Biochemistry Commons^™

Nuclear Receptor Coactivator 3 In Endoplasmic Reticulum Stress And Stress Granule Dynamics In Pancreatic Cancer, Andrew Kisling

Theses & Dissertations

Pancreatic cancer is predicted to be the second-leading cause of cancer-related deaths within the next decade. Nuclear receptor coactivator 3 (NCOA3/SRC3/AIB1) regulates an array of metabolic and signaling pathways and has been established by our group and others as a critical regulator pancreatic cancer progression and metastasis. A recent study demonstrated NCOA3 regulation by the IRE1α-XBP1 axis of the unfolded protein response (UPR), suggesting a link between NCOA3 and cellular stress management. Furthermore, NCOA3 has been shown to directly bind to a scaffolding protein of stress granules (SGs). Since SG assembly is regulated by the UPR, we hypothesized that NCOA3 …

Functional Characterization Of Cancer-Associated Dna Polymerase Ε Variants, Stephanie R. Barbari

Theses & Dissertations

Replicative DNA polymerases ε (Polε) and δ (Polδ) achieve high fidelity DNA synthesis through a precise balance of polymerization and exonucleolytic proofreading. Errors that escape proofreading are corrected by DNA mismatch repair (MMR). Ultramutated human cancers with proficient MMR carry alterations in the exonuclease domain of Polε, which were initially predicted to abolish proofreading. However, functional studies in yeast of the most recurrent Polε-P286R variant suggested defects beyond a loss of exonuclease activity. Indeed, biochemical analysis of the yeast Polε-P286R analog revealed increased polymerization capacity in addition to decreased proofreading, which enables efficient mismatch extension and bypass of replication-blocking non-B …

A Pkcα-Mediated Growth Suppressive Mek-Erk Signaling Axis In Intestinal Epithelial Cells, Navneet Kaur

Theses & Dissertations

Members of the protein kinase C (PKC) family of serine/threonine kinases are involved in regulation of fundamental cellular functions, including proliferation, differentiation, survival, migration, and transformation. Increasing evidence points to anti-proliferative and tumor suppressive role of PKCs. Our laboratory and others have reported that the classical PKC isozyme, PKCαnegatively regulates proliferation and tumorigenesis in the intestinal epithelium. Our laboratory has further determined that PKCα signaling induces a program of cell cycle withdrawal in intestinal epithelial cells that involves downregulation of the pro-proliferative proteins, cyclin D1 and Id1, and upregulation of the cyclin dependent kinase (CDK) inhibitor, p21^Cip1. Unexpectedly, …

Molecular Mechanisms Of Aberrant Protein Glycosylation In Pancreatic Cancer Stemness And Metastasis, Frank Leon

Theses & Dissertations

A myriad of genetic and other abnormal changes underlies the aggressiveness and dissemination properties observed in pancreatic cancer (PC). Aberrant protein glycosylation is a commonly observed feature in PC. The modification of protein O-glycosylation is mediated by glycosyltransferases, which attach and sequentially elongate monosaccharides on Serine/Threonine (Ser/Thr) motifs. Aberrant glycosylation is recognized as an emerging hallmark of cancer where a disruption in normal glycosylation results in irregular O-glycans.

This dissertation research has investigated the consequences of aberrant protein glycosylation on stemness and enhancement of metastatic properties in pancreatic ductal adenocarcinoma (PDAC). Several publications have reported aberrant O-glycosylation increases in oncogenic …

A Link Between Methylglyoxal And Heart Failure During Hiv-1 Infection, Prasanta K. Dasg, Fadhel A. Alomar, Jesse L. Cox, Joellyn Mcmillan, Bryan T. Hackfort, Edward Makarov, Brenda Morsey, Howard S. Fox, Howard E. Gendelman, Santhi Gorantla, Keshore R. Bidasee

