Biochemistry Commons^™

Loss Of Caspase-8 Function In Combination With Smac Mimetic Treatment Sensitizes Head And Neck Squamous Carcinoma To Radiation Through Induction Of Necroptosis., Burak Uzunparmak

Dissertations and Theses (Open Access)

Caspase-8 (CASP8) is one of the most frequently mutated genes in Head and Neck Squamous Carcinomas (HNSCC), and mutations of CASP8 are associated with poor overall survival. The distribution of these mutations in HNSCC suggests that they are likely to be inactivating. Inhibition of CASP8 has been reported to sensitize cancer cells to necroptosis, a unique cell death mechanism. Here, we evaluated how CASP8 regulates necroptosis in HSNCC using cell line models and syngeneic mouse xenografts. In vitro, knockdown of CASP8 rendered HNSCCs susceptible to necroptosis induced by a second mitochondria-derived activator of caspase (SMAC) mimetic, Birinapant, when combined …

Protection Against Atherosclerosis By A Non-Native Pentameric Crp That Shares Its Ligand Recognition Functions With An Evolutionarily Distant Crp, Asmita Pathak

Electronic Theses and Dissertations

C-reactive protein (CRP) is an acute phase protein of the innate immune system that has been evolutionarily conserved. Human CRP is known to exist in two different pentameric conformations; native CRP and non-native CRP that possess differential ligand recognition functions. The structure of CRP evolved from arthropods to humans, in terms of subunit composition, disulfide bonds, and glycosylation pattern. Along with change in structure, the gene expression pattern of CRP also evolved from a constitutive protein in lower invertebrates to an acute phase protein in humans. The objective of this study was to determine the function of a non-native pentameric …

Electrophysiological Characterization Of The Inhibitory Effects Of 2-Amino-4-Bis (Aryloxy Benzyl) Amino Butanoic Acids On Alanine Serine Cysteine Transporter 2 And Sodium Coupled Neutral Amino Acid Transporter 2, Paul Serguei Zakrepine

Undergraduate Honors Theses

Alanine Serine Cysteine Transporter 2 (ASCT2) is a member of the solute carrier 1A (SLC1A) family of transport proteins. It is a Na+ dependent, obligatory neutral amino acid exchanger with the capability to transport glutamine and it is a primary glutamine transport protein in cancer cells. This glutamine transport capability confers an important physiological role for ASCT2 in the maintenance of intracellular amino acid pools for various metabolic and cell signaling pathways. Because of this, ASCT2 is found to be overexpressed in many cancers, which rely heavily on glutamine as an essential nutrient for cell survival and growth. A wealth …

A Novel Mode Of Action Of C-Reactive Protein In Protecting Against Streptococcus Pneumoniae Infection And Synergy With Antibiotics, Donald Ngwa

Electronic Theses and Dissertations

C-reactive protein (CRP) is a part of the innate immune system, is synthesized in the liver, its blood level increases in inflammatory states, and it binds to Streptococcus pneumoniae. The conformation of CRP is altered under conditions mimicking an inflammatory milieu and this non-native CRP also binds to immobilized/aggregated/pathogenic proteins. Experiments in mice have revealed that one of the functions of CRP is to protect against pneumococcal infection. For protection, CRP must be injected into mice within two hours of administering pneumococci, thus, CRP is protective against early-stage infection but not against late-stage infection. It is unknown how CRP protects …

Characterization Of Beryllium Ion Complexation In The Presence Of Biological Buffers Using Isothermal Titration Calorimetry, Guillermo Alexander Ramirez

UNLV Theses, Dissertations, Professional Papers, and Capstones

Be2+ ion is a biologically active metal that is capable of binding to proteins and has been shown to affect various cellular processes. When treated with Be2+, certain cancer cells display cytostatic effects. GSK3β is a regulatory kinase involved in the β-catenin pathway that may be involved in producing these cytostatic effects when Be2+ binds to it. In order to determine binding parameters between Be2+ and GSK3β, isothermal titration calorimetry (ITC) can be utilized. However, titrations at physiological pH cannot be carried out due to Be2+ unique speciation at neutral pH ranges. Significant precipitation occurs at pH 6 and higher …

Investigating The Mechanisms Responsible For Cephalosporin Resistance In Clostridioides Difficile Strain 630, Lara Anna Turello

UNLV Theses, Dissertations, Professional Papers, and Capstones

Clostridioides difficile infection (CDI) is one of the most common nosocomial infections worldwide. A major risk factor for CDI is antibiotic therapy, due to C. difficile’s resistance to a myriad of antibiotics—one of which are cephalosporins. Cephalosporins are ß-lactam antibiotics that function by binding to the active site of penicillin-binding proteins (PBPs), thus inhibiting peptidoglycan synthesis and leading to cell lysis. Gram-positive bacteria can counteract ß-lactams by (i) producing ß-lactamases, (ii) expressing modified PBPs, or (iii) by expressing efflux pumps.

