Biology Commons^™

Identification Of Clonal Evolution Pattern And Mutation Event Associated With Relapsed/Refractory Diffuse Large B-Cell Lymphoma Using Next-Generation Sequencing, Cheng Wang

Theses & Dissertations

Diffuse large B-cell lymphoma (DLBCL) is an aggressive lymphoid malignancy. About 30% of DLBCL cases respond poorly to initial treatment and eventually relapse. For these patients, the current treatment regimen is quite limited, and the prognosis is poor. Gene mutations and genetic alterations play an important role in lymphomagenesis. However, the genetic alterations or gene mutations underlying the disease resistance/relapse in DLBCL are still unknown. The clonal evolution during the process of disease progression is elusive as well. Our goal is to study the genetic alterations in DLBCL, particularly paired diagnostic and relapsed/refractory DLBCL, to better understand the mutation landscape …

Mechanisms By Which Mnte-2-Pyp Suppresses Prostate Cancer Cell Growth, Yuxiang Zhu

Theses & Dissertations

Prostate cancer patients are often treated with radiotherapy. MnTE-2-PyP, is a superoxide dismutase (SOD) mimic and a known radioprotector of normal tissues. Our recent work demonstrates that MnTE-2-PyP also inhibits prostate cancer progression with radiotherapy; however, the mechanisms remain unclear. In this thesis, we identified that MnTE-2-PyP-induced intracellular H2O2 levels are critical in inhibiting growth of prostate cancer cells. We found that MnTE-2-PyP induced protein oxidations in PC3 cells and one major group of oxidized protein targets were involved in energy metabolism. The oxidative phosphorylation rates were significantly enhanced in both PC3 and LNCaP cells with MnTE-2-PyP treatment, but mitochondrial …

Engineering Mesothelin-Binding Proteins As Targeted Cancer Diagnostics And Therapeutics, Allison Rita Sirois

Doctoral Dissertations

Cancer is a significant global health concern; and traditional therapies, including chemotherapeutics, are often simultaneously toxic yet ineffective. There is a critical need to develop targeted cancer therapeutics which specifically inhibit molecules or molecular pathways essential for tumor growth and maintenance. Furthermore, a targeted therapy is only effective when a patient's tumor expresses the molecular target; therefore, companion diagnostics, including molecular imaging agents, are a necessary counterpart of targeted therapies. Mesothelin (MSLN) is a cell surface protein overexpressed in numerous cancers, including triple-negative breast, pancreatic, ovarian, liver, and lung, with limited expression in normal tissues. Aberrant MSLN expression promotes tumor …

Elucidating The Role Of Ecdysoneless In Mrna Processing, Irfana Saleem

Theses & Dissertations

The mammalian orthologue of the evolutionarily conserved Ecdysoneless (ECD) protein is required for embryogenesis, cell cycle progression and mitigation of ER stress. However, the molecular mechanisms of ECD function in mammalian cells remain unclear. Here, using mass spectrometry analysis of the mammalian ECD interactome, we identified several components of the mRNA export complexes as binding partners of ECD and then characterized the functional interaction of ECD with key mRNA export-related DEAD BOX protein helicase DDX39A and its associated partners. FISH analysis of Poly-A-tailed mRNAs revealed that ECD depletion/deletion blocks the mRNA export from the nucleus to the cytoplasm. We have …

Sine Oculis Homeobox Homolog 1 (Six1) Plays A Critical Role In The Progression Of Pulmonary Fibrosis., Cory Wilson

Dissertations & Theses (Open Access)

Idiopathic pulmonary fibrosis (IPF) is the most common idiopathic interstitial pneumonia with a median survival time of 2-4 years after diagnosis. The alarming mortality rate is due to the lack of effective treatments. IPF is a chronic disease that is characterized by alveolar destruction due to increasing extracellular matrix deposition that leads to poor lung compliance, impaired gas exchange, and ultimately respiratory failure. Repetitive alveolar epithelial injury is a central process to the underlying pathology with injury to the type II alveolar epithelial cells (AT2) specifically being a key player in the pathogenesis of IPF. Recent studies have shown that …

The Effect Of Nuclear Perturbations On The 3d Organization Of The Genome, Rosela Golloshi

