Biochemistry Commons^™

Mechanisms Of Regulation Of Mrna 3' Processing By P53 Pathway, Emral Cakmak Devany

Dissertations, Theses, and Capstone Projects

Although the p53 network has been intensively studied, genetic analyses long hinted at the existence of components that remained elusive. This dissertation focuses on the study of the regulation of mRNA 3' processing during DNA damage response (DDR) by the p53 pathway and the regulation of p53 expression by the mRNA 3' processing machinery. The results in this dissertation revealed new roles of tumor suppressor p53 in mRNA 3' processing. In Chapter II, I showed that p53 inhibits the cleavage step of polyadenylation reaction and that cells with different levels of p53 expression have different mRNA processing profiles. As part …

Role Of The Polyadenylation Factor Cstf-50 In Regulating The Brca1/Bard1 E3 Ubiquitin (Ub) Ligase Activity, Danae Fonseca

Dissertations, Theses, and Capstone Projects

The cellular response to DNA damage is an intricate mechanism that involves the interplay among several pathways. The studies presented in this dissertation focus on the determination and characterization of the role of mRNA processing factor CstF-50 and escort protein p97 in the regulation of the BRCA1/BARD1 E3 ubiquitin (Ub) ligase activity during the DNA damage response (DDR).

As part of the studies presented in Chapter II, I determined that the polyadenylation factor CstF plays a direct role in DDR, specifically in transcription-coupled repair (TCR), and that it localizes with RNA polymerase II (RNAP II) and BARD1 to sites of …

Oxidation Of Cellular Amino Acid Pools Leads To Cytotoxic Mistranslation Of The Genetic Code, Tammy J. Bullwinkle, Noah M. Reynolds, Medha Raina, Adil Moghal, Eleftheria Matsa, Andrei Rajkovic, Huseyin Kayadibi, Farbod Fazlollahi, Christopher Ryan, Nathaniel Howitz, Kym F. Faull, Beth A. Lazazzera, Michael Ibba

Biology, Chemistry, and Environmental Sciences Faculty Articles and Research

Aminoacyl-tRNA synthetases use a variety of mechanisms to ensure fidelity of the genetic code and ultimately select the correct amino acids to be used in protein synthesis. The physiological necessity of these quality control mechanisms in different environments remains unclear, as the cost vs benefit of accurate protein synthesis is difficult to predict. We show that in Escherichia coli, a non-coded amino acid produced through oxidative damage is a significant threat to the accuracy of protein synthesis and must be cleared by phenylalanine-tRNA synthetase in order to prevent cellular toxicity caused by mis-synthesized proteins. These findings demonstrate how stress …

Bio-Compatible Polymer Coatings Using Low Temperature, Atmospheric Pressure Plasma, Susan Farhat, Mary Gilliam, Ali Zand, Montserrat Rabago-Smith

Chemistry & Biochemistry Presentations And Conference Materials

Current research has been dedicated to investigating the viability of atmospheric pressure plasmas for use in coating technology. In addition to being more cost effective and efficient, atmospheric pressure plasma offers a more streamlined process, as it can be employed directly into the production line. Atmospheric pressure plasma has been used in applications including biocompatibility, hydrophilicity/hydrophobicity, and coating with antibacterial films. Polyethylene is used as a biocompatible surface for ball and socket joint replacements, which are under constant wear. Atmospheric pressure plasma treatment was used to change the surface chemistry by grafting various biocompatible polymers to the polyethylene surface, as …

Automating Dicentric Chromosome Detection From Cytogenetic Biodosimetry Data., Peter K Rogan, Yanxin Li, Asanka Wickramasinghe, Akila Subasinghe, Natasha Caminsky, Wahab Khan, Jagath Samarabandu, Ruth Wilkins, Farrah Flegal, Joan H Knoll

