Molecular Biology Commons^™

The Development Of A Comprehensive Antifungal Susceptibility Testing Assay For Vulvovaginal Candidiasis Therapy, David Hardaker

Graduate School of Biomedical Sciences Theses and Dissertations

Vulvovaginal candidiasis is the most common fungal infection of the female urogenital tract, commonly caused by Candida albicans and C. glabrata. However, treatment can be difficult when caused by non-albicans strains due to resistance to the oral antifungal drug fluconazole. The mechanism through which strains of Candida, particularly C. glabrata, develop resistance to different antifungal classes has not been completely characterized. The ergosterol biosynthesis pathway, an important component of the cell membrane, is the major target of antifungals such as fluconazole, an inhibitor of the ERG 11 gene. Current research shows that an upregulation of specific genes in C. glabrata …

Molecular Chaperone Tools For Use Against Neurodegenerative Diseases, Matthew Tinkham

Senior Honors Projects

A noted characteristic found in several neurodegenerative disorders, including Alzheimer’s Disease, Parkinson’s Disease, Huntington’s Disease and bovine spongiform encephalopathy, is the accumulation of amyloid plaques in the brain. Amyloid plaques contain deposits of fibrillar aggregates of misfolded proteins that disrupt normal functionality in neurons. Certain variants of these misfolded proteins are self-replicating; these self-replicating amyloids are termed prions (for infectious protein). We are interested in how protein misfolding contributes to amyloid formation and how molecular chaperone proteins can change the formation of amyloid deposits. Chaperone proteins function by catalyzing the proper folding of other proteins, the refolding of misfolded proteins, …

Biology And Control Of Rice False Smut Caused By Ustilaginoidea Virens (Teleomorph Villosiclava Virens), Andrew Clayton Jecmen

Graduate Theses and Dissertations

Rice false smut (FS), a disease caused by Ustilaginoidea virens (Cke.) Takahashi (1896), was first reported in northeastern Arkansas counties in 1997. The first objective of this research was to establish a collection of U. virens isolates from geographically diverse regions of Arkansas. Three U. virens isolates and chlamydospores from `Templeton' and `Clearfield-151' rice cultivars were used to determine the effects of temperature and pH on mycelial growth and germination. A nested-PCR protocol and histological methods were used to determine if U. virens infects and colonizes rice seedlings and spikelets on panicles. The sensitivity of three U. virens isolates was …

The Effect Of Small Molecule 390 On Cxcr4 Receptors, Selam B. Zenebe-Gete '14, Shruti R. Topudurti '14, Shum Andrew, Richard J. Miller

Student Publications & Research

CXCR4 is the chemokine receptor which aids in chemotaxis of stem cells, such as those in the bone marrow or the brain. SDF-1 is the natural ligand for the CXCR4 receptor. Similarities between novel molecule 390 synthesized by the Miller Lab and SDF-1 make this novel small molecule a possible agonist of the CXCR4 receptor. To determine whether 390 is an agonist to the CXCR4 receptor, we transfected cells with CXCR4 and exposed them to no agonist [vehicle control], SDF-1, or varying concentrations of our agonist drug. Next, we took calcium images using the dye fura-2, which indicates changes in …

The Use Of A Small Molecule To Improve The Thermostability Of Dna Junctions, Arik Shams

Honors Theses

The short-term goal of this research project is to employ small molecules as a means to stabilize four-way DNA junctions (4WJs) composed of natural DNA and chimeric nucleic acids. The long-term goal of the project is utilizing the 4WJs as extracellular therapeutic inhibitors of DNA binding proteins [i.e. Histones and High Mobility Group Protein B (HMGB1b)]. A number of studies have shown that classical intracellular DNA-binding proteins have a variety of deleterious side-effects when present in the extracellular milieu. In order to develop a successful 4WJ therapeutic, we are focused on using modified nucleic acids to enhance the stability of …

Numerical Assessment Of Sequence Conservation In Flu-Virus Hemagglutinin, Scott S. Norton

