No description available.

Gopherus polyphemus, commonly known as the Gopher Tortoise, is a dryland reptile native to the southeastern United States. It is commonly a resident of longleaf pine and dry oak sand hill habitats. It is considered a keystone species because they dig deep burrows that provide shelter to them as well as many other animals. Habitat loss, fragmentation, and disease are major threats and have caused this species to be federally listed as a threatened species under the Endangered Species Act (ESA). Disease is a major threat to the gopher tortoise’s survival, and with declining populations, the need to investigate pathogens is crucial. Herpesvirus, is known to contribute to upper respiratory tract diseases (URTD) in G. polyphemus and is the primary focus of this project. Due to high mutation rates in the virus, a modified version of PCR, nested PCR, was conducted on eye and nose swabs and blood samples obtained from G. polyphemus to detect the presence of the alpha herpesvirus pathogen. The positive samples were then sent for genetic sequencing to confirm the occurrence of the pathogen. The detectability of Herpesvirus in eye and nose swabs was compared to blood and lymph samples and statistical tests concluded that both sample types had the same detectability.

No description available.

Combinatorial approaches in metabolic engineering can make use of randomized mutations and/or overexpression of randomized DNA fragments. When DNA fragments are obtained from a common genome or metagenome and packaged into the same expression vector, this is referred to as a DNA library. Generating quality DNA libraries that incorporate broad genetic diversity is challenging, despite the availability of published protocols. In response, a novel, efficient, and reproducible technique for creating DNA libraries was created in this research based on whole genome amplification using degenerate oligonucleotide primed PCR (DOP-PCR). The approach can produce DNA libraries from nanograms of a template genome or the metagenome of multiple microbial populations. The DOP-PCR primers contain random bases, and thermodynamics of hairpin formation was used to design primers capable of binding randomly to template DNA for amplification with minimal bias. Next-generation high-throughput sequencing was used to determine the design is capable of amplifying up to 98% of template genomic DNA and consistently out-performed other DOP-PCR primers. Application of these new DOP-PCR amplified DNA libraries was demonstrated in multiple strain enrichments to isolate genetic library fragments capable of (i) increasing tolerance of E. coli ER2256 to toxic levels of 1-butanol by doubling the growth rate of the culture, (ii) redirecting metabolism to ethanol and pyruvate production (over 250% increase in yield) in Clostridium cellulolyticum when consuming cellobiose, and (iii) enhancing L-arginine production when used in conjunction with a new synthetic gene circuit. / Ph. D.

Ultra-cold dilute gases of neutral atoms are attractive candidates for creating controlled mesoscopic quantum systems. In particular, quantum degenerate gases of bosonic and fermionic atoms can be used to model the correlated many-body behaviour of Bose and Fermi condensed matter systems, and to study matter wave interference and coherence. This thesis describes the experimental realization and manipulation of Bose-Einstein condensates (BECs) of 87Rb and degenerate Fermi gases (DFGs) of 40K using static and dynamic magnetic atom chip traps. Atom chips are versatile modern tools used to manipulate atomic gases. The chips consist of micrometre-scale conductors supported by a planar insulating substrate, and can be used to create confining potentials for neutral atoms tens or hundreds of micrometres from the chip surface. We demonstrate for the first time that a DFG can be produced via sympathetic cooling with a BEC using a simple single-vacuum-chamber apparatus. The large 40K-87Rb collision rate afforded by the strongly confining atom chip potential permits rapid cooling of 40K to quantum degeneracy via sympathetic cooling with 87Rb. By studying 40K-87Rb cross-thermalization as a function of temperature, we observe the Ramsauer-Townsend reduction in the 40K-87Rb elastic scattering cross-section. We achieve DFG temperatures as low as T = 0.1TF , and observe Fermi pressure in the time-of-flight expansion of the gas. This thesis also describes the radio-frequency (RF) manipulation of trapped atoms to create dressed state double-well potentials for BEC and DFG.We demonstrate for the first time that RF-dressed potentials are species-selective, permitting the formation of simultaneous 87Rb double-well and 40K single-well potentials using a 40K-87Rb mixture. We also develop tools to measure fluctuations of the relative atom number and relative phase of a dynamically split 87Rb BEC. In particular, we observe atom number fluctuations at the shot-noise level using time-of-flight absorption imaging. These measurement tools lay the foundation for future investigations of number squeezing and matter wave coherence in BEC and DFG systems.

