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)

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.

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

Microelectrode arrays (MEAs) provide advanced neural recordings for the implementation of brain-computer interface (BCI) devices. However, MEAs lose recording quality over time, limiting clinical and chronic pre-clinical applications. Chronic failure is often attributed to the neuroinflammatory response following implantation, which remains widely under-characterized. Following decades of largely immunohistochemical characterization of the response, recent efforts have begun to include measurements of changes in gene expression profiles. In the initial studies measuring gene expression, temporal characterization of acute and chronic gene expression identified several key inflammatory pathways upregulated, including the complement system and toll-like receptor pathways. However, spatially resolved analysis and the correlation between gene expression and protein expression had previously not been reported. This dissertation expands on previous gene expression studies by conducting the first large-scale proteomic analysis of MEA implantation, and applying more rigorous spatial characterization as a function of the extent of changes in gene or protein expression as a function of binned distance from the MEA-tissue interface. With each chapter, we further expand on our proteomic analysis, demonstrating the importance of distance-based segmentation on both the significance of the proteins and our interpretations of the results. By integrating spatially resolved transcriptomic and proteomic analyses, we uncover new insights into the molecular mechanisms of neuroinflammation and neurodegeneration following MEA implantation. With 62 proteins and over 21,000 genes analyzed at 4, 8, and 16 weeks post-implantation, we provide numerous potential therapeutic targets, including microglial, astrocytic, T-cell, and neuronal genes and proteins.

Doctor of Philosophy, The Ohio State University, 2023, Neuroscience Graduate Studies Program

Single nucleotide variants (SNVs) in the gene encoding Kinesin Family Member 5A (KIF5A), a neuronal motor protein subunit involved in transport along microtubules, have been associated with amyotrophic lateral sclerosis (ALS). ALS is a rapidly progressive and fatal neurodegenerative disease that primarily affects motor neurons. Numerous ALS-associated KIF5A SNVs are clustered near splice site junctions of the penultimate exon 27 and are predicted to alter the carboxy-terminal (C-term) cargo-binding domain of KIF5A. Mis-splicing of exon 27, resulting in exon exclusion, is proposed to be the mechanism by which these SNVs cause ALS. Whether all KIF5A SNVs proximal to exon 27 result in exon exclusion is unclear. To address this question, we designed an in vitro minigene splicing assay in HEK293 cells which revealed heterogeneous site-specific effects on splicing: only 5´ splice site (5´ss) SNVs resulted in exon skipping. We also quantified splicing in select CRISPR-edited human stem cells differentiated to motor neurons and in neuronal tissues from a 5´ss SNV knock-in mouse (Mouse: c.3005+1G>A; Human homolog: c.3020+1G>A), which showed the same result. Moreover, survival of representative 3´ splice site (3´ss), 5´ss, and truncated C-term (ΔC) variant KIF5A (v-KIF5A) motor neurons was significantly reduced compared to wildtype (WT) motor neurons, and overt morphological changes were apparent. While total KIF5A mRNA levels were comparable across cell lines, total KIF5A protein levels were decreased for v-KIF5A lines, suggesting an impairment of protein synthesis or stability. Thus, despite the heterogeneous effect on RNA splicing, KIF5A SNVs near exon 27 similarly reduce the availability of the KIF5A protein, leading to axonal transport defects and motor neuron pathology.

