Digital Commons Network^™

Characterization Of A Hypothetical Protein Critical For The Symbiotic Interaction Of Aeromonas Veronii And Hirudo Verbana, Kaitlin Vaughan

Honors Scholar Theses

The digestive tract symbiosis of the medicinal leech, Hirudo verbana, is a model system for studying the genes required for microbial colonization of digestive tracts, as H. verbana has only two species of bacteria that dominate the crop microbiota, Aeromonas veronii and a Rikenella-like bacterium. Signature-tagged mutagenesis (STM) of the A.

veronii strain, HM21R, revealed genes required for the colonization of the digestive tract. One of these mutants, JG573, has an interrupted gene that is predicted to encode a hypothetical protein. The region flanking the transposon insertion of this mutant was sequenced by primer walking.

Comparison of the flanking DNA …

Contribution Of The Novel C-Terminal Domain To The Ribosome Binding Activities Of Virulence Regulator Bipa, Heeren Makanji

Honors Scholar Theses

Bacterial GTPases regulate many cell functions, including the stress response, signal recognition, protein synthesis, and cell differentiation, through a molecular switch that is activated and deactivated depending on their nucleotide bound state (1). A member of the translational family of bacterial GTPases along with LepA and EF-G, BipA is a 67 kD protein that is essential for virulence and the stress response. Crystal structures from the Robinson lab have shown a unique C-terminal domain on BipA that has been implicated in ribosome binding. Using N-terminal deletion constructs, we have shown that the C-terminal domain is necessary, but not sufficient, to …

Knockdown Of Kiaa0319 Reduces Dendritic Spine Density, Daniel Young Kim

Honors Scholar Theses

Developmental Dyslexia is a reading disorder that affects individuals that possess otherwise normal intelligence. Until the four candidate dyslexia susceptibility genes were discovered, the cause of cortical malformations found in post mortem dyslexic brains was unclear. Normal brain development is crucial for the proper wiring of the neural circuitry that allow an individual to perform cognitive tasks like reading. For years, familial and twin studies have suggested that there was a genetic basis to the causation of dyslexia. Kiaa0319 was among the candidate dyslexia susceptibility genes that were ascertained. KIAA0319 is located on Chromosome 6p22.2-22.3 and has been found to …

Genetic Variations In A Well Conserved 5-Untranslated Region Of Hepatitis C Virus Genome Isolated In Pakistan, Anila Yasmeen, Anwar Ali Siddiqui, Saeed Hamidb, Taranum Sultana, Wasim Jafri, Mats A.A. Perssonc

Department of Biological & Biomedical Sciences

The diversity and extent of sequence variations between hepatitis C virus (HCV) isolates from Pakistan were studied and the probable effects of these variations were assessed on secondary viral structures. Sequencing and phylogenetic analysis was performed on 33 samples, of which 25 were typed as genotype 3 by RFLP (restriction fragment length polymorphism) and 8 remained unresolved. Rooted neighbour-joining (NJ) tree revealed that 28 isolates were HCV type 3a and 5 isolates were typed as 3b. The majority of unresolved samples clustered in a different branch of genotype 3, supported by a bootstrap value of 71%. Another, cluster, cluster I, …

Improved Red-Emitting Firefly Luciferase Mutant For Biotechnical Applications, Audrey L. Davis

Chemistry Honors Papers

Luciferase from the North American firefly Photinus Pyralis catalyzes a highly efficient bioluminescent reaction that produces yellow-green light (557 nm at pH 7.8). This bioluminescence system has been adapted for a variety of applications including gene reporter assays, detection of bacteria and toxins, whole-cell biosensor measurements, and in vivo imaging. A luciferase variant with a red-shifted bioluminescence spectra and high specific activity, two qualities that are challenging to achieve simultaneously, would be especially useful when paired with a green-emitting enzyme in a dual-color reporter assay, or used alone for improved imaging in living animals.

