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Analysis Of Human Papillomavirus Capsid Proteins: Insights Into Capsid Assembly, Willie A. Hughes

School of Biological Sciences: Dissertations, Theses, and Student Research

Papillomaviruses (PVs) are double stranded (ds)-DNA viruses (~8-kbp), which infect mucosal and cutaneous epithelial cells from various mammalian species, causing tumors in both epithelial cell-types. During the late-phase, the capsid proteins (L1 and L2), are expressed to encapsidate the viral genome generating infectious virion particles required for PV. Natural PV infections produce morphologically homogenous progeny virions 55-nm in diameter. Transient transfection systems allow individual expression of the capsid proteins, which are able to produce low-levels of infectious virion-like particles (VLPs) and non-infectious VLPs that have the capacity to resemble and function as wild-type virions.

Results: The research herein demonstrates …

2013: Proceedings Of The 16th International Congress Of Speleology, Czech Republic, Brno, July 21-28, 2013 Volume 2 International Congress Of Speleology Ics Proceedings, International Congress Of Speleology

KIP Talks and Conferences

Produced by the Organizing Committee of the 16th International Congress of Speleology. Published by the Czech Speleological Society and the SPELEO2013 and in the co-operation with the International Union of SpeleologyEdited by Michal Filippi, Pavel Bosák Contents: Preface Session: Exploration And Cave TechniquesRecent Investigations In The Gálapagos Islands, Ecuador / Aaron Addison, Theofilos Toulkeridis, Steven Taylor, Glenn Osburn, Geoffery Hoese, Vicente Delgado -- Quartz Sandstone Caves On Table Mountains Of Venezuela / Marek Audy, Richard Bouda -- Northern Velebit Deep Caves / Darko Bakšić, Dalibor Paar, Andrej Stroj, Damir Lacković -- Best-Practice Training Approaches For Mitigating Caving Hazards And Enhancing …

Regenerating The Enthesis: Characterizing Tendon To Bone Interface Development On Polymer Scaffolds Under Cyclic Strain Application, Lauren Eichaker

Electronic Theses and Dissertations Archive

This research is the application of cyclic strain to a polyester terepthalate (PET) scaffold seeded with fibroblast cells on one half and osteoblast cells on the other half for 28 days. The apparatus ensured that osteoblasts received no applied strain except that from the flowing media. Fibroblasts received strain (0%, 2.5%, and 5%) in the form of 0.089 Hz load cycles, which incorporated 10 seconds of rest, 4 hours per day. This preliminary research showed that fibroblasts can respond to strain application and media flow by depositing approximately 2 times more glycosaminoglycans and collagen matrix onto the PET scaffold per …

Studies Toward The Synthesis Of Lyconadin A And Cranomycin, Brad M. Loertscher

Theses and Dissertations

Lyconadin A is a pentacyclic Lycopodium alkaloid isolated from the club moss Lycopodium companatum with anticancer activity. Our approach sought to incorporate a 7-exo–6-exo acyl radical cyclization cascade to access the bicyclo[5.4.0]undecane framework of lyconadin A. Our studies created methodology for the synthesis of 5-alkyl and 3,5-dialkyl-6-carbomethoxy-2-pyridones and sterically demanding epoxide substrates. These epoxide substrates underwent an unanticipated Payne rearrangement.Cranomycin is a potent antibiotic with antiprotozoal activity. Structurally it is a cyclopentane ring system with substitution at each carbon in the ring. Another interesting structural aspect is the existence of three contiguous quaternary stereocenters including two tertiary alcohols and a …

Interview With Jane West - Oh 274, Martha Jane Cato West

Winthrop University Oral History Program

In her July 15, 2013 interview with Martha Manning, Jane Cato West (Class of 1968) details her time at Winthrop as a Biology major in the 1960s. Briefly, West discusses student life and Winthrop traditions, but she provides insight into her life student teaching at Florence High School. Additionally, West includes her experience in required courses like English and Math, as well as experiments conducted in her Biology courses. West concludes the interview with her overall perceptions of Winthrop.

