Genetics and Genomics Commons^™

Managing Stress: A Study Of Stress Response Mechanisms In Mycobacteria, Augusto C. Hunt Serracin

Biology Dissertations

Mycobacteria encompass many pathogenic species known to cause severe disease in humans. A well-known example is Mycobacterium tuberculosis (Mtb), the causative agent of the lung disease tuberculosis, which kills millions of humans worldwide yearly. Pathogenic mycobacteria like Mtb are challenging to treat because of their innate ability to adapt to environmental stress. Their unique cell physiology and conserved stress responses allow them to combat biological insults, regulate growth, and regulate genes involved in stress; all these responses increase tolerance to antibiotics. The current therapies to treat mycobacterial infections are lengthy and, at times, unsuccessful, partly due to antibiotic tolerance. A …

The Evolution Of Transposable Elements As Cis-Regulatory Elements In Mammals, Alan Y. Du

Arts & Sciences Electronic Theses and Dissertations

Transposable elements (TEs) are mobile genetic elements that make up a large proportion of mammalian genomes. Although TEs are highly prevalent genomic sequences, they have been understudied as they were once labeled as “junk DNA.” Despite their initial status as simple genomic parasites, recent studies have implicated TEs as cis-regulatory elements, supplying promoters, enhancers, and boundary elements. Functional testing of regulatory activity, however, remains a significant bottleneck. Nonetheless, due to their repetitive nature, TEs provide a unique model to examine the evolution of cis-regulatory elements, which has traditionally been difficult to study due to lack of homology at the sequence …

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

Doctoral Dissertations

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

Computational Analysis Of Transcriptional And Post-Transcriptional Feedback Loops In Development And Cell Differentiation, Benjamin Rigel Nordick

Masters Theses

Regulation of gene expression is critical to organism development and health. Positive and negative feedback in networks of gene regulatory interactions are associated with the maintenance of distinct cell states/types or oscillations, respectively. Recent computational studies identified two structures of positive feedback relevant to establishment of cell type: interconnected transcriptional “high-feedback” loops and a purely post-transcriptional feedback loop arising from multiple microRNA molecules cooperatively regulating one mRNA. The goals of this work were to develop methods for analyzing often-unintuitive high-feedback loops in large networks, generalize the two new regulatory structures to consider oscillation, and further explore the ability of post-transcriptional …

Tetr Family Regulator Farr Variation Controls Antimicrobial Fatty Acid Efflux In Staphylococcus Aureus, Camryn M. Bonn

Electronic Thesis and Dissertation Repository

To colonize human skin and survive within abscesses, Staphylococcus aureus has evolved mechanisms to evade host innate defenses. USA300 has become the predominate community-acquired methicillin-resistant S. aureus (CA-MRSA) clone, which can be in part attributed to detoxification of unsaturated free fatty acids (uFFA) found in sebum and the nares. Our lab has previously identified the TetR family regulator FarR responsible for induction of the resistance-nodulation-division (RND) superfamily efflux pump FarE to promote efflux of toxic uFFA. However, RND family efflux pumps remain poorly characterized in Gram-positive species and the mechanism by which FarR regulates FarE has yet to be determined. …

An Investigation Of Epigenetic Mechanisms Driving The Biology Of Head And Neck Squamous Cell Carcinoma, Scot Carson Callahan

Dissertations & Theses (Open Access)

Head and neck squamous cell carcinoma (HNSCC) is the 6th most common cancer worldwide and is associated with significant morbidity and mortality. To date, the majority of work in the field has focused on genomic alterations such as mutations and copy number alterations. However, the clinical success of targeted therapies that exploit known genomic alterations, such as EGFR mutations, has remained mixed. Over the past decade, the importance of epigenetic regulators has come to the forefront, with the realization that many of these genes are mutated in cancer. Despite this realization, the role of epigenetics in regulating tumorigenesis, progression and …