Honors Scholar Theses

The flu virus was investigated to find a common recognition domain to which an antibody against human-infected viruses can bind. If such a target site is structurally and electrostaticly conserved or invariant, only a single antibody would be required to attack the virus in all cases. The sequence of one of the viral surface proteins contains 24 amino acids that do not vary through mutation. However, these amino acids are neither contiguous in sequence or in space, and the ones that are associated with each other are not readily accessible to an antibody. They do provide a first impression of …

Characterization Of Udp-Arabinopyranose Mutase Genes In The Arabidopsis Cell Wall Mutant Mur5, Christopher A. Hart

Honors Scholar Theses

The genome of Arabidopsis thaliana contains several coding regions for UDP-arabinopyranose mutases (UAMs) that are also known as reversibly glycosylated polypeptides (RGPs). The mur5 cell wall mutant of Arabidopsis shows a 30% decrease in cell wall arabinose content, and a missense mutation in the Reversibly Glycosylated Polypeptide 2 gene was recently proposed to cause this mutant phenotype. Through a traditional complementation analysis, mur5 and a T-DNA insertion mutant in the RGP2 gene were shown not to complement each other, indicating that the two genes are mutant alleles of the same locus. The mur5 SNP located in RGP2 caused a more …

Functional Analysis Of Cytosolic Hsp70 Nucleotide Exchange Factor Networks In Yeast, Jennifer Lynn Abrams

Dissertations and Theses (Open Access)

The Hsp70 class of molecular chaperones play critical roles in protein homeostasis via an ATP-dependent folding cycle. Cytosolic Hsp70s in the budding yeast Saccharomyces cerevisiae, Ssa and Ssb, interact with up to three distinct nucleotide exchange factors (NEFs) homologous to human counterparts; Sse1/Sse2/HSP110, Fes1/HspBP1, and Snl1/Bag1. In an effort to understand the differential functional contributions of the cytosolic NEFs to protein homeostasis (“proteostasis”), I carried out comparative genetic, biochemical and cell biological analyses. For these studies, I developed protocols to monitor protein disaggregation and reactivation in a near real-time coupled assay that revealed the importance of aggregate dynamics in the …

Mechanisms Of Action And Co-Optive Evolution For Hypervariable Courtship Pheromones In Plethodontid Salamanders., Wilburn Beau Wilburn

Electronic Theses and Dissertations

Pheromones are an important type of chemical cue used by most animals to convey information between individuals. For more than 100 million years, male plethodontid salamanders have utilized a system of non-volatile, proteinaceous pheromones to regulate female mating behavior and receptivity. One of these pheromone components, Plethodontid Modulating Factor (PMF), is a hypervariable protein related to the three-finger protein (TFP) superfamily. Previous studies revealed that PMF persists as a rapidly evolving multi-isoform mixture. However, many characteristics of PMF as a pheromone remained undetermined, including gene structure and transcriptional regulation, translational regulation, protein structure, evolutionary mechanisms, and the isoform effects on …

Augmentation Of Ras-Induced Cell Transformation : A New Role For Mir-200a In Malignancy., Lindsey Erin Becker

Electronic Theses and Dissertations

Cancer is a multistep disease that begins with malignant cell transformation and frequently culminates in metastasis and death. MicroRNAs (miRNAs) are small regulatory 21-25-nt RNA molecules and are frequently deregulated in cancer. The majority of miRNAs are estimated to be co-expressed with neighboring miRNAs as clusters. Many miRNA clusters coordinately regulate multiple members of cellular signaling pathways or protein interaction networks. miR-200a is a member of the miR-200 family, which are known to be strong inhibitors of the epithelial to mesenchymal transition. As such, the tumor suppressive role of miR-200a in oncogenesis has been well studied; however, recent studies have …

Characterization Of Ftsa-Ftsn Interaction During Escherichia Coli Cell Division, [email protected] K. Busiek

