Biochemistry, Biophysics, and Structural Biology Commons^™

Interactions Of Eukaryotic Translation Initiation Factors And 3' Untranslated Region Of Barley Yellow Dwarf Virus Mrna During Protein Synthesis: A Study Of Equilibrium Binding, Kinetics And Thermodynamics, Bidisha Banerjee

Dissertations, Theses, and Capstone Projects

Eukaryotic initiation factor (eIF) 4F binding to mRNA is the first committed step in cap-dependent protein synthesis. Barley Yellow Dwarf Virus (BYDV) employs a cap-independent mechanism of translation initiation which is mediated by a structural element BTE (BYDV translation element) located in the 3’ UTR of its mRNA. eIF4F bound the BTE and a translational inactive mutant with high affinity; thus questioning the role of eIF4F in translation of BYDV. To examine the effects of eIF4F in BYDV translation initiation, BTE mutants with widely different in vitro translation efficiencies ranging from 5-164% compared to WT were studied. Using fluorescence anisotropy …

Structure And Function In Bacteriophage Phi6, James Carpino

Dissertations, Theses, and Capstone Projects

The present study of bacteriophage Phi6 has been preceded by a great number of exploratory studies of its structure and function, and these studies have formed a basis for Phi6's development into a model organism. In this study, two aspects of the model organism have been examined. 1. There are several uncharacterized and presumed untranslated regions (UTRs) in Phi6's 13.3 kilobase-pair dsRNA genome. I examined the impact of specific modification to the 3' UTR of the small segment of bacteriophage Phi6. I determined that modification to the purported UTR of the small segment resulted in severe fitness costs, supporting a …

Recruitment Of The Ribosomal 40s Subunit To The 3'Untranslated Region Of A Viral Mrna, Via The Eif4 Complex, Facilitates Cap-Independent Translation, Sohani Das Sharma

Dissertations, Theses, and Capstone Projects

Translation of uncapped plant viral RNAs can be facilitated by either an internal ribosomal entry site (IRES) in the 5' untranslated region (UTR) or a cap-independent translation element (CITE) in the 3' UTR. Barley yellow dwarf virus (BYDV) mRNA, which lacks both cap and poly(A) tail, has a translation element (3'BTE) in its 3' UTR that is essential for efficient translation initiation at the 5'-proximal AUG. This mechanism requires binding of the eukaryotic initiation factor 4G (eIF4G) subunit of the heterodimer eIF4F to the 3'BTE and base pairing between the 3'BTE and the 5' UTR. Here we investigate how this …

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 …

Biophysical Characterization Of The Votu Proteases From The Cchf And Dugbe Nairoviruses, Glenn C. Capodagli

Electronic Theses and Dissertations

My research focuses on understanding the substrate specificity of the viral homolog of the ovarian tumor domain protease superfamily (vOTU) from nairoviruses, and the structural reasons for their specificities. The vOTU from the Crimean-Congo Hemorrhagic Fever Virus (CCHFV) has been implicated in the down-regulation of the innate immune response through its ability to cleave post-translational modifications via Ubiquitin (Ub) as well as the Ub-like interferon-stimulated gene 15 (ISG15). vOTU homologs have been found in numerous viruses across several families. Moreover, the effects of these viruses range in severity from mild flu-like symptoms to mortality depending on the species of the …

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 …

The Human Metapneumovirus Small Hydrophobic Protein Has Properties Consistent With Those Of A Viroporin And Can Modulate Viral Fusogenic Activity, Cyril Masante, Farah El Najjar, Andres Chang, Angela Jones, Carole L. Moncman, Rebecca Ellis Dutch

Molecular and Cellular Biochemistry Faculty Publications

Human metapneumovirus (HMPV) encodes three glycoproteins: the glycoprotein, which plays a role in glycosaminoglycan binding, the fusion (F) protein, which is necessary and sufficient for both viral binding to the target cell and fusion between the cellular plasma membrane and the viral membrane, and the small hydrophobic (SH) protein, whose function is unclear. The SH protein of the closely related respiratory syncytial virus has been suggested to function as a viroporin, as it forms oligomeric structures consistent with a pore and alters membrane permeability. Our analysis indicates that both the full-length HMPV SH protein and the isolated SH protein transmembrane …

