Life Sciences Commons^™

Characterization Of Cytidylyltransferase Enzyme Activity Through High Performance Liquid Chromatography, James Brault

Theses and Dissertations

The cytidylyltransferases are a family of enzymes that utilize cytidine 5â?? triphosphate (CTP) to synthesize molecules that are precursors to membrane phospholipids. There are four well known enzymes: CTP: phosphoethanolamine cytidylyltransferase (ECT), CTP: glycerol-3-phosphate cytidylyltransferase (GCT), 2-C-methyl-D-erythritol-4-phosphate cytidylyltransferase synthetase (CMS), and CTP: phosphocholine cytidylyltransferase (CCT). Previously, a radioisotope tagging method was employed to study cytidylyltransferase catalysis. Using CCT as a model, a method utilizing high performance liquid chromatography (HPLC) was developed to replace the radioisotope scintillation technique. The development of this new HPLC method is cheaper, more efficient, and more accurate than the previously established method.

The targets of separation …

Arylboronates As H2o2 Or Photo-Inducible Dna Cross-Linking Agents: Design, Synthesis, Mechanism, And Anticancer Activity, Yibin Wang

Theses and Dissertations

Interest in the development of cancer therapies with improved selectivity and reduced host toxicity has been growing. In this thesis, we designed and synthesized a series of novel non-toxic arylboronic ester and biarylboronic ester derivatives that can be activated by hydrogen peroxide (H2O2) to induce DNA interstrand cross-link formation. The mechanism of DNA cross-linking induced by these arylboronates involves generation of phenol intermediates 1 followed by departure of leaving group (L) leading to quinone methides (QMs) 2, which directly cross-link DNA via alkylation. The QM formation is the rate-determining step for DNA cross-linking. The activity and selectivity of these compounds …

Transport Mechanisms For Human Fecal Indicator Bacteria In An Urban Stormwater Basin In Southeastern Wisconsin, Chelsea M. Corson

Theses and Dissertations

Discharge of stormwater runoff to receiving waters is a known source of human pathogens; however the primary mechanisms by which these pathogens enter the stormwater system have yet to be quantified. This study builds upon and utilizes prior research findings in an attempt to explain the influence of the age of the pipes within stormwater and sanitary conveyance systems, rainfall and hydrogeological characteristics, and select infrastructure variables that contribute to the observed contamination of an urban stormwater basin in Southeastern Wisconsin.

Over the course of approximately two years from 2012 to 2014, a total of 260 samples from 22 stormwater …

The Mixing Of A River Into Coastal Waters At Two Beaches: Environmental Factors, E. Coli Contributions And Applications For Predictive Models, Adrian Jordan Koski

Theses and Dissertations

Beach closures and public health protection are confounded by analytical procedures that result in delays in notification of adverse water quality conditions and the lack of affordable analytical methods to identify pollutant sources. Attempts have been made to develop predictive frameworks using ancillary hydrometeorological data to statistically anticipate deteriorated water quality. Many urban coastal beaches are impacted by river runoff. In Kenosha Wisconsin, beach sanitary survey data from two beaches adjacent to the mouth of the Pike River were examined to ascertain whether simple river-lake mixing models identified river influence on coastal water quality and improved predictions of beach advisories. …

Iodine-131: Measurement And Application Of A Novel Tracer In Lake Michigan, Michael Patrick Montenero

Theses and Dissertations

Iodine-131 is a short-lived (half-life=8.0233 days), gamma emitting, radiopharmaceutical that, when excreted by patients, enters aquatic systems via sewage effluent discharged from water reclamation facilities (WRFs). Here, I report on 131I activities in the nearshore of southwest Lake Michigan in the vicinity of Milwaukee, Wisconsin. This is the first report on 131I activity in any of the Great Lakes of North America.

The flux of 131I from Milwaukee’s two WRFs was monitored from July 2013 to December 2014. Mean discharge of 131I from the Jones Island WRF was (0.664 ± 0.012)×108 Bq d-1 (mean effluent 131I activity: ~0.25 Bq L-1; …

The Identification And Quantification Of Sewage Contamination In The Milwaukee Estuary, Hayley Templar

Theses and Dissertations

Sewage contamination from failing infrastructure and sewer overflows is a major environmental and human health concern in waterways, especially in urban communities bordering the Great Lakes such as Milwaukee, Wisconsin. Culture-based fecal indicator bacteria, such as Escherichia coli, enterococci, and fecal coliforms are traditionally used to indicate the presence of a human health risk due to fecal contamination. These indicators, however, fail to distinguish between sources of fecal contamination (human vs. non-human). Two human-specific fecal indicators, human Bacteroides and human Lachnospiraceae, were used to identify and quantify sewage contamination in the Milwaukee estuary, which discharges to Lake Michigan, as well …