The Role Of Ccaat Binding Factor In The Regulation Of Catalase Gene Expression In Candida Albicans, Zahra Al-Rumaih

Graduate Theses and Dissertations

Candida albicans is a fungal opportunistic human pathogen. Its infections range from surficial infections like skin rash to fatal systemic infections. Filamentation growth mode is associated with C. albicans virulence because it helps penetration of the host’s epithelial cells. The CCAAT-binding factor (CBF) is a conserved heterooligomeric transcription factor found in 30% of eukaryotes genes. In C. albicans it is composed of 4 major subunits, including Hap2, Hap3, Hap4, and Hap5. Hap2 and Hap5 are essential for DNA binding and function. Hap4 has 3 homologous subunits: Hap41 and Hap42 are putative subunits of CBP. Hap43 is the only Hap4 subunit …

Regulation Of Genome Architecture By Chromatin Remodeling In The Brain, Jared Vega Goodman

Arts & Sciences Electronic Theses and Dissertations

Brain development requires exquisite control of gene expression to establish and refine the proper circuitry of the nervous system. Gene expression control is under the purview of several cellular processes, including chromatin regulation in the form of DNA modification, histone modification, and nucleosome remodeling. Chromatin remodeling enzymes are the major effectors of nucleosome remodeling. These enzymes are clearly involved in brain development – mutations in chromatin remodeling enzymes are likely causative for neurodevelopmental disorders of cognition. Chromatin remodeling enzymes have discrete molecular functions and binding profiles and similarly control distinct phases of nervous system maturation. Chd4 is a Chd family …

Genetic Mouse Models Of Liver Disease: Potential Roles Of Zhx2 (Afr1) And Afr2 In Damage And Regeneration, Courtney P. Turpin

Theses and Dissertations--Pharmacology and Nutritional Sciences

The liver is the largest internal organ in mammals and responsible for carrying out various processes, including lipid and carbohydrate metabolism, detoxification of chemicals, and production of serum proteins. Liver damage, which can be caused by a variety of agents including viral infection, environmental toxins, alcohol and excessive dietary fats, can cause dysregulation of these critical functions, leading to worsening liver pathophysiology and impacting health. However, the liver has the remarkable ability to regenerate when damaged. Hepatocytes, which comprise a majority of liver cells, are relatively quiescent under healthy conditions. Upon injury, remaining hepatocytes can proliferate to recover from liver …

Employing High Probability Gene Choice Elements To Understand Singular Odorant Receptor Expression, Raena Mina

Dissertations, Theses, and Capstone Projects

The ability to detect odorous chemicals in the environment is the oldest of the senses necessary for survival, from escaping danger, finding mates, to locating food. It is said that humans can identify and discriminate up to a trillion different odor mixtures. For chemoreception to have such a high discriminatory power, would require a diverse population of cells dedicated for odor detection. These detector cells are the olfactory sensory neurons (OSNs), which express odorant receptors (ORs) that bind to chemical odors in the environment. In order to increase specificity and sensitivity, an essential property in olfaction is for each OSN …

Thyroxine-Dependent And -Independent Effects On Premature Aging And Myelination In Atrx Mutant Mice, Megan E. Rowland

Electronic Thesis and Dissertation Repository

ATRX is an ATP-dependent chromatin remodeler required to safeguard genomic integrity. Conditional deletion of Atrx in the mouse embryonic forebrain and anterior pituitary in Atrx^Foxg1Cre mice phenocopies mouse models of progeria which display increased DNA damage, coupled with reduced lifespan, growth and subcutaneous fat. These mice also have severely low circulating levels of insulin like growth factor 1 (IGF-1) and (T4) which have been reported in models of premature aging. Based on evidence that Igf1 is activated by the ligand-bound thyroid hormone receptor, I tested whether T4 supplementation could restore IGF-1 levels and ameliorate premature aging phenotypes in Atrx …

From Single Cells To Human Disease: High-Resolution Phenotyping Of Male Infertility Models Using Single-Cell Rna Sequencing, Min Jung