Bachelor of Science, Wittenberg University, 2022, Biology

Obsessive-compulsive disorder (OCD) is very common, affecting about 2% of the world's population. Currently, there are very few effective treatments for OCD including medications such as serotonin reuptake inhibitors (SRIs) and varying therapies. N-acetyl cysteine, an over-the-counter supplement, has been implicated as a potential treatment for OCD. This experiment tested how N-acetyl cysteine (NAC) affects OCD-induced mice, specifically looking at isolated gene involvement. qPCR was used to analyze the gene expression on Nrxn1, Gfap, Reep3, Grm1, and Grm2. By studying the specific gene expression in NAC-treated, OCD-induced mice we hope to gain a better understanding of this correlation and the implications this may have for ongoing OCD treatment as well as gain a better understanding of the neurological pathways that affect OCD. Nrxn1, Gfap, and Reep3 showed minimal amounts of expression even in normal mice, suggesting there may not be a relationship between these genes and OCD, or that these genes are low expressing genes across all groups, not just the OCD treated groups. Grm1 and Grm2 had larger amounts of expression, with decreasing expression between 1-week and 3-week treatments of NAC+RU suggesting a relationship between OCD and glutamate receptors. Futures studies could focus on researching interactions between OCD and other glutamate receptors such as Grm3 and Grm5.

Doctor of Philosophy (PhD), Wright State University, 2022, Biomedical Sciences PhD

Gene expression in mammalian cells requires complex nuclear choreography, and there is increasing evidence that spatiotemporal organization of chromatin and nuclear compartments plays an important role in gene expression. In this dissertation, I examined the function of SON, a splicing factor with a known role in nuclear organization, in chromatin-mediated gene expression. SON association with a transcriptionally inactive U2OS 2-6-3 reporter gene array provided a useful model to study SON's chromatin dynamics. I demonstrated that SON associates with the inactive but not the activated array, and that SON's RNA binding domains are not necessary for that association. Second, I discovered a new role for SON in maintaining chromatin condensation. Whereas chromatin decondensation is typically correlated with transcription activation, I have demonstrated that reporter transcripts are not produced at decondensed SON-depleted U2OS 2-6-3 reporter gene loci, and that SON-depleted loci contain histone H3 that is trimethylated on lysine 9, a marker for transcriptionally silent chromatin. We found that SON depleted reporter loci are still transcriptionally activatable, and that inhibiting transcription elongation is not sufficient to condense the enlarged SON depleted reporter locus. These findings suggest that higher order chromatin structure and transcription activation are functionally distinct mechanisms of gene regulation that can be uncoupled. Finally, I investigated SON's role in genome-wide chromatin organization. SON-depleted cells are more susceptible to DNase digestion, implicating SON in the maintenance of chromatin stability globally. In conclusion, this study demonstrates a new function for the splicing factor SON in maintaining chromatin organization.

Master of Science in Biological Sciences, Youngstown State University, 2021, Department of Biological Sciences and Chemistry

Gene expression is a crucial process in muscle functioning which occurs throughout the skeletal myogenic process. The gene regulatory network involved in the later process could be essential in shedding some light in muscle aging and muscle related diseases. This study employed an experimental design to determine the expression of Acetylcholine receptor and galectin 3 gene in C2C12 cells which are mouse muscle cells that are immortalized and capable of allowing the description of transcriptional steps through myogenesis. The C2C12 cells were studied over extensive time course of 30 days with the cells being seeded, media changed, and cells pelleted at specific time points for RNA isolation. Following the RNeasy kit protocol the RNA was isolated and quantified by nanodrop spectrophotometry. Analysis of the Acetylcholine receptor and galectin-3 gene was done by quantitative Real-Time Polymerase Chain Reaction(qRT-PCR). The expression of the said genes was measured for each of the three trials that was done and averaged. Inaddition to determining the expression levels of these genes, this level of expression was compared at different time points and correlated with changes in tissue morphology. During the onset of myogenesis, Acetylcholine receptor was highly expressed compared to Galectin-3. As the muscles mature the expression of Galectin-3 seem to increase as compared to Acetylcholine receptor. This gene expression analysis was normalized to GAPDH. According to this study, it can be concluded that changes in expression of these genes during maturation of muscles are good indicators of aging in muscle cultures.