Genomic analysis of C. difficile strain 630 revealed the presence of at least 31 putative ß-lactam resistance genes that encode …

Characterization Of Avidin And Case9 Single Protein Molecules By A Solid-State Nanopore Device, Haopeng Li

Graduate Theses and Dissertations

The shape and charge of a protein play significant roles in protein dynamics in the biological system of humans and animals. Characterizing and quantifying the shape and charge of a protein at the single-molecule level remains a challenge. Solid-state nanopores made of silicon nitride (SiNx) have emerged as novel platforms for biosensing such as diagnostics for single-molecule detection and DNA sequencing. SSN detection is based on measuring the variations in ionic conductance as charged biomolecules translocate through nanometer-sized channels driven by an external voltage applied across the membrane. In this paper, we observe the translocation of asymmetric cylindrical structure CRISPR-Cas9 …

Antimicrobial Activity Of Extracts From The Leaves Of Marrubium Vulgare, Ashley Cravens

Undergraduate Theses

Natural products have served as powerful therapeutics against pathogenic bacteria since the golden age of antibiotics of the mid-20th century. In the United States, antibiotics are a key component of modern medicine and are one of the top written prescriptions every year. However, overuse and misuse of antibiotics has led to an increasing frequency of antibiotic-resistant infections. These infections are difficult and expensive to treat, often resulting in increased length of illness, hospital stays, and mortality rates. This demonstrates a clear need for novel antibiotics in for modern medicine. Murrubium vulgare (white horehound) is a shrub found in the Appalachia …

A Study Of The Antioxidant Versus Pro-Oxidant Nature Of The Amyloid Beta Peptide And An Analysis Of The Natural Products, Isorhamnetin And Narignenin, As Antioxidants, Kaylee Holmes

Honors Theses

Alzheimer’s disease is a neurodegenerative disorder with no cure. Due to the widespread effects of this disease, abundant research efforts have gone towards finding a cure. The amyloid beta (Ab) peptide has been shown to be a potential cause of the disease due to destructive effects on tissues that it can have both by itself and through reactive oxygen species (ROS) generation. This study was performed in order to assess the structural properties of Ab₄₂monomers, fibrils and oligomers, to assess the antioxidant versus pro-oxidant behavior of the Ab peptide, and to assess the antioxidant nature of the natural …

Mutagenesis Of Claudins To Probe In Vivo Interactions And Assemblies, Currey Zalman, Alex J. Vecchio

UCARE: Research Products

Paracellular transport of solutes and the control of the flow of molecules through the intracellular space in vertebrate epithelia is directed by tight junctions (TJs). Claudins form paracellular barriers and pores that determine tight junction permeability. This investigation attempts to explain the molecular bases for destruction and reconstruction of tight junctions within epithelial cells, occurring via both natural and disease-causing mechanisms. This interdisciplinary research is important in the advancement of our understanding of human biology and health, as different disruptions to epithelial tight junctions are hallmarks of many human diseases. The overall objective was to take previously made Claudin containing …

Meeting Radiation Dosimetry Capacity Requirements Of Population-Scale Exposures By Geostatistical Sampling., Peter K Rogan, Eliseos J Mucaki, Ruipeng Lu, Ben C Shirley, Edward Waller, Joan H M Knoll

Biochemistry Publications

BACKGROUND: Accurate radiation dose estimates are critical for determining eligibility for therapies by timely triaging of exposed individuals after large-scale radiation events. However, the universal assessment of a large population subjected to a nuclear spill incident or detonation is not feasible. Even with high-throughput dosimetry analysis, test volumes far exceed the capacities of first responders to measure radiation exposures directly, or to acquire and process samples for follow-on biodosimetry testing.

AIM: To significantly reduce data acquisition and processing requirements for triaging of treatment-eligible exposures in population-scale radiation incidents.

