Biochemistry, Biophysics, and Structural Biology Commons^™

The Chemistry Of Red Lipstick: The Impact Red Lipstick Has On Society, Lilliana Weldeslassie

Electronic Theses & Dissertations (2024 - present)

Cosmetic chemistry is deeply embedded in everyday life, shaping the products people use from morning to night. Among these, red lipstick stands out as a formulation that blends complex chemistry with a cultural meaning. This thesis examines the scientific foundations of red lipstick through its chemical composition, pigment structure, toxicological history, analytical methods, and evolving sustainability practices. Historically, red lipsticks relied on high-risk ingredients such as lead, mercury, and other toxic metals, reflecting an era before chemical safety and regulatory oversight were incorporated.²¹ Modern formulations have established safer synthetic dyes, natural waxes, plant-based oils, and stabilizers created to optimize …

Bio-Orthogonal Chemistry-Based Strategy To Turn-On And Turn-Off Crispr-Cas9 Gene Editing In Solution And In Live Cells, Bhoomika Pandit

Electronic Theses & Dissertations (2024 - present)

The CRISPR–Cas9 system is a widely popular tool for genome engineering. There is a strong interest in developing tools for temporal control of CRISPR-Cas9 activity to address some of the challenges and to broaden the scope of potential applications. In this thesis I describe two biorthogonal based approaches to either Turn-ON and Turn-OFF CRISPR-Cas9 gene editing.

In first project work I describe a bio-orthogonal chemistry-based approach to Turn-ON Cas9 nuclease activity with temporal precision. We report a TCO-acylimidazole reagent that acylates 2′-OH groups of RNA. Poly-acylation (“cloaking”) of RNA was optimized in vitro using a model 18-nt oligonucleotide, as well …

Photo And Spatial Control Of Rna Structures And Functions: Exploring Positional Effects And Photo-Responsiveness Of Azobenzene Modified Nucleotides, Jinxi Du

Electronic Theses & Dissertations (2024 - present)

RNA molecules perform many important biological functions by forming complex three-dimensional structures stabilized by base pairing, tertiary interactions, and metal ion coordination. Because RNA function depends strongly on its structure, methods that allow reversible control of RNA conformation and activity are important for understanding RNA behavior and for potential therapeutic applications. However, achieving reversible and site-specific control of RNA structure, especially at the single-nucleotide level, remains challenging. In this dissertation, I developed and applied azobenzene-modified nucleotides as a chemical tool to enable optical and spatial control of RNA structure and function.

The first part of this dissertation focuses on establishing …

Channel-Opening Kinetics Of Complex Kainate Receptors, Noah S. Saunders

Electronic Theses & Dissertations (2024 - present)

Ionotropic glutamate receptors (iGluRs) are found both pre- and postsynaptically in neuronal membranes, and mediate the majority of fast excitatory synaptic transmission in response to the binding of glutamate, a major excitatory neurotransmitter in the central nervous system (CNS). Ionotropic glutamate receptors are divided into three distinct subtypes: kainate, α-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid (AMPA), and N-methyl-D-aspartic acid (NMDA) receptors. Auxiliary proteins specific to each receptor subtype also play a role in tuning both receptor expression and gating properties, such as neuropilin and tolloid-like (NETO) proteins that modulate kainate receptors, and transmembrane AMPA receptor regulatory proteins (TARPs) that regulate AMPA receptors. Like …

Development Of Novel Small Molecule Therapeutics For Myotonic Dystrophy, Xhesika Azis

Biological Sciences

Myotonic Dystrophy type 1 (DM1) results from expanded CUG repeat RNA that sequesters MBNL proteins and disrupts alternative splicing. Small molecules that bind toxic repeat RNA and release MBNL proteins represent a promising therapeutic strategy. This thesis examines newly synthesized modified polycyclic compounds (MPCs) engineered to target CUG RNA with enhanced specificity and efficacy. Through Suzuki–Miyaura coupling and benzoquinone-mediated cyclization, MPC03 was synthesized and characterized by NMR and LC–MS.