Biochemistry Publications

We present a prototype software system with sufficient capacity and speed to estimate radiation exposures in a mass casualty event by counting dicentric chromosomes (DCs) in metaphase cells from many individuals. Top-ranked metaphase cell images are segmented by classifying and defining chromosomes with an active contour gradient vector field (GVF) and by determining centromere locations along the centreline. The centreline is extracted by discrete curve evolution (DCE) skeleton branch pruning and curve interpolation. Centromere detection minimises the global width and DAPI-staining intensity profiles along the centreline. A second centromere is identified by reapplying this procedure after masking the first. Dicentrics …

Hpv16 E6* Induces Oxidative Stress And Dna Damage, Vonetta M. Williams

Loma Linda University Electronic Theses, Dissertations & Projects

High risk types of Human Papillomavirus are the causative agents of virtually all cases of cervical cancer, 50-90% of other anogenital cancers and approximately 30% of oral and pharyngeal cancers. The high-risk types encode two viral oncogenes, E6 and E7, which work together to initiate cell transformation. The approximately 50 amino acid product of the E6* transcript is expressed during the early stages of HPV infection. In this study, we found that expression of E6* increased the level of reactive oxygen species (ROS) in both HPV+ and HPV- cells. This increased oxidative stress led to higher levels of DNA damage. …

Effect Of Maternal Hypoxia On Fetal Development: Programming Of Hie Phenotype In Neonatal Rat Brain, Pablo J. Gonzalez-Rodriguez

Loma Linda University Electronic Theses, Dissertations & Projects

Developmental programming of health and disease correlates the adverse intrauterine environment and the risk of disease later in life as cardiovascular disease, metabolic diseases, renal dysfunction or neurobehavioral disorders among others. Maternal hypoxia is one of the most common intrauterine growth restricted environment during pregnancy. Perinatal hypoxic-ischemic encephalopathy is an important cause of brain injury in the newborn due to a systematic asphyxia. Our study aims to test the hypothesis that maternal hypoxia affect the organogenesis of the kidney by affecting the kidney structure and focusing on the roles of AT1R and AT2R, while the brain development will also be …

Quantitative Characterization Of Conserved Noncoding Regions By Flow Cytometry, Amber Brown

Loma Linda University Electronic Theses, Dissertations & Projects

Spatial and temporal regulation of developmental gene transcription often involves regulatory sequences found in noncoding DNA separate from the gene’s promoter. Conservation of a noncoding region (CNR) across divergent species may indicate a regulatory region critical to basic morphogenesis. CNR-green fluorescent protein (GFP) constructs can demonstrate spatial and temporal CNR activity by microscopy visualization. However, characterization of regulatory modules within a CNR requires quantitative, in addition to qualitative, analysis. The study presented here describes the development and implementation of a novel application of flow cytometry in the quantitative characterization of CNRs. The technique couples fluorescent microscopy localization with flow cytometry …

Biological Surveys Of Selected Lower Grand River Streams: Ionia, Kent, Muskegon, And Ottawa Counties, Michigan, August-September 2014, Michigan Department Of Environmental Quality Water Resources Division

Faculty and Professional Research

The biologic integrity and physical habitat conditions of the lower Grand River (Hydrologic Unit Code (HUC) 04050006) and selected tributaries were surveyed during August and September 2014 by staff of the Surface Water Assessment Section (SWAS), Water Resources Division (WRD). The objectives of this study were to: 1. Evaluate the attainment status of the other indigenous aquatic life and wildlife (OIALW) designated use. 2. Identify and investigate effects of nonpoint sources (NPS) of pollution. 3. Satisfy monitoring requests submitted by internal and external customers.

Exosomal Survivin-T34a: A Novel, Potential Cancer Therapeutic, Jonathan Richard Aspe

Loma Linda University Electronic Theses, Dissertations & Projects

Pancreatic cancer is the fourth most common cause of cancer fatality in American men and women with a less than 5% survival rate. Currently, if diagnosed early, surgical resection remains the only viable cure. However, only 20% of pancreatic cancer patients meet these criteria. It is therefore necessary to discover new therapies or therapeutic combinations in order to impact significantly this deadly disease. The anti-metabolite agent Gemcitabine is currently being employed to treat pancreatic cancer. While Gem-citabine has shown significant benefit in clinical applications, its ability to more than modestly impact pancreatic cancer is limited. It has been speculated that …

