Doctor of Philosophy (PhD), Ohio University, 2024, Molecular and Cellular Biology (Arts and Sciences)

Gravity is a fundamental driving force of plant evolution, profoundly influencing numerous developmental and growth processes in plants. Gravity's most evident impact is the provision of directional cues to germinating seeds, guiding the roots downward and shoots upward. Known as gravitropism, this directional response to gravity is crucial to plants' overall health and productivity. Although biochemical and physiological studies have identified key ionic, chemical, and genetic factors involved in gravitropic signaling, the coordination of these actors remains poorly understood. Recent advances in omics technologies and the emergence of ways to isolate the effects of gravity on plants such as spaceflight experiments aboard the International Space Station (ISS), ground-based simulated gravities using clinostat and random positioning machines, and simple reorientation experiments have provided opportunities to investigate the molecular intricacies of this signaling cascade. Hence, this dissertation utilized both transcriptomics and proteomics to investigate gravitropic signaling in Arabidopsis plants during spaceflight in the Biological Research In Canister – Light Emitting Diode (BRIC LED) hardware. The results revealed key adaptive responses to the spaceflight environment, including destabilization and rearrangement of cell wall components, increased metabolic energy demands, and hypersensitivity of the photosystem. These adaptations were accompanied by a lack of direct correlation between transcriptomics and proteomics datasets, prompting further analysis using statistical and machine learning models. It was found that comparisons at the metabolic pathways level provided more comprehensive insights than simple gene-to-protein correlations. In addition, a meta-analysis of four existing plant proteomics datasets from spaceflight experiments aboard the ISS was conducted to assess variability. Factors such as spaceflight hardware, seedling age, li (open full item for complete abstract)

Committee: Sarah Wyatt (Advisor); Michael Held (Committee Member); Erin Murphy (Committee Member); Allan Showalter (Committee Member) Subjects: Bioinformatics; Cellular Biology; Molecular Biology; Plant Biology

Master of Science, The Ohio State University, 2024, Evolution, Ecology and Organismal Biology

Artificial propagation, called in vitro propagation, has been commonly used to metamorphose juvenile freshwater mussels without the need of a fish host, making it a useful tool for conservation biology. To improve our success of in vitro propagation, we must first expand our current limited knowledge of the larval development of mussels. The key to this is understanding what nutrition is needed for the successful development and propagation of healthy juvenile mussels. In this study, we compare media of various compositions to assess the growth of larval mussels. Growth is evaluated via analysis of the transcriptome, which can reveal internal processes happening within an organism. This study combines the accessibility of in vitro propagation with gene expression analysis of larval growth between growth media of different compositions with the goal of improving in vitro juvenile mussel propagation. Glochidia were extracted from adult Lampsilis siliquoidea mussels, pooled, and separated into three media groups: Leibovitz's L-15 Medium (L-15), Medium 199 (M199), and M199 with 50μL of lipids from concentrate (M199 + lipids). Glochidia developed in an incubator until signs of metamorphosis were present. Percent metamorphosis in the newly metamorphosed juveniles propagated in each of the three media was calculated and compared. Juveniles were collected from each dish, rinsed with sterile ultrapure water, and snap frozen in liquid nitrogen. RNA was extracted from the samples and sequenced on the Illumina NovaSeq 6000 sequencer with output as 100-base-pair paired-end reads. Assembly of the de novo transcriptome was performed and differentially expressed transcripts between the three groups were identified. Percent metamorphosis was significantly different between the L-15 medium and the M199 medium, but not different between the M199 medium and M199 medium with the addition of lipids. Differential expression was detected in 22,066 transcripts between L-15 and M199, a (open full item for complete abstract)

Committee: Ieva Roznere (Advisor); Jim Hood (Committee Member); Lindsey Bruckerhoff (Committee Member); Meg Daly (Advisor) Subjects: Conservation; Organismal Biology; Zoology

Master of Science, The Ohio State University, 2024, Horticulture and Crop Science