The biological activity of these compounds was assessed in DM1 patient-derived myotubes and fibroblasts. MPC03 consistently produced dose-dependent rescue of multiple MBNL-regulated exons, restoring splicing patterns toward those observed in healthy …

Conserved A-Rich Regions In The 3’ Utr Of Zika Virus Differentially Affect Viral Gene Expression, Kristen Kaytes

Electronic Theses & Dissertations (2024 - present)

Following its discovery in 1947, Zika virus garnered little attention in the global stage until a rapidly spreading epidemic brough the virus to the global stage in 2015. Continuous advances in research have begun to further the understanding of the molecular biology of Zika virus, however much is still unknown. Much of our understanding of the virus comes from cross reference to other viruses within the same family, such as Dengue virus and West Nile virus. A commonality of these viruses is that they resemble cellular mRNAs and have a single-stranded positive-sense RNA genome that contains a 5’-cap but lacks …

Development Of Dna Nanoswitches With Aptamer Based Detection For Thrombin, Camryn A. Beckles

Electronic Theses & Dissertations (2024 - present)

Bio-transducers are devices capable of converting the binding signals from molecular recognition events into readable signals for analytical detection. There is a need for modular bio-transducers that can specifically detect a wide range of analytes using a unified readout technique, as this approach could dramatically reduce costs of healthcare diagnostics and environmental monitoring.

To create such a modular transducer, the molecular recognition properties of aptamers will be used and integrated with the already established biosensing capabilities of DNA nanoswitches that reconfigure their shape in the presence of their target molecule. In this design, the detector strands of the nanoswitch will …

Investigating Rna Dysfunction Of Inherited Neuromuscular And Neurodevelopmental Disease, Jacob H. Schroader

Electronic Theses & Dissertations (2024 - present)

ITPase deficiency is a rare but fatal, autosomal recessive enzyme deficiency involving encephalopathy, microcephaly, congenital cataracts, hypotonia, developmental delay, and dilated cardiomyopathy. Within a decade since the original description of the severe form in humans, there are huge gaps in the field regarding the underlying molecular mechanisms driving pathogenesis resulting from ITPase deficiency. Past studies have focused on characterization of the organism level ITPase-deficient phenotype, but the molecular and cellular characterization remains to be fully described. Due to the biochemical function and established biological role of the ITPase enzyme, investigation into the consequences of inosine accumulation and misincorporation into RNA …

Interfacing Neural Models: Biocompatibility And Fabrication Of A Flexible, Self-Folding Microelectrode Array, Fernando A. Pesantez Torres

Electronic Theses & Dissertations (2024 - present)

Neurodegenerative diseases pose a formidable challenge in modern medicine, necessitating the development of advanced research tools that can elucidate their complex pathophysiology. Recent advancements in neurodegenerative disease research have led to the development of three-dimensional (3D) neurodegenerative organoids using human induced pluripotent stem cells (hiPSCs). These organoids closely mimic human brain architecture and functionality, providing a valuable tool for understanding complex diseases. Additionally, the ability to generate and study brain organoids consistently and in large quantities holds potential for a controlled in vitro setting and high-throughput drug screening. However, these models are complex systems requiring specialized maintenance, analysis, and manipulation …

Physiological Structure, Activity, And Interactions Of The Formin, Human Diaphanous Homologue 1, Aaron Premo

Electronic Theses & Dissertations (2024 - present)

Human Diaphanous Homologue 1 (DIAPH1) is a 143 kDa functional protein that plays a critical role in the regulation of actin dynamics within eukaryotic cells. As a formin, DIAPH1 facilitates the assembly of actin filaments from globular actin monomers, a process essential for cellular structure, motility, and other fundamental cellular processes. Beyond its structural role in actin polymerization, DIAPH1 is implicated in several diseases, including diabetes, cancer, and inflammation, as well as complications like hearing loss. Despite its significance in human health, the functional and structural properties of DIAPH1, particularly in human cells, remain less explored compared to related proteins, …

Technological Development Of In-Cell Nmr: Microfluidic, Metabolomic, And Fluxomic Approaches, Nicholas Sciolino

Electronic Theses & Dissertations (2024 - present)

In the fields of structural biology, metabolomics, and fluxomics, there is a driving, technique-based concern when it comes to high-resolution spectrometry and its marriage to biological and physiological relevance. Sample preparation often involves cellular perturbation, lysate separation schemes, combinations with non-biological reagents, and timeline slack. Conceptually, the farther we get from the cell, the greater the potential disparity between what exists in vivo and our in vitro manipulations. This is particularly true when seeking to collect data on transfected targets of interest, and on sensitive metabolic equilibria that occur on the order of minutes. The question remains: if we are …

Characterization Of Adaptive Quorum Sensing In Pseudomonas Aeruginosa, Kayla Simanek

