MA

thesisDuring the latter half of the 20th century the number of theories being defended in the field of practical reason has proliferated dramatically. This proliferation, however, threatens to undermine the justificatory aim of practical reason, for if these different theories yield different practical inferences, then we seem to be in a dilemma: we have to either give reasons for our reasons, or accept that there aren't any such reasons, which would render our actions (even if they were made after some sort of rational deliberation) completely arbitrary. This thesis argues that currently in the field of practical reason there isn't any method or set form of argumentation aimed at providing reasons for our reasons, and that therefore nihilism, or the view that we don't have good reasons for doing what we do, seems to be the best attitude to take regarding theories of practical reason and human agency. This conclusion is then defended against three objections that stem from the views of J. David Velleman, Christine M. Korsgaard, and John McDowell

Immune Gene Diversity and Populations Structure of Reticulated Flatwoods Salamander (Ambystoma bishopi)

Reticulated flatwoods salamander (Ambystoma bishopi) populations began decreasing dramatically in the late 1900s. Contemporary populations are small, isolated, and may be susceptible to inbreeding and reduced adaptive potential because of low genetic variation. Genetic variation at immune genes is especially important as it influences disease susceptibility and adaptation to emerging infectious pathogens, a central conservation concern for declining amphibians. Connectivity between isolated populations is also vital to maintain genetic diversity and avoid inbreeding. I collected tissue samples from across the extant range of this salamander to examine genetic variation and population structure in: immune genes broadly (immunome), the major histocompatibility complex (MHC) class Iα and IIβ exons, as well as the mitochondrial control region. I also screened for ranavirus, a pathogen associated with amphibian declines worldwide. Overall, I found low MHC variation when compared to other amphibian species but mitochondrial diversity similar to other Ambystomatids. I also found moderate diversity in the immunome with possible gene duplication. I did not detect ranavirus at any site. MHC class Iα sequencing revealed only three highly similar alleles while MHC class IIβ sequencing found five alleles. However, unique variation still exists across this species’ range with private alleles at several sites. I hypothesize that a combination of factors may have contributed to low MHC diversity, specifically, a historic disease outbreak and/or a population bottleneck. Ultimately, MHC data indicates that the reticulated flatwoods salamander is at an elevated risk from infectious diseases due to low levels of immunogenetic variation necessary to combat novel pathogens. Population structure and migration between major sites was calculated using all three genetic marker types (immunome, MHC, and mitochondria). Population structure for immunome and MHC data was low between major breeding sites, but mitochondrial structure was higher. This pattern is indicative of male biased dispersal with females dispersing at a lower rate than males. Using program Migrate-N and BayesAss I calculated migration rates and found historic gene flow between salamander breeding sites. Since there is low population structure and historic migration between sites, I suggest human mediated dispersal of this species to re-establish gene flow and extirpated populations

Master of Science

thesisDue to the complex failure modes associated with composites, a structural health monitoring system capable of accurately locating the source of strength-reducing events is desirable in order to reduce inspection time and time out of service. Various active and passive inspection techniques exist but most require large footprints and extensive cabling to monitor full scale structures. This work derives various location techniques by coupling modal acoustic emissions with phased array techniques to detect and accurately locate the source of strength-reducing events such as impacts. Phased array techniques provide a method to more accurately track phase points for determining arrival times used to back-calculate the source, as well as providing a method that can incorporate anisotropic wave speeds. To increase accuracy by neglecting local to global material changes, the local velocity profile per component was found and built into the derived location algorithms. The location algorithms were then tested on two full scale composite structures based on strength and stiffness critical design considerations. It was found that with two arrays, each with dimensions of 1 inches in width and 8 inches in length and consisting of four sensors each, events could be accurately located over a 65 ft2 region on the stiffness critical structure with an average error of 10 inches and over a 100 ft2 region on the strength critical structure with an average error of 9 inches

Production of FAME biodiesel in E. coli by direct methylation with an insect enzyme.