Our lab previously reported a red-emitting …

Human Cerebral Neuropathology Of Type 2 Diabetes Mellitus, Peter T. Nelson, Charles D. Smith, Erin L. Abner, Frederick A. Schmitt, Stephen W. Scheff, Gregory J. Davis, Jeffrey N. Keller, Gregory A. Jicha, Daron Davis, Wang-Xia Wang, Adria Hartman, Douglas G. Katz, William R. Markesbery

Pathology and Laboratory Medicine Faculty Publications

The cerebral neuropathology of Type 2 diabetes (CNDM2) has not been positively defined. This review includes a description of CNDM2 research from before the ‘Pubmed Era’. Recent neuroimaging studies have focused on cerebrovascular and white matter pathology. These and prior studies about cerebrovascular histopathology in diabetes are reviewed. Evidence is also described for and against the link between CNDM2 and Alzheimer's disease pathogenesis. To study this matter directly, we evaluated data from University of Kentucky Alzheimer's Disease Center (UK ADC) patients recruited while non-demented and followed longitudinally. Of patients who had come to autopsy (N = 234), 139 met …

Purification Of Proteorhodopsin By Using Citrate And Phosphate To Induce Selective Precipitation, Jonathan Kim

Renée Crown University Honors Thesis Projects - All

Abstract not Included

Identifying Proteins That Interact With The Novel Saccharomyces Cerevisiae Proteins Pdr19 And Pdr20 And Bioinformatic Characterization Of Genes Involved In Ttg Cellular Responses, Casey White

Renée Crown University Honors Thesis Projects - All

One of the most critical structures in cellular biology is the plasma membrane, due to its ability to respond to environmental stresses. Saccharomyces cerevisiae is a model, single-celled eukaryote that has been used to investigate many aspects of cell biology. A recent genetic screen in yeast for plasma membrane homeostatic proteins identified three related proteins of unknown molecular function that participate in these processes. These proteins, termed PDR19, PDR20, and PDR21 for Pleiotropic Drug Resistance, are each approximately one hundred amino acids in size and share a small conserved domain, namely the core sequence KITRYDL. In the case of PDR21 …

Enhancing Bacterial Expression Of Mammalian Gprotein Coupled Receptors The Creation Of A Proteorhodopsin‐Bovine Rhodopsin Chimera, Chauncey Brown Jr.

Renée Crown University Honors Thesis Projects - All

Bovine (cow) rhodopsin is a 7‐transmembrane (7TM), lightabsorbing protein located in rod cells. It is activated by the photoisomerization of retinal, a Vitamin A derivative. This light‐triggered reaction activates the G‐Protein Coupled Receptor (GPCR), resulting in a signaling cascade within the cell. When previously cloned in an E. coli expression vector in the Braiman Lab, bovine rhodopsin expression was not successful, possibly due to E. coli’s lack of recognition of the foreign Nterminus portion of the protein, which may be a prerequisite for proper folding and insertion into the membrane. Our proposed solution is to create a chimera protein, replacing …

Fatal Flu: History, Science, And Politics Of The 1918 Influenza Pandemic, Suzanne Vroman

Renée Crown University Honors Thesis Projects - All

In 1918 an influenza pandemic killed over 50 million people world wide including 675,000 in the United States alone. This Capstone Thesis asks the question: what caused the 1918 pandemic to become so fatal? In order to understand how the influenza outbreak of 1918 turned into one of the world’s deadliest pandemics, I took a unique approach to tackling the mystery of the “Spanish Influenza,” by interpreting the high fatality rate from both a social and natural scientific approach. This project is broken into two parts.

