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Identifying Epidermal Enriched Genes Required For Planarian Regeneration- Sp. Schmidtea Mediterranea, Pallob Barai

Theses and Dissertations--Biology

The outer epithelial layer covering an organism, commonly known as the epidermis, is crucial for maintaining homeostasis and for the wound healing processes after injury. The planarian epidermis allows flatworms to heal their wounds and virtually restore any missing tissues. Immediately after amputation, planarians contract their muscle and stretch their epidermis to heal the wound area. However, how the planarian epidermis coordinates with other tissues and mechanisms after the initial wound healing processes begins is not understood in detail. I hypothesized that epidermal cell stretching upon wound healing induces transcriptional changes that are required for effective regeneration. To test this …

Assessing Ear Pinna Repair In The Mrl/Mpj Mouse Strain, Fatemeh Safaee

Theses and Dissertations--Biology

The outcome of tissue repair varies across species. Vertebrates such as salamanders have the ability to not only heal scar-free but also completely regenerate lost appendages. In contrast, most mammals heal their wounds with fibrotic scarring. Understanding the key drivers of these divergent injury responses remains a major unanswered question in animal biology. Previous work with the Murphy’s Roth Large (MRL/MpJ) inbred mouse strain suggested they have the ability to rapidly close small (2mm) ear holes. While this ability was originally published as an example of regeneration, subsequent work by other groups suggested that it might represent something more akin …

The Role Of Protein Tyrosine Phosphatase Receptor Type F In Intestinal Homeostasis And Colorectal Cancer, Ashley T. Skaggs

Theses and Dissertations--Molecular and Cellular Biochemistry

Protein phosphorylation defines one of the most important regulatory mechanisms in cell signaling. PTPRF, protein tyrosine phosphatase receptor type F, belongs to the class I R2A subfamily of protein tyrosine phosphatases (PTP). The overall objective of this dissertation is to investigate the molecular mechanisms by which PTPRF regulates normal and cancer stem cells by controlling Wnt signaling.

Dysregulation of Wnt signaling promotes the initiation and progression of colorectal cancer (CRC). We first determined the functional important of PTPRF in regulating Wnt signaling in CRC. Combining cell culture, 3D tumor organoid and xenograft models, results from our study establish PTPRF as …

A Multidisciplinary Characterization Of The Enzymology And Biology Of Reversible Glucan Phosphorylation In Toxoplasma Gondii , Robert Murphy

Theses and Dissertations--Molecular and Cellular Biochemistry

Toxoplasma gondii is an opportunistic, protozoan parasite of all warm-blooded animals, infecting roughly one-third of humans worldwide. Humans acquire infections by consuming T. gondii tissue cysts in undercooked meat or from oocysts shed in cat feces. Encysted parasites convert into rapidly growing tachyzoites that disseminate throughout the body, defining the acute phase of infection. Under host immune pressure, tachyzoites convert into bradyzoites that populate tissue cysts found in CNS or muscle tissue and persist for the lifetime of the host, defining the chronic phase of infection. Tissue cysts are responsible for transmission via carnivory, but also possess the ability to …

Defining Patient Cohorts For Guiding Clinical Trials And Treatment In Lafora Disease: A Model For The Rare Disease Community, Katherine Janae Donohue

Theses and Dissertations--Molecular and Cellular Biochemistry

In the US, approximately 8000 rare diseases have been identified. Combined, rare diseases impact more than 30 million people in the U.S. alone, with 75% of those being children. However, research, funding, and therapeutic development for the rare disease community remains challenging because of the incredible diversity – not only between diseases, but often even within a single disease.