Sub-zero freezing temperatures cause 5-15% of annual crop losses to worldwide grapevine cultivation. Based on their cold hardiness, i.e., the ability to survive under low temperature conditions, grapevine genotypes can be classified as a) cold sensitive, such as Vitis vinifera (-18℃ to -22℃ critical range), and b) cold hardy, such as Vitis labrusca (-26℃ to -29℃). During spring, late-spring frost conditions can cause injury to young shoots emerging from dormant buds, affecting grapevine yield and wine quality. Enhancing cold hardiness and frost tolerance can improve grapevine's survivability under extreme low temperature conditions. Cold hardy wild grapevine species, such as native North American Vitis labrusca, are being utilized for the development of cold hardy hybrid cultivars, however, most of these species have low-chilling requirements, leading to early budburst in spring. Therefore, despite being cold hardy as dormant buds, it is unknown if the young shoots of Vitis labrusca have higher frost tolerance than those of Vitis vinifera cultivars. Our goal was to determine the difference in frost tolerance and transcriptomic response related to low temperatures between young shoots of cold hardy V. labrusca acc. ‘GREM4' and cold sensitive V. vinifera cv. ‘Cabernet Sauvignon'. Results showed that ‘GREM4' shoots had significantly higher frost tolerance than those of ‘Cabernet Sauvignon'. Transcriptomic analysis for chill (4℃) and freeze (-2℃) stress revealed that 'GREM4' shoots exhibited upregulation of genes encoding cell-wall-associated receptor kinases and extensin proteins under both chill and freeze stress. Moreover, genes encoding 3-ketoacyl-coenzymeA synthase (KCS), a key enzyme involved in wax biosynthesis, and genes related to sugar transport and metabolism were differentially expressed between ‘GREM4' and ‘Cabernet Sauvignon'. Interaction analysis between species and temperature treatments revealed that the gene encoding abscisic acid (ABA) degrading enzym (open full item for complete abstract)

Committee: Andrea Gschwend (Advisor); Imed Dami (Advisor); Eric Stockinger (Committee Member); Jonathan Fresnedo-Ramirez (Committee Member) Subjects: Genetics; Horticulture; Plant Sciences

Doctor of Philosophy, Case Western Reserve University, 2024, Pharmacology

Globally, an estimated 420 million people today suffer from debilitating vision loss caused by age-related macular degeneration (AMD), diabetic retinopathy (DR), retinitis pigmentosa (RP), or glaucoma; a large majority of these cases (up to 90%) have only minimally effective or no treatment options available. These chronic, progressive retinal diseases arise from a complex interplay of genetic and environmental factors that disrupt, and eventually compromise, cellular and tissue stability. Such disruptions accumulate with repeated exposures to stress over time, leading to progressive visual impairment and, in many cases, legal blindness. Despite decades of research, effective treatments to preserve eyesight have remained elusive for the millions of patients suffering from these debilitating disorders, especially in the vast majority of cases that are in early stages of disease progression, wherein lies the greatest opportunity to slow or halt vision loss. In the coming decades, population aging will exacerbate the increase in global prevalence of vision impairment and blindness, thus underscoring a critical, unmet need for innovative, new ophthalmic medications. In pre-clinical studies, we demonstrated the efficacy of prototypical ‘stress resilience-enhancing drugs' (SREDs) that preserved both retinal morphology and function across a variety of genetic and environmental animal models of AMD, DR, RP, and glaucoma. These small-molecule therapies can be subdivided according to primary mechanism of action, resulting in two distinct subclasses of SREDs: 1) epigenetic modulators that include inhibitors of select histone deacetylases (HDACi) or methyltransferases (SUVi); and 2) selective inhibitors of cyclic nucleotide phosphodiesterases (PDEi). With pharmacological inhibition of histone deacetylase 11 (HDAC11) or suppressor of variegation 3-9 homolog 2 (SUV39H2), key histone-modifying enzymes involved in promoting reduced chromatin accessibility, stress-induced retinal (open full item for complete abstract)

Committee: Krzysztof Palczewski (Advisor); Philip Kiser (Advisor); Walter Boron (Committee Member); Johannes von Lintig (Committee Member); George Dubyak (Committee Member); John Mieyal (Committee Chair) Subjects: Medicine; Ophthalmology; Pharmaceuticals; Pharmacology

Doctor of Philosophy, The Ohio State University, 2024, Dentistry

Despite having been introduced over 10 years ago, there is little research into the effects of electronic cigarettes (e-cigs, electronic nicotine delivery systems, or ENDS) on health outcomes. These devices create an aerosol mixture by heating propylene glycol, glycerol, nicotine, additives and flavorings. Although concerns have been voiced about these devices, usage continues to increase, partially because they are marketed as a safer alternative to traditional cigarettes and as a smoking cessation aid. However, the chemicals in ENDS may deliver toxins to a variety of body systems, necessitating an urgent need for investigation into their biological effects. The oral cavity is the initial point of contact and the primary repository of nicotine deposition, which places the oral microbial environment at a high potential to be impacted by ENDS. Oral microbial homeostasis relies on an intricate balance between the host and their microbiome, but disruptions to this equilibrium can have wide-reaching effects. The purpose of this investigation was to examine the multi- faceted impacts of ENDS on the different systems within the oral cavity, ranging from the microbiome to the human host, and the signaling molecules that connect these two. A tandem approach of in vitro and in vivo techniques was utilized to recapitulate the oral microenvironment and identify the mechanistic changes while also allowing for clinical correlations to be made. Systems were analyzed with a multi omics approach consisting of host transcriptomics, metatranscriptomics and metabolomics in combination with mass spectrometry and immunohistochemistry to identify potential biomarkers and risk for disease.