Master of Computer Science (M.C.S.), University of Dayton, 2021, Computer Science

Facial recognition with mask/noise has consistently been a challenging task in computer vision, which involves human wearing a facial mask. Masked Face Analysis via Multi-task deep learning is a method which will answer to many questions. In this thesis, we propose a unifying framework to simultaneously predict human age, gender, and emotions. This method is divided into three major steps; firstly, Creation of the dataset, Secondly, 3 individual classification models used for the system to learn the labelled (Age, Expression and Gender) images, Thirdly, the multi-task deep learning (MTDL) model; which takes the inputs as the data and shares their weight combined and gives the prediction of the person's (with mask) age, expression and gender. However, this novel framework will give better output then the existing methods

Master of Science in Biomedical Engineering (MSBME), Wright State University, 2019, Biomedical Engineering

Triple-negative breast cancer (TNBC) is characterized by the absence of expression of the estrogen receptor, progesterone receptor and human epidermal growth factor receptor 2 (HER2). Therefore, TNBC is unresponsive to targeted hormonal therapies, which limits treatment options to nonselective chemotherapeutic agents. Basal-like breast cancers (BLBCs) represent a subset of about 70% of TNBCs, more frequently affecting younger patients, being more prevalent in African-American women and significantly more aggressive than tumors of other molecular subtypes, with high rates of proliferation and extremely poor clinical outcomes. Proper classification of BLBCs using current pathological tools has been a major challenge. Although TNBCs have many BLBC characteristics, the relationship between clinically defined TNBC and the gene expression profile of BLBC is not fully examined. The purpose of this study is to assemble publicly-available TNBC gene expression datasets generated by Affymetrix gene chips and define a set of genes, or gene signature, that can classify TNBC samples between BLBC and Non-BLBC subtypes. We compiled over 3,500 breast cancer gene expression profiles from several individual publicly available datasets and extracted Affymetrix gene expression data for 580 TNBC cases. Several popular data mining methods along with dimensionality reduction and feature selection techniques were applied to the resultant dataset to build predictive models to understand molecular characteristics and mechanisms associated with BLBCs and to classify them more accurately according to important features extracted through microarray data analysis of BLBC and Non-BLBC cases. Our result can lead to proper identification and diagnosis of BLBCs, which can potentially direct clinical implications by dictating the most effective therapy.

Doctor of Philosophy, The Ohio State University, 2019, Microbiology

The Arctic system has been undergoing a rampant change during the Anthropocene. This anthropogenic change has allowed for additional physical and biological positive feedback processes that in turn accelerate warming in the arctic and subarctic systems. Microbial community/functional dynamics are both (i) dramatically impacted by these rapid changes and (ii) key players in the biological positive feedback process that accelerates the change. Recent technological, analytical, and computational advances have allowed us to ask systems-level questions that encompass microbial and viral community dynamics (along with their potential functional dynamics) and high-resolution environmental measurements. This research took a systems-level approach to look for the first time at (i) the characteristics of Arctic marine viruses in a global context, and (ii) microbial community gene expression in a rapidly changing permafrost thaw gradient. Additionally, novel viral sequences recovered from the marine and terrestrial ecosystems studied here were used to build new resources and tools that accelerate viral discovery in nature. First, studying marine viral macro- and microdiversity from the Arctic Ocean to the Southern Ocean, enabled by the Tara Oceans Expedition, revealed the Arctic Ocean as a hotspot of viral diversity, with ~42% of the recovered viral populations originating from the Arctic Ocean viromes. In total 195,728 viral populations >10 kb were recovered from the global ocean to constitute the Global Ocean Viromes 2.0 (GOV2.0) dataset. Viral communities assorted into five distinct global ecological zones and the arctic viral communities formed their own distinct ecological zone. Additionally, this work revealed unexpected patterns and ecological drivers of viral diversity (at the community, inter-, and intrapopulation levels), within the Arctic Ocean, across latitudes, and across the depth of the global ocean. Second, genome-resolved metaproteomic study of microbial gene (open full item for complete abstract)

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.

