Physical Sciences and Mathematics Commons^™

Methods Development In Qualitative And Quantitative Proteomics, Ting Liu

University of Kentucky Doctoral Dissertations

Proteomics based on liquid chromatography coupled to mass spectrometry has developed rapidly in the last decade and become a powerful tool for protein mixtures analysis. LC-MS based proteomics involves four steps, sample preparation, liquid chromatography, mass spectrometry and bioinformatics. Improvements in each step have extended its applications to new biological research areas. This dissertation mainly focuses on method developments in both qualitative and quantitative proteomics.

The first part of this dissertation focuses on qualitative analysis of T. gondii Parasitophorous Vacuole Membrane (PVM) proteins, which is very important for T. gondii’s survival. The hypothesis of this study is that proteomic …

Algebraic And Combinatorial Properties Of Certain Toric Ideals In Theory And Applications, Sonja Petrovic

University of Kentucky Doctoral Dissertations

This work focuses on commutative algebra, its combinatorial and computational aspects, and its interactions with statistics. The main objects of interest are projective varieties in Pⁿ, algebraic properties of their coordinate rings, and the combinatorial invariants, such as Hilbert series and Gröbner fans, of their defining ideals. Specifically, the ideals in this work are all toric ideals, and they come in three flavors: they are defining ideals of a family of classical varieties called rational normal scrolls, cut ideals that can be associated to a graph, and phylogenetic ideals arising in a new and increasingly popular area of …

Mechanistic Investigations Of The Trans Excision-Splicing And Trans Insertion-Splicing Reaction, Perry Patrick Dotson Ii

University of Kentucky Doctoral Dissertations

Group I intron-derived ribozymes are catalytic RNAs that have been engineered to catalyze a variety of different reactions, in addition to the native self-splicing reaction. One such ribozyme, derived from a group I intron of Pneumocystis carinii, can modify RNA transcripts through either the excision or insertion of RNA sequences. These reactions are mediated through the trans excision-splicing (TES) or trans insertionsplicing (TIS) reaction pathways. To increase our current understanding of these reactions, as well as their general applicability, a mechanistic and kinetic framework for the TES reaction was established. Furthermore, additional ribozymes were investigated for their ability to …

Precision Measurements Of The Neutron Electric Form Factor At High Momentum Transfers, Ameya Suresh Kolarkar

University of Kentucky Doctoral Dissertations

The neutron, although electrically neutral, is composed of elementary charged particles and as a result, possesses a charge distribution within. The charge distribution can be studied by measuring a quantity called the neutron electric form factor, Gⁿ_E. Experiment E02-013 at Jefferson Lab’s Hall A measured Gⁿ_E at high four-momentum transfer values of Q2 = 1.2, 1.7, 2.5 and 3.4 (GeV/c)² in double polarized semi-exclusive ³He(e, e'n) scattering in quasi-elestic kinematics by measuring the transverse asymmetry A_T of the cross section.

The neutron electric form factor is essential to …

The H-Vectors Of Matroids And The Arithmetic Degree Of Squarefree Strongly Stable Ideals, Erik Stokes

University of Kentucky Doctoral Dissertations

Making use of algebraic and combinatorial techniques, we study two topics: the arithmetic degree of squarefree strongly stable ideals and the h-vectors of matroid complexes.

For a squarefree monomial ideal, I, the arithmetic degree of I is the number of facets of the simplicial complex which has I as its Stanley-Reisner ideal. We consider the case when I is squarefree strongly stable, in which case we give an exact formula for the arithmetic degree in terms of the minimal generators of I as well as a lower bound resembling that from the Multiplicity Conjecture. Using this, we can …

Benzene-1,3-Diamidoethanethiol (Bdeth2) And Its Metal Compounds, Kamruz Md Zaman

University of Kentucky Doctoral Dissertations

There is a global need to find a permanent and readily implemented solution to the problem of heavy metal pollution in aqueous environments. A dithiol compound, benzene-1,3-diamidoethanethiol (BDETH₂), also known as N,N'-bis(2-mercaptoethyl) isophthalamide or N,N'-bis(2-mercaptoethyl)-1,3-benzenedicarboxamide, capable of binding divalent metal ions, has been synthesized and characterized. A broad range of BDET-metal compounds, spanning the periodic chart, has been prepared and characterized by IR, MS, EA, Raman, XAFS and TGA. The characteristics of the BDET-M compounds were determined through secondary reactions. In an effort to derivatize BDET-M compounds through alkylalumination a new cyclic compound, 1,3- bis(4,5-dihydrothiazolo)benzene, has …

