Master of Science in Biomedical Sciences (MSBS), University of Toledo, 2018, Biomedical Sciences (Bioinformatics and Proteomics/Genomics)

Oropharyngeal candidiasis (OPC) is a fungal infection of the oral cavity caused by a human commensal fungus called Candida albicans. Even though C. albicans is a commensal, it can become pathogenic in immunocompromised patients. IL-17-mediated antifungal immunity has been implicated as the major pathway for fungal defense in the oral cavity. The IL-17 pathway has been found to regulate the release of antimicrobial peptides (AMPs) downstream, including murine ß-defensin 3 (mBD3). Murine ß-defensin 3 is an antimicrobial peptide involved in the protection of the oral mucosa against pathogens. Murine BD3 can protect the oral mucosa through its direct antimicrobial activity, but it has also been found to have chemotactic properties as well. The human homolog of mBD3, human ß-defensin 2 (hBD2), has been found to bind CCR6. CCR6 is found on the surface of cells like memory T-cells, dendritic cells (DCs), Th17 cells, and Treg cells. Studies have shown that hBD2 binding to CCR6 on the surface of memory T-cells and DC's can induce chemotaxis, and other studies have suggested the same could be true for Th17 cells and Treg cells. The goal of this experiment was to study the chemotactic ability of mBD3 via RNA-sequencing to explore how the presence/absence of Defb3 leads to changes in transcriptional regulation while in the presence/absence of an OPC infection. The RNA-sequencing results reveal that there are very few differences in transcript expression between wild-type mice and Defb3 knockout mice. One difference in transcript expression between Defb3 knockout mice and WT mice is found in Sycp1. Sycp1 is expressed at higher levels in Defb3 knockout infected mice when compared with WT infected mice and Defb3 knockout sham mice when compared to WT sham mice. The DNA-binding ability of Sycp1 makes it an interesting candidate for future studies.

Committee: Heather Conti (Committee Chair); Sadik Khuder (Committee Member); Alexei Fedorov (Committee Member) Subjects: Bioinformatics; Biology; Immunology

Master of Science in Biological Sciences, Youngstown State University, 2023, Department of Biological Sciences and Chemistry

Burying beetles have served as a model to answer diverse questions about the evolution of social behavior in insects and to understand the physiological and evolutionary mechanisms involved in the manifestation of parental care behavior. More recently, an increasing number of genomic and transcriptomic resources have become available in Nicrophorus spp. This study utilizes this data to assay sources of variation in the Nicrophorus orbicollis transcriptome with the specific aims to 1) evaluate the extent of alternative splicing in this species and 2) assess differential expression and alternative splicing in genes that are associated with distinct parental behavioral phenotypes in male and female burying beetles during breeding. This was achieved by differential expression analysis of N. orbicollis transcriptomes for parents showing high and low care provisioning behavior. Two algorithms were used to increase predictive accuracy in detecting alternatively spliced genes. Genes that were alternatively spliced and differentially expressed between behavioral groups were subject to further functional characterization. An overall profile of alternative splicing was determined, indicating that many transcripts resulting from alternative splicing were the result of several types of alternative splicing events. There was also evidence for a higher occurrence of intron retention events than exon skipping events. Additionally, the occurrence of alternative splicing was not found to be more common in differentially expressed genes for any specific biological process associated with parental care behavior. Still, evidence for alternative splicing within genes relevant to variability of the parental care phenotype was presented and potential behavioral implications were discussed.

