Biochemistry, Biophysics, and Structural Biology Commons^™

Metabolic Reprogramming In Kras-Driven Cancer Cells, Ahmet Hatipoglu

Dissertations, Theses, and Capstone Projects

Cancer cells require nutrient uptake for anabolic reactions needed for cellular growth and proliferation. The mammalian target of rapamycin (mTOR) is a key regulator of cellular growth that links nutrient availability and growth factor signals. mTOR mediated signaling pathways are often dysregulated in a wide range of cancers. We previously reported that KRas-driven cancer cells sense exogenous lipids via de novo production of phosphatidic acid, which ultimately activates both mTOR complexes – mTORC1 and mTORC2. Activated mTORC2 phosphorylates the survival kinase Akt at Ser 473 which is required for full Akt activation. A direct substrate of Akt and a major …

Identifying Co-Factors That Drive Tra-1 Activator Function, Jibran Imtiaz, Youngquan Shen, Ronald Ellis

Stratford Campus Research Day

Gli proteins are involved in cell fate determination, proliferation, and patterning in many species and are major effectors of Hedgehog (Hh) signaling. There are three Gli proteins in humans, and mutations or errors in their regulation lead to a variety of developmental disorders or cancer. However, the mechanisms by which they interact with co-factors are poorly understood. We are analyzing co-factors of Gli proteins using TRA-1 in Caenorhabditis nematodes. The TRA-1 zinc fingers are structurally like those of other Gli proteins, and TRA-1 can be cleaved like other Gli proteins to form a repressor. However, its function has changed during …

The Involvement Of Ubiquitin In Med13 Cyclin C Degradation Following Cellular Stress, Ayesha Gurnani, Brittany Friedson, Katrina Cooper

Stratford Campus Research Day

The Cdk8 Kinase Module is a dissociable regulator of cellular stress response genes, with degradation of its components Med13 and cyclin C eventually determining cell fate decisions such as engaging cell survival or cell death mechanisms. We aimed to explore the roles of ubiquitin in degradation of the Cdk8 Kinase Module following nitrogen starvation, with respect to the potential involvement of deubiquitinating enzyme Doa4, lysine linkage at position K63, and E2 ubiquitin conjugating enzymes Ubc4 and Ubc5. We utilized Western blot analysis to observe nitrogen starvation-induced degradation of Med13-HA in wild-type, doa4 mutant, and K63R yeast strains; degradation of cyclin …

Analyzing Conformational Changes In The Binding Of Hiv-1 Matrix Protein, N And C Terminals, To Calmodulin, Nousha Karimi, Fabian Valdez, Davis Mau, K. Sakamaki

Student Scholar Symposium Abstracts and Posters

Worldwide, more than 38 million people are living with human immunodeficiency virus (HIV), about 84 million people have become infected with HIV since the start of the epidemic, and 40.1 million of those diagnoses led to death. HIV Type-1 is the most common type of HIV, attacking the body’s immune system by destroying CD4 cells. The virus attaches itself to the CD4 cell, taking control of its DNA and replicating itself to release more HIV into the bloodstream. The Gag proteins of HIV-1 are crucial players in the virus’ assembly, release, and maturation; it utilizes its essential matrix protein (MA) …

The Tricarboxylic Acid Cycle As A Central Regulator Of The Rate Of Aging: Implications For Metabolic Interventions, Jonathan M. Borkum

Psychology Faculty Scholarship

Certain metabolic interventions such as caloric restriction, fasting, exercise, and a ketogenic diet extend lifespan and/or health span. However, their benefits are limited and their connections to the underlying mechanisms of aging are not fully clear. Here, these connections are explored in terms of the tricarboxylic acid (TCA) cycle (Krebs cycle, citric acid cycle) to suggest reasons for the loss of effectiveness and ways of overcoming it. Specifically, the metabolic interventions deplete acetate and likely reduce the conversion of oxaloacetate to aspartate, thereby inhibiting the mammalian target of rapamycin (mTOR) and upregulating autophagy. Synthesis of glutathione may provide a high-capacity …

Mitochondrial Roles In Developmentally Programmed Heart Disease, Eli John Louwagie

Dissertations and Theses

Offspring of diabetic and obese mothers (ODOM) have greater risks of heart disease at birth and later in life. However, prevention is hindered because underlying mechanisms are poorly understood. Mounting studies in the Developmental Origins of Health and Disease field suggest that mitochondria play key roles in developmentally programmed heart disease similar to the roles they play in cardiomyopathy in adults with diabetes and obesity. However, whether mitochondria are responsible for the short[1]and long-term cardiac disease seen in ODOM remains unknown. Here, we sought to delineate the roles of mitochondria in the hearts of ODOM, determine whether mitochondria are playing …

