Genetics and Genomics Commons^™

The Sos Response In Escherichia Coli K12: An Exploration Of Mutations In Lexa And Reca Using Fluorescence Microscopy, Steven Van Alstine

Doctoral Dissertations

Faithful replication of the genome is paramount for maintaining the fitness of an organism. Therefore, life has evolved inducible mechanisms to be able to repair damaged DNA and maintain evolutionary fitness. The SOS response is a highly conserved DNA damage inducible response that is tightly regulated. Multiple factors contribute to the ability of the cell to perform proper DNA repair and induction of the SOS response including the amount of RecA, mutations in RecA that affect competition for DNA, and other proteins that interact with the RecA filament. The complex relationship between RecA and LexA is the subject of this …

Intracellular Delivery Of Therapeutic Biomolecules Through Versatile Polymer Nanotechnology, David C. Luther

Doctoral Dissertations

Advancing pharmaceutical technology has made it possible to treat diseases once considered ‘undruggable.’ Access to these new pharmaceutical targets is possible thanks to the advent of protein and nucleic acid therapeutics. Responses to the COVID-19 pandemic, as well as cutting-edge treatments for cancer and multiple sclerosis have centered on these biologic therapies, promising even greater value in the future. However, their utility is limited at a cellular level by inability to cross the plasma membrane. Nanocarrier technologies encapsulate therapeutics and facilitate uptake into the cell but are often trapped and degraded in endosomes. Arginine-functionalized gold nanoparticles (Arg-NPs) provide efficient, direct …

Investigation Of Basil Downy Mildew Pathogen Survival, New Pathotype Development And Sources Of Quantitative, Kelly S. Allen

Doctoral Dissertations

Basil downy mildew (BDM) caused by the oomycete pathogen Peronospora belbahrii, threatens sweet basil (Ocimum basilicum) production worldwide. Chemical and cultural control options for BDM are limited, and resistant cultivars have only recently become available for commercial production. To address this challenging agricultural disease, this research investigates BDM epidemiology, occurrences of new pathotypes, and molecular plant-pathogen interactions leading to host resistance or susceptibility. A reproducible low-resource inoculation protocol was developed to harvest P. belbahrii inoculum and propagate BDM for further research. The survival of P. belbahrii sporangia was examined using an in vitro assay to assess germination …

What I Talk About When I Talk About Integration Of Single-Cell Data, Yang Xu

Doctoral Dissertations

Over the past decade, single-cell technologies evolved from profiling hundreds of cells to millions of cells, and emerged from a single modality of data to cover multiple views at single-cell resolution, including genome, epigenome, transcriptome, and so on. With advance of these single-cell technologies, the booming of multimodal single-cell data creates a valuable resource for us to understand cellular heterogeneity and molecular mechanism at a comprehensive level. However, the large-scale multimodal single-cell data also presents a huge computational challenge for insightful integrative analysis. Here, I will lay out problems in data integration that single-cell research community is interested in and …

Genome Evolution In The Salicaceae: Genetic Novelty, Horizontal Gene Transfer, And Comparative Genomics, Timothy Yates

Doctoral Dissertations

Genome evolution is a powerful force which shapes genomes over time through processes like mutation, horizontal transfer, and sexual reproduction. Although questions which aim to explore genome evolution are broad, they are all understood through the discovery and comparison of genetic variation. For example, genetic diversity may explain differences in phenotypes, etiology of disease, and is essential for phylogenomic analysis. Recently, the democratization of next generation and third generation DNA sequencing technologies have allowed for genomics to produce large amounts of sequence data. This has facilitated the capture of genetic variation at species and population scales.

Populus and Salix are …

Mechanisms By Which Xenorhabdus Nematophila Interacts With Hosts Using Integrated -Omics Approaches, Nicholas C. Mucci

Doctoral Dissertations

Nearly all organisms exist in proximity to microbes. These microbes perform most of the essential metabolic processes necessary for homeostasis, forming the nearly hidden support system of Earth. Microbial symbiosis, which is defined as the long-term physical association between host and microbes, relies on communication between the microbial community and their host organism. These interactions among higher order organisms (such as animals, plants, and fungi) and their bacteria links metabolic processes between interkingdom consortia. Many questions on microbial behavior within a host remain poorly understood, such as the colonization efficiency among different microbial species, or how environmental context changes their …