Department of Biochemistry: Faculty Publications

Early-onset heart failure (HF) continues to be a major cause of morbidity and mortality in people living with human immunodeficiency virus type one (HIV-1) infection (PLWH), yet the molecular causes for this remain poorly understood. Herein NOD.Cg- Prkdc^scidIl2rg^tm1Wjl/SzJ humanized mice (Hu-mice), plasma from PLWH, and autopsied cardiac tissues from deceased HIV seropositive individuals were used to assess if there is a link between the glycolysis byproduct methylglyoxal (MG) and HF in the setting of HIV-1 infection. At five weeks post HIV infection, Hu-mice developed grade III-IV diastolic dysfunction (DD) with an associated two-fold increase in plasma …

A Review Of Calcineurin Biophysics With Implications For Cardiac Physiology, Ryan B. Williams

Theses and Dissertations

Calmodulin is a prevalent calcium sensing protein found in all cells. Three genes exist for calmodulin and all three of these genes encode for the exact same protein sequence. Recently mutations in the amino acid sequence of calmodulin have been identified in living human patients. Thus far, patients harboring these mutations in the calmodulin sequence have only displayed an altered cardiac related phenotype. Calcineurin is involved in many key physiological processes and its activity is regulated by calcium and calmodulin. In order to assess whether or not calcineurin contributes to calmodulinopathy (a pathological state arising from dysfunctional calmodulin), a comprehensive …

Initial Characterization Of Prna From Burkholderia Ambifaria: Developing An Nadph-Dependent Activity Assay For Tryptophan Halogenation, Mahmuda Akter

Theses and Dissertations

Some bacteria produce a potent antifungal agent (pyrrolnitrin) from tryptophan using four dioxygen dependent steps to outcompete other microbes. Each step of this process is catalyzed by an oxygenase encoded by the prnABCD cassette. The first enzymatic step in pyrrolnitrin biosynthesis is the regioselective chlorination of tryptophan to form 7-chlorotryptophan. This halogenation is catalyzed by PrnA, a Flavin dependent oxygenase, which has been isolated and characterized from P. fluorescens. The pyrrolnitrin biosynthesis pathway (prnABCD) has been also observed in the Burkholderia genus. This thesis comprises my studies on the expression, purification, and characterization of PrnA from Burkholderia ambifaria. Beyond the …

Granulins In Norm And Neurodegenerative Pathologies, Anukool Bhopatkar

Dissertations

Granulins (GRNs) are small, cysteine-rich modules produced from the proteolytic cleavage of the precursor protein called progranulin (PGRN). GRNs are present in the form of seven tandem repeats within the precursor and are known to be produced in the extracellular and in lysosomal environments. In physiology, PGRN and GRNs plays pleiotropic roles such as neuronal growth and differentiation, immunomodulation, wound healing. Recent studies have implicated pathological role for PGRN in Alzheimer disease (AD) and frontotemporal dementia (FTD) but specific mechanism(s) remains unclear. However, potential interactions between GRNs and Ab42 and TDP-43 seem like a plausible underlying mechanism. Studies presented here …

Discovering Virally Encoded Proteins That Block Type Iv Crispr Immune Systems, Andrew Williams

Fall Student Research Symposium 2021

Bacteria and the viruses that infect them have been at war from the beginnings of life until today. Due to selective pressure from viral infection, bacteria have evolved various biological defense systems, including CRISPR-Cas systems that use a genetic memory of previous viral encounters to protect against future invasions. However, recently it has been shown that viruses have evolved counter-strategies to evade CRISPR systems. Virally encoded proteins called anti-CRISPRs use a variety of mechanisms to block the activity of CRISPR immune systems in order to infect bacterial cells. The Jackson lab at USU recently showed that a Type IV-A CRISPR-Cas …

Characterization Of The Atpase Activity Of Casding, Christian Cahoon

Fall Student Research Symposium 2021

The battle between bacteria and phage has been ongoing for eons. This battle has generated the evolutionary pressure necessary for the development of microbial immune systems. Characterization of these systems has led to the discovery of molecular tools such CRISPR-Cas systems. This system uses a genetic memory of past viral infections coupled with associated proteins to form ribonucleoprotein complexes which seek out and destroy foreign genetic elements. These systems have been repurposed by scientists to create powerful gene editing tools such as Cas9. With such powerful molecular tools being discovered, we have pursued the characterization of a relatively unknown system, …

