STUDENT ABSTRACTS

Current thought on galactic evolution suggests that this process is dominated by two or more “heating” mechanisms, which increase the random motions of stars in the system. A convenient manner of quantifying this heating is through the comparison of the random motion occurring parallel to and perpendicular to the plane of the galactic disk, a ratio known as the velocity ellipsoid ratio. Since each of the proposed heating mechanisms acts on different components of a star’s motion and varies differently with galactic morphology, the trend in velocity-ellipsoid ratios over a range of galactic types can be used to ascertain the validity of competing theories. Recent work has shown that it is possible to extract his information from external galaxies by observing the major and minor axes of systems with intermediate inclination. Prior to this project, such analyses had only been performed on two external spirals, and while the results suggested that a trend in velocity ellipsoid ratio does exist, the error bars were too large to be conclusive. Presented here is the study of four additional external galaxies, covering a slightly larger range in morphological type. The results are consistent with a decreasing velocity-ellipsoid ratio in later-type spirals; however the error bars inherent in this analysis continue to restrict the strength of the conclusions that can be drawn.

Temporary occlusion of blood flow to the brain -- ischemia -- is associated with extensive cell death in the hippocampus as well as impairments in memory. Recent findings suggest that pretreatment with estradiol may minimize the extent of damage to the hippocampus. This investigation examined the effects of transient global ischemia on working memory, the potential protective effects of estradiol, as well as potential sex differences in the effects of ischemia and estradiol on memory and hippocampal morphology. Male and female Sprague-Dawley rats were gonadectomized and implanted with silastic capsules containing either 17_-Estradiol or Cholesterol vehicle. Half the animals in each group were subjected to transient global ischemia through the use of a 4-vessel occlusion procedure; the others underwent a sham procedure. Working memory was then assessed with a water T-maze task, in which animals were required to alternate left and right at the choice point. Rats performed 20 trials per day for 4 days, after which they were perfused. Estradiol-treated rats made significantly more alternation errors than their cholesterol-treated counterparts. Male ischemic rats also performed worse on the task than did male rats in the sham surgical condition. Plasma samples were taken at the time of perfusion and assayed for estradiol levels using a radioimmunoassay. Higher levels of estradiol were present in the estradiol-treated females than in the cholesterol-treated females, but levels of estradiol in estradiol-treated males did not significantly surpass levels in cholesterol-treated males. Preliminary histological analysis of coronally sliced brain sections did not reveal differences in CA1 pyramidal neuron density between test groups for either sex. These findings are discussed in light of an existing literature supporting estradiol’s facilitative and neuroprotective effects on working memory.

We examined substrate-borne vibrational signaling in the treehopper Publilia concava (Hemiptera: Membracidae), which participates in a mutualism with Myrmica ants. The ants defend the treehoppers against predators in exchange for nutritious secretions. We found that adult treehoppers produce three distinct vibrational signals, which we call a chirp, a sigh, and a scratch. Nymphs produce one signal, a groan.

Chirps are produced by both males and females in the context of encounters with predators. Females that are unwilling to mate also chirp when approached by a male. In ant choice tests, 34% more ants (1.16±0.16 versus 0.86±0.22) attended an artificial nectary where the chirp signal was being played than a nectary with no signal. These results suggest that P. concava adults may be able to regulate levels of attendant ants by producing vibrational signals.

A second signal, a sigh, is produced only by males. Isolated males produce this signal spontaneously. We did not identify a call specific to females. In observations of a mating pair in the laboratory, the male produced occasional sighs before the pair encountered each other on the goldenrod plant. Additionally, every attempt at copulation was preceded by a train of five sighs. This suggests that the signal may play an important role in mate attraction and courtship, consistent with observations from other membracid species.

A third signal, a scratch, occurs frequently but is not associated with a clear behavioral or environmental context of production.

Aggregations of P. concava nymphs produced one vibrational signal, a groan. Groans occurred in response to the presentation of a crushed conspecific nymph, and were accompanied by nymphs moving away from their original feeding site. An experiment designed to examine the context of groan production more closely lacked the audio sensitivity necessary to identify groans, which are of very low frequency and amplitude. Further investigation is required to clarify the context and function of this signal.

We observed the results of increasing host plant quality on an ant-treehopper mutualism. The ants protect the treehoppers from predators and may increase feeding rates. During the summer of 2002 we created a two-treatment experiment in Hopkins Memorial Forest, Williamstown MA. Host plant quality and ant presence were the variables used. Predators were excluded from the treatments. We censed the plants for the number of ants tending and treehopper population size throughout the summer. Results show that fertilizer significantly increased treehopper weight and survivorship. Fertilizer also significantly increased the surface area and nitrogen content of the leaves of goldenrod. Ant tending had a marginally significant affect on the survivorship of treehoppers. Ants had the greatest affect on survivorship during mid-summer (between July 24th and August 14th). Fertilization had the greatest affect in the early summer (between July 8th and 23rd) and had a marginally significant affect during mid-summer. Fertilizer positively increased the maturation rate of treehoppers. Per-capita tending and the variance in tending of treehoppers are positively correlated to treehopper survivorship during the early portion of the summer. These results imply that the maturation rate of treehoppers is very important to their survivorship. The data shows little support for the hypothesis that bottom up regulation is an important component of the relationship between ants and treehoppers in this system.

Nest predation is an important source of mortality for the veery (Catharus fuscescens), and the white-footed mouse (Peromyscus leucopus) is an important nest predator. We conducted artificial nest experiments in conjunction with the monitoring of real veery nests in order to explore the effects of local habitat and nest substrate on nest predation. We found a negative effect of the invasive shrub barberry (Berberis thunbergii) on nest mortality that was present only in lowland areas, and we found that predation rates in upland areas were less than half of those in lowland areas. Predation by mice, which accounted for over 70% of predation events, explained both trends. Mouse densities in upland and lowland habitats were tested in a trapping study and no difference was found. Data on mouse movement paths were collected in upland and lowland sites and compared to the correlated random walk model of movement. Mouse paths did not follow a correlated random walk, and the structure of paths in lowland areas was not found to be more efficient than in upland areas. We conclude that patterns of nest predation by mice can only be explained by a mechanism that specifically affects the likelihood of a mouse perceiving or deciding to attack a nest without affecting general foraging patterns.

