Digital Commons Network^™

Eukaryotic Initiation Factor 3 Interactions With Structural Elements Of Barley Yellow Dwarf Virus Untranslated Regions Reveal Details Of A New Cap-Independent Translation Initiation Model, Paul S. Powell

Dissertations, Theses, and Capstone Projects

Barley Yellow Dwarf Virus (BYDV) is a positive strand RNA plant virus that translates without using a 5′ 7-methylguanosine cap or a 3′ poly-adenosine tail, features that are required for canonical mRNA translation. BYDV’s non-canonical translation relies on RNA structures in the 5′ and 3′ untranslated regions (UTRs) to recruit eukaryotic initiation factors (eIFs) and ribosomes. BYDV’s 3′ translation enhancer (BTE) is a cruciform structure capable of recruiting the cap-binding complex eIF4F, the large scaffolding complex eIF3, and the 40S ribosomal subunit. Together eIF3, eIF4F, and BTE influence factor binding and 40S recruitment on the 5′ UTR and play a …

The College Experience Podcast: Connecting Student Services For College Success, Lucila Sanchez

Dissertations, Theses, and Capstone Projects

What do we know about orienting college students on how to successfully manage the college experience? With this podcast, I aim to answer that question. The podcast aims to serve two purposes. The first purpose is to transmit the information to the students. The secondary purpose is to support student development by increasing knowledge about a wide range of topics as well as available services and resources. The goal is for students to become more aware of how they can access and use these services most effectively and how to manage their time to access essential services that support their …

Making Sense Of Pre-Symbolic Trauma: A Qualitative Study On The Lived Experiences Of Adults Who Were Born Extremely Prematurely, Noia Efrat

Dissertations, Theses, and Capstone Projects

The psychological experiences of adults (n=5) who were born at or before the threshold for extreme prematurity (weeks) was examined using Interpretive Phenomenological Analysis (IPA) (Smith, Flowers & Larkin, 2009). Subjects were interviewed to learn about how their extreme prematurity has become organized and integrated on the levels of fantasy, identity and personality. Results showed that dysregulation and the propensity to self-contain on both somatic and affective levels were common themes across cases, supporting current research connecting the ongoing impacts of prematurity to the context of overstimulation and fundamental absence in the first months of life in the NICU. Despite …

Representation Learning For Chemical Activity Predictions, Mohamed S. Ayed

Dissertations, Theses, and Capstone Projects

Computational prediction of a phenotypic response upon the chemical perturbation on a biological system plays an important role in drug discovery and many other applications. Chemical fingerprints derived from chemical structures are a widely used feature to build machine learning models. However, the fingerprints ignore the biological context, thus, they suffer from several problems such as the activity cliff and curse of dimensionality. Fundamentally, the chemical modulation of biological activities is a multi-scale process. It is the genome-wide chemical-target interactions that modulate chemical phenotypic responses. Thus, the genome-scale chemical-target interaction profile will more directly correlate with in vitro and in …

Understanding The Proton Transport In Non-Aqueous Histidine-Based Nanostructures, Jiang Bian

Dissertations, Theses, and Capstone Projects

Over the past two decades, proton transport has been extensively studied because of the many applications to the development of new technological devices. In particular, understanding proton transport permits the design of new materials with desired properties for constructing effective proton exchange membranes (PEM) in fuel cells. Current PEM technology involves biocummulative perfluorinated membranes that operate under hydrated conditions, for which the proton conductivity is limited by the usually high temperature that fuel cells operate. Therefore, it is of great interest to study the alternative systems that have the potential to conduct protons, in particular, those that are able to …

Adapting Small Unmanned Aerial Systems For Behavioral Research With Coastal Marine Mammals, Eric Angel Ramos

Dissertations, Theses, and Capstone Projects

Marine mammals inhabit aquatic worlds where their subsurface behavior, cryptic surface profiles, and movements make them difficult to study. New tools are needed to study coastal marine mammals in a world increasing impacted by climate change related shifts in weather and animal distribution patterns. Unmanned aerial systems (UAS) are important remote-sensing tools for studying a range of wildlife including terrestrial and aquatic flora and fauna. These systems offer flexible platforms for adding sensor packages needed for different applications, for example, most are equipped with high-resolution cameras and GPS sensors. The vantage point from an aerial platform dramatically improves the ability …

An In Silico Approach To Investigate The Structural And Biochemical Basis Of The Rna Binding Functions Of Nucleolin, Avdar San

