Digital Commons Network^™

Elucidating The First Protective Mutation From Inherited Alzheimer’S Disease - Apolipoprotein E3 Christchurch (Apoe3ch) And Insights Into Apoe Ligand-Receptor Interactions, Yun Chen

Arts & Sciences Graduate Student Theses and Dissertations

Alzheimer’s disease (AD) is the major cause of dementia. An inherited form of AD (dominant inherited AD) starts much earlier in life, often in the fourth and fifth decade. A recent case report described an individual who was resistant to dominantly inherited AD caused by a PSEN1-E280A mutation and was a homozygous carrier of the APOE3 Christchurch (APOE3ch) variant. A clear separation between amyloid and tau pathology occurred in this unique AD case. However, whether APOE3ch contributed to the protective effect remains unclear. In this thesis, we generated a humanized APOE3ch knock-in mouse and crossed it to an amyloid-β (Aβ) …

International Consensus On Fasting Terminology, Daniela A. Koppold, Carolin Breinlinger, Etienne Hanslian, Christian Kessler, Holger Cramer, Anika Rajput Khokhar, Courtney M. Peterson, Grant Tinsley, Claudio Vernieri, Richard J. Bloomer, Michael Boschmann, Nicola L. Bragazzi, Sebastian Brandhorst, Kelsey Gabel, Alan C. Goldhamer, Martin M. Grajower, Michelle Harvie, Leonie Heilbronn, Benjamin D. Horne, Spyridon N. Karras, Jost Langhorst, Eva Lischka, Frank Madeo, Sarah J. Mitchell, Ioannis Eleemon Papagiannopoulos-Vatopaidinos, Maria Papagiannopoulou, Hanno Pijl, Eric Ravussin, Martha Ritzmann-Widderich, Krista Varady, Lilian Adamidou, Melika Chihaoui, Rafael De Cabo, Mohamed Hassanein

Clinical Research Faculty Publications

Although fasting is increasingly applied for disease prevention and treatment, consensus on terminology is lacking. Using Delphi methodology, an international, multidisciplinary panel of researchers and clinicians standardized definitions of various fasting approaches in humans. Five online surveys and a live online conference were conducted with 38 experts, 25 of whom completed all 5 surveys. Consensus was achieved for the following terms: “fasting” (voluntary abstinence from some or all foods or foods and beverages), “modified fasting” (restriction of energy intake to max. 25% of energy needs), “fluid-only fasting,” “alternate-day fasting,” “short-term fasting” (lasting 2–3 days), “prolonged fasting” (≥4 consecutive days), and …

Identification And Characterization Of A Skin Microbiome On Caenorhabditis Elegans Suggests Environmental Microbes Confer Cuticle Protection, Nadia B Haghani, Robert H Lampe, Buck S Samuel, Sreekanth H Chalasani, Molly A Matty

Faculty, Staff and Students Publications

In the wild, C. elegans are emersed in environments teeming with a veritable menagerie of microorganisms. The C. elegans cuticular surface serves as a barrier and first point of contact with their microbial environments. In this study, we identify microbes from C. elegans natural habitats that associate with its cuticle, constituting a simple “skin microbiome.” We rear our animals on a modified CeMbio, mCeMbio, a consortium of ecologically relevant microbes. We first combine standard microbiological methods with an adapted micro skin-swabbing tool to describe the skin-resident bacteria on the C. elegans surface. Furthermore, we conduct 16S rRNA gene sequencing studies …

Analysis And Tritrophic Associations Of Bats, Bat Flies, And Laboulbeniales Microfungi In Kenya, Ally Willis

Masters Theses & Specialist Projects

Bats (Chiroptera) are host to diverse lineages of ectoparasitic arthropods including ticks, mites, fleas, bat bugs, and bat flies (Arthropoda). Streblidae and Nycteribiidae are families in the dipteran superfamily Hippoboscoidea, and these hematophagous ectoparasites and their host associations are relatively well studied in the American tropics but not as well in east Africa. One of the main properties of host-parasite systems is host specificity, with some Eastern Hemisphere species (Nycteribiidae) appearing to display a lower level. The morphology of bat flies may drive (or be the result of) niche partitioning on the landscape of the host. Streblid bat flies in …

