Rhododendrons are plants native to the Northern hemisphere, comprising over 1000 species, most of which have eye-catching flowers. The native Rhododendron of the Pacific NW, R. macrophyllum, harbors a degree of DNA sequence variation exceptional for a single species. Our study focuses on RPB2d, the gene encoding the second largest subunit of RNA polymerase II. Within intron 4 of R. macrophyllum RPB2d, there exist four conserved haplotypes, which have a structured geographical distribution. (Puget Sound differs from Oregon Cascades differs from Oregon Coast.) This surprising pattern of intraspecies variation inspired my project of looking into the degree and pattern of genetic homogenization in these populations by recombination events within and near the RPB2d gene. Thus far, I have sequenced most introns throughout RPB2d and some of the non-coding region upstream. The results have shown that the intron 4 haplotypes are linked to specific variants in intron 1. However, the later introns (6-13, 13-15, and 23-24) are uncoupled from the intron 4 haplotypes and show increasing recombination. About 1 kb upstream, there is a 341 bp DNA sequence inversion in certain plants. An inversion is a segment of a chromosome that has been reattached on the same chromosome in the same location, but in the opposite direction. The inversion found in most RPB2d genes of R. macrophyllum is not found in other species or in haplotypes 1 and 4, the ones most similar to other species. The data continues to show that fewer recombination events occur in introns closer to the inversion. My research is now focused on how the inversion limits the rate of recombination. The next step will be to sample heavily from homozygous populations to see if there is a normal rate of recombination. This regulation could help explain the persistence of varied haplotypes in intron 4.

Most procedures for DNA transformation of chloroplasts involve the use of circular DNA as vectors and green leaves as the target tissue. Although such procedures are successful with some plants, they are inefficient and do not work with other plants, especially monocots. In maize, plastid DNA (ptDNA) is comprised largely of linear molecules. Furthermore, ptDNA is rapidly degraded as the cells become green. In consequence, the introduction of transgenes into maize chloroplasts has been problematic. In order to create vectors for monocot transformation, the plastid chromosome is most efficiently targeted in its natural form. Previous work suggests that the plastid chromosome is found primarily in a complex, branched linear form with defined ends. We chose one of these ends, “End 1,” which is near an origin of replication, as our target for transgene integration. We constructed vectors with the “End 1” gene sequences and a mannose-metabolizing transgene, PMI, as the selectable marker. Plastid transformation was performed by particle bombardment using gold microcarriers coated with either the circular or linear vector. The successful introduction of a transgene using the “End 1” DNA sequence indicates that the transgene integrates either by end joining of the linear vector to the linear ptDNA or by homologous strand invasion. Thus, using a linear vector with an end sequence produces optimized results when engineering monocot plastid transformants.

Thermostability is the capacity of an organism to survive and thrive at high temperatures and is a characteristic with many biotechnological applications, such as food processing. We are seeking to understand the mechanisms of thermostability in viruses by using an RNA virus, phi-6 Cystovirus. We are evolving the phi-6 virus to become thermostable by exposing it to a target temperature of 61°C over many generations (wild type viruses grow at 25°C). In order to see if exposure to different intermediate temperatures affects the genetic pathway to thermostability, we will expose the phi-6 virus to different temperature regimes prior to reaching the target temperature. The temperature treatments are sudden, where the virus is exposed to the target temperature throughout the entire course of the experiment, moderate, where the virus is exposed to the target temperature halfway through the experiment, and gradual, where the virus is exposed to the target temperature on the final day of the experiment. The genome of phi-6 has already been characterized, which enables us to compare the genome of the evolved, thermostable phi-6 viruses to the ancestor and allows us to study the genetic basis of thermostability. In future studies, we hope to use these thermostable viruses to learn about costs and benefits of maintaining thermostability.

