Digital Commons Network^™

Local Adaptation Of Two Cryptic Species, Lasthenia Californica And Lasthenia Gracilis, To Distinct Regions Within A Serpentine Outcrop, Teri Barry

Master's Theses

Intraspecific variation providing tolerance to specific edaphic conditions may contribute to population differentiation, speciation, and species coexistence. This process is often examined using reciprocal transplant experiments of closely related species in contrasting edaphic conditions. The two cryptic species Lasthenia californica and L. gracilis occur on a serpentine outcrop in parapatry at Jasper Ridge Biological Preserve. I hypothesized that each species would demonstrate greater fitness in its home range. A reciprocal transplant experiment was conducted in the field to determine home site advantage. Seedlings from each species were planted in both home ranges and in the transition zone where both species …

Mastermind-Like 1-Dependent Notch Target Gene Activation Requires A Sequence-Paired Site And A Tata Box, Cassandra Agbayani Ramos

Master's Theses

Notch signaling plays an important role in mammalian cellular proliferation, apoptosis, and differentiation. To activate target genes, the Notch intracellular domain (NICD) forms a complex with CBF1 and Mastermind-like protein (MAM). The Notch activation complex binds to a response element containing the consensus sequence RTGRGAR (R= purine) on target gene promoters. The promoter of one well characterized target gene, Hes1, contains four Notch response elements (NREs). Site-directed mutagenesis and reporter gene assays were used to examine the activation of Hes1 by mutating individual and combinations of NREs. Results indicated that NREs 2 and 4 are important for Hes1 activity, confirming …

Computational Approaches For Structure Based Drug Design And Protein Structure-Function Prediction, Sai Lakshmana Kumar Vankayala

USF Tampa Graduate Theses and Dissertations

This dissertation thesis consists of a series of chapters that are interwoven by solving interesting biological problems, employing various computational methodologies. These techniques provide meaningful physical insights to promote the scientific fields of interest. Focus of chapter 1 concerns, the importance of computational tools like docking studies in advancing structure based drug design processes. This chapter also addresses the prime concerns like scoring functions, sampling algorithms and flexible docking studies that hamper the docking successes. Information about the different kinds of flexible dockings in terms of accuracy, time limitations and success studies are presented. Later the importance of Induced fit …

Force Generation By Kinesin And Myosin Cytoskeletal Motor Proteins, F. Jon Kull, Sharyn A. Endow

Dartmouth Scholarship

Kinesins and myosins hydrolyze ATP, producing force that drives spindle assembly, vesicle transport and muscle contraction. How do motors do this? Here we discuss mechanisms of motor force transduction, based on their mechanochemical cycles and conformational changes observed in crystal structures. Distortion or twisting of the central β-sheet - proposed to trigger actin-induced Pi and ADP release by myosin, and microtubule-induced ADP release by kinesins - is shown in a movie depicting the transition between myosin ATP-like and nucleotide-free states. Structural changes in the switch I region form a tube that governs ATP hydrolysis and Pi release by the motors, …

Oligodeoxynucleotide Synthesis Using Protecting Groups And A Linker Cleavable Under Non-Nucleophilic Conditions, Xi Lin

Dissertations, Master's Theses and Master's Reports - Open

Oligodeoxynucleotides (ODNs) containing latent electrophilic groups can be highly useful in antisense drug development and many other applications such as chemical biology and medicine, where covalent cross-linking of ODNs with mRNA, protein and ODN is required. However, such ODN analogues cannot be synthesized using traditional technologies due to the strongly nucleophilic conditions used in traditional deprotection/cleavage process.

To solve this long lasting and highly challenging problem in nucleic acid chemistry, I used the 1,3-dithian-2-yl-methoxycarbonyl (Dmoc) function to protect the exo-amino groups on the nucleobases dA, dC and dG, and to design the linker between the nascent ODN and solid support. …

Microfluidic Impedance-Metric Biosensor For Monitoring Carbon Nanotube-Induced Epithelial Permeability, Zhouchun Huang

Graduate Theses, Dissertations, and Problem Reports (ETD)

Carbon nanomaterials, including carbon nanotubes (CNTs) gain increasing interest in commercial and biomedical applications. Adverse health effects of engineered CNTs may result from either direct exposure during production, inadvertent exposure during use of by-products, and/or release of these materials into the environment. Recent studies have shown that CNTs can induce cytotoxicity, apoptosis, DNA damage, and tumor formation in animals, suggesting their potential toxicity in humans. To address the current needs in developing in vitro cell assays for assessment of the adverse health effects of CNTs in lung respiratory, we have developed a microfluidic impedance-metric biosensor for investigation of multi-walled CNTs …