Regulation Of L-Type Voltage-Dependnet Calcium Channels By The Rem Gtpase, Chunyan Pang

University of Kentucky Doctoral Dissertations

The Rem, Rem2, Rad, and Gem/Kir GTPases, comprise a novel subfamily of the small Ras-related GTP-binding proteins known as the RGK GTPases, and have been shown to function as potent negative regulators of high voltage-activated (HVA) Ca²⁺ channels upon overexpression. HVA Ca²⁺ channels modulate Ca²⁺ influx in response to membrane depolarization to regulate a wide variety of cellular functions and they minimally consist of a pore-forming α1 subunit, an intracellular β subunit, and a transmembrane complex α₂/δ subunit. While the mechanisms underlying RGK-mediated Ca²⁺ channel regulation remain poorly defined, it appears that both membrane …

A Systematic Study Of Thermodynamic And Transport Properties Of Layered CaN+1(Ru1-XCrX)NO3n+1, Vinobalan Durairaj

University of Kentucky Doctoral Dissertations

Orbital degrees of freedom play vital role in prompting novel phenomena in ruthenium based Ruddlesden-Popper compounds through coupling of orbits to spin and lattice. Physical properties are then particularly susceptible to small perturbations by external magnetic fields and/or slight structural changes. Current study pertains to the impact when a more-extended 4d Ruthenium ion is replaced by a less-extended 3d Chromium ion.

Perovskite CaRuO₃ (n=∞) is characterized by borderline magnetism and non- Fermi liquid behavior – common occurrences in quantum critical compounds. Remarkably, Cr substitution as low as x=0.05 abruptly drives CaRu_1−xCr_xO₃ from a paramagnetic …

Empirical Processes And Roc Curves With An Application To Linear Combinations Of Diagnostic Tests, Costel Chirila

University of Kentucky Doctoral Dissertations

The Receiver Operating Characteristic (ROC) curve is the plot of Sensitivity vs. 1- Specificity of a quantitative diagnostic test, for a wide range of cut-off points c. The empirical ROC curve is probably the most used nonparametric estimator of the ROC curve. The asymptotic properties of this estimator were first developed by Hsieh and Turnbull (1996) based on strong approximations for quantile processes. Jensen et al. (2000) provided a general method to obtain regional confidence bands for the empirical ROC curve, based on its asymptotic distribution.

Since most biomarkers do not have high enough sensitivity and specificity to …

Carbon Nanotube Supported Metal Catalysts For NoX Reduction Using Hydrocarbon Reductants, Eduardo Santillan-Jimenez

University of Kentucky Doctoral Dissertations

Nitrogen oxides (NO_x) are atmospheric pollutants that pose a serious threat to both the environment and human health. Although catalytic deNO_x technologies for engines working under stoichiometric air-to-fuel ratios (i.e., most gasoline engines) are already available, their performance is unsatisfactory under excess air conditions like those under which diesel engines operate.

The selective catalytic reduction of NO_x with hydrocarbon reductants (HC-SCR) is a potential deNO_xsolution for diesel engines, whose operating temperatures are 150-500 ºC. Given that is unlikely for a single catalyst to show acceptable activity throughout this entire temperature span, the use of …

Paleogene Mirelands Of The Upper Mississippi Embayment, Western Kentucky, Jennifer Marie Klein O'Keefe

University of Kentucky Doctoral Dissertations

Detailed petrography, geochemistry, and palynology together describe the depositional environments and paleoecology of an abandoned meander-fill system in western Kentucky. Oriented block petrography reveals alternating clay-rich and attrinite-rich zones of variable thickness. Woody tissues, where present, do not show dessication features and deflation layers could not be identified. Overall, petrography is indicative of a topogenous mire. Mire palyno-assemblages are less diverse than assemblages reported from clays in the region. Castanea-Cupuliferoidaepollenites assemblages dominate the entire system and other tree pollen are common; fungal spores are relatively uncommon. Weighted statistical analyses reveal ecological groupings beyond this dominance and define botanical succession within …