Committee: Stefania C. Panaitof PhD (Advisor); Xiangjia Min PhD (Committee Member); Jonathan Caguiat PhD (Committee Member) Subjects: Animals; Bioinformatics; Genetics; Molecular Biology

Master of Science in Biological Sciences, Youngstown State University, 2022, Department of Biological Sciences and Chemistry

Potato (Solanum tuberosum L.) is the third most important food crop in the world following rice and wheat. Due to its high calories, it is a good source of energy and nutrients such as proteins, vitamins and minerals. Thus, potato plays an important role in providing food, nutritional and economic security of the world. To further improve the quantity and quality of potato as a food crop, it is imperative to understand the transcriptome diversity, gene expression dynamics and associated developing methods. The aim of this study is to identify the alternative spliced events of genes and their differential expression in nitrogen-treated and drought-stressed potato plants. In nitrogen grown potato plants, alternative acceptor site was observed to be most dominant alternative spliced events while intron retention was dominant in drought-stressed potato plants. Additionally, differential gene and isoform expressions of four different varieties of drought-stressed leaf samples of potato plants were analyzed by cuffdiff module of cufflinks V2.2.1 package. Statistically significant (P ≤ 0.05) differential gene expressions with corresponding transcript isoforms were identified such as 10 (up-regulated) and 13 (down-regulated) in Algeria cultivars, 24 (up-regulated) and 21 (down-regulated) in Desiree cultivars with 39 transcript isoforms generated, 33 (up-regulated) and 51 (down-regulated) with 62 generated transcript isoforms in Saturna cultivars, 43 (up-regulated) , 32 (down-regulated) and 55 transcript isoforms generated in Milva cultivars. Overall, conserved alternative spliced genes and alternative spliced events were identified in both nitrogen-treated and drought-stressed potato plants. Furthermore, among the differentially expressed genes, PYR1-like (pyrabactin resistance 1) and heat shock protein families were most upregulated genes. These genes play a crucial role in enhancing development in potato plants under extreme conditions of drought.

Committee: Xiangjia Min PhD (Advisor); David Asch PhD (Committee Member); Jonathan Caguiat PhD (Committee Member) Subjects: Agriculture; Bioinformatics; Biology

Doctor of Philosophy, Case Western Reserve University, 2022, Systems Biology and Bioinformatics

The evolution of therapeutic resistance in cancer is a complex and nearly inescapable process driven by evolutionary dynamics. As the genomic characterization of cancer has provided insight into the mechanisms of oncogenesis, tumor growth, and metastasis we have developed targeted therapeutics to provide personalized treatment based on mutation status. Yet, most cancer patients are not helped by these drugs, with just over 7\% of cancer patients in the United States benefiting from genome-driven care in 2020. In this work, we propose that an evolutionary-driven problem requires an evolutionary-inspired solution. We present a novel method for extracting therapeutic response biomarkers in cancer, and demonstrate its utility in large, publicly-available datasets, tightly-controlled in silico experiments, and translational efforts. Our procedure exploits principles of convergent evolution to find patterns across tumors with distinct evolutionary histories and mutational profiles. First, we use this signature extraction method to predict collateral treatment response in Ewing's sarcoma cell lines. While evolving resistance to standard of care treatment across multiple evolutionary replicates of a Ewing's sarcoma cell line, we compared gene expression between responders and non-responders to a variety of second-line treatments. Differential gene expression results were compiled to generate biomarkers of therapeutic response which are hypothesized to be clinically relevant, but require further validation. Next, we use epithelial cell lines from the Genomics of Drug Sensitivity in Cancer (GDSC) database to extract the Cisplatin Response Signature (CisSig). CisSig is predictive of cisplatin IC50 in GDSC cell lines, clinical trends in tumor sample databases, and survival outcomes in patients who received cisplatin-containing chemotherapy. Finally, we propose translational efforts to move two gene expression signatures, CisSig and the genome-adjusted radiation dose (GARD), (open full item for complete abstract)

Committee: David Lodowski (Committee Chair); Jacob Scott (Advisor); Drew Adams (Committee Member); Mark Chance (Committee Member) Subjects: Bioinformatics; Oncology; Radiation; Systems Science