Doctoral Dissertations

Cells in our body experience constant mechanical forces that influence biological functions such as growth and development. The nucleus has been implicated as a key mechanosensor and can directly influence chromatin organization and epigenetic alterations leading to gene expression changes. However, the mechanism by which such mechanical forces lead to genomic alterations and expression of mechanosensitive genes is not fully understood. The work presented in this dissertation investigates the effect of mechanical and epigenetic perturbations on the 3D genome organization. To investigate this 3D genome folding, we use Chromosome Conformation Capture followed by high throughput sequencing (Hi-C) (Chapter-1) which identifies …

Drivers Of Rickettsial Pathogen Transmission And Spillover In Local Tick Populations In Southeastern Virginia, Alexandra Cumbie

Biomedical Sciences Theses & Dissertations

Cases of spotted fever group rickettsiosis are becoming more prevalent in the United States. In Virginia, there are three human-biting ticks which are largely responsible for the spread of rickettsial pathogens and the increase in disease cases. These species include Dermacentor variabilis, Amblyomma americanum, and Amblyomma maculatum; all of which are vectors of rickettsial agents to vertebrate hosts. These species are sympatric as adults and have the potential to share large and small mammal hosts. Their interactions on and off host and their associated rickettsiae were the focus of this dissertation work. Amblyomma americanum is the vector …

Posttranslational Modification And Protein Disorder Regulate Protein-Protein Interactions And Dna Binding Specificity Of P53, Robin Levy

USF Tampa Graduate Theses and Dissertations

p53 is an intrinsically disordered transcription factor that suppresses tumor development by arresting the cell cycle and promoting DNA repair. p53 deletions or mutations can lead to cancer due to the inability of cells to respond to stress. The protein levels and post-translational modification state of p53 changes in response to cellular stress like DNA damage. Previous studies have shown that p53 can undergo coupled folding and binding with the E3 ubiquitin ligase, Mdm2, and the histone deacetylase, p300. In normal cells, p53 is kept at a low level by Mdm2, which marks it with ubiquitin, targeting p53 for proteasome …

Role Of Ceramide-1 Phosphate In Regulation Of Sphingolipid And Eicosanoid Metabolism In Lung Epithelial Cells, Brittany A. Dudley

USF Tampa Graduate Theses and Dissertations

Ceramide 1-Phosphate (C1P) is a sphingolipid metabolite which plays a large role in inflammation, cell survival and proliferation¹. C1P is known to have both pro- and anti-apoptotic roles in lung cancer cells, governed by ceramide kinase (CERK), upstream of precursor ceramide (Cer)². Previous work reveals C1P serves as the liaison between sphingolipid and eicosanoid synthesis, by decreasing the dissociation rate of group IVA cytosolic PLA₂ (cPLA_2α) from the Golgi membrane, C1P directly activates this phospholipase for downstream eicosanoid synthesis and subsequent inflammatory response³. CERK has been discovered to modulate eicosanoid synthesis, …

Molecular Identification And Characterization Of Viral Pathogens Infecting Sweet Cherry, Aaron J. Simkovich

Electronic Thesis and Dissertation Repository

Stone fruits are a valuable crop grown worldwide, however pathogens such as viruses threaten fruit production by reducing tree health and fruit yield. In an orchard within the Niagara region of Ontario, symptoms typical of viral infection such as chlorosis and leaf deformation were seen on sweet cherry (Prunus avium L.) trees. Next generation sequencing was performed on symptomatic and asymptomatic leaves and four viruses were identified. On the tree displaying the most severe symptoms, Prune dwarf virus (PDV), was the only virus detected. A survey conducted during this work showed 42% of cherry trees on a single …

Mechanisms Of Cross-Presentation By Cdc1s, Derek James Theisen

Arts & Sciences Electronic Theses and Dissertations

Classical dendritic cells (cDCs) are specialized antigen presenting cells that can be divided into distinct subsets based on the types of pathogens they respond to and the type of immune response they generate. The cDC1 subset is specialized in priming CD8 T cell responses through the process of cross-presentation. During cross-presentation, exogenous protein antigens are taken up by cDC1 and presented on MHCI molecules, allowing for the priming of CD8 T cells during conditions when DCs themselves are not directly infected. The ability to cross-present in vivo is unique to cDC1, and is essential for anti-viral responses and rejection of …

Testing The Combined Module Swapping And Repair By Modification Strategies: A Step Toward Universal Toolbox, Catherine A. Martini

Biology Theses

The crux of synthetic biology is the engineering of biological components to modulate the activity of specific DNA-based promoter(s) to drive gene expression; thus, providing a means to modulate pathways between signal detection and cellular response. However, the longstanding frustration of synthetic biologists has been the inability to transfer those engineered components between cellular systems — this lack of “modular universality” or “universal toolbox” impedes research by forcing a metaphorical reinvention of the wheel in new systems. The modular swapping strategy expanded the available “toolbox” with customizable hybrid repressors formed from “swapping” the DNA-recognition modules (DRMs) and environmental-sensing modules (ESMs) …