Dissertations, Theses, and Capstone Projects

Nucleolin (NCL) is a stress responsive multifunctional nucleolar protein and accounts for 10% of the total nucleolar protein content. NCL belongs to the class of RNA binding proteins (RBPs) that regulate many important cellular processes through their interactions with different RNA molecules. The dysregulation of RBPs and the RNA metabolism pathways they intersect is a known driver of tumorigenesis. NCL regulates ribosome biogenesis, chromatin remodeling, microRNA processing, and gene expression on multiple levels. The RNA-protein interactions of NCL are primarily driven by its four RNA binding domains (RBDs). NCL is known to interact with a growing list of primary-miRNA (pri-miRNA) …

Maternal Wellness: Self, Matrescence, Obstetric Violence, And Self-Care, Vanessa V. Vales-Lewis

Dissertations, Theses, and Capstone Projects

In this dissertation, I engage in a self-study through an examination of my experience of matrescence (i.e., the transition to motherhood). I discuss my praxis in the development of a self-study on maternal wellness as it applies to my well-being as both a researcher and the researched. In Chapter 1, I preface this study by highlighting critical scholars and the bricoleurs who have been foundational in my undertaking of this work on a narrative study on maternal wellness. Using bricolage as part of a research methodological framework that involved key scholarly methodologies of authentic inquiry, emergence and contingence, and narratology, …

Committed To The Fragment: Feminist Literature And The Promise Of Wellness, Lynne Beckenstein

Dissertations, Theses, and Capstone Projects

“I have never been able to blind myself” to the cruelty of a world that “destroys its own young in passing…out of not noticing or caring about the destruction,” Audre Lorde tells us in her 1980 “mythobiography” Zami: A New Spelling of My Name. This quality, Lorde says, “according to one popular definition of mental health, makes me mentally unhealthy.” In rejecting psychological self-possession as a sign of wellness, this passage also rejects it as one of sovereignty’s conditions. At the time of Lorde’s writing, this version of sovereignty already dominated the landscape of therapeutic culture in the United States, …

Role Of Metals In Human Immune System: Study Of Metal-Dependent Structural Changes Of S100a12 Protein, Aleksey Aleshintsev

Dissertations, Theses, and Capstone Projects

S100A12 protein belongs to the S100 family of calcium-binding proteins and participates in the innate immune system. Antimicrobial proteins from the S100 family of the proteins (S100A12, S100A8/A9, etc.) are secreted and expressed by neutrophils during microbial infection and perform their antimicrobial activity through metal sequestration. While most S100 proteins function intracellularly, S100A12 is highly expressed and secreted into the extracellular space by neutrophils during infection. Sequestration of Zn²⁺ by S100A12 is aided by the nanomolar zinc binding affinity of the protein at neutral pH conditions, which is further enhanced upon calcium-binding. The Zn²⁺ binding scaffold in S100A12 …

Surveilling The Fat Disidencia: Policing The Bodies Of Plus-Size Black Women On Instagram, Daniela V. Verdejo Salazar

Dissertations, Theses, and Capstone Projects

Instagram has shaped how we network and share content with others, making interactions far more accessible for everyone who uses this platform daily. Unfortunately, it has also given space to some surveilling mechanisms that tend to police and norm how users and their bodies should present themselves to the rest of the world.

The body can be understood as a manifestation, a presence, and a performance. As Judith Butler argues, the body is also a political space where ideas of resistance and vulnerability take place, and I will understand the body as a combination of the physical manifestation of it …

Structural And Biochemical Investigations Of The Initiation Of Dna Replication In Bacteriophage Lambda And Escherichia Coli, Jillian D. Chase

Dissertations, Theses, and Capstone Projects

Faithful transmission of genetic information is requisite for the propagation of all life. DNA replication in each of the three domains of life requires the separation of double stranded DNA (dsDNA) into single stranded DNA (ssDNA) which then serves as a template for genomic duplication of each original DNA strand. Initiation of replication events occurs by tightly regulated processes during which specialized proteins are loaded at a specific locus within the genome, termed the origin of replication, in preparation of bidirectional replication events. A replicative helicase must be loaded or assembled on both strands of DNA at the origin to …

Girl Friends, Camila Santander

Dissertations, Theses, and Capstone Projects

Friendships between women are common and essential parts of women's lives; however, they are often overlooked. This capstone project titled Girl Friends is a film on which eight women are interviewed and asked about their friendships with other women. They discuss the importance of having female friends and how they create love, support, and companionship. The interviewees also talk about female friendships and romantic partners coexisting, the pressures to find a romantic partner to find fulfillment, as opposed to good friends. Additionally, they describe how friendships between women can be competitive and catty, and how female relationships can change as …