Arts & Sciences Electronic Theses and Dissertations

Male infertility is a complex disease that can result in significant emotional distress and treatment costs. Globally, male infertility affects 7% of males, and while its incidence is rising, its etiology remains elusive. In order to improve patient care, it is critical to identify the nature of spermatogenic failure in as many men as possible. The extensive cellular heterogeneity of testis has limited the application of bulk expression measurements to capture crucial information to dissect molecular mechanisms of defects in the infertile patients. Thus, the application of single-cell RNA-sequencing on male germ cells provides an amazing new set of scientific …

Inference And Analysis Of Multilayered Mirna-Mediated Networks In Cancer, Duc Do

Dissertations (1934 -)

MicroRNAs (miRNAs) are small noncoding transcripts that can regulate gene expression, thereby controlling diverse biological processes. Aberrant disruptions of miRNA expression and their interactions with other biological agents (e.g., coding and noncoding transcripts) have been associated with several types of cancer. The goal of this dissertation is to use multidimensional genomic data to model two different gene regulation mechanisms by miRNAs in cancer. This dissertation results from two research projects. The first project investigates a miRNA-mediated gene regulation mechanism called competing endogenous RNA (ceRNA) interactions, which suggests that some transcripts can indirectly regulate one another's activity through their interactions with …

Functional Similarity Of Prd-Containing Virulence Regulators In Bacillus Anthracis, Malik Raynor

Dissertations & Theses (Open Access)

Bacillus anthracis produces three regulators, AtxA, AcpA, and AcpB, that control virulence gene expression and are members of an emerging class of regulators termed “PCVRs” (Phosphoenolpyruvate-dependent phosphotransferase regulation Domain-Containing Virulence Regulators). AtxA controls expression of the toxin genes; lef, cya, and pag, and is the master virulence regulator and archetype PCVR. AcpA and AcpB are less well studied. AcpA and AcpB independently positively control transcription of the capsule biosynthetic operon capBCADE, and culture conditions that enhance AtxA activity result in capBCADE transcription in strains lacking acpA and acpB. RNA-Seq was used to assess the regulons of the …

Alternative Splicing Of Cytoplasmic Polyadenylation Element Binding Protein 2 Is Modulated Via Serine Arginine Splicing Factor 3 In Cancer Metastasis, James T. Deligio, James Thomas Deligio

Theses and Dissertations

Our laboratory delineated a role for alternative pre-mRNA splicing (AS) in triple negative breast cancer (TNBC). We found the translational regulator cytosolic polyadenylation element binding protein 2 (CPEB2) which has two isoforms, CPEB2A and CPEB2B, is alternatively spliced during acquisition of anoikis resistance (AnR) and metastasis. The splicing event which determines the CPEB2 isoform is via inclusion/ exclusion of exon four in the mature mRNA transcript. The loss of CPEB2A with a concomitant increase in CPEB2B is required for TNBC cells to metastasize in vivo. We examined RNAseq profiles of TNBC cells which had CPEB2 isoforms specifically downregulated to …

Transcriptional Regulation Of Cell-Type Specific Expression In The Arabidopsis Root, Keegan M. Leckie

Electronic Thesis and Dissertation Repository

Characterizing transcription factor interactions with their corresponding binding sites is crucial for understanding how gene expression is regulated by DNA sequence. A more comprehensive understanding of this process could have benefits in synthetic promoter design and creation of genetically modified organisms. Herein, the promoters of genes exhibiting cell-type specific expression within a single layer of the Arabidopsis root are analyzed to identify cis-regulatory motifs implicated in cell-type specific expression. De novo motif prediction identifies multiple motif candidates overly represented in the promoter sequences of co-expressed genes specific for epidermal, cortex, and endodermal expression. Several endodermal specific putative motifs are …