Branching Into Rnai: Synthesis, Characterization And Biology Of Branch And Hyperbranch Sirnas, Anthony Muriithi Maina

Seton Hall University Dissertations and Theses (ETDs)

The cancer epidemic continues to afflict millions of humans world-wide each year and despite a renewed hope with the development of new and improved forms of therapy, a cure for cancer remains an elusive goal. This is partly related to the rise of resilient forms of tumors that have evolved with resistance towards conventional chemotherapy and radiation treatments. Moreover, these non-specific therapeutic regimens are highly toxic, leading to severe immunosuppressive effects which poisons the body and compromises the road towards remission. In an effort to mitigate these limitations, cancer-targeting approaches are currently experiencing a renaissance in the translation of new …

Reduced Amino Acid Specificity Of Mammalian Tyrosyl-Trna Synthetase Is Associated With Elevated Mistranslation Of Tyr Codons, Medha Raina, Adil Moghal, Amanda Kano, Mathew Jerums, Paul D. Schnier, Shun Luo, Rohini Deshpande, Pavel D. Bondarenko, Henry Lin, Michael Ibba

Biology, Chemistry, and Environmental Sciences Faculty Articles and Research

Quality control operates at different steps in translation to limit errors to approximately one mistranslated codon per 10,000 codons during mRNA-directed protein synthesis. Recent studies have suggested that error rates may actually vary considerably during translation under different growth conditions. Here we examined the misincorporation of Phe at Tyr codons during synthesis of a recombinant antibody produced in tyrosine-limited Chinese hamster ovary (CHO) cells. Tyr to Phe replacements were previously found to occur throughout the antibody at a rate of up to 0.7% irrespective of the identity or context of the Tyr codon translated. Despite this comparatively high mistranslation rate, …

The Effects Of Jasmonic Acid And Chemicals In The Ja Pathway On The Defense Systems And Gene Expression In Moss, Physcomitrella Patens And Amblystegium Serpens, Allison Shanks

Undergraduate Honors Thesis Collection

Systemic acquired resistance (SAR) is a defense system used by plants that results in increased resistance to future pathogen infection following an initial pathogen exposure. SAR in vascular plants has been well documented; however, a similar defense system has only recently been documented in non-vascular plants. It is believed that chemicals in the jasmonic acid (JA) pathway are able to activate the SAR response in vascular plants. The non-vascular plant, Amb/ystegium serpens, will be used as a model to test if SAR is triggered by JA and two other molecules in the JA pathway, 12-oxo-phytodieonic acid, and methyl jasmonate. To …

Amino Acid Racemase Enzyme Assays, Atanas D. Radkov, Luke A. Moe

Plant and Soil Sciences Faculty Publications

Amino acid racemases are enzymes that invert the α-carbon stereochemistry of amino acids (AAs), interconverting amino acids between their L- and D-enantiomers in a reversible reaction. In bacteria, they are known to have catabolic physiological functions but are also involved in the synthesis of many D-AAs, including D-glutamate and D-alanine, which are necessary components of the peptidoglycan layer of the bacterial cell wall. As such, amino acid racemases represent significant targets for the development of bactericidal compounds. Amino acid racemases are also regarded by the biotechnological industry as important catalysts for the production of economically relevant D-AAs. Here, we provide …

Reclaiming The Efficacy Of Β-Lactam–Β-Lactamase Inhibitor Combinations: Avibactam Restores The Susceptibility Of Cmy-2-Producing Escherichia Coli To Ceftazidime, Krisztina M. Papp-Wallace, Marisa L. Winkler, Julian A. Gatta, Magdalena A. Taracila, Sujatha Chilakala, Yan Xu, J. Kristie Johnson, Robert A. Bonomo