Conservation, Comparative Genomics And Species Delimitation Of The Reindeer Lichens (Cladonia), Jordan R. Hoffman

Dissertations, Theses, and Capstone Projects

The genus Cladonia represents one of the most speciose genera of lichenized fungi, with more than 500 known species encompassing a diverse array of morphologies and habits. These lichens form keystone species in many habitats, serving a variety of ecological roles. However, despite being among of the more well studied lichens, there is much still unknown or under-studied about them. As is the case with most lichen study systems, phylogenetic study has been limited to a small number of partial loci, while adoption of next-generation sequence methods has been slow. As a consequence, there are still knowledge gaps in Cladonia …

Paddling Along The Voltage Gated Sodium Channel Galaxy With Sea Anemone Toxins: Structural Studies Of The Interaction Between The Paddle Motif From Nav1.5div And Sea Anemone Toxin, Adel K. Hussein

Dissertations, Theses, and Capstone Projects

Voltage gated sodium channels (VGSC) are membrane proteins that serve an important function in the central nervous system (CNS), peripheral nervous system (PNS), and cardiac muscles amongst others. The main function of VGSC is in the propagation of electrical signals by depolarizing excitable cells. Nine mammalian VGSC subtypes have been characterized, Na_V1.1 – Na_V1.9, that are expressed in a tissue specific manner, each with unique gating properties. Numerous diseases have been linked to defects in VGSC including epilepsy, mental retardation, long QT syndrome, and Brugada disease. Furthermore, these channels are one of the primary targets of …

Understanding Species Interactions And Their Impacts In Restored Communities, Jennifer Zhu

Dissertations, Theses, and Capstone Projects

Species interactions may mediate the ability of organisms to survive in a community and provide valued services but are rarely fully considered in restoration planning. To address this, I considered how service provisioning will change as restored marsh communities mature and the value of incorporating antipredator training into captive-rearing programs.

For chapter 1, I explored how a facultative mutualism between Atlantic ribbed mussels Geukensia demissa and cordgrass Spartina alterniflora may enhance marsh growth and nitrogen cycling in a eutrophic setting. I created experimental plots in Jamaica Bay, NY, that contained live mussels, mussel shells, or no mussels (control) and measured …

February Cvm Library Newsletter

CVM Library Newsletters

February CVM Library Newsletter

Mule Deer Do More With Less: Comparing Their Nutritional Requirements And Tolerances With White-Tailed Deer, Anna R. Staudenmaier, Lisa A. Shipley, Meghan J. Camp, Jennifer S. Forbey, Ann E. Hagerman, Abigail E. Brandt, Daniel H. Thornton

Biology Faculty Publications and Presentations

Congeneric species often share ecological niche space resulting in competitive interactions that either limit co-occurrence or lead to niche partitioning. Differences in fundamental nutritional niches mediated through character displacement or isolation during evolution are potential mechanisms that could explain overlapping distribution patterns of congenerics. We directly compared nutritional requirements and tolerances that influence the fundamental niche of mule (Odocoileus hemionus) and white-tailed deer (O. virginianus), which occur in allopatry and sympatry in similar realized ecological niches across their ranges in North America. Digestible energy and protein requirements and tolerances for plant fiber and plant secondary …

Alterations Of Host-Gut Microbiome Interactions In Multiple Sclerosis, Claudia Cantoni, Laura Ghezzi, Emily Evans, Li Deng, Alberto Locca, Robert Mikesell, Kathleen Obert, Amber Salter, Anne H Cross, Phillip I Tarr, Laura Piccio, Yanjiao Zhou, Et Al

Open Access Publications

BACKGROUND: Multiple sclerosis (MS) has a complex genetic, immune and metabolic pathophysiology. Recent studies implicated the gut microbiome in MS pathogenesis. However, interactions between the microbiome and host immune system, metabolism and diet have not been studied over time in this disorder.

METHODS: We performed a six-month longitudinal multi-omics study of 49 participants (24 untreated relapse remitting MS patients and 25 age, sex, race matched healthy control individuals. Gut microbiome composition and function were characterized using 16S and metagenomic shotgun sequencing. Flow cytometry was used to characterize blood immune cell populations and cytokine profiles. Circulating metabolites were profiled by untargeted …

Mitochondrial Pyruvate Carrier Inhibitors Improve Metabolic Parameters In Diet-Induced Obese Mice, Wesley T Hodges, Chaowapong Jarasvaraparn, Daniel Ferguson, Kristine Griffett, Lauren E Gill, Yana Chen, Ma Xenia G Ilagan, Lamees Hegazy, Bahaa Elgendy, Kevin Cho, Gary J Patti, Kyle S Mccommis, Brian N Finck