Transcription Factor Binding Profiles Reveal Cyclic Expression Of Human Protein-Coding Genes And Non-Coding Rnas, Chao Cheng, Matthew Ung, Gavin D. Grant, Michael L. Whitfield

Dartmouth Scholarship

Cell cycle is a complex and highly supervised process that must proceed with regulatory precision to achieve successful cellular division. Despite the wide application, microarray time course experiments have several limitations in identifying cell cycle genes. We thus propose a computational model to predict human cell cycle genes based on transcription factor (TF) binding and regulatory motif information in their promoters. We utilize ENCODE ChIP-seq data and motif information as predictors to discriminate cell cycle against non-cell cycle genes. Our results show that both the trans- TF features and the cis- motif features are predictive of cell cycle genes, and …

An Approximation Method To Calculate Complicated Expectations, Mohammad Moradi, Jennifer Brown

Journal of Statistics Applications & Probability

In some adaptive sampling designs, expectations need to be calculated as sampling progresses. For situations when these calculations need to be done in the field where there is no access to computers, or for very complicated and computer intensive calculations, we introduce an approximation method. The method to approximate the expectation is based on conditioning on small set of points. An application of the approximation method is described for a sample design with a complicated estimator.

Genomic Analysis Of Stress Response Against Arsenic In Caenorhabditis Elegans, Surasri N. Sahu, Jada Lewis, Isha Patel, Serdar Bozdag, Jeong H. Lee, Robert Sprando, Hediye Nese Cinar

Mathematics, Statistics and Computer Science Faculty Research and Publications

Arsenic, a known human carcinogen, is widely distributed around the world and found in particularly high concentrations in certain regions including Southwestern US, Eastern Europe, India, China, Taiwan and Mexico. Chronic arsenic poisoning affects millions of people worldwide and is associated with increased risk of many diseases including arthrosclerosis, diabetes and cancer. In this study, we explored genome level global responses to high and low levels of arsenic exposure in Caenorhabditis elegans using Affymetrix expression microarrays. This experimental design allows us to do microarray analysis of dose-response relationships of global gene expression patterns. High dose (0.03%) exposure caused stronger global …

Neural Correlates Of The Extreme Male Brain Theory In Adolescents With And Without Autism Spectrum Disorders, Audrey Meyer Carson

Dissertations (1934 -)

The Extreme Male Brain (EMB) theory (Baron-Cohen, 2003) is a behavioral theory of autism spectrum disorders (ASD), suggesting that the triad of behavioral impairments in ASD can be conceptualized psychologically as impairment in empathizing, coupled with a superior capacity for systemizing. Despite studies of the behavioral manifestations of this theory, it lacks neurological findings, specifically evidence of less coordinated activity between the left and right hemisphere in ASD (i.e. more lateralized activity). This study attempted to investigate neural correlates of the EMB theory utilizing EEG coherence, an index of neural connectivity, to determine if a more lateralized profile exists in …

Don't Give Your Kid That Shot!: The Public Health Threat Posed By Anti-Vaccine Speech And Why Such Speech Is Not Guaranteed Full Protection Under The First Amendment, Amanda C. Naprawa

Cardozo Public Law, Policy & Ethics Journal

The article argues that antivaccination speech poses a significant threat to public health, and the law should be utilized to regulate such speech to prevent the spread of preventable diseases and protect vulnerable populations through herd immunity. While the First Amendment protects free speech, legal measures such as the FTC regulating false advertising and potential vaccine disparagement statutes can be effective tools in curbing harmful misinformation. The article emphasizes the need for a balanced approach that respects individual rights while safeguarding community health, supported by scientific consensus on vaccine safety and legal precedents like Jacobson v. Massachusetts.

Biology, Saint Mary's College Of California

Academic Catalog

No abstract provided.

Relationship Between Serum And Brain Carotenoids, Α-Tocopherol, And Retinol Concentrations And Cognitive Performance In The Oldest Old From The Georgia Centenarian Study, Elizabeth J. Johnson, Rohini Vishwanathan, Mary Ann Johnson, Dorothy B. Hausman, Adam Davey, Tammy M. Scott, Robert C. Green, L. Stephen Miller, Marla Gearing, John Woodard, Peter T. Nelson, Hae-Yun Chung, Wolfgang Schalch, Jonas Wittwer, Leonard W. Poon

