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Characterizing And Epitope Mapping Single-Domain Antibodies On Borrelia Burgdorferi Protein Ospa, Saiful Basir
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 …
Evaluating The Health Impacts Of Fruit And Vegetable Intake At The Individual Level And Food Pantry Level Among Food Pantry Users, Jiacheng Chen
Evaluating The Health Impacts Of Fruit And Vegetable Intake At The Individual Level And Food Pantry Level Among Food Pantry Users, Jiacheng Chen
Legacy Theses & Dissertations (2009 - 2024)
Background: Chronic diseases impose heavy burdens on individuals and the healthcare system in the US. Many factors were found to be associated with chronic diseases, including demographics, family history, social environmental factors, and individual behavioral factors such as diet and physical activity. Among those factors, fruit and vegetable intake can have substantial health impacts via a variety of causal pathways. Fruit and vegetable (F&V) consumption is generally lower among individuals living in households experiencing food insecurity and rely on food assistance programs. Decreased F&V intake among food pantry users may negatively impact health. However, conducting quantitative analysis on this population …
Understanding SjöGren's Syndrome As A Systemic Autoimmune Disorder, Gaietchyne Chery
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 …
Vircy-Seq : A Protocol For Characterizing Viral Activity, Tyler James Dion
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 …
Development Of Nucleic Acid Diagnostics For Targeted And Non-Targeted Biosensing, Christopher William Smith
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 …
An Ims-Ms/Md Workflow For Determining Higher Order Structure And Dynamics Of Nucleic Acids, Rebecca D'Esposito
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.
Parallel Networks That Govern The Transcriptional Response To Stress, Serene Anne Durham
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 …
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
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 …
Amyloid Fibril Formation And Polymorphism : A Critical Role Of Sulfur-Containing Amino Acid Residues, Tatiana Quiñones-Ruiz
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 …
Potentially Cis-Acting Super-Enhancer Long Noncoding Rnas As Biomarkers In Triple Negative Breast Cancer Progression, Kavipriya Kovai Palanivel
Potentially Cis-Acting Super-Enhancer Long Noncoding Rnas As Biomarkers In Triple Negative Breast Cancer Progression, Kavipriya Kovai Palanivel
Biological Sciences
Triple negative breast cancer (TNBC) is defined by the lack of estrogen receptors (ER), the lack of progesterone receptors (PR), and normal human epidermal growth factor 2 (HER2) protein levels in breast tumors. Therefore, TNBC is an aggressive type of breast cancer due to limited treatment options for patients. Determining genes that regulate the progression of tumors to TNBC may help develop new therapeutic techniques. Many super-enhancer long noncoding RNAs (SElncRNAs) are found to be differentially expressed in cancer cells. Super-enhancer activity heavily influences target gene transcription and is often augmented through cis-acting SE-lncRNA activity. Therefore, we hypothesize cis-acting SE-lncRNAs …
Optophysiology Of D. Melanogaster Neuromuscular Synapses Using Gcamp, Kavindra Dasrat
Optophysiology Of D. Melanogaster Neuromuscular Synapses Using Gcamp, Kavindra Dasrat
Biological Sciences
An activity-dependent increase in postsynaptic currents produced by a single vesicle of neurotransmitter is an important mechanism for synaptic plasticity in the central nervous system (CNS) and possibly involved in learning and memory. We have found a similar form of postsynaptic potentiation at the D. Melanogaster neuromuscular junction (NMJ) where a brief increase in impulse activity results in an increase in the amplitude of spontaneous miniature excitatory postsynaptic currents (mEPSCs), resulting in miniature excitatory postsynaptic potentials (mEPSPs). To visualize sites of postsynaptic potentiation along the synaptic terminal, we have used a Ca2+ indicator, GCaMP to observe postsynaptic Ca2+ signals. Since …
Toward Long Non-Coding Rna Detection Using Dna Nanoswitches, Ché-Doni Platt
Toward Long Non-Coding Rna Detection Using Dna Nanoswitches, Ché-Doni Platt
Biological Sciences
Long non-coding RNAs (lncRNAs) are transcripts that are over 200 nucleotides and do not encode proteins. LncRNAs are involved in a wide spectrum of biological processes ranging from cell proliferation, apoptosis, and nutrient sensing to cell differentiation. Further, lncRNAs have been reported to play an important role in a wide range of pathophysiological processes and are linked to diseases such as cancer. Thus, lncRNAs are becoming increasingly important as biomarkers to study biological and disease processes. In our work, we develop a DNA nanoswitch-based assay for detecting long RNAs. The DNA nanoswitch is a reconfigurable device that undergoes a conformational …
