic lip (the interface between the roof plate and neuroepithelium). In addition to granule cells, the Atoh1 lineage also gives rise to different types of neurons including cerebellar nuclei neurons. In the current study, I have investigated the …

The Effects Of Mapk Signaling On The Development Of Cerebellar Granule Cells, Kerry Morgan

Honors Scholar Theses

The granule cells are the most abundant neuronal type in the human brain. Rapid proliferation of granule cell progenitors results in dramatic expansion and folding of the cerebellar cortex during postnatal development. Mis-regulation of this proliferation process causes medulloblastoma, the most prevalent childhood brain tumor. In the developing cerebellum, granule cells are derived from Atoh1-expressing cells, which arise from the upper rhombic lip (the interface between the roof plate and neuroepithelium). In addition to granule cells, the Atoh1 lineage also gives rise to different types of neurons including cerebellar nuclei neurons. In the current study, I have investigated the …

Discovery Of Novel Ubiquitin- And Methylation-Dependent Interactions Using Protein Domain Microarrays, Jianji Chen

Dissertations and Theses (Open Access)

Post-translational modifications (PTMs) drive signal transduction by interacting with "reader" proteins. Protein domain microarray is a high throughput platform to identify novel readers for PTMs. In this dissertation, I applied two protein domain microarrays identifying novel readers for histone H2Aub1 and H2Bub1, and H3TM K4me3. Ubiquitinations of histone H2A at K119 (H2Aub1) and histone H2B at K120 (H2Bub1) function in distinct transcription regulation and DNA damage repair pathways, likely mediated by specific "reader" proteins. There are only two H2Aub1-specific readers identified and no known H2Bub1-specific readers. Using a ubiquitin-binding domain microarray, I discovered the phospholipase A2-activating protein (PLAA) PFU domain …

Rare Variant Association Studies In Crohn’S Disease And Colorectal Cancer: Methods And Applications, Jiun-Sheng Chen

Dissertations and Theses (Open Access)

Genetic factors account for a substantial portion of Crohn’s disease and colorectal cancer (CRC) risk. Patients with Crohn’s disease, a condition that causes chronic inflammation of the gastrointestinal tract, are at increased risk of colorectal cancer morbidity and mortality. Genome-wide association studies using single marker approaches have identified loci responsible for these diseases, but disease susceptibility from rare variants is incompletely understood. This dissertation includes three chapters, two association studies for Crohn’s disease and CRC, and a statistical method to improve the power of statistical tests.

For Crohn’s disease, we performed targeted sequencing of 101 genes in 205 children with …

Genomic Studies Of Beaf-32 In Drosophila, John Keller Mckowen Iii

LSU Doctoral Dissertations

Compared to humans, the model organism Drosophila melanogaster is particularly gene dense and encodes several insulator binding proteins (IBP) to aid in its genome organization. Our focus of research is a particular IBP, Boundary Element-Associated Factor of 32kD (BEAF). BEAF primarily binds near the promoters of constitutively active housekeeping genes. It is thought to help maintain the active state of these genes by preventing the spread of repressive chromatin. Additionally, the enhancer blocking activity of BEAF is thought to prevent aberrant activation or silencing of genes. BEAF appears to be ubiquitously expressed among cells and tissues, albeit at varying levels. …

Insights Into Leptopilina Spp. Immune-Suppressive Strategies Using Mixed-Omics And Molecular Approaches, Brian Wey

Dissertations, Theses, and Capstone Projects

Host-parasite interactions influence the biology of each over the course of evolution. Parasite success allows for the passage of potent virulence strategies from generation to generation. Host success passes stronger immunity and resistance strategies to the following generations as well. Only by studying both partners within their natural contexts can we begin to understand the relationship between the two and how immune mechanisms and virulence strategies interact as a molecular arms race.

