Cell Biology Commons^™

Role And Regulation Of Snon/Skil And Plscr1 Located At 3q26.2 And 3q23, Respectively, In Ovarian Cancer Pathophysiology, Madhav Karthik Kodigepalli

USF Tampa Graduate Theses and Dissertations

Ovarian cancer is one of the most common causes of gynecological cancer related deaths in women. In 2014, the estimated number of deaths due to ovarian cancer is 14,270 with occurrence of over 22, 240 new cases (National Cancer Institute, http://seer.cancer.gov/statfacts/html/ovary.html). Despite improvement in treatment strategies, the 5-year survival rate is still below 50% mainly due to chemoresistance and relapse. Amplification of chromosomal region 3q26 is a common characteristic in various epithelial cancers including ovarian cancer. This region harbors various oncogenes including the TGFβ signaling mediators EVI1 and SnoN/SkiL, PKCι and PIK3CA amplified at 3q26.2 and 3q26.3, respectively, in ovarian …

Transcriptional Regulation Of Sinorhizobium Meliloti Cell Cycle-Related Genes In The Δcbra Mutant And Root Nodules Of Medicago Sativa, Corey S. Hazekamp

Graduate Masters Theses

Sinorhizobium meliloti is a Gram-negative alphaproteobacterium and nitrogen-fixing symbiont, which undergoes a novel cell cycle modification during its' host-microbe interaction. I intend to monitor the transcriptional regulation of cell cycle-related genes during free-loving growth, in addition to monitoring their expression during symbiosis. Using genes known to be regulated by CtrA in C. crescentus or predicted to be regulated by CtrA in S. meliloti, I aim to show how certain cell cycle genes are regulated in S. meliloti. In C. crescentus, CtrA acts as a transcription factor that is active when phosphorylated and inactive when not phosphorylated. In …

Karst Estuaries: A Newly Described Ecosystem Governed By Aquifer Hydrology, Damian M. Menning

USF Tampa Graduate Theses and Dissertations

The overall goal of this dissertation is to define the hydrological, geochemical, and biological characteristics of a Karst Estuary. These types of estuaries represent a unique ecosystem created by freshwater inputs from direct flow through karst conduits and/or diffuse flow through a karst matrix. In order to determine the characteristics of a Karst Estuary we monitored short-term tidal fluctuations, long-term rainfall patterns, aquifer levels, spring discharge, multiple geochemical parameters, microbial communities in the water column and sediment, and macrofaunal communities in the sediment along a transect from a submarine spring through the Gulf of Mexico. Four sites were selected along …

Robust Meta-Analysis Shows That Glioma Transcriptional Subtyping Complements Traditional Approaches, Sanghoon Lee, Stephen Piccolo, Kristina Allen-Brady

Faculty Publications

Background Gliomas traditionally have been sub-classified
based on histopathological observations. However, this ap-
proach is subject to inter-observer variability, and histopatho-
logical features may not reflect the biological mechanisms that
drive tumor growth. High-throughput transcriptional profiling
has shown promise in objectively and reproducibly identify-
ing glioma subtypes. Most prior studies have typically used
only modest sample sizes and have sometimes overlooked
important data-processing steps to ensure sample quality and
to evaluate the robustness of quantitative findings. The pur-
pose of our study was to define robust glioma subtypes by
applying rigorous preprocessing and validation steps to 1,952
microarray samples aggregated …

Serotonergic Signaling Pathways That Suppress Amyloid Beta In Mouse Models Of Ad, Jonathan Robert Fisher

All Theses and Dissertations (ETDs)

A diagnosis of Alzheimer's disease is one of the most devastating things one can hear. This terrible disease robs people of their ability to remember cherished events as their brains become riddled with beta amyloid plaques. Alzheimer's is especially terrifying because there currently are no effective treatments for slowing or stopping the disease. However, recent research has shown that plaque formation is correlated to concentrations of amyloid beta. This discovery suggests that limiting amyloid beta production could potentially halt the disease. One promising avenue for slowing amyloid beta production is serotonergic signaling.