Doctor of Philosophy, The Ohio State University, 2018, Translational Plant Sciences

The exhaustion of oil fields together with the undesirable effects of its use has turned sugarcane into an attractive crop for the biofuel market. The position of Brazil as the world's major sugarcane producer and the need to expand the planted area to less favorable soils makes the study of drought essential. This work has the aim of providing a comprehensive analysis of sugarcane drought responses in the physiological and molecular levels. In order to do that I followed four strategies. First, I performed the analysis of physiology and transcriptome (microarray) of drought stressed sugarcane plants at 4 days of stress, 6 days of stress and re-watering of a greenhouse experiment. The plant material analyzed was leaves and roots. Second, aiming to complement the data obtained, it was performed RNA-Seq analysis from the most discrepant condition (identified by microarray), from both leaves and roots, third, I performed the analysis of a drought progression experiment through physiology and RT-qPCR of selected genes and forth I built co-expression networks to detect interesting patterns. Physiology analysis showed that plants were under moderate to severe water stress with decreases of up to 97% in photosynthesis. Microarray data identified 575 unique SAS differentially expressed. The analysis of the identified sequences allowed the observation that in leaves after 4 days of stress, the plant is mostly transducing the signal from the environment, while after 6 days and after rehydration there is a functional response of the plant, with re-watering leading the metabolism back to homeostasis. In the case of roots, it was observed a similar response, however roots take longer to go back to the initial condition, with down-regulated genes even after re-watering. There are also pathways presenting a distinct pattern in the analyzed tissues, such as the case of Phenylpropanoid Biosynthesis pathway. Furthermore, while in leaves there is a restriction on photosynthesis, on ro (open full item for complete abstract)

Doctor of Philosophy, The Ohio State University, 2014, Integrated Biomedical Science Graduate Program

Genetic differences are one of the main contributors to diversity in clinical phenotypes. This project identifies and defines genetic factors affecting dopamine dysregulation focusing on three genes in dopamine signaling: DBH, COMT and SNCA. To study this I measure allelic expression, selecting RNA samples from post-mortem human tissue that are heterozygous for a marker SNP, and quantitate the expression of each allele. Dopamine beta-hydroxylase (DBH) encodes an enzyme which converts dopamine to norepinephrine. A promoter SNP, rs1611115 has been associated with low DBH and high dopamine plasma levels; however, underlying mechanisms remain uncertain. I found a tissue-specific effect of rs1611115 in liver, with up to 11 fold differences in allelic and overall mRNA expression (p<0.0004 to 2x10-7 and p<0.0001 respectively), indicating decreased transcription. Interestingly, locus coeruleus and adrenal gland, the main sources of DBH in the body, did not demonstrate this robust effect; only small AEI ratios were detected in these tissues. More frequent than rs1611115 and in linkage disequilibrium with it, a second SNP, rs1108580 was associated with reduced allelic mRNA expression in all tissues tested. This dual mechanism accounts for the previously described genotype effect on DBH plasma levels, with a novel role for liver as an important source of variability in DBH levels. In combination, rs161115 and rs1108580 contribute to strongly reduced mRNA expression in the liver, reducing transcription in a tissue selective manner. In mice, Dbh mRNA levels in the liver correlated with cardiovascular risk phenotypes. Using a PheWAS (phenome-wide association study) analysis, the minor alleles of rs1611115 and rs1108580 were associated with sympathetic phenotypes including angina pectoris. Testing the combined effects of rs1611115 and rs1108580 indicated robust protection against myocardial infarction in three clinical cohorts. These results demonstrate profound effec (open full item for complete abstract)

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)