Dissertations and Theses (Open Access)

Division of a bacterial cell into two equal daughter cells requires precise assembly and constriction of the division machinery, or divisome. The Escherichia coli divisome includes nearly a dozen essential cell division proteins that assemble at midcell between segregating sister chromosomes. FtsZ, a homolog of eukaryotic tubulin, is the first essential cell division protein to localize at midcell where it polymerizes into a ring-shaped scaffold (Z ring). Establishment of the Z ring is required for recruitment of downstream cell division proteins including FtsA, a cytoplasmic protein that tethers the Z ring to the inner membrane. Following localization of FtsA and …

Diabetes And Obesity Induce Transcriptomic And Metabolomic Changes Enhancing Pancreatic Cancer Aggressiveness, Guermarie Velázquez Torres

Dissertations and Theses (Open Access)

Pancreatic cancer is one of the most aggressive types of cancer, with poor prognosis that lacks effective diagnostic markers and therapies. It is expected that in 2014 the incidence and the mortality of pancreatic cancer in the United States will be 46,420 and 39,590 respectively. Diabetes and obesity are modifiable risk factors associated with accelerated pancreatic carcinogenesis and tumor progression, but the biological mechanisms are not completely understood. The purpose of this study is to demonstrate direct evidence for the mechanisms mediating these epidemiologic phenomena. Our hypothesis is that obesity and diabetes mellitus type 2 (DM2) accelerate pancreatic cancer and …

The Regulation Of Microrna Biogenesis By Ribosome-Interacting Proteins, Brian Pickering

Dissertations and Theses (Open Access)

MicroRNA (miRNA) are small, non-coding RNAs that affect gene expression through degradation of complementary mRNA targets or inhibition of translation. As they affect approximately 50% of all cellular processes, miRNA are tightly regulated by the cell through transcriptional and post-transcriptional mechanisms. Transcribed miRNA are capped and polyadenylated (referred to as pri-miRNA) which are cleaved by Drosha and DGCR8 to generate 60-90 nucleotide precursor miRNA. The precursors are cleaved again by Dicer and loaded into the RNA-induced silencing complex (RISC) of which Argonaute 2 is the functional component. Many of the proteins involved in miRNA biogenesis share a common role in …

The Mechanism Of Small Rna Biogenesis, Degradation, And Function In Arabidopsis, Meng Xie

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

Eukaryotic small RNAs play important roles in many biological processes through sequence-specific RNA silencing. In plants, there are mainly two small RNAs triggering gene silencing: microRNAs (miRNAs) and small interfering RNAs (siRNAs). The biogenesis and precise regulation of small RNA abundance are crucial for plant growth, development, genomic stability, and the resistance to both abiotic and biotic stresses. In this study, we used Arabidopsis thaliana, the model plant, to study the mechanism of RNA-directed DNA methylation (RdDM), in which siRNAs can trigger DNA methylation and gene silencing. In addition, we investigated the mechanism of miRNA biogenesis and degradation. For …

Clpxp Modulates Cell Growth And Morphology In Cell Shape Mutants Of E.Coli, Ryann Murphy

Senior Honors Projects

ClpXP modulates cell growth and morphology in cell shape mutants of E. coli

Ryann Murphy¹ and Jodi L. Camberg¹

¹University of Rhode Island, Department of Cell and Molecular Biology, Kingston, RI, 02881

Penicillin Binding Proteins (PBPs) are a family of prokaryotic membrane proteins named for their propensity to bind the antibiotic penicillin and are involved in remodeling and deposition of peptidoglycan. In wild type Escherichia coli cells, the uniform rod shape is conserved across generations. E.coli cells containing multiple deletions of Low Molecular Weight (LMW) PBPs exhibit irregular shapes. LMW PBP5 (dacA) is a potential …

Molecular Analyses Of Microbial Abundance And Diversity In The Water Column Of Anchialine Caves In Mallorca, Spain, Damian Menning, Liana M. Boop, Elaina D. Graham, James R. Garey