Committee: Binnaz Leblebicioglu (Advisor); Purnima Kumar (Advisor); Shareef Dabdoub (Committee Member); Haikady Nagaraja (Committee Member); Emmanouil Chatzakis (Committee Member) Subjects: Dentistry

Doctor of Philosophy, The Ohio State University, 2024, Translational Plant Sciences

Grapevine (Vitis) is the world's most valuable fruit crop, therefore, reducing yield losses to stressors is paramount. Vitis labrusca, a wild North American grapevine, is well adapted to its local environment, exhibiting stout pathogen resistance. Meanwhile, Vitis vinifera grapevine, grown worldwide for winemaking, is native to Europe and is highly susceptible to biotic stressors, particularly fungal and insect pests. V. labrusca has been long utilized in Vitis breeding programs to imbue resistance. Therefore, in this dissertation, we determined if V. labrusca acc. ‘GREM4' was more insect herbivory resistant than V. vinifera cv. ‘PN40024' and investigated the morphological, genetic, and metabolomic factors which may contribute to resistance. In an herbivory choice assay, Japanese beetles (Popillia japonica), a major pest of grapevine, preferred to feed upon ‘PN40024' compared to ‘GREM4'. Further, increased leaf area was consumed on ‘PN40024' compared to ‘GREM4' in a time course (30min, 1h, and 4h) feeding assay. These results reported ‘GREM4' is resistant to Japanese beetle herbivory compared to ‘PN40024'. To determine morphological adaptations that may impact defense, trichomes were next investigated. Trichome densities were greater on ‘GREM4' compared to ‘PN40024' leaves. In trichome-focused herbivory studies, beetles exhibited a preference for lower trichome density sides of leaves and, when provided tissues with equal trichome densities for both ‘GREM4' and ‘PN40024', more leaf tissue was still lost from ‘PN40024' compared to ‘GREM4'. These results report that trichomes play a role in resistance but are not the sole factor. Therefore, we conducted a comparative transcriptomic analysis to identify differences in gene expression upon insect herbivory between the two species. When comparing constitutive expression differences prior to insect herbivory, genes with greater expression in ‘GREM4' were enriched in secondary metabolite biosynthesis while enr (open full item for complete abstract)

Committee: Andrea Gschwend (Advisor); Jay Hollick (Committee Member); Joshua Blakeslee (Committee Member); Jyan-Chyun Jang (Committee Member); Laura Kubatko (Committee Member); Pablo Valverde (Committee Member) Subjects: Agriculture; Bioinformatics; Genetics; Molecular Biology; Plant Biology; Plant Sciences

Doctor of Philosophy, Case Western Reserve University, 2024, Biomedical Engineering

Intracortical microelectrodes (IMEs) are a type of brain-computer interface that allows for the recording of neural signals to communicate between the brain and computers. IMEs can be used to restore motor function in people with spinal cord injury, treatment of neurological disorders, and are a strong basic science tool for understanding the brain. Unfortunately, implanted IMEs consistently see a steady decline in recording ability over time, leading to failure of the device. Damage to the blood-brain barrier (BBB) from IME implantation is a key contributor to device failure. After BBB breach, neurotoxic molecules invade the brain and cause a downstream cascade of neuroinflammation and oxidative stress that further damages the BBB, brain tissue, and the IME itself. Attempts to minimize BBB damage to improve neuroinflammation and IME longevity have shown limited success. Given the lack of solutions to the chronic stability of neural recordings, further investigation into understanding and minimizing the effects of BBB damage is warranted. In my dissertation, I investigate multiple strategies to mitigate and expand our understanding of how BBB damage can impact IME performance. Thermal damage to underlying vasculature because of cranial drilling has been shown to impact BBB permeability. To combat this, I developed a standardized surgical approach to limit surgeon variability and reduce thermal damage on the BBB. Next, I utilized the antioxidant dimethyl fumarate to promote BBB healing and reduce oxidative stress, resulting in acute improvements to IME function without long-term stability. Lastly, I investigated what unknown molecules enter the brain through the permeable BBB and contribute to neuroinflammation. I was the first to discover that gut-derived bacteria invade the site of implantation through the damaged BBB, which can be modulated with antibiotics to alter neuroinflammation and IME performance. New therapeutics can be developed utilizing this connecti (open full item for complete abstract)

Committee: Jeffrey Capadona (Advisor); Anirban Sen Gupta (Committee Chair); A. Bolu Ajiboye (Committee Member); Andrew Shoffstall (Committee Member); Gary Wnek (Committee Member) Subjects: Biomedical Engineering; Engineering