PhD, University of Cincinnati, 2008, Medicine : Environmental Health

Variation in activity of cytochrome P450s is one of the major factors responsible for interindividual difference in drug clearance rate which may cause serious toxicity or inefficacy of clinically used drugs. Such variation was reported to be determined at mRNA level for major P450 genes albeit it to a various degree. Little is known about mechanisms underlying the huge expression variation of most P450 genes among individuals. Identification of genetic variants affecting expression levels of P450 genes can lead to a cost-effective personalized medicine. This dissertation aims to 1) determine the genetic diversity and genetic structure of the CYP1A1_1A2 region; 2) search for determinants of interindividual variation in expression level of seven cytochrome P450 genes; 3) identify cis-acting genetic variants affecting the expression level of CYP1A1 and CYP1A2. Single nucleotide polymorphisms in a 39.6kb segment encompassing the whole CYP1A1 and CYP1A2 genes and the spacer region were identified. The linkage disequilibrium structure, haplotypes and tagSNPs in this region were determined. A humanized BAC-transgenic mouse line was established as a in vivo platform to study activity of different haplotypes of the human CYP1A1_1A2 region. Four factors were identified as major determinants of interindividual variability in expression level of P450 genes in human liver with various contribution for each P450 gene. These four factors include (1) the functional efficacy of global regulators affecting expression level of most active genes; (2) the expression level of specific P450 regulators; (3) exposure to environmental factors responsible for activation or modulation of activity of specific P450 regulators; (4) the presence of cis-acting genetic variants in P450 genes. At least four major cis-acting regulatory SNPs (rSNP) were demonstrated to exist in regulation of CYP1A1 or CYP1A2 expression. One of the four rSNPs was CYP1A1-940C>T (rs4646418), which is located in a G-rich (open full item for complete abstract)

Doctor of Philosophy, The Ohio State University, 2007, Neuroscience

My studies are to test the hypothesis that functional polymorphisms of OPRM1 and DRD2 modulate the susceptibility to mental disorders. I first determined whether there is an mRNA allele expression difference between two alleles of OPRM1 and DRD2 in relevant tissue (postmortem brain samples). Primer extension assays (SNaPshot) was used to detect allele-specific mRNA expression in human postmortem brain tissues using indicator SNP A118G for OPRM1 and three SNPs (rs6275, rs6277, and rs6279) for DRD2, respectively. Allelic expression imbalance (AEI) has been revealed for both OPRM1 and DRD2. The main efforts of this project were to search for functional polymorphisms or other factors responsible for the observed AEI of OPRM1 and DRD2. For OPRM1, in vitro studies were conducted to verify the effects of A118G on transcription and translation in transfected CHO cells. As for DRD2, genotyping and association studies were used to scan for polymorphisms correlated with AEI, and one SNP (rs12364283) in the upstream regulatory region of DRD2 was highly associated with AEI and its effects were confirmed by reporter gene assay in HEK and SH-SY5Y cells. Moreover, two highly linked intronic SNPs (rs2283265 and rs1076560) were associated with reduced formation of the DRD2S (short) splice variant relative to DRD2L (long) – two splice variants thought to have distinct roles in dopamine signaling. Consistent with this finding, we found the minor allele of the two intronic SNPs was associated with greater neuronal activity in healthy humans assessed with fMRI during working memory. These results reveal novel functional genetic DRD2 variants which affect its expression and physiology of subcortical and cortical brain regions during working memory, a mechanism that may be relevant to several mental disorders. Another clinical case-control study (Stanley collections, Bethesta, MD) revealed much higher allele frequency of rs12364283 (c2 = 6.89, P = 0.009 (n = 95)) in schizophrenia subjects, (open full item for complete abstract)

Doctor of Philosophy, The Ohio State University, 2004, Veterinary Biosciences

Human T-lymphotropic virus type-1 (HTLV-1), a deltaretrovirus cause adult T-cell leukemia/lymphoma and other lymphocyte-mediated disorders. HTLV-1 provirus encodes various regulatory and accessory genes, including p30(II). Our laboratory has identified the functional properties of pX ORF-II encoded p30(II), but the role of this viral protein in virus replication or pathogenesis remains unclear. We have reported that HTLV-1 p30(II), a nuclear-localizing protein, interacts with CBP/p300, disrupts CREB-Tax-CBP/p300 complex formation at HTLV-1 Tax-Responsive Elements repeats (TRE) and differentially modulates CREB and TRE-mediated transcription. We have also recently demonstrated that p30(II) is critical in maintaining viral loads in vivo. Herein, we further characterized the role of p30(II) in regulation of cellular gene expression, using microarrays and identified alterations of interrelated pathways of cell-proliferation, T-cell signaling, apoptosis and cell-cycle in p30(II)-expressing T-lymphocytes. We are the first to test the overall effect of an HTLV-1 accessory protein, on cellular gene expression and demonstrate that p30(II) activates transcription factors involved in T-cell signaling/activation, such as NFAT, NF-KB and AP-1. We further characterized the role of p30(II) in regulation of viral gene expression, by identifying motifs critical in binding p300 and regulating TRE-mediated transcription. By analysing the amino acid domain of p30(II) critical for repressing LTR-mediated transcription, we identified a lysine residue at amino acid 106 of p30(II), that is critical for repressing TRE-mediated transcription. Additionally, we found that p300 reverses p30(II)-dependent repression of TRE-mediated transcription, in a dose-responsive manner. Our data confirms the role of p30(II) as a regulator of viral gene transcription, in association with p300. However, unlike wildtype p300, p300 HAT mutants only partially rescue p30(II)-mediated LTR repression. Additionally, (open full item for complete abstract)