International Journal of Speleology

Water column samples from the island of Mallorca, Spain were collected from one site in Cova des Pas de Vallgornera (Vallgornera) and three sites (Llac Martel, Llac Negre, and Llac de les Delícies) in Coves del Drac (Drac). Vallgornera is located on the southern coast of Mallorca approximately 57 km southwest of Coves del Drac. Drac is Europe's most visited tourist cave, whereas Vallgornera is closed to the public. Water samples were analyzed for water chemistry using spectrophotometric methods, by quantitative PCR for estimated total abundance of microbial communities, and by length heterogeneity PCR for species richness and relative species …

Potential Targeted Therapeutic Strategies For Overcoming Resistance In Braf Wild Type Melanoma, Vito William Rebecca

USF Tampa Graduate Theses and Dissertations

Melanoma manifests itself from the malignant transformation of melanocytes and represents the deadliest form of skin cancer, being responsible for the disproportionate majority of all skin cancer deaths. The 2002 discovery that 50% of all melanoma patients possess activating BRAF mutations ignited a significant paradigm shift in the way the melanoma field approached research and how patients were treated [1]. The era of targeted therapy had begun and with it came successful targeted BRAF inhibitor therapy regimens, which have accomplished improved clinical benefit (response rate, progression free survival, and overall survival) compared with treatment with chemotherapy in three phase III …

Structure-Based Design Of Novel Inhibitors And Ultra High Resolution Analysis Of Ctx-M Beta-Lactamase, Derek Allen Nichols

USF Tampa Graduate Theses and Dissertations

The emergence of CTX-M class-A extended-spectrum β-lactamases, which confer resistance to second and third-generation cephalosporins, poses a serious health threat to the public. CTX-M β-lactamases use a catalytic serine to hydrolyze the β-lactam ring. Specifically, the hydrolysis reaction catalyzed by CTX-M β-lactamase proceeds through a pre-covalent complex, a high-energy tetrahedral acylation intermediate, a low-energy acyl-enzyme complex, a high-energy tetrahedral deacylation intermediate after attack via a catalytic water, and lastly, the hydrolyzed β-lactam ring product which is released from the enzyme complex. The crystallographic structure of CTX-M at sub-angstrom resolution has enabled us to study enzyme catalysis as well as perform …

Determining The Presence Of Carbapenem Antibiotic Resistance In Clinical Isolates, Fidelis Uzoma Enyinnaya

UNLV Theses, Dissertations, Professional Papers, and Capstones

Carbapenems are β-lactam antibiotics reserved for the treatment of severe microbial infections, especially those targeting the Enterobacteriaceae. Introduced in the 1980s, carbapenems have been used successfully in hospitals, and in the 1990s resistance was discovered. Carbapenem resistance is conferred through the production of carbapenemases. In the U.S., the most common carbapenemase is Klebsiella pneumoniae carbapenemase (KPC). In 2012, the National Healthcare Safety Network reported a carbapenem resistance rate of 13.0% among Klebsiella pneumoniae infections, and indicated that the mortality rate associated with carbapenem resistant Enterobacteriaceae (CRE) infections ranged from 48.0-71.9%. According to the Food and Drug Administration (FDA), carbapenem resistance …

Quorum Sensing Molecules For Unicellular Organisms: Spectroscopic And Computational Study Of Conformational Behavior, Daniel Tollefson

Undergraduate Research Symposium

Quorum sensing plays a vital role in unicellular communications. Until recently, it was thought that unicellular bacteria were non-cooperative; that they did not communicate among each other as a larger community. They do, in fact, communicate via small molecules that are created and released into the extracellular environment. Detailed knowledge regarding the interactions of these quorum sensing molecules (QSM) with the molecular and cellular-scale environments can lead to the manipulation of quorum sensing within a population. The function of these molecules requires that they can readily diffuse through the polar environment of aqueous solution and the nonpolar environment of cell …