LD is an ultra-rare childhood dementia and epilepsy caused by mutations in one of two driver genes: EPM2A, which encodes for the glycogen phosphatase laforin, and EPM2B/NHLRC1, which encodes the E3 ubiquitin ligase malin. Children with LD …

Simple Control For Complex Pandemics, Sarah C. Fay, Dalton J. Jones, Munther A. Dahleh, A.E. Hosoi

Engineering: Faculty Publications

he COVID-19 pandemic began over two years ago, yet schools, businesses, and other organiza- tions are still struggling to keep the risk of disease outbreak low while returning to (near) normal functionality. Observations from these past years suggest that this goal can be achieved through the right balance of mitigation strategies, which may include some combination of mask use, vac- cinations, viral testing, and contact tracing. The choice of mitigation measures will be uniquely based on the needs and available resources of each organization. This article presents practical guidance for creating these policies based on an analytical model of disease …

Tirso De Molina’S El Melancólico And The Performative Authenticity Of Early Modern (Pseudo-)Melancholy, Paul Michael Johnson

Global Language Studies Faculty publications

La melancolía se ha convertido casi en sinónimo de la temprana modernidad, no ya como una aflicción crónica de la psicología médica, sino como un sentimiento definitorio del periodo en términos generales. Esto es de aplicación especial para el caso de España, cuya reputación como creadora de melancólicos fue legendaria dentro y fuera de sus fronteras. Recientemente se ha dudado sobre su autenticidad, y los estudiosos han cuestionado cuánto en esa melancolía era condición psicológica, o bien moda pasajera, obsesión auto-creada, histeria colectiva imaginada o performance dramática. Este ensayo analiza las implicaciones mutuas de la melancolía y la incertidumbre en …

Coming Of Age In Post-Climate Change Florida In Karen Russell's "The Gondoliers", Christopher Nank

The Marjorie Kinnan Rawlings Journal of Florida Literature

No abstract provided.

The Case For Alternate Media Requirement Expressions In Systems Engineering, Jason Kolligs

Dissertations

“Requirements” are often presented as a necessary, if not mandated, component or tool of the systems engineering process. Despite their place in engineering, low quality requirements are the first potential mistakes of an engineering project and their effects are potentially felt downstream in the form of increased costs and schedule overruns. Innovations to improve requirements engineering have historically omitted the requirement media. This research provides the rationale and process heuristics to include alternate media requirement expressions within systems engineering which shifts accountability to higher context requirement expressions that may require less cognitive load while decreasing effort and schedule thereby potentially …

Mrna-Sequencing Pipeline And Pathway Analysis To Determine The Effects Of Bisphenol A On Fragile X Syndrome In Drosophila Melanogaster, Rashi Raghulan

Master's Projects

Neurological disorders (NDDs), like Fragile X Syndrome (FXS), are becoming more prevalent. One outstanding question in the field is how genetic risk factors for NDDs, like Fmr1, converge with environmental risk factors like bisphenol A (BPA). Our research compares and contrasts the different molecular impacts of BPA exposure in wild-type and FXS flies using mRNA-sequencing analysis. This analysis identifies the mutation in the Fmr1 gene is shown to have a stronger effect on the Drosophila than the presence of BPA, resulting in significant differential gene expression that perturbed several neurological pathways. Moreover, numerous genes responsible for genetic human diseases have …

The Impact Of Bisphenol A And Its Analogues On Neurodevelopmental Transcriptomes In Drosophila Melanogaster, An Nguyen

Master's Projects

Bisphenol A (BPA) is an endocrine-disrupting compound (EDC) that can act as an agonist or antagonist to interfere with multiple signaling pathways, including neurological pathways. The impact of BPA related to neurodevelopmental disorders (NDDs) is one of the biggest concerns in BPA exposure in humans. Therefore, BPA analogues are used to replace BPA in manufacturing and BPA-free products. However, most BPA analogues, including Bisphenol F (BPF) and Bisphenol S (BPS), act the same way as BPA on estrogen and androgen receptors. RNASequencing (RNA-seq) analysis was used to investigate the impact of BPA, BPF, and BPS on neurodevelopmental transcriptomes in Drosophila …

An Investigation Of Segmental Duplications Across Topologically Associating Domains, Sara Bell

Master's Projects

High-throughput chromosome conformation capture (Hi-C) reveals organization within genomes. Topologically associating domains (TADs) make up one level of organization and are identified by applying algorithms to Hi-C data. TADs have boundaries disrupted by structural variants (SVs), hypothesized to form due to recombination that occurs between segmental duplications (SDs). Little research is available about the effects of SDs at TAD boundaries. This project aimed to understand the distribution of SDs near TADs and determine any overlap between the two features. We analyzed public data and found SDs to have low breakpoint frequency and coverage at TAD boundaries. We then processed a …

