The study of protein evolution and adaptation resides at the junction between the disciplines of biological chemistry and evolutionary biology. We chose the B. thetaiotaomicron tetracycline resistant enzyme TetX2, as our model system to study the biophysical basis for adaptation to antibiotics; a phenomenon that continuously poses global health challenges. In the work presented here, experimental evolution and biophysical characterization were used to identify and link the physicochemical properties of TetX2 and its adaptive mutants to increased resistance to minocycline. Bacteroides thetaiotaomicron TetX2 was previously identified as a novel oxidoreductase with broad activity against tetracyclines. Experimental evolution of E. coli expressing a chromosomal copy of tet(X2) was used to identify an adaptive mutation (TetX2 T280A ) that confers higher resistance to minocycline and tigecycline. In addition to TetX2 T280A , a family of variants of TetX2 with single amino acid changes in TetX2 sequence that conferred equal or higher resistance towards MCN was identified by error-prone mutagenesis. Changes in fitness of E. coli carrying a single chromosomal copy of either wild-type or one of the mutant alleles were assessed by growth rate assays over a range of minocycline concentrations. Despite similar in vivo performances of TetX2 T280A and two other variants (TetX2 N371I and TetX2 N371T ), TetX2 T280A was the only successful mutant in the adaption experiment suggesting that mutational supply may play an important role in evolutionary dynamics of populations undergoing adaptation. The most surprising result is that the differences in growth rates among TetX2 variants arise from small changes in in vitro catalytic activity and in vivo protein expression. The steady-state kinetic studies with minocycline and NADPH suggest a binary mechanism for antibiotic inactivation by TetX2 which is supported by the structural characteristics of the enzyme. The atomic structures of the best adaptive mutant TetX2 T280A in complex with minocycline and tigecycline reveal the details of substrate recognition and show that the site of the mutation is ∼18 Å away from the active site suggesting an indirect mechanism for improved catalysis. Taken together, our data show that very small changes in the in vitro biochemical properties and expression levels can have surprisingly large fitness effects and are important during adaption. In addition, a promising preliminary mathematical model suggests that based on kinetic activity and in vivo expression levels the success of bacteria undergoing adaptation to antibiotics can be predicted.

In this thesis, we will study the smooth linear section of the Grassmannian Gr(2, n). Explicitly, we give a criterion for the rationality of such linear section in terms of its codimension in the Plü ̈cker embedding in projective space. Moreover, to obtain a better understanding of the birational parametrization of these linear sections, we analyze their Hodge structures in the cases of even and odd codimensions. To be more precise, we provide numerous examples which suggest certain patterns of Hodge diamonds corresponding to even and odd cases and derive the proof of general patterns for codimension 3 smooth linear section of Gr(2, n) corresponding to odd and even n. / page 29 is missing from hardcopy

In this thesis an in depth analysis of nanoparticle synthesis utilizing carbon monoxide as a reducing agent is presented. Synthesized nanoparticle mono and polydispersity was examined via particle distribution profiles, statistical, and spectral analysis and compared against other reduction methods. The size and monodispersity of the gold nanoparticles produced with carbon monoxide were tunable by altering the concentration of HAuCl 4 and gas injection flow rates. The carbon monoxide based reduction method offered excellent tunability over a broad range of sizes while maintaining a high level of monodispersity when compared to the other reduction methods. The mechanisms involved in the size dependent optical response of the synthesized nanoparticles were identified. It was also found that speciation of aqueous HAuCl 4 influences the size, structure, and properties of Au colloids. Ensemble extinction spectra and TEM images provide clear evidence that CO reduction offers a high level of tunability compared to other synthesis methods.

We have used the narrow 2 S 1/2 [arrow right] 3 P 3/2 transition in the ultraviolet (UV) to laser cool and magneto-optically trap (MOT) 6 Li atoms. Laser cooling of lithium atoms is usually performed on the 2 S 1/2 [arrow right] 2 P 3/2 (D2) transition, where temperatures of twice the Doppler limit, or ∼300 μ K for lithium, are achieved. The linewidth of the UV transition is seven times narrower than the D2 line, resulting in a lower Doppler limit. We show that a MOT operating on the UV transition reaches temperatures as low as 59 μ K. We load 6 million atoms from this UV MOT into a 1070 nm optical dipole trap (ODT). We show that the light shift of the UV transition in the ODT is small and blue-shifted, facilitating efficient loading. Evaporative cooling of a two spin-state mixture of 6 Li in the ODT produces a quantum degenerate Fermi gas with 3 million atoms in only 11 seconds.

A novel electrostatic analyzer (ESA) simulation method that differs significantly from traditional methods is presented in this study, the "reverse-fly" simulation method. The simulation process and its applications are discussed in detail. This method is tested by comparing its results to the published test data of three experimental instruments; The Proton Electrostatic Analyzer-High Geometric Factor (PESA-H) instrument on the Wind mission [Lin, et al. 1995], the 2π-Toroidal Analyzer (2πTA) of Young, et al., [1988], and the Hot Plasma Composition Analyzer (HPCA) to be used in the upcoming Magnetospheric Multi-scale (MMS) mission. The strong agreement between simulation and experimental results verifies the accuracy of this technique. Our results reveal detailed properties of ESA response that are not practical to assess using laboratory data. This simulation method then is used to compare the transmission characteristics of five published ESA geometries to efficiently determine the optimal ESA geometry for use in future space missions. We show that the simulation methods described here are an important contribution to instrument design and development techniques and are critical to efficient and accurate verification of instrument performance.