The first part of this paper gives a historical analysis of the 1918 …

Generation Of An Fsh Inducible Inh-[Alpha]-Flag-Gg-Icer I[Gamma] Ovarian Specific Gene Construct, Goce Bogdanoski

Theses, Dissertations and Culminating Projects

Avian animal models have led to many essential discoveries in molecular biology and biochemistry, including the discovery of vitamins, the chemistry behind vision and the development of transgenic hens as natural bioreactors for pharmaceutically relevant proteins. Hyperovulation in domesticated hens is considered a highly desirable genetic trait, a feature that has been explored in multiple studies and remains the focus of many biotech companies. Unlocking the molecular mechanism that controls ovulation may provide a basis for development in new reproductive technologies.

Previous research done on rodents provided data and identified a single transcription factor, the Inducible cAMP Early Repressor (ICER), …

Methyl Septanoside Hydrolysis As A Measure Of Carbohydrate Ring Flexibility: Substrate Synthesis And Kinetics Analysis, Shawn Michael Miller

Honors Scholar Theses

A number of seven-membered ring systems have been found to have promising enzyme inhibiting properties. The common explanation for their efficacy is the apparent improved flexibility that the ring-system has over smaller rings. In an attempt to probe the validity of this hypothesis, unnatural seven-membered ring carbohydrates have been generated and subjected to kinetics analysis using hydrolysis. In particular, methyl α- and β-D-glycero-D-guloseptanoside were subjected to acid-catalyzed hydrolysis and monitored via HNMR experiments. The rate constants of the reactions were determined and compared to the hydrolysis rate constants of comparable pyranose carbohydrates and found to be significantly faster, indicating an …

Characterization Of The Substrate Specificity And Mechanism Of Protein Arginine Methyltransferase 1, Whitney Lyn Wooderchak

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

Protein arginine methyltransferases (PRMTs) posttranslationally modify protein arginine residues. Type I PRMTs catalyze the formation of monomethylarginine (MMA) and asymmetric dimethylarginine (ADMA) via methyl group transfer from S-adenosyl methionine onto protein arginine residues. Type II PRMTs generate MMA and symmetric dimethylarginine. PRMT-methylation affects many biological processes. Although PRMTs are vital to normal development and function, PRMT-methylation is also linked to cardiovascular disease, stroke, multiple sclerosis, and cancer.

Thus far, nine human PRMT isoforms have been identified with orthologues present in yeast, plants, and fish. PRMT1 predominates, performing an estimated 85% of all protein arginine methylation in vivo. Yet, the substrate …

Characterization Of The Catalytic Mechanism Of The Carboxyltransferase Component Of Escherichia Coli Acetyl-Coa Carboxylase Leading To Rational Inhibitor Identification And The Development Of Enzymatic Mimics, Nabil K. Thalji

Honors Capstones

No abstract provided.

Understanding The Role Of Histones During Chromosome Segregation: A Study Of The Effects Of Histone Gene Dosage In Saccharomyces Cerevisiae, Rebecca Leigh Danforth

Graduate Theses and Dissertations

Chromatin plays a role in all cellular functions that involve DNA. These include, but are not limited to replication, recombination, transcription, and chromosome segregation. Chromosome segregation is an extremely well conserved cellular process and is essential for maintaining the genetic integrity of a cell. There is very strong evidence indicating that chromatin structure is critical for maintaining the fidelity of chromosome transmission, but its specific role(s) in this process remains unclear. Chromatin is comprised of arrays of nucleosomes that serve to compact DNA. These nucleosomes consist of 146 bp of DNA that is wrapped around a histone octamer; two each …

The Membrane Interface Of Chloroplast Signal Recognition Particle-Dependent Protein Targeting, Naomi Jane Marty

Graduate Theses and Dissertations

A novel signal recognition particle (SRP) found in the chloroplast (cpSRP) works in combination with the cpSRP receptor, cpFtsY, to facilitate the post-translational targeting of a family of nuclear-encoded thylakoid proteins to the Alb3 translocase in thylakoid membranes. Work here focused on understanding events at the membrane that take place to ensure targeting of the cpSRP-dependent substrate to Alb3. Specifically, we sought to understand the structural and functional role of membrane binding by cpFtsY, a protein that exhibits the ability to partition between the membrane (thylakoid) and soluble (stroma) phase during protein targeting. We also sought to understand whether a …