Multi-Omic Systems Biological Analysis Of Host-Microbe Interactions, Piet Jones

Doctoral Dissertations

Systems biology offers the opportunity to understand the complex mechanisms of various biological phenomena. The wealth of data that is produced, at an increasing rate, provides the potential to meet this opportunity. Here we take an applied approach to integrate multiple omic level data sources in order to generate biologically relevant hypotheses. We apply a novel analysis pipeline to model both, in concert, the microbial and transcriptomic signature from COVID-19 positive patients. We show patients may suffer from an increased microbial burden, with an increased pathogen potential. Gene expression evidence further shows patients may exhibit a compromised barrier immunity, owing …

The Influence Of Climate Change On The Ecology Of The Arctic Ground Squirrel In Denali National Park, Ak., Nigel A. Golden

Doctoral Dissertations

This dissertation research focuses on the ecology of the Arctic ground squirrel (Urocitellus parryii) in Denali National Park and Preserve, AK. The Arctic ground squirrels is a species of interest for monitoring efforts under the National Park Services’ Vital Signs Monitoring Program under the Vital Signs Monitoring program. The focus of this program is to monitor what is considered to be the most significant indicators of ecological conditions of the specific park resources that are of the greatest concern. The CAKN designated the Arctic ground squirrel (Urocitellus parryii) as one indicator species of park ecosystems. Despite being easy to observe …

Genomic Organization And Expression Of The Wc1 Hybrid Coreceptor And Pattern Recognition Receptor On Porcine Gamma Delta T Cells, Lauren Le Page

Doctoral Dissertations

gd T cells are a crucial component of the immune response to a number of increasingly relevant and largely zoonotic pathogens to which efficacious vaccination is lacking. In ruminants and swine, gd T cells represent a major population of peripheral blood and epithelial tissue-resident lymphocytes. gdT cells respond to both protein and non-protein antigens independently of MHC presentation and possess immunological memory. Upon activation, gamma delta T cells illicit a variety of effector functions and play an indispensable role of orchestrating the downstream immune response. These characteristics make gamma delta T cells a promising candidate for recruitment by vaccination, however, …

The Neurobiological Underpinnings Of Depression-Related Maternal Behavior Deficits, Sarah B. Winokur

Doctoral Dissertations

Maternal caregiving is a dynamic process that requires extensive cognitive, motivational, and affective processing. World-wide, approximately 17% of mothers are diagnosed with postpartum depression yearly (Wang et al., 2021). Untreated, mothers with postpartum depression experience deficits in cognition, motivation, affect, and parenting (Arteche et al., 2011; Dix and Meunier, 2009; Lovejoy et al., 2000). Although postpartum depression is related to compromised parenting, to date, few studies have examined the neurobiological mechanisms by which maternal behavior is compromised in postpartum depression (Field, 2010; Murray et al., 1996)_. This dissertation aims to examine how depression neurobiologically disrupts parenting abilities. These studies …

Genetic And Environmental Regulation Of Plant Growth, Kirk J-M Mackinnon

Doctoral Dissertations

Field grown crops are continually exposed to a variety of external stimuli that influence plant responses. Light, temperature, and water availability interact to affect many economically important traits including growth rate, size, and lifespan. My research is focused on the intersection of genetic and environmental factors influencing plant growth. Specifically, I am interested in elucidating the regulation of rhythmic genes in response to photo- and thermocycles and identifying novel candidate genes associated with growth and drought traits. Understanding the gene regulatory networks that mediate time-of-day signaling is vital to identifying candidate genes across the pan-genome associated with traits of interest.

Mapping Selected Polyphenols Metabolism By Gut Bacteria And Their Genes, Ermin Zhao

Doctoral Dissertations

The human gut microbiome is a huge enzyme repository for dietary polyphenols metabolism, especially considering most of the polyphenols cannot be digested in the host and their biological functions are limited. Poor bioaccessibility based on traditional pharmaceutical ADME (absorption, distribution, metabolism, and excretion) assessment is the main problem facing the widely medical application of most polyphenols. Gut bacteria have the potential to mediate a wide range of biotransformation reactions of polyphenols, which leads to the production of many bioactive metabolites. In the past decades, mounting evidence in traditional ADME study have demonstrated gut bacteria play an irreplaceable role in dietary …