This dissertation presents evidence for a direct sequence …

Electrophoresis Staining: A New Method Of Whole Mount Staining, Mitchell G. Ayers, Sarah Calve, Zhiyu Li

The Summer Undergraduate Research Fellowship (SURF) Symposium

Advances in tissue clearing techniques have allowed almost a ten-fold increase in the viewing depth of confocal microscopy. This allows for intact cellular structures to be rendered in 3D. However, viewing tissues to this depth is often limited to endogenous fluorescence as passive diffusion of antibodies via whole mount staining can take weeks. Our lab is developing a new method involving electrophoresis as a driving force that will promote active antibody binding deep into tissue, reducing the amount of time needed to stain for cellular structures. Due to the inherent charge within antibodies, they are able to be directionally forced …

Antiviral Responses In Mouse Embryonic Stem Cells: Differential Development Of Cellular Mechanisms In Type I Interferon Production And Response, Ruoxing Wang

Dissertations

Embryonic stem cells (ESCs) have been recognized as a promising cell source for regenerative medicine. Intensive research over the past decade has led to the possibility that ESC-derived cells will be used for the treatment of human diseases. However, increasing evidence indicates that ESC-derived cells generated by the current differentiation methods are not fully functional. It is recently recognized that ESC-derived cells lack innate immunity to a wide range of infectious agents and inflammatory cytokines. When used in patients, ESC-derived cells would be placed in wounded sites that are exposed to various pathogens and inflammatory cytokines; therefore, their viability and …

Identification And Characterization Of Msab Gene Involved In Biofilm Formation And Virulence In Staphylococcus Aureus, Amelsaad Elbarasi

Master's Theses

Staphylococcus aureus is an important human pathogen that causes a wide variety of life-threatening infections ranging from minor skin and oral infections to severe infections, such as bacteremia, pneumonia, osteomyelitis, or endocarditis due to the presence and secretion of a large number of virulence factors that are controlled by global virulence regulators in complex networks. Furthermore, S. aureus infections have become a threat to public health because of their high potential to form biofilm, and their ability to resist a wide range of antibiotics has exacerbated further. Therefore, understanding the regulatory networks and developing a drug targeting these networks has …

Role Of Msaa Gene In Regulation Of The Msaabcr Operon And Biofilm Development In Staphylococcus Aureus, Ahmed Alzuway

Master's Theses

Staphylococcus aureus is an important human pathogen that causes wide variety of diseases ranging from chronic biofilm associated infection to acute life threatening infection such as bacteremia, pneumonia, osteomyelitis, or endocarditis, despite the progress with antibiotics used in the treatment of bacterial infections. Furthermore, increased use of prosthetic and indwelling devices in modern medical practices has led to increased infections due to S. aureus. Treating S. aureus infections have become difficult owing to its ability to resist most of the antibiotics; this problem is further exacerbated by ability of MRSA strains to form biofilms. Emergence of community-acquired methicillin resistance …

Strategies To Sensitize Bladder Cancer Cells To Small Molecule Inhibitors Targeting The Pi3k Pathway, Giovanni Nitti

Dissertations and Theses (Open Access)

After many years of cancer research, it is well accepted by the scientific community that the future cure for this disease lies in a personalized therapeutic approach. Anticipating therapeutic outcome based on the genetic signature of a tumor has become the new paradigm. The PI3K pathway represents an ideal target for bladder cancer, as many of the key proteins of this pathway are altered or mutated in this particular type of cancer. Several small molecule inhibitors have been developed to target this pathway, but their efficacy has been shown to be heterogeneous among different cell lines and mostly cytostatic but …

Roles For B-Raf Kinase In The Specific Regulation Of Α4Β1 Integrin In T Cells, Wells S. Brown

Dissertations and Theses (Open Access)

The regulation of integrin-mediated adhesion is of vital importance to adaptive and innate immunity. Integrins are versatile proteins and mediate T cell migration and trafficking by binding to ECM or other cells, as well as initiating intracellular signaling cascades promoting survival or activation. The mitogen activated-protein kinase (MAPK) pathway is known to be downstream from integrins and regulate survival, differentiation, and motility. However, secondary roles for canonical MAPK pathway members are being discovered. We show chemical inhibition of RAF by Sorafenib or shRNA-mediated knockdown of B-Raf reduces T cell resistance to shear stress to α4β1 integrin ligands vascular cell adhesion …