In this work, we focus on a natural host-parasite pair, the Drosophila-Leptopilina model. Leptopilina species are parasites of several fruit fly species, including Drosophila melanogaster. This model …

Composition And Homology In The Taxonomic Classification Of Escherichia Coli, Tanya Irani

Theses and Dissertations (Comprehensive)

As new techniques have been introduced, specifically the possibility of complete genome sequencing, better methods of defining bacterial species have also been proposed. One of the most recently proposed methods, using bioinformatic techniques, is to calculate the average nucleotide identity (ANI) between the homologous genome segments of different isolates. Another method for species discrimination that has been tested successfully is the similarity of DNA compositional signatures. However, in a recent update, DNA signatures split the available Escherichia coli complete genomes into three groups. To check if this result was consistent with such genomes belonging to different species, we tested methods …

Population Genetics Of A Reintroduced Fisher (Pekania Pennanti) Population In West Virginia, Caroline E. Harms

Graduate Theses, Dissertations, and Problem Reports (ETD)

Fishers (Pekania pennanti) were reintroduced in West Virginia in 1969 with no population wide genetic analysis ever having been conducted. Genetic analysis of reintroduced populations is vital to assess genetic diversity as an indicative of population viability. My objective was to collect fisher samples throughout West Virginia, nearby states where fisher may be migrating (PA and NY), and the New Hampshire source population to provide a full genetic interpretation of the reintroduced West Virginia population. Genetic analysis was used to measure genetic diversity, admixture or delineation of subpopulations, and effective population size. Sample location and genetic data were …

Decoding The Evolutionary Response To Prostate Cancer Therapy Using Plasma Genome Sequencing, Naveen Ramesh

Dissertations and Theses (Open Access)

Investigating genome evolution in response to therapy is difficult in human tissue samples due to the difficulty in accessing metastatic tumor sites and logistical challenges of collecting longitudinal samples. To overcome these issues, we developed an unbiased whole-genome plasma DNA sequencing approach called PEGASUS that concurrently measures genomic copy number and exome mutations from archival cryostored plasma samples. This approach was applied to study longitudinal blood plasma samples from prostate cancer patients. A molecular characterization of archival plasma DNA from 233 patients and genomic profiling of 101 patients identified clinical correlations of aneuploid plasma DNA profiles with poor survival, increased …

Quantifying Structure And Variation In Complex Phylogenetic Data, Genevieve Geraldine Mount

LSU Doctoral Dissertations

Identifying the source and structure of variation in nature is crucial to understanding fundamental aspects of evolution. Despite a recent plethora of genetic and morphological data, many interesting questions about the relationships between different groups remain unresolved. My dissertation evaluates three approaches for identifying and quantifying the variation within phylogenetic datasets. Characterizing variation within datasets and across analytical methods gives insight into biologically interesting characters, unusual evolutionary processes, and areas for model improvement.

Network-based community detection approaches offer a powerful tool to describe variation in phylogenetic signal across the genome (i.e., gene tree variation). In Chapter 2, I investigate the …

Identification Of Trim24 Domain Essentiality In Primary Trim24coe Carcinosarcoma Cell Lines, Cem Dede

Dissertations and Theses (Open Access)

Regulation of transcriptional control is a critical feature for organismal development and survival. Because of its effects on chromatin-controlled expression, disruptions of this delicately tuned mechanism are an important factor in development of tumorigenesis. Therefore, there is a growing interest in targeting these control mechanisms for their potential therapeutic values.

Our lab previously discovered the epigenetic regulator function of Tripartite motif protein 24 (TRIM24) through its H3K4me0 and H3K23ac dual histone signature reader function, its negative regulatory effect on the p53 tumor suppressor, in addition to its shown oncogenic driving capacity on immortalized mammary epithelial cells when overexpressed. Although TRIM24 …

Transposable Element Expression In Human Embryo Single-Cell Rna-Seq Data, Corinne Sexton

UNLV Theses, Dissertations, Professional Papers, and Capstones

Transposable elements (TEs) are genetic sequences which are mobile within the genome, including DNA transposons and retrotransposons. Though the vast majority are no longer able to move or duplicate in humans, they still are actively transcribed in both germline and somatic cells, particularly in early human development. TEs are expressed in an extremely cell-type and stage specific pattern during embryogenesis, suggesting that they may either have a regulatory role in the cell or be transcribed along with cell-specific genes. However, earlier studies have focused on hESC models or early embryos up to day 6, with differing patterns of TE expression. …