Epigenetic Regulation Of Lymphocyte Development And Transformation, Yue Huang

Arts & Sciences Electronic Theses and Dissertations

Cell identity and function rely on intricately controlled programs of gene regulation, alterations of which underlie many diseases, including cancer. Epigenetic analyses of normal and diseased cells have started to elucidate different facets of epigenetic mechanisms for gene regulation. These include changes in nucleosome density, histone modifications, factor binding and chromosomal architecture. All of these aspects contribute to the activities of regulatory elements conferring promoter, enhancer and insulator functions and the cis-regulatory circuits formed by these elements. Despite this progress, an urgent need remains to profile these features and to study how they cooperatively function in normal and pathogenic settings. …

Antisense Afp Transcripts In Mouse Liver And Their Potential Role In Afp Gene Regulation, Maria S. Dixon

Theses and Dissertations--Microbiology, Immunology, and Molecular Genetics

Hepatocellular carcinoma (HCC) is the most common form of primary liver cancer, ranking the sixth most common cancer and third most common cause of cancer mortality worldwide. Alpha-fetoprotein (AFP) is a plasma protein that is highly expressed in the fetal liver and shut off after birth. AFP expression is elevated in regenerating adult liver and HCC and has been used extensively as a diagnostic marker of liver cancer. We have been studying mouse liver gene regulation to better understand mechanisms by which changes in gene expression contribute to liver development, homeostasis and disease. Zinc Fingers and Homeoboxes 2 (Zhx2) has …

The Regulation Of The Phosphatidate Phosphatase Gene Pah1 And Its Regulatory Role On Cell Homeostasis, Goldie Libby Sherr

Dissertations, Theses, and Capstone Projects

The Saccharomyces cerevisiae gene, PAH1, encodes a phosphatidate (PA) phosphatase that plays a fundamental role in lipid metabolism. PA phosphatases are key enzymes that catalyze the PA dephosphorylation reaction to form diacylglycerides, the first step in the synthesis of triacylglycerols. Pah1p, one of the main PA phosphatases in yeast, has not only emerged as a key player in lipid biosynthetic pathways, but also acts as an important regulator of nuclear membrane biogenesis, the transcriptional regulation of many inositol-sensitive upstream activating sequence (UAS_INO)containing genes needed for phospholipid synthesis, vacuole homeostasis, and lipid droplet formation. Due to its …

The Implications Of Chromatin Remodelers' Acetylation In Ino1 Activation, Michelle M. Esposito

Dissertations, Theses, and Capstone Projects

It is known that histone acetylases (HATs) regulate gene expression, but only recently have new functional implications about remodelers’ acetylation emerged. For instance, the HAT, Gcn5p, is capable of acetylating the catalytic subunit of the nucleosome remodeling complex SWI/SNF, Snf2p, which results in the dissociation of the complex from chromatin. The implications of this acetylation and subsequent dissociation have yet to be explored with regard to transcriptional regulation and other possible mechanisms. To further understand the implications of remodeler acetylation, I used a yeast model system examining the expression of the inositol-3-phosphate synthase gene INO1. Through chromatin immunoprecipitation (ChIP) …

Expression Of Zinc Fingers And Homeoboxes 2 (Zhx2) And Zhx2 Target Genes In Multiple Tissues Of Wild-Type And Zhx2 Knockout Mice, Minen Al-Kafajy

Theses and Dissertations--Microbiology, Immunology, and Molecular Genetics

The Spear lab has had a long-standing interest in gene regulation in the liver during development and disease. Several years ago, these studies identified a novel transcriptional regulator called Zinc fingers and homeoboxes 2 (Zhx2), which is a member of a small family that includes Zhx1 and Zhx3. All Zhx proteins contain two amino-terminal C2-H2 zinc fingers and four or five carboxy-terminal homeodomains. Previous studies indicate that Zhx proteins can form homodimers and heterodimers with each other.