City Of Milpitas Trash Capture Device Program: An Evaluation Of System Performance And Compliance With The Municipal Regional Permit, Joseph Aguilera

Master's Projects

Water pollution negatively impacts the environment and human population. The problem persists despite various mitigation efforts, strategies, and the implementation of regulatory requirements. It is estimated that Californians dispose of approximately 40 million tons of consumer items and waste materials annually (California Department of Resource Recycling and Recovery, 2019). As the population increases, it is expected that negative impacts of trash on the environment will be exacerbated. To address this, municipalities in California apply various methods to reduce trash before it enters ocean waters.

The primary vehicle for urban trash pollutants to reach ocean waters is through storm water conveyance …

Hidden Markov Models With Momentum, Andrew Miller

Master's Projects

Momentum is a popular technique for improving convergence rates during gradient descent. In this research, we experiment with adding momentum to the Baum-Welch expectation-maximization algorithm for training Hidden Markov Models. We compare discrete Hidden Markov Models trained with and without momentum on English text and malware opcode data. The effectiveness of momentum is determined by measuring the changes in model score and classification accuracy due to momentum. Experiments indicate that adding momentum to Baum-Welch can reduce the number of iterations required for initial convergence during HMM training, particularly in cases where the model is slow to converge. However, momentum does …

Modeling Sequencing Artifacts For Next Generation Sequencing, Yvonna Leung

Master's Projects

Advancements in Next Generation Sequencing (NGS) have enabled detection of genetic alterations at large scales with high throughputs. NGS offers advantages over the established sequencing method, Sanger sequencing, by processing large sections of the genome simultaneously at a lower cost with higher accuracy. However, recent research has shown that sequencing artifacts are introduced at various steps in the NGS workflow. These artifacts are the result of an accumulation of errors from multiple steps, such as library preparation and downstream processes, and can result in variants being identified that aren’t actually present in the sequenced genome. Therefore, there is a need …

Mirna-Seq Analysis Pipeline And R Shiny App, Alexis Torres

Master's Projects

ABSTRACT Thrombosis in the internal jugular vein (IJV) has been identified as a risk factor for astronauts undergoing spaceflight, following a 2019 study in which one astronaut developed a thrombus, and several others experienced stagnant or retrograde blood flow. To better understand this phenomenon, a model that simulates the effects of microgravity on blood flow in the IJV is being developed. mRNA and microRNA NGS sequencing will be used to study the transcriptome of human umbilical vein endothelial cells (HUVEC) in simulated microgravity conditions. A microRNA sequencing (miRNA-seq) pipeline has been developed to quantify the miRNA sequencing results. A graphical …

Comparison Of An Oxford Nanopore Technologies Sequencing Platform To Existing Sequencing Methods For Differential Expression Studies, Nikola Klier

Master's Projects

As the genomics revolution continues, there is constant pressure to make sequencing technology more accessible and practical for a growing series of applications. Existing sequencing technologies are often prohibitively expensive, limiting their use for novel diagnostic and research applications. Additionally, existing technologies are often limited by short read lengths, which may present problems to certain quantitative sequencing applications. One such application is Differential Expression Analysis, in which RNA-Seq is performed in paired samples under different experimental conditions to identify differences in gene expression. In this study, an Oxford Nanopore Technologies sequencing platform was used to conduct a differential expression study …

Reuse Considerations For Successful Complex Systems Integration, Logan Grumbach

Dissertations

As systems have become increasingly complex, engineers are relying on reuse of components and subsystems as a method to curb complexity. However, integrating these reuse components and subsystems have historically often resulted in catastrophic failures. Technical principles key to integration success and the role of reuse in these principles are not currently defined. The objective of this research is to, first, derive and validate a set of technical integration principles and subsequently to explore how incorporating reuse impacts integration success. This research uses historical system integration data and a combination of qualitative analysis techniques and quantitative techniques to draw conclusions …