Structure And Evolution Of Lizard Immunity Genes, Trent Santonastaso

University of New Orleans Theses and Dissertations

One of the most important gene families to play a role in adaptive immunity is the major histocompatibility complex (MHC). MHC class II loci are considered to be the most variable loci in the vertebrate genome, and studies have shown that this variability can be maintained through complex co-evolutionary dynamics between host and parasite. Despite the rich body of research into the MHC, there is comparatively little understanding of its genomic architecture in reptiles. Similarly, loci associated with innate immunity have received little attention in reptiles compared to other vertebrates. In the first chapter, we investigated the structure and organization …

Transcriptional Control Of Virulence Genes In The Bacterial Pathogen Shigella Flexneri, Joy Asami Mckenna

UNLV Theses, Dissertations, Professional Papers, and Capstones

Shigella species, the causal agents of bacillary dysentery, use a type III secretion system (T3SS) to inject two waves of virulence proteins, known as effectors, into the human colonic epithelium to subvert host cell machinery. Transcriptional regulation of these virulence genes is controlled by the three-tiered VirF/VirB/MxiE signaling cascade. Of these, VirB has the largest regulon (~50 genes); however, VirB regulatory properties are poorly understood. To date, VirB is known to function to counter or 'anti-silence' transcriptional silencing mediated by the histone-like nucleoid structuring protein H-NS. To better understand VirB regulation, my colleagues and I chose to better define the …

Origin Of Gene Specificity In The Nitrogen-Fixing Symbiosis, Christina Marie Stonoha-Arther

Doctoral Dissertations

Many legumes form a symbiosis with nitrogen-fixing bacteria found in the soil. This relationship is beneficial to both the plant and the bacteria; the plant receives nitrogen that is otherwise limited, and the bacteria receive fixed carbon. Upon sensing the bacteria, the plant forms a new organ (the nodule) where the bacteria are housed within the cells. Many genes are required for the proper formation and function of nodules; this dissertation is broadly focused on how genes required for nitrogen-fixing symbiosis are co-opted from other cellular processes and how they are specialized for symbiosis. Protein trafficking from the plant to …

Characterization Of The Overexpression Of The Native H+-Pumping Pyrophosphatase In The Microalga Picochlorum Soloecismus, Kimberly T. Wright

Biology ETDs

Microalgae are of interest for the creation of sustainable and cost competitive alternatives to petroleum-based fuels and chemicals. However, cultivation, extraction and processing of algal biomass requires improved yields to achieve economic feasibility. The advancement of microalgal biotechnology and various genetic engineering techniques allow the improvement of microalgae biomass for this purpose. Here, the characterization of the overexpression of the native vacuolar H+ pumping pyrophosphate (AVP1) in Picochlorum soloecismus was examined. AVP1 overexpression causes biomass increase in relevant plant crops. When overexpressed in this microalga it increases carbon storage in the form of starch in a closed laboratory photobioreactor. However, …

A Health Evaluation Of Gulf Of Mexico Golden Tilefish (Lopholatilus Chamaeleonticeps) And Red Snapper (Lutjanus Campechanus) Following The Deepwater Horizon Oil Spill, Kristina Leigh Deak

USF Tampa Graduate Theses and Dissertations

A lack of baseline heath indices for offshore Gulf of Mexico (GoM) teleosts complicated impact assessments of the Deepwater Horizon (DWH) oil spill. While measurement of contaminant levels in fish after a pollution event can document exposure, such data fail to provide meaningful information about how this contact affects an animal's physiology. Controlled exposure studies have highlighted the utility of biomarkers that may indicate deleterious, long-lasting effects of pollutant exposure on various life stages of fish, however, their extrapolation to wild-caught, non-model species is challenging. In an increasingly chemically-saturated environment, it can also be difficult to separate the influence of …

Changes In Gene Expression Profiles In Müller Glia Following Exposure To An Α7 Nicotinic Acetylcholine Receptor Agonist, Megan L. Stanchfield

