Molecular Biology Commons^™

The Pathophysiological Mechanisms Of Alzheimer's Disease; Investigating Therapeutic Interventions For Disease Onset, Alexandra A. Sandberg

Electronic Theses and Dissertations

Alzheimer’s Disease is a multifarious disease that progressively affects more people as both the proportion of older adults in the population and life expectancy increase in both the United States and worldwide. This devastating disease is a result of rampant neuronal loss in the memory centers of the brain that robs the independence of those who are diagnosed and places a heavy burden on those who care for them. Traditionally speaking, research has focused on the hallmark pathology of amyloid plaques, targeting them to try and prevent disease onset. However, countless failures in clinical trials aimed at this said pathology …

Antioxidant Biomarkers And Nutraceutical Therapeutics In Neurodegeneration And Neurotrauma, Lilia A. Koza

Electronic Theses and Dissertations

Mild traumatic brain injury (mTBI), yielding a Glascow Coma Scale of 13-15, is the most commonly occurring severity of TBI. Pathology from mTBI consists of blood brain barrier disruption, neuroinflammation, oxidative stress, excitotoxicity, mitochondrial dysfunction, protein aggregation, axonal degeneration, and resulting neuronal death. These processes deplete the body’s endogenous antioxidant system. We report a retrospective analysis of antioxidant blood biomarkers in patients with a history of mTBI from a local sports medicine clinic, Resilience Code. We found persistent sex-specific antioxidant depletions in mTBI patients associated with worsened symptomology.

Certain populations, such as athletes, are at high risk for repetitive mTBI …

Organellar Zn2+ Homeostasis And The Role Of Trpml Channels In Neuronal Lysosome Physiology And Axonal Transport, Taylor Franklin Minckley

Electronic Theses and Dissertations

Zinc (Zn²⁺) is crucial for proper cellular function, and as such it is important to measure and track Zn²⁺ dynamics in living cells. Fluorescent sensors have been used to estimate Zn²⁺ content of subcellular compartments, but little is known about endolysosomal Zn2+ homeostasis. Similarly, although numerous sensors have been reported, it is unclear whether and how Zn²⁺ can be released from intracellular compartments into the cytosol due to a lack of probes that can detect physiological dynamics of cytosolic Zn²⁺. My dissertation started with comparing and characterizing different Zn²⁺ sensors including the …

Characterization Of Cofilin And Its Potential Role In The Epha4 Pathway, Brian Donald Condron

Master's Theses and Doctoral Dissertations

EphA4 is a receptor tyrosine kinase that is responsible for cellular adhesion and locomotion using repulsion signaling in early development of Xenopus laevis. EphA4 regulates cellular locomotion by controlling proteins within its signal transduction pathway, which may include the protein cofilin. Cofilin actively severs and removes actin monomers, thus altering the actin cytoskeleton, leading to the cessation of cellular crawl. During the gastrulation phase of embryonic development, individual cells are relocating to create the three primary germ layers of the organism. Failure of this process to occur results in attrition of the embryos, frequently by way of embryonic exogastrulation. …

Phosphatidylserine Externalization On Non-Apoptotic Cells And Lipid Scramblases In C. Elegans, Julia Frondoni

Electronic Theses and Dissertations

Cell corpse clearance is key for animals to avoid inflammation and autoimmune disease. To better understand the “eat me” signal of phosphatidylserine (PS) exposure for non-apoptotic corpse clearance, we attempted to disrupt the externalization of PS on C. elegans polar bodies. The second polar body undergoes a non-apoptotic form of cell death, loses membrane integrity, externalizes PS and is cleared by embryonic cells during early development. During apoptotic and necrotic cell death, PS asymmetry is disrupted by lipid scramblases, which translocate phospholipids between the leaflets of the lipid bilayer. We found neither apoptotic nor necrotic scramblases are required for PS …

The Importance Of Protein Context In Spinocerebellar Ataxia Type 3, Sean Luis Johnson

Wayne State University Dissertations

Spinocerebellar Ataxia Type 3 (SCA3) is a member of the family of polyglutamine (polyQ) neurodegenerative disorders that includes Huntington's Disease and several other SCAs. SCA3, the most common dominant ataxia in the world, is caused by polyQ tract expansion in the protein, ataxin-3. How SCA3 occurs and how to treat it remain unresolved issues. The primary culprit of toxicity in all polyQ diseases is the glutamine repeat: its abnormal expansion leads to neuronal dysfunction and death. With that said, there is indisputable evidence that the way polyQ-dependent toxicity presents—areas impacted, cellular processes perturbed—is predicated in large part on regions outside …