Surfaces Modulate Β-Amyloid Peptide Aggregation Associated With Alzheimer's Disease., Elizabeth Anne Yates

Graduate Theses, Dissertations, and Problem Reports (ETD)

A hallmark of Alzheimer's disease, a late onset neurodegenerative disease, is the presence of neuritic amyloid plaques deposited within the brain composed of β-amyloid (Aβ) peptide aggregates. Aβ can aggregate into a variety of polymorphic aggregate structures under different chemical environments, specifically affected by the presence of differing surfaces. There are several point mutations clustered around the central hydrophobic core of Aβ (E22G Arctic mutation, E22K Italian mutation, D23N Iowa mutation, and A21G Flemish mutation). These mutations are associated with hereditary diseases ranging from almost pure cerebral amyloid angiopathy to typical Alzheimer's disease pathology with both plaques and tangles. To …

Integrative Analysis Using Module-Guided Random Forests Reveals Correlated Genetic Factors Related To Mouse Weight, Zheng Chen, Weixiong Zhang

Open Access Publications

No abstract provided.

The Role Of The Immune Response In Age-Related Macular Degeneration, Scott M. Whitcup, Akrit Sodhi, John P. Atkinson, V Michael Holers, Debasish Sinha, Barbel Rohrer, Andrew D. Dick

Open Access Publications

No abstract provided.

Design Of A Running Robot And The Effects Of Foot Placement In The Transverse Plane, Timothy James Sullivan

Open Access Theses

The purpose of this thesis is to make advances in the design of humanoid bipedal running robots. We focus on achieving dynamic running locomotion because it is one metric by which we can measure how far robotic technologies have advanced, in relation to existing benchmarks set by humans and other animals. Designing a running human-inspired robot is challenging because human bodies are exceptionally complex mechanisms to mimic. There are only a few humanoid robots designed specifically for running and the existing robots are either constrained to a plane, do not yet exhibit human-like motion, or are unstable.

One aspect of …

Method Development Using Laser Ablation And Solution Icpms And Their Application In Environmental Science And Forensic Provenance Studies, Kaixuan Bu

Electronic Theses and Dissertations

Inductively coupled plasma mass spectrometry (ICPMS) is an analytical technique that can be used to determine multiple elements and isotope ratios in a wide variety of samples. In this work, four projects are described that involve the method development using laser ablation (LA) and solution-based ICPMS and their application in environmental science and forensic (provenance) investigations. In the first project, plutonium (Pu) concentrations and 240Pu/ 239Pu atom ratios were measured in kelp, lichen, aquatic moss, and horse mussel collected on or near Amchitka Island, a former nuclear test in Alaska, and at a background site. The Pu in terrestrial and …

Mechanisms Models And Biomarkers In Amyotrophic Lateral Sclerosis, Martin R. Turner, Robert Bowser, Lucie Bruijn, Luc Dupuis, Albert Ludolph, Michael Mcgrath, Giovanni Manfredi, Nicholas Maragakis, Robert G. Miller, Seth L. Pullman, Seward B. Rutkove, Pamela J. Shaw, Jeremy M. Shefner, Kenneth H. Fischbeck

Neurology

The last 30 years have seen a major advance in the understanding of the clinical and pathological heterogeneity of amyotrophic lateral sclerosis (ALS), and its overlap with frontotemporal dementia. Multiple, seemingly disparate biochemical pathways converge on a common clinical syndrome characterized by progressive loss of upper and lower motor neurons. Pathogenic themes in ALS include excitotoxicity, oxidative stress, mitochondrial dysfunction, neuroinflammation, altered energy metabolism, and most recently RNA mis-processing. The transgenic rodent, overexpressing mutant superoxide dismutase-1, is now only one of several models of ALS pathogenesis. The nematode, fruit fly and zebrafish all offer fresh insight, and the development of …

Heterostyly In Linum Aretioides, Aykut Güvensen, Özcan Seçmen, Serdar Gökhan Şenol

Turkish Journal of Botany

The petal width; sepal, pistil, and stamen lengths; and changes in pollen sizes associated with heterostyly of different morphs in populations of Linum aretioides Boiss. were investigated. Fruit sets were compared in 2 populations and it was investigated whether the Bozdağ population has a heteromorphic incompatibility system. It was observed that the stamen lengths of thrum morphs of Bozdağ were shorter than those of thrum morphs of Babadağ. Pistil lengths of both morphs of Bozdağ were longer than those of morphs of Babadağ. Pollen shapes of both morphs were prolate-spheroidal and subprolate, respectively, in the Bozdağ population and subprolate in …