The Mobility Of Fecal Indicator Microorganisms Within A Karst Groundwater Basin In The Inner Bluegrass Region, Kentucky, James Wade Ward

University of Kentucky Doctoral Dissertations

This project implemented novel approaches to assess the source, age, concentration and mobility of fecal indicator microorganisms within a karst groundwater system. Research was conducted in the well-characterized Blue Hole Spring karst groundwater basin in Versailles, Woodford County, Kentucky. At this site the AC/TC ratio and fecal coliform (FC) bacteria counts were used to delineate sources of fecal inputs and determine relative age of the fecal matter. An aging experiment using indicator bacteria (total coliform (TC) and atypical colonies (AC)), which approximated subsurface conditions, indicated that changes in the AC/TC ratio are likely to be retarded during bacterial transport through …

Nitroreductase: Evidence For A Fluxional Low-Temperature State And Its Possible Role In Enzyme Activity, Peng Zhang

University of Kentucky Doctoral Dissertations

The enzyme nitroreductase (NR) catalyzes two-electron reduction of high explosives such as trinitrotoluene (TNT), a wide variety of other toxic nitroaromatic compounds, as well as riboflavin derivatives, using a tightly-bound flavin mononucleotide (FMN) cofactor. It has important environmental and clinical implications. Previous studies have focused on elucidating NRs catalytic mechanism and solving its crystal structure.

In this dissertation work, we first develop and implement new strategies for labeling NR with stable isotopes, and report a completely re-designed protocol for NRs purification. Then we report the successful assignment of over half of NRs backbone resonances using 3d-NMR methods. The most significant …

Interactions Between Structures In The Appalachian And Ouachita Foreland Beneath The Gulf Coastal Plain, Donald Matthew Surles

University of Kentucky Doctoral Dissertations

In Alabama, the Paleozoic Appalachian thrust belt plunges southwest beneath the Mesozoic-Cenozoic Gulf Coastal Plain. In Arkansas, the Paleozoic Ouachita thrust belt plunges southeast beneath the Coastal Plain. The strikes of the exposed thrust belts suggest an intersection beneath the Coastal Plain. Well data and seismic reflection profiles confirm the strike and intersection of the thrust belts, and provide information to determine the structure and general stratigraphy of each thrust belt. In east-central Mississippi, the Appalachian thrust belt curves from the regional northeast trace to westward at the intersection with the southeastern terminus of the Ouachita thrust belt, to northwest …

Polymorphism Of Four Enantiotropic Crystalline Systems Containing Ni(Ii), H2O, 15-Crown-5 And No3-, Maxime Andre Siegler

University of Kentucky Doctoral Dissertations

The series of compounds [M(H₂O)₂(15-crown-5)](NO₃)₂, M = Mg, Mn, Co, Cu and Zn, has been extended to include two new phases for M = Fe and two new phases for M = Ni. The system [M(H₂O)₂(15-crown-5)](NO₃)₂ is remarkable for having many high-Z’ phases (Z’ > 1) with similar packing and for having solid-solid phase transitions through which there is no significant loss of crystallinity. The synthesis of the analogous Ni complex was carried out. Single-crystal X-ray diffraction showed …

Computer Simulation And Modeling Of Physical And Biological Processes Using Partial Differential Equations, Wensheng Shen

University of Kentucky Doctoral Dissertations

Scientific research in areas of physics, chemistry, and biology traditionally depends purely on experimental and theoretical methods. Recently numerical simulation is emerging as the third way of science discovery beyond the experimental and theoretical approaches. This work describes some general procedures in numerical computation, and presents several applications of numerical modeling in bioheat transfer and biomechanics, jet diffusion flame, and bio-molecular interactions of proteins in blood circulation.

A three-dimensional (3D) multilayer model based on the skin physical structure is developed to investigate the transient thermal response of human skin subject to external heating. The temperature distribution of the skin is …

A Systematic Study On The Thermodynamic And Transport Properties Of Layered Ruthenates, Xiunu Lin

University of Kentucky Doctoral Dissertations

In the 4d transition metal oxides, the extension of the 4d orbitals leads to comparable and thus competitive kinetic and coulomb energies. As a result, small perturbations can induce significant changes in their physical properties, giving rise to a class of exotic phenomena that are rarely found in other materials. The ruthenates materials with readily tunable parameters open an avenue to study the strong electronic correlation in the rarely explored territory: the 4d transition metal oxides.