METHODS: Physical radiation plumes modelled nuclear detonation scenarios of simulated exposures at …

Methylation Of Salmonella Typhimurium Flagella Promotes Bacterial Adhesion And Host Cell Invasion, Julia A Horstmann, Michele Lunelli, Hélène Cazzola, Johannes Heidemann, Caroline Kühne, Pascal Steffen, Sandra Szefs, Claire Rossi, Ravi K Lokareddy, Chu Wang, Laurine Lemaire, Kelly T Hughes, Charlotte Uetrecht, Hartmut Schlüter, Guntram A Grassl, Theresia E B Stradal, Yannick Rossez, Michael Kolbe, Marc Erhardt

Department of Biochemistry and Molecular Biology Faculty Papers

The long external filament of bacterial flagella is composed of several thousand copies of a single protein, flagellin. Here, we explore the role played by lysine methylation of flagellin in Salmonella, which requires the methylase FliB. We show that both flagellins of Salmonella enterica serovar Typhimurium, FliC and FljB, are methylated at surface-exposed lysine residues by FliB. A Salmonella Typhimurium mutant deficient in flagellin methylation is outcompeted for gut colonization in a gastroenteritis mouse model, and methylation of flagellin promotes bacterial invasion of epithelial cells in vitro. Lysine methylation increases the surface hydrophobicity of flagellin, and enhances flagella-dependent adhesion of …

Towards The Development Of Low-Cost And Easily-Deployable Sensing Platforms For Phosphate, Maureen Pontarelli, Thomas Koch

Chemistry & Biochemistry Student Scholarship

Maureen Pontarelli ’20
Major: Chemistry

Thomas Koch '20
Major: Biochemistry

Faculty Mentor: Dr. John Breen, Chemistry and Biochemistry

206— Binding Of Telomeric Dna G-Quadruplexes By Abietane Diterpene Natural Products, Tarryn Franciosa, Sarah Ostrowski

GREAT Day Posters

G-quadruplexes are non-canonical higher order DNA structures formed from guanine rich sequences, made up of stacked G-tetrads stabilized by Hoogsteen base pairing and K+ ions. G-quadruplexes are overrepresented in the promoter regions of oncogenes and the 5’UTR of mRNA1. As a result, G-Quadruplexes have been implicated as targets for possible anti-cancer therapeutic agents to treat previously “undruggable” targets like the c-myc and ras oncogenes1. The human telomeric repeat, [5’G3(T2AG3)3], is a repeating, single stranded DNA sequence that can form G-quadruplexes. Telomerase, an enzyme expressed in ~90% of all cancers, is responsible for extending telomeric repeats, making cancer cells immortal. It …

Optimization Of Adc Linkers: Design And Evaluation Of A Fret-Based Adc Linker-Library, Jared T. Miller

Undergraduate Honors Theses

Success of Antibody-drug conjugates (ADCs) relies on the maintained integrity of a chemical linker fusing a therapeutic payload to a monoclonal antibody. Recent reports have revealed the lead linker ValCitPABC has poor stability in rodent models compared to mammalian counterparts, resulting in many clinical investigations predicting poorer ADC efficacy due to premature payload release in these model systems. Optimization of this chemical linker to be resistant both in mouse and human models would streamline ADC progression into clinical trials. Herein we describe the synthesis and development of a FRET-based assay for evaluating linker stability in vitro. Evaluation of lysosomal release …

295— Biomimicry: Investigating The Active Site Model Of Lactate Racemase, Stephanie Podguski, Maisy Ross

GREAT Day Posters

Because of humans’ heavy impact on nature with industrialization and resource extraction, biomimetics, also known as biomimicry, is a study that has emerged. Biomimetics utilizes observations from nature to comprehend the principles of underlying mechanisms and apply concepts that may benefit science, medicine, engineering and the like. An area of biochemistry we are applying this to is the lactate racemase enzyme.This metalloenzyme is found in many prokaryotic organisms and catalyzes the interconversion between the two optical isomers of lactic acid. The structure of this enzyme consists of a square-planar nickel (II) ion coordinated by a histidine residue and a pincer …

385— Optimizing Nitrogen Concentrations To Maximize Lipid Yields For Biodiesel Production, Wady Jacoby, Daria Zhogina, Pavel Ananev, Lauren Saggese, Max Muller, Barnabas Gikonyo

GREAT Day Posters

Select subspecies of microalgae are considered to be the most promising candidates for third generation renewable resources of biodiesel. Algae not only ingest excess carbon emissions from the atmosphere, they also convert it into energy-dense lipids which can be harvested, and then transformed into biodiesel. However, before the fuel industry can adopt algae farming as a realistic alternative to fossil fuels, the process of harvesting algal lipids must be optimized further. Our research aims to make algal lipid extraction more realistic by determining the ideal growing conditions of the algae species Chlorella Vulgaris. Our research this semester focused on two …

Possible Roles For Essential Oils In Chemoprevention And Suppression Of Cancer, Chad Kirk Lillestolen