This paper challenges the Kantian account of autonomous moral decision-making. Kant’s definition of autonomy, I argue, is excessively narrow and does not place sufficient importance on the contextual factors which one encounters when attempting to act as an ethical agent in the empirical realm. An intersectional view of autonomous moral decision-making such as that put forth by Meyers takes these considerations more fully into account. By way of an exemplification illustrating a "real-world" scenario, I show how an application of Kant’s definition generates seemingly irresolvable conflicts. Then, through utilization of an intersectional definition of autonomy, I demonstrate how this alternative moral reasoning system allows for a more holistic understanding of individuals and the multiplicity of factors which shape and influence their situations and choices.

In this project, we explore conditions that are critical for de novo evolution of cooperation and altruism in a bacterial system. Previous theoretical work has shown that there is a competitive advantage to defection and selfishness, but the ubiquity of cooperation in nature suggests that cooperation may be adaptive. Here, we aim to uncover environments and genetic conditions that actually promote greater cooperation. We use an engineered cooperative strain of Escherichia coli. Through a bistable genetic switch, single cells have the capability to be either a producer cell that makes the cellulase enzyme to break down cellulose, or a consumer cell that eats the byproducts of cellulose breakdown. Our first aim is to characterize the social dynamics of this synthetic system and determine if a social dilemma is in fact occurring—i.e., is there a cost to producing cellulase, and can cheaters that do not produce cellulase displace the cooperators that do? Our second aim is to evolve the system over many generations and analyze how it changes. Uncovering the conditions favoring higher cooperation (e.g., greater production of cellulase) provides insight into how cooperation can evolve and how populations circumvent social dilemmas. We hope to use evolution as a tool to tune the synthetic genetic circuit for maximal cellulose breakdown. On a broader scale, these conditions that favor cooperation may have practical applications in waste degradation and biofuel production.

The evolution of multicellularity is one of the most important yet least understood biological phenomena. What selective pressures drive this major evolutionary transition? To address this question, we use a theoretical approach to model the spatial properties of cell groups in a simulation entitled Tree-Multicellularity (TreeMu). In TreeMu a simple multicellular organism is represented as a graph, with nodes representing cells, and edges representing physical connections between cells. Like cells, nodes carry intrinsic attributes, such as reproduction, mutation and death rates; these dictate life processes and define an individual's fitness. Like multicellular groups, graphs have similar properties that emerge from individual contributions. When a node dies it splits the graph in two, analogous to group level reproduction. We explore how the evolution of a node's death rate affects multicellular growth. In the simulation we implement an evolutionary algorithm that selects for 'multicellular' graphs of large sizes by removing small groups from the population. Preliminary data supports a tradeoff between group size and reproduction. TreeMu provides a computational framework to explore the dynamics of multicellular evolution.

With the rise of atmospheric carbon dioxide, understanding the various facets of the carbon cycle is critical. In temperate coastal systems, the phytoplankton group of diatoms play a key role in the carbon cycle by sequestering carbon from the atmosphere into deep ocean sediments. Many scientists turn to laboratory culturing experiments to make predictions about the response of phytoplankton to changes in climate. But do these laboratory studies serve as realistic proxies for environmental responses? This study will compare growth rates of phytoplankton communities from Barkley Sound, British Columbia using field and laboratory experiments. Field experiments will comprise an in situ community growth rate measured using diffusion chambers in addition to on-ship incubations measuring the community growth rate in response to added nutrients. Field samples will be used to isolate the three dominant diatom species into a mixed-species culture for laboratory experiments. An analogous culture using laboratory isolates of the same species will be created, and the two cultures will be kept in a semi-continuous batch culture experiment tracking the growth rates in response to added nutrients. Comparisons of the growth rates in situ, shipboard, and in the laboratory will indicate how growth rates differ between natural phytoplankton assemblages and laboratory settings. Growth rates will be calculated using changes in chlorophyll a levels, a proxy for cell densities. If growth rates are much higher in the laboratory cultures than in the wild cultures, the implication is that there are limitations to growth in the natural environment that should be factored in when correlating laboratory experiments to the responses of natural phytoplankton assemblages. However, if there is no significant difference in growth rates between the experiments, then the laboratory conditions can provide similar conditions as in the field and laboratory culture experiments and can be easily used to predict environmental responses.