Regulation And Function Of Zeb1 Acetylation In Lung Adenocarcinoma Progression And Metastasis, Mabel Perez-Oquendo

Dissertations and Theses (Open Access)

Lung cancer metastasis is leading the causes of cancer-related mortality in the United States and worldwide. Epithelial-to-mesenchymal transition (EMT) is a model for metastasis that results in loss of specialized epithelial cell contacts and acquisition of mesenchymal invasive capacity. Zinc finger E-box-binding homeobox 1 (ZEB1) recognizes and binds to E-boxes of epithelial gene promoters to repress its transcription. ZEB1 has inconsistent molecular weights, which have been attributed to post-translational modifications (PTMs). In the presented dissertation, I specifically addressed the gap in the molecular mechanisms by which PTMs of ZEB1 regulate its ability to induce EMT and how its activity might …

Rational Design, Synthesis And Biology Of Immunostimulatory Peptides, Nelson Casanova

Seton Hall University Dissertations and Theses (ETDs)

This dissertation reports the design, synthesis, characterization, and biological studies of three uniquely structured peptides, derived from ubiquitinated multiple myeloma proteins and ubiquitinated B7H6 ligand. The peptides were made into linear or branched shapes, with the branched peptides containing both major histocompatibility complex (MHC) class two and NKp30 binding motifs properties in one peptide. This results in an immunocytotoxic response (via cytokines and chemokines) of both natural killer cells and cytotoxic T lymphocytes (CTLs). These shapes were determined for data comparison but also to increase cytokine proliferation, the shapes help with healthy cell aviation. Thus, the linear monomer (contains a …

Neuronal Or Intestinal Knockdown Of C. Elegans Nadk-1 Decreases Oxygen Consumption And Reactive Oxygen Species, Jake Regan

Electronic Theses and Dissertations

Reactive oxygen species (ROS) such as H2O2 can damage cellular components and are formed as a byproduct of mitochondrial oxidative metabolism. Studies using the nematode C. elegans have found that increasing ROS during development or early adulthood can extend lifespan, while increasing ROS during later adulthood normally decreases lifespan. NADPH provides the reducing power for several cellular antioxidants and is synthesized in a two-step reaction from NAD+ with the first step being catalyzed by NAD kinase (NADK). In this study, the effects of knocking down C. elegans cytoplasmic NADK, nadk-1 globally or in a neuron or intestine-specific manner starting from …

Studying The Phosphorylation Of Isocitrate Dehydrogenase In Humans, Hannah Smith

Chemistry & Biochemistry Undergraduate Honors Theses

Isocitrate dehydrogenase is an important enzyme in the citric acid cycle where it catalyzes the oxidative decarboxylation of isocitrate to alpha-ketoglutarate. While there are three isoforms of isocitrate dehydrogenase (IDH1, IDH2, and IDH3), this research will focus on IDH1. The phosphorylation of isocitrate dehydrogenase is a process that has been linked to the formation of both luminal-like and basal-like breast cancer. Despite these correlations, the mechanisms that cause breast cancer development are unknown. To examine this, an enzyme activity assay for each phosphorylation variant and crystallization were conducted. The results of these indicate that phosphorylation at each site (IDH1-T77, IDH1-S188, …

Nicotinamide Riboside And Beta-Hydroxybutyrate Activate Parallel Pathways For C. Elegans Lifespan Extension, Mckenzie Peters

Undergraduate Honors Theses

Supplementation with nicotinamide riboside (NR), a form of vitamin B3 and a precursor of nicotinamide adenine dinucleotide (NAD⁺) extends lifespan in the nematode C. elegans and delays aging-related pathologies in mammals. During aging, levels of NAD⁺ decline causing metabolic dysfunction and oxidative damage. Studies in C. elegans found that when NR was administered during larval development it induced the mitochondrial unfolded protein response (UPR^mt), which is frequently associated with lifespan extension. Both calorie restriction (CR) and ketogenic diets (KD) have been shown to extend lifespan, in part through increasing NAD⁺ and through increasing levels …

Development Of A Cannabinoid Testing Method Using Blood Collection Cards And Lc-Ms/Ms, Lindsey K. Reynolds, Matt J. Vergne

Student Works

Cannabis is one of the most widely used drugs in the world. Marijuana is a type of cannabis with high amount of Δ9-tetrahydrocannabinol (Δ9-THC) which is psychoactive and intoxicating. Δ9-THC affects alertness and concentration, reducing driving skills when one is intoxicated. Law enforcement of driving under the influence of drugs (DUID) is difficult for police because there is no rapid way to test for Δ9- THC intoxication at the scene of an accident or police stop. Currently, police have to take suspects to a facility to acquire blood samples for testing and the average time before testing is more than …