The Small Molecule Bcl-2 Inhibitor Ha14-1 Potentiates The Lethality Of A Regimen Combining Mek1/2 And Chk1 Inhibitors In Multiple Myeloma Cells, Leena Youssefian

Theses and Dissertations

Previously, we have found that the co-administration of MEK1/2 inhibitors and Chk1 inhibitors synergistically induce multiple myeloma cell apoptosis through upregulation of the BH3-only pro-apoptotic protein Bim. However, these apoptotic events were largely blocked by the characteristic over-expression of Bcl-2 of Bcl-xL in multiple myeloma cells. HA14-1, a small molecule Bcl-2 inhibitor, may therefore circumvent this resistance to apoptosis by blocking Bcl-2 and Bcl-xL anti-apoptotic protein actions. In our project, we hypothesize that the co-administration of HA14-1 with MEK/Chk1 inhibitors will enhance apoptosis in multiple myeloma (MM) cells. To test this hypothesis, we exposed MM cells U266 and RPMI8226, or …

A Comparative Study Of The Structural Features And Kinetic Properties Of The Mofe And Vfe Proteins From Azotobacter Vinelandii, Miguel Alejandro Pabon Sanclemente

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

Biological nitrogen fixation is accomplished in the bacterium Azotobacter vinelandii by means of three metalloenzymes: The molybdenum, vanadium, and iron-only nitrogenase. The knowledge regarding biological nitrogen fixation has come from studies on the Mo-dependent reaction. However, the V- and Fe-only-dependent reduction of nitrogen remains largely unknown.

By using homology modeling techniques, the protein folds that contain the metal cluster active sites for the V- and Fe-only nitrogenases were constructed. The models uncovered similarities and differences existing among the nitrogenases regarding the identity of the amino acid residues lining pivotal structural features for the correct functioning of the proteins. These differences, …

Identifying Biomarkers For Resistance To Novel Cisplatin Analogues In Human Lung, Breast And Prostate Cancers, Becky Michelle Hess

UNLV Theses, Dissertations, Professional Papers, and Capstones

Cisplatin is a common therapeutic agent used in cancer treatment. Unfortunately, resistance to cisplatin in addition to severe side effects limits its use in cancer treatment. Two novel cisplatin analogues, 4DB and 4TB were shown to have varying cytotoxicity in lung, breast and prostate cancer cells. The hypothesis for this study states that the differences in 4DB and 4TB cytotoxicity among different tissue types is due to the type and efficiency of DNA repair mechanisms involved in response to these drugs.

To test the hypothesis, proteins involved in the rate limiting step of nucleotide excision repair (NER) and mismatch repair …

Rational Drug Design: An Information Driven Approach To The Design Of An Anthracycline Analog, Charlene Rebecca Young

Boise State University Theses and Dissertations

Over the past fifty years anthracyclines have been used to treat a wide variety of cancers. Combination therapies with anthracyclines have the potential to greatly increase treatment success. Despite the great potential of anthracyclines in the treatment of cancer, their use has been limited due to the risk of chronic cardiotoxicity. The reduction of anthracyclines to an alcohol metabolite has been linked to the development of cardiotoxic side effects. One of the principal enzymes responsible for catalyzing the formation of the anthracycline alcohol metabolite is human carbonyl reductase 1(HCBR). Controlling the reduction of anthracyclines by HCBR may offer a means …

Role Of The Porphyromonas Gingivalis Ecf Sigma Factor, Sigh, In Oxidative Stress Response, Sara Sarrafee