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

Long non-coding RNAs (lncRNAs) are transcripts that are longer than 200 bp and have little to no coding potential. Although lncRNAs are linked to various diseases in humans, lncRNAs in pathogens are rarely observed. Understanding these key regulatory molecules in infectious organisms may lead to potential drug targets. Schistosoma mansoni is a parasitic flatworm that causes schistosomiasis and affects over 200 million people worldwide. Schistosomes require a molluscan host and a mammalian host, but the molluscan sporocyst stage has largely been overlooked. Therefore, the transcriptome of mature in vivo sporocysts has never been investigated. In this thesis, we describe a computational pipeline that filters out snail transcripts from sporocyst transcriptome in order to identify lncRNAs in sporocyst and adult S. mansoni. We then demonstrate that each life stage has a distinct lncRNA expression pattern. Next, we use co-expression networks to identify lncRNAs clustering with protein-coding genes to narrow down the potential functions of the novel lncRNAs. Overall, we devise a novel method to study in vivo sporocyst transcriptome and show lncRNAs are developmentally regulated in S. mansoni. The subsequent chapters concern Trypanosoma brucei, a parasitic protozoan that causes Human African Trypanosomiasis that affects over 57 million people across Africa. T. brucei research heavily relies on the cell lines that have been established more than fifty years ago. Continuous culturing over decades may have accumulated changes in T. brucei. Since lncRNAs evolve faster than protein-coding genes, we hypothesized that lncRNAs may be the ideal tool to examine the accumulated potential changes in T. brucei. We constructed more stringent pipeline to identify lncRNAs in cell line and wildtype T. brucei. We then show that lncRNAs are differentially expressed between the two strains. Overall, we designed a lncRNA identification pipeline with improved specificity, and demonstrate th (open full item for complete abstract)

Committee: Emmitt Jolly (Advisor); Gabriella Wolff (Committee Chair); Blanton Tolbert (Committee Member); Yolanda Fortenberry (Committee Member); Christopher Cullis (Committee Member) Subjects: Bioinformatics; Biology; Molecular Biology

Master of Sciences, Case Western Reserve University, 2020, EECS - Computer and Information Sciences

Microarray and RNA-seq are two transcriptomics data types. Comparison between microarray and RNA-seq was popular in recent research fields. But few works analyzed both data types on the same sample groups and fewer have discussed whether different analytical methods or statistical models will impact on the results. To get an insight of what role analytical method and statistical model play, and also to eliminate variances that might be caused by data types, we applied microarray and RNA-seq data into 5 analytical methods across 4 statistical models to contrast the similarities and differences. In this thesis, we processed and transformed raw microarray and RNA-seq data to fit in 5 different analytical methods across 4 statistical models. We did differential expression analysis on both data for all methods and evaluated the results. Both data types showed high consistency in those two methods applying the same model. All statistical models gave similar detected differentially expressed genes, the extent of similarity varied basing on specific pairs chosen to be compared. Among all analytical methods, NBPSeq and NOIseq are the most consistent for microarray while DESeq and baySeq are the most consistent for RNA-seq. Between data types, RNA-seq gives more detected differentially expressed genes. Overall, statistical models and data types both impact greatly on differential analysis results while analytical method seems trivial.

Committee: Fredrick Schumacher (Committee Chair); Jing Li (Committee Member); Mehmet Koyuturk (Committee Member); Satya Sahoo (Committee Member) Subjects: Bioinformatics

Doctor of Philosophy (PhD), Ohio University, 2020, Plant Biology (Arts and Sciences)

Flowering plants produce two different kinds of flowers: chasmogamous, open flowers that promote cross-pollination, and cleistogamous, small mechanically sealed flowers that force self-pollination. Typically, plants produce either chasmogamous or cleistogamous flowers. However, some species contain a chasmogamous/cleistogamous mixed breeding system and develop both flowers at different locations along the plant or at different times of the season. The temporal separation of chasmogamous and cleistogamous flowers is hypothesized to be influenced by the environment. However, the specific environmental cues and genetic mechanisms that signal for the induction and differentiation of each flower type remain largely unknown. To analyze the environmental variables driving separate, seasonal development of chasmogamous and cleistogamous flowers in Viola pubescens, bud counts and measurements of light quantity, canopy cover, photoperiod, temperature, soil moisture, and soil pH were collected over a native population in 2016 and 2017. Statistical analyses confirm that the two flowers develop in response to differing environmental factors and distinguish which factors are significantly associated with chasmogamous versus cleistogamous bud presence, the number of buds produced, and specific threshold values at which each bud type is most likely to develop. To enable genetic investigations, the V. pubescens draft genome was assembled using DNA and RNA sequencing data from eight diverse tissues, which together generated 38,081 gene models including 81 novel cyclotide genes. Gene expression was visualized for each tissue and highlighted transcriptional networks specific to chasmogamous and cleistogamous flowers. Functional annotation of the flower-specific genes indicate that chasmogamous flowers are enriched with genes involved in environmental sensing and repressing precocious development, while cleistogamous flowers contain up-regulated genes involved in DNA topology and microR (open full item for complete abstract)