Synthesis, Structural, Morphological Characterization, And Cytotoxicity Assays Of Metal Complexes Decorated Sio2 Nanoparticles Against Breast Cancer Cell Lines (Mda-Mb-231), Alya'a J. Ahmed, Mahasin F. Alias

Baghdad Science Journal

This study examines the new synthesis of Pt (IV) and Au (III) Mannich base complexes derived from ciprofloxacin. The complexes were then used as precursors to prepare SiO2/PtO2 and SiO2/Au2O3 nanoparticles by depositing the synthesized complexes on porous silica nanoparticles. Elemental analysis, FT-IR, UV-vis, molar conductivity measurements, and melting point were used to characterize this ligand and its metal complexes. Elemental analysis data show that the general formula of the metal complexes formed is [M(L)2Cl2] nCl.H2O, where L = Mannich base ligand and M = Au(III) and Pt(IV), and n = 1,2 respectively with octahedral structure. The chemical structure and …

Boron Neutron Capture Therapy Of Cancer: Where Do We Stand Now?, Rolf F. Barth, Gong Wu, Maria Da Graca H. Vicente, John C. Grecula, Nilendu Gupta

Faculty Publications

No abstract provided.

Using Wasp Specimens In Taxonomic, Biogeographic, Evolution, And Informal Education Studies, Brenna Lynn Decker

All Graduate Theses and Dissertations, Fall 2023 to Present

Entomology collections hold an untapped wealth of information, from insect morphology, genetics, locality and association data, and potential for use in education. Especially with insects that generate initial fears, such as wasps, seeing insect specimens provides a safe environment to learn about their behaviors. Wasps are insects in the order Hymenoptera, along with ants and bees. The public may hold fears against wasps, due to their negative portrayal in various media, but they serve as integral components of a functional ecosystem. Even with their importance, many groups of wasps are still highly understudies. This dissertation aims to tackle this fear …

Ai-Driven Deep Learning Techniques In Protein Structure Prediction, Lingtao Chen, Qiaomu Li, Kazi Fahim Ahmad Nasif, Ying Xie, Bobin Deng, Shuteng Niu, Seyedamin Pouriyeh, Zhiyu Dai, Jiawei Chen, Chloe Yixin Xie

2020-Current year OA Pubs

Protein structure prediction is important for understanding their function and behavior. This review study presents a comprehensive review of the computational models used in predicting protein structure. It covers the progression from established protein modeling to state-of-the-art artificial intelligence (AI) frameworks. The paper will start with a brief introduction to protein structures, protein modeling, and AI. The section on established protein modeling will discuss homology modeling, ab initio modeling, and threading. The next section is deep learning-based models. It introduces some state-of-the-art AI models, such as AlphaFold (AlphaFold, AlphaFold2, AlphaFold3), RoseTTAFold, ProteinBERT, etc. This section also discusses how AI techniques …

Engineered Nucleic-Acid Binding Intrinsically Disordered Proteins For Biomedical Applications, Telmo Diez Perez

Biomedical Engineering ETDs

This dissertation explores the use of intrinsically disorder proteins (IDPs) in biomedical applications related to the detection and biosensing of nucleic-acid species. We engineer several low critical solution temperature (LCST) nucleic-acid binding elastin-like polypeptides (ELPs) as model IDPs and study their potential in biomedical application via interactions with short single-stranded (ss) DNA, tRNA and viral RNAs. First, we engineer a simple polycationic ELP capable of recruiting DNA on demand in a DNA-protein-rich condensate via LLPS. Moreover, we develop a modified Flory-Huggins theory to quantify the partitioning of DNA and protein upon coacervate formation with and without salts. We then design …

Insulin Resistance In Women Correlates With Chromatin Histone Lysine Acetylation, Inflammatory Signaling, And Accelerated Aging, Christina Vidal, Jackelyn Alva-Ornelas, Nancy Zhuo Chen, Parijat Senapati, Jerneja Tomsic, Vanessa Myriam Robles, Cristal Resto, Nancy Sanchez, Angelica Sanchez, Terry Hyslop, Nour Emwas, Dana Aljaber, Nick Bachelder, Ernest Martinez, David Ann, Veronica Jones, Robert Winn, Lucio Miele, Augusto Ochoa, Eric Dietze, Rama Natarajan, Dustin Schones, Victoria Seewaldt

Kimmel Cancer Center Faculty Papers

BACKGROUND: Epigenetic changes link medical, social, and environmental factors with cardiovascular and kidney disease and, more recently, with cancer. The mechanistic link between metabolic health and epigenetic changes is only starting to be investigated. In our in vitro and in vivo studies, we performed a broad analysis of the link between hyperinsulinemia and chromatin acetylation; our top "hit" was chromatin opening at H3K9ac.