The Role Of Sars-Cov-2 Orf8 Protein Arks Motif On Novobiocin Binding, Si Chun Chiu, My T. Nguyen

Celebrating Scholarship and Creativity Day (2018-)

The discovery of the SARS-CoV-2 virus during the COVID-19 pandemic required scientists to develop medical solutions to reduce infectivity, severity of symptoms, and death. Although vaccines and drugs provided urgent assistance, the need to continue developing better drugs is necessary long term, and understanding the structure of the virus and finding potential inhibitors would prove vital to discovering solutions to this worldwide health problem. This experimental project focuses on targeting the unique accessory protein, Open Reading Frame 8 (ORF8) in SARS-CoV-2 through studying its interactions with a repurposable drug, novobiocin. Importantly, ORF8 specializes in helping evade immune system checks by …

Testing Of Indazole Inhibitors Of Kasa, A Vital Enzyme Of M. Tuberculosis, Karissa Highlander

Student Research Submissions

Tuberculosis is a disease that affects the lungs caused by Mycobacterium tuberculosis (M. tuberculosis). Although drug treatment options exist, increased rates of antibiotic resistant strains have become more prevalent in recent years, driving a need for new treatment approaches. KasA, a β-ketoacyl synthase, has been found to synthesize parts of the cell wall and been identified as an attractive drug target. Previous medicinal chemistry research has been completed to synthesize six effective competitive inhibitors of KasA that would potentially block the enzyme from binding the substrate, preventing elongation of the backbone and creation of the mycolic fatty acids that …

Toward The Design, Synthesis, And Characterization Of Abiotic Coiled-Coil Peptides Via Solid-Phase Copper-Catalyzed Azide-Alkyne Cycloaddition (Sp-Cuaac) Click Reaction For The Preparation Of Controlled Self-Assembly Molecular Building Block, Liaquat Ali

Chemistry Theses

The production of cutting-edge materials, the development of novel medications, drug delivery systems, technological advancements, and biosynthesizing all depend on molecular building blocks. Proteins are required for the creation of intricate, well-organized structures, and coiled-coil protein domains are vital subunits for the oligomerization of protein complexes, gene expression, and the structural components of biological materials. The numerous interactions between a wide variety of amino acids make it difficult to assemble protein complexes with a particular shape. In the current study, we successfully designed and synthesized four different 32-residue peptides, each of which had two modified amino azide residues. These peptides …

Apoptosis Induction In Jurkat T-Lymphocytes By Proton Pump Inhibitors (Ppis), Shreya Murali, Randall Reif

Student Research Submissions

Apoptosis, commonly known as programmed cell death, constantly occurs in humans. As a cancer cell increases in acidity, apoptosis is induced. In healthy cells, proton pump proteins allow for H⁺ ions to permeate cellular membranes, regulating pH. However, proton pump inhibitors (PPIs), such as omeprazole, prevent proton movement. In previous studies, omeprazole induced cell death in Jurkat T lymphocytes; however, there was no confirmation of whether the cells died through apoptosis, or through necrosis, where the cell bursts. By using Annexin-V staining, the effects of omeprazole, dexlansoprazole, and esomeprazole on apoptosis induction can be measured. Cell death was observed …

Study Of Protein Extraction Techniques For M. Foliorum Phages, Lola Sibaud, Anna Elgersma

Student Academic Conference

Characterizing phages is becoming increasingly important in biochemistry and biotechnology due to their potential to treat bacterial infections without need for antibiotics. Last year, students attempted to isolate proteins from Microbacterium foliorum infecting phages Babydotz and Rosadiaz. Proteins were successfully extracted; however, after further analysis it was shown that the obtained proteins belonged to the host bacteria and not the phages. The purpose of this study was to find a method to separate phage from host bacterial debris to successfully isolate phage proteins and analyze them later. Isolating phage proteins could help us characterize more phages and know more about …

Novel Plant Peroxidase Investigation For Use In Various Biochemical And Practical Applications, Sally Hess

Liberty University Research Week

Undergraduate

Basic

Activation Of Nrf2 Pathway By Natural Products, Genesis Schat, Madelyn Sedlachek

Liberty University Research Week

Undergraduate

Basic

Characterization Of A Sas3 Homolog In The Human Pathogenic Yeast Cryptococcus Neoformans, Lillianne Bartone

Liberty University Research Week

Undergraduate

Basic