Biochemistry Commons^™

Studies Into The Structure And Function Of Various Domains Of Obscurin And Titin, Rachel A. Policke

Senior Honors Projects, 2010-2019

Muscles give our bodies the ability to move by stretching and contracting. While contraction is accomplished by the well-known actin-myosin interaction, not much is known about stretch. Two integral muscle proteins involved in stretch are titin and obscurin; both are long rope-like protein molecules that seem to act as molecular springs. Mutations in these two proteins can lead to diseases such as hypertrophic cardiomyopathy and muscular dystrophy, as well as a variety of cancers. In an effort to understand muscle stretch and signaling on a more fundamental level, here we present the high resolution structure of obscurin Ig59, a domain …

The Role Of Semaphorin 5a In Pancreatic Cancer Progression And Metastasis, Sugandha Saxena Dr.

Theses & Dissertations

Pancreatic cancer (PC) is an aggressive disease with an overall 5-year survival rate of less than 7%, statistics that have not changed in almost five decades. Metastasis is one of the leading causes of mortality in PC. Accumulating evidence suggests that axon guidance molecules, such as semaphorins, are involved in cancer progression, invasion, and metastasis. Recent genomic characterization of pancreatic ductal adenocarcinoma revealed aberration in axon guidance pathway genes as well. Previous reports from our laboratory have identified one such molecule Semaphorin5A (SEMA5A) as a putative cell adhesion molecule which is involved in organ-specific homing during PC metastasis. My dissertation …

Aberrant Glycosylation In Pancreatic Cancer Progression, Seema Chugh

Theses & Dissertations

Aberrant changes in O-glycosylation patterns underlie pancreatic ductal adenocarcinoma (PDAC) progression and metastasis. Glycosylation is a post-translational modification in which carbohydrate moieties are attached to the protein substrate. My dissertation is focused on mucin-type O-glycosylation, which is the predominant form of O-glycosylation and is regulated by a myriad of glycosyltransferases.

PDAC is one of the most lethal diseases and the mechanistic involvement of aberrant O-glycosylation in its progression and metastasis is unknown. The aberrant glycosylation refers to the appearance of unusual carbohydrate structures such as truncated carbohydrate antigens, often referred to as tumor-associated carbohydrate antigens.

In this dissertation, my goal …

The Rise And Fall Of The Bovine Corpus Luteum, Heather Talbott

Theses & Dissertations

This dissertation describes a study of the mechanisms regulating the genesis and subsequent involution of the temporary endocrine structure, the corpus luteum (CL), through the use of a bovine model. The CL is essential for maintaining a suitable uterine environment for embryo implantation and early development through secretion of the steroid hormone progesterone. The “Rise and Fall” of the CL occurs within each estrous cycle whereby the CL must form from the ruptured follicle, secrete sufficient progesterone for uterine maturation, and at the end of the cycle (or pregnancy) regress to allow new follicular development. During the rise of the …

Epigenetic Regulation Of Salicylic Acid-Mediated Plant Defense, Phillip Key

Senior Theses

Plant pathogens remain a significant threat to the stability of modern agricultural systems, and the investigation of mechanisms to improve the security of food resources has led to the partial characterization of plant immune response. With this progress, there is a newfound ability to analyze the relative pathogen resistance capability of specifically modified organisms, and in doing so, it is possible to identify individual alterations that might play a role in creating a more robust immune response. In this study, ten Arabidopsis thaliana mutants were infiltrated with Pseudomonas syringae pv. morsprunorum alongside positive and negative control Col-0 Wild-Type and npr1-2. …

Paper Microzone Plates As Analytical Tools For Studying Enzyme Stability: A Case Study On The Stabilization Of Horseradish Peroxidase Using Trehalose And Su-8 Epoxy Novolac Resin, Kirsten A. Ganaja, Cory Chaplan, Jingyi Zhang, Nathaniel W. Martinez, Andres W. Martinez

Chemistry and Biochemistry

Paper microzone plates in combination with a noncontact liquid handling robot were demonstrated as tools for studying the stability of enzymes stored on paper. The effect of trehalose and SU-8 epoxy novolac resin (SU-8) on the stability of horseradish peroxidase (HRP) was studied in both a short-term experiment, where the activity of various concentrations of HRP dried on paper were measured after 1 h, and a long-term experiment, where the activity of a single concentration of HRP dried and stored on paper was monitored for 61 days. SU-8 was found to stabilize HRP up to 35 times more than trehalose …

Mechanism Of Lck Activation In Driving Leukemia Cell Proliferation, Hannah E. Dobson

Senior Honors Projects

Leukemia is a type of cancer that develops in blood-forming tissues of the immune system. These tissues can include the bone marrow or sites within the lymphatic system such as the lymph nodes. Leukemia progresses from a mutational event within a white blood cell. Often this mutation alters the cell’s normal life cycle, resulting in uninhibited cell division and growth. With this uncontrolled cell proliferation, mutated white blood cells accumulate and begin interfering with the functioning of healthy cells.