Streptomycetes are ubiquitous soil-dwelling bacteria, which exhibit an unusually complex life cycle. Unlike many bacteria, streptomycetes progress through several morphological stages, which result in the formation of spores. In this study, genes and gene products involved in the developmental decisions leading to sporulation in Streptomyces coelicolor were investigated. Earlier phenotypic screens had identified the whiJ gene cluster, which consists of three open reading frames (orf1, orf3 and orf5), as important for successful sporulation. In particular, whiJ orf3 and whiJ orf5 mutants were unable to sporulate. Protein sequence homology revealed that the Orf3 protein contains a Helix-Turn-Helix domain, while promoter studies showed that the whiJ orf3 promoter is only activated in the presence of wild type whiJ orf3, implying that Orf3 may be an autoregulatory transcription factor, which interacts with its own promoter.

To test if WhiJ Orf3 binds to its promoter DNA, purification of native Orf3 from E. coli was attempted using two different affinity tags (a HisoTag and an intein-tag). When Orf3 could not be obtained in a soluble form, insoluble Orf3oHis inclusion bodies were solubilized, denatured and allowed to refold. This protein was tested for binding to the whiJ promoter DNA using an electrophoretic mobility shift assay and was found not to bind to the whiJ promoter. This was attributed to the lack of correctly folded protein in the sample. Attempts to determine Orf3 binding using induced E. coli extract were unsuccessful, due to binding of the whiJ promoter to a component of E. coli in the absence of whiJ. For the characterization of Orf3 to proceed, new techniques for Orf3 purification will need to be established.

The bacteria Agrobacterium tumefaciens infects plant cells by transferring DNA (T-DNA) containing enzymes that spur the production of growth factors and opines into host cells. The virC operon is one of a group of operons encoding proteins necessary for virulence located with the T-DNA on the Ti plasmid, and contains two genes: virC1 and virC2. In order to examine the possibility that these proteins are responsible for tethering the pTi to the transfer pore, which would increase the transfer efficiency of the T-DNA, we performed a variety of assays. Dihybrid analysis showed that VirC1 and VirC2 do not engage in homotypic or heterotypic protein interactions in yeast. Gel shift assays demonstrated that VirC1 binds specifically to overdrive, a sequence near one of the T-DNA border sequences that is thought to be important for inducing single stranded nicks at that border. However, the dihybrid work indicated that VirC1 might bind other DNA sequences as well. Using a variation of transposon insertion mutagenesis, we attempted to make multiple mutations in VirC1, but were unable to due to the lethality of virC1 insertions in E. coli and problems with our experimental method. Complementation assays indicated that a virC operon located on a plasmid can restore virulence to virC--- A. tumefaciens strains, and that this virC operon can come from the same pTi that is mutated in the bacterium, or a dissimilar pTi. This opens the door for experiments examining the importance of VirC1‚s ATPase motif in vivo, and whether or not VirC1 and VirC2 are translationally coupled. One possible role of the virC operon in the infection process is as an intermediary that increases T-DNA production when the pTi is tethered near the transfer pore. This putative action would tie together all the data about virC collected in this study and existing in the literature.

Ygl232w is a 33.5-kDa protein encoded on Chromosome VII of the Saccharomyces cerevisiae genome. No known lab has characterized or specifically investigated Ygl232w. However, during investigation of a novel temperature-sensitive yeast strain called pus4_ts, the Raymond lab found that a genetic screen identified YGL232w as a possible factor contributing to pus4_ts’s unexpected temperature-sensitive phenotype. This suggested that the Ygl232w protein might have a functional interaction with the enzyme Pus4 (pseudouridine synthase 4), a tRNA-modification protein operating in the process of tRNA maturation. This hypothesis is supported by the presence of a domain called THUMP (believed to function in RNA binding) in the Ygl232w protein sequence. In this study we isolated and cloned wild-type YGL232w in a plasmid vector and found that it could independently rescue pus4_ts cells from temperature sensitivity, confirming that YGL232w interacts genetically with PUS4 and suggesting it might also play a role in tRNA maturation. This possibility was examined by analyzing Ygl232w’s location and affects within the cell, looking for characteristics corresponding to those of tRNA maturation proteins. We determined that that Ygl232w appears necessary for proper cell growth in pus4_ts cells and that Ygl232w appears to localize to the nucleus (as EGFP-tagged Ygl232w fluoresces there). These two characteristics correspond with those expected of a tRNA maturation protein. However, further studies are needed to confidently identify Ygl232w as a tRNA maturation protein. In particular the protein needs to be purified and its binding characteristics examined. Towards that end, we have also created a potential system for expression and purification of the Ygl232w protein from yeast.