Time-Resolved, Near Atomic Resolution Structural Studies At The Free Electron Laser, Jason James Tenboer

Theses and Dissertations

Time-resolved serial femtosecond crystallography (TR-SFX) employs X-ray free electron lasers (XFELs) to provide X-ray pulses of femtosecond (fs) duration with 1012 photons per pulse. These XFELs are more than a billion times more brilliant than 3rd generation synchrotron X-ray sources. For structure determination, protein crystals on the micrometer length scale (microcrystals) are injected into the X-ray beam and the resulting diffraction patterns are recorded on fast-readout pixel detectors. Although these intense pulses deposit enough energy to ultimately destroy the protein, the processes that lead to diffraction occur before the crystal is destroyed. This so-called diffraction-before-destruction principle overcomes radiation damage, which …

Porphyrin As A Spectroscopic Probe Of Net Electric Fields In Heme Proteins, Hannah Elizabeth Wagie

Theses and Dissertations

Heme proteins have diverse functions as well as varied structures but share the same organic, conjugated cofactor. Similarly varied approaches have been taken to deduce how heme can take on different roles based on its protein environment. A unique approach is to view the protein matrix as a constellation of point charges that generates a defined, reproducible, net internal electric field that has influence over the electronic properties of the heme cofactor. This work considers how porphyrins, the basic chromophore building block of heme, can be used as a native spectroscopic sensor of internal electric field at the active site …

Theoretical Investigation Of Interactions And Relaxation In Biological Macromolecules, Koki Yokoi

Theses and Dissertations

One of the major challenges posed to our quantitative understanding of structure, dynamics, and function of biological macromolecules has been the high level of complexity of biological structures. In the present work, we studied interactions between G protein-coupled receptors (GPCRs), and also introduced a theoretical model of relaxation in complex systems, in order to help understand interactions and relaxation in biological macromolecules.

GPCRs are the largest and most diverse family of membrane receptors that play key roles in mediating signal transduction between outside and inside of a cell. Oligomerization of GPCRs and its possible role in function and signaling currently …

Decomposition And Nitrogen Dynamics Of Turtle Grass (Thalassia Testudinum) In A Subtropical Estuarine System, Monica Delgado

Theses and Dissertations

Seagrass beds are pivotal in the functioning of coastal ecosystems in terms of productivity, organic matter turnover and nutrient cycling. Aiming to document decay and nitrogen (N) dynamics of turtle grass (Thalassia testudinum) in a subtropical estuarine system, decomposition patterns of leaves and rhizomes were characterized and compared. Nitrogen usage during decomposition of tissues, and of live tissues and epiphytes growing on live leaves, was also quantified and compared. Stable isotope ratios allowed tracing N within the seagrass bed, following N incorporation into seagrass tissues from the surrounding media (water, sediment). Leaves had a higher N content and decomposed at …

Using An Agent-Based Model To Study The Effect Of Reproductive Skew On Mongoose Populations, Stacy Lee Mowry

Theses and Dissertations

Reproductive skew is the name given to the unequal partitioning of breeding

within social groups. Within these groups a mating hierarchy emerges wherein one dominant mating pair holds an unproportional majority of the group's reproductive benefit, while other members mate infrequently, yet allocate energy and resources toward the offspring of the dominant group members. In this paper, we use an agent-based model, which mimics dwarf and banded mongoose populations, to investigate how reproductive skew aftects the speed natural selection, and thus how reproductive skew affects fitness. The results of the model show that due to the geometric structure of skewed …

Image-Charge Detection €“ Novel Instrumentation And Applications, Brandon Lee Barney

Theses and Dissertations

Image-charge detection is an analytical technique in which a highly-charged particle is detected by the magnitude of the image current that it generates in a detecting electrode. This current is represented as a voltage between the charged particle and the sensing electrode. It is a single particle detection method, ideal for the analysis of large, variable mass particles such as biological cells. Some of the physical properties of Bacillus subtilis spores were explored using different applications of image-charge detection. B. subtilis is a gram-negative spore-forming bacteria that has been shown to exhibit extremophile behavior. The particular extremophile behavior that was …

Modeling Radiation Effectiveness For Inactivation Of Bacillus Spores, Emily A. Knight