Zhx2 regulates numerous hepatic genes, including alpha-fetoprotein (AFP) and H19. Genes controlling lipid and cholesterol homeostasis are also regulated by …

Investigation Of Bacterial Rna-Directed Dna Methylation Via Dcm And Hfq, Dandan Li

Wayne State University Theses

Bacterial small RNAs and the RNA chaperone Hfq play crucial roles in post-transcriptional gene regulation, often as parts of stress-response pathways, but little is known about their roles in regulation of gene transcription. A recent report showed that changes in methylation patterns caused by DNA cytosine methyltransferase (Dcm) were linked to gene regulation occurring during the transition to stationary phase. Here, we show that Dcm involves in the stress responses under nutrient starvation and cold stress. Dcm and Hfq together mediate gene expression under cold stress. Hfq promotes Dcm-catalyzed cytosine methylation at specific sites near the rpoS promoter, which is …

Systems Biology Approaches To Probe Gene Regulation In Bacteria, Diogo F. Troggian Veiga

Dissertations & Theses (Open Access)

Mechanisms that allow pathogens to colonize the host are not the product of isolated genes, but instead emerge from the concerted operation of regulatory networks. Therefore, identifying components and the systemic behavior of networks is necessary to a better understanding of gene regulation and pathogenesis. To this end, I have developed systems biology approaches to study transcriptional and post-transcriptional gene regulation in bacteria, with an emphasis in the human pathogen Mycobacterium tuberculosis (Mtb).

First, I developed a network response method to identify parts of the Mtb global transcriptional regulatory network utilized by the pathogen to counteract phagosomal stresses …

Mechanistic Studies Of A Novel Ppar-Gamma Mutant That Causes Lipodystrophy And Diabetes, Olga Astapova

Wayne State University Dissertations

PPAR-gamma is a nuclear receptor that plays a central role in metabolic regulation by regulating extensive gene expression networks in adipose, liver, skeletal muscle and many other tissues. Human PPAR-gamma mutations are rare and cause a monogenetic form of severe type II diabetes with metabolic syndrome, known as familiar partial lypodystrophy. The E157D PPAR-gamma mutant causes atypical lipodystrophy in a large Canadian kindred, presenting with multiple musculoskeletal, neurological and hematological abnormalities in addition to the classic lipodystrophy features of insulin-resistant diabetes, hypertension and dyslipidemia. This mutation is localized to the p-box of PPAR-gamma, a small region that interacts directly with …

Functional Analysis Of The Cyp6a8 Gene Promoter Of Drosophila Melanogaster For Caffeine- And Phenobarbital-Inducibility By Site-Directed Mutagenesis, Olivia Nichole Hill

Masters Theses

Cytochrome P450 enzymes (CYPs), found in almost all organisms, are involved in endobiotic metabolism and detoxification of xenobiotic compounds, such as drugs, pollutants, and insecticides. In insects, CYPs play a major role in conferring resistance to various insecticides including DDT. In Drosophila and other insects, DDT-resistant strains exhibit increased expression of multiple P450 genes; however, the mechanism of overexpression is unknown. Since many CYP genes including Cyp6a8 of Drosophila are induced by caffeine and other xenobiotics, these chemicals are used as tools to understand the regulation of these genes. Previously it was shown that the 0.8-kb (-1/-732) and 0.2-kb (-1/-170) …

Modification Of Ontogenic Expression Due To Relocation Of The Ry+ Gene In Drosophila Melanogaster, Allen A. Badgett Jr.

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

The ry⁺ gene of Drosophila melanogaster and its associated enzyme, xanthine dehydrogenase, were employed in an analysis of the relationship between regulation and the location of a gene in the genome. Enzyme assays as an indication of gene activity were performed on genotypes containing zero, one and two doses of ry⁺ genes. Xanthine dehydrogenase activity of rosy genes in normal and relocated positions was determined during development.

The results indicate: 1) the gene ry⁺ is differentially active during ontogeny; 2) the activity during ontogeny is proportional to the number of ry⁺ genes present in the genome; …