Committee: Harvey Ballard Jr. (Advisor); Sarah Wyatt (Advisor); David Rosenthal (Committee Member); Ronan Carroll (Committee Chair) Subjects: Bioinformatics; Biology; Developmental Biology; Ecology; Environmental Science; Genetics; Plant Biology; Plant Sciences

Master of Science in Biological Sciences, Youngstown State University, 2019, Department of Biological Sciences and Chemistry

Stenotrophomonas maltophilia Oak Ridge Strain OR02 (S. maltophilia 02), which was isolated from a heavy metal contaminated site in Oak Ridge, TN, grows in the presences of toxic levels of heavy metals, including selenite. Selenium exists in four different valences as selenate (+6), selenite (+4), elemental selenium (0) and selenide (-2). Selenate (SeO42-) and selenite (SeO32-) are soluble, uncolored forms of selenium and elemental selenium forms an insoluble red precipitate. Microbes that use selenium, import it into the cell as selenite, reduce it to selenide and incorporate it into selenocysteine. When environmental selenite concentrations are higher than required, some bacteria reduce it to insoluble elemental selenium and methylate it to form volatile methyl selenide. When S. maltophilia 02 is growing in the presence of 0.5 mM sodium selenite, it produces an insoluble red precipitate and a stale garlic odor, which are presumably elemental selenium and methyl selenide, respectively. A subtractive hybridization technique was used in an attempt to identify genes that are expressed in response to high concentrations of selenite. S. maltophilia 02 was grown to early log phase and exposed to 0.5 mM selenite. After two hours of selenite exposure, RNA was extracted from untreated and treated cultures. The RNA was converted to double stranded cDNA and cut with the four-base cutter, restriction endonuclease, Sau3AI. After ligating linkers to the digested cDNA, it was amplified by PCR. The PCR reaction on the untreated cDNA was labeled with dCTP and dUTP biotin. The PCR reaction on the treated cDNA did not contain biotin labeled nucleotides. PCR products from both reactions were mixed, heated at 98°C to denature the DNA and allowed to hybridize at 68°C for 24 hours. The hybridization mixture was added to streptavidin magnetic beads and exposed to a magnetic stand to remove the cDNA from RNA that was present under both the treated and untreated conditions. The remaining cDN (open full item for complete abstract)

Committee: Jonathan Caguiat PhD (Advisor); David Asch PhD (Committee Member); Xiangjia Min PhD (Committee Member) Subjects: Biology; Genetics; Microbiology; Molecular Biology

Master of Science in Botany, Miami University, 2018, Botany

One path of the evolution of dioecy from hermaphroditism is via mutations at two loci, yet reversions to gynodioecy occur in some plants, including Carica papaya. Papaya has an XY chromosome system and hermaphrodites have a unique Y chromosome (Yh). The sex-determining regions of the Y and Yh chromosomes are nearly identical in nucleotide sequence; however, males and hermaphrodites differ morphologically. I predicted that the morphological differences and the sexual reversion are due to differentially expressed genes (DEGs). I conducted RNA-seq to identify DEGs during different floral developmental stages. Linkage Group 1 (the sex chromosome) was significantly enriched for DEGs compared to the other eleven linkage groups, and most of these genes were found in the pseudoautosomal regions (PAR). Sex-biased genes in papaya can be found on the PARs of the sex chromosomes and may serve as way to resolve sexually antagonistic loci.