The bilayered system, Ca₃Ru₂O₇, belongs to the Ruddlesden-Popper series in which the physical properties are intimately linked to …

Solution And Solid State Interactions Between Ionic Π-Systems, Jing Chen

University of Kentucky Doctoral Dissertations

Although attractive interactions between π systems (π-π interaction) have been known for many years, understanding of its origin is still incomplete. Quantitative measuring of π-stacking is challenging due to the weak nature of the π-π interaction. This dissertation aims at elucidating a quantitative conformational analysis by NMR ring current anisotropy of an organic compound capable of intramolecular π-stacking in solution and studying charge effects on the stacking of π-systems. This dissertation offers four contributions to the area. (1) A general approach to four-state, conformational analysis based on the magnetic anisotropy of molecules undergoing fast dynamic exchange is described. (2) Study …

Studies Of Unusual Packing And Of Polymorphism In Two Crystal Systems, Xiang Hao

University of Kentucky Doctoral Dissertations

Crystal structures of anhydrous pinacol, the hexagonal pinacol, pinacol monohydrate, and pinacol hexahydrate were studied. In all the structures crystal packing is unusual and complicated. The origin of the complexity may be the difficulty in filling space densely and while also satisfying the H-bonding requirements when the molecule has few internal degrees of freedom.

Five 15-crown-5 complexes of M(NO₃)₂ (M = Cu, Zn, Mg, Co, Mn) were synthesized and characterized using X-ray diffraction and differential scanning calorimetry. The system is rich in polymorphs. Nine definite solid-state phases were identified. More phases probably exist in the solid state …

Methods Development And Application Of Two Dimensional Chromatography And Tandem Mass Spectrometry In Proteomics, Brett Romain Wenner

University of Kentucky Doctoral Dissertations

Although molybdenum blue solutions have been known for more than twocenturies, an understanding of their chemical nature is only beginning to emerge.This dissertation aimed at elucidating the structural nature of the polydisperse,nanoscopic components in the solution phases and the solid states of partiallyreduced polyoxomolybdate (Mo-POM). The study offered at least fourcontributions to the area: (1) a rational protocol for the molecular recognition ofMo-POM with de novo organic hosts. (2) demonstration of kinetic precipitation ofa dynamic mixture of polyoxomolybdates and application of the technique to thestudy of the dynamic mixture by TEM (3) characterization of the Mo-POMnanostructures by an unusual combination …

Geometric And Kinematic Evolution Of The Bessemer Transverse Zone, Alabama Alleghanian Thrust Belt, Margaret Colette Brewer

University of Kentucky Doctoral Dissertations

Transverse zones are important syn-kinematic components of thrust belt development. Various scales of data were utilized to develop three-dimensional geometric and kinematic models for the Bessemer transverse zone (BTZ) of the Alabama Alleghanian thrust belt.

Regional analysis of the BTZ began with the examination of geologic maps (1:250,000, 1:48,000, and 1:24,000 scales), seismic reflection profiles, well data, and previous stratigraphic research. All Paleozoic-age stratigraphic contacts, major thrust faults and associated folds, and various unnamed minor structures were compiled to create two strike-perpendicular, and five-strike parallel, cross sections transecting the extent of the BTZ at a scale of 1:100,000. The balanced …

Controls On Middle To Late Ordovician Synorogenic Deposition In The Southeastern Corner Of Laurentia, German Bayona

University of Kentucky Doctoral Dissertations

Middle and Upper Ordovician strata in the southernmost Appalachians document initial collision along the southeastern margin of Laurentia during the Blountian orogeny, an early phase of the Taconic orogeny. Coeval drowning and exposure of different parts of the former platform and variations in stratal architecture have been attributed to tectonic and depositional loading along the collisional margin. Stratigraphic correlations, using a bentonite-graptoliteconodont time framework, a palinspastic map, and a map of subsurface basement structures, suggest that basement-fault reactivation, flexural subsidence, and eustasy variously controlled uplift, subsidence, and deposition at different sites within the peripheral foreland basin. This dissertation documents how …