Joint Entropy Of Continuously Differentiable Ultrasonic Waveforms, M S. Hughes, John E. Mccarthy, J N. Marsh, S A. Wickline

Mathematics Faculty Research

This study is based on an extension of the concept of joint entropy of two random variables to continuous functions, such as backscattered ultrasound. For two continuous random variables, X and Y, the joint probability density p(x,y) is ordinarily a continuous function of x and y that takes on values in a two dimensional region of the real plane. However, in the case where X=f(t) and Y=g(t) are both continuously differentiable functions, X and Y are concentrated exclusively on a curve, γ(t)=(f(t),g(t)), in the x,y plane. This concentration can only be represented using a mathematically "singular" object such as a …

“It’S Not About Health; It’S About Sex, Pumpkin”: Reproductive Autonomy, Medicalization, And Contraceptive Rhetoric In The Wake Of The War On Women, Alyson Lise Guthrie

English

The purpose of this study is to better understand the ways in which contemporary women describe their contraceptive needs in the wake of the war on women, primarily in the context of the Sandra Fluke and Rush Limbaugh controversy. After surveying contemporary American women, this study aligns with previous research in finding that the majority of participants describe their contraceptive needs in a variety of ways, but primarily as a means for planning, preventing, or delaying pregnancy. However, women who were not in committed relationships were much more likely to cite medical reasons for their contraceptive use, and much less …

Identification Of A Histidine Metal Ligand In The Arge-Encoded N-Acetyl-L-Ornithine Deacetylase From Escherichia Coli, Wade C. Mcgregor, Danuta M. Gillner, Sabina I. Swierczek, Dali Liu, Richard C. Holz

Chemistry: Faculty Publications and Other Works

The H355A, H355K, H80A, and H80K mutant enzymes of the argE-encoded N-acetyl-L-ornithine deacetylase (ArgE) from Escherichia coli were prepared, however, only the H355A enzyme was found to be soluble. Kinetic analysis of the Co(II)-loaded H355A exhibited activity levels that were 380-fold less than Co(II)-loaded WT ArgE. Electronic absorption spectra of Co(II)-loaded H355A-ArgE indicate that the bound Co(II) ion resides in a distorted, five-coordinate environment and Isothermal Titration Calorimetry (ITC) data for Zn(II) binding to the H355A enzyme provided a dissociation constant (K_d) of 39 μM. A three-dimensional homology model of ArgE was generated using the …

Investigation Of A Novel Magnesium And Acidified Ethanol System For The Degradation Of Persistent Organic Pollutants, Phillip Maloney

Electronic Theses and Dissertations

For centuries chemists have sought to improve humankind’s quality of life and address many of society’s most pressing needs through the development of chemical processes and synthesis of new compounds, often with phenomenal results. Unfortunately, there also are many examples where these chemicals have had unintended, detrimental consequences that are not apparent until years or decades after their initial use. There are numerous halogenated molecules in this category that are globally dispersed, resistant to natural degradation processes, bioaccumulative, and toxic to living organisms. Chemicals such as these are classified as persistent organic pollutants (POPs), and due to their negative environmental …

Biogeography And Systematics Of The Nerodia Clarkii/Nerodia Fasciata Clade In Florida, Gregory Territo

Electronic Theses and Dissertations

Biogeography provides a window into the evolutionary history of populations, and helps explain the diversity and distribution of life through time. Viewed from a systematic perspective, biogeographic studies generate convincing arguments to explain the relationships among organisms and categorize them into useful taxonomies. When taxonomies do not reflect evolutionary histories, inaccurate representations of biodiversity confound future studies and conservation efforts. Two thamnophiine snakes, Nerodia clarkii and Nerodia fasciata, harbor unique morphological and ecological adaptations that obscured natural groupings, leading to controversial taxonomic delimitations. Additionally, population declines documented in N. clarkii compressicauda and N. clarkii taeniata led managers to list N. …

Identification Of A Histidine Metal Ligand In The Arge-Encoded N-Acetyl-L-Ornithine Deacetylase From Escherichia Coli, Wade C. Mcgregor, Danuta Gillner, Sabina I. Swierczek, Dali Liu, Richard C. Holz