Caloric restriction (CR) has been shown to cause a decrease in blood pressure as well as a reduction in sympathetic nervous system activity (Swoap et al.) Atrial natriuretic peptide (ANP) is a peptide hormone released from the heart atria in response to high blood pressure. The primary target of ANP lowers blood pressure through alterations in blood volume. Blood volume is a major factor in the long-term regulation of arterial blood pressure, because it influences several aspects of cardiac function, including venous pressure, venous return, end-diastolic volume, stroke volume, and cardiac output. Reciprocally, arterial pressure has a major influence on blood volume, as well, by altering plasma volume through regulating total-body sodium and water balance in the kidneys. Together these factors form a negative-feedback loop system that serves to stabilize total-body fluid and blood pressure. ANP exerts its hypotensive effect through actions on the kidney to induce natriuresis, or sodium loss, and on the cardiovascular system to induce vasodilation and decreased peripheral vascular resistance. We hypothesized that ANP plays a role in the cardiovascular effects of CR by acting through the primary receptor for ANP, NPR-1, to induce natriuresis, resulting in decreased blood volume, and therefore hypotension. Through the use of a knockout mouse that lacks the NPR-1 receptor, we expected to see no drop in blood pressure in response to a 50% reduction in calorie intake, implicating this receptor in the hypotensive actions of CR. We also expected to see an increase in sodium excretion through the urine, along with an up-regulation of serum ANP levels during CR relative to the ad libitum fed state. We found that NPR-1-/- mice do not experience a drop in blood pressure in response to CR, partially confirming our hypothesis. However, the results of urine assays suggested that the hypotensive effect of CR is not regulated by changes in sodium excretion, and the results of serum ANP assays suggest that an alternate hormone plays the hypotensive role in CR. Therefore, we propose that the drop in blood pressure in response to CR is due to the regulation of vascular parameters by a different peptide hormone than ANP that also exerts if effects through the NPR-1 receptor.

We studied Empria obscurata, a nearctic sawfly on Isle Royale Wilderness National Park. We report a new host plant, Potentilla fruiticosa, and describe new details of morphology and development. The larva is remarkable because its transparency causes it to appear the color of the food it eats and to match its background. This may be adaptive as cryptic coloration. The larvae can eat both the flowers and leaves of their host plant. The larval stage is concurrent with the flowering season of P. fruiticosa. Larvae that eat flowers in addition to leaves end to grow slightly faster than larvae that eat only one or the other. Their transparency allows them to maintain crypsis while utilizing both food sources.

To determine the relative contribution of phylogeny and habitat on floral longevity, we studied the floral longevity of four species on Isle Royale National Park, MI. Floral longevity is a measure of how long each individual flower blooms. We compared floral longevity of four species in two phylogenetic lines and two different habitats. Sisyrinchium montanum and Iris versicolor are monocots in the Iridaceae family. Ledum groenlandicum and Moneses uniflora are eudicots in the Ericaceae family. On Isle Royale, the former species of each family lives on the rocky shoreline while the latter lives in a forested habitat. We used pollinator exclosures and controlled pollinations to determine the effect of pollination on the longevity of each species.

Both habitat and phylogeny appear to affect floral longevity. The Iridaceous species had a fixed lifespan, but both Ericaceous species had a variable longevity. Moneses uniflora showed a change in longevity due to pollination, and the longevity of Ledum groenlandicum varied depending on the position of the flower in the inflorescence. Species in the forest lived longer and had larger flowers than their rocky shoreline counterparts.

Although floral longevity varies among family and habitat, all the study species have similar breeding systems. Through pollen tube observations, we see a strong tendency toward the ability of these species to self-pollinate. This may be a consequence of island colonization, but it is also indicative of a more widespread trend for plants to have a secondary method of pollination.

Bird song is a learned behavior that is subject to evolutionary pressure through female selection and male-male competition. To compare the relative importance of cultural and genetic effects on the male house finches' songs it is necessary to develop a tool to measure genetic relatedness. This project focuses on developing polymorphic microsatellite markers as that tool. Three polymorphic microsatellites were found using developed in closely related species. However, at least six primers are required to collect statistically significant measures of relatedness. A separate protocol was developed to find new microsatellites using RAPD primer enhanced genomic libraries and biotin tagged microsatellite probes. Current evidence suggests that this protocol has successfully isolated microsatellite containing sequences; although the presence of microsatellites has not yet been confirmed through a sequencing reaction. Further research should focus on completing the protocol to isolate new microsatellites and finding at least three more polymorphic microsatellite markers in the house finch. Calculations of genetic relatedness, as performed here with the microsatellites developed to date, can then be combined with measurements of song relatedness. This will provide a powerful tool for researching the different effects of genetics and culture on house finch song.

The Streptomyces coelicolor organism is capable of surviving numerous environmental stresses. The organism employs 51 extra-cytoplasmic function (ECF) sigma factors in its defense against all kinds of osmotic, oxidative/reductive, temperature, pH and antibiotic stresses. In the present study, green fluorescent protein and XylE reporters were used to determine the stress that leads to the transcriptional activation of the ECF sigma factor, sigU. Data from the green fluorescent protein reporter indicate that incubating cells at pH 2 for one hour or incubation in 0.06% hydrogen peroxide for three hours both potentially lead to transcriptional activation of the sigU promoter.

I studied tadpole phenotypes in a natural population of the Chorus Frog, Pseudacris triseriata on Isle Royale, MI. These tadpoles occupy pools which vary in importance of mortality factors, the most important of which are dragonfly predation, crowding, wave wash and drying. Prior field experiments showed that the phenotype of these tadpoles is plastic and these shape changes enhance survivorship and growth. The purpose of this study is to test whether body shapes of the tadpoles vary according to these mortality factors, and whether phenotypic differences are causes by plasticity or selection under natural conditions. Observations of the patterns of shape upheld the experimental results that there are two distinctive phenotypes expressed by individuals and dragonfly and non-dragonfly pools. I found that tadpoles in the natural population differ as expected between dragonfly and non-dragonfly pools: compared to tadpoles in non-dragonfly pools, those in pools with dragonflies have higher tail fins, a more anterior location of fin attachment, more forward placement of the fin peak, and thicker tail muscle. However, the expression of these traits in a natural setting is temporally determined with a change in tail fin height, fin attachment location, and fin peak occurring prior to the study period. Late in development for individuals in dragonfly pools, it is apparent that the tail fin height reduces and the point of tail fin attachment is moving backward on the body. The muscle height does not show signs of diverging prior to the time period of this study and a reversion of the direction of shape change occurs for the fin peak with dragonfly pools initially having a forward location that, after this study, has a more posterior placement. No consistent differences in shape were correlated with pool location (a measure of risk to wave wash), pool size (a measure of desiccation), or density (a measure of crowding). A 7-10 d recapture experiment that traced a matched subset of the population, showed changes in shape were made by individuals, indicating a plastic response. Tadpoles in dragonfly pools developed higher fins, thicker muscles, and a more forward location of the attachment of the fin to the body. I found no differences in growth rate related to body shape in this group of tads. Therefore, in a natural setting, plasticity was not shown to convey a benefit in the overall fitness of individuals.

