Biology Commons^™

The Effect Of Nuclear Perturbations On The 3d Organization Of The Genome, Rosela Golloshi

Doctoral Dissertations

Cells in our body experience constant mechanical forces that influence biological functions such as growth and development. The nucleus has been implicated as a key mechanosensor and can directly influence chromatin organization and epigenetic alterations leading to gene expression changes. However, the mechanism by which such mechanical forces lead to genomic alterations and expression of mechanosensitive genes is not fully understood. The work presented in this dissertation investigates the effect of mechanical and epigenetic perturbations on the 3D genome organization. To investigate this 3D genome folding, we use Chromosome Conformation Capture followed by high throughput sequencing (Hi-C) (Chapter-1) which identifies …

Ixodes Scapularis Src Kinase Is Required For Rickettsial Pathogen Survival In Ticks, Jeremy W. Turck

Biological Sciences Theses & Dissertations

Anaplasma phagocytophilum is an obligate intracellular bacterium that causes disease in humans and animals. It is the causative agent for human anaplasmosis. A. phagocytophilum uses certain strategies to infect both vertebrates and invertebrates. It uses Ixodes scapularis ticks as a vector for spreading infection to other mammal species. This bacterium has a specific path for infection through the salivary glands of its vector host. It also suppresses certain functions such as the inhibition of apoptosis and ROS production in order to increase its survival in ticks. Src kinase, a non-receptor protein-tyrosine kinase, is a major player in cell signaling. Src …

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 …

Multiple Roles Of Nup1 In Arabidopsis Growth And Development, Raj K. Thapa

Electronic Thesis and Dissertation Repository

The nuclear pore complex (NPC) is the gateway between the nucleus and cytoplasm, which provides the passage for transport of RNA, protein, and other molecules into and out of the nucleus. NPC is conserved across all eukaryotes and plays a vital role in various cellular processes. However, compared to other organisms, the study of NPC in plants is limited. Although more than 30 different types of nucleoporin proteins in the model plant Arabidopsis thaliana have been identified, none of those proteins has been studied in detail. In this thesis, I focused on one such protein named NUCLEOPORIN1 (NUP1) and investigated …

Transgenerational Plasticity Causes Differences In Uv-Tolerance Of Intertidal And Subtidal Populations Of The Purple Sea Urchin, Strongylocentrotus Purpuratus, Yareli Alvarez, Nikki L. Adams

Master's Theses

Planktonic larvae of marine organisms are increasingly being exposed and required to respond to a changing physical environment. Adult sea urchins occupy both intertidal and subtidal waters and broadcast spawn gametes into the water column to contend with variable physical conditions. To answer how populations of invertebrates residing at different depths adequately prepare their offspring to cope with different levels of ultraviolet radiation (UVR), we collected adult purple sea urchins, Strongylocentrotus purpuratus, from four sites (two intertidal and two subtidal (~15 m deep)) on the central coast of CA to compare UV tolerance in offspring. Our measurements of UVA …

Classification Of Bacterial Motility Using Machine Learning, Yue Ma

Masters Theses

Cells can display a diverse set of motility behaviors, and these behaviors may reflect a cell’s functional state. Automated, and accurate cell motility analysis is essential to cell studies where the analysis of motility pattern is required. The results of such analysis can be used for diagnostic or curative decisions. Deep learning area has made astonishing progresses in the past several years. For computer vision tasks, different convolutional neural networks (CNN) and optimizers have been proposed to fix some problems. For time sequence data, recurrent neural networks (RNN) have been widely used.

This project leveraged on these recent advances to …

Regulators Of Ectopic Calcification In A Mouse Model Of Dish: A Multi-Omics Perspective, Matthew A. Veras

Electronic Thesis and Dissertation Repository

Diffuse idiopathic skeletal hyperostosis (DISH) is a non-inflammatory spondyloarthropathy and the second most common form of arthritis characterized by formation of ectopic mineral along the spine. Pathological findings in DISH include regional calcification of the anterior longitudinal ligament, paraspinal connective tissues, and annulus fibrosus (AF) of the intervertebral disc (IVD). Clinical symptoms of DISH include increased spine stiffness, decreased spinal range of motion, and in severe cases dysphagia and spinal cord/nerve root compression. The molecular pathways responsible for DISH have not been delineated and as such, there are no disease-modifying treatments. Clinical treatment for DISH is limited to surgical resection …

A Genomic Analysis Of Bobcat Populations In North America With A Comparison To The Canada Lynx: An Assessment Of Local Adaptation To Unique Ecoregions And Phylogeography, Jennifer C. Broderick

Electronic Theses and Dissertations

Bobcats (Lynx rufus) are an ecologically and genetically diverse species with a large contiguous range throughout North America. The species not only has a wide array of phenotypic variation compared to other mammals, but shows marked adaptability across ecozones with differing ecological influences. It is these various selective pressures in distinctive parts of the continent that have likely led to localized adaptations within the bobcat metapopulations. The species is also marked by its ability to maintain connectivity and populations in anthropogenically developed areas, an advantage it has over other felids, including its close relative the Canada lynx ( …

Understanding Intercellular Signaling During Lung Injury-Repair, Margo Patricia Cain

Dissertations & Theses (Open Access)

The mammalian lung is a complex system of specialized cell types with precise spatial organization designed to cooperate to perform gas exchange. These cell types together coordinate organ development, homeostasis, and repair after injury through signals either presented or secreted, known as ligands, to be received by receptors on the surface of another, or in some cases, the same cell. The alveolar region of the lung, the primary region of gas exchange, responds to various types of injuries with different lung repair mechanisms. In order to explore how the various cell types in the lung communicate to drive tissue repair …