METHODS: Building on our published preclinical studies, here, we performed a detailed analysis of the link between insulin resistance, chromatin acetylation, and inflammation using an initial test set of 28 women and validation sets of 245, 22, …

A Constructivist Grounded Theory Exploration Of Intergenerational Trauma Among Lgbtq+ Bipoc Individuals, Satveer Kler

Dissertations

Many scholars have argued that existing conceptualizations of trauma such as the Diagnostic and Statistical Manual of Mental Disorders (5th Ed.; DSM-5) conceptualization are inapplicable for individuals of marginalized communities. Individuals of marginalized communities may experience historical trauma, racial trauma, identity-related trauma, or collective trauma. Moreover, the effects of these forms of trauma may persist throughout different generations via biological transmission (e.g., epigenetics) or via interpersonal transmission (e.g., emotion socialization, cultural socialization, attachment, communication styles, behavioral socialization). The generational effects of these forms of trauma are referred to as intergenerational trauma. There has been a paucity of empirical explorations of …

Molecular Insights Into Propylthiouracil As A Thyroid Peroxidase Inhibitor: A Computational Study Approach, Dwi Anita Suryandari, Luluk Yunaini, Hadi Sunaryo, Khaerunissa Anbar Istiadi, Irandi Putra Pratomo

Indonesian Journal of Medical Chemistry and Bioinformatics

Thyroid peroxidase (TPO) is a crucial enzyme in the biosynthesis of thyroid hormones, catalyzing the iodination of tyrosine residues in thyroglobulin and the coupling of iodotyrosines to form thyroxine (T4) and triiodothyronine (T3). Propylthiouracil (PTU) is an antithyroid drug commonly used to manage hyperthyroidism by inhibiting TPO. Understanding the molecular interactions between TPO and PTU can provide insights into the inhibitory mechanisms and guide the design of more effective antithyroid medications. Objective: This study aims to elucidate the binding interactions between TPO and PTU through molecular docking, providing a detailed understanding of how PTU inhibits TPO activity. Methods: …

Phylogenetic Analysis Of Anthropomorphic Rock Art: A Study Of Material Culture Evolution, Muhammad Faisal Chair, Ali Akbar

International Review of Humanities Studies

This paper provides an explanation of the application of phylogenetic analysis, derived from biology, to be applied in archaeology with the aim of observing evolutionary phenomena, the development of ideas, and the dissemination of ideas from material culture. Phylogenetics will be applied to data on anthropomorphic motifs at five rock art sites in West Sumatra: Gua Lidah Air, Gua Runjo, Ngalau Tompok Syohiah, Batu Basurek, and Gua Basurek. The main stages in this analysis involve collecting representative data in the category of distinctive values from each rock art site. Distinctive values data is obtained through observation and identification of morphological …

Gabaa Receptor Subunit Composition Regulates Circadian Rhythms In Rest–Wake And Synchrony Among Cells In The Suprachiasmatic Nucleus, Daniel Granados-Fuentes, Peter Lambert, Tatiana Simon, Steven Mennerick, Erik D Herzog

2020-Current year OA Pubs

The mammalian circadian clock located in the suprachiasmatic nucleus (SCN) produces robust daily rhythms including rest-wake. SCN neurons synthesize and respond to γ-aminobutyric acid (GABA), but its role remains unresolved. We tested the hypothesis that γ2- and δ-subunits of the GABA

The Role Of Sensing Modalities In Shaping Collective Motion And Group Behavior, Poorendra P. Ramlall

Doctoral Dissertations and Master's Theses

Collective behavior refers to the coordinated movements that emerge from simple interactions between individuals within a group. Traditionally, researchers have modeled these interactions assuming individuals can sense their surroundings in all directions, like having eyes all around their heads. While this is a useful simplification, it does not capture the diverse ways animals actually sense the world. In this thesis, we take inspiration from the natural world, particularly from animals like bats and dolphins that use a combination of hearing and sight to navigate their environments. We explore how combining these sensory cues in a three-dimensional space affects the way …