Theses and Dissertations

Periodontal disease affects a majority of the US population. Porphyromonas gingivalis is the major etiological agent for development and progression of the disease. P. gingivalis is a hemin-dependent, obligate anaerobe that is found predominantly in periodontal pockets in infected patients. So for, little is known regarding the mechanisms which allow P. gingivalis to survive and sustain itself in the oral cavity. To better understand the adaptive mechanisms of the bacterium to the varying conditions in the oral cavity, regulatory mechanisms must be characterized. Sigma factors (σ) are responsible for initiating transcription by guiding RNA polymerase binding to specific DNA promoter …

The Second Generation Proteasome Inhibitor Carfilzomib Interacts Synergistically With Hdac Inhibitors In Diffuse Large B-Cell Lymphoma Cells Through Multiple Mechanisms And Circumvents Bortezomib Resistance, Dmitry Lembersky

Theses and Dissertations

Mechanisms underlying the interactions between the proteasome inhibitor carfilzomib and HDAC inhibitors were examined in both germinal center (GC) and activated B-cell (ABC) subtypes of human diffuse large B-cell lymphoma (DLBCL). Simultaneous exposure to minimally toxic concentrations of carfilzomib and HDAC inhibitor vorinostat resulted in the release of mitochondrial pro-apoptotic proteins SMAC and cytochrome c, pro-apoptotic caspase activation, and synergistic induction in apoptosis in both ABC and GC DLBCL subtypes. These events were associated with a marked increase in the stress kinase JNK, ROS generation, G2-M cell cycle arrest, as well as induction of DNA damage. Genetic knockdown of JNK …

The Role Of Brca1 In Dna Double-Strand Break Repair, Seth Dever

Theses and Dissertations

Mutations in the breast cancer susceptibility 1 (BRCA1) gene are linked to breast as well as ovarian cancers. However, most cancer-causing mutations within the BRCA1 gene have been found in the N’ and C’ terminal regions of the BRCA1 protein, both believed to be important for DNA double-strand break (DSB) repair. The BRCA1 C’ terminal (BRCT) repeats have been implicated in phospho-serine protein binding whereas the N’ terminal RING domain interacts with the BARD1 protein to form a hetero-dimeric complex with E3 ubiquitin ligase activity. The BRCA1 BRCT domain binds CtIP, BACH1, and RAP80, all of which have been directly …

Scribble As A Possible Binding Partner For The Map Kinases Erk2 And Erk6, William Allen

Theses and Dissertations

We worked on finding a new kinase regulator to develop basic data to be used for cancer prevention. Our work found a link between three previously unrelated proteins involved in cancer, ERK2 and ERK6 and Scribble. The MAP kinase cascade is involved in cell proliferation, which is highly deregulated in cancer. Through the screening of ERK6 associating molecules, we found the cell polarity, and cell cycle related molecule Scribble. Furthermore, we found that Scribble was a dual-specific kinase regulator. We clearly demonstrated that these ERKs interact with Scribble through the LRR and the PDZ domains of Scribble. We hypothesize that …

Ionic Selectivity In L-Type Calcium Channels By Electrostatics And Hard-Core Repulsion, Dezso Boda, Douglas Henderson, Monika Valisko, Bob Eisenberg, Dirk Gillespie

Faculty Publications

A physical model of selective "ion binding" in the L-type calcium channel is constructed, and consequences of the model are compared with experimental data. This reduced model treats only ions and the carboxylate oxygens of the EEEE locus explicitly and restricts interactions to hard-core repulsion and ion–ion and ion–dielectric electrostatic forces. The structural atoms provide a flexible environment for passing cations, thus resulting in a self-organized induced-fit model of the selectivity filter. Experimental conditions involving binary mixtures of alkali and/or alkaline earth metal ions are computed using equilibrium Monte Carlo simulations in the grand canonical ensemble. The model pore rejects …

The Zinc Finger Protein Zn72d And Dead Box Helicase Belle Interact And Control Maleless Mrna And Protein Levels, Kathleen A. Worringer, Feixia Chu, Barbara Panning