Darwinian natural selection produces an organism that is adapted to its environment, an organism whose traits (phenotype) are tuned in critical ways to its habitat. If organisms and their phenotypes are so finely tuned to their environment, how can they deal with changes to that environment? One strategy is to evolve the ability to change phenotype in response to a change in the environment, or phenotypic plasticity. Theory predicts phenotypic plasticity to be adaptive when (1) organisms experience different environments either spatially or temporally and (2) different environments favor different phenotypes. In some cases, changes may be accompanied by cues that provide reliable information about future selection. Previous studies modeling adaptive plasticity suggest plasticity to be favored when the environmental cue always predicts the correct selection and not when the environmental cue is unreliable. We experimentally tested theoretical predictions about the de novo evolution of adaptive phenotypic plasticity with a clustering phenotype of baker's yeast by selecting alternately for large or small clusters. Selection for size was cued by alternate forms of growth media and this cue was either a reliable predictor of future selection or an unreliable predictor. After a preliminary run of the experiment, we have found indications of an emergent plastic response in one of our replicates from the reliable cue treatment. This provides a biological example that is consistent with accepted theoretical predictions.

Exoplanets are planets outside our solar system, and the current explosion in exoplanet discoveries is revolutionizing our understanding of the potential for extraterrestrial life. This prolific era of detections has stemmed largely from the unprecedented observing capabilities of NASA's Kepler Space Telescope. The Kepler Spacecraft collects high precision time-series photometric data on a fixed group of approximately 160,000 stars. The data are represented by temporal lightcurves (i.e. brightness vs. time) that can be used to detect transiting exoplanets, the topic of our research. Transits are events where an orbiting planet partially eclipses its host star, casting a small shadow on the telescope. To detect transit signals, we rely on the Quasi-Periodic Automated Transit Search Algorithm (QATS). As an automated tool, QATS provides a crucial means to reduce the Kepler dataset to a manageable size. However, since the algorithm is sensitive to stellar variability, eclipsing binary stars, and systematic artifacts of the spacecraft, additional analysis is required to separate true detections from false positives. Determining the best way to do this is the present focus of our work. Concurrently, we are exploring the potential for QATS not only to determine orbital period, but also to constrain transit depth and duration (properties related to the size of the exoplanet and to the density of the stellar host). While this increases the complexity of the QATS algorithm and the amount of output to manage, it provides greater potential for a fully automated transit search process with results that are more descriptive of the exoplanet systems detected.

The presence of fungal symbionts residing in the root tissue of plants is a well-documented occurrence, yet questions regarding the identification and comparison of fungal partners in mycorrhizal relationships have been largely unanswered. Ericoid mycorrhizae, an example of a mycorrhizal relationship, are found in host plants within the order Ericales. Ericales, which contains such familiar species as persimmon, blueberry and Rhododendron, are able to persist in edaphic conditions due to their fungal symbionts. These symbionts form hyphal coils inside plant cell membranes, and thereby exchange crucial nutrients with the host plant. This project aims to evaluate the specificity between fungal communities and their host Rhododendron species, with the expectation that differing communities may exist, even in closely related hosts. Using known techniques to extract fungal DNA from the root systems of Rhododendron species in varying conditions and proximity, this DNA is then used to generate species based communities within specific Rhododendron hosts. By using type-cultures and genomic sequencing, comparisons of the presence or absence of fungal species within host roots can be made. This will shed light on infection intensity, and specificity between roots and fungal symbionts. Anticipated results of high levels of specificity between host plant and fungus could prompt questions regarding the importance of fungal symbionts in genus Rhododendron, especially with regards to the speciation between individual host plants.