Investigation Of Nuclear Envelope-Associated Progeria Proteins During Nuclear Envelope Rupture, Rhiannon Marie Sears

Dissertations and Theses

The nuclear envelope (NE) is a specialized extension of the endoplasmic reticulum critical for the proper protection and organization of the genome. This interphase-only structure is host to several proteins and their interacting constituents that have various and diverse cellular roles. Mutations in NE constituents are associated with several human diseases. A subset of these diseases, known as progeria syndromes, are characterized by the premature presentation of physiological aging in a variety of tissues. Mutations in the genes LMNA and BANF1, which encode the A-type lamins and barrier-to-autointegration factor (BAF), can lead to these multisystem progeroid diseases. Though the underlying …

Phip Variants Associated With Chung–Jansen Syndrome Disrupt Replication Fork Stability And Genome Integrity, Neysha Tirado-Class, Caitlin Hathaway, Wendy K. Chung, Huzefa Dungrawala

Molecular Biosciences Faculty Publications

Chung–Jansen syndrome (CJS) is a rare, autosomal dominant disorder characterized by developmental delay, intellectual disability/cognitive impairment, behavioral challenges, obesity, and dysmorphic features. CJS is associated with heterozygous variants in PHIP (Pleckstrin-Homology Interacting Protein), a gene that encodes one of several substrate receptors for Cullin4-RING (CRL4) E3 ubiquitin ligase complex. Full-length PHIP, also called DCAF14, was recently identified to function as a replication stress response protein. Herein, we report the identification of two PHIP missense variants identified by exome sequencing in unrelated individuals with CJS. The variants p.D488V and p.E963G occur in different functional elements of DCAF14-WD40 repeat domain and pleckstrin …

Sequence Properties Of An Intramolecular Interaction That Inhibits P53 Dna Binding, Emily Gregory, Gary W. Daughdrill

Molecular Biosciences Faculty Publications

An intramolecular interaction between the p53 transactivation and DNA binding domains inhibits DNA binding. To study this autoinhibition, we used a fragment of p53, referred to as ND WT, containing the N-terminal transactivation domains (TAD1 and TAD2), a proline rich region (PRR), and the DNA binding domain (DBD). We mutated acidic, nonpolar, and aromatic amino acids in TAD2 to disrupt the interaction with DBD and measured the effects on DNA binding affinity at different ionic strengths using fluorescence anisotropy. We observed a large increase in DNA binding affinity for the mutants consistent with reduced autoinhibition. The ΔΔG between DBD and …

Exploring The Functionality Of Putative Bop3 Post-Translational Modifications, Liliya Tkachuk, Rebecca Adams Phd

[Archive] Belmont University Research Symposium (BURS)

All eukaryotic cells require that transcribed mRNAs undergo export form the nucleus to the cytoplasm where they can be translated into proteins. This process requires a host of proteins which are conserved between the unicellular budding yeast, S. cerevisiae, and humans. During this process, Mex67 and other associated proteins facilitate the mRNA to travel across the nuclear pore complex (NPC), doorways embedded in the nuclear envelope. Upon the exit of mRNA, Mex67 is released and recycled back into the nucleus to provide the export of more mRNA. This release occurs through the action of Dbp5, whose activity is regulated …

Establishing A Biochemical System For The Purification And Atpase Activity Of Gst-Dbp5, Sarah R. Utley, Rachel E. Rigsby Phd, Rebecca L. Adams Phd

Science University Research Symposium (SURS)

The export of mRNA out of the nucleus is a crucial step for eukaryotic gene expression. The export of mRNA transcripts is aided by Mex67, which allows export through the nuclear pore complex doorways in the nuclear envelope. Once out of the nucleus, a protein known as Dbp5, bound to ATP, Gle1, and Nup42 aids in the directionality of mRNA export by helping remove Mex67 from the mRNA strand. Following interaction with RNA, Dbp5 then hydrolyzes ATP so that it unbinds the mRNA, allowing for enzyme recycling. Previous efforts worked towards the purification of Dbp5, but the attempts were unsuccessful …

The Promise And Perils Of Molecular Combing, Jeanmarie Mishler

Master's Theses and Doctoral Dissertations

Dynamic Molecular Combing (DMC) is a method of making visible single molecules of DNA. The method stretches the molecules, attaching them to a glass coverslip; labels them with an intercalating dye or fluorescent antibodies; and images the molecules with fluorescent microscopy. After combing, fluorescent in situ hybridization (FISH) can be used to inspect regions on the DNA molecule. DMC is especially technically challenging for undergraduate research laboratories. To make the technique accessible to an undergraduate laboratory this project addresses three challenges: pH of buffer solution, NaOH exposure time, and halogenated thymidine exposure time in yeast (Saccharomyces cerevisiae). A serial pH …