Emerging Roles Of Intragenic Enhancers In Gene Expression Of Gadd45a, Ekaterina Sazon
Emerging Roles Of Intragenic Enhancers In Gene Expression Of Gadd45a, Ekaterina Sazon
Biological Sciences
Non-coding regulatory elements in the eukaryotic genomic DNA, like enhancers and promoters, control gene expression. Transcription factors recognize and bind to DNA sequences within these regulatory regions and affect said regulatory elements. The extent and specific circumstances regarding transcription factors are long-standing questions in the field. In this thesis, we wanted to investigate how transcription factors work in a particular case of enhancers, known as intragenic enhancers. We designed reporter gene assays that looked at the well-studied model transcription factor p53’s regulation on its target gene GADD45A in basal and stress conditions. We determined that GADD45A is a p53-dependent gene, …
Using The Centrifuge Force Microscope As A Single-Molecule Technique For Studying Base-Stacking Interactions, Kevin Thomas
Using The Centrifuge Force Microscope As A Single-Molecule Technique For Studying Base-Stacking Interactions, Kevin Thomas
Biological Sciences
A wide range of single-molecule techniques has streamlined the process of applying and studying the effects of force on individual molecules. The centrifuge force microscope (CFM) is one such technique that allows for high-throughput single-molecule pulling experiments. It is relatively inexpensive and user-friendly, making it a suitable tool to study the effects of force on various biomolecular interactions. A benchtop centrifuge can be used to apply centrifugal force to molecular constructs that are tethered between a glass slide and a microsphere. Molecular events like bond dissociation result in the removal of the microsphere from the surface, which is observed by …
Circadian Modulation Of Astrocyte Morphology And Synaptic Transmission, Saad Ahmad
Circadian Modulation Of Astrocyte Morphology And Synaptic Transmission, Saad Ahmad
Biological Sciences
The circadian rhythm affects behavior and physiology in many animal species. Our previous work in mice showed that within the hippocampus, a subordinate circadian oscillator, astrocytes change their proximity to excitatory synapses. Here we obtain 3D reconstructions of biocytin-filled hippocampal astrocytes processed with protein retention expansion microscopy and imaged using two-photon laser scanning microscopy. Our findings identify the subtle changes in astrocyte morphologies that encode information about time-of-day in hippocampal astrocytes. These findings shed light on fundamental mechanisms that allow the function of hippocampal circuits to adapt to different times of the day. This will help us understand how structural …
The Role Of Angiocrine Factors In The Progression Of Salivary Disease, Owen Zon
The Role Of Angiocrine Factors In The Progression Of Salivary Disease, Owen Zon
Biological Sciences
In our blood vessels, cells called endothelial cells line the inside of veins and arteries. Due to the discovery that endothelial cells actually organogenesis during embryogenesis, our interest in these cells has increased to a new understanding of their functions in tissue repair and regeneration. These cells are no longer only considered passive modes of transport for bodily fluids and nutrients, but, with new research in the fibrosis of liver cells, are also considered to be key players in the repair of damaged organs and tissue. These cells release signals known as angiocrine factors that act in damaged areas of …
Investigating The Roles Of Rna Modification And Associated Enzymes On Stress Response And Connections To Human Diseases, Carrson Widen
Investigating The Roles Of Rna Modification And Associated Enzymes On Stress Response And Connections To Human Diseases, Carrson Widen
Biological Sciences
Transfer RNAs decode messenger RNA using anticodon – codon interactions to deliver specific amino acids to a growing peptide chain. Enzyme-catalyzed modifications on specific nucleotides on tRNAs increase their stability and help mediate the speed and fidelity of translation, giving these modifications regulatory potential. RNA modifications are catalyzed by writer enzymes, and I predicted that writers are important in the cellular responses to stress. I have evaluated the following E. coli modification enzyme mutants: miaA, mnmE, dtd, tmcA, lysU, yeaK, and iscS, from the corresponding Keio E. coli gene deletion library. Writer mutants were exposed to hydrogen peroxide to induce …
Characterization Of The Role Of The Replicase And Quasispecies Diversity In Flaviviral Evolution And Host Adaptation, Haley Caldwell
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.