Senior Honors Theses

Cancer represents one of the costliest and most prevalent diseases to afflict the modern world, even though treatments have evolved steadily over the years and produce an increasingly positive outlook with each development and innovation. Essential oils have been used medicinally- among other purposes- for thousands of years and have begun to attract attention for possible applications to the field of oncology. Numerous investigations and publications have shed light on the possible chemopreventative (antioxidant and antimetastatic) uses of these oils, alongside cancer suppressive (apoptosis-inducing and cytotoxic) abilities that they may possess. With the high annual incidence of cancer and the …

Chem 490: Characterization Of Cellular Targets And Derivatization Of A Lipogenic Pt Anticancer Therapeutic, Keira D. Naff, Jonathan D. White

Virtual 2020 Spring Student Showcase for Research and Creative Inquiry

Platinum-based compounds have been a centerpiece of anticancer chemotherapies since the 1970s. Despite their widespread use, a seemingly endless challenge with these drugs is their toxicity, stemming from non-specific binding of Pt to cellular targets in healthy cells. Within the last few decades only a small number of new platinum-based drugs have demonstrated improved efficacy in any clinical trials, and none have received regulatory approval in the USA. Most of these efforts have focused on either developing improved methods of drug delivery, or on developing non-classical Pt complexes with alternative binding modes. We have begun to explore tethering Pt compounds …

Progress Presentation On The Proposed Function Of Protein 4diu Through Bioinformatics Analyses, Melissa Hoff

Biochemistry and Molecular Biology Presentations

The BASIL project is a scientific inquiry project that aims to determine the function of a protein from its structure. Biochemistry students completed wet lab work, while structural biology students worked in silico. The purpose of this study was to determine the function of the protein with PDB ID: 4DIU. Bioinformatics analyses were completed using several databases: BLAST, Dali, Pfam, and Moltimate, and imaging of the protein was completed using PyMOL software. The BLAST database aligned the primary sequence with known protein sequences. The Dali database compared protein structure with known structures through global alignment. The Pfam database matched our …

Modeling The Alkaline Hydrolysis Of Diaryl Sulfate Diesters: A Mechanistic Study, Klaudia Szeler, Nicholas H. Williams, Alvan C. Hengge, Shina C. Kamerlin

Chemistry and Biochemistry Faculty Publications

Phosphate and sulfate esters have important roles in regulating cellular processes. However, while there has been substantial experimental and computational investigation of the mechanisms and the transition states involved in phosphate ester hydrolysis, there is far less work on sulfate ester hydrolysis. Here, we report a detailed computational study of the alkaline hydrolysis of diaryl sulfate diesters, using different DFT functionals as well as mixed implicit/explicit solvation with varying numbers of explicit water molecules. We consider the impact of the computational model on computed linear free-energy relationships (LFER) and the nature of the transition states (TS) involved. We obtain good …

Examining The Roles Of The Conserved Mrna Deadenylase Complex On Drosophila Neuronal Structures, Megan Mccaughey, Scott Barbee

DU Undergraduate Research Journal Archive

The most common cause of inherited mental deficiency and monogenetic cause of autism is Fragile X Syndrome (FXS). There is little known about the origins of this disease which will be investigated in the present study. The series of experiments conducted examined the potential role of mRNA deadenylation proteins as contributing factors to the pathogenesis of FXS using Drosophila melanogaster as a model organism. One of the main complexes involved in deadenylation is the CNOT complex, which is comprised of many proteins, including POP2, TWIN, and NOT3. Each protein plays a unique role within the CNOT complex. This goal of …

Synthesized Tripodal Amine As Potential Anti-Cancer Therapeutic, Abigail G. Mcnamee

Honors College Theses

Cancer remains a prevalent disease today. This disease may manifest itself in many different ways and affect a variety of tissues with everything from the brain to the blood. With this wide diversity of cancer types, treatment can be complicated since there is not a “one size fits all” treatment for the disease. Surgery, radiation, and chemotherapy are all options that must be weighed with their benefits and side effects. Ultimately though, there are not enough effective treatment options available for every type of cancer. This leaves many with the grim prognosis of never being cured. With this clear need …

Investigating The Toxicology Of Intramuscular Injected Cnt-Ab In Mice Followed By Microwave Hyperthermia., Conner Clark

Honors College Theses

The advent of carbon nanotubes (CNTs) has led to a wide range of research in various fields including cancer therapy for targeting specific localized and site-specific treatment. Carbon nanotubes bound to tumor specific antibodies (Ab) offers specific treatment for cancer cells without affecting surrounding tissue. This treatment makes use of infrared absorptive properties of nanotubes to incinerate both the nanotube and its associated tumor in vivo. We seek to affirm the initial results of CNT in cancer therapy by investigating the toxicological effect in mice injected with CNT-Ab followed by microwave hypothermia. After 1-week post-injection, mice were sacrificed followed …