Electronic Theses & Dissertations (2024 - present)

Pseudomonas aeruginosa is an opportunistic pathogen that is highly antibiotic resistant and causes tens of thousands of infections each year. It persists in hospitals by forming biofilms on medical equipment like ventilators and catheters, making it difficult to eradicate. Biofilm formation, among other virulence factors of P. aeruginosa, is regulated through quorum sensing, a mechanism of bacterial communication. Quorum sensing is primarily coordinated through LuxI-R type systems comprised of an autoinducer synthase and receptor, respectively. Canonically, the first system to be expressed is LasI-R, and LasR upregulates the second arm of the quorum sensing network, the RhlI-R system. Research …

Development Of Selective Rna Aptamers For Kainate Receptors, Samantha Ingenito

Legacy Theses & Dissertations (2009 - 2024)

Ionotropic glutamate receptors (iGluRs) play a major role in mediating the excitatoryfunctions in the central nervous system (CNS). iGluRs are ligand-gated ion channels that are activated when glutamate binds to the extracellular ligand binding domain, thereby leading to the opening of the ion channels. Three subtypes of iGluRs include kainate receptors, α-amino-3- hydroxy-5-methyl-4-isoxazole propionate (AMPA) receptors, and N-methyl-D-aspartate (NMDA) receptors. Abnormal and dysregulation of these receptors have cytotoxic effects for neurons and have been implicated in various neurological diseases. For instance, elevated expression of a key AMPA receptor subunit has been linked to conditions such as ALS, where cytotoxic levels …

Identifying Novel Therapeutics And Modifiers Of Myotonic Dystrophy Type 1, Jesus Alberto Frias

Legacy Theses & Dissertations (2009 - 2024)

The expansion of microsatellite repeats within the human genome has been identified as the cause of numerous hereditary diseases, including myotonic dystrophy (DM). DM is an autosomal dominant disease with a worldwide prevalence of ~1:8000 individuals. DM presents multisystemic symptoms such as myotonia, cardiac conduction defects, muscle wasting and weakness, insulin resistance, and cataracts. There are two genetically distinct, yet clinically similar types of DM: DM type 1 (DM1), caused by CTG repeat expansions in the 3’ UTR of the dystrophia myotonica protein kinase (DMPK) gene and DM type 2 (DM2), resulting from CCTG repeat expansions in the first intron …

Chemical Biology Approach To Study Rna Modifications, Ya Ying Zheng

Legacy Theses & Dissertations (2009 - 2024)

Nucleic acid modifications have gained compelling interest for their pivotal roles in cellular and biological processes. These modifications introduced a new layer of regulation without altering the original genetic sequence. In this burgeoning field of epitranscriptomics, many of the chemical modifications have emerged as potential biomarkers in therapeutic applications. Inosine is an essential post-transcriptional RNA modification that has functional roles in modulating the fate of all RNAs. The enzyme ADAR catalyzes the deamination of adenosine to inosine. This can also lead to change in the eukaryotic transcriptome due to A-G miscoding since inosine preferentially base pairs with cytosine. Moreover, hyper-editing …

The Study Of Ribosome-Amplified Metabolism, Rambo, Effect In Vitro And In Live Cells, Jianchao Yu

Electronic Theses & Dissertations (2024 - present)

Quinary interactions arise due to the extreme macromolecular crowding inside live cells. Quinary interactions affect intracellular protein stability, activity, and homeostasis. Ribosomes, traditionally known for their role in protein synthesis, have been found to engage in quinary interactions with metabolic enzymes, modulating their activity and thereby revealing a potential regulatory role for ribosomes in cellular metabolism. This phenomenon, termed the Ribosome-Amplified MetaBOlism (RAMBO) effect, was investigated in this dissertation through a series of in vitro and in vivo studies using primarily Nuclear Magnetic Resonance (NMR) spectroscopy.