Sanders-Brown Center on Aging Faculty Publications

Oxidative stress is involved in age-related cognitive decline. The dietary antioxidants, carotenoids, tocopherols, and vitamin A may play a role in the prevention or delay in cognitive decline. In this study, sera were obtained from 78 octogenarians and 220 centenarians from the Georgia Centenarian Study. Brain tissues were obtained from 47 centenarian decedents. Samples were analyzed for carotenoids, α-tocopherol, and retinol using HPLC. Analyte concentrations were compared with cognitive tests designed to evaluate global cognition, dementia, depression and cognitive domains (memory, processing speed, attention, and executive functioning). Serum lutein, zeaxanthin, and β-carotene concentrations were most consistently related to better cognition …

Brovine: Mammary Gland Gene Database, Therin C. Irwin

Computer Science and Software Engineering

Brovine is used by the Animal Science department at Cal Poly to catalog and analyze genetic information. Brovine, or the Mammary Gland Gene Database, is a system used to store and categorize genetic information which is gathered through experimentation and through TESS, a web application that lets users search through catalogs of similar genetic information. This document describes the purpose, use, and maintenance of Brovine.

Fitness: Philosophical Problems, Grant Ramsey, Charles H. Pence

Faculty Publications

Fitness plays many roles throughout evolutionary theory, from a measure of populations in the wild to a central element in abstract theoretical presentations of natural selection. It has thus been the subject of an extensive philosophical literature, which has primarily centred on the way to understand the relationship between fitness values and reproductive outcomes. If fitness is a probabilistic or statistical quantity, how is it to be defined in general theoretical contexts? How can it be measured? Can a single conceptual model for fitness be offered that applies to all biological cases, or must fitness measures be case-specific? Philosophers have …

Synthesis And Antifungal Evaluation Of Barbiturate Saponins And Progress Towards Cysteinyl Metal Peptides, Monika Madhav

LSU New Orleans Theses and Dissertations

Invasive fungal infections are a major threat to immune-compromised patients. There is a critical need to develop new antifungal agents because of increasing resistance to the common antifungal drugs.

In the first part of this dissertation, methods for preparation of novel barbiturate saponin as antifungals and their biological activities would be described. Barbiturates and steroidal saponins have shown remarkable antifungal activity in the biological assays. Therefore, attempts were directed to combine the barbiturate with the steroid to give novel antifungal agents. The need for extensive SAR studies and to better understand these compounds efforts were directed to synthesize novel saponin …

Growth And Energetic Condition Of Dolly Varden Char In Coastal Arctic Waters, Jason T. Stolarski

Fisheries

Dolly Varden char Salvelinus malma are a dominant member of the nearshore Arctic icthyofauna and support one of the largest subsistence fisheries within Arctic coastal communities in Alaska. Despite this importance, numerous aspects of Dolly Varden ecology remain poorly understood, which inhibits efforts to assess the biological consequences of anthropogenic disturbances such as hydrocarbon extraction and climate change within nearshore areas. The goal of this research was to develop and apply new techniques to measure and assess the biological integrity of Dolly Varden populations. To do so, I evaluated the precision of age determination generated from scales, otoliths, and fin …

2013 Spring Commencement, Harding University

Commencement Programs

Program for the Harding University Commencement on May 11.

Commencement Speaker: David B. Burks

Effect Of Positional Dependence In Recognizing Transcription Factor Binding Sites, Saad A. Quader

Master's Theses

Background: Many consensus-based and Position Weight Matrix-based methods for recognizing transcription factor binding sites are not well suited to the variability in the lengths of binding sites. Besides, many methods discard known binding sites while building the model. Moreover, the impact of Information Content (IC) and the positional dependence of nucleotides within an aligned set of TFBSs has not been well researched for modeling variable-length binding sites. In this paper, we propose ML-Consensus, a consensus model for variable-length binding sites which does not exclude any input binding sites. We consider Pairwise Score (PS) as a measure of positional dependence of …

05-08-2013 Swosu Biology Students Receive Awards, Southwestern Oklahoma State University

THE BARK ARCHIVE 2013

Southwestern Oklahoma State University’s Biological Sciences Department recently held its annual honors banquet on the Weatherford campus. Scholarships and awards were presented to outstanding biology students at the end-of-year ceremony.

A Study Of The Niche Structure And Habitat Utilization Of Urban Dwelling Winter Birds, Thomas Huff

Honors Theses

A study was conducted to evaluate the distribution of urban birds relative to differences in habitat as determined by zoning type. A total of 1,948 individual birds and a total of 33 species were sampled across the four different zones (industrial, commercial, residential, and public use.) The industrial use zone contained the highest number of individuals whereas commercial zones contained the fewest. However, the four zones contained approximately equal species richness.