Open Access Publications

The mitochondrial pyruvate carrier (MPC) is an inner mitochondrial membrane complex that plays a critical role in intermediary metabolism. Inhibition of the MPC, especially in liver, may have efficacy for treating type 2 diabetes mellitus. Herein, we examined the antidiabetic effects of zaprinast and 7ACC2, small molecules which have been reported to act as MPC inhibitors. Both compounds activated a bioluminescence resonance energy transfer-based MPC reporter assay (reporter sensitive to pyruvate) and potently inhibited pyruvate-mediated respiration in isolated mitochondria. Furthermore, zaprinast and 7ACC2 acutely improved glucose tolerance in diet-induced obese mice in vivo. Although some findings were suggestive of improved …

The Foundations And Development Of Lipidomics, Xianlin Han, Richard W Gross

Open Access Publications

For over a century, the importance of lipid metabolism in biology was recognized but difficult to mechanistically understand due to the lack of sensitive and robust technologies for identification and quantification of lipid molecular species. The enabling technological breakthroughs emerged in the 1980s with the development of soft ionization methods (Electrospray Ionization and Matrix Assisted Laser Desorption/Ionization) that could identify and quantify intact individual lipid molecular species. These soft ionization technologies laid the foundations for what was to be later named the field of lipidomics. Further innovative advances in multistage fragmentation, dramatic improvements in resolution and mass accuracy, and multiplexed …

Protocol Versus Practice: Deviations From 2 Guidelines In Low-Risk Twin Deliveries In The United States, Julia M. Morris, Andrea Bertotti

Sociology & Criminology Faculty Research

Background

Medical guidelines recommend vaginal delivery for low-risk twin pregnancies because cesareans increase the probability of maternal morbidity and mortality. Yet, vaginal delivery rates for twins are considerably lower than for comparable singletons. One explanation for this disparity argues that greater risk associated with twins warrants increased surgical intervention. An alternative explanation is that twin deliveries are more likely to deviate from protocols that advise vaginal birth.

Methods

Using the 2017 Natality Detail File (N = 3,197,401), we measured alignment of vaginal birth and trial of labor (TOL) with the American College of Obstetricians and Gynecologists’ guidelines for twin and …

Dna Ligase Iv Mutations Confer Shorter Lifespan And Increased Sensitivity To Nutrient Stress In Drosophila Melanogaster, Rashmi Joshi, Surya Jyoti Banerjee, Jennifer Curtiss, Amanda K. Ashley

Faculty Publications - Biological Sciences

The nonhomologous end-joining pathway is a primary DNA double-strand break repair pathway in eukaryotes. DNA ligase IV (Lig4) catalyzes the final step of DNA end ligation in this pathway. Partial loss of Lig4 in mammals causes Lig4 syndrome, while complete loss is embryonically lethal. DNA ligase 4 (DNAlig4) null Drosophila melanogaster is viable, but sensitive to ionizing radiation during early development. We proposed to explore if DNAlig4 loss induced other long-term sensitivities and defects in D. melanogaster. We demonstrated that DNAlig4 mutant strains had decreased lifespan and lower resistance to nutrient deprivation, indicating Lig4 is required for maintaining health and …

Neural Control Of Stopping And Stabilizing The Arm, Shanie A. L. Jayasinghe, Robert A. Scheidt, Robert L. Sainburg

Biomedical Engineering Faculty Research and Publications

Stopping is a crucial yet under-studied action for planning and producing meaningful and efficient movements. In this review, we discuss classical human psychophysics studies as well as those using engineered systems that aim to develop models of motor control of the upper limb. We present evidence for a hybrid model of motor control, which has an evolutionary advantage due to division of labor between cerebral hemispheres. Stopping is a fundamental aspect of movement that deserves more attention in research than it currently receives. Such research may provide a basis for understanding arm stabilization deficits that can occur following central nervous …

Developing Peri-Operative Rehabilitation In Degenerative Cervical Myelopathy [Ao Spine Recode-Dcm Research Priority Number 6]: An Unexplored Opportunity?, Timothy F. Boerger, Allison S. Hyngstrom, Julio C. Furlan, Sukhvinder Klasi-Ryan, Armin Curt, Brian K. Kwon, Shekar N. Kurpad, Michael G. Fehlings, James S. Harrop, Bizhan Aarabi, Vafa Rahimi-Movaghar, James D. Guest, Jefferson R. Wilson, Benjamin M. Davies, Mark R. N. Kotter, Paul A. Koljonen

Physical Therapy Faculty Research and Publications

Study Design

Narrative review.