Egfr Modulates Microrna Maturation In Response To Hypoxia Through Phosphorylation Of Argonaute2, Jia Shen

Dissertations and Theses (Open Access)

MicroRNAs (miRNAs) are generated by two-step processing to yield small RNAs that negatively regulate target gene expression at posttranscriptional level. Deregulation of miRNAs has been linked to diverse pathological processes, including cancer. Recent studies have also implicated miRNAs in regulatory roles to cope with a spectrum of stresses, such as hypoxia, which is frequently encountered in the poorly angiogenic core of a solid tumor. However, the upstream regulators of miRNA biogenesis machineries remain obscure, raising the question of how tumor cells efficiently coordinate and impose specificity on miRNA expression and function in response to stresses. Here, we show that EGFR, …

Brit1/Mcph1 Mediates The Dna Damage Response By Inducing P53 Stability And Promoting Atr Signaling, Edward Wang

Dissertations and Theses (Open Access)

The BRCT-repeat inhibitor of hTERT (BRIT1)/MCPH1 protein promotes the process of homologous recombination (HR) to repair DNA double strand breaks (DSBs). In response to DSBs, BRIT1 foci form at damaged sites, and recruits downstream repair proteins including 53BP1, MDC1, NBS1, and the SWI/SNF complex to the DSB region to promote DNA repair. BRIT1 copy number deficiency correlates with increased genomic instability in ovarian cancer specimens and breast cancer cell lines. Here, we propose that additional functions of BRIT1 include a direct interaction with the p53 tumor suppressor protein to promote p53 stability, and binding and recruitment of TopBP1 to sites …

Energy Stress Causes Chaperones To Assemble Into Cytoplasmic Complexes, Kimberly J. Cope

Dissertations and Theses (Open Access)

The majority of proteins require molecular chaperones to assist their folding into tertiary and quaternary structures. Certain stresses can compromise the weak hydrophobic forces responsible for these structures and lead to protein unfolding, misfolding, and aggregation. Aggregates of proteins are hallmarks of devastating diseases such as Alzheimer’s, Parkinson’s, and Huntington’s diseases. Fortunately, bacteria, plants, and fungi have a potent disaggregase, named Hsp104 in Saccharomyces cerevisiae. Recently, heat-induced aggregates, termed Q-bodies, were found to contain three molecular chaperones: Hsp70, Hsp104, and Hsp42. Their coalescence from small puncta into larger inclusions required Hsp104. During glucose deprivation, a stress that isn’t known to …

Impedance Biosensors For The Rapid Detection Of Viral And Bacterial Pathogens Using Avian Influenza Virus Subtypes H5n1 And H7n2 And Escherichia Coli O157:H7 As Model Targets, Jacob David Lum

Graduate Theses and Dissertations

This research investigated impedance biosensors for the rapid detection of viral and bacterial pathogens using avian influenza virus (AIV) subtypes H5N1 and H7N2 and Escherichia coli O157:H7 as the model targets, which were chosen due to their impact on the agricultural and food industries. For the detection of AIV H7N2, a single stranded DNA aptamer was selected using systematic evolution of ligands by exponential enrichment (SELEX). The selected aptamer and a previously selected aptamer against AIV H5N1 were used in a microfluidics chip with an embedded interdigitated array microelectrode to fabricate an impedance biosensor for specific detection of AIV H7N2 …

Construction Of 3d Biomimetic Tissue Niches For Directing Pancreatic Lineage Differentiation Of Human Embryonic Stem Cells, Weiwei Wang

Graduate Theses and Dissertations

The potential of human embryonic stem cells (hESCs) to differentiate into insulin producing beta cells offers great hope for cell-based therapy for diabetes treatment. However, in vitro pancreatic differentiation of hESCs remains challenging. In the past decade, most protocols for differentiating pancreatic cells have been focused on the use of signaling molecule cocktails on 2D substrates. Studies on embryonic development biology strongly suggest that extracellular matrix (ECM) plays a critical role on hESCs behavior. In this work, we first established a 3D collagen scaffold culture system for hESCs differentiating into definitive endoderm (DE), which is the first and most important …