Estradiol administration has been shown to be neuroprotective with regard to the hippocampal damage resulting from transient global ischemia. While such ischemic events are associated with performance deficits on spatial learning and memory tasks, little is known about the behavioral consequences of pre-ischemic exposure to estradiol. Additionally, it is unclear whether estradiol‚s cellular protection is a direct antioxidant effect or requires the binding of estradiol to central estrogen receptors in the brain. The present study examines the neural and behavioral effects of transient global ischemia in male rats as well as the mechanism and degree to which estradiol administered prior to the ischemic event may protect against these consequences. In the first experiment, ischemic rats trained on the Morris Water Maze exhibited learning impairments relative to controls. In the second experiment, 54 male Sprague-Dawley rats were castrated at 35 days of age and implanted subcutaneously with a 10 mm silastic capsule containing either 25% 17â-estradiol in cholesterol, 25% 17á-estradiol in cholesterol, or cholesterol alone. Two weeks later, rats experienced either 10 minutes of transient global ischemia via 4-vessel occlusion or sham surgical procedures. One week following the ischemic or sham procedure, all rats were tested on the Morris Water Maze. On the first day of testing, each rat received 8 pretraining trials with a visible platform. On the following day, each rat received 12 trials in a different room with the platform hidden below the surface of the water. The latency to escape and the length of the swim path were recorded for each trial. One week following behavioral testing, plasma samples were collected for RIA assay of estradiol levels and the rats were perfused. All groups showed rapid acquisition of the visible platform task. When tested with the hidden platform, however, ischemic rats that were pretreated with cholesterol or 17á-estradiol performed significantly worse than all other groups. Pretreatment with 17â-estradiol prevented this impairment in performance indicating that estradiol neuroprotection is dependent upon estrogen receptor-mediated mechanisms. Ongoing histological analysis suggests corresponding protection of cellular death by 17â-estradiol pretreatment.

Time-series analysis was used to understand the factors controlling the natural dynamics of chorus frog (Pseudacris triseriata) populations on islands in Isle Royale National Park, MI. The populations possess a return tendency with stochasticity on three islands composed primarily of wave wash. The basic structure of the population dynamics is a damped equilibrium. The island populations are also synchronous, which implies a common climate-mediated factor affecting them. Conspicuous spikes appear to occur as part of a distinct rule change between regulation at low and high levels and are correlated to changes in the spatial patterns of occupied breeding habitat rather than to population increases within established habitat patches. This correlation implies that either population levels drive habitat-use patterns or that the availability of habitat regulates population levels. Two models were generated for future investigation: 1) the role of adult behavior and limits to dispersal in determining available habitat and governing chorus frog population dynamics and 2) the role of post-metamorphic survival in driving adult population dynamics. Both models constitute new directions that had not previously been considered important in chorus frog population dynamics.

Muscle fiber-type transition coincides with changes in energy utilization pathways. Metabolic gene expression precedes changes in contractile gene expression upon muscle transition. Considering this temporal relationship in gene expression, I hypothesized that changes in energetic pathways in muscle can influence alterations in contractile gene expression. I used both in vitro and in vivo techniques along with the drug WY-14,643 to test this hypothesis. WY-14,643 is a synthetic PPARα ligand that increases PDK4 expression which inhibits the pyruvate dehydrogenase complex, and causes the subsequent suppression of the glycolytic pathway leading to an increase in fatty acid oxidation. I used WY-14,643 to assess the effect of this shift in metabolism on the expression of fast and slow muscle genes. I transfected C2C12 cells with plasmids containing the promoters of fast and slow genes upstream to a luciferase reporter gene, and treated these cells with WY-14,643. I fed WY-14,643 to hindlimb suspended and nonsuspended rats for one week to compare changes in myosin heavy chain (MHC) in the slow soleus and fast EDL muscles, along with changes in muscle fiber-type expression in the heart. My transfection results demonstrate a possible increase in slow βMHC promoter activity due to WY-14,643 treatment. My experiment using the rat hindlimb suspension model did not lead to conclusive results about WY-14,643's effect on fiber-type gene expression of the rat hindlimb. However, I am able to report a possible increase in βMHC gene expression in the heart of WY-14,643 treated animals. These results support the possibility that metabolic pathways may influence the expression of contractile genes in ‘fast’ or ‘slow’ muscle.

There is much diversity in the mechanisms used to create segmented body plans. Within the polychaetes, the basal class of the annelids, the mechanism of segment formation is not well described. Segments can form sequentially from a posterior growth zone, or from the synchronous differentiation of the segmental precursor cells. This project traced the formation of segmental precursor cells in the polychaete Capitella capitata by staining for the ribosomal gene cp17, which is upregulated in rapidly diving cells including the segmental precursor cells. Capitella forms its segments in two phases. The rapidly dividing segmental precursor cells of each appear simultaneously and persist for a significant length of time. The first stage of segmental formation produces ventral-lateral bands of segmental precursor cells. The second stage, occurring in the stage 12 trochophore, produces stripes of segmental precursor cells which correspond to the precociously formed segments. The segmental precursor cells were produced before the segments are morphologically visible in the stage 13 trochophore. These data indicate that Capitella do not produce segments sequentially like most polychaetes, and may represent a novel variation on a basal mechanism of segmentation.