Committee: Richard Moore (Advisor); Rob Baker (Committee Member); Dan Gladish (Committee Member) Subjects: Botany

Doctor of Psychology (PsyD), Wright State University, 2019, School of Professional Psychology

Previous research on gender conflict and strain quantitatively measured traditional masculinity ideology from western societal norms. The current study added to the previous research and qualitatively studied masculinity performance in men from different cultures: Black, Asian, Latino. Results from this study added to masculinity research due to the mixed method approach of both quantitative and qualitative research in males from diverse groups. Information gained from this study enabled masculinity to be operationally defined by different cultural focus groups and compared in order to explore distinct masculinity expression. Information was gained by measuring traditional masculinity ideology quantitatively on the Male Role Norms Inventory-Short Form (MRNI-SF). In addition, the males participated in separate focus groups to provide narratives of their masculinity performance beyond their traditional masculine ideology measured on the MRNI-SF. The current study showed that traditional masculine gender ideology was similar within all males, but how they expressed their masculine ideology appeared different in the Black, Asian, and Latino focus groups. Information from the current study will add to the masculinity research and increase understanding on the complexity of masculinity expression due to the integration of multiple cultural variables. Such knowledge will also enhance the cultural competence of providers and improve mental health resources for diverse men.

Committee: Steven Kniffley Jr. sy.D., M.P.A., ABPP (Committee Chair); Scott Fraser Ph.D., ABPP (Committee Member); Chris Modica Ph.D. (Committee Member) Subjects: African American Studies; African Americans; African Literature; Asian American Studies; Asian Studies; Black Studies; Clinical Psychology; Counseling Education; Counseling Psychology; Gender; Gender Studies; Hispanic American Studies; Hispanic Americans; Latin American History; Latin American Literature; Latin American Studies; Mental Health; Psychology; Psychotherapy; Quantitative Psychology; Social Psychology; Social Research

Master of Science (MS), Wright State University, 2016, Biochemistry and Molecular Biology

ΔNp63α, the most physiologically relevant isoform of p63, a p53 family member protein, maintains the proliferative capacity of the basal layer of epithelial tissues and is highly expressed in non-melanoma skin cancer. It has been implicated in a variety of different cancers, including breast, lung, and prostate cancers, however the complex role it plays in disease remains poorly understood. Elucidating ΔNp63α's regulatory network may provide insight into its role in epithelial tissues and in cancer progression. The objective of this thesis is to investigate ΔNp63α's upstream regulation in the context of non-melanoma skin cancer as well as expand on ΔNp63α's downstream function through its modulation of target microRNAs (miRNAs). Non-melanoma skin cancer is primarily a result of excessive exposure to ultraviolet (UV) radiation. ΔNp63α appears to be regulated by post-translational modifications such as phosphorylation, which can lead to its degradation in a ubiquitin-mediated, proteasome-dependent manner. cJun N-terminal kinase (JNK), a stress activated protein kinase (SAPK), is potently activated by UV stress and has been shown to phosphorylate p53 and p73. I hypothesized that UV-induced JNK activation can similarly regulate ΔNp63α via phosphorylation. Anisomycin and UV induced JNK activation were shown to produce an electrophoretic mobility shift in ΔNp63α, suggesting it was phosphorylated. Co-expression of JNK and ΔNp63α also exhibited an enhanced electrophoretic mobility shift in ΔNp63α following UV and anisomycin treatment. Phosphorylation was confirmed using an in vitro kinase assay with recombinant JNK and p63 proteins. Mass spectrometry analysis of immunoprecipitated ΔNp63α protein from UV treated H1299 cells transfected with ΔNp63α and in vitro kinase assay samples identified several phosphorylated residues, some of which are highly conserved in p73. Mutation of these potential JNK targeted residues alone did not prevent an electrophoretic mobility shift, h (open full item for complete abstract)

Committee: Madhavi Kadakia Ph.D. (Advisor); Weiwen Long Ph.D. (Committee Member); Michael Raymer Ph.D. (Committee Member) Subjects: Bioinformatics; Molecular Biology