Doctor of Philosophy, The Ohio State University, 2023, Plant Pathology

Plants continually confront a multitude of environmental challenges that can impede their growth, development, and survival, and thereby have evolved a remarkable array of responses to environmental stresses to ensure their persistence on the landscape and optimize growth. These stress responses are remarkably plastic and adaptable to a changing environment and have been the subject of intense research interest. The study of plant stress responses provides critical insights into fundamental physiological processes and has practical implications for agriculture, conservation, and ecosystem management. Understanding the intricate signaling cascades and molecular components that underlie plant stress responses is essential for developing strategies to enhance stress tolerance in crops, mitigate the impact of climate change on ecosystems, and conserve plant biodiversity. In recurring encounters of tree species with both abiotic stress and pathogenic invasions, delimiting stress responses will be instrumental for conservation and management practices. Building on current understanding of induced resistance in the Pinus nigra - Diplodia spp. pathosystem, we hypothesized that, (1) predisposition of Austrian pine to abiotic stress such as climate change (CC) leads to increased susceptibility to pathogenic infections by Diplodia spp. and this heightened susceptibility is explainable by a detailed analysis of the transcriptional regulation of both the host and pathogen, (2) attack of Austrian pine by D. pinea results in a systemic induced resistance (SIR) phenotype that intensifies over time, and (3) this phenotype is mediated by the accumulation of terpenoids and is explainable by a detailed analysis of signaling pathways involving phytohormones in specific patterns. The test of the first hypothesis is described in Chapter 2. We subjected Austrian pine trees to simulated CC conditions of high temperatures and prolonged water scarcity, followed by infection with either D. p (open full item for complete abstract)

Committee: Pierluigi Bonello (Advisor); Guo-Liang Wang (Committee Member); Tea Meulia (Committee Member); Jason Slot (Committee Member); David Mackey (Committee Member) Subjects: Plant Pathology

Doctor of Philosophy, The Ohio State University, 2023, Computer Science and Engineering

In many biomedical contexts, multiple types of BDMs (e.g., metabolites, genes, proteins, chromatin states, and DNA methylation sites) associate with one another directly or indirectly in groups or chains to impact phenotype or outcome. Certain significant associations often help in data interpretation and novel hypotheses generation, motivating researchers to identify the most impactful groups of BDM associations between multiple types of data. However, many state-of-the-art models focus either on individual BDM associations independently of one another or implement black box predictors of outcome that are agnostic of BDM associations. Moreover, collection of multiple types of BDMs in a subject (i.e., multi-omics data) is not always feasible, motivating the need to infer one omic type of data from another. This dissertation tackles the related problems of (1) using inter-omics approaches to infer BDM types from other related BDM types in specific contexts, (2) finding groups of multi-omics data BDMs associated with outcome through multivariate statistical analysis and graph-based predictive models, and (3) interpreting groups of multi-omics data BDMs associated with outcome in a functional context using existing knowledge. This dissertation addresses the problem of using inter-omics approaches to infer BDM types from other related BDM types in two domains of note: (1) regulatory element annotation, and (2) protein abundance prediction. First, this dissertation introduces the Self Organizing Map with Variable Neighborhoods (SOM-VN), designed to annotate regulatory elements across whole human genomes using shapes found in chromatin accessibility assays. The novelty of SOM-VN is that, while most computational tools for annotating regulatory elements require a suite of resource-intensive experimental assays, SOM-VN uses only a single assay to annotate regulatory elements. SOM-VN is validated on chromatin accessibility assays from multiple H1, HeLa, A549, and GM12878 ce (open full item for complete abstract)

Committee: Raghu Machiraju (Advisor); Ewy Mathé (Advisor); Andrew Perrault (Committee Member); Rachel Kopec (Committee Member); Rachel Kelly (Committee Member) Subjects: Applied Mathematics; Artificial Intelligence; Bioinformatics; Biomedical Research; Biostatistics; Computer Science

Doctor of Philosophy, The Ohio State University, 2023, Plant Pathology

Phytophthora root and stem rot is one of the top ten most yield-limiting soybean [Glycine max (L.) Merr] diseases in the U.S. and Canada. The causal agent of this disease, Phytophthora sojae (Kaufmann & Gerdemann), is an oomycete (water mold) organism that is often managed by using disease-resistant soybean cultivars containing a single Rps gene to a specific pathotype of the pathogen combined with quantitative disease resistance (QDR). Due to the limitation of the number of effective Rps genes available, as the populations of this pathogen have adapted to these genes, it is a necessity to find new Rps genes and identify perfect markers for QDR genes, which have a smaller effect but can resist all pathotypes of P. sojae, that can be used in the development of modern soybean cultivars. In this dissertation, the main approach for all three chapters is to examine the mechanisms of disease resistance in soybeans towards P. sojae using different forward and reverse genetic approaches. A previous study found more than 100 candidate genes by mapping the expression quantitative disease-resistance loci (eQDRL) from the Conrad × Sloan population. To explore and validate the functions of these genes, a fast neutron (FN) population from the University of Minnesota, derived from soybean cultivar M92-220, with these genes deleted was employed. Thus, the first chapter's first objective was to compare cultivars M92-220 and Conrad at phenotypic and transcriptomic levels for their QDR resistance to determine if the molecular mechanisms associated with the eQDRLs were similar to those previously found in Conrad. Then, the next objective was to explore how the loss of the candidate genes using mutants that were highly susceptible would affect the soybean resistance response following inoculation with P. sojae by examining the three most susceptible FN mutants. Conrad and M92-220 were found to share high levels of QDR in the phenotypic assay as well as having several similar defense-r (open full item for complete abstract)