Chemistry Faculty Research and Publications

The H355A, H355K, H80A, and H80K mutant enzymes of the argE-encoded N-acetyl-L-ornithine deacetylase (ArgE) from Escherichia coli were prepared, however, only the H355A enzyme was found to be soluble. Kinetic analysis of the Co(II)-loaded H355A exhibited activity levels that were 380-fold less than Co(II)-loaded WT ArgE. Electronic absorption spectra of Co(II)-loaded H355A-ArgE indicate that the bound Co(II) ion resides in a distorted, five-coordinate environment and Isothermal Titration Calorimetry (ITC) data for Zn(II) binding to the H355A enzyme provided a dissociation constant (K_d) of 39 μM. A three-dimensional homology model of ArgE was generated using the …

The Complex Transcriptional Landscape Of The Anucleate Human Platelet., Paul F. Bray, Steven E. Mckenzie, Leonard Edelstein, Srikanth Nagalla, Kathleen Delgrosso, Adam Ertel, Joan Kupper, Yi Jing, Eric R. Londin, Phillipe Loher, Huang-Wen Chen, Paolo Fortina, Isidore Rigoutsos

Cardeza Foundation for Hematologic Research

BACKGROUND: Human blood platelets are essential to maintaining normal hemostasis, and platelet dysfunction often causes bleeding or thrombosis. Estimates of genome-wide platelet RNA expression using microarrays have provided insights to the platelet transcriptome but were limited by the number of known transcripts. The goal of this effort was to deep-sequence RNA from leukocyte-depleted platelets to capture the complex profile of all expressed transcripts.

RESULTS: From each of four healthy individuals we generated long RNA (≥40 nucleotides) profiles from total and ribosomal-RNA depleted RNA preparations, as well as short RNA (<40 >nucleotides) profiles. Analysis of ~1 billion reads revealed that coding …

Synthesis Of The Western Hemisphere Of Theonellamide C, Saroj Yadav

LSU Doctoral Dissertations

Theonellamides A-F were isolated from Theonella swinhoei by Fusetani and co-workers. Despite considerable synthetic effort to produce theonellamide F by the Shioiri group in the early 1990’s, the total synthesis of a theonellamide has yet to be reported. We report herein our efforts toward some of the required amino acid residues and construction of the western ring of theonellamide C. We describe the synthesis of an uncoded amino acid, (2S,4R)-ɣ-hydroxy-α-amino adipic acid (Ahad), a building block for theonellamide C. We initially investigated the Corey-Lygo method for the catalytic asymmetric generation of the Cα stereocenter. Unfortunately, the alkylation of glycine benzophenone …

Polymer Microsystems For The Enrichment Of Circulating Tumor Cells And Their Clinical Demonstration, Joyce W. Kamande

LSU Doctoral Dissertations

Cancer research is centered on the discovery of new biomarkers that could unlock the obscurities behind the mechanisms that cause cancer or those associated with its spread (i.e., metastatic disease). Circulating tumor cells (CTCs) have emerged as attractive biomarkers for the management of many cancer-related diseases due primarily to the ease of securing them from a simple blood draw. However, their rarity (~1 CTC per mL of whole blood) makes enrichment analytically challenging. Microfluidic systems are viewed as exquisite platforms for the clinical analysis of CTCs due to their ability to be used in an automated fashion, minimizing sample loss …

Laser Ablation Sample Transfer For Mass Spectrometry, Sung-Gun Park

LSU Doctoral Dissertations

In this research, a new ambient sampling technique for mass spectrometry was developed that uses an infrared laser to ablate materials under ambient conditions that are captured in a solvent or on a surface. An infrared optical parametric oscillator (OPO) laser system at 3 μm wavelength was focused onto samples for ablation at atmospheric pressure. The ablated materials were transferred to a solvent or surface. For off-line electrospray ionization (ESI) and matrix-assisted laser desorption/ionization (MALDI) analysis, the ablated material was captured in a static solvent droplet that was deposited on a MALDI target or flow-injected into a nanoelectrospray source. The …

From The Horse's Mouth, Jennifer K. Cox

Electronic Theses and Dissertations 2010 - 2019

This thesis challenges dualistic human and animal ontologies by interpreting science fiction (sf) literature, and argues that whereas words can equivocate and obscure meaning, bodies do not lie. Linguistics and semiology extend the definition of "language" to include human and nonhuman gestures and movement, and posthumanist theory expands definitions of "human" and "animal" to explore species boundaries. Scrutinizing opposing dualisms ultimately questions Western epistemology and authority, allowing for an exploration of embodied animal communications within the larger discourse on species and speciesism. This perspective results in a more comprehensive understanding of the interdependence of all species: human, animal, and "other." …