The avian song system is often used to study the neural correlates of vocal learning. The central motor pathway consists of several hierarchical, sequential, and essentially ipsilateral connections. Similarly, the motor nerve projections to the bipartite vocal organ, the syrinx, are ipsilateral as well. Furthermore, the syringeal muscles are bilaterally paired and each syringeal lumen contains a separate oscillatory source. Thus, though functionally identical the two halves of the avian song system are independent and act in parallel. This allows for lateralization within the song system; the right side of the song system is dominant in the control of acoustical features in zebra finch song. Although the precise location of the asymmetry (central v. peripheral) is unknown, recent research suggests that song is lateralized at the level of the syrinx. The bilateral tracheosyringeal nerve transection and regrowth experiments presented here support these findings, as the side of syringeal innervation strongly affected control of acoustical properties of song, whereas the side of the central source (CNS) did not. Independent of the side of CNS, subjects with innervation of the right side of the syrinx approached intact measures of entropy, continuity and pitch to a significantly greater extent than their counterparts with innervation of the left side. Although the specific mechanisms of peripheral lateralization are not well understood, these findings suggest that caution should be exercised in using the avian system as a model for vocal learning, a human hemispheric asymmetry.

Agrobacterium tumefaciens is an oncogenic plant pathogen that inserts a fragment of DNA into the plant host cell. This DNA encodes proteins responsible for the production of plant growth hormones and a food source for the bacteria. Wounded plant cells release sugars and phenolic compounds such as acetosyringone (AS), which cause the bacterium to express a set of virulence (vir) genes. The Vir proteins are encoded on the Ti (tumor inducing) plasmid and are responsible for mobilizing the transferred DNA (T-DNA). Bacterial genes are organized into functional groups called operons, and a single promoter controls each operon. The virB operon encodes proteins that constitute a conserved extracellular transport apparatus called a Type IV Secretion System (T4SS). Previous work has shown that a secondary, internal promoter sequence exists within the virB operon, between virB6 and virB7. Susan Levin '02 proved that the internal promoter is capable of promoting transcription from a promoterless lacZ plasmid construct (Levin 2001). In this study, we have shown that a protein similar to the bacterial repressor Ros may regulate the internal promoter, and that the promoter and genes involved in attachment to host cells may compete for regulatory factors. We theorize that transcription from the internal promoter is sensitive to the accumulation of an unidentified virulence factor, possibly the T-DNA itself. It may also only specifically control the transcription of virB8, which nucleates assembly of the other VirBs.

Ceramides, present in cell membranes, are lipids bearing a primary amine on the C-2 carbon. Some of their functions include regulating cell membrane integrity and involvement in cell-cell recognition, intercellular signaling, and signal transduction pathways. Ceramides are also the central molecule in sphingolipid structure and metabolism, and so, are derivatives of long chain bases with a fatty acid (of variable length) bound to the C-2 amine. They can be characterized into two main classes – nonhydroxy and hydroxy ceramides. Previous studies indicate the possibility of ceramides/sphingolipids being mediators of apoptosis – programmed cell death. The goal of this thesis was to develop an experimental method that could be utilized to answer the following question: Do ceramides play a role in the initial signal transduction pathway that leads to apoptosis? Hence, the goal involved the development of an analytical tool that will be used to identify, quantify and track sphingolipid concentrations in cells. The proposed steps for analysis and quantification are: (1) Extraction of sphingolipids / ceramides; (2) Reduction of ceramides to ceramines; (3) Labeling of ceramine by derivatization; and (4) Quantification by fluorescence analysis. Reduction of the ceramides, even as low as the 1 mg scale, was demonstrated and was confirmed by spectroscopic analyses. In addition, the corresponding ceramines were shown to undergo FMOC-Cl labeling to give FMOC derivatives that were then analyzed by RPHPLC with a fluorescence detector. Only limited and tentative assignments for the FMOC-derivatized ceramines have been made; thus analysis via HPLC still requires further investigation.

Hay-scented fern (Dennstaedtia punctilobula) is a local plant species native to the Northeast and found in Hopkins Forest. The mechanism by which this plant species out competes others in the forest has been examined in the chemistry lab of Professor David Richardson and the biology lab of Professor Hank Art. The work in these two labs has been aimed at demonstrating that hay-scented fern achieves competitive advantage through the release of allelochemicals. Previous research had culminated in the discovery by Jude Dumfeh and Nisha David that certain fractions of the hay-scented fern crude extract showed strong growth inhibition activity in lettuce seed germination/growth bioassays. Attempts to recreate the activity in the field had been unsuccessful prior this year.

A new approach was taken this year to reproduce the activity observed in lab. Soil samples were collected from Hopkins Forest, from within a hay-scented fern patch, from the boundary of the fern patch, and from outside the fern patch. Seedling growth and germination for broccoli, lettuce, and radish seeds in the different samples was recorded for 16 days. The compiled data supported our qualitative observations and indicated that there was significant activity occurring in the soil samples collected from within and on the boundary of the fern patch. These data indicate, for the first time, that the soil in which hay-scented fern grows is allelopathic, strongly supporting the hypothesis that this plant employs allelochemicals to gain an advantage. TLC analysis revealed certain saccharide compounds present in the active soil were also present in a particular active fraction of the crude fern extract. Detailed spectroscopic analysis of these compounds led to the determination of their identity, but the findings did not reveal conclusive answers about the allelopathic mechanism responsible for hay-scented fern dominance in the field.

The family of 4,4’ and 5,5’ disubstituted 2,2’ bipyridine ligands and platinum complexes, which were previously synthesized, have been shown to exhibit columnar liquid crystalline mesophases, and it has recently been shown by fluorescence that there are likely metal-metal interactions between the metal centers of these stacks of columns. We began to test possible methods for doping these platinum-bipyridine complexes, including chemical oxidation by the addition of an oxidizer such as bromine or iodine and a novel approach to doping involving the addition of the cobalt-bipyridine analogue as a way to remove electrons from the platinum-bipyridine system. The chemical oxidation looks very promising, as an immediate color change was seen upon oxidation, and the crystals that formed are needle-like, which is indicative of chains of the platinum complex.