Doctor of Philosophy, Miami University, 2016, Biology

The ocular lens is an excellent model to study cell signaling, cell survival and cell differentiation. The lens is comprised of only two cell types: proliferative lens epithelial cells and terminally differentiated lens fiber cells. The lens fiber differentiation process involves specific changes in gene expression between the two cell types. However, a comprehensive understanding of gene expression changes during lens fiber differentiation remains incomplete. Furthermore, despite the wealth of knowledge of transcription factors involved in lens cell proliferation, survival and lens fiber differentiation, little information exists about the role of DNA methylation and miRNAs in these processes. This study presents the first application of RNA-seq to provide a comprehensive view of both the relative abundance and differential expression of mRNAs and long intergenic non-coding RNAs from lens epithelial cells and lens fiber cells. We also investigated the role of DNA methylation in lens development. We found that while Dnmt1 inactivation at the lens placode stage led to lens DNA hypomethylation and severe lens epithelial apoptosis, lens fiber cell differentiation remained largely unaffected. The simultaneous deletion of phosphatase and tensin homolog (Pten) elevated the level of phosphorylated AKT and rescued many of the morphological defects and cell death in DNMT1- deficient lenses. With a different Cre driver (MLR10) we demonstrated that a small number of lens epithelial cells escaped Dnmt1-deletion and over-proliferated to compensate for the loss of Dnmt1-deleted cells, suggesting that lens epithelium possess a substantial capacity for self- renewal. Inactivation of both Dnmt3a and Dnmt3b by either the Le-Cre or MLR10-Cre transgene did not result in any obvious lens phenotype prior to 10 months of age, indicating that de novo DNA methylation, at least as mediated by both DNMT3A and DNMT3B, is dispensable for normal lens development. Our comparative miRNA-Seq data a (open full item for complete abstract)

Committee: Michael Robinson (Advisor) Subjects: Biology; Biomedical Research; Genetics; Zoology

Doctor of Philosophy, The Ohio State University, 2014, Horticulture and Crop Science

The genetic diversity in the crop landraces and crop wild relatives (CWRs) of the world is the `biological cornerstone' of food security—we must ensure that it is conserved. Two important steps that could assist the in-situ conservation of this germplasm are: 1) determining how natural selection has shaped the distribution of functional genetic diversity across the landscape; and 2) identifying potential threats to this diversity. In addition, the former could assist landrace farmers in securing germplasm capable of withstanding future biotic and abiotic shifts by producing information on the locations of pertinent genetic diversity. In this body of work we provide examples of each of these steps—one from the maize landraces of Chiapas, Mexico (step 1) and the other from the sunflower system of the US (step 2). First, we sought understanding of how natural selection has shaped functional genetic diversity in Zea mays ssp. mays (maize) landraces grown along an elevational cline in Chiapas, Mexico by using RNA-seq approaches. We collected maize landraces from three elevational zones (highland, ~2100 m; midland, ~1550 m; and lowland, ~600 m) and planted them in a midland common garden. RNA-seq was performed on young leaf tissue. Weighted gene co-expression network analysis was used to identify co-expressed gene modules among landraces. Association analysis was then performed between landrace module expression values and environmental parameters of landrace origin. We identified an apparent tradeoff between an ABA dependent abiotic stress response in the lowland landraces and a possible plasma membrane repair/signaling response in the highland landraces. We then used the RNA-seq dataset to find signals of genetic differentiation in phenylpropanoid, flavonoid, and lignin biosynthesis between highland and lowland maize landraces. Genes differentially expressed between highland and lowland landraces were compared to a list of known and predicted genes involv (open full item for complete abstract)

Committee: Kristin Mercer Dr. (Advisor); Erich Grotewold Dr. (Committee Member); Leah McHale Dr. (Committee Member); Andrew Michel Dr. (Committee Member) Subjects: Agriculture; Biology; Conservation; Ecology; Horticulture; Molecular Biology; Plant Biology; Plant Sciences; Sustainability