The Incidence And Aetiology Of Hospitalised Community-Acquired Pneumonia Among Vietnamese Adults: A Prospective Surveillance In Central Vietnam, Kensuke Takahashi, Motoi Suzuki, Le Minh, Nguyen Anh, Luu Thi Huong, Tran Vo Son, Phan Long, Nguyen Thi Ai, Le Tho, Konosuke Morimoto, Paul E. Kilgore, Dang Anh, Koya Ariyoshi, Lay Yoshida

Wayne State University Associated BioMed Central Scholarship

Abstract

Background

Lower respiratory tract infection (LRTI) including Community-acquired pneumonia (CAP) is a common infectious disease that is associated with significant morbidity and mortality. The patterns of aetiological pathogens differ by region and country. Special attention must be paid to CAP in Southeast Asia (SEA), a region facing rapid demographic transition. Estimates burden and aetiological patterns of CAP are essential for the clinical and public health management. The purposes of the study are to determine the incidence, aetiological pathogens, clinical pictures and risk factors of community-acquired pneumonia (CAP) in the Vietnamese adult population.

Methods

A prospective surveillance for hospitalised adult …

Insects As Indicators Of Environmental Stress, De Anna Estella Beasley

Theses and Dissertations

In the face of climate change-related events and anthropogenic disturbances, understanding the impacts of these events on species richness, abundance and distribution is important for us to mitigate biodiversity loss and better predict consequences for the environment and for human life. Insects are excellent models for understanding the consequences of environmental stress due to the sensitivity of their development and behavior. The overall focus of my dissertation research is the investigation of fluctuating asymmetry and oviposition behavior as indicators of environmental stress. My research includes a meta-analysis of published literature, and empirical research that was part of a collaborative initiative …

Ecology Of The Late Neogene Extinctions: Perspectives From The Plio-Pleistocene Of Florida, Shubhabrata Paul

USF Tampa Graduate Theses and Dissertations

The ecological impact of past extinction events is one of the central issues in paleobiology. In face of present environmental changes, a better understanding of past extinctions will enable us to identify the magnitude of biodiversity crises and their underlying processes. The Late Neogene was a time of extraordinary climatic reorganization, including Northern Hemisphere glaciation, the rise of the Central American Isthmus, and associated changes in environmental conditions. Therefore, the Late Neogene extinctions of marine molluscs of South Florida present an ideal platform to examine the interaction between environmental changes and biotic response. In the present study, three different aspects …

Melungeon Portraits: Lived Experience And Identity, Tamara L. Stachowicz

Antioch University Dissertations & Theses

The desire to claim an ethnicity may be in response to an institutional and systemic political movement towards multiculturalism where ethnic difference is something to be recognized and celebrated (Jimenez, 2010; Tatum, 1997). Those who were a member of a dominant or advantaged group took that element of their identity for granted (Tatum, 1997). Identity work has included reflections and congruence between how individuals see themselves and how they perceive others to see them, including Optimal Distinctiveness Theory where one determines the optimal amount of individual distinctiveness needed to feel a healthy group and personal identity (Brewer, 2012). When most …

Oligomers Of Beta-L-Arabinosides Of Hydroxyproline : Synthesis Of The Carbohydrate Epitope Of The Art V 1 Allergen, Ning Xie

LSU Doctoral Dissertations

The pollen of mugwort is a major contributor to hay fever in Europe and North America. The chemical structure of Art v 1, the major allergen of mugwort, has been elucidated. A notable motif in Art v 1 – characterized by clusters of contiguous â-arabinosides of hydroxyproline – was found to be a key recognition element for antibodies generated in response to the natural protein. This dissertation details the chemical synthesis of oligomers of â-arabinosides of hydroxyproline and the search to establish the minimal carbohydrate epitope of Art v 1. The â-arabinoside motif, being a 1,2-cis glycoside, presents a considerable …

Surface Studies Of Organic Thin Films Using Scanning Probe Microscopy And Nanofabrication, Venetia Denae Lyles

LSU Doctoral Dissertations

Porphyrins and metalloporphyrins have unique chemical and electronic properties and thus provide useful model structures for nanoscale studies of the role of chemical structure for electronic properties. Porphyrins have been proposed as viable materials for molecular-based information-storage devices, gas sensors, photovoltaic cells, organic light-emitting diodes and molecular wires. The function and efficiency of porphyrins in devices is largely attributable to molecular architecture and how the molecules are self-organized. Modifications of the porphyrin macrocycle, peripheral groups or bound metal ions can generate a range of electrical, photoelectrical or magnetic properties. The conductive properties are greatly influenced at the molecular level by …