Firstly, an NMR-based direct enzyme assay compatible with ribosome was developed and validated using …

Crispr-Cas Enabled Dna Nanotechnology For Advanced Pathogen Detection, Mahera J. Kachwala

Legacy Theses & Dissertations (2009 - 2024)

The ever-growing list of carcinogens, toxicants, pathogens, and other disease-causing agents necessitates the development of new and improved mechanisms of disease detection. A better understanding of events leading up to the diseased state and early diagnosis is imperative for the timely management and targeted treatment of diseases affecting the biological world. Recent achievements in DNA nanotechnology have led to the prominence of DNA-based technologies for multiplexed biological sensing, high-throughput analysis, and improved diagnostics. Typical methods of disease detection employ complex multi-step procedures and advanced equipment, which significantly reduces their accessibility while elevating their cost. DNA functionalized sensing systems that examine …

Identification Of Genes Conferring Resistance To 2-Amino-3-Methylimidazo [4,5-F] Quinoline Genotoxicity In Budding Yeast Using High-Throughput And Targeted Approaches, Michael J. Dolan

Legacy Theses & Dissertations (2009 - 2024)

Heterocyclic aromatic amines (HAAs) are potent carcinogenic agents found in charred read meat and cigarette smoke. We hypothesize that HAAs may contribute to red meat being a risk factor for colorectal cancer (CRC). At present, few eukaryotic genes conferring resistance to HAAs have been identified. In this research, the genome of Saccharomyces cerevisiae (budding yeast) was profiled using next-generation sequencing to identify genes conferring resistance to one such HAA, 2-amino-3-methylimidazo[4,5-f] quinoline (IQ).CYP1A2 and NAT2 activate IQ to become a mutagenic nitrenium compound. Deletion libraries expressing human CYP1A2 and NAT2 or no human genes were exposed to either 400 or 800 …

Vircy-Seq : A Protocol For Characterizing Viral Activity, Tyler James Dion

Legacy Theses & Dissertations (2009 - 2024)

The main purpose of pharmaceutical production is to produce safe effective medicine for patient use. In an effort to ensure patient safety constant surveillance for viruses takes place. The detection of a viral nucleic acid in a pharmaceutical production setting results in investigations to assess its infectious potential. This is an intensive, expensive process that entails many tests such as the observation of hemadsorption, cytopathic effects (CPE), and more. These tests are typically specific and only capture certain viruses, as factors like CPE can only be observed in some viral species. A new investigational method that is effective on all …

Understanding SjöGren's Syndrome As A Systemic Autoimmune Disorder, Gaietchyne Chery

Legacy Theses & Dissertations (2009 - 2024)

Sjögren’s syndrome is an autoimmune condition characterized by a dysfunction in the lachrymal and salivary glands which results in dry eyes and dry mouth. Since its first description in 1892, the disease is one of the most common autoimmune diseases after lupus erythematosus and rheumatoid arthritis in the United States. Despite its high prevalence in the general population, Sjögren’s syndrome remains hard to diagnose due to the wide range of symptoms associated with the disease that is also shared by other conditions. Furthermore, the mechanisms behind the pathogenesis are not properly understood even though multiple factors have been proposed to …

Development Of Nucleic Acid Diagnostics For Targeted And Non-Targeted Biosensing, Christopher William Smith

Legacy Theses & Dissertations (2009 - 2024)

The field of nucleic acid technology is rapidly expanding with new impactful discoveriesbeing made each year. Starting from the discovery of the double-helix structure, cloning, gene editing, polymerase chain reaction (PCR), CRISPR technology, and even the late mRNA vaccines; nucleic acid technology is at the forefront of improving medicine. Nucleic acid technology is extremely versatile due to its easy programmability, automated cheap synthesis, and even its catalog for numerous chemical modifications that can be used to alter structure stability. For example, the number of permutations that can be made with DNA just by altering the code for adenine (A), cytosine …

Characterizing And Epitope Mapping Single-Domain Antibodies On Borrelia Burgdorferi Protein Ospa, Saiful Basir

Legacy Theses & Dissertations (2009 - 2024)

Epitope mapping a protein that enables pathogenesis is crucial for the development of therapies and prophylactics that can inhibit the pathogen’s function and its transmission of disease. The lipoprotein OspA enables Lyme Disease etiologic pathogen, Borrelia burgdorferi, to inhabit the tick midgut until transmission occurs. Anti-OspA mAbs and their smaller VHH counterparts are highly specific and tailored to bind proteins such as OspA, reproducibly, at established binding sites or epitopes. Previous studies found an array of mAbs that successfully bound OspA and have already been used in epitope mapping. To our knowledge, this is the first use of VHHs in …

Amyloid Fibril Formation And Polymorphism : A Critical Role Of Sulfur-Containing Amino Acid Residues, Tatiana Quiñones-Ruiz

Legacy Theses & Dissertations (2009 - 2024)

