Biochemistry, Biophysics, and Structural Biology Commons^™

Nutritional Supplementation And Skeletal Muscle Health In Chronic Diseases, Hexirui Wu

Graduate Theses and Dissertations

Prevalence of chronic diseases in the United States keeps increasing in recent years. There are approximately four in ten adults having chronic diseases in America. Chronic diseases include obesity, aging, heart diseases, cancer and many others. This thesis mainly focuses on obesity and aging. Skeletal muscle performance is impaired in obesity and aging conditions. One common reason causing this could be higher fat mass and lower muscle mass. However, there is no study showing what pathways are involved in the imbalance of body composition. Therefore, the first objective of the thesis is to determine gene expression of selected pathways in …

Structure And Mechanism Of Human Diacylglycerol O-Acyltransferase 1, Lie Wang, Hongwu Qian, Yin Nian, Yimo Han, Zhenning Ren, Hanzhi Zhang, Liya Hu, B V Venkataram Prasad, Arthur Laganowsky, Nieng Yan, Ming Zhou

Faculty, Staff and Students Publications

Diacylglycerol O-acyltransferase-1 (DGAT1) synthesizes triacylglycerides and is required for dietary fat absorption and fat storage in humans1. DGAT1 belongs to the superfamily of membrane-bound O-acyltransferases (MBOAT) that are found in all kingdoms of life and involved in acylation of lipids and proteins2,3. It remains unclear how human DGAT1 (hDGAT1) or other mammalian members of the MBOAT family recognize their substrates and catalyze their reactions. The absence of three-dimensional structures also hampers rational targeting of hDGAT1 for therapeutic purposes. Here we present the structure of hDGAT1 in complex with a substrate oleoyl Coenzyme A solved …

Cloning, Expression, Purification And Characterization Of Heparin-Binding Pocket Of Recombinant Fgf1, Quratulayn Ashraf

Graduate Theses and Dissertations

Fibroblast growth factors are polypeptide members of the FGF family, which to date comprises of at least 22 members. They belong to a group of growth factors and are involved in a variety of cellular processes including wound healing, angiogenesis, differentiation and development (organogenesis). Amongst FGF members, human acidic FGF-1 and basic FGF-2 are the most characterized. FGF-1 and FGF-2 are known to share more than 80% sequence similarity and have an identical structural fold. However, their biological roles are quite different. FGFs bind to heparin and heparan sulfate ligands through their heparin-binding pockets. The interactions are primarily electrostatic in …

Focal Adhesion Kinase And Src Mediate Microvascular Hyperpermeability Caused By Fibrinogen- Γc- Terminal Fragments, Richard S. Beard Jr.

Biomedical Research Institute Publications and Presentations

Objectives

We previously reported microvascular leakage resulting from fibrinogen-γ chain C-terminal products (γC) occurred via a RhoA-dependent mechanism. The objective of this study was to further elucidate the signaling mechanism by which γC induces endothelial hyperpermeability. Since it is known that γC binds and activates endothelial αvβ3, a transmembrane integrin receptor involved in intracellular signaling mediated by the tyrosine kinases FAK and Src, we hypothesized that γC alters endothelial barrier function by activating the FAK-Src pathway leading to junction dissociation and RhoA driven cytoskeletal stress-fiber formation.

Methods and results

Using intravital microscopy of rat mesenteric microvessels, we show increased extravasation …

An Analysis Of Crispr-Cas Gene Editing In Agriculture, Ashley Laliberte

Honors Scholar Theses

The CRISPR-Cas system is a promising form of gene editing, especially for the agriculture industry. The ability to make single-nucleotide edits within a gene of interest, without the need to introduce foreign DNA, is a powerful tool for designing healthier and more efficient crops and food animals. This system provides opportunity for increased nutritional value, decreased food waste, and more economically and environmentally sustainable food production. Though this biotechnology is facing mechanistic limitations due to off-target effects and inefficient homology-directed repair, vast improvements have already been made to improve its efficacy. The CRISPR-Cas system is already the most advanced form …

Effect Of Zinc On Microcystis Aeruginosa And Its Toxin Production, Jose L. Perez

Seton Hall University Dissertations and Theses (ETDs)