Since the French and Spanish occupation of Hispaniola and specifically the US occupation from 1915-1934, Dominicans and Haitians have lived in a borderlands of blackness. However, these imaginary boundaries have been entwined with the African American response to the US occupation in Haiti. There have been many studies on the relationship between Dominicans and Haitians, but few have complicated how the relationship of African Americans living in Hispaniola played a fundamental role in shaping the multiple dimensions of blackness. By drawing upon Antonio Gramsci's theory of cultural hegemony, Stuart Hall's concept of cultural identity and diasporas in the Caribbean, in conjunction with Michael Omi and Howard Winant's work on racial formation in the United States, my research aims to draw the connections between these three groups and determine how these understandings have transformed preexisting definitions of blackness on the island. This paper is significant for comprehending the complexity of Dominican and Haitian identity, as well as locating the mechanisms of Western power, privilege and discourse. My research contributes to scholarship on the cultural production of blackness and race in the Caribbean and the United States.

Knowing the sources of archaeological materials is helpful in understanding how they were acquired, that is, by trade or travel, and how these methods change over time. We analyzed magnetic susceptibility and elemental concentrations in ochre samples from four South African Middle Stone Age sites spanning 60-20 ky BP. We measured elemental concentrations on 13 geological ochre samples and 60 archaeological ochre samples using portable x-ray fluorescence spectroscopy (pXRF). Magnetic susceptibility, a sample’s ability to be magnetized, was also measured on these samples using the the Bartington MS2. These analyses will help distinguish between each sample and identify different types of ochre. Analysis of these data will determine provenance of the archaeological samples of ochre, an important step towards understanding the process by which they were procured. We show how procurement strategies varied between the four sites and over time.

Sulawesi, in northern Indonesia, is strategically positioned to test competing models of modern human expansion, and trajectories of cultural change and interaction. Recent excavations in South Sulawesi have revealed a long and continuous archaeological sequence spanning most of the Holocene. We used sedimentological methods to investigate site formation and the environment of deposition at Gua Mo'o hono. These methods include the analyses of chemical and physical attributres of sediments, and particle size analysis. For determining the basic chemical  properties of the Sulewesi sediment samples, we used measurements of pH, electrical conductivity, organic carbon proportion by mass, and carbonate proportion by mass. For determining the basic physical properties of the sediment samples, we determined the color using the Munsell color chart by analyzing hue, value, chroma, viewing conditions, sample freshness, and the moisture content, as well as by measuring the magnetic susceptibility of the samples. Lastly, for dertermining particle size distribution of sediment samples, we use the pipette method and camsizer method of sediment granulometry. Our results present the environmental context to human occupation at the site. We discuss the relationship between the environmental and major cultural changes such as the introduction of ceramics at this site. The expected results are an improved understanding of the environment of site formation and the climatic conditions for humans that occupied the site.

It is well documented that low levels of antibiotics are present in both surface water sources and in soil near industrial, large-scale farms. However, very little work has been done exploring the selective pressure for the evolution of resistance at these sub-inhibitory antibiotic concentrations. It is our concern that mutations acquired in a low antibiotic environment may be “potentiating:” that is, the presence of these first mutations opens more mutational paths after a shift to a high antibiotic environment. The converse may also be true in terms of “dooming” mutations that close off evolutionary paths in the new environment. Here we aim to investigate the prevalence of potentiating and dooming mutations and to understand their role in adaptive evolution. We study these phenomena by performing evolution experiments with Escherichia coli grown in a permissive environment (low drug concentration) followed later by a sudden shift to a new environment that imposes a strong selective pressure (high drug concentration). Here the permissive environment serves to generate mutational diversity and the harsh selective environment serves to assess the evolutionary potential of mutant isolates relative to their wild type ancestor. This will increase our knowledge of the evolution of antibiotic resistance and as well as the unintended but potentially dangerous effects of long term selection in the presence of low levels of antibiotics.