Ultra-cold dilute gases of neutral atoms are attractive candidates for creating controlled mesoscopic quantum systems. In particular, quantum degenerate gases of bosonic and fermionic atoms can be used to model the correlated many-body behaviour of Bose and Fermi condensed matter systems, and to study matter wave interference and coherence. This thesis describes the experimental realization and manipulation of Bose-Einstein condensates (BECs) of 87Rb and degenerate Fermi gases (DFGs) of 40K using static and dynamic magnetic atom chip traps. Atom chips are versatile modern tools used to manipulate atomic gases. The chips consist of micrometre-scale conductors supported by a planar insulating substrate, and can be used to create confining potentials for neutral atoms tens or hundreds of micrometres from the chip surface. We demonstrate for the first time that a DFG can be produced via sympathetic cooling with a BEC using a simple single-vacuum-chamber apparatus. The large 40K-87Rb collision rate afforded by the strongly confining atom chip potential permits rapid cooling of 40K to quantum degeneracy via sympathetic cooling with 87Rb. By studying 40K-87Rb cross-thermalization as a function of temperature, we observe the Ramsauer-Townsend reduction in the 40K-87Rb elastic scattering cross-section. We achieve DFG temperatures as low as T = 0.1TF , and observe Fermi pressure in the time-of-flight expansion of the gas. This thesis also describes the radio-frequency (RF) manipulation of trapped atoms to create dressed state double-well potentials for BEC and DFG.We demonstrate for the first time that RF-dressed potentials are species-selective, permitting the formation of simultaneous 87Rb double-well and 40K single-well potentials using a 40K-87Rb mixture. We also develop tools to measure fluctuations of the relative atom number and relative phase of a dynamically split 87Rb BEC. In particular, we observe atom number fluctuations at the shot-noise level using time-of-flight absorption imaging. These measurement tools lay the foundation for future investigations of number squeezing and matter wave coherence in BEC and DFG systems.

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The obstruction to the existence of Fredholm problems for elliptic differentail operators on manifolds with edges is a topological invariant of the operator. We give an explicit general formula for this invariant. As an application we compute this obstruction for geometric operators.

This dissertation presents the implementation of a technique to generate atomic Fock states of Lithium 6 with ultra-high fidelity, called laser culling. Fock states, atomic states with a definite number of particles, are a mandatory step for studying few-body quantum phenomena such as quantum tunneling, quantum entanglement, and serve as building blocks for quantum simulators. The creation of ultra-high fidelity Fock states begins with a degenerate Fermi gas in an optical dipole trap. Being fermions, lithium-6 atoms fill the energy levels of the dipole trap with 2 atoms per energy level. Introducing a magnetic field gradient creates a linear potential that tilts the potential produced by the optical dipole trap. The initially bound energy levels become quasi-bound states, each with a different lifetime. By exploiting the difference between these lifetimes, one can generate a single pair of atoms in the ground state of the trap with fidelities that can exceed 99.9%. This dissertation first presents the details of the design and construction of an apparatus for laser culling, and then reports on the progress made towards the creation of atomic Fock states with ultra-high fidelity. / text

We consider bounded weak solutions u of a degenerate parabolic-hyperbolic equation defined in a subset [mathematical symbols]. We define strong notion of trace at the boundary [mathematical symbols] reached by L¹ convergence for a large class of functionals of u. Such functionals depend on the flux function of the degenerate parabolic-hyperbolic equation and on the boundary. We also prove the well-posedness of the entropy solution for scalar conservation laws with a strong boundary condition with the above trace result as applications. / text