Mushroom Body-Specific Gene Regulation By The Swi/Snf Chromatin Remodeling Complex, Kevin Cj Nixon

Electronic Thesis and Dissertation Repository

Over the lifetime of an organism, neurons must establish, remodel, and maintain precise connections in order to form neural circuits that are required for proper nervous system functioning. Disruptions in these processes can lead to neurodevelopmental disorders such as intellectual disability (ID) and autism spectrum disorder. Mutations in genes encoding subunits of the SWI/SNF chromatin remodeling complex have been implicated in ID, yet the role of this complex in neurons is poorly understood. In this project, I established cell-type specific methods to examine the effect of SWI/SNF subunit knockdowns on gene transcription and chromatin structure in the memory-forming neurons of …

The Role Of Influenza Infection On Cell Metabolism, Megha Mokkapati

Williams Honors College, Honors Research Projects

In this particular study global metabolomics LCMS data was analyzed to determine the effect of influenza infection on host metabolic processes. Specifically, wild-type male and female mouse lung samples from mice infected with PR8 (H1N1) or both PR8 and a reinfection of X31 (H3N2) were analyzed. The LC/MS(liquid chromatography-mass spectrometry) based global metabolomics will be performed on the samples using hydrophilic interaction liquid chromatography to separate polar analytes from the tissues (Dettmer, Aronov, 2007). Metabolites impacted by influenza infection in all samples will be analyzed to compare male and female mice, as well as differences between PR8 infection and X31 …

Categorization Of Orthologous Gene Clusters In 92 Ascomycota Genomes Reveals Functions Important For Fungal Phytopathogenicity, Daniel Curtis Peterson

Graduate Research Theses & Dissertations

Ascomycota fungi are mostly saprophytic in nature, living off dead or decaying matter. However, a small subset of these fungi possess the ability to infect live hosts and cause disease while obtaining nutrients. Phytopathogenic Ascomycota are responsible for substantial economic losses each year, destroying valuable crops. Previous genomic studies have been conducted to annotate sequenced genes and proteins of these fungi with predicted functions, and those annotations are publicly accessible through online databases. Through these means, several genes have been identified to play a role in pathogenicity in some agriculturally relevant fungi. Through a bioinformatic analysis approach the present study …

Biological And Computational Studies Of The Structure And Function Of Pul103, A Human Cytomegalovirus Tegument Protein, Ashley N. Anderson

Wayne State University Dissertations

Human cytomegalovirus (HCMV) is an enveloped, single segment, double-stranded DNA virus. HCMV infection causes disease in immunocompromised (HIV patients, transplant recipients) and immunodeficient (fetuses, neonates) populations. Current treatments are effective but are either limited in use or can lead to organ damage and/or antiviral resistance, and no vaccines are available. Additional antiviral targets are needed. HCMV pUL103 is a potential antiviral target. pUL103 is a conserved herpesvirus protein present in the tegument, layer of proteins and RNA between the envelope and capsid of HCMV virions. pUL103 helps reorganize cellular secretory machinery (Golgi, endosomes) to form the cytoplasmic virion assembly compartment …

Interspecific Gene Flow Potentiates Adaptive Evolution In A Hybrid Zone Formed Between Pinus Strobiformis And Pinus Flexilis, Mitra Menon

Theses and Dissertations

Species range margins are often characterised by high degrees of habitat fragmentation resulting in low genetic diversity and higher gene flow from populations at the core of the species range. Interspecific gene flow from a closely related species with abutting range margins can increase standing genetic diversity and generate novel allelic combinations thereby alleviating limits to adaptive evolution in range margin populations. Hybridization driven interspecific gene flow has played a key role in the demographic history of several conifer due to their life history characteristics such as weak crossability barriers and long generation times. Nevertheless, demonstrating whether introgression is adaptive …

Plasticity And The Impact Of Increasing Temperature On A Tropical Ectotherm, Adam A. Rosso

Electronic Theses and Dissertations

Organisms may respond to climate change through behavior, genetic adaptation, and/or phenotypic plasticity. Tropical ectotherms are thought to be especially vulnerable to climate change because most have a narrow range of thermal tolerance while living close to their upper thermal tolerance limits. Additionally, many tropical species live in closed-canopy forests, which provide homogenous thermal landscapes that prevent behavioral compensation for stressfully warm temperatures. Finally, tropical ectotherms are thought to have decreased capacity for phenotypic plasticity because they have evolved in thermally stable environments. We tested gene expression patterns and phenotypic plasticity in the Panamanian slender anole by a) measuring changes …

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 …

Deriving Statistical Inference From The Application Of Artificial Neural Networks To Clinical Metabolomics Data, Kevin M. Mendez

Theses: Doctorates and Masters

Metabolomics data are complex with a high degree of multicollinearity. As such, multivariate linear projection methods, such as partial least squares discriminant analysis (PLS-DA) have become standard. Non-linear projections methods, typified by Artificial Neural Networks (ANNs) may be more appropriate to model potential nonlinear latent covariance; however, they are not widely used due to difficulty in deriving statistical inference, and thus biological interpretation. Herein, we illustrate the utility of ANNs for clinical metabolomics using publicly available data sets and develop an open framework for deriving and visualising statistical inference from ANNs equivalent to standard PLS-DA methods.