Scientists are unsure of the exact mechanisms required for leukemia development. However, recently scientists identified four characteristic mutations in the protein …

Birc6 Mediates Imatinib Resistance Independently Of Mcl-1, Denis O. Okumu, Michael P. East, Merlin Levine, Laura E. Herring, Raymond Zhang, Thomas S.K. Gilbert, David Litchfield, Yanping Zhang, Lee M. Graves

Biochemistry Publications

© 2017 Okumu et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Baculoviral IAP repeat containing 6 (BIRC6) is a member of the inhibitors of apoptosis proteins (IAPs), a family of functionally and structurally related proteins that inhibit apoptosis. BIRC6 has been implicated in drug resistance in several different human cancers, however mechanisms regulating BIRC6 have not been extensively explored. Our phosphoproteomic analysis of an imatinib-resistant chronic myelogenous leukemia (CML) cell line (MYL-R) …

Determination Of The Substrate Specificity Of Citrus Paradisi Flavonol Specific 3-O-Glucosyltransferase Mutant D344p, Nathan R. Spaulding

Undergraduate Honors Theses

Plants produce a vast array of secondary metabolites. A group of phenolic compounds, the flavonoids, are metabolites ubiquitous among plants and are known to aid in processes such as plant reproduction, UV defense, pigmentation and development. In relation to human health, flavonoids have been found to possess anti-inflammatory, anti-cancer, and antioxidant properties. Flavonoid’s ability to participate in so many interactions is due in part to their subclass variation and further chemical modification. One such modification is glucosylation, where a glucose molecule is added to the flavonoid substrate. The enzymes that catalyze these reactions are known as glucosyltransferases (GT). Citrus paradisi …

Enzyme Kinetics Studies To Guide Mathematical Modeling Of Microdialysis Sampling To Predict In Situ Biochemistry, Justin M. Klucher

Chemistry & Biochemistry Undergraduate Honors Theses

Microdialysis is a diffusion-based sampling method that can be useful for monitoring various biological systems. Matrix metalloproteinases are a class of enzymes responsible for remodeling the extracellular matrix that, when dysregulated, are linked to various diseases. The delivery method of microdialysis is of particular interest as a sampling technique for enzymatic reactions. Microdialysis was performed in vitro using a model enzyme, porcine pancreatic elastase, because it is a useful substitute for matrix metalloproteinases. A colorimetric substrate for elastase, succinyl-ala-ala-ala-p-nitroanilide, and its product p-nitroaniline were measured using a UV-Vis spectrophotometer. Using an expanded Beer’s Law equation, both analytes’ concentrations were determined …

Evaluation Of Different Probiotic Strains Supplemented In Commercial Broiler Rations And Their Influences On Performance, Yield, And Intestinal Microbiota., Justin M. Glasscock

Electronic Theses and Dissertations

The objective of this study was to evaluate Bacillus megaterium, Bacillus licheniformis, and Bacillus subtilis, as probiotic strains compared to Bacitracin Methylene Disalicylate (BMD) 50 as the antibiotic growth promotor, supplemented in commercial broiler rations and their influences on performance, yield, and intestinal microbiota. This trial was completed as a randomized-block design with 4,800 birds split into 96, 5’x10’ pens, and randomly assigned to one of eight treatment groups. The birds were placed at a stocking density of 1.00 ft²/bird, (50 birds/pen), and reared on used pine shaving for 55 days. Throughout the study, bird …

Ubr-5, A Conserved Hect-Type E3 Ubiquitin Ligase, Negatively Regulates Notch-Type Signaling In Caenorhabditis Elegans, Anniya Gu

Renée Crown University Honors Thesis Projects - All

Germline stem cell proliferation in C. elegans is regulated by the distal tip cell (DTC) located at the distal end of each gonad arm. The DTC signals germ cells, through a Notch-type signaling pathway, to proliferate. As germ cells move farther away from the DTC, they transition into meiosis and produce gametes. There are two Notch-type receptors in C. elegans, GLP-1 and LIN-12, which play a role in regulating cell fate decisions. Whenever GLP-1 function is lost, all the germ cells exit mitosis and enter meiosis. If this happens early in development, then the animal is sterile because it does …

Uncovering The Identity And Metabolism Of Bacterial Coa-Rna, Joseph R. Spangler

Dissertations

Coenzyme A is an indispensable molecule in all known life with roles in metabolism, gene regulation, and macromolecule synthesis. As CoA is derived from RNA itself, it’s incorporation into RNA by in vitro methods has proven useful in research probing the origin of life based on the RNA World theory. The discovery in contemporary bacteria of RNA modified with CoA, however, provided an unexpected twist to previously well-characterized bacterial systems. The identity of sequences associated with CoA-RNA has been elusive since their discovery in 2009 based on the difficulties in isolation while maintaining RNA quality. The aim of this study …