Committee: Feng Qu (Advisor); Anne Dorrance (Committee Member); Guo Liang Wang (Committee Member); Xia Ye (Committee Member); Leah McHale (Committee Member) Subjects: Plant Biology; Plant Pathology; Plant Sciences

MS, University of Cincinnati, 2023, Medicine: Immunology

Transcriptomic analyses represent one of the most powerful tools available to researchers for investigating gene expression, a fundamental principle in the central dogma of biology, utilizing next generation sequencing (NGS) technologies. As the technologies for acquiring RNA sequencing data advance, so do the tools used for data analysis. The ability to process and analyze sequencing data from any experimental context is an invaluable skill. This paper endeavors to provide an understanding of the current technologies and methods available for obtaining and analyzing high-quality transcriptomic data, as well as outline a workflow for executing a bulk RNA sequencing experiment within the context of liver studies.

Committee: Rana Herro Ph.D. (Committee Chair); Ty Troutman Ph.D. (Committee Member); Jonathan Katz Ph.D. (Committee Member) Subjects: Immunology

PhD, University of Cincinnati, 2023, Engineering and Applied Science: Computer Science and Engineering

Graphs have become a convenient approach for representing complex real-world systems that contain a collection of objects and their relationships. They are extensively used to model data in various domains, including computer science, statistical physics, linguistics, and biological and social sciences. For instance, in the biological domain, networks are used to represent the interactions between proteins. Traditional network clustering and community detection algorithms are then applied for candidate gene prioritization and in silico biomarker discovery. However, given the ever-increasing size and complexity of networks, machine learning has become the primary approach for analyzing such graphs. The success of these models is highly dependent on the quality of user-designed input features. Alternatively, representation learning models work toward learning relevant representations of input data suitable for the task at hand. The learned representations can then be reused in subsequent downstream tasks as inputs. In addition, they can be used to determine the explanatory factors shared by two or more independent learning tasks. Recently, there has been a surge in representation learning frameworks for graph-structured data to learn node embeddings. However, computational frameworks capable of analyzing multiple networks simultaneously are still limited. Such implementations are particularly useful for research problems, such as in silico biomarker discovery, where multiple transcriptomic studies associated with a given disease are available but seldom used. In this dissertation, we developed novel feature learning frameworks capable of embedding network nodes from multiple datasets. In the first part of our work, we developed a skip-gram-based multi-task feature learning model that is capable of combining multiple supervised and/or unsupervised task objectives to learn continuous features of discrete entities. We used this model to extract contextualized gene (open full item for complete abstract)

Committee: Anil Jegga DVM MRes (Committee Chair); Raj Bhatnagar Ph.D. (Committee Member); Ali Minai Ph.D. (Committee Member); Yizong Cheng Ph.D. (Committee Member); Jing Chen Ph.D. (Committee Member) Subjects: Computer Science

PhD, University of Cincinnati, 2023, Arts and Sciences: Biological Sciences

Chemical contaminants present in the environment have the potential to negatively impact fish. This study encompasses two chemical contaminants of concern: the synthetic estrogen, 17α-ethynylestradiol (EE2) and the neonicotinoid insecticide, imidacloprid (IMI). In chapters 2 and 3, I investigate the effects of EE2 exposure on an estrogen receptor gene (esr1) in adult fathead minnows (Pimephales promelas) through evaluation of epigenetic, transcriptomic and isoform usage end points. This was accomplished by conducting a 48h exposure of adult male fathead minnows to two doses of EE2 and conducting necropsies to remove brain and liver tissues for comparison to untreated female fish. Furthermore, a subset of male fish was subjected to a 7d and 14d depuration period to evaluate the lasting effects of EE2 exposure. A targeted approach was used to evaluate DNA methylation and transcriptomic changes to esr1. I found that EE2 induced significant esr1 expression in liver tissues for both experimental groups compared to control. Targeted bisulfite sequencing revealed DNA methylation changes in both the esr1 promoter and gene body regions of exposed male fish which exhibited a female pattern. Evidence was found for some methylation marks to persist after chemical exposure, even when gene expression changes were no longer significant. Next, an RNAseq dataset was utilized to detect differential isoform usage of esr1 through comparison to reference sequences predicted by genome assembly models. The results of this study revealed significant differential isoform usage in liver tissue from male fathead minnows for esr1 transcript variants to look more similar to isoform usage found for female fathead minnows indicating that regulatory mechanisms of esr1 may play a pivotal role in the inter-sex and gonadal sex changes in fish known to occur in the presence of EE2. The study presented in chapter 4 investigates the effects of IMI exposure to zebrafish in early life stages. In (open full item for complete abstract)