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 …

The Evolution Of Respiratory O2/No Reductases: An Out-Of-The-Phylogenetic-Box Perspective, Anne-Lise Ducluzeau, Barbara Schoepp-Cothenet, Robert Van Lis, Frauke Baymann, Michael J. Russell, Wilfgang Nitschke

Department of Biochemistry: Faculty Publications

Complex life on our planet crucially depends on strong redox disequilibria afforded by the almost ubiquitous presence of highly oxidizing molecular oxygen. However, the history of O₂-levels in the atmosphere is complex and prior to the Great Oxidation Event some 2.3 billion years ago, the amount of O₂ in the biosphere is considered to have been extremely low as compared with present-day values. Therefore the evolutionary histories of life and of O₂-levels are likely intricately intertwined. The obvious biological proxy for inferring the impact of changing O₂-levels on life is the evolutionary history …

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.

Y- Box Protein 2 (Ybx2) Is A Major Mrna Specific Regulator Of Translation In Spermatogenesis And The Translational Regulation Of The Sperm Mitochondria Associated Cysteine Rich Protein (Smcp) Mrna, Tamjid A. Chowdhury

Graduate Doctoral Dissertations

Spermatogenesis is the process by which diploid stem cells differentiate into haploid male gametes, spermatozoa. As haploid cells differentiate into spermatozoa, they undergo profound changes in morphology and physiology, including total reorganization of chromatin in the nucleus which results in the inability to synthesize new mRNAs about one week before the differentiation of sperm is complete. Consequently, many mRNAs, such as the protamine 1 (Prm1) mRNA and sperm mitochondria-associated cysteine rich-protein (Smcp) mRNA, are transcribed in early haploid spermatogenic cells and stored as translationally inactive messenger ribonucleoprotein particles (free-mRNPs) for several days to a week before the mRNA is translated …

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 …

The Effect Of Tuning Cold Plasma Composition On Glioblastoma Cell Viability, Xiaoqian Cheng, Jonathan H. Sherman, William Murphy, Edward Ratovitski, Jerome Canady, Michael Keidar

Biochemistry and Molecular Medicine Faculty Publications

Previous research in cold atmospheric plasma (CAP) and cancer cell interaction has repeatedly proven that the cold plasma induced cell death. It is postulated that the reactive oxygen species (ROS) and reactive nitrogen species (RNS) play a major role in the CAP cancer therapy. In this paper, we seek to determine a mechanism of CAP therapy on glioblastoma cells (U87) through an understanding of the composition of the plasma, including treatment time, voltage, flow-rate and plasma-gas composition. In order to determine the threshold of plasma treatment on U87, normal human astrocytes (E6/E7) were used as the comparison cell line. Our …

Implications Of The Landauer Limit For Quantum Logic, F. Matthew Mihelic

Faculty Publications

The design of any system of quantum logic must take into account the implications of the Landauer limit for logical bits. Useful computation implies a deterministic outcome, and so any system of quantum computation must produce a final deterministic outcome, which in a quantum computer requires a quantum decision that produces a deterministic qubit. All information is physical, and any bit of information can be considered to exist in a physicality represented as a decision between the two wells of a double well potential in which the energy barrier between the two wells must be greater than kT·ln2. Any proposed …

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 …

Identification Of The Transcriptional Co-Repressor Complex And Its Functions In Arabidopsis Thaliana, Barsha Shrestha

LSU New Orleans Theses and Dissertations

No abstract provided.