Work was also begun on another type of ligand en route to an additional set of metallomesogens. The synthetic path for the preparation of the Schiff-base ligands was determined, and the C2 and C12 length versions have been successfully synthesized. With an understanding of what the ligands’ NMR’s should look like, nickel and palladium were coordinated to the C2 Schiff-base ligand. Both because color changes were observed and because there were shifts in these complexes’ NMR’s, the synthesis of these complexes looks promising. These ligands, when complexed to platinum and cobalt, will be useful for future doping studies.

We record the fundamental and lower overtones of the C-H stretching transition in pentafluoroethane and the two tetrafluoroethanes with Fourier transform infrared spectroscopy and long pathlength absorption spectroscopy. The 5th overtone of these three hydrofluoroethanes and of the hexafluoropropanes we record with cavity ringdown spectroscopy. We compare experimental oscillator strengths (absolute intensities) with calculated values from a B3LYP/6-311++G(2d,2p) density functional calculation. The three hydrofluoroethanes agree with the predicted order-of-magnitude decrease for each successive overtone, although theory increasingly over-predicts intensities at higher overtones, especially for the tetrafluoroethanes.

The spectra of the hydrofluoroethanes studied show Fermi-resonant coupling between the C-H stretching mode and the C-H bending modes. No significant evidence of coupling between the two stretching modes in the tetrafluoroethanes is found at overtone levels. The complexity of the spectra at low overtones and the over-predicted intensity at high overtones suggest that other modes, such as C-C stretches, play a role in the vibrational dynamics of these molecules.

We fit our data to local-mode, Fermi-resonance potentials of varying complexity. Including only one bending mode gives us superior fits, and we report a Fermi-resonance parameter of 91.9 cm–1 for 1,1,1,2-tetrafluoroethane and of 57.2 cm–1 for 1,1,2,2-tetrafluoroethane. Our analysis suggests that the bends in the two C-H bonds may be significantly coupled, and a mixed-basis approach may prove more successful. From our model fitting, we report values of 3081.2(2.9) cm-1, 3090.2 (10.3) cm-1, and 3078.7(12.5) cm-1, for ω, and 56.814(0.458) cm-1, 59.59(1.65) cm-1, and 56.53(2.01) cm-1, for ωx of 1,1,1,2-tetrafluoroethane, 1,1,2,2-tetrafluoroethane, and pentafluoroethane, respectively.

Bacillus Subtilis is fairly unique in that cells are able to undergo genetic competence followed by sporulation when survival is threatened. Cells that become competent develop a complex DNA binding and uptake machinery which allows exogenous DNA to be assimilated and integrated into the genome. The resulting genetic variation increases the survivability of spores. In the laboratory, competence is triggered by nutritional limitation and high cell density. The transcription factor ComK controls the expression of well over a hundred competence genes including the recA gene. The ComK mediated activation of the recA gene is the focus of these studies as this gene plays a pivotal role in the competence program, enabling recombination of assimilated DNA. Previous studies showed that Comk was able to activate the recA gene without displacement of its repressor, LexA. Furthermore, LexA has been found to bind the recA promoter upstream of its usual binding site on other SOS genes, in a region that overlaps with the binding site for the alpha subunit of RNA polymerase, which transcribes genes. Based on this information a model has been proposed in which LexA blocks the alpha subunit access to its binding site on the recA promoter. Within this model, ComK activates the recA gene by either providing novel or strengthened binding sites for the alpha subunit on the recA promoter, or enables alpha to physically displace LexA, thus allowing transcription to occur. To test this model, the interactions of the alpha subunit of B. subtilis RNA polymerase with the recA promoter were characterized. The previously cloned rpoA gene was induced to produce alpha in BL21 (DE3) gold cells, the alpha subunit purified and its binding to the recA promoter analyzed using mobility shift assays. The size of the subunit was found to be ~38 kDa. Alpha was found to bind the recA promoter in the absence of the rest of the RNA polymerase subunits. A binding constant of 95.5 nM for the recA promoter was measured, showing an affinity that suggests specific binding. Furthermore, two binding sites for alpha were observed on the recA promoter.

Hennoxazole A demands attention from synthetic and medicinal chemists. This compound shows potential as a therapeutic agent for Herpes Simplex I, and as a peripheral anesthetic. It also provides a case study for synthesis of bisoxazole-containing marine natural products. A number of bioactive marine natural products incorporate a bisoxazole unit into their structures. In particular, all of the hennoxazoles contain a skipped triene side-chain, a tetrahydropyran derivative, a 2,4-linked bisoxazole core, and five stereogenic centers.

Described herein are efforts toward the asymmetric total synthesis of hennoxazole A. Three very powerful reactions suggest the promise of this general synthetic plan. Employing a chiral auxiliary, a single aldol-type reaction directly and diastereoselectively converts an acetal to an ether. A later aldol reaction attempts to overcome the intrinsic 1,3-anti selectivity through use of a chiral auxiliary, to diastereoselectively produce an alcohol with a 1,3-syn relationship. After this reaction, a malonate addition displaces the chiral auxiliary, while adding the ester functionality required for further elaboration.

Two analogs of benzocanthinone, 9H-indolo[3,2,1-de]phenanthridin-9-one and 9H-benzo[c]indolo[3,2,1-de][2,6]naphthyridin-9-one, were prepared in two and four steps, respectively. The key step in both syntheses was an intramolecular radical cyclization of an aryl halide. The present work established the preferred halo substituent and its location in the key intermediate. It is believed that this methodology will prove to be applicable to the formation of isomers of benzocanthinone, an antibacterial agent derived from natural sources.

Since Java exploded on the scene in 1996, there have been numerous proposed language extensions that add generic types to the language. These approaches have suffered either from the same code bloat Found in C++’s template system or from run time overhead in incurred by excess type casts and bridge method calls. In the latter case, the superfluous casts and method calls exist to appease the Java bytecode verifier.

We will consider a language extension, LOOJ, developed a Williams by Kim Bruce and his past thesis students that adds generics as well as the notions of This Type and exact types to the Java Programming Language. Using information stored in “comments” in the Java class files, we will describe a smart bytecode verifier that allows safe execution of Java bytecode containing generic types and without excess type casts or bridge methods.