Developing Standards For Gender-Responsive Human Rights Due Diligence, Constance Z. Wagner, Nancy Kaymar Stafford

All Faculty Scholarship

This article addresses the current state of gender-responsive human rights due diligence (GR-HRDD) standards and advocates for greater attention to be paid to women’s human rights in the due diligence process. The 2011 United Nations Guiding Principles on Business and Human Rights (UNGPs) created a global framework for recognizing, preventing, and addressing the risk of adverse impacts of human rights violations linked to business activities. The responsibility of businesses to respect human rights under the UNGPs includes implementing a human rights due diligence process. Although the UNGPs do not provide guidance on the process for integrating women’s rights into human …

Your Body, Your Cells? Direct-To-Consumer Marketing Of Autologous Stem Cell Therapies In The United States, Japan, And Australia, Kathleen C. Laird

Vanderbilt Journal of Transnational Law

Stem cell tourism has relocated; patients in search of stem cell therapies to treat nearly any disease can find clinics selling miracle cures without traveling beyond their national borders. Businesses marketing unproven autologous stem cell therapies are now plentiful in highly regulated, wealthy countries, including the United States, Japan, and Australia. Despite regulatory oversight of stem cell therapies and strong support for scientific innovation in these countries, the internet and social media have facilitated the rapid growth and success of a new industry selling unproven treatments directly to consumers. Clinics selling unproven autologous stem cell therapies have succeeded by developing …

Model Of A Biotic Hard Substrate Community: Paleoecology Of Large Trepostome Bryozoans From The Upper Ordovician (Katian) Of The Cincinnati Region, Usa, Kate Runciman

Senior Independent Study Theses

The calcite skeletons of trepostome bryozoan colonies from the Upper Ordovician (Katian) of the Cincinnati region record the diverse interactions and growth responses these colonies experienced. Trepostome specimens from three Cincinnatian strata; the Bellevue Member, the Bull Fork Formation, and the Whitewater Formation, were studied within this project. These three strata were deposited in a shallow epicontinental sea environment that was located in the southern subtropics, approximately 20-23°S at the time of deposition. The focus of this project was the paleoecology of large trepostome bryozoans, which was studied by examining bryozoan growth patterns, trace fossils, and sedimentation. Microscopic examination of …

Natural Resource Management Newsletter, January 2022, Department Of Natural Resource Management

NRM Newsletter

CAFES Awards: Teacher of the Year & Student Club Honorable Mention 2021
NRM Affiliate Professor Receives Fulbright to Norway
Service Awards
Elisha YT Summer Internship
Deva Raj Khanal 2021 ASPT Research Award
Gary Larson Memorial Burr Oak at Dakota Nature Park in Brookings
Oak Lake Field Station Jon Haertel Undergraduate Research Award
Undergraduate Research, Scholarship and Creative Activity Day (URSCAD)
Seven Wokini Challenge Grants Awarded for FY 2022 - Lan Xu
Fire School at Oak Lake Field Station
USDA project to produce wildflower seeds, improve soil health
Pollinators in an Agricultural Context
Welcome new faculty members: Alison, Chris, Amanda & …

The Role Of Son In Chromatin-Mediated Gene Expression, Melissa Jordan Ward

Browse all Theses and Dissertations

Gene expression in mammalian cells requires complex nuclear choreography, and there is increasing evidence that spatiotemporal organization of chromatin and nuclear compartments plays an important role in gene expression. In this dissertation, I examined the function of SON, a splicing factor with a known role in nuclear organization, in chromatin-mediated gene expression. SON association with a transcriptionally inactive U2OS 2-6-3 reporter gene array provided a useful model to study SON’s chromatin dynamics. I demonstrated that SON associates with the inactive but not the activated array, and that SON’s RNA binding domains are not necessary for that association. Second, I discovered …