Novel Long Non-Coding Rna Cdlinc Promotes Nsclc Progression, Christina J. Moss

USF Tampa Graduate Theses and Dissertations

Non-small cell lung cancer (NSCLC) is the leading cause of cancer death worldwide with a low 5-year survival rate of only around 21%. This low 5-year survival rate is due to two main reasons. First, NSCLC is often diagnosed at the later stages when it has already metastasized. Second, NSCLC is an incredibly diverse, heterogenous disease making it very hard to target the true molecular oncogenic drivers. New targets for personalized therapeutics are needed based on the expression status of each individual lung cancer tumor.

One way of looking for these new therapeutics is to begin by identifying the oncogenotype …

Evolutionary Inference From Admixed Genomes: Implications Of Hybridization For Biodiversity Dynamics And Conservation, Tyler Chafin

Graduate Theses and Dissertations

Hybridization as a macroevolutionary mechanism has been historically underappreciated among vertebrate biologists. Yet, the advent and subsequent proliferation of next-generation sequencing methods has increasingly shown hybridization to be a pervasive agent influencing evolution in many branches of the Tree of Life (to include ancestral hominids). Despite this, the dynamics of hybridization with regards to speciation and extinction remain poorly understood. To this end, I here examine the role of hybridization in the context of historical divergence and contemporary decline of several threatened and endangered North American taxa, with the goal to illuminate implications of hybridization for promoting—or impeding—population persistence in …

Molecular Differentiation Of Astragalus Species And Varieties From The Western United States: The Chloroplast Dna Bridge Between Evolution And Molecular Systematics, Marwa Neyaz, Daniel Cook, Rebecca Creamer

Poisonous Plant Research (PPR)

Locoweeds are the most widespread poisonous plant problem in the world and have been reported in the Western United States since the 1800s, causing tremendous losses in livestock. Consumption of locoweeds by grazing animals stimulates the neurological disease, locoism, characterized by weight loss, ataxia, and lack of muscular coordination. The name locoweed is used for Astragalus and Oxytropis species known to contain swainsonine, the toxic principle produced by the plant endophytic fungus Undifilum. Astragalus includes 2,500-3,000 species and many varieties that have almost identical morphological characteristics that overlap among species, leading to improper identification. Therefore, the aim of this study …

On The Distribution Of Genetic Variation In Ecological Communities, Isaac Overcast

Dissertations, Theses, and Capstone Projects

Biodiversity in ecological communities is structured hierarchically across spatial and temporal scales. Many open questions remain as to how this structure accumulates. For example, what are the relative contributions of dispersal versus in situ speciation? Or, how important are stochastic drift versus deterministic processes? Up to this point, these questions have been investigated by isolated disciplines (e.g. macroecology, comparative phylogeography, macroevolution) using tools and data that tend to focus on only one axis of community scale data (e.g. phylogenies, relative abundances, and/or trait information). Yet we know that there are feedbacks among processes that respond on short, medium, and long …

Pseudomonas And Bacillus Soil Isolates Produce Antibiotics, Chelsea Brandt, Dr. Lori Scott

Identifying and Characterizing Novel Antibiotic Producing Microbes From the Soil

The recent emergence of antibiotic resistance bacterial strains presents a significant challenge and threat to human healthcare. While new methods of treatment such as bacteriophage therapy and combinations of existing antibiotics are being researched, the human population is in dire need of new antibiotics to replace those that are ineffective. This research addresses this need by identifying antibiotic producing bacteria in a soil sample from Davenport, IA. This project is a collaboration with the Tiny Earth Project Initiative (TEPI), which is a global network of educators and students focused on studentsourcing antibiotic discovery from soil. Microbiology lab techniques and 16S …

Using Cuda To Enhance Data Processing Of Variant Call Format Files For Statistical Genetic Analysis, Heather Mckinnon