Industrial zones supported the greatest number of cavity nesting and seed eating species. Residential and public use zones contained greater numbers of insectivorous and cup nesting species. In the …

Genetic Structure In The Coral, Montastraea Cavernosa: Assessing Genetic Differentiation Among And Within Mesophotic Reefs, Daniel A. Brazeau, Michael P. Lesser, Marc Slattery

Pharmaceutical Sciences Faculty Publications

Mesophotic coral reefs (30–150 m) have recently received increased attention as a potential source of larvae (e.g., the refugia hypothesis) to repopulate a select subset of the shallow water (,30 m) coral fauna. To test the refugia hypothesis we used highly polymorphic Amplified Fragment Length Polymorphism (AFLP) markers as a means to assess small-scale genetic heterogeneity between geographic locations and across depth clines in the Caribbean coral, Montastraea cavernosa. Zooxanthellae-free DNA extracts of coral samples (N = 105) were analyzed from four depths, shallow (3–10 m), medium (15– 25 m), deep (30–50 m) and very deep (60–90 m) from Little …

I. Stereochemical Control Of Chiral Assembly And Liquid Crystal Phase Formation Of Nonamphiphilic Molecules In Water Ii. Control Bacterial Quorum Sensing And Quorum Sensing-Mediated Activities Using Small Unnatural Molecules, Sijie Yang

Chemistry - Dissertations

The primary goal of this research is to utilize organic synthesis as a tool to prepare small molecules that find potential application in different areas including colloidal and material science, biological chemistry, and medicinal chemistry.

Chapter 1 describes the interpretation of the conformation of nonamphiphilic mesogen disodium cromoglycate (5´DSCG) when it exists as part of an assembly in water. The study of thermodynamic incompatibility and miscibility suggest that a previously proposed model for the assembly of 5´DSCG may be applicable to nonamphiphilic organic dyes and other mesogens.

Chapter 2 presents a study of stereochemical control on assembly and liquid crystal …

Proteomic Studies Of The Influenza Virus-Human Cell Interactions: The Responses Of Host Cell Protein Expression To Viral Infection And The Novel Host Proteins That Interact With Virus Protein Ns1, Yimeng Wang

Graduate Theses and Dissertations

Influenza A viruses (IAVs) continue to be a threat to human health. Despite extensive studies, the mechanisms underlying the IAVs-host interactions during IAV infection remain elusive. We employed quantitative proteomic methods to systematically explore the host cell protein expression responses to IAV infection and examine the function of a critical IAV protein called NS1 by identifying its host binding partners. Specifically, we used a 2-dimentional gel electrophoresis (2-DE) based proteomic method to screen host proteins whose expression was substantially altered by IAV. One critical protein named IκB kinase-gamma (IKKγ) was found to be significantly down-regulated during IAV infection. Functional studies …

Synthesis Of Dibenzofurans Via A Palladium Catalyzed Oxidative Ring Closure Reaction, Sadia Akram

Senior Honors Theses

The cannabinoid partial agonist BAY 59-3704 has been identified as an attractive target to explore structure-activity relationships at cannabinoid receptors for the development of a therapeutic agent for psychostimulant addiction. This thesis will describe the studies associated with the optimization of a palladium-catalyzed oxidative ring closure reaction for the synthesisof dibenzofuran analogues from substituted diaryl ethers. These dibenzofurans are viewed as rigid analogues of BAY 59-3704 and will provide useful information about molecular interactions at cannabinoid receptors. The scope and limitations of the palladium-catalyzed oxidative ring closure reaction as it relates to the synthesis of the target dibenzofuran analogues will …

Functional Characterization Of Type-B Response Regulators In The Arabidopsis Cytokinin Response, Kristine Hill, Dennis E. Mathews, Hyo Jung Kim, Ian H. Street, Sarah L. Wildes, Yi-Hsuan Chiang, Michael G. Mason, Jose M. Alonso, Joseph R. Ecker, Joseph K. Kieber, G. Eric Schaller