Caspase-Dependent Signaling Underlies Glioblastoma Cell Death In Response To The Fungal Metabolite, Fusarochromanone, Elahe Mahdavian, Monique Marshall, Patrick M. Martin, Patrice Cagle, Brian A. Salvatore, Quincy A. Quick

Biology Faculty Research

Fungal metabolites continue to show promise as a viable class of anticancer agents. In the present study, we investigated the efficacy of the fungal metabolite, fusarochromanone (FC101), for its antitumor activities in glioblastomas, which have a median survival of less than two years and a poor clinical response to surgical resection, radiation therapy and chemotherapy. Using clinically applicable doses, we demonstrated that FC101 induced glioblastoma apoptotic cell death via caspase dependent signaling, as indicated by the cleavage of poly(ADP-ribose) polymerase, glioblastoma (PARP). FC101 also induced differential reactive oxygen species (ROS) levels in glioblastoma cells, contrasting a defined role of oxidative …

Effects Of Nutritional Level Of Concentrate‐Based Diets On Meat Quality And Expression Levels Of Genes Related To Meat Quality In Hainan Black Goats, Dingfa Wang, Luli Zhou, Hanlin Zhou, Guanyu Hou, Liguang Shi, Mao Li, Xianzhou Huang, Song Guan

Faculty Publications

The present study investigated the effects of the nutritional levels of diets on meat quality and related gene expression in Hainan black goat. Twenty-four goats were divided into six dietary treatments and were fed a concentrate-based diet with two levels of crude protein (CP) (15% or 17%) and three levels of digestive energy (DE) (11.72, 12.55 or 13.39 MJ/kg DM) for 90 days. Goats fed the concentrate-based diet with 17% CP had significantly (P < 0.05) higher average daily gains (ADG) and better feed conversion rates (FCR). The pH 24h value tended to decrease (P < 0.05) with increasing DE levels. The tenderness of Longissimus dorsi muscle (LD) and Semimembranosus muscle (SM) reduced with increasing CP levels (P < 0.05). With increasing DE levels, tenderness was increased (P < 0.05). The heart fatty acid-binding protein (H-FABP) mRNA expression levels in LD and SM increased with increasing DE levels (P < 0.05), but decreased with increasing CP levels (P < 0.05). The calpastatin (CAST) and μ-calpain mRNA expressions levels in LD and SM were affected significantly (P < 0.05) by CP and DE levels in the diet. Therefore, the nutritional levels of diets affect meat quality and expression levels of genes associated with meat quality in Hainan black goats.

Bi-Directional Signaling Between Melanoma And The Microenvironment Generates A Protective Niche That Mediates Therapeutic Escape, Inna Fedorenko

USF Tampa Graduate Theses and Dissertations

Very few cancer patients are cured through drug therapy alone, with the majority exhibiting acquired resistance. To date, most studies of therapeutic escape have focused upon tumor-intrinsic mechanisms of drug resistance with little attention paid to the role of normal host cells in preventing complete tumor eradication. In the present study we implicate co-operative bi-directional signaling between melanoma cells and fibroblasts in the generation of a pro-survival niche that mediates drug resistance. Mass-spectrometry based phosphoproteomics was used to show that BRAF inhibition and chemotherapy drugs enhanced the survival of both melanoma cells and fibroblasts through the induction of fibronectin (FN)/integrin …

Regulation Of Strand-Specific Processing In Human Pre-Mir-371 And Its Mouse Homologs, Jianting Shi