All Graduate Projects

Utilizing the power of GPU parallel processing with CUDA can speed up the processing of Variant Call Format (VCF) files and statistical analysis of genomic data. A software package designed toward this purpose would be beneficial to genetic researchers by saving them time which they could spend on other aspects of their research. A data set containing genetics from a study of trichome production in Mimulus guttatus, or yellow monkey flower, was used to develop a package to test the effectiveness of GPU parallel processing versus serial executions. After a serial version of the code was generated and benchmarked, OpenACC …

Machine Learning Methods For The Analysis Of Metagenomes, Vito Adrian Cantu Alessio Robles

CGU Theses & Dissertations

As of October 2020, there are 18.6 × 1015 DNA base pairs publicly available in the Sequence Read Archive and this number is growing at an exponential rate. As DNA sequencing prices continue to drop, many research groups around the world have incorporated high throughput sequencing in their research, giving us access to sequences from many distinct ecosystems. This has revolutionized the field of metagenomics, which aims to fully characterize all organisms and their interactions in a particular system. Nevertheless, the plethora of available data has made its analysis difficult as traditional techniques such as genome assembly or sequence alignment …

Spatial And Temporal Genetic Structure Of Winter-Run Steelhead (Oncorhynchus Mykiss) Returning To The Mad River, California, Steven R. Fong

Cal Poly Humboldt theses and projects

Distinct populations of steelhead in the wild are in decline. The propagation of steelhead in hatcheries has been used to boost population numbers for recreational fisheries and for use in conservation. However, hatchery breeding practices of steelhead can result in changes in genetic structure. I investigated the genetic structure of winter-run steelhead (Oncorhynchus mykiss) returning to the Mad River, California, where a hatchery has been used enhance production for recreational fisheries since 1971. Genetic variability in Mad River steelhead was evaluated using 96 single nucleotide polymorphisms (SNPs) among 4203 individuals, including the Mad River and nearby locations, and …

The Host Gatekeeper: Using The Flagellar Pathway To Understand Symbiont Host Adaptation, Adam R. Pollio

Graduate Theses, Dissertations, and Problem Reports (ETD)

The acquisition of microbial partners is a strategy used by a diverse group of arthropods to overcome ecological barriers that might normally make certain niches uninhabitable. The unique phylogenetic opportunities attainable from the natural experiment of the Sodalis-allied clade allow for better understanding of how molecular structures evolve through time. Here, we focus on the evolution of the flagellar synthesis pathway, due to its complexity and ability to diverge in response to ecological pressures. We used this molecular pathway and natural experiment to show that normal evolutionary outcomes associated with symbiosis (i.e., genome reduction) do not explain the predicted conservation …

Wading In A Glycan Sea: Investigations Of, And Developing Bioinformatic Tools For, Carbohydrate Active Enzymes And Gene Clusters In Prokaryotes, Catherine Ann Ausland

Graduate Research Theses & Dissertations

Carbohydrates are immensely important biomolecule found in all organisms on earth, serving roles in structure, energy storage, protection and/or cell signaling. Carbohydrates are composed of an immense diversity of linkages, monosaccharide moieties and substitutions making them likely the most diverse biomolecule on earth, as well as the most abundant, being synthesized by plants and algae. Carbohydrates are synthesized and degraded by all organisms on earth through the expression of carbohydrate active enzymes, or ‘CAZymes’. In bacteria, CAZymes have been characterized to cluster in with transporters, regulators and/or other genes in so-called ‘polysaccharide utilization loci’, or PULs, to degrade carbohydrate substrates …

Mechanisms And Consequences Of Myb Gene Activation In Salivary Gland Tumors, Candace Frerich

Biomedical Sciences ETDs

Salivary gland adenoid cystic carcinoma (ACC) is an aggressive tumor with a tendency to infiltrate surrounding nerves and metastasize to distant sites. The standard treatment often fails to control local tumor recurrence and distant metastases and no approved targeted therapeutic options exist for these tumors. The goal of our studies was to reveal the molecular mechanisms driving ACC tumor development and novel drug targets to improve patient morbidity and mortality.