Dartmouth Scholarship

Cytokinins play critical roles in plant growth and development, with the transcriptional response to cytokinin being mediated by the type-B response regulators. In Arabidopsis (Arabidopsis thaliana), type-B response regulators (ARABIDOPSIS RESPONSE REGULATORS [ARRs]) form three subfamilies based on phylogenic analysis, with subfamily 1 having seven members and subfamilies 2 and 3 each having two members. Cytokinin responses are predominantly mediated by subfamily 1 members, with cytokinin-mediated effects on root growth and root meristem size correlating with type-B ARR expression levels. To determine which type-B ARRs can functionally substitute for the subfamily 1 members ARR1 or ARR12, we …

The Effect Of Epigallocatechin Gallate (Egcg) On Caeonorhabdits Elegance Exposed To Modelled Microgravity, Sieanna Marissa Blackwood

Theses (Pre-2016)

Antioxidants are substances found in many foods, nuts, grains, fruits and vegetables. Antioxidants protect cells from the damage caused from free radicals. Epigallocatechin gallate (EGCG) is the main constituent of green tea. Studies show that EGCG protects against oxidative stress. There is indication that EGCG can prevent neurodegenerative diseases such as Alzheimer's, Parkinson's, and Huntington's disease. Caenorhabditis elegans are used as model organisms to better understand the effect of zero gravity on organisms. With the widespread popularity of space flight, scientists continue to better understand the consequences of microgravity on organism. Microgravity weakens the muscular, skeletal, nervous system, reproductive and …

Reproductive Biology And Impacts Of Energy Development On Physaria Congesta And Physaria Obcordata (Brassicaceae), Two Rare And Threatened Plants In The Piceance Basin, Colorado, Sarah Lynn Clark

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

Oil and gas development has increased profoundly over the last 20 years in the United States. A large underground deposit of natural gas has been found in the Piceance Basin, which is located in the northwestern part of the state of Colorado. This deposit occurs in an area inhabited by two rare mustard species commonly named the Dudley Bluffs bladderpod and the Dudley Bluffs twinpod. These two plant species are also listed as threatened by the US Fish and Wildlife Service. Concerns about gas development effects on these rare plants have motivated research that quantifies these potential impacts. Through funding …

Tgf-B Signaling Pathway, Er-A And The Heterogeneity Of Breast Cancer Risk Among Hispanic And Non-Hispanic White Women., Stephanie Denkhoff Boone

Electronic Theses and Dissertations

Many risk factors for breast cancer differ between race/ethnic groups. Few studies have included Hispanic women: a genetically admixed population that differs from other ethnic groups for breast cancer incidence, survival, and tumor phenotype. The objective of this study was to determine if genetic variation in ERa and TGF-ß signaling genes (TGF-ß1, TGF-ßR1, RUNX1, RUNX2, RUNX3) is associated with breast cancer risk, and if these associations differ between Hispanic and non-Hispanic white women (NHW). Data from The Breast Cancer Health Disparities (BCHD) study were used. BCHD is a multi-site consortium including two case-control studies within the U.S. and one in …

Ovarian Modifications In Mice Exposed To Whole-Body Irradiation., Jacob Marion Poole

Undergraduate Honors Theses

This experiment was designed to determine the involvement of varying levels of whole-body irradiation on ovarian follicular and corpora luteal development in mice. Previous research has indicated reduced counts of ovarian follicles and corpora lutea in mice flown in space. These differences may be the result of microgravity, increased exposure to radiation, or some combination of both. Fifty-six mice were divided into three groups (apocynin-treated, nox2 knockout, and wild-type control) before exposure to 0 Gy, 0.5 Gy, or 2.0 Gy radiation. The tissues were harvested, preserved, run through the appropriate paraffin embedding procedures, serially sectioned, mounted on microscope slides, and …

Interactions Between Ions And Lysenin Nanochannels And Their Potential Applications As Biosensors, Radwan Awwad Al Faouri

Graduate Theses and Dissertations

Lysenin is classified as a pore-forming toxin protein that is isolated from the earthworm Eisenia fetida and consists of 297 amino acids [1]. Lysenin inserts large conducting pores (3.0-4.7 nm in diameter) into artificial membranes (BLM) which include sphingomyelin. These pores (channels) are open and oriented upon insertion into the bilayer lipid membrane. Lysenin channels gate at positive voltages (voltage-induced gating), but not at negative voltages. Lysenin pores also exhibit activity modulation in response to changes in ionic strength and pH, indicating that electrostatic interaction is responsible for Lysenin conductance activities. In this line of inquiries, and by modulating Lysenin …