The Global Cancer Genomics Consortium's Third Annual Symposium: From Oncogenomics To Cancer Care, Luis Costa, Sandra Casimiro, Sudeep Gupta, Stefan Knapp, M. Radhakrishna Pillai, Mazakazu Toi, Rajendra Badwe, Maria Carmo-Fonesca, Rakesh Kumar

Biochemistry and Molecular Medicine Faculty Publications

The Global Cancer Genomics Consortium (GCGC) is a cohesive network of oncologists, cancer biologists and structural and genomics experts residing in six institutions from Lisbon, United Kingdom, Japan, India, and United States. The team is using its combined resources and infrastructures to address carefully selected, shared, burning questions in cancer medicine. The Third Annual Symposium was organized by the Institute of Molecular Medicine, Lisbon Medical School, Lisbon, Portugal, from September 18 to 20, 2013. To highlight the benefits and limitations of recent advances in cancer genomics, the meeting focused on how to better translate our gains in oncogenomics to cancer …

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, …

Investigation Of Fshr-L Protein Function In Regulating Synaptic Transmission At The Neuromuscular Junction In C. Elegans, Julie Christine Kolnik

Undergraduate Honors Thesis Collection

euronal communication (synaptic transmission) is critical for nervous system function. This communication occurs at specialized junctions called synapses where chemical neurotransmitters signal from presynaptic to postsynaptic cells. Additional signaling via neuropeptide activated G protein-coupled receptors (GPCRs) fine-tunes synaptic communication. GPCRs are a large family of transmembrane receptor proteins that bind extracellular neurotransmitters and neuropeptides to activate intracellular signaling pathways. My project investigated the function of FSHR-l, a GPCR and potential neuropeptide receptor, in regulating synaptic transmission at the neuromuscular junction (NMJ) in Caenorhabditis elegans roundworms, which share conservation of nervous system structure and function with humans. Worms lacking the fshr-I …

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 …

A Comparison Of Angiography Versus Intravascular Ultrasound In The Treatment Of Peripheral Arterial Disease, Michael Pompliano

Senior Theses

Peripheral Arterial Disease is a growing epidemic throughout the United States. It is estimated that 8 to 12 million Americans currently suffer from PAD, a disease of the circulatory system that limits blood flow to your hands and feet. This limited blood flow is due to the narrowing of the arteries that supply blood throughout your body and can disrupt the balance of the nerves and tissues that make up your extremities. If left untreated, it can cause irreparable, life- threatening damage that may result in amputation of the diseased limb. Although the mechanism of PAD is known and well …

Conformationally Stabilized Hiv Envelope Immunogens, Peter Kwong, John Mascola, Gary Nabel, Richard Wyatt, Barna Dey, Ling Xu, Tongqing Zhou, Joseph Sodroski, Wen Yuan, Shi-Hua Xiang

School of Veterinary and Biomedical Sciences: Faculty Publications

Isolated immunogens including a HIV-1 gp120 polypeptide or immunogenic fragment thereof stabilized in a CD4 bound confirmation by crosslinked cysteines, and methods of their use are disclosed. The immunogens are useful, for example, for generating an immune response to HIV-1 gp120 in a Subject.

Basal Nf-Κb Controls Il-7 Responsiveness Of Quiescent Naïve T Cells, Michelle L. Miller, Luqiu Chen, Ping Zhou, Xindong Liu, Monica Michelotti, Nicole Tramontini Gunn, Sarah E. Powers, Xiaoping Zhu, Cesar Evaristo, Maria-Luisa Alegre, Luciana L. Molinero

Biology Department Faculty Articles

T cells are essential for immune defenses against pathogens, such that viability of naïve T cells before antigen encounter is critical to preserve a polyclonal repertoire and prevent immunodeficiencies. The viability of naïve T cells before antigen recognition is ensured by IL-7, which drives expression of the prosurvival factor Bcl-2. Quiescent naïve T cells have low basal activity of the transcription factor NF-κB, which was assumed to have no functional consequences. In contrast to this postulate, our data show that basal nuclear NF-κB activity plays an important role in the transcription of IL-7 receptor α-subunit (CD127), enabling responsiveness of naïve …

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 …