Modeling Als-Associated Matrin-3 Toxicity In Yeast, Widad El-Zein

Browse all Theses and Dissertations

ALS is a neurodegenerative disease characterized by degeneration of upper and lower motor neurons in the brain and spinal cord leading to progressive paralysis and ultimately death. Perturbations in RNA metabolism and RNA binding proteins have emerged as underlying defects in ALS pathogenesis. Matrin-3 is a multifunctional RNA binding protein that has been linked to familial and sporadic ALS. Matrin-3 is normally found in the nucleus, but mutations in the gene cause mislocalization of the protein from the nucleus into the cytoplasm of neuronal cells where it forms protein aggregates. In this study, we show that over-expressing human MATR3 in …

The Role Of Pi4kb In Cellular Localization Of Small Gtpases, Parisa Sadrpour

Browse all Theses and Dissertations

Constitutively active oncogenic mutant K-Ras is one the principal contributors to human cancers including 90% of pancreatic, 50% of colorectal and 32% of non-small cell lung cancers. However, except for K-Ras G12C oncogenic mutant, which only presents in about 13% of non-small cell lung cancer patients, there is no anti-K-Ras therapy for a considerable subset of K-Ras mutations in human tumors, reflecting challenges for targeting oncogenic K-Ras activity. K-Ras is a membrane-bound small GTPase; when active, it triggers multiple signaling pathways regulating a variety of key cellular functions such as cell growth, proliferation and survival. To initiate these signaling cascades, …

Reconstruction Of Gut Microbiome Via Intermittent Feeding, Kourtney Sprague

Browse all Theses and Dissertations

The benefits of intermittent fasting have been studied across many facets of health. It is known that physiologically fasting results in a metabolic switch from liver-derived glucose to adipose cell derived ketones to be used as energy and signaling molecules. Fasting down-regulates inflammation, increases expression of antioxidant defenses, and activates pathways for DNA repair and autophagy. While fasting or intermittent feeding effects on host physiology have been identified, the relationship between fasting and gut microbiome is not as well known. In times of gut rest, resident microbes undergo detoxication and motility, and in times of activity, gut microbes undergo DNA …

Outcome Of Vital Pulp Therapy On Immature Permanent Teeth With Calcium Silicate-Based Materials: Retrospective Cohort Study, Brian I. Hone

Theses and Dissertations

Introduction: The purpose of vital pulp therapy is to maintain pulp viability by eliminating bacteria from the dentin-pulp complex and to establish an environment in which apexogenesis can occur. The aim of this retrospective cohort study was to evaluate the clinical and radiographic outcomes of vital pulp therapy on immature permanent teeth using different calcium silicate-based materials. Methods: This study was carried out in the Virginia Commonwealth University Graduate Endodontics department in Richmond, Virginia. Vital pulp therapy cases performed by graduate endodontic residents were retrospectively searched and charts were reviewed to determine inclusion into this study. All cases …

Getting To Know You: Relationship Formation Across Development In Octodon Degus, Amber Lynn Thatcher

Graduate Student Theses, Dissertations, & Professional Papers

Social relationships are a necessary part of group formation and cohesion across many animal species and can increase the health and fitness of the individuals involved. These benefits are seen across the lifespan, although the exact advantages and functions differ across developmental stages. Our current understanding of how relationships are formed and maintained is incomplete. Previous findings suggest that a measure of stability may be a useful method for understanding how relationships are formed and how this process may differ across development. The goal of this dissertation is to investigate the variability of social interactions over time and how it …

Soft Law: The Optimal Legal Framework For Global Financial Regulation, Yussuf A. Aleem

Emory Business Law Review

The regulation of global finance comprises an unorthodox legal framework. Unlike other areas of economic regulation or international law, more generally, this framework is not directed through intergovernmental organizations with formal legal status. Moreover, commitments (or best practice standards) made by various regulatory officials are non-binding and subject to significant variation. This departure is especially unique when comparing financial regulation to areas such as international trade law or environmental law.[1]

The purpose of this Paper is to provide a positive analysis explaining the prevalence of this form of “soft” law, and normatively suggest why such a framework is the …

A Case Of Postural Orthostatic Tachycardia Syndrome And Anxiety, Nadia Anabtawi, Clinton Martin, Janaki Nimmagadda, Richard Shelton

UAB Huntsville Research Day - All Presentations

2022 clinical vignette poster