Committee: Ronald DeBry Ph.D. (Committee Chair); Joshua Benoit Ph.D. (Committee Member); Erik Pilgrim Ph.D. (Committee Member); Daniel Buchholz Ph.D. (Committee Member); Adam Biales Ph.D. (Committee Member) Subjects: Biology

Doctor of Philosophy, The Ohio State University, 2023, Biomedical Sciences

Alzheimer's Disease (AD) is a debilitating neurodegenerative disorder characterized by the progressive and selective accumulation of neurofibrillary tangles in specific areas of the brain over the course of disease. Composed of aggregated tau protein, these tangles appear to spread from the earliest affected regions to networked brain regions across the synapse, templating additional pathology in a prion-like manner. However, the cerebellum appears to resist this prion-like insult, despite connectivity to early and profoundly affected regions. The selective vulnerability and resistance of specific brain regions and cell types to prion-like tau pathology offers a window into disease etiology and endogenous mechanisms of neuroprotection. The objective of this work was to untangle the adaptive changes to disease that respond in parallel and in contrast between differentially vulnerable tissues to provide new insight into disease etiology and new targets for biological validation in disease models. First, we define a unique gene expression approach termed Ratio of Ratios that tests differential gene expression across AD and control in the vulnerable prefrontal cortex and the resistant cerebellum. We apply this along with Desirability Function Analysis to a publicly available microarray data set to sort genes into priority groups demonstrating contrasting differential expression between regions that associates with selective vulnerability, and parallel differential expression between regions that is nonspecific to vulnerability. Among contrasting genes, we find a neuronal and endothelial proteostasis signature where chaperones are selectively upregulated in the cerebellum. Among parallel genes, we find a microglial, astrocytic, and endothelial signature of immune and stress activation. Using transcription factor interaction network analysis, we report potential key regulators of these contrasting and parallel responses. We also show that the identified chaperone p (open full item for complete abstract)

Committee: Jeffrey Kuret (Advisor); Karl Obrietan (Committee Member); Andrea Tedeschi (Committee Member); Hongjun Fu (Committee Member) Subjects: Bioinformatics; Biology; Biomedical Research; Neurosciences

Doctor of Philosophy, Case Western Reserve University, 2022, Biology

Flax is a dual-purpose crop for both the seeds and linseed oil; as with other major crops, abiotic stress imparted by both varying environmental conditions and climate change have significant effects on the plant's viability. In particular, nutrient deprivation is well-characterized at both the phenotypic and molecular level in four varieties of flax (Bethune, Pl, S, and L). While, salt stress susceptibility and tolerance is much less understood in the aforementioned flax varieties. The primary aims of this project included: 1. characterize the phenotype and genotype of four flax varieties under salt stress to be compared to nutrient deprivation, 2. determine the transcriptomic changes of the four flax varieties under salt stress versus nutrient deprivation, and 3. characterize the flax soil microbiome (rhizosphere) to identify punitive plant growth promoting rhizobacteria (PGPR) and/or well-known PGPR. The first portion of the project focused on collecting data pertaining to several phenotypic metrics (height, branching, flowering, and seed setting/collection), as well as genotypic characteristics. Such genotypic regions of interested included LIS-1 to determine if this region was inserted under salt stress, as well as, characterize of several molecular markers (scaffold regions) to identify genotypic patterns specific to salt stress. While, the second portion consisted of RNA sequencing of Bethune, Pl, S and L under salt stress (0.08 M NaCl and 0.15 M NaCl). Additionally, RNA sequencing of S and L under nutrient deprivation was conducted. These data illustrated that many candidate transcripts are those implicated in general stress response, as there was not consistent differential expression per each stress condition within or between flax varieties. Finally, the third portion consisted of 16S ITS V4 sequencing which allowed for metagenomic analysis of the Bethune, Pl, S, and L soil microbiomes under 0.08 M NaCl, 0.015 M NaCl, and nutrient deprivation. This al (open full item for complete abstract)

Committee: Christopher Cullis (Advisor) Subjects: Agriculture; Biochemistry; Bioinformatics; Biology; Botany; Developmental Biology; Environmental Science