Protein aggregation that results in the formation of amyloid fibrils has been linked to many neurodegenerative disorders, including Alzheimer’s disease and Parkinson’s disease. The sulfur atoms in methionine (Met) and cysteine (Cys) residues of proteins can be readily oxidized, significantly affecting their properties. Oxidation of sulfur-containing amino acids has recently been shown to affect protein fibrillation. This work presents novel findings on Cys and Met redox reactions that are related to the formation of amyloid fibrils and on the polymorphism of a model fibrillogenic protein, hen egg white lysozyme (HEWL). Biophysical techniques including Raman spectroscopy, atomic force microscopy, electron paramagnetic …

An Ims-Ms/Md Workflow For Determining Higher Order Structure And Dynamics Of Nucleic Acids, Rebecca D'Esposito

Legacy Theses & Dissertations (2009 - 2024)

Ion mobility spectrometry - mass spectrometry (IMS-MS) has potential for the investigation of structure and dynamics in large biopolymers, which will come to full fruition only with a firmer understanding of how to interpret the experimental data. Numerous studies have employed elements of nucleic acid (NA) secondary structure, such as duplexes and hairpins, to explore the relationships between structure, experimental conditions, and actual observations. When combined with molecular dynamics simulations (MDS), IMS-MS can be effectively employed to perform structural elucidation of biomolecules that are not readily amenable to established techniques employed for structural analysis.

N6-Methyladenosine Rna Modifications In Myogenesis / Narrative Competence And Cognitive Mapping As A Culturally Sustaining Pedagogy In The Education Of Emergent Bilinguals, Marina Danielle Infantado

Legacy Theses & Dissertations (2009 - 2024)

Myogenesis involves skeletal muscle stem cells (MuSCs) that produce and regenerate skeletal muscle during regular growth and repair. However, when this system fails to function normally, it can lead to musculoskeletal diseases like Duchenne Muscular Dystrophy (DMD). Therefore, it is important to study the molecular mechanisms behind this developmental process in order to seek therapies and solutions for these types of diseases. Our interest lies in the field of epitranscriptomics, which focuses on post-transcriptional ribonucleic acid (RNA) modifications, particularly N6-methyladenosine (m6A), which involves the addition of a methyl group to the adenosine nucleotide, a process that is mediated by the …

Parallel Networks That Govern The Transcriptional Response To Stress, Serene Anne Durham

Legacy Theses & Dissertations (2009 - 2024)

The transcription factor, p53, plays a pivotal role in the oversight of many stimulus-dependent pathways. Its ability to respond to a wide variety of cellular stress stimuli by activating a broad range of target genes has led it to be characterized as a stress-dependent transcription factor. Our research focuses on deconvoluting the varied transcriptional response to distinct stress signals in an attempt to define the regulatory strategies leading to gene activation after cell stress. We have found that distinct stress response networks, some of which are p53-independent, are converging at activation of a common set of target genes. Our data …

Characterization Of The Role Of The Replicase And Quasispecies Diversity In Flaviviral Evolution And Host Adaptation, Haley Caldwell

Legacy Theses & Dissertations (2009 - 2024)

Flaviviruses include several emerging and re-emerging arboviruses that cause millions of infections each year. Although relatively well-studied, much remains unknown regarding the mechanisms and means by which these viruses adapt to different hosts and rapidly alternate between hosts. Different aspects of flaviviral biology impact host switching, viral fitness, and the generation of viral diversity during genome replication by the NS3 and NS5 proteins. Together these factors may impact host plasticity.

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 …

Synthesis Of Oligonucleotides Containing Unnatural Backbone And Regulation Of Crispr Activity Using Inverse Electron Demand Diels-Alder Chemistry, Alyssa Hoy

Legacy Theses & Dissertations (2009 - 2024)

This thesis describes the synthesis of an oligonucleotide containing an unnatural neutralbackbone. The backbone was constructed using bio-orthogonal inverse electron demand Diels- Alder chemistry between trans-cyclooctene (TCO) and tetrazine (Tz). A TCO phosphoramidite was synthesized and attached to solid support for strand propagation. Uridine monomers containing either bis-TCO or bis-Tz were also synthesized. The oligonucleotide strand was formed by sequential ligation of the bis-Tz and bis-TCO monomers. The oligonucleotide was analyzed using mass spectrometry. This thesis also describes the synthesis of sgRNAs containing non-canonical nucleobases, m1A, m6A, s2U and s4U using the ‘split-and-click’ methodology. The synthetic sgRNAs were assembled using …