We first analyzed clinical and RNA-sequencing (RNA-seq) data for 68 formalin-fixed paraffin-embedded (FFPE) ACC tumor samples and described previously unappreciated molecular heterogeneity that predicts patient outcome. The poor outcome subgroup …

Sequence Analysis Of The Ren1 Genomic Region From The Grapevine ‘Kishmish Vatkana’, Dani Joseph

Graduate Theses/Dissertations

The REN1 region of the grapevine ‘Kishmish Vatkana’ was mapped as the locus that confers resistance to the economically important disease, grape powdery mildew. The purpose of this work was to extend the nucleotide sequence information of this region. By sequencing a heretofore unknown bacterial artificial chromosome clone, the sequence information of this region was extended by 46,890 nucleotides. Sequencing was performed using the third-generation sequencing method, named Oxford Nanopore Technology (ONT). In order to improve the accuracy of the sequence data, a modified ONT library preparation method was developed. ONT sequencing of a library prepared with the modified protocol …

Multi-Polygenic Risk Score Prediction Model For Bipolar Disorder, Travis Mize

UNLV Theses, Dissertations, Professional Papers, and Capstones

Bipolar disorder (BP), a severe mental disorder characterized by recurring manic and depressive episodes, has been shown to have a strong genetic underpinning. Current theory suggests that it is the summation of risk alleles, spread across the entirety of the genome, which contributes to the development of BP, as well as other polygenic traits. The comorbid nature of these polygenic traits are often problematic for diagnosticians as the symptomology of the disorders may vary substantially between individuals and can create diagnostic confusion. To alleviate issues such as these, a more objective measure, to be used alongside current diagnostic procedures, is …

P53r245w Mutation Elicits Metastatic Phenotype In Pten Deficient Prostate Cancer, Ky Pham

Dissertations and Theses (Open Access)

Trp53 mutations are the most frequent genetic alterations in prostate cancer and are associated with more aggressive disease and worse overall survival. The majority of Trp53 mutations in prostate cancer are missense mutations, resulting in amino acid substitutions with profound effect. In addition to the loss of wild type function, missense mutations in Trp53 result in a gain-of-function (GOF) phenotype. This GOF phenotype confers biologic advantages to the tumor cells, enabling them to metastasize and invade distant organs. In this study, we generated mice carrying a conditional prostate-specific p53R245W mutant and Pten deletion to access the role of this common …

Fusarium Euwallacea: A Serious Threat To The Native And Ornamental Trees And Shrubs In Southern California, Greg Tyler, Yixing Zheng, Michael Kulinich, Hagop Atamian

Student Scholar Symposium Abstracts and Posters

Fusarium Euwallacea is a fungus that has established symbiotic relationship with the beetle Euwallacea aff. fornicata. The beetle bores through the tree bark and into the sapwood making long tunnels inside the trees. The beetle carries the F. Euwallacea in a specialized structure on its body called mandibular mycangia and cultivates the fungus in the tunnels on which the beetle feeds to grow and reproduce. The growth of the fungus obstructs water and mineral transport in the plant xylem tissue, resulting in dieback, wilt and mortality of the host tree. Fungi are known to secrete proteins called effectors in …

Co-Occurrence Of Manganese Oxidase Genes Indicates Lateral Transfer Between Classes Of Proteobacteria, Jacob Olichney

Student Scholar Showcase

Pseudomonas putida GB-1 is a model organism for the study of manganese oxidation in bacteria, however, the frequency of co-localization of multiple known and suspected manganese oxidizing proteins, as well as their occurrence between species, is unknown. Eight different genes isolated from known manganese oxidizing bacteria (MnxG, MopA, McoA, PputGB1_2552, PputGB1_2553, MoxA, MofA, and Bacillus MnxG) were tested individually using BioPython and BLAST (Basic Local Alignment Search Tool) on multiple genomic databases. BLAST searches had an expect value cutoff of 1e-50, limiting gene homologs to those with high sequence similarity. The abundance of homologous genes across classes of proteobacteria point …