Biochemistry, Biophysics, and Structural Biology Commons^™

Single-Amino-Acid Alterations In A Highly Conserved Central Region Of Vesicular Stomatitis Virus N Protein Differentially Affect The Viral Nucleocapsid Template Functions, Debasis Nayak, Debasis Panda, Subash C. Das, Ming Lou, Asit K. Pattnaik

School of Veterinary and Biomedical Sciences: Faculty Publications

The nucleocapsid protein (N) of vesicular stomatitis virus and other rhabdoviruses plays a central role in the assembly and template functions of the viral N-RNA complex. The crystal structure of the viral N-RNA complex suggests that the central region of the N protein interacts with the viral RNA. Sequence alignment of rhabdovirus N proteins revealed several highly conserved regions, one of which spanned residues 282 to 291 (GLSSKSPYSS) in the central region of the molecule. Alanine-scanning mutagenesis of this region suggested that replacement of the tyrosine residue at position 289 (Y289) with alanine resulted in an N-RNA template that is …

Pot1‐Independent Single‐Strand Telomeric Dna Binding Activities In Brassicaceae, Eugene V. Shakirov, Thomas D. Mcknight, Dorothy E. Shippen

Biological Sciences Faculty Research

Telomeres define the ends of linear eukaryotic chromosomes and are required for genome maintenance and continued cell proliferation. The extreme ends of telomeres terminate in a single‐strand protrusion, termed the G‐overhang, which, in vertebrates and fission yeast, is bound by evolutionarily conserved members of the POT1 (protection of telomeres) protein family. Unlike most other model organisms, the flowering plant Arabidopsis thaliana encodes two divergent POT1‐like proteins. Here we show that the single‐strand telomeric DNA binding activity present in A. thaliana nuclear extracts is not dependent on POT1a or POT1b proteins. Furthermore, in contrast to POT1 proteins from yeast and vertebrates, …

Expression Of Chemokines And Vegfs In Hnscc, Crystal Cunningham

Theses and Dissertations

Head and neck squamous cell carcinoma (HNSCC) is the sixth most common malignancy worldwide. The 5-year survival rate when the cancer remains as a primary tumor is 81% but when it metastasizes to distant sites, defined as a metastatic cancer, it decreases dramatically to 26%. Approaches to prevent these cancers from undergoing these metastatic changes can greatly improve the survival and outcome of these cancer victims. This current study is examining the expression profiles of chemokines and VEGFs in HNSCC. By investigation the underlying pathways involved in the expressions of chemokines and VEGFS we hope to sort out the transcriptional …

Genetic Analysis Of Ribosome Stalling And Rescue, Douglas Ray Tanner

Theses and Dissertations

In eubacteria, ribosome stalling on broken messenger RNA transcripts can lead to cell death. The trans-translation quality control mechanism rescues many of these stalled ribosomes. In this process, tmRNA enters stalled ribosomes by mimicking a transfer RNA, accepting the stalled nascent peptide. The ribosome then releases the broken mRNA and resumes translation on a coding region within tmRNA itself. Translation of tmRNA marks the nascent peptide for destruction by the addition of a short proteolysis tag and the ribosome is released at a stop codon within the tmRNA open reading frame. An intriguing aspect of trans-translation is that …

Synthesis And Evaluation Of Stimulatory Properties Of Glycolipids For Natural Killer T Cells, Xiangtian Long

Theses and Dissertations

Natural killer T cells (NKT cells) are a subset of T cells. They regulate a wide range of diseases including infection, tumor growth, and autoimmune diseases, through recognizing glycolipid antigens in the context of CD1d. An understanding of the scope of glycolipid antigens would facilitate use of this cell type in controlling immune responses. Till today, a lysosomal glycolipid, isoglobotrihexosylceramide (iGb3), is the only natural glycolipid that has been found to be recognized by both human and mouse NKT cells. To elucidate the molecular basis of this specific recognition, iGb3 variants were designed and prepared: i) replacement of the C26 …

Effects Of Estrogen On Muscle Damage In Response To An Acute Resistance Exercise Protocol, Megan R. Wolf

Honors Scholar Theses

Creatine Kinase (CK) is used as a measure of exercise-induced muscle membrane damage. During acute eccentric (muscle lengthening) exercise, muscle sarcolemma, sarcoplasmic reticulum, and Z-lines are damaged, thus causing muscle proteins and enzymes to leak into the interstitial fluid.

Strenuous eccentric exercise produces an elevation of oxygen free radicals, which further increases muscle damage. Muscle soreness and fatigue can be attributed to this membrane damage. Estradiol, however, may preserve membrane stability post-exercise (Brancaccio, Maffulli, & Limongelli, 2007; Carter, Dobridge, & Hackney, 2001; Tiidus, 2001). Because estradiol has a similar structure to Vitamin E, which is known to have antioxidant properties, …

Analysis Of The Phosphorylated Forms Of Protein Kinase R, Christine Quartararo

Honors Scholar Theses

Protein Kinase R (PKR) is induced by interferon and activated by dsRNA. Subsequent autophosphorylation and phosphorylation of eIF2alpha inhibits viral replication. In the latent state PKR exists as an unphosphorylated monomer. Work in the Cole laboratory has shown two additional states, a phosphorylated monomeric state (pPKRm) and a phosphorylated dimeric state (pPKRd). RNA serves as a scaffold bringing two PKRs together allowing dimerization and autophosphorylation to occur. The contribution of each state to the function of PKR remains unclear. Western blots were performed to examine the phosphorylation states of the essential residues,

T446 and T451. Activity assays have shown activation …

The Role Of Raf Kinase Inhibitor Protein In Cell Motility, Kathryn Grive

Honors Scholar Theses

Raf Kinase Inhibitor Protein (RKIP) has been identified as a phosphatidylethanolamine-binding protein capable of inhibiting Raf-1 kinase, an enzyme significant in cell proliferation and cancer development. When properly functioning, RKIP can mediate the expression of Raf-1 kinase and help prevent uncontrolled cell division. RKIP also has suggested, but unclear, roles in spindle fiber formation during mitosis, regulation of apoptosis, and cell motility. The Fenteany laboratory in the Chemistry Department identified a new small molecule, named Locostatin, as a cell migration inhibitor in mammalian cells, with RKIP as its primary molecular target.

Dictyostelium discoideum possess two RKIP proteins, RKIP-A and RKIP-B. …

Characterizing The Role Of Phaeobacter In The Mortality Of The Squid, Euprymna Scolopes, Brian Shawn Wong Won

Honors Scholar Theses

The subject of our study is the Hawaiian bobtail squid, Euprymna scolopes, which is known for its model symbiotic relationship with the bioluminescent bacterium, Vibrio fischeri. The interactions between E. scolopes and V. fischeri provide an exemplary model of the biochemical and molecular dynamics of symbiosis since both members can be cultivated separately and V. fischeri can be genetically modified 1. However, in a laboratory setting, the mortality of embryonic E. scolopes can be a recurrent problem. In many of these fatalities, the egg cases display a pink-hued biofilm, and rosy pigmentation has also been noted in the deaths of …

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 …

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.

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), …

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 …

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 …

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 …

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 …

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 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 …

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 …

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, …

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 …