PhD, University of Cincinnati, 2009, Engineering : Biomedical Engineering

Applying clustering algorithms to identify groups of co-expressed genes is an important step in the analysis of high-throughput genomics data in order to elucidate affected biological pathways and transcriptional regulatory mechanisms. As these data are becoming ever more abundant the integration with both, existing biological knowledge and other experimental data becomes as crucial as the ability to perform such analysis in a meaningful but virtually unsupervised fashion.Clustering analysis often relies on ad-hoc methods such as k-means or hierarchical clustering with Euclidean distance but model-based methods such as the Bayesian Infinite Mixtures approach have been shown to produce better, more reproducible results. Further improvements have been accomplished by context-specific gene clustering algorithms designed to determine groups of co-expressed genes within a given subset of biological samples termed context. The complementary problem of finding differentially co-expressed genes given two or more contexts has been addressed but relies on the a priori definition of contexts and has not been used to facilitate the clustering of biological samples. Here we describe a new computational method using Bayesian infinite mixture models to cluster genes simultaneously utilizing the concept of differential co-expression as a unique similarity measure to find groups of similar samples. We compute a novel per-gene differential co-expression score that is reproducible and biologically meaningful. To evaluate, annotate, and display clustering results we present the integrated software package CLEAN which contains functionality for performing Clustering Enrichment Analysis, a method to functionally annotate clustering results and to assign a novel gene-specific functional coherence score. We apply our method to a number of simulated datasets comparing it to other commonly used clustering algorithms, and we re-analyze several breast cancer studies. We find that our unsuper (open full item for complete abstract)

Committee: Mario Medvedovic PhD (Committee Chair); Bruce Aronow PhD (Committee Member); Michael Wagner PhD (Committee Member); Jaroslaw Meller PhD (Committee Member) Subjects: Bioinformatics

PhD, University of Cincinnati, 2006, Arts and Sciences : Biological Sciences

This project studied the transcriptional response in larval fathead minnows to three different stressors, copper, zinc and heat. Differential display was used to identity stress-responsive genes in the genetically uncharacterized Pimephales promelas larvae. Two hundred and sixty-one clearly sequenced candidate bands were identified as being differentially expressed by copper, of which 148 were unique genes. One hundred and sixty-eight clearly sequenced candidate bands showed differential expression by zinc, 100 of which were unique genes. One hundred and sixty-seven heat-responsive differentially expressed bands were obtained, of which 107 were unique genes. Eight-five novel ESTs for the fathead minnow were homologous to functional genes from the NCBI database. In addition, this study identified 143 cDNAs homologous to genomic sequences of undetermined function within the NCBI database. Twenty-three dose-responsive genes that were identified in samples from two different stress experiments were quantified using an alternative more sensitive technique, real-time PCR. Gene expression was validated for two independent data sets from each of the stress experiments. Two genes, carboxypeptidase B and 60S ribosomal protein L12, were consistently repressed by copper in all gene assays. One gene, carboxypeptidase B, was consitently repressed by zinc in all gene assays of two independent experiments. One gene, fast muscle troponin I, was consistently repressed in response to thermal stress using samples from two independent experiments.

Committee: Dr. Stephen Keller (Advisor) Subjects:

Doctor of Philosophy, The Ohio State University, 2007, Integrated Biomedical Science