Theses and Dissertations

This research models and analyzes the inactivation of Bacillus spores following a radiation exposure and the process enacted by the Bacillus spore to repair the resulting damage. Irradiation of a spore and the medium surrounding the spore induces chemical reactions that produce reactive oxygen species (ROS). This research will consider the reaction- diffusion of these ROS throughout the spore. These ROS can react with the spore's DNA and enzymes to degrade them to such an extent that the DNA cannot be repaired or replicated, thus causing spore death. In order to survive a dose of radiation, a spore must repair …

Neurobehavioral And Gene Expression Effects Of Early Embryonic Methylmercury Exposure In Yellow Perch (Perca Flavescens) And Zebrafish (Danio Rerio) Larvae, Francisco Xavier Mora Zamorano

Theses and Dissertations

Methylmercury (MeHg) is a pervasive and persistent neurotoxic environmental pollutant known to affect the behavior of fish, birds and mammals. The present study addresses the neurobehavioral and gene expression effects of MeHg in yellow perch (Perca flavescens) and zebrafish (Danio rerio) embryos. The rationale for this study originated from an interest to understand the behavioral and molecular phenotypes of environmental MeHg exposure in the yellow perch, an ecologically and economically relevant species of the North American Great Lakes region. Both MeHg and the yellow perch coexist in a common ecosystem: the North American Great Lakes. However, the effects of this …

Functional Diversity Of Regional Marine Paleocommunities After The Permo-Triassic Mass Extinction: Case Studies From Panthalassa And Paleo-Tethys, Ashley Ann Dineen

Theses and Dissertations

The Permo-Triassic mass extinction (PTME) was the largest biodiversity collapse in Earth’s history. Published data has been interpreted as indicating that marine ecological devastation following the PTME was protracted and may have lasted 5 million years into the Middle Triassic (Anisian). However, a review of previous literature shows that understanding of biotic recovery is usually based on only a few components of the ecosystem, such as on taxonomic diversity, a single genus/phylum, or shallow water facies. Typically, paleocommunities are considered fully recovered when dominance and diversity are regained and normal ecosystem functioning has resumed. However, to more fully characterize Triassic …

Three Essays On Enhancing Clinical Trial Subject Recruitment Using Natural Language Processing And Text Mining, Euisung Jung

Theses and Dissertations

Patient recruitment and enrollment are critical factors for a successful clinical trial; however, recruitment tends to be the most common problem in most clinical trials. The success of a clinical trial depends on efficiently recruiting suitable patients to conduct the trial. Every clinical trial research has a protocol, which describes what will be done in the study and how it will be conducted. Also, the protocol ensures the safety of the trial subjects and the integrity of the data collected. The eligibility criteria section of clinical trial protocols is important because it specifies the necessary conditions that participants have to …

Mechanistic Study Of Heme Protein-Mediated Nitric Oxide Dioxygenation Using Photolytically Produced Nitric Oxide, Karl Joseph Koebke

Theses and Dissertations

The previously reported NO precursor [Mn(PaPy2Q)(NO)]ClO4 (1), where (PaPy2QH) is N,N-bis(2-pyridylmethyl)-amine-N-ethyl-2-quinoline-2-carboxamide, was synthesized and proven capable of producing as much as 180 µM NO when irradiated by a single 3 mJ 500nm laser pulse, in a 0.15 cm path cell, without the need for additional sacrificial reductants or oxidants. Species 1 was first used to study the reaction of nitric oxide with oxy-myoglobin (oxyMb) to form ferric myoglobin (metMb) and nitrate. This reaction had long been assumed to proceed via the same iron-bound peroxynitrite intermediate (metMb(OONO)) as the metMb-catalyzed isomerization of peroxynitrite to nitrate. Recent research showed that the metMb-catalyzed …

Analytical Approaches In Investigating The Kinetics Of Water-Molecule Complexes In Tropospheric Reactions, William J. Keeton

Theses and Dissertations

Ozone is a heavily monitored pollutant. Ozone is not directly emitted into the atmosphere, but rather the product of chemical reactions. Ground level ozone occurs when nitrogen oxides (NOx) and volatile organic compounds (VOCs) react with each other in the presence of sunlight. The primary precursors of ozone are anthropogenically emitted, and as a result, tropospheric ozone has cost millions of dollars in damages and has hurt the health of countless people. This dissertation is a collection of work that aims to provide insight into atmospheric reactions that result in tropospheric ozone and the instrumentation to study such reactions. While …

Histone Deacetylase 6 (Hdac6) Is Critical For Tumor Cell Survival And Promotes The Pro-Survival Activity Of 14-3-3Ζ Viadeacetylation Of Lysines Within The14-3-3Ζ Binding Pocket, Jeffrey Benjamin Mortenson