Epigenetic Buffering In Introduced House Sparrows, M. Ellesse Lauer

College of Graduate Studies: Theses & Dissertations

Epigenetic buffering, as an environmentally induced increase in variance of epigenetic states that increases phenotypic variation to buffer populations against decreased fitness, may be a factor that resolves the genetic paradox of introduced species. DNA methylation is a molecular mechanism that could facilitate epigenetic buffering by changing in response to environmental stress. Therefore, epigenetic buffering can be detected through increased variance in DNA methylation in novel or heterogeneous environments. Introduced house sparrows (Passer domesticus) have well-documented phenotypic changes with low genetic diversity, high epigenetic diversity, and high variance in DNA methylation that provide a characteristic signature of epigenetic buffering. …

Evaluation Of Oasl And Herc5’S Role In The Non-Lytic Clearance Of Influenza A Virus From Club Cells, Steve Crisafulli

West Chester University Master’s Theses

Influenza A virus (IAV) is a highly infectious pathogen responsible for causing severe respiratory illness and death in humans and animals worldwide. Due to highly effective strategies to negate host antiviral defenses, IAV leads to the death of nearly all infected cells. Furthermore, IAV induces high levels of genome-damaging oxidative stress within infected cells and suppresses the cellular mismatch repair (MMR) mechanism, thereby inhibiting expression of key antiviral genes, which further contributes to cell death. However, recent studies have demonstrated that a subset of respiratory epithelial cells, called club cells, are able to non-lytically clear IAV and continue to survive …

The Role Of Irf-1 In Spontaneous Mouse Glioma, Aakash B. Vaidya

Theses and Dissertations

Glioblastoma Multiforme has been shown to be one of the deadliest primary brain cancers. One of the reasons why GBM is so deadly, is a unique immunosuppressive tumor microenvironment that promotes GBM growth and progression. Both astrocyte and microglia have been implicated in immunosuppression. In this study, we explored the role of Interferon Regulatory Factor 1 (IRF-1) in astrocytes and glioma cells on the growth of spontaneous glioma tumors. IRF-1 is regulated by the JAK/STAT pathway and induces expression of Programmed death ligand 1 (PD-L1). PD-L1 downregulates immune responses to glioma. We found that IRF-1 had no effect on spontaneous …

Targeting Bcl-2 Family Proteins In Therapy Induced Senescent Cancer Cell Models, Wade Cook

Theses and Dissertations

Non-small Cell Lung Cancer (NSCLC) originates from numerous different cell types in the lungs and is among the deadliest of cancers. Head and Neck Squamous Cell Carcinomas (HNSCC) are derived from the mucosal membranes of the oral cavity, pharynx, and larynx. Both NSCLC and HNSCC are predominately caused by tobacco smoke inhalation and as such mutations in the tumor suppressor gene TP53 are common. Since similarities exist in the root cause of NSCLC and HNSCC, they may also share similarities in treatment methods. Cisplatin is a platinum-based DNA damaging agent that has been used as a cancer chemotherapy for decades. …

Structure Of A Monomeric Photosystem Ii Core Complex From A Cyanobacterium Acclimated To Far-Red Light Reveals The Functions Of Chlorophylls D And F, Christopher J. Gisriel, Gaozhong Shen, Ming-Yang Ho, Vasily Kurashov, David A. Flesher

Faculty Publications

Far-red light (FRL) photoacclimation in cyanobacteria provides a selective growth advantage for some terrestrial cyanobacteria by expanding the range of photosynthetically active radiation to include far-red/near-infrared light (700-800 nm). During this photoacclimation process, photosystem II (PSII), the water:plastoquinone photooxidoreductase involved in oxygenic photosynthesis, is modified. The resulting FRL-PSII is comprised of FRL-specific core subunits and binds chlorophyll (Chl) d and Chl f molecules in place of several of the Chl a molecules found when cells are grown in visible light. These new Chls effectively lower the energy canonically thought to define the "red limit" for light required to drive photochemical …

Leveraging Queueing Theory To Develop Advanced Synthetic Biological Circuits, Prajakta K. Jadhav

Electronic Theses and Dissertations

The complexity and redundancy in the network topology of the cell hinder our understanding of the natural system, making it challenging to engineer living organisms with the desired functionality. The long-term goal of synthetic biology and bioengineering is to engineer cells to perform specific functions with increased robustness. The robust engineered systems can be easily applied to different species with the same outcome. An effective approach is a bottom-up approach where we tease apart the biological pathways and study them independently. Understanding the underlying mechanisms of biological pathways can be further applied to construct complex biological circuits that function similarly …