Molecular, Cellular & Biomedical Sciences

Background: The Male Specific Lethal (MSL) complex is enriched on the single X chromosome in male Drosophila cells and functions to upregulate X-linked gene expression and equalize X-linked gene dosage with XX females. The zinc finger protein Zn72D is required for productive splicing of the maleless (mle) transcript, which encodes an essential subunit of the MSL complex. In the absence of Zn72D, MLE levels are decreased, and as a result, the MSL complex no longer localizes to the X chromosome and dosage compensation is disrupted. To understand the Molecular basis of Zn72D function, we identified proteins that interact with Zn72D. …

Consequences Of Hyaluronan Metabolism On Cell Cycle Progression In Prostate Tumor Growth And Metastasis, Alamelu G. Bharadwaj

Department of Biochemistry: Dissertations, Theses, and Student Research

Progression of Prostate cancer (CaP), depends on a complex series of interactions between the tumor and extracellular matrix (ECM) leading to tumor growth and metastasis. Hyaluronan (HA), an ECM component, is elevated in CaP and its accumulation in the tumor microenvironment is dependent on its synthetic enzyme, hyaluronan synthase (HAS), and turnover enzyme, hyaluronidase (Hyal). Although Hyal1 expression can independently prognosticate CaP, and HAS expression shows increase in aggressive prostate cancer cells, the functional relevance of this correlation is unexplored. In these studies we aim to dissect the roles of HAS and Hyal1 in prostate cancer.

Stably overexpressed hyaluronan synthases …

Synthesis Of 2,4,5-Triaminocyclohexane Carboxylic Acid As A Novel 2-Deoxystreptamine Mimetic, Sarah Elizabeth Roberts

Theses and Dissertations

RNAs have become increasingly recognized as possible drug targets due to their involvement in important biochemical functions, as well as their unique but well-defined structures. Recently published crystal structures depict the binding of a series of aminoglycosides- or more specifically- 2-deoxystretamine (2-DOS), the most preserved central scaffold of aminoglycosides, to a conserved 5'-GU-3'region on their target RNAs. A novel unnatural γ-amino acid, 1, has been synthesized using 2-deoxystreptamine as a template through structure-based rational design. The unnatural amino acid has been designed to replace a glycosidic linkage with an amide bond, which may limit the promiscuous binding characteristics of aminoglycosides …

Novel Mechanisms Regulating Cytokine-Induced Gene Expression In Astrocytes And Glioblastoma Cells, Lauren Bryan

Theses and Dissertations

Chronic inflammation in the brain results in the development of several CNS diseases, including Alzheimer’s and Parkinson’s diseases, multiple sclerosis, and tumors. IL-1, a pro-inflammatory cytokine released by activated microglia and astrocytes, instigates the expression of factors promoting the progression of these CNS disorders, including cytokines, chemokines, and components of matrix remodeling systems, such as the plasminogen activator system. IL-1 also increases the mRNA expression and activity of SphK, the enzyme that phosphorylates Sph to form S1P, a bio-active sphingolipid. This thesis demonstrates that IL-1 and S1P enhance the mRNA and protein expression of PAI-1 and uPAR, two key components …

Molecular Mechanisms For Regulation Of Gene Expression By Lysophosphatidic Acid In Ovarian Carcinoma Cells, Regina Oyesanya

Theses and Dissertations

Lysophosphatidic acid (LPA) is a potent bioactive phospholipid mediator that functions through multiple G protein couple receptors (GPCRs). LPA is elevated in ascites of ovarian cancer patients and is involved in growth, survival and metastasis of ovarian cancer cells. Gene promoter analyses revealed that some LPA-target genes share similar sets of binding sites for prominent transcription factors posing the possibility of a general mechanism for activation of their expression by LPA. Detailed investigation of the mechanisms of regulation of cyclooxygenase 2 (Cox-2), a paradigm of LPA-regulated genes, showed that LPA robustly upregulated the expression of Cox-2 in ovarian cancer cells …