The genetic investigation of human disorders largely through linkage mapping has led to the discovery of candidate genes and mutations as risk factors for those disorders where there is a high degree of penetrance. While twin studies have provided evidence that there are major genetic contributions to multifactorial diseases like coronary artery disease, it has proven difficult to find and replicate significant genetic associations for such diseases. Searching for genetic variants with evidence of a direct molecular impact on the expression and function of candidate genes vital to disease etiology is one valid approach to this problem. There is a growing appreciation that one major class of variation acts at the level of mRNA expression. Traditional tools for studying this class of variation (e.g., reporter gene assays) have severe limitations, mainly in lacking the in vivo context where the alleles have their functional impact. This dissertation relies on the application of a relatively novel technique: measurement of allelic expression imbalances (AEI) between chromosomes in human tissues. Using these measurements as phenotypic traits, I demonstrate that cis-acting alleles affecting mRNA expression can be readily mapped. In the largest survey to date of AEI in human tissues I find AEI in disease candidate genes is quite common, and that functional contributors to these expression phenotypes are often not regulatory polymorphisms, but polymorphisms found directly within the mRNAs and affecting mRNA processing and functions. Computational analysis of mRNA structures and genetic variation within human genomes indicates that modulation of mRNA structural plasticity to polymorphism is likely one contributor to human phenotypic variability. Focusing on a number of cardiovascular disease candidate genes I make a number of novel findings: 1) a strong ACE AEI phenotype common in the African-American population is mapped to specific upstream regulatory alleles and is signif (open full item for complete abstract)

Committee: Wolfgang Sadee (Advisor) Subjects:

Master of Science, Miami University, 2009, Botany

Gene duplication can lead to increased morphological complexity by giving rise to new genes and gene functions. The classic Ohno model predicts new gene duplicates will be functionally redundant. However, this model does not address functional divergence due to differential expression. To test this possibility, the developmental expression patterns of 18 pairs of unlinked recent duplicates in Arabidopsis thaliana were characterized. These duplicates have a Ks less than 5%, are less than 2 my old, and are specific to the A. thaliana lineage. The coding regions of these duplicates are generally complete, although they share only an average 616 bp of upstream regulatory sequence. We found that the majority of duplicate loci have non-redundant expression patterns, suggesting functional divergence occurs soon after duplication for unlinked duplicates. Furthermore, comparison of expression data from this study to online databases suggests these databases cannot reliably differentiate expression patterns among recent duplicate genes.

Committee: Richard Moore Dr. (Advisor); Qingshun Li Dr. (Committee Member); Martin Stevens Dr. (Committee Member) Subjects: Botany; Genetics; Molecular Biology

Master of Science, University of Akron, 2010, Biology

The transcription factor Sry is expressed in male embryos where it initiates testis development. It is also transcribed in several adult tissues of various species. Tissue specific differences in the expression profile of the 6 or 7 rat Sry loci have been reported in adult male testis, adrenal, and kidney of the SHR/y strain, indicating likely differential locus functions. The promoter of Acsl3, an enzyme in fatty acid metabolism, contains putative Sry response elements, implicating Sry as a potential regulator of Acsl3 gene activity. It was hypothesized that Sry is expressed in adult cerebral cortex, ventricle, atrium, aorta, and skeletal muscle in adult normotensive WKY, borderline hypertensive SHR/y, and hypertensive SHR male rats with differential locus expression in cerebral cortex and ventricle. Further, total Sry transcript expression was expected to correlate with Acsl3 transcript expression. RNA isolated from skeletal muscle, atrium, aorta, ventricle, and cerebral cortex of 15-20 week old WKY, SHR/y, and SHR male rats was reverse transcribed to cDNA. Total Sry and Acsl3 transcript expression was determined by real-time PCR using Sry and Acsl3 specific primers. Individual Sry locus expression in ventricle and cerebral cortex was determined by fragment analysis using standard PCR and fluorescent-tagged primers. Sry transcripts were detected in all five tissues. Total Sry expression in cerebral cortex was between 3.9 and 42.3 fold (P<0.05) greater than in aorta, skeletal muscle, and ventricle in all three strains. Within each tissue, proportional expression of individual Sry loci differed (P<0.05): Sry1, Sry2, and Sry3A/3C differed in WKY cerebral cortex; Sry1 differed from Sry2 and Sry3/3A/3C in SHR cerebral cortex and SHR/y cerebral cortex; and Sry1 differed from Sry2 in WKY ventricle and SHR/y ventricle. Within each strain, tissue specific differences were present for Sry1 and Sry2 in all three strains; Sry3A/3C in WKY; and Sry3/3A/3C in SHR/y. Strain prop (open full item for complete abstract)

Committee: Amy Milsted Dr. (Advisor) Subjects: Molecular Biology