Most biodiesel currently in use consists of fatty acid methyl esters (FAMEs) produced by transesterification of plant oils with methanol. To reduce competition with food supplies, it would be desirable to directly produce biodiesel in microorganisms. To date, the most effective pathway for the production of biodiesel in bacteria yields fatty acid ethyl esters (FAEEs) at up to ~1.5 g/L. A much simpler route to biodiesel produces FAMEs by direct S-adenosyl-L-methionine (SAM) dependent methylation of free fatty acids, but FAME production by this route has been limited to only ~16 mg/L. Here we employ an alternative, broad spectrum methyltransferase, Drosophila melanogaster Juvenile Hormone Acid O-Methyltransferase (DmJHAMT). By introducing DmJHAMT in E. coli engineered to produce medium chain fatty acids and overproduce SAM, we obtain medium chain FAMEs at titers of 0.56 g/L, a 35-fold increase over titers previously achieved. Although considerable improvements will be needed for viable bacterial production of FAMEs and FAEEs for biofuels, it may be easier to optimize and transport the FAME production pathway to other microorganisms because it involves fewer enzymes

Expression of regions of Apm1p in E coli. and purification of the expressed proteins [abstract]

Abstract only availableAn active area of cell biological research is the study of intracellular protein trafficking. Improper function of protein trafficking has pathological consequences, as the malfunction of certain transport systems can give rise to certain cancers. Our lab focuses on the dynamic mechanisms of transport between the trans-Golgi network (TGN) and endosomes using the model protein Ste13p. The goal of my project is to deepen our understanding of Ste13p retrieval from the early endosome to the TGN via binding of the adaptor complex (AP-1). Previous research suggests that the C-terminal domain of the AP-1 subunit Apm1p interacts with a sorting signal contained within amino acids 1-12 of the cytosolic domain of Ste13p. With this in mind, we developed plasmids that expressed different regions of the C-terminal domain of Apm1p in E coli. The hope was to find a construct that provided both high expression and ease of purification. As part of a collaboration, we intended to discover how the 1-12 region of Ste13p binds to Apm1p on an atomic level. Each construct was contained within the expression vector pET28a(+) which is under the control of a T7 promoter. The results led us to choose Apm1p 161-475 as the best construct. Using a nickel column, we purified this Apm1p construct due to the nickel's binding affinity for the engineered 6xHistidine tag. Soon, we will perform a pull down assay to confirm the binding of Apm1 161-475 to a peptide that represents amino acids 1-12 of Ste13- GST. After completion of the assay, we will send our construct to our collaborator who will co-crystallize the AP-1 derivative with a Ste13p peptide to structurally define the binding between these two proteins. Structural data will make it easier to understand how mutations could affect the binding of the signal with the adaptor protein, thus allowing more detailed manipulations of both proteins

Asymptotically Normal Estimation of Local Latent Network Curvature

Network data, commonly used throughout the physical, social, and biological sciences, consist of nodes (individuals) and the edges (interactions) between them. One way to represent the complex, high-dimensional structure in network data is to embed the graph into a low-dimensional geometric space. Curvature of this space, in particular, provides insights about structure in the graph, such as the propensity to form triangles or present tree-like structure. We derive an estimating function for curvature based on triangle side lengths and the midpoints between sides where the only input is a distance matrix and also establish asymptotic normality. We next introduce a novel latent distance matrix estimator for networks as well as an efficient algorithm to compute the estimate via solving iterative quadratic programs. We apply this method to the Los Alamos National Laboratory Unified Network and Host dataset and show how curvature estimates can be used to detect a red-team attack faster than naive methods, as well as discover non-constant latent curvature in coauthorship networks in physics.Comment: 77 page

Hypergeometric decomposition of symmetric K3 quartic pencils

We study the hypergeometric functions associated to five one-parameter deformations of Delsarte K3 quartic hypersurfaces in projective space. We compute all of their Picard--Fuchs differential equations; we count points using Gauss sums and rewrite this in terms of finite field hypergeometric sums; then we match up each differential equation to a factor of the zeta function, and we write this in terms of global L-functions. This computation gives a complete, explicit description of the motives for these pencils in terms of hypergeometric motives.Comment: 70 pages, minor revision, to appear in Research in the Mathematical Science