An Interaction Between Centrosome Scaffold Proteins And A Retrotransposon Nucleocapsid Protein May Alter Asymmetric Centrosome Inheritance, Lanilei Doctora
An Interaction Between Centrosome Scaffold Proteins And A Retrotransposon Nucleocapsid Protein May Alter Asymmetric Centrosome Inheritance, Lanilei Doctora
Legacy Theses & Dissertations (2009 - 2024)
Nearly all eukaryotic genomes harbor mobile genetic elements known as retrotransposons. The mRNA ofthese elements undergo reverse transcription, yielding cDNA that is inserted in a new location in the host genome. We study Saccharomyces cerevisiae Ty1 elements, an active family of retrovirus-like retrotransposons, and the mechanism behind its regulation of spindle pole body (SPB) inheritance. Ty1 retromobility is activated during growth at 20˚C. In a manuscript that includes my work (Murphy et al., 2022, manuscript in preparation), we report that essential SPB proteins Nud1 and Spc42 are sequestered in the Ty1 retrosome, the site of Ty1 nucleocapsid assembly, in a …
Bioinformatics Analysis Of The Transcriptomic Profiles Of Duchenne Muscular Dystrophy Patients / Narrative Competence And Cognitive Mapping As A Culturally Sustaining Pedagogy In The Education Of Emergent Bilinguals, Bianca Gonzalez
Legacy Theses & Dissertations (2009 - 2024)
Duchenne Muscular Dystrophy (DMD) is a muscle-wasting disease that primarily affects boys characterized by loss of the dystrophin gene. Dystrophin is necessary for proper muscle growth, muscles that lack dystrophin are more prone to damage. In this thesis, a bioinformatics approach was used to evaluate the transcriptomic profiles of two datasets obtained from DMD patients. The two datasets were analyzed separately, as well as combined to identify differentially expressed genes. The first dataset, GSE6011, has 23 DMD samples and 14 controls. The second, GSE38417, consists of 16 DMD samples and six controls. Differential gene expression of both datasets combined found …
Translation Control Tunes Drosophila Oogenesis, Elliot T. Martin
Translation Control Tunes Drosophila Oogenesis, Elliot T. Martin
Legacy Theses & Dissertations (2009 - 2024)
The decision of a stem cell to either self-renew or differentiate is controlled by specific cellularpathways that can act at the level of transcription, translation, or post-translation. To study the regulation of these pathways in-vivo, I have used the female Drosophila germline as a model system. Each of the steps from germline stem cell (GSC) to egg require changes in cellular pathways. These changes can occur at the level of transcription, post-transciption, translation, or post-translation . Decades of research has elucidated many of the changes to gene that occur during oogenesis, however, many players in this process still remain mysterious. …
Megacity : A Reservoir Of Toxic Environmental Contaminants And Health Disease Burden, Omosehin Daniel Moyebi
Megacity : A Reservoir Of Toxic Environmental Contaminants And Health Disease Burden, Omosehin Daniel Moyebi
Legacy Theses & Dissertations (2009 - 2024)
Ambient air pollution is a global environmental problem of concern with more than 95% of the world population living in areas with unhealthy air. World Health Organization (WHO) in 2019 stated that air pollution is a principal environmental risk to human health with about 7 million premature air pollution-related deaths annually. Several epidemiological studies have linked morbidity due to cardiovascular diseases (CVDs) to ambient air pollution exposure, especially in North America and Europe. However, the effect of air pollution in Karachi, Pakistan is understudied, which is the case for many urban centers in the developing countries. Karachi is a megacity …
Environmental Factors And Human Health Interactions : Ultrafine Particles, Temperature Variability, And Proximity To Power Stations, Ian Ryan
Legacy Theses & Dissertations (2009 - 2024)
Background: Air pollution leads to more than four million premature deaths worldwide and nearly 200,000 in the US each year. While there is extensive research relating PM2.5 to hospital visits for various health outcomes, there is relatively little research on ultrafine particles (UFPs), a particularly small and dangerous air pollutant. Another important exposure is temperature due to its association with dehydration, heat stress, and cardiovascular-related hospital admissions. However, relatively little research has been conducted on diurnal temperature range (DTR), or the range of temperature within a single day, which is an important indicator of climate change. Importantly, the interaction between …
Exploring The Response To Arsenic Using Trna Modification Detection, Writer Mediated Protection And Codon Usage Analytics, Anwesha Sarkar
Exploring The Response To Arsenic Using Trna Modification Detection, Writer Mediated Protection And Codon Usage Analytics, Anwesha Sarkar
Legacy Theses & Dissertations (2009 - 2024)
Transfer ribonucleic acid (tRNA) is a non-coding RNA which interacts with the messenger RNA (mRNA) to facilitate protein synthesis. tRNA is also one of the most heavily modified RNAs with the collection of modifications, termed as the tRNA epitranscriptome, ranging from simple methylation to complex hypermodification catalyzed by RNA epitranscriptomic writers. Detecting tRNA modifications is an evolving field and the state-of-the-art technologies that include next generation sequencing and mass spectrometry of intact and derivatized RNAs is described in the chapter one. Liquid chromatography coupled with mass spectrometry has previously been used to show that arsenic promotes increases in the levels …