Increased Cd11b+ Immune Cells Contribute To Thoracic Aortic Aneurysm Rupture, Lucynda Pham

Wayne State University Theses

A life-threatening clinical manifestation of Marfan Syndrome (MFS) is the development of thoracic aortic aneurysms (TAA) which can lead to dissection and or rupture. MFS is caused by mutations in extracellular matrix (ECM) protein, Fibrillin-1 (FBN1) which forms the structural component of elastic microfibrils. It is unclear how mutations in FBN1 cause aneurysm development and progression. In recent years, inflammation and immune cells are being considered an important biological process that contributes to TAA. However, the exact roles of the immune cells are unknown. Here we find increased CD11b+ cells recruited and infiltrated into the vessel wall and their spatial …

Characterization Of L-Malic Acid-Capped Cds Quantum Dots And Examination Of The Nanoncrystal's Biosensor Ability, Andrei A. Potapenko

Honors Theses and Capstones

Ligand-capped quantum dots are microscopic semiconductors commonly used in biomedical research and therapy for cell imaging and drug delivery. Despite the abundance of in vivo applications, the nature of interactions between the nanocrystals and the amino acids comprising human proteins remains insufficiently investigated. In this work, we report on the synthesis, ligand exchange, and characterization of the L-malic acid-capped CdS quantum dots via various spectroscopic techniques. We also assess the ligand-capped nanocrystals as potential probes for some amino acids. We determine that in the presence of L-cysteine, the L-malic acid-capped CdS quantum dots fluorescence signal quenches drastically, thus indicating a …

Inhibition Of Lysine Acetyltransferases Kat 3a/3b And Its Effect On Poliovirus Proliferation, Eduards Norkvests

Legacy Theses & Dissertations (2009 - 2024)

Ribosomes have been traditionally viewed as invariable machinery, but in recent years more and more evidence for their heterogeneity has emerged. Core ribosomal proteins, ribosomal-associated proteins, and post-translational modifications all contribute to the variations found within these crucial subcellular components.In our research, we focused on lysine acetylation – a post translational modification found on many ribosomal proteins. We used a chemical inhibitor of acetyltransferases KAT 3A and KAT 3B to observe the effect that inhibiting acetylation may have in the context of translation. By using poliovirus to shut off conventional cellular translation, we were able to look at a narrow …

Salivary Gland Stromal Heterogeneity And Epithelial Controls, Nicholas L. Moskwa

Legacy Theses & Dissertations (2009 - 2024)

Organogenesis is the process organs go through where cellular communications coordinate all a developing organ needs. What organs need are more cells, in the right place, doing the right job. In the salivary gland, we know that stromal cells are important for organogenesis and that they coordinate the epithelium’s form and functions. However, specific stromal contributions have focused on epithelial quantity and placement. There is less information about how the stroma directs the epithelium towards certain functions. Here we used organoids as a model for understanding what stromal signaling directs epithelial cell fate. We found that stromal cell state is …

Exploring The Roles Of Stress, Codon Usage, And Rna Modifications In Myotonic Dystrophy Type 1, Afrooz Golestanian

Legacy Theses & Dissertations (2009 - 2024)

Myotonic dystrophy (DM), the most common form of muscular dystrophy, is a neuromuscular disease caused by microsatellite repeat expansions. It can represent a multi-systemic autosomal dominant disease with DM1 and DM2 subtypes. A cytosine-thymine-guanine (CTG) triplet repeat in the 3’ untranslated region (3’UTR) of myotonic dystrophy protein kinase (DMPK) gene causes DM1 disease, which leads to the production of a longer, abnormal and toxic mRNA. The toxic DMPK mRNA sequester the splicing proteins such as Muscle blind-like (MBNL) and rbFOX which leads to gene expression alteration. Repeat associated non-AUG (RAN) translation also occurs in DM1. Mitochondrial dysregulation has also been …

Genetic Analysis Of Vibrio Cholerae During Its Hyperinfectious State In Danio Rerio (Zebrafish), Ravipaul Singh

Wayne State University Theses

ABSTRACTGENETIC ANALYSIS OF VIBRIO CHOLERAE DURING ITS HYPERINFECTIOUS STATE IN DANIO RERIO (ZEBRAFISH) by RAVIPAUL SINGH AUGUST 2022 Advisor: Dr. Jeffrey Withey Major: Biochemistry and Molecular Biology Degree: Master of Science Vibrio cholerae is a gram-negative, comma-shaped, monotrichous bacillus and the causative agent of the diarrheal disease cholera. V. cholerae is a natural resident of aquatic environments such as rivers and estuaries and is a highly motile bacterium. Upon entering the human host, V. cholerae travels to its site of colonization in the small intestine and upregulates its virulence factors. Upon escape from the host, V. cholerae can enter a …