Theses and Dissertations

Our understanding of non-histone acetylation as a means of cellular regulation is in its infancy. Using a mass spectrometry approach we identified acetylated lysine residues and monitored acetylation changes across the proteome as a consequence of metabolic stress (hypoxia). We observed changes in acetylation status of non-histone lysines in tumor cells. Through the use of small molecule inhibitors of histone deacetylase enzymes (HDACs) and siRNA screening identified HDAC6 as a pro-survival regulator of lysine acetylation during hypoxia. The phospho-binding protein 14-3-3ζ acts as a signaling hub controlling a network of interacting partners and oncogenic pathways. We show here that lysines …

An Approach To An Agave Problem: The Bioremediation Of Agricultural Waste By Yeast Fermentations, Joshua Michael Jarodsky

Theses and Dissertations

The agricultural waste products created by industries, such as the Tequila manufacturing industry, create thousands of tons of waste material every year. This agricultural waste often becomes an environmental and ecological problem for fields and surrounding areas. The purpose of this study is to determine the potential of using the yeast Kluyveromyces marxianus 7-1 and Kluyveromyces marxianus 8-1 to ferment the leaf waste from the harvesting of the Agave tequilana as a form of bioremediation. Fermentations (anaerobic, under constant shaking, and at room temperature) were monitored for colony forming units, pH of fermentation broth, concentration of reducing sugars, and protein …

A Study Of Allylic Aminations As Catalyzed By Heterobimetallic Pd-Ti Complexes, Diana Lauren Ellis

Theses and Dissertations

Heterobimetallic complexes present a unique approach to catalyzing challenging reactions. By having two metals in close proximity to each other, the metals are able to interact and alter their electronics in a way that simple organic ligands (carbon, nitrogen, sulfur etc.) cannot. Our studies of heterobimetallic complexes focus on a Pd–Ti complex. The complex features a dative interaction between the palladium and the titanium held together by a phosphonamide scaffold. This interaction increases the electrophilicity of the palladium and makes it a very suitable catalyst for allylic amination reactions. We have conducted extensive studies of this catalyst in allylic aminations, …

Female Reproductive Impacts Of Dietary Methylmercury In Yellow Perch (Perca Flavescens) And Zebrafish (Danio Rerio), Abigail Rachael Debofsky

Theses and Dissertations

This study sought to evaluate the effects of dietary MeHg exposure on female teleost reproduction and phenotypically-anchor gene dysregulation in adult yellow perch (Perca flavescens) and zebrafish (Danio rerio) in order to establish relevant biomarkers relating exposure and subsequent reproductive effects. Yellow perch were used in the study for their socioeconomic importance within the Great Lakes basin, and their significance to the food web. Utilization of zebrafish allowed for a detailed analysis of the molecular effects of MeHg and established its relevance as a model for other fish species. MeHg exposures at environmentally relevant levels were done in zebrafish for …

Scattering Correction Methods Of Infrared Spectra Using Graphics Processing Units, Asher Imtiaz

Theses and Dissertations

Fourier transform infrared (FTIR) microspectroscopy has been used for many years as a technique that provides distinctive structure-specific infrared spectra for a wide range of materials (e.g., biological (tissues, cells, bacteria, viruses), polymers, energy related, composites, minerals). The mid-infrared radiation can strongly scatter from distinct particles, with diameters ranging between 2-20 micrometer. Transmission measurements of samples (approximately 100 micrometers x 100 micrometers x 10 micrometers) with distinct particles. will be dominated by this scattering (Mie scattering). The scattering distorts the measured spectra, and the absorption spectra appear different from pure absorbance spectra. This thesis presents development and implementation of two …

Synthesis And Characterization Of Carbonized Poly (Divinylbenzene) Microspheres For Carbon/Nanodiamond/Polymer-Based Core-Shell Materials And Applications Of This Mixed-Mode Phase To High-Performance Liquid Chromatography, Chuan-Hsi Hung

Theses and Dissertations

This work focuses on improving the quality of carbon-based core-shell materials for high performance liquid chromatography (HPLC) via the characterization of the core materials, and also the development of chromatographic methods (separations) for them. In the early part of this work, I applied organic synthesis to make uniform, spherical poly(divinylbenzene) (PDVB) microspheres, and then carbonized them to prepare carbon core materials for core-shell particle synthesis. Here, I studied in detail the surface and material properties of these particles with multiple instruments, which allowed me to describe the physical and chemical changes that took place during each treatment. The uniform, spherical …