Characterizing The Mechanisms Of C. Elegans Prmt1 Temperature Dependence, Arianna Towne

Fall Student Research Symposium 2021

Over time, cellular enzymes evolve through amino acid mutations which allow them to remain functional at temperatures specific to the host organism. This activity may be partially or completely lost when enzymes are removed from their optimal temperature range, as is observed for the C. elegans protein arginine methyltransferase 1 (cPRMT1). This construct demonstrates maximum enzymatic activity at the C. elegans optimum of 20°C, but no activity at 37°C where activity for mammalian PRMT1 variants is observed. Given dysregulation of PRMT1 has been linked to various disease states, we are interested in exploiting the biophysical mechanisms of cPRMT1 temperature dependence …

Determining The Nucleic Acid Binding Affinities Of Crispr-Associated Ding (Casding), Matt Armbrust

Fall Student Research Symposium 2021

CRISPR-Cas systems are adaptive prokaryotic immune systems that enable host cells to defend against attack from foreign nucleic acids such as phage infections or plasmids. CRISPR-Cas systems are diverse and encompass 2 classes, 6 types, and 33 subtypes. The Type IV-A CRISPR-Cas system from Pseudomonas aeruginosa strain 83 is composed of five different genes (csf1, csf2, csf3, cas6, and dinG). Type IV-A systems are poorly understood, and currently there is little research detailing their biological and biochemical mechanism of immunity. CasDinG, an ancillary protein within the Type IV-A system, is required for an immune response in vivo. However, the role …

Single-Variable Porous Nanomaterial Series From Polymer Structure-Directing Agents, Morgan Stefik

Faculty Publications

Block polymer structure-directing agents (SDA) enable the production of porous nanoscale materials. Most strategies rely upon polymer equilibration where diverse morphologies are realized in porous functional materials. This review details how solvent selectivity determines the polymer SDA behaviors, spanning from bulk-type to solution-type. Equilibrating behavior of either type, however, obscures nanostructure cause-and-effect since the resulting sample series convolve multiple spatial variations. Solution-type SDA behaviors include both dynamic and persistent micelles. Persistent micelle templates (PMT) use high solvent selectivity for kinetic entrapment. PMTs enable independent wall thickness control with demonstrated 2 Å precision alterations. Unimodal PMT pore size distributions have spanned …

Charting A New Frontier Integrating Mathematical Modeling In Complex Biological Systems From Molecules To Ecosystems, Katharine A. White, Kira D. Mcentire, Nicole R. Buan, Lecia Robinson, Elisar Barbar

Department of Biochemistry: Faculty Publications

Advances in quantitative biology data collection and analysis across scales (molecular, cellular, organismal, and ecological) have transformed how we understand, categorize, and predict complex biological systems. This surge of quantitative data creates an opportunity to apply, develop, and evaluate mathematical models of biological systems and explore novel methods of analysis. Simultaneously, thanks to increased computational power, mathematicians, engineers, and physical scientists have developed sophisticated models of biological systems at different scales. Novel modeling schemes can offer deeper understanding of principles in biology, but there is still a disconnect between modeling and experimental biology that limits our ability to fully realize …

Spectroscopic Studies Of The Interaction Between Phosphorus Heterocycles And Cytochrome P450, Dumei Ma, Libo Zhang, Yingwu Yin, Yuxing Gao, Qian Wang

Faculty Publications

P450 fatty acid decarboxylase OleT from Staphylococcus aureus (OleT_SA) is a novel cytochrome P450 enzyme that catalyzes the oxidative decarboxylation of fatty acids to yield primarily terminal alkenes and CO₂ or minor α- and β-hydroxylated fatty acids as side-products. In this work, the interactions between a series of cycloalkyl phosphorus heterocycles (CPHs) and OleT_SA were investigated in detail by fluorescence titration experiment, ultraviolet–visible (UV–vis) and ³¹P NMR spectroscopies. Fluorescence titration experiment results clearly showed that a dynamic quenching occurred when CPH-6, a representative CPHs, interacted with OleT_SA with a binding constant value of 15.2 …