The Role Of Diet In The Onset Of Depression: A Biochemical Connection Between Nutrition And Mental Health, Katlin Wildeman

Senior Honors Theses

Depression is a major clinical concern, having a complex onset and the presence of multiple, often unidentifiable causes. Depression affects millions of individuals worldwide, with a high prevalence in regions of the world with a Western-style diet as compared to regions with a Mediterranean diet. A Western-style diet consists of foods high in sugar, fat, and processed meats and grains, whereas the Mediterranean diet contains significantly more vegetables, fruits, lean meats, and whole grains. The link between diet and mental health disorders has implications for individuals of all ages who are hesitant to turn to medication. In addition to presenting …

Aminoacyl-Trna Synthetases, Miguel Angel Rubio Gomez, Michael Ibba

Biology, Chemistry, and Environmental Sciences Faculty Articles and Research

The aminoacyl-tRNA synthetases are an essential and universally distributed family of enzymes that plays a critical role in protein synthesis, pairing tRNAs with their cognate amino acids for decoding mRNAs according to the genetic code. Synthetases help to ensure accurate translation of the genetic code by using both highly accurate cognate substrate recognition and stringent proofreading of noncognate products. While alterations in the quality control mechanisms of synthetases are generally detrimental to cellular viability, recent studies suggest that in some instances such changes facilitate adaption to stress conditions. Beyond their central role in translation, synthetases are also emerging as key …

The Classification Of An Unknown Protein 3h04, Britney Dyszel

Biochemistry and Molecular Biology Presentations

An unclassified protein in the Protein Data Bank, 3H04, was selected as a protein of interest. Research was performed in silico to gain key information on the structure, sequence, and homology of protein 3H04. This research was guided using the BASIL Project’s protocols on in silico research. Several databases were utilized to study protein 3H04. Based on the data gathered, unclassified protein 3H04 is an aminopeptidase that cleaves prolyl-dipeptidyl peptide bonds through alpha beta hydrolase function.

The Role Of Conformational Dynamics In Isocyanide Hydratase Catalysis, Medhanjali Dasgupta

Department of Biochemistry: Dissertations, Theses, and Student Research

Post-translational modification of cysteine residues can regulate protein function and is essential for catalysis by cysteine-dependent enzymes. Covalent modifications neutralize charge on the reactive cysteine thiolate anion and thus alter the active site electrostatic environment. Although a vast number of enzymes rely on cysteine modification for function, precisely how altered structural and electrostatic states of cysteine affect protein dynamics, which in turn, affects catalysis, remains poorly understood.

Here we use X-ray crystallography, computer simulations, site directed mutagenesis and enzyme kinetics to characterize how covalent modification of the active site cysteine residue in the enzyme, isocyanide hydratase (ICH), affects the protein …

Polyglucosan Body Structure In Lafora Disease, M. Kathryn Brewer, Jean-Luc Putaux, Alberto Rondon, Annette M. Uittenbogaard, Mitchell A. Sullivan, Matthew S. Gentry

Lafora Epilepsy Cure Initiative Faculty Publications

Abnormal carbohydrate structures known as polyglucosan bodies (PGBs) are associated with neurodegenerative disorders, glycogen storage diseases (GSDs), and aging. A hallmark of the GSD Lafora disease (LD), a fatal childhood epilepsy caused by recessive mutations in the EPM2A or EPM2B genes, are cytoplasmic PGBs known as Lafora bodies (LBs). LBs result from aberrant glycogen metabolism and drive disease progression. They are abundant in brain, muscle and heart of LD patients and Epm2a^-/- and Epm2b^-/- mice. LBs and PGBs are histologically reminiscent of starch, semicrystalline carbohydrates synthesized for glucose storage in plants. In this study, we define LB architecture, …

Characterization Of A Split-Nluc Assay For Monitoring Changes In Alpha-Synuclein Solubility In Living Cells, Baolong Truong

Honors Program: Senior Projects (Public)

Alpha-synuclein is the primary constituent of Lewy Bodies, protein aggregates associated with Parkinson’s Disease, Dementia with Lewy Bodies, and Multiple Systems Dystrophy. Given the terminal nature of these synucleinopathies, the need for an assay that can report on alpha-synuclein aggregation levels in living systems is critical. Western blotting represents one potential approach to this problem; however, this technique can often be limited by selectivity of available antibodies and experimental reproducibility. Herein, we describe a novel luminescence-based assay capable of detecting alpha-synuclein solubility in bacterial cells. This platform can report on the influence of disease-relevant mutations and small molecules. Antibodies are …