Application Of Coumarin Derivatives In Dna-Associated Study: Mutation Detection, Site-Specific Labeling, Photoinduced Interstrand Cross-Links And Ligation Reactions, Huabing Sun

Theses and Dissertations

Coumarin derivatives have been widely utilized as cross-linking agents in polymer science, being fluoroprobes in biochemistry and as medicines in pharmacy. But the coumarin's fluorogenic properties and reactivities in DNA were rarely reported and unclear, which limits its bioapplications due to possible side reactions towards biomolecules. In this thesis, we investigated the activity of coumarin moiety towards natural DNA and expanded its application in DNA-associated study. We have found that coumarin derivatives can serve as perfect DNA cross-linking agents, as alkylation agents for site-specific labeling, and fluoroprobes for single nucleotide polymorphism (SNP) analysis, which provided a novel insight of biotoxicity …

Paleoecology Of Glacial And Non Glacial Carboniferous Faunas During The Late Paleozoic Ice Age In Patagonia, Nicole Braun

Theses and Dissertations

The Late Paleozoic Ice Age (LPIA) records the only icehouse to greenhouse transition in Earth’s history that involved complex marine and terrestrial life and serves as an analogue for Quaternary climate change. Identifying biotic responses to paleoenvironmental variations during the LPIA is important in order to understand how our modern fauna may respond to contemporary climate change. Low-paleolatitude (far-field) marine faunas far from ice centers have been recognized and used as a global proxy for biotic responses to the LPIA, but the biotic responses in high-paleolatitude (near-field) regions close to Gondwanan ice centers have received much less attention. We tested …

Paleoredox Geochemistry And Bioturbation Levels Of The Exceptionally Preserved Early Cambrian Indian Springs Biota, Poleta Formation, Nevada, Usa, Jonah Meron Novek

Theses and Dissertations

The early Cambrian Indian Springs biota, western Nevada, USA exhibits Burgess Shale-type (BST) preservation of a diverse array of animal phyla, including the earliest definitive echinoderms. It therefore provides an important window on animal life during the Cambrian radiation. The objective of this study is to analyze the trace metal paleoredox geochemistry and bioturbation levels of this BST deposit in order to characterize the paleoenvironmental conditions in which these animals lived and their fossils were preserved. A total of 28 rock samples were collected from outcrops at three previously reported intervals of exceptional preservation at the Indian Springs locality, as …

Microbially Induced Sedimentary Structures As An Ecological Niche In Subtidal Early Triassic Environments Of Eastern Panthalassa, Erin Wimer

Theses and Dissertations

Early Triassic microbially induced sedimentary structures (MISS) are a critical link in understanding the dynamics between changing environmental conditions and their effect on marine communities. The Permo-Triassic mass extinction (PTME) resulted in vacated ecospace and reduced bioturbation that allowed MISS to expand into Early Triassic subtidal environments. Data from southern Idaho and Montana indicate that MISS inhabited and proliferated in subtidal marine environments during the Griesbachian. This propagation led to changes in shallow substrate geochemical conditions that directly affected macrofaunal communities. The proliferation of microbial mats would have created anoxic and euxinic porewaters and made vertical bioturbation physiologically difficult. Geochemical …

Immunoassays Of Potential Cancer Biomarkers In Microfluidic Devices, Jayson Virola Pagaduan

Theses and Dissertations

Laboratory test results are important in making decisions regarding a patient's diagnosis and response to treatment. These tests often measure the biomarkers found in biological fluids such blood, urine, and saliva. Immunoassay is one type of laboratory test used to measure the level of biomarkers using specific antibodies. Microfluidics offer several advantages such as speed, small sample volume requirement, portability, integration, and automation. These advantages are motivating to develop microfluidic platforms of conventional laboratory tests. I have fabricated polymer microfluidic devices and developed immunoassays on-chip for potential cancer markers. Silicon template devices were fabricated using standard photolithographic techniques. The template …

Investigating Seed Dispersal Distances And Long Distance Dispersal Mechanisms Of The Invasive Plant, Alliaria Petiolata, Christopher Loebach

Theses and Dissertations

Alliaria petiolata, an herbaceous plant, has aggressively invaded North American woodlands. It has been extensively studied to understand why it is a successful invader, but certain aspects of its biology have been understudied such as seed dispersal distances and long distance dispersal mechanisms (LDDM). My thesis experimentally measured A. petiolata seed dispersal distances and determined if epizoochory (external animal transport) is a LDDM. To measure dispersal distances, seed traps were placed around three A. petiolata seed point sources to capture dispersed seeds at increasing distances away from the point sources. Eight mathematical functions that describe dispersal distances were fitted to …