Engineering Fluorescently Labeled Human Fibroblast Growth Factor One Mutants And Characterizing Their Photophysics Properties Towards Designing Fret Assays, Mamello Mohale

Graduate Theses and Dissertations

Human fibroblast growth factor one (hFGF1) belongs to a family of 22 FGF members produced by fibroblast cells. Cell signaling during physiological processes of angiogenesis and wound healing occurs when hFGF1 binds to its receptor (FGFR). However, when heterogenous homeostasis is not maintained, fibroblast cells exhibit excessive proliferation which can lead to a myriad of cancers. smFRET is an ultrasensitive distant dependent (1-10 nm) technique capable of resolving such heterogeneity in structural dynamics and binding affinities (Kd). Therefore, we successfully designed and characterized fluorescently labeled hFGF1 tracers which span the visible light region of the electromagnetic spectrum for use in …

Characterization Of The Multifunctional Enzyme Proline Utilization A, Yizi Mao

Department of Biochemistry: Dissertations, Theses, and Student Research

Proline is a unique and important amino acid. Proline is a proteogenic amino acid and its metabolism is involved in many critical cellular functions. Therefore, proline metabolism is tightly regulated, and dysfunction of proline metabolism is related to human diseases. The first step of proline oxidization to ∆¹-pyrroline-5-carboxylic acid (P5C) is catalyzed by proline dehydrogenase (PRODH). P5C is then non-enzymatically hydrolyzed to glutamate-γ-semialdehyde (GSA), which can be further oxidized to glutamate by P5C dehydrogenase (P5CDH/GSALDH). In Gram-negative bacteria, the PRODH and P5CDH enzymes are expressed as one polypeptide called proline utilization A (PutA). In some Gram-negative bacteria an …

V-Myb Avian Myel Oblast Viral Oncogene Homolog Like 1 (Mybl1) Knockdown And Its Role In A Triple Negative Breast Cancer, Nabras Mahmoud Abdulrahman

Theses (2016-Present)

Triple Negative Breast Cancer (TNBC) is defined as negative for three genes, estrogen receptor (ESR), progesterone receptor (PR) and Human epidermal growth factor receptor (HER2-neu) genes. Previous data show the V-Myb Avian Myel oblast Viral Oncogene Homolog Like 1 (MYBL1) gene is over-expressed in Triple negative breast cancer cell line (MDA-MB231). MYBL1 belongs to the MYB family of genes which are transcription factors and proto-oncogenes which are associated with cell cycle regulation, apoptosis, and differentiation, all of which are key events associated with cancers. It could be that MYBL1 contributes to these same processes in TNBC. Instead of studying MYBL1’s …

Liposomes: Production And Applications For Controlled Drug Delivery, Gamid Abatchev

Boise State University Theses and Dissertations

This dissertation recognizes the enormous potential presented by the ever-evolving development of liposomes as drug carriers and seeks to offer further investigation into their useful production and utilization. The first chapter presents the basic principles governing their formation by self-assembly in water solutions, briefly describes the most common production methods, and points out essential past advances that led to their use as drug carriers. Chapter two exemplifies production of liposomes by the traditional methods of extrusion and sonication, detailing passive and active loading, as well as physical characterization by Dynamic Light Scattering, microscopy imaging, and fluorescence spectroscopy. In the next …

Enzymatic Degradation Of Microcystin-Lr By Microcystinase (Mlra), Faisal Alqhtani

Graduate Theses and Dissertations

Microcystin-LR (MC-LR) is affecting the water supply worldwide. Hence, a way to eliminate this toxin is an essential target. In this study, successful cloning of the mlrA gene and producing MlrA enzyme that can degrade the cyclic MC-LR to linearized MC-LR was done. MlrA protein was expressed in Escherichia coli BL-21 (E. coli). Also, enhancing the MlrA yield by adding nickel to LB media was a success in producing more MlrA enzyme from the same volume. Even though the enzyme showed no activity after adding Ni, the enzyme was expressed at a higher yield. Furthermore, it was to investigate adding …