Master of Science in Biomedical Sciences (MSBS), University of Toledo, 2022, Biomedical Sciences (Bioinformatics and Proteomics/Genomics)

Temporal Lobe Epilepsy (TLE) is one of the most common neurological disorders and is characterized by recurrent and spontaneous seizures. Although TLE genetic and electrophysiological markers such as gamma oscillations are well characterized, alterations in the interactions between neurons predisposing a cortical region to seizures are not fully understood. To study these non-linear interactions, we incorporated RNA expression changes into a microcircuit computer model of the hippocampus, an area strongly implicated in TLE. Cellular deconvolution of bulk RNAseq data with single-cell transcriptomic data from the hippocampi of pilocarpine-induced temporal lobe epilepsy mice revealed three distinct cell clusters characterized as pyramidal (PYR) cells, oriens-lacunosum moleculare (OLM) interneurons, and parvalbumin-positive (PV) interneurons. We used the differential expression (log fold change) of genes coding for the Alpha-Amino-3-Hydroxy-5-Methyl-4-Isoxazole Propionic Acid (AMPA), N-methyl-D-aspartate (NMDA), and Gamma-aminobutyric acid type A (GABAA) receptor subunits in the control and epileptic conditions for each cell cluster to guide scaling of receptor density iv in the model. The model was composed of 800 PYR, 200 PV and 200 OLM neurons. PYR cells of the model activate PV, OLM, and other pyramidal cells via NMDA and AMPA receptors; in return, the PV and OLM interneurons inhibit PYR cells by acting on their GABAA receptors. Guided by the RNA expression data, we ran simulations where we increased the density of PYR AMPAR, OLM NMDAR, PV AMPAR, and PV GABAAR scaling. PYR GABAAR subunits were both upregulated and downregulated and thus, both changes were implemented when running simulations. Our simulations showed two dynamical changes with the RNA sequence changes. The first is the expected increased seizure susceptibility, reflected as increased gamma power. That pattern took place with pyramidal AMPAR/GABAAR upscaling. The second pattern was a surprising reduc (open full item for complete abstract)

Committee: Robert Mccullumsmith (Advisor); Rammohan Shukla (Committee Co-Chair); Mohamed Sherif (Committee Member); Bruce Bamber (Committee Member); Imran Ali (Committee Member) Subjects: Bioinformatics; Biophysics; Neurosciences

Master of Science in Biomedical Sciences (MSBS), University of Toledo, 2022, Biomedical Sciences (Bioinformatics and Proteomics/Genomics)

Suicide is defined as the act of self-injurious behavior that results in an outcome of death. Nearly 800,000 people are estimated to die by suicide each year. Approximately 90% of those that die by suicide are suspected to have a comorbid neuropsychiatric condition, such as major depressive disorder (MDD), schizophrenia (SCZ), or bipolar disorder (BP). Given this clear correlation, studies of suicide have been largely conducted in the context of gene transcription associated with neuropsychiatric disorders. Such approaches, like RNAseq and microarray technologies, have been invaluable in assessing gene expression changes in the brain in subjects diagnosed with a neuropsychiatric disorder, offering significant insight into the biological processes that are perturbed in these disorders and therefore associated with an outcome of suicide. In this analysis, we utilized public postmortem brain tissue datasets from frontal cortical regions (i.e. DLPFC, frontal cortex, prefrontal cortex) to identify transcriptional gene signature specific to suicide across multiple neuropsychiatric disorders (MDD, SCZ, BP). Three RNAseq (150 total subjects) and four microarray (322 total subjects) datasets were collected from 4 NCBI GEO to construct a meta-analysis of various neuropsychiatric disorders. We assessed differentially expressed genes (DEGs) between suicide and natural death groups. We further explored DEG results using full transcriptome (GSEA) and targeted transcriptome (EnrichR) pathway analysis. As chronic psychological stress is associated with an increase in suicidal risk, we identified DEGs from mouse models of chronic stress. We explored these DEGs using similar pathway analyses as human data for comparison. Results in human data show dysfunction in mitochondrial pathways, purine metabolism and purinergic signaling pathways, as well as neuroinflammation associated pathways which have prior implications in suicide risk and underlying pathology of MDD, SCZ, and BP. We ad (open full item for complete abstract)

Committee: Robert Smith (Committee Co-Chair); Cheryl McCullumsmith (Committee Member); Rammohan Shukla (Committee Member); Sinead O'Donovan (Committee Co-Chair) Subjects: Bioinformatics; Biology; Biomedical Research; Neurosciences

Master of Science (MS), University of Toledo, 2022, Biomedical Sciences (Bioinformatics and Proteomics/Genomics)