Objective

Degenerative cervical myelopathy is one of the most frequent impairments of the spinal cord encountered internationally in adults. Currently, surgical decompression is the recommended treatment for people with DCM (PwCM) presenting with moderate to severe symptoms or neurological deficits. However, despite surgical intervention, not all patients make a complete recovery due to the irreversible tissue damage within the spinal cord. The objective of this review is to describe the state and gaps in the current literature on rehabilitation for PwCM and possible innovative rehabilitation strategies.

Methods

Literature search.

Results

In other neurological disorders such as …

Mental Health In The Uk Biobank: A Roadmap To Self-Report Measures And Neuroimaging Correlates, Rosie K. Dutt, Kayla Hannon, Ty O. Easley, Joseph C. Griffis, Wei Zhang, Janine D. Bijsterbosch

Statistical and Data Sciences: Faculty Publications

The UK Biobank (UKB) is a highly promising dataset for brain biomarker research into population mental health due to its unprecedented sample size and extensive phenotypic, imaging, and biological measurements. In this study, we aimed to provide a shared foundation for UKB neuroimaging research into mental health with a focus on anxiety and depression. We compared UKB self-report measures and revealed important timing effects between scan acquisition and separate online acquisition of some mental health measures. To overcome these timing effects, we introduced and validated the Recent Depressive Symptoms (RDS-4) score which we recommend for state-dependent and longitudinal research in …

The Antibacterial Effect And The Incidence Of Post-Operative Pain After The Application Of Nano-Based Intracanal Medications During Endodontic Retreatment: A Randomized Controlled Clinical Trial, Shehabeldin Mohamed Saber Prof.Dr.

Dentistry

Objective: This clinical trial aimed to evaluate the effect of nano-silver and nano-calcium hydroxide intracanal medicaments (ICM) during retreatment regarding their antibacterial effect and their effect on post-operative pain and flare-ups. Materials and methods: Sixty-nine patients scheduled for endodontic retreatment were included in this randomized clinical trial and randomly allocated to 3 equal groups (n = 23) according to the type of ICM used. The first microbial sampling (S1) representing the original microbiota was obtained after the removal of the old canal filling. After chemo-mechanical debridement, another sample (S2) was obtained representing the microbial state before ICM application. Patients were …

Propagation Of Inflowing Urban Stormwater Pulses Through Reservoir Embayments, Megan Fork, Ryan A. Mcmanamay, James B. Heffernan

Biology Faculty Publications

Flashy hydrology and high solute loads in stormflow are well-studied effects of the built environment on urban streams. The physical and chemical interactions between inflowing stormwater of urban streams and their termination in large impoundments, however, is poorly understood. Determining the spatial distribution of urban stormwater in reservoirs is an important step in understanding the effects of the heat and contaminant loads in these systems, which provide multiple services for adjacent cities. Here, we show that signals of stormwater from a small urban stream can propagate more than 800 m from the stream mouth. Stormflow can also break down the …

Rapid Reductions In Breast Density Following Tamoxifen Therapy As Evaluated By Whole-Breast Ultrasound Tomography, Gretchen L. Gierach, Mark Sak, Shaoqi Fan, Ruth M. Pfeiffer, Maya Palakal, Cody Ramin, Lisa Bey-Knight, Michael S. Simon, David Gorski, Haythem Y. Ali, Peter Littrup, Mark E. Sherman, Nebojsa Duric

Hematology/Oncology Articles

PURPOSE: Women whose mammographic breast density declines within 12-18 months of initiating tamoxifen for chemoprevention or adjuvant treatment show improved therapeutic responses compared with those whose density is unchanged. We tested whether measuring changes in sound speed (a surrogate of breast density) using ultrasound tomography (UST) could enable rapid identification of favorable responses to tamoxifen.

METHODS: We evaluated serial density measures at baseline and at 1 to 3, 4 to 6, and 12+ months among 74 women (aged 30-70 years) following initiation of tamoxifen for clinical indications, including an elevated risk of breast cancer (20%) and diagnoses of in situ …

Preemption & Gender & Racial (In)Equity: Why State Tort Law Is Needed In The Cosmetic Context, Marie C. Boyd

Faculty Publications

Much of the legal scholarship on the preemption of state tort law in the food and drug context and beyond has focused on issues of federalism. While the literature has considered the relationship between state tort law and the regulatory system, it has not generally explored the impact the federal preemption of state tort law may have on women and people of color. Similarly, while the literature has grappled with gender and racial justice issues in the tort system, including in the context of tort reform, it has largely not examined the gender and racial equity issues raised by federal …