Most memory access has two important properties: temporal locality and spatial locality. We take advantage of these qualities through use of multiple levels of caches to bridge the gap between processor speed and main memory access speed. But what happens when these assumptions do not hold true: specifically, when memory accesses do not have temporal locality? In this talk we will examine read-once data accesses, or memory access without temporal locality.

Examples of this type of access include socket and other network message passing, and display of multimedia files. We will investigate how these accesses patterns affect performance using Current caches, and what improvements may be made to the hardware to account for of the lack of temporal locality in the data.

Recent work in the field of global visibility has focused on efficient storage and representation of visibility events. Many of the data structures currently in use rely on the determination of non-occluded lines tangent to four objects in the scene. However, little is known regarding the expected number and characterizations of these “quad-tangents” in arbitrary graphics scenes. This talk will introduce a reliable and robust method for determination of quad-tangents, and present a few of the more interesting subtopics explored along the way.

Real-world software has to be flexible. Users demand new features, platform requirements change, our understanding evolves. We can plan for change with better design, but there are usually some cases we miss. Do we have to kiss our design goodbye in these cases, or can we transform it into a more suitable design? This talk introduces refactoring, a technique for improving the design of existing code, along with Aspect-Oriented programming, a promising extension of the Object-Oriented approach.

Geographic Information Systems (GIS) provide an effective method for calculating minimum, long-term erosion rates in the Tertiary fill basins of the southern Rocky Mountains and adjacent High Plains. Basins that formed initially during the Laramide orogeny (70 to 50 Ma) filled with sediment by Oligocene time and experienced periods of erosion and deposition through the Miocene before erosion dominated in Late Cenozoic times. Erosion and incision were driven by base-level fall resulting from uplift from the Rio Grande Rift and concomitant climate change. Material stripped from Colorado and Wyoming was deposited in western Nebraska, forming the “gangplank” of the Cheyenne Tablelands. Better understanding of basin histories in the greater Colorado area will help clarify timing of erosional and depositional events and shed light on the erosional history of the southern Rockies.

A digital paleosurface, an approximation of the original depositional surface, can be created using the geologic and geomorphic features of preserved basin fill remnants, the Eocene erosion surface and volcanic rocks. Elevations of geologic and geomorphic features record the minimum elevation of depositional surfaces and were compared to digital topography (DEMs) to determine volume of material that has been eroded from the basins. Paleosurface models generated using spline, local polynomial interpolation and inverse distance weighted interpolations showed little variance in the resulting calculated erosion rates. Although this GIS technique is relatively untested, models using paleosurfaces for Nebraska, an area of simple geology and structure, give reasonable calculated erosion rates. This gives me confidence applying the method to the more complicated north-central Colorado basins.

My calculations of long-term erosion rates range from ~20 m/m.y. in western Nebraska to ~34 m/m.y. in north-central Colorado’s North Park and Middle Park basin, similar to minimum rates calculated by other researchers in the southern Rocky Mountains. The choice of paleosurface model adds little uncertainty to calculated erosion rates, future work should concentrate on refining the geologic and geomorphic-based elevation data and remove uncertainties produced by late Cenozoic deformation. My model values for long-term erosion of north-central Colorado basins are minimums.

Eight lake sediment cores were taken from three sites in western Ireland. The sediment in the cores had been deposited in the lake from the end of the last glaciation through the recent Holocene. While the cores consisted mostly of biogenically precipitated marl (calcium carbonate), most also contained a section of clay (up to 20 cm thick). This clay has been interpreted to represent the abrupt Younger Dryas (YD) cold event, which lasted from about 11,000 to 10,000 14C yr B.P. Strong evidence for the YD cooling from pollen, stable isotopes, and faunal counts has been found in lake and deep-ocean sediment cores and ice cores throughout the North Atlantic region; because of Ireland’s location in the North Atlantic, its climate was expected to have been significantly impacted by the YD.

In this project, high-resolution (1 sample/1-2 cm) analyses of major and trace elements were performed on samples from a section of core containing the clay interval to determine if the clay does represent the YD and to look for other potential climate-related variations. The sampled core (LINC-1) was extracted from the banks of Lough Inchiquin, near the town of Corrofin, Co. Clare, Ireland. It was selected over the other cores because it was the only one containing the entire clay interval, and geochemical analyses were therefore expected to reflect the change in mineralogy associated with the transition into and out of the clay. On each sample, six major elements (Ca, Fe, Mg, Mn, K, and Na) and two trace elements (Cu and Sr) were analyzed on an Inductively-Coupled Plasma Atomic-Emission spectrophotometer (ICP-AES) and an Atomic Absorption spectrometer (AA). All eight elements showed variation related to the change in core lithology: carbonate-enriched elements (Ca and Sr) decreased during the clay interval and clay-enriched elements (Fe, Mg, Mn, K, Na, and Cu) all increased. Individual elements showed other trends over the clay interval, as well. For example, Fe and Mg concentrations were highly variable, which may have been related to their occasional substitution (when temperatures were moderately cold) for calcium in calcite. Magnesium input may have also been affected by changes in groundwater saturation with respect to dolomite (more dolomite would have resulted in more Mg in subsurface waters entering the lake). In addition, manganese and sodium both increased during the clay in the ICP-AES (full digest) results, but not in the AA (partial digest) results. This was probably due to the incomplete digestion of the samples in the AA preparation, and therefore also reflects a change from insoluble clay deposition to soluble carbonate deposition over this interval.

Element variations unrelated to the clay were also found within the sampled interval. The pre-YD oscillation (PRYO) may correspond to the well-documented Killarney Oscillation (KO), based on local sedimentation rates and established dates for the KO, and the post-YD oscillation (POYO) may represent the Preboreal Oscillation. These two variations also appear in the stable isotope results from the LINC-1 core, indicating that major and trace element geochemistry may be capable of showing climate change. Thus other variations with similar geochemical signatures may also represent climate variations. This indicates that the clay interval probably does represent the YD cold event, and that smaller variations within the clay may reflect climate changes during the YD.