Effect Of Allosteric Site Binding On Smyd2 Conformational Ensemble, Jacob Daniel Sobota

Wayne State University Theses

Molecular dynamics simulation allows for the simulation of proteins with precise control over what ligands are present at what sites. The conformational ensemble of a protein can be obtained from MD simulation with and without binding at an allosteric site and compared between to gain insight at what effects binding at an allosteric site has on a protein’s structure. SMYD2, a critical regulator of cellular processes, was recently found to have a novel secondary binding site with allosteric effects on its activity. The discovery of an allosteric site has implications for drug design in the inhibition of SMYD2 to treat …

Mhc Diversity Analysis Of Spheniscus Demersus For In Situ And Ex Situ Populations, Antonieta Van Den Berg Monsalve

Undergraduate Honors Thesis Projects

The South African Penguin has been listed as endangered by the International Union for Conservation of Nature. Major histocompatibility complex (MHC) alleles provide valuable statistics because of their variation in terms of vertebrate genomes and are pertinent to immune and reproductive health. A greater number of MHC alleles correlates with survivability of a population because the genes control the immune and reproductive systems. Legacy research by Otterbein alumni and Dr. Simon Lawrance studied MHC samples from wild, in situ, and captive, ex situ, penguin populations. By comparing these populations' major histocompatibility complexes through biostatistical analysis, contributions to conservation of the …

A Look Into Alzheimer’S Disease—Interventions At The Molecular Level, Priscila Feliciano Nieves

Honors Undergraduate Theses

There are puzzle pieces to the cure for Alzheimer’s Disease (AD), and such can emerge by inspecting the biomolecular interactions and their effects on neuronal cells. The upcoming presented literature review will cover the molecular changes caused by AD pathological progression, explore the relationship between non-AD molecules and AD molecules in the body, and analyze potential contributing factors in AD. In addition, the information to be provided will highlight medicinal alternatives respective to a particular stage in AD.

A Study Of Cobalt (Iii) Oxide Nanoparticle Delivery Of Sirna Molecules Directed Against Signaling Intermediates Of The P2y2 Receptor, Rachel Blair Stroud

Graduate Theses/Dissertations

G protein-coupled receptors are evolutionarily ubiquitous sensors of extracellular signals, propagating intracellular signal cascades through heterotrimeric G proteins. P2Y₂ receptors are GPCRs which are activated by extracellular nucleotides to mediate signaling cascades via Gαq coupling. Many GPCRs are subject to a common mechanism for signal termination involving phosphorylation of the C-terminal tail followed by β-arrestin binding and subsequent endocytic internalization of the complex. This effect has been described for the P2Y₂ R in the 1321N1 astrocytoma cell line, and UTP-induced activation and desensitization profiles have been previously defined. There is need to develop molecular vehicles for safe and …

Function And Expression Of Ribonucleotide Reductase-Encoding Genes In Flavobacterium Johnsoniae, Hunter Scott Doheny

All Graduate Theses, Dissertations, and Other Capstone Projects

Ribonucleotide reductases (RNRs) are essential enzymes that are involved in DNA synthesis. While this makes them ideal targets for antiproliferative drugs, most known RNR targeting agents are nonspecific. This poses a problem when considering antimicrobials, but several groups of bacteria have RNRs that utilize unique mechanisms that could be exploited if fully understood. One such bacteria, Flavobacterium johnsoniae, has the gene for a class Id RNR with a novel activation mechanism. Class Id RNRs belong to the aerobic class I RNRs and seem to have a unique metallocofactor and activation mechanism involving superoxide and manganese. The goal of this research …

Antibacterial Activity Of Commiphora Molmol (Myrrha) Against The Yeast, Mohammad Hassan Alshehri

Selected Full-Text Master Theses 2021-

Commiphora molmol (myrrha) is widely used as a traditional medicine around the globe against inflammatory diseases. It is also considered to be effective as anti-fungal, anti-cancer and anti-oxidant agent. The minimum inhibitory concentration, bactericidal activity and heat stability of antibiotic component in myrrha oil extract has been investigated. The MIC was determined in nutrient free buffer and in nutrient rich peptone glucose buffer. The results showed that MIC was 0.6% in nutrient free buffer as no growth was shown by cells, whereas, in peptone glucose media a slight increase in cell count was seen. It can be concluded that it …