As multi-omics studies gain popularity, more insight is gained on the biological mechanisms that cause and influence disease. This study combined a transcriptomic approach and functional proteomic approach to gain a holistic understanding of End-Stage Renal Disease (ESRD), renal allograft status, and immunosuppression status on a molecular level. Functional proteomics approaches like kinomics consider post-translational modifications such as phosphorylation that alter protein function. The kinome is the comprehensive list of all protein kinases within an organism and the study of these protein kinases is critical in the understanding of cellular communication. Kinase activity quantified by phosphorylation can reveal key biological pathways. This study aims to assess the active kinome profiles from peripheral blood mononuclear cells (PBMCs) from renal transplant patients. Active kinome profiles of PBMCs will provide information about the cellular communication that facilitates immune response. The information gathered from the PBMC active kinome profile may also be used to predict response to immunosuppressant drugs based on the observed activity of protein kinase signaling networks. The effects of immunosuppressive drugs are well understood on a transcriptomic level but have yet to be explored on a kinomic level. Immunosuppressive drugs perturb kinase signaling networks, therefore the baseline active kinome profile might act as a biomarker for trait-based immune system function. This can then allow for the prediction of a patient's potential allograft acceptance or rejection based on their active kinome profile and how it relates to immunosuppressant drug signatures. Additionally, PBMC samples can be treated with kinase inhibitors that model the effect of an immunosuppressant medication on the protein kinase signaling networks in vitro. The impact an inhibitor has on the protein kinase activity can be used to determine optimal treatment. Furthermore, active kinome p (open full item for complete abstract)

Committee: Robert Smith (Advisor); Stanislaw Stepkowski (Committee Member); Puneet Sindhwani (Committee Member); Kunal Yadav (Committee Member) Subjects: Bioinformatics; Biomedical Research; Immunology; Medicine; Molecular Biology; Statistics

Master of Science, Miami University, 2021, Biology

Ectotherms can respond to changing climate through behavioral plasticity, physiological plasticity, and adaption. Adaptive versus plastic responses to stimuli can affect gene expression. The desert horned lizard (Phrynosoma platyrhinos) inhabits climatic extremes: the Great Basin Desert where it can get below freezing for half of the year, and the Mojave Desert containing some of the hottest and driest places on Earth. I conducted a common garden experiment by dividing lizards from the Great Basin and Mojave deserts into three groups: cold treatment, hot treatment, and an unstressed group with access to a temperature gradient. After exposure for two weeks, I collected liver and brain tissue for RNA sequencing. Differential gene expression analyses showed that both origin (Great Basin versus Mojave) and treatment (temperature exposure) contributed to overall responses. The presence of genes differentially expressed by both origins in response to thermal stress indicates conserved, plastic responses. Further, a large portion of genes were differentially expressed as population-specific responses to thermal stress, indicative of adaptive mechanisms.

Committee: Tereza Jezkova (Advisor); Paul Schaeffer (Committee Member); David J. Berg (Committee Member); Michael O'Connell (Committee Member) Subjects: Biology

Doctor of Philosophy, Case Western Reserve University, 2021, Biology

Schistosome infection affects over 250 million people worldwide, leading to extensive morbidity and death. Although this parasitic helminth immiserates millions annually, significant gaps exist in our understanding of translational regulation. Further analysis of the basic biology of schistosomes is required to develop new, more effective treatment modalities. In this thesis, we perform global translational analysis of cercariae and early schistosomula and transcriptomic and proteomic analysis of cercariae. The cercariae are comprised of two macrostructures, the head and the tail. The cercarial head has limited motility but contains proteases and mucins required for host invasion. The cercarial tail is highly motile and is necessary for swimming and motility. Given the cercarial tail functions, we hypothesize that the tail requires translation to maintain metabolism for motility. Given that cercarial transformation is not affected by translational inhibition, we hypothesize that the cercarial head is translationally repressed. In this thesis, we present two major studies. The first study directly tested the global translation rates in cercarial heads and tails. We found that neither the head nor tail undergoes transcription, translation is also severely limited in the cercarial head, but to the contrary, the cercarial tail has extensive translational activity. We also found that translation is required for swimming behavior. The global translation analysis did not identify the mechanisms that control these differences in translation, so we performed transcriptomic and proteomic analyses of cercarial heads and tails. In the second study, we analyze heads' and tails' transcriptomes and proteomes. We found that the probable drivers of translational differences in heads and tails are the storage and ratios of ribosomal components. The pattern of increased ribosomal component proteins extends into schistosomula and paired adults as well. We also report that transcri (open full item for complete abstract)

Committee: Emmitt Jolly PhD (Advisor); Blanton Tolbert PhD (Committee Member); Brian McDermott PhD (Committee Member); Chris Cullis PhD (Committee Member); Yolanda Fortenberry PhD (Committee Chair) Subjects: Biology; Biomedical Research