Twenty-Three Years Of Pcr-Based Seafood Authentication Assay Development: What Have We Learned?, Maleeka Singh, Robert G. Young, Rosalee S. Hellberg, Robert H. Hanner, Maria G. Corradini, Jeffrey M. Garber

Food Science Faculty Articles and Research

Seafood is a prime target for fraudulent activities due to the complexity of its supply chain, high demand, and difficult discrimination among species once morphological characteristics are removed. Instances of seafood fraud are expected to increase due to growing demand. This manuscript reviews the application of DNA-based methods for commercial fish authentication and identification from 2000 to 2023. It explores (1) the most common types of commercial fish used in assay development, (2) the type of method used, (3) the gene region most often targeted, (4) provides a case study of currently published assays or primer-probe pairs used for DNA …

Risk Factors Associated With Pyogenic Spinal Infections Among Intravenous Drug Users And Nonusers, Vivek Biololikar, Brendan Gleason, Lee Kripke, Robert Merrill, Colin Whitaker, Jon Handal

Einstein Health Papers

PURPOSE: To identify the differences in patient factors, presentation, treatment course, and outcomes of intravenous drug users (IVDA) vs. nonusers (non-IVDA) presenting with pyogenic spinal infections.

METHODS: We identified all cases involving spinal infections at our institution between May 2017 and January 2023. Postsurgical infections were excluded, and patients were separated into IVDA and non-IVDA groups. The patient charts were reviewed and analyzed for statistical or clinically significant differences using RStudio (2019 version 3.6.2). Our institutional review board approved this study, IRB# 2020-277, iRISID-2023-1384.

RESULTS: Fifty patients (29 males and 21 females) with primary pyogenic spinal infections were included in …

Energy Safety Management: A Training Model To Improve Flight Safety, Juan R. Merkt, Matthijs H. J. Amelink, David G. Sizoo

Journal of Aviation Technology and Engineering

Failing to properly manage an airplane’s energy state can be unforgiving. Mismanagement of mechanical energy (altitude and/or airspeed) is a contributing factor to three common types of fatal accidents in aviation: loss of control in flight, approach and landing accidents, and controlled flight into terrain. Recognizing the importance of energy management, the Federal Aviation Administration has incorporated new elements into the Airman Certification Standards, emphasizing knowledge of energy management concepts and the consequences of mishandling an airplane’s energy state. Unfortunately, no adequate guidance has been available in terms of defining key energy management concepts or suggesting how these should be …

Advances In Stereoselective Glycosylation: Electron-Withdrawing Groups, Benzyne-Mediated Stereoinversion, And Visible-Light Photochemistry For 1,2-Cis O-Glycosylation, Erik Giovanni Alvarez Valenzuela

LSU Doctoral Dissertations

The symbiotic relationship between humans and their microbiota is essential for health, with imbalances in the complex microbiota ecosystem linked to a variety of disorders ranging from neurodegenerative to gastrointestinal diseases. Bacteria within the human microbiota, comprising over 1000 known species, are densely and diversely coated with oligosaccharides crucial for functions like cell recognition, communication, signaling, adhesion, proliferation, and pathogenic inhibition. However, studying the structure-activity relationships of these sugars which are also secreted by bacteria is challenging due to difficulties in obtaining homogenous samples from natural sources.

Chemical synthesis offers a solution by enabling the production of well-defined oligosaccharides in …

Molecular Docking, Synthesis And Evaluation For Antioxidant And Antibacterial Activity Of New Oxazepane And Benzoxazepine Derivatives, Athra G. Sager, Jawad Kadhim Abaies, Zeena R. Katoof

Baghdad Science Journal

In the field of molecular simulations, molecular docking is a method that can determine the optimal and preferred orientation of a certain molecule related to another when they are coupled to create a stable complex. The strength of the association, or binding affinity, between two molecules can be predicted using knowledge of their preferred orientation. In this study, a series of prepared compounds were evaluated for their binding modes, potential interactions, and target binding locations. Some derivatives 1,3-oxazepane, and 1,3-benzoxazepine were prepared from three Schiff bases compounds (1S-3S). The compounds (1S-3S) were reacted with succinic anhydride and phthalic anhydride to …