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)

Bachelor of Science, Wittenberg University, 2024, Biochemistry/Molecular Biology

Obsessive compulsive disorder (OCD) is a neuropsychiatric disorder in which individuals can suffer from obsession, compulsions, and uncontrollable thoughts. Current treatments for OCD are not effective for all individuals, but an over-the-counter drug, N-acetyl cysteine (NAC), has shown promising therapeutic effects for those affiliated with OCD. In a past behavioral study, mice were separated into groups and given NAC for one or three weeks and then given RU24969, which is a 5-HT1B serotonin receptor agonist that induces perseverative behavior, a common characteristic of OCD in mice. The mouse brains were then homogenized, mRNA was extracted, and cDNA was created. The Quantitative Polymerase Chain Reaction (qPCR) analysis was used to measure gene expression in six chosen genes: CNTN4, TNR, GRIK3, GRIA2, SLC6A4, and ADRA2A and two reference genes. Gene expression was measured in seven different treatment groups with varying conditions including normal mice, those with OCD like symptoms, and those treated with NAC. These genes are involved in the nervous system in some way, which could mean there is a link between their activity and OCD. The trend in the data for these genes showed significant increases in gene expression in the 1-week NAC + water treatment and decreases in the 3-week NAC + RU treatment.

Doctor of Philosophy, Case Western Reserve University, 2025, Biochemistry

Appropriate levels of gene expression are required for cellular fitness and survival. Messenger RNAs (mRNAs) play a central role in gene expression and thus must be tightly regulated. Despite most mRNAs undergoing degradation through the same decay pathway, mRNA half-lives are highly disparate and can vary by orders of magnitude. Some transcript-specific features, such as stable structures in the 5' UTR or regulatory sequences in the 3' UTR, can affect mRNA expression. However, these elements are not sufficient to explain the variation in mRNA stability observed transcriptome-wide. Our lab originally identified codon optimality as a global determinant of mRNA stability. Codon optimality refers to how efficiently each codon is translated and is dependent on the relative availability of charged cognate tRNAs. The most likely explanation for the observed link between codon optimality and mRNA stability is that ribosome decoding rates influence mRNA stability. However, a transcriptome-wide link between the contribution of codons to translation rate and to mRNA stability has not been previously established. Using ribosome profiling in Saccharomyces cerevisiae, we demonstrate that codon-level and transcript-level elongation rates indeed globally correlate with mRNA stability. Chemical modification of mRNA nucleosides provides an additional layer of regulation. Prior to our work, N4-acetylcytidine (ac4C) was an understudied modification solely found to exist in polyA-selected mRNA by HPLC/MS-MS. Through a collaborative effort, we identified more than 2,000 human mRNAs that are modified with ac4C, and our studies revealed novel roles for ac4C in promoting mRNA stability and translation. We also find that the acetylating enzyme N-acetyltransferase 10 (NAT10) associates with translating ribosomes, suggesting that it may monitor translation and co-translationally acetylate mRNA. Furthermore, ac4C displayed stronger base-pairing interactions with guanosine (open full item for complete abstract)