Characterization Of P43lgrn-3, Kelly G. Hill

Honors Theses

Alzheimer’s Disease (AD) is a progressive neurodegenerative disorder characterized by extensive memory loss and cognitive deficits, which occur due to severe neuronal loss. Two hallmark lesions, intracellular neurofibrillary tangles composed of hyperphosphorylated tau and extracellular neuritic plaques formed by the aggregation of amyloid-β (Aβ), are responsible for the progressive neuronal loss seen in AD brains. Neurotoxic Aβ aggregates are also known to cause inflammation within the brain. It has recently come to light that severe and acute inflammation, such as seen in traumatic brain injury (TBI), may also lead to AD-type dementia. This has raised the question whether some of …

The Preparation Of Synthetic Myod Mrna For Cellular Differentiation And Innate Immune Response Downstream Application, James D. Grenn

Honors Theses

The development of therapeutic immune responses from the manipulation of embryonic stem cells (ESCs) via induction of synthetic RNA with 5’ capped and 3’ poly(A)tailed ends would lead to development of stem cell therapy. A necessary step in attaining such a goal is to first produce an mRNA transcript from a plasmid containing the open reading frame (ORF) for a transcription factor for cellular activation.

In this research, the DNA plasmid pMD4 encoding MyoD was transcribed into synthetic mRNA. The plasmid was first amplified using Polymerase Chain Reaction (PCR), and analyzed using gel electrophoresis. The amplified template was purified via …

Altering The Structure Of Carboxysomal Carbonic Anhydrase Csosca To Determine The Necessity Of The N-Terminal Domain In Csosca Function, Dana L. Dillistone

Honors Theses

In this project, a DNA construct was designed and developed to remove the first fifty amino acids of the CsoSCA protein in the chemolithotrophic bacterium Halothiobacillus neapolitanus. The csoS3 gene codes for a carbonic anhydrase enzyme (CsoSCA) that is unique to a structure called a carboxysome. Carboxysomes are polyhedral microcompartments where carbon fixation is housed. The carbonic anhydrase is a shell-associated protein that improves the catalytic efficiency of ribulose-bisphosphate carboxylase/oxygenase (RuBisCO), the enzyme that catalyzes the fixation of carbon. By deleting the first fifty amino acids of the carbonic anhydrase, the necessity of the amino acids in carboxysome function was …

Elucidating The Interplay Between Sodium Selenite On The Tick Amblyomma Maculatum Selenoprotein Gene Expression, Afnan M. Beauti

Honors Theses

Selenium (Se) is an element recognized as an essential micronutrient in eukaryote organisms. Selenoproteins contain selenium as selenocysteine, the 21st amino acid. Selenium plays a role in cell growth and functioning. At low concentrations, it can induce growth and at high concentrations, it can cause a cell to stop growing and potentially have toxic effects on the cell and organism. When selenium levels are high, oxidative stress results by the production of reactive oxidative species. Selenoproteins, however, can aid the antioxidant response in the cell. Ticks are arthropods of interest, as they are one of few that contain many selenogenes, …

Phopsphorylation And Ubiquitin Modification At Dna Damage Sites In Response To Double-Strand Breaks, Atanu Paul

Dissertations and Theses (Open Access)

Genomes of all organisms are continuously damaged by numerous exogenous and endogenous sources leading to different kinds of DNA lesions, which if not repaired efficiently may trigger wide-scale genomic instability, a hallmark of cancer development. To overcome this, cells have evolved a sophisticated sensory network called the DNA damage response (DDR) comprised of a large number of distinct protein complexes categorized as sensor, mediator, transducer and effector proteins that amplify the DNA damage signal and activate cell cycle checkpoint to initiate DNA repair or trigger apoptosis where the defect is beyond repair. This intricate signaling pathway is tightly regulated by …

Role Of Mir-29b-1 And Mir-29a In Endocrine-Resistant Breast Cancer., Penn Muluhngwi

Electronic Theses and Dissertations

Therapies targeting estrogen receptor α (ERα) including selective estrogen receptor modulators (SERMs), e.g., tamoxifen (TAM); selective estrogen receptor downregulators (SERDs), e.g., fulvestrant (ICI 182,780); and aromatase inhibitors (AI), e.g., letrozole, are successfully used in treating breast cancer patients whose initial tumor expresses ERα. Unfortunately, the effectiveness of endocrine therapies is limited as ~ 40% of breast cancer patients will eventually acquire resistance to them. The role of miRNAs in the progression of endocrine-resistant breast cancer is of keen interest in developing biomarkers and therapies to counter metastatic disease. This dissertation begins with a review on miRNAs implicated …

Genetically Encoded Fluorescent Protein Biosensor For Nitric Oxide, Wenjia Zhai

Department of Chemistry: Dissertations, Theses, and Student Research

Nitric oxide (NO) is an important molecule in living cells for signaling, thus a specific sensor to detect its level in live cells is needed. Currently there are a few small molecule probes for the detection of NO. A common shortcoming of these probes is their unavoidable leakage from the target cells. In this project, I seek to develop a novel green fluorescent protein (GFP)-based biosensor to detect cellular NO. This GFP-based sensor is genetically encodable and can potentially avoid the possible false positive result due to the leakage. I synthesized an unnatural amino acid (unAA) and examined its incorporation …