Chemistry Faculty Publications

CMY-2 is a plasmid-encoded Ambler class C cephalosporinase that is widely disseminated in Enterobacteriaceae and is responsible for expanded-spectrum cephalosporin resistance. As a result of resistance to both ceftazidime and β-lactamase inhibitors in strains carrying blaCMY, novel β-lactam–β-lactamase inhibitor combinations are sought to combat this significant threat to β-lactam therapy. Avibactam is a bridged diazabicyclo [3.2.1]octanone non-β-lactam β-lactamase inhibitor in clinical development that reversibly inactivates serine β-lactamases. To define the spectrum of activity of ceftazidime-avibactam, we tested the susceptibilities of Escherichia coli clinical isolates that carry blaCMY-2 or blaCMY-69 and investigated the inactivation kinetics of CMY-2. Our analysis showed that …

2-Acylamido Analogues Of N-Acetylglucosamine Prime Formation Of Chitin Oligosaccharides By Yeast Chitin Synthase 2, Jacob Gyore, Archana Parameswar, Carleigh Hebbard, Younghoon Oh, Erfei Bi, Alexei Demchenko, Neil Price, Peter Orlean

Chemistry & Biochemistry Faculty Works

Chitin, a homopolymer of β1,4-linked N-acetylglucosamine (GlcNAc) residues, is a key component of the cell walls of fungi and the exoskeletons of arthropods. Chitin synthases transfer GlcNAc from UDP-GlcNAc to preexisting chitin chains in reactions that are typically stimulated by free GlcNAc. The effect of GlcNAc was probed by using a yeast strain expressing a single chitin synthase, Chs2, by examining formation of chitin oligosaccharides (COs) and insoluble chitin, and by replacing GlcNAc with 2-acylamido analogues of GlcNAc. Synthesis of COs was strongly dependent on inclusion of GlcNAc in chitin synthase incubations, and N,N′-diacetylchitobiose (GlcNAc2) was the major reaction product. …

Mutagenesis Of 8-Oxoguanine Adjacent To An Abasic Site In Escherichia Coli Cells Proficient Or Deficient In Dna Polymerase Iv, Savas T. Tsikis

Honors Scholar Theses

It is well established that clustered DNA damages or multiply damaged sites (MDS) are the result of ionizing radiation and that they are characterized by an enhanced mutagenic potential. As a model MDS, we have evaluated the mutagenic and cytotoxic properties of the ubiquitous oxidative DNA damage 8-oxoguanine (G^8-oxo) adjacent to the abasic site lesion (Z) using a single stranded M13mp7L2 vector. The recombinant DNA was used to transform wild type E. coli strains and strains deficient in the translesion DNA polymerase of the Y-family, DNA polymerase IV, in the presence or absence of SOS induction. The percent …

Defining The Sites Of Interaction Of The Fancd2, Fance, And Fancl Proteins, Joseph Mcclanaghan

Senior Honors Projects

Fanconi anemia (FA) is a rare genetic disease characterized by congenital defects, bone marrow failure and increased cancer susceptibility. FA is caused by mutations in any one of 16 genes. These genes encode for proteins that function in the FA-BRCA pathway to repair damaged DNA. Because of its important r­­­ole in DNA repair, this pathway is considered a major cellular tumor suppressor pathway, i.e. is critical for the prevention of cancer. Underscoring this fact, several of the FA genes - including BRCA2, BRIP1, PALB2, and RAD51C - are bona fide breast and ovarian cancer susceptibility genes.

My …

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, …

Phthalates And Phthalate Alternatives: Effects On Proliferative And Estrogenic Target Genes In Ishikawa Cells, Ranjani Sundar '15, Ping Yin, Serdar E. Bulun

Student Publications & Research

Phthalates are used as plasticizers in many of the products found in medical, household, and industrial applications. Much research has not been completed on the effects of these phthalates as potential endocrine disrupting chemicals (EDCs). As these chemicals are ingested, the mechanism by which they affect the reproductive system is largely unknown. The purpose of this study was to observe how 2 phthalates, Di-n-butyl phthalate (DBP) and Diisononyl phthalate (DINP), and 2 phthalate alternatives, Dioctyl terephthalate (DOTP) and BHT (butylated hydroxytoluene)affect uterine cells in comparison to a vehicle treatment and 17β-Estradiol treatment. Changes in expression of mRNA were observed using …