Synthesis And Biological Studies Of 4‐Methyl-7‐Ethylcoumarin Derivatives Containing Azo Group, Muntather Hossam Kazem, Luma S. Ahamed

Baghdad Science Journal

New 4-methyl-7-ethylcoumarin derivatives bearing the azo group were synthesized through series ‎of sequential reactions and tested for their biological activity. Starting from 4‎-methyl-7-ethylcoumarin ‎ prepared from a reaction of m-ethyl phenol and ethyl acetoacetate by pechmann ‎condensation reaction, nitration of 4 -methyl-7-ethyl coumarin using nitric acid was carried out in the ‎presence of sulfuric acid to produce one isomer from 4-methyl-7-ethyl-8-nitrocoumarin under the ‎cold condition at (2-5Cº). Then reducing nitro group used iron metal in an acidic medium to form ‎corresponding amino coumarin, which was converted to azo dyes by reacting its diazonium salt ‎with different phenol derivatives. Mass, FT-IR, …

Archaeoentomology: Arthropods And Humans, Current Works In Archaeoentomology, Paz Vigil

Department of Entomology: Distance Master of Science Projects

This paper presents a brief literature review, exploring human and insect interaction, and how such research aids the ongoing construction of the archaeological and entomological record. This field, a combined subset of both entomology and archaeology, is both complex and rich as well as young and still growing. This literature review is not meant to be an exhaustive or comprehensive exploration of this subject, but it will serve as part of a foundation for those interested in the topic or wanting to conduct further exploratory study in this field. The intent is to highlight the practical applications of Archaeoentomology, using …

Ballc And Ballcools: Efficient Formatting And Operating For Single-Cell Dna Methylation Data, Wei Tian, Wubin Ding, Jiawei Shen, Daofeng Li, Ting Wang, Joseph R Ecker

2020-Current year OA Pubs

MOTIVATION: With single-cell DNA methylation studies yielding vast datasets, existing data formats struggle with the unique challenges of storage and efficient operations, highlighting a need for improved solutions.

RESULTS: BAllC (Binary All Cytosines) emerges as a tailored format for methylation data, addressing these challenges. BAllCools, its complementary software toolkit, enhances parsing, indexing, and querying capabilities, promising superior operational speeds and reduced storage needs.

AVAILABILITY AND IMPLEMENTATION: https://github.com/jksr/ballcools.

The Dynamic Trpv2 Ion Channel Proximity Proteome Reveals Functional Links Of Calcium Flux With Cellular Adhesion Factors Ncam And L1cam In Neurite Outgrowth, Pamela N Gallo, Elaine Mihelc, Robyn Eisert, Gary A Bradshaw, Florian Dimek, Andreas Leffler, Marian Kalocsay, Vera Moiseenkova-Bell

Faculty, Staff and Student Publications

TRPV2 voltage-insensitive, calcium-permeable ion channels play important roles in cancer progression, immune response, and neuronal development. Despite TRPV2's physiological impact, underlying endogenous proteins mediating TRPV2 responses and affected signaling pathways remain elusive. Using quantitative peroxidase-catalyzed (APEX2) proximity proteomics we uncover dynamic changes in the TRPV2-proximal proteome and identify calcium signaling and cell adhesion factors recruited to the molecular channel neighborhood in response to activation. Quantitative TRPV2 proximity proteomics further revealed activation-induced enrichment of protein clusters with biological functions in neural and cellular projection. We demonstrate a functional connection between TRPV2 and the neural immunoglobulin cell adhesion molecules NCAM and L1CAM. …

Navigating The Critical Translational Questions For Implementing Flash In The Clinic, Billy W Loo, Ioannis I Verginadis, Brita Singers Sørensen, Anthony E Mascia, John P Perentesis, Albert C Koong, Emil Schüler, Erinn B Rankin, Peter G Maxim, Charles L Limoli, Marie-Catherine Vozenin

Faculty, Staff and Student Publications

The "FLASH effect" is an increased therapeutic index, that is, reduced normal tissue toxicity for a given degree of anti-cancer efficacy, produced by ultra-rapid irradiation delivered on time scales orders of magnitude shorter than currently conventional in the clinic for the same doses. This phenomenon has been observed in numerous preclinical in vivo tumor and normal tissue models. While the underlying biological mechanism(s) remain to be elucidated, a path to clinical implementation of FLASH can be paved by addressing several critical translational questions. Technological questions pertinent to each beam type (eg, electron, proton, photon) also dictate the logical progression of …