The burial and exhumation history of saprolite in the modern Front Range can help us better understand how modern weathering processes and measured short-term erosion rates may apply to long-term landscape evolution. The geomorphology of the Front Range near Nederland, Colorado has evolved since erosion of the Laramide orogen began in early Cenozoic time. West of Nederland, Colorado, the Front Range has been sculpted by glacial and periglacial processes over the last 106 years; glaciers disappeared at the end of the Pinedale glaciation at about 12 ka. East of the glaciated area, gently rolling uplands underlain by saprolite and steep, narrow inner canyon areas expose bedrock and thin surficial deposits that reflect the influence of weathering, slope and fluvial processes. I used field mapping of roadcuts and a compilation of well logs for the greater Nederland area to determine the extent and thickness of deeply weathered material in the gently rolling uplands in the area. Geographic Information Systems (GIS) analyses were then used to analyze the distribution and depth of weathered and alluvial material.

Patterns of saprolite thickness are defined primarily by Bull Lake and Pinedale glacial limits. Deep weathered material is widespread in adjacent non-glaciated areas, and can be found preserved on topographic highs above the areas scoured by Pleistocene valley glaciers. Valley glaciers eroded deep saprolite, but an average of 5 m of weathered material remains in glaciated valleys today. Alluvial deposits thicker than 3 m are scarce in my study area; most deep deposits are located within glacial limits to the west and southwest of Nederland.

Saprolite is thought to form slowly in climates as dry (~50 to 120 cm/yr precipitation) as those of the modern Front Range. Where saprolite forms, it requires ≥100,000 years for 1 m of fresh bedrock to become completely grussified. Thick mantles of saprolite preserved near Nederland may have been buried soon after formation, possibly in late Eocene time, and exhumed in late Cenozoic time. Miocene fill material on Winiger Ridge to the southeast of Nederland preserves a paleovalley that incised material stratigraphically higher than the saprolite of my study area. These geologic relations suggest burial of an Eocene surface in this section of the Front Range. Assuming that 40 m of weathered material lay beneath the Eocene surface, most saprolite has been stripped to leave the present landscape with a mean saprolite cover of 5 to 6 meters. Cosmogenic nuclides suggest that weathered Precambrian bedrock of the Colorado Front Range is eroding at a rate of 18-30 m/m.y. Using a mean saprolite depth of 5 m for the study area, erosion at this rate would remove most of the weathered material from the modern landscape in about 250 k.y. Extrapolating this rate back in time suggests that exposure occurred at ~ 2 to 3 Ma, approximately the same time as the first continental-scale glaciation of North America.

Removal of the weathered material from the Front Range landscape could have both local and global implications. Locally, removal of weathered material is critical for how relief continues to evolve in the Front Range west of Boulder. On a broader spatial scale, widespread exposure of fresh bedrock may enhance chemical weathering, which Molnar and England (1991) believe can lead to atmospheric drawdown of CO2 and subsequent global cooling.

Monadnocks are geologic phenomena that stand up above the surrounding peneplain because the material around them has been eroded away. At several locations around the globe and across time, monadnocks have been interpreted as paleoislands. A cluster of five monadnocks is located at the western terminus of Varangerfjord outside of Karlebotn, East Finnmark, Norway at 70º 8’ N, 28º 35’ E. These monadnocks and the surrounding deposits were studied in detail to determine the depositional environment and the possibility of a paleoisland interpretation. The monadnocks are composed of gneiss of granitic and tonalitic composition that dates from ~1800-3000 Ma. They are surrounded by 570-580 Ma quartzite of the Smallfjord Formation, and show a present topographic relief of between 4-22 m.

There is a 100-m thick exposure of the Smallfjord Formation at Oaibaccanjarga, 3.2 km east of the monadnocks. A detailed stratigraphic column was constructed at this locality. Its base is composed of a diamictite deposit that has been interpreted as a glacially deposited and reworked till. It sits unconformably on a striated quartzite pavement belonging to the Veidnesbotn Formation. The diamictite was left behind as a glacier retreated to the southeast. Glacial advance and retreat carved out a paleovalley that was subsequently filled by water and sediment in a transgressive valley fill sequence. The deposits sitting on the diamictite are composed of medium-grained quartzite with shale laminations that occasionally show soft-sediment deformation. The majority of the section is composed of medium-bedded quartzite that is often massive, but occasionally shows lenticular structures and ripple-like bedding. The deposits are characteristic of a shallow marine environment.

Previous workers have found evidence of currents from the east and southeast, which correspond to local delta front deposits that indicate flow from the same direction. This study has located paleocurrent indicators that show that there is also a history of currents running to the northeast in the sediment around the monadnocks. These currents were generated by tidal action through inlets that developed in a barrier bar system at the mouth of an estuary. The fluvial currents from the east and southeast, and the tidal currents from the southwest converged in the relative calm of the central basin within the estuary that developed in the paleovalley.

The monadnocks were located in the central basin. One of the monadnocks provided significant facies data. Nine conglomerate grids and 11 thin sections were analyzed to reveal two distinct facies on the monadnock. The southwestern edge is composed of fine-grained, quartz-dominated deposits, while the northeastern side is dominated by coarse-grained conglomerate that is higher in feldspar and mica content due to addition of minerals from the gneiss as it eroded. The original source for the conglomerate was glacially deposited material, left behind by glacial retreat. This was slumped off the monadnock and was reworked and carried away by the tidal currents on the southwestern side, while the northeastern deposits remained relatively undisturbed, being sheltered from waves and currents.

The monadnocks, located in the Varanger estuary were part of a larger global system. East Finnmark, Norway was part of the continent of Baltica, which was located between 30 and 40º S latitude during the Late Precambrian, but was oriented as it is today. At this orientation and latitude, the mouth of the