Role Of H3k4 Methylation In Myogenesis, Regeneration, And Muscle Disease / Narrative Competence And Cognitive Mapping As A Culturally Sustaining Pedagogy In The Education Of Emergent Bilinguals, Hannah Emily Shippas
Role Of H3k4 Methylation In Myogenesis, Regeneration, And Muscle Disease / Narrative Competence And Cognitive Mapping As A Culturally Sustaining Pedagogy In The Education Of Emergent Bilinguals, Hannah Emily Shippas
Legacy Theses & Dissertations (2009 - 2024)
Muscles are a crucial part of an organism’s wellbeing, as defects in distinct types of muscles can be lethal. Our voluntary muscles, skeletal muscles, go through distinct regeneration phases before reaching maturity. With its own pool of stem cells, muscles have a large potential for regeneration. This potential has led scientists into looking closely at the steps that lead a muscle stem cell into muscle fiber, also known as myogenesis. As a muscle cell moves through myogenesis, genes are led to be turned on/off with different epigenetic mechanisms, one being histone modifications. A methylation modification on the 4th Lysine on …
Cis-Acting Super-Enhancer Lncrnas As Biomarkers To Early-Stage Breast Cancer, Ali Salman Ropri
Cis-Acting Super-Enhancer Lncrnas As Biomarkers To Early-Stage Breast Cancer, Ali Salman Ropri
Legacy Theses & Dissertations (2009 - 2024)
Abstract
Disability In An American Indian Community : Prevalence, Distribution, And The Role Of Polychlorinated Biphenyls, Thoin Farzana Begum
Disability In An American Indian Community : Prevalence, Distribution, And The Role Of Polychlorinated Biphenyls, Thoin Farzana Begum
Legacy Theses & Dissertations (2009 - 2024)
The Akwesasne reservation along the St. Lawrence River has experienced significant exposure to several persistent organic pollutants due to rapid industrialization. The Aluminum Company of America, General Motors, and Reynolds Metals operated aluminum foundries that used polychlorinated biphenyls (PCBs) as hydraulic fluids, which contaminated the community environment, the soil, air and water, and community food sources with PCBs. We administered the World Health Organization Disability Assessment Schedule II (WHODAS II) to 119 Akwesasne Mohawk adults residing along the St. Lawrence River in New York. We used exploratory factor analysis to summarize the 36- items comprising the WHODAS II. The 7 …
Evaluation Of Aquatic Plant Survey Methods For Efficacy In Invasive Species Detection, Izaac Cooper
Evaluation Of Aquatic Plant Survey Methods For Efficacy In Invasive Species Detection, Izaac Cooper
Legacy Theses & Dissertations (2009 - 2024)
Aquatic invasive plants can often be ecologically devastating to ecosystems where they are introduced. This devastation has been widely apparent in the United States, including many locations in New York State over many decades, following anthropogenic transport of species from their native ranges. Due to the difficulty involved in eradicating these plants once they have become fully established, there is keen interest in strategies for early detection to assist with prevention and monitoring to mitigate future management costs. Invasive species detection research aims to find methods for detecting new invaders more effectively. I evaluated three detection methods for their effectiveness …
Developing High-Resolution Meteorological Datasets To Assess The Short-Term Association Between Meteorological Factors And Green Space And Mental Disorders, Xinlei Deng
Legacy Theses & Dissertations (2009 - 2024)
Global climate change is linked to the frequency and intensity of local climate extremes such as heatwaves, cold spells, and flooding. Scientific evidence indicates that heatwaves and higher ambient temperature could increase the risk of hospital admission and emergency department (ED) visits for mental disorders (MDs). On the other hand, urban green space is considered a way to reduce heat island effects and provide comfort for area residents. However, there still exist huge research gaps. Except for temperature, few studies have examined how other meteorological factors (relative humidity (RH), solar radiation (SR), heat index (HI), and rainfall) are associated with …
Genetic Regulation Within Cellular Stress Response Pathways, Jhos M. Dufflart
Genetic Regulation Within Cellular Stress Response Pathways, Jhos M. Dufflart
Legacy Theses & Dissertations (2009 - 2024)
Cellular stress is something that a cell deals with on a regular basis. Fortunately, there are several different mechanisms that are set in place in order to deal with them. Depending on the stress present in the cell there will be different stress response pathways that are activated in order to mitigate the stress or initiate cellular death mechanisms. Transcription factors (TFs) are key components within these pathways, and this will be the focus of this thesis. TFs within mammalian stress response pathways are tasked with the essential regulation of multiple genes within these pathways and are oftentimes linked with …