Masters Theses

Previous studies from this lab have determined that dedifferentiation of Müller glia (MG) occurs after application of an α7 nicotinic acetylcholine receptor agonist, PNU-282987 (PNU), to retinal pigment epithelial (RPE) cells in adult rodents. This study was designed to explore the role of the HB-EGF/Ascl1/Lin28a signaling pathway in MG dedifferentiation to retinal progenitor cells. RNAseq was performed on MG following contact with RPE-J cells treated with PNU-282987. Up- or down-regulated genes were compared with published literature of MG dedifferentiation that occurs in lower vertebrate regeneration or with transcript profiles during early mammalian development. Between 8-12 hours, up-regulation was observed in …

Insights Into Desiccation Tolerance: Properties Of Late Embryogenesis Abundant Proteins From Embryos Of Artemia Franciscana, Blase Matthew Leblanc

LSU Doctoral Dissertations

LEA proteins are a family of intrinsically disordered proteins that are expressed in various life stages of anhydrobiotic organisms and have been strongly associated with survival during water stress. The brine shrimp Artemia franciscana is the only known anhydrobiotic animal that expresses LEA proteins from Groups 1, 3, and 6. Here, I report that AfrLEA6, a novel Group 6 LEA protein, is most highly expressed in embryos during diapause and decreases throughout pre-emergence development. Notably, there is an acute drop in expression upon termination of the diapause state and the titer of AfrLEA6 during diapause is 10-fold lower than values …

Notch-Mediated Regulation Of Atrial Arrhythmogenesis, Catherine Lipovsky

Arts & Sciences Electronic Theses and Dissertations

Abnormalities in electrical impulse generation and/or propagation that affect the heartճ normal rhythm are extremely common. Clinically, cardiac arrhythmias are prevalent worldwide, yet the molecular mechanisms underlying their pathology remain largely unknown. Current treatments for arrhythmias primarily target symptoms rather than the underlying cause and these treatments have limited efficacy. The most common risk factor for developing an arrhythmia is a previous cardiac injury; however, the mechanisms underlying this are not well described. My thesis work has demonstrated that the Notch signaling pathway, which is crucial for cardiac patterning and development and is normally quiescent in adult cardiomyocytes (CMs), is …

Elucidating The Effect Of Myopathy-Causing Mutations And Second-Site Suppressors On Client Processing By J-Domain Proteins, Melanie Y. Pullen

Arts & Sciences Electronic Theses and Dissertations

Defects in protein quality control may lead to protein misfolding and aggregation often associated with protein conformational disorders such as Alzheimerճ Disease and Limb Girdle Muscular Dystrophy, among others. Molecular chaperones protect against protein misfolding and aggregation. A chaperone of interest is the ubiquitously expressed type II Hsp40 co-chaperone DNAJB6, which assists in protein folding and disaggregation. Mutations within the DNAJB6 G/F domain have been associated with the dominantly inherited disease Limb-Girdle Muscular Dystrophy type 1D (LGMD1D), now referred to as LGMDD1. Our collaborators recently discovered novel LGMDD1-associated mutations in the J-domain of DNAJB6. In the enclosed body of work, …

Development Of An In Vitro Culture System For Cryptosporidium Parvum, Georgia Wilke

Arts & Sciences Electronic Theses and Dissertations

Cryptosporidium is a genus of protozoan parasites that causes diarrheal disease in humans and other animals. There are two major species that cause disease in humans: C. parvum, which infects both humans and animals, and C. hominis, which primarily infects humans. A recent study investigating the etiologies of pediatric diarrheal illness in Africa and South Asia found that Cryptosporidium is the 2nd most prevalent cause of diarrhea in infants and may be a contributing factor to chronic malnutrition. This discovery has led to renewed interest in studying this parasite and a reexamination of the barriers to studying Cryptosporidium. The main …

Testing The Potential Of Environmental Dna: Genetic Monitoring Of Estuarine And Coastal Bottlenose Dolphin (Tursiops Truncatus) Stocks In South Carolina, Kathryn Greiner-Ferris

Electronic Theses and Dissertations

Environmental DNA (eDNA) analysis is a non-invasive monitoring technique that can detect and potentially monitor elusive marine mammals. To date, the majority of eDNA studies have been performed in freshwater environments, partially due to methodological challenges posed by higher salinities and increased dilution effects of large water masses in marine environments. The objective of this study was to design and optimize species-specific oligonucleotide PCR primers to accurately detect and quantify common bottlenose dolphin (Tursiops truncatus) eDNA collected from the marine environment and to evaluate potential trends between eDNA concentration and dolphin abundance and seasonality. Primer pairs were designed to target …

Cloning And Expression Of Hydra Innexin 2, A Gap Junction Protein Required For Coordinated Contraction Of The Body Column, Ashley O'Brien