Drosophila Nhe2 Overexpression Induces Autophagic Cell Death, Jobelle Peralta, Blake Dupriest, Daniel Orozco, Juan Reyna Pacheco, Laura Martins, Rachel Ann Soriano, Alan Wong, Ramy Wong, Bree Grillo-Hill

Faculty Research, Scholarly, and Creative Activity

Autophagy is a conserved catabolic process where double membrane-bound structures form around macromolecules or organelles targeted for degradation. Autophagosomes fuse with lysosomes to facilitate degradation and macromolecule recycling for homeostasis or growth in a cell autonomous manner. In cancer cells, autophagy is often up-regulated and helps cancer cells survive nutrient deprivation and stressful growth conditions. Here, we propose that the increased intracellular pH (pHi) common to cancer cells is sufficient to induce autophagic cell death. We previously developed tools to increase pHi in the Drosophila eye via overexpression of DNhe2, resulting in aberrant patterning and reduced tissue size. We examined …

Cornus Officinalis Extract Activates The Keap1/Nrf2 Pathway And Delays T1d Onset In The Nod Mouse, Justin D. Fletcher

USF Tampa Graduate Theses and Dissertations

Type 1 diabetes (T1D) is an autoimmune disorder that results in the destruction of the insulin producing pancreatic β cells. The only therapeutic option following T1D clinical onset is exogenous insulin supplementation. At present, there is no cure for T1D and attempted interventional therapy has been focused on modulating the immune system. Few attempts have been pursued at preserving β cell function and survival. Here we provide a novel approach using extract from the fruit of the Cornus officinalis (CO) tree to preserve β cell function through the prevention of β cell stress. CO has been used in traditional Chinese …

Trust And Its Implications For Trauma, Casidhe C. Daniels

Doctoral Dissertations and Projects

Trust presents as a complex and frequently misunderstood building block. While people often demonstrate an inherent belief that trust is naturally engrained in others, adverse life events and traumatic experiences can alter a person’s level of trust. Trust has the ability to change and become redefined. This can occur in a negative manner when trauma is incurred. While the individual’s is often innocent because of the challenges they have experiences, successes, failures, and traumatic events develop an ability to trust others and to what degree they face the lingering implications and diagnoses result.

Differentiating Dynamic System Outcomes In Cam Photosynthesis Through Sonification, Duncan Turley

Civil and Environmental Engineering Undergraduate Honors Theses

Sonification is a powerful tool that is harnessed by modern engineers to represent information through audio, and is beginning to be used to interpret more complex data sets. Sonification can be used to facilitate the listeners' ability to grasp microscopic or complex changes in the state of a system. This study uses the assigning of sound patterns to model outputs that indicate chaotic or non-chaotic systems in Crassulacean acid metabolism photosynthesis. Using sound allows the interpretation of chaotic data without the more time intensive processes typically used, such as of Fast Fourier Transformations. Based on past research, it is known …

Antiviral And Cytotoxic Activities And Chemical Profiles Of Two Species Of Abies Nordmanniana From Türkiye, Nazli Sarikahya, Gaye Sümer Okkali, Furkan Ozan Çöven, Sevda Zeinali̇, Gülce Gucur, Ayşe Di̇la Çağlar, Ece Uyar, Ahmet Ceyhan Gören, Ayşe Nalbantsoy

Turkish Journal of Chemistry

Abies is an important genus of the family Pinaceae, with about 50 species found in the highlands of Asia, Europe, North Africa, and North and Central America. The principal aim of the present work was to investigate the chemical content and biological potential of the resin and cone from Abies nordmanniana subsp. bornmulleriana and Abies nordmanniana subsp. equi-trojani, respectively. The flavonoid and phenolic contents of the resin and cones were evaluated using liquid chromatography-high resolution mass spectrometry (LC-HRMS). Additionally, the essential oil and fatty acid compositions were analyzed using gas chromatography-mass spectrometry (GC-MS) and gas chromatography-flame ionization detector (GC-FID).. Cytotoxicity …