Cyanobacteria harmful algal blooms (CHABs) are globally increasing biomasses of detrimental cyanobacteria due to anthropogenic water phosphorous and nitrogen loading and climate change. CHABs often produce secondary metabolites, cyanotoxins, that cause harmful effects to organisms, most water systems, and socioeconomic infrastructures. Additionally, the presence of heavy metal pollutant runoff in CHAB affected environments may result in CHAB population changes – aggravating toxigenicity. Zinc metal resistance and stress response were studied in microcystin (MC) cyanotoxin-producing Microcystis aeruginosa UTEX LB 2385 (M. aeruginosa UTEX LB 2385) and non-MC producing Microcystis aeruginosa UTEX LB 2386 (M. aeruginosa UTEX LB 2386) cyanobacteria. Molecular analysis …

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 …

The Role Of Reactive Oxygen Species In The Gut Immune Response Of Cat Fleas (Ctenocephalides Felis), Clark Hall

Honors College Theses

Fleas transmit numerous deadly and debilitating diseases, including the causative agents of murine typhus and plague. Because initial entry of these infectious agents occurs while blood feeding, the immune response in the flea gut is considered to be the first line of defense against invading microbes. However, relatively few studies have identified the flea immune molecules that effectively resist or limit infection in the gut. In other hematophagous insects, an immediate immune response to imbibed pathogens is the generation of reactive oxygen species (ROS). In this study, we utilized cat fleas (Ctenocephalides felis) to investigate whether natural infections …

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 …

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 …

Mycobacteriophage Morphology As A Diagnostic For Cluster Assignment, Ethan Dionne

Chemistry & Biochemistry Student Scholarship

Major: Biochemistry

Faculty Mentor: Dr. Kathleen A. Cornely, Chemistry and Biochemistry

Phages are viral bodies that infect bacterial hosts, and have shown promising applications as alternatives to antibiotics for the treatment of bacterial infections. This project examines the morphology of siphoviridae mycobacteriophage, which have long, flexible, non-contractile tails as well as the characteristic head, called a capsid. Using electron microscopy photos of sequenced phages, tail length and capsid diameter were measured and compared to further characterize morphological relationships between genetically distinct phages. The data presented has the potential to work as a diagnostic tool to classify unsequenced phages to genetically …

Surface Mutations Promote Metal Ion Affinity In Haemophilus Influenzae Carbonic Anhydrase, Ella Sheehan

Chemistry & Biochemistry Student Scholarship

Major: Biochemistry
Faculty Mentor: Dr. Kathleen Cornely, Chemistry and Biochemistry

αβ-Carbonic anhydrases are metalloenzymes that are essential to the growth of bacteria, making them a target for antibiotic research in the drug industry. These enzymes contain zinc ions that catalyze the hydration of carbon dioxide to bicarbonate for homeostatic balance. To enhance isolation, surface mutations were completed to introduce histidine residues because they demonstrate affinity for Ni-NTA resin in a column chromatography procedure. After generation and isolation of these mutants, the mutant HICA proteins can be used in a kinetic assay to observe the effect of mutation on the rate …

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

Exploration Of K2 Mycobacteriophages With Bred​, Colby Agostino, Olivia Schmitt

Chemistry & Biochemistry Student Scholarship

Colby Agostino ’22
Major: Biochemistry and Computer Science

Olivia Schmitt ’22
Major: Biochemistry

Faculty Mentor: Dr. Kathleen A. Cornely, Chemistry and Biochemistry

ZoeJ and Marcoliusprime are mycobacteriophage capable of infecting tuberculosis causing bacteria via the lytic and lysogenic cycles. The lytic cycle is the form of viral replication that results in cell death. Lysogeny involves phage DNA being integrated with the DNA of the host cell and preserved through binary fission. However, the bacteria causing tuberculosis do not die in the lysogenic phase. This research project will involve creating mutants of ZoeJ and Marcoliusprime that will not contain the genes …

Development Of New Methodology Towards Accessing 2-Imidazoline Scaffolds For Combatting Tuberculosis And Multiple Myeloma By Proteasome Modulation, Karen Saldarriaga, Victoria Rasmussen

Chemistry & Biochemistry Student Scholarship

Karen Saldarriaga ’20
Major: Biochemistry

Victoria Rasmussen '20
Major: Biology and Psychology

Faculty Mentor: Dr. Travis K. Bethel, Chemistry and Biochemistry

Multiple Myeloma (MM) is a disorder of differentiated B cells in which the inhibition of the proteasome is standard care. The current drug, bortezomib, used to treat MM is ineffective against drug tolerance where 97% of all patients become intolerant within a few years. Imidazoline scaffolds are capable of overcoming that resistance and delaying MM tumor growth. We believe we will be able to effectively yield imidazolines. Synthesis will occur with commercially available starting materials, making the process less …

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 …