One of the fundamental problems in Algebraic Geometry is to study solutions to certain systems of polynomial equations in several variables, or in other words, find rational points on a given variety which is defined by equations. In this paper, we discuss the existence of del Pezzo surface of degree 1 and 2 with a unique rational point over any finite field [Special characters omitted.] , and we will give a lower bound on the number of rational points to each q. Furthermore, we will give explicit equations of del Pezzo surfaces with a unique rational point. Also we will discuss the rationality property of the del Pezzo surfaces especially in lower degrees.

xviii, 124 p. : ill. (some col.) / This dissertation discusses three topics on scenarios beyond the Standard Model. Topic one is the effects from a fourth generation of quarks and leptons on electroweak baryogenesis in the early universe. The Standard Model is incapable of electroweak baryogenesis due to an insufficiently strong enough electroweak phase transition (EWPT) as well as insufficient CP violation. We show that the presence of heavy fourth generation fermions solves the first problem but requires additional bosons to be included to stabilize the electroweak vacuum. Introducing supersymmetric partners of the heavy fermions, we find that the EWPT can be made strong enough and new sources of CP violation are present. Topic two relates to the lepton avor problem in supersymmetry. In the Minimal Supersymmetric Standard Model (MSSM), the off-diagonal elements in the slepton mass matrix must be suppressed at the 10-3 level to avoid experimental bounds from lepton avor changing processes. This dissertation shows that an enlarged R-parity can alleviate the lepton avor problem. An analysis of all sensitive parameters was performed in the mass range below 1 TeV, and we find that slepton maximal mixing is possible without violating bounds from the lepton avor changing processes: μ [arrow right] eγ; μ [arrow right] e conversion, and μ [arrow right] 3e. Topic three is the collider phenomenology of quirky dark matter. In this model, quirks are particles that are gauged under the electroweak group, as well as a \dark" color SU (2) group. The hadronization scale of this color group is well below the quirk masses. As a result, the dark color strings never break. Quirk and anti-quirk pairs can be produced at the LHC. Once produced, they immediately form a bound state of high angular momentum. The quirk pair rapidly shed angular momentum by emitting soft radiation before they annihilate into observable signals. This dissertation presents the decay branching ratios of quirkonia where quirks obtain their masses through electroweak symmetry breaking. This dissertation includes previously published and unpublished co-authored material. / Committee in charge: Dr. Davison Soper: Chair; Dr. Graham Kribs: Advisor; Dr. Ray Frey: Member; Dr. Michael Kellman: Outside Member

xv, 219 p. : ill. (some col.) / Chemists have long recognized the potential of the BN bond to mimic CC double bonds in aromatic systems. Phenyl and indole are two of the most important arenes in natural systems, as well as medicine, applied chemistry, and materials science. Despite the potential of BN arenes as phenyl and indole mimics in biomolecules, few isoelectronic and isostructural BN biomolecules have been synthesized. Substitution of BN for C=C imparts tunability to aromatic systems, giving new and potentially valuable properties to the resulting molecules. Our group has sought to expand the utility of BN arenes by developing the synthetic arsenal available to chemists seeking to incorporate the BN bond into biological and other organic molecules of importance. The scope of this dissertation is twofold: (1) development of the first "fused" BN indole, including a survey of its reactivity towards electrophiles, synthesis of the parent N -H compound with complete characterization, and a comparison to natural indole and (2) expansion of the synthetic methodologies for constructing 1,2-dihydro-1,2-azaborine derivatives, including complete structural characterization of a family of "pre-aromatic" and aromatic compounds and a protection-free synthesis of azaborines. The contributions outlined in this dissertation expand both the fundamental understanding of BN isosterism in aromatic molecules and the synthetic toolbox for chemists seeking to incorporate BN arenes into biological and other organic motifs. This dissertation includes previously published and unpublished coauthored material. / Committee in charge: Professor Kenneth M. Doxsee, Chair; Professor Shih-Yuan Liu, Advisor; Professor Victoria J. DeRose, Member; Professor Michael M. Haley, Member; Professor Janis Weeks, Outside Member

The purpose of this work was to investigate a general synthetic route to 1-Methyl-4-Isopropyl-Hydroxy Bicyclo (3.1.0) Hexane.

Five electrochemical test methods were evaluated for prediction of tinplate performance during this study. In addition, test packs were performed which provided some tinplate performance data. Three of the electrochemical methods gave inconclusive results in predicting tinplate performance. Two of these were anodic polarization in citric acid solutions involving different cell configurations. Another was anodic polarization of stress fractured samples in citric acid solution. One method, measuring the tin/steel alloy couple potential and current, gave results which appeared to predict tinplate performance, but the procedure was time consuming and the results were not easily reproducible. One method gave results which predicted tinplate performance and is recommended for use by the industry. This method measured tin dissolution rate and peak current as a function of time. The best performing tinplates gave lower peak currents and longer dissolution times. New electrochemical test cells were designed for four of the test electrochemical methods. One cell was designed to do five tinplate samples at once. A computerized test apparatus was developed for two of the test methods. This test apparatus greatly improved data handling and storage. A software program was configured to collect and evaluate data for the two computerized electrochemical methods.