Biology Theses

In invertebrates gap junctions are formed by the innexin family of proteins. Remarkably, the genome of Hydra magnipapillata contains 17 innexin genes. This study focused on Hydra innexin-2 (h-Inx2) which is expressed in nerve cells and plays a role in contraction of the body column. The gene sequence of H-Inx2 was obtained from the National Center for Biotechnology Information (NCBI), the gene was synthesized externally and transferred to a vector suitable for expression in Xenopus oocytes (pcDNA3.1 CT-GFP TOPO). The TOPO CT-GFP vector includes a priming site for RNA polymerase which allows in vitro preparation of RNA. Another advantage is …

Investigating The Redox Sensitivity Of Mitf Splice Variants, Rachel Berryman

Senior Theses

Within pigment-producing cells known as melanocytes, the transcription factor MITF is intimately involved in regulating genes associated with cell cycle maintenance and melanocyte differentiation. Research, however, has provided conflicting results on the relationship between the expression levels of MITF and melanocyte cell fate. To complicate matters, two splice variants of MITF exist, differing by only 18 base pairs. These variants have been observed at variable levels of expression in melanocyte and melanoma cells, raising the question as to their functional purpose. Building upon previous research by the Leachman/Cassidy lab that identified the redox sensitivity of MITF while additionally establishing a …

Rapid Evolution Of Starvation Resistance In Drosophila: Physiological And Molecular Mechanisms, Austin Joseph Mckenna

UNLV Theses, Dissertations, Professional Papers, and Capstones

The Gibbs lab has maintained starvation-selected Drosophila melanogaster for >130 generations. These starvation-selected flies evolved an obese phenotype with a suite of physiological differences compared to control-fed flies. Previous studies have shown that long-term starvation-selected Drosophila contain more lipids, have lower metabolic rates and develop more slowly than controls. This dissertation encompasses 1) Examining the molecular mechanisms contributing to starvation resistance, 2) Functional validation of the candidate plin1 allele, and 3) Rapid physiological and genomic evolution in starvation-selected Drosophila.

Starvation-selected Drosophila survive starvation conditions much longer than control-fed flies. This study took a simple approach to identify possible differences in …

The Role Of Reactive Oxygen Species In The Gut Immune Response Of Cat Fleas (Ctenocephalides Felis), Clark Hall

Honors College Theses

Fleas transmit numerous deadly and debilitating diseases, including the causative agents of murine typhus and plague. Because initial entry of these infectious agents occurs while blood feeding, the immune response in the flea gut is considered to be the first line of defense against invading microbes. However, relatively few studies have identified the flea immune molecules that effectively resist or limit infection in the gut. In other hematophagous insects, an immediate immune response to imbibed pathogens is the generation of reactive oxygen species (ROS). In this study, we utilized cat fleas (Ctenocephalides felis) to investigate whether natural infections …

Understanding How Human Lipoxygenases Bind Molecular Oxygen And Arachidonic Acid Substrate, Austin Paul Primeaux

Honors Theses

No abstract provided.

Optimization Of Methods For Cross-Species Infection Of Cell Cultures With Wolbachia, Sarah J. Lane

Honors Thesis

The common intracellular endosymbiont genus of bacteria called Wolbachia is of interest due to the promise it shows for playing a role in disease control. Wolbachia have a number of widely variable effects on its many species of host insects. In combination with these roles, Wolbachia largely affects reproduction and development of its host species. It can lead to feminization and cytoplasmic incompatibility (Werren et al. 2008). Furthermore, this species is vertically transmitted which means that it passes from mother to offspring (Caragata et al., 2016). In combination with its effects on reproduction, which can allow Wolbachia to propagate through …

Tpr-Containing Proteins Control Protein Organization And Homeostasis For The Endoplasmic Reticulum, Jill Bradley-Graham

Doctoral Dissertations

The endoplasmic reticulum (ER) is a complex, multifunctional organelle comprised of a continuous membrane and lumen that is organized into several functional regions. It plays various roles including protein translocation, folding, quality control, secretion, calcium signaling, and lipid biogenesis. Cellular protein homeostasis is maintained by a complicated chaperone network, and the largest functional family within this network consists of proteins containing tetratricopeptide repeats (TPRs). TPRs are well-studied structural motifs that mediate intermolecular protein-protein interactions, supporting interactions with a wide range of ligands or substrates. Nine TPR-containing proteins have been shown to localize to the ER and control protein organization and …