Graduate School of Biomedical Sciences Theses and Dissertations

MicroRNAs (miRNAs) are small noncoding RNAs, known to regulate genes by inducing target mRNA degradation or translational repression. This regulatory function has been shown to assist developmental timing control and increasingly more evidence reveals some of the miRNAs may have tissue/cell type-specific function, showing the potential to assist cell differentiation. Mouse miR-290-295 cluster is embryonic stem cell (ESCs)-specific miRNA cluster and human miR-371-373 cluster has been verified to be its functional homolog. We have previously demonstrated that human pre-miR-371 is processed into multiple miRNA species, which represent the seeds of the mouse of miR-290-5p, miR-292-5p, miR-292-3p-iso2 and miR-293-3p. Deep sequencing …

Case Study: From Gummy Bears To Celery Stalks: Diffusion And Osmosis, Kevin M. Bonney

Publications and Research

The article describes a case study which interperses information on diffusion and osmosis with content review and knowledge application questions, as well as simple experiment that can be conducted without the use of a laboratory. Topics discussed include biological membranes, the use of gummy bears to demonstrate osmosis and osmosis in animal cells. Also mentioned is osmosis in plants. It notes that the case study was developed for use in an introductory undergraduate biology course.

Key Residues Of Human Cytoplasmic Protein Tyrosine Phosphatase-A And -B For Substrate Binding And Specificity, Byunghyun Park

Open Access Theses

Reversible tyrosine phosphorylation plays an important role in signaling pathways that are essential for regulating cellular growth, differentiation and metabolism. Moreover, several human diseases such as diabetes, obesity and cancers are associated with the deregulation of protein tyrosine phosphatases (PTPs). Several studies provide evidence that PTPs not only contribute to cellular differentiation, but over-expression of these molecules also leads to transformation of non-transfomed cells as well. Based on these results, designing specific PTP inhibitors may ultimately function as potential therapeutic agents to treat various diseases including cancer, diabetes, and autoimmune diseases. EphA2 is a receptor tyrosine kinase which is hypo-phosphorylated …

Experimental And Computational Analysis Of The Synucleins, Agatha Munyanyi

Theses and Dissertations in Biomedical Sciences

The synuclein proteins α, β and γ which are located in the brain, have been a subject of intense research. Of particular interest is α-synuclein, which is found in misfolded forms in Lewy bodies that are associated with Parkinson's disease. Despite the efforts of researchers across the world, the physiological structure and function of the synucleins remains elusive. In recent years, highly controversial reports by some investigators indicate that in its natural form, α-synuclein exists as a tetramer instead of as an intrinsically unstructured monomer. This dissertation presents results of the experimental and computational analysis of the synucleins. First, we …

Phosphoinositides: Minor Lipids Make A Major Impact On Photoreceptor Cell Functions, Raju V. S. Rajala, Ammaji Rajala, Andrew J. Morris, Robert E. Anderson

Internal Medicine Faculty Publications

Activation of the phosphoinositide (PI) cycle generates the second messengers that control various aspects of cellular signaling. We have previously shown that two PI cycle enzymes, type II phosphatidylinositol 5-phosphate 4-kinase (PIPK IIα) and phosphoinositide 3-kinase (PI3K), are activated through light stimulation. In our earlier studies, we measured enzyme activities, instead of directly measuring the products, due to lack of sensitive analytical techniques. Cells have very low levels of PIs, compared to other lipids, so special techniques and sensitive analytical instruments are necessary for their identification and quantification. There are also other considerations, such as different responses in different cell …

Manipulating The Tumor Microenvironment For Therapeutic Benefit, Kate M. Bailey

USF Tampa Graduate Theses and Dissertations

The physical tumor microenvironment contributes significantly to carcinogenesis, cancer progression and metastatic dissemination. Two main components of the tumor microenvironment, hypoxia and acidosis, are present in nearly every solid tumor and act as powerful selection forces against the tumor. Hypoxia and acidosis promote tumor heterogeneity and contribute to chemotherapy and radiotherapy resistance. This dissertation interrogates methods to target the tumor microenvironment including two novel studies describing mechanisms of buffer therapy resistance and targeting tumor hypoxia with vasodilators to enhance the efficacy of a hypoxia activated prodrug, TH-302.

In the first study, mechanisms of buffer therapy resistance were identified and detailed. …

Fty720 (Fingolimod) Provides Insight Into The Molecular Mechanisms Of Multiple Sclerosis, Madelyn Elizabeth Crawford

Pursuit - The Journal of Undergraduate Research at The University of Tennessee

Multiple sclerosis (MS) is a neurodegenerative disorder caused by a prolonged immune- mediated inflammatory response that targets myelin. Nearly all of the drugs approved for the treatment of MS are general immunosuppressants or only function in symptom management. The oral medication fingolimod, however, is reported to have direct therapeutic effects on cells of the central nervous system in addition to immunomodulatory functions. Fingolimod is known to interact with sphingosine-1-phosphate (S1P) receptors, and the most widely- accepted theory for its mechanism of action is functional antagonism of the receptor. This review examines significant neuromodulatory effects achieved by functional antagonism of the …

Identification Of Novel Small Rnas And Characterization Of The 6s Rna Of Coxiella Burnetii, Indu Warrier, Linda D. Hicks, James M. Battisti, Rahul Raghavan, Michael F. Minnick

Biology Faculty Publications and Presentations

Coxiella burnetii, an obligate intracellular bacterial pathogen that causes Q fever, undergoes a biphasic developmental cycle that alternates between a metabolically-active large cell variant (LCV) and a dormant small cell variant (SCV). As such, the bacterium undoubtedly employs complex modes of regulating its lifecycle, metabolism and pathogenesis. Small RNAs (sRNAs) have been shown to play important regulatory roles in controlling metabolism and virulence in several pathogenic bacteria. We hypothesize that sRNAs are involved in regulating growth and development of C. burnetii and its infection of host cells. To address the hypothesis and identify potential sRNAs, we subjected total RNA isolated …

Chlorovirus Skp1 And Core Ankyrin-Repeat Protein Interplay And Mimicry Of Cellular Ubiquitin Ligase Machinery, Eric Andrew Noel

School of Biological Sciences: Dissertations, Theses, and Student Research

The ubiquitin-proteasome system is a common target of several unrelated viruses that have evolved convergent strategies to redirect host ubiquitin machinery to serve their own needs. Members of the genus Chlorovirus, a group of large dsDNA viruses that infect certain freshwater chlorella-like green algae, encode a conserved Skp1 homolog and ankyrin-repeat (ANK) proteins, some of which contain C-terminal domains characteristic of cellular F-boxes or related viral PRANC domains. These observations suggested that this unique combination of chlorovirus proteins either interact with or imitate the key components of the SCF (Skp1-Cul1-F-box) ubiquitin ligases. Using mass spectrometry, we identified two functional …

The Role Of The N-Terminus On The Enzymatic Activity Of Dutpase From Dictyostelium Discoideum, Kyle C. Varon

School of Biological Sciences: Dissertations, Theses, and Student Research

The enzyme deoxyuridine triphosphatase (dUTPase) (EC 3.6.1.23) converts dUTP to dUMP, thus shifting the dUTP to dUMP ratio in the cell. The molecule dUTP is subject to mis-incorporation into DNA due to lack of distinguishing by DNA polymerase. Uracil incorporation can be repaired with base excision repair mechanisms but may create overwhelming DNA strand breaks proving to be detrimental to the cell. Most dUTPases of eukaryotes are homotrimeric and contain five highly conserved motifs responsible for catalysis and substrate binding. Many dUTPases of eukaryotes possess a leading and core region in their sequence. The core region is composed of the …

Localization And Functional Analysis Of Dictyostelium Discoideum Gtpases, Rabs And Rab2, Katherine V. Maringer

Theses and Dissertations

Dictyostelium discoideum is a simple eukaryotic amoeba that has proven useful in studying various aspects of endosomal and lysosomal membrane trafficking, as well as development. The Rab family of small molecular weight GTPases has been implemented in several cellular processes to include various vesicle trafficking roles, cell-cell signaling, and development. This study focuses on the localization and function of two Dictyostelium GTPases, RabS, and Rab2 which we hypothesized to both localize to the Golgi, and the contractile vacuole system. Expression of GFP-tagged DdRab2, and DdRabS proteins revealed similar localization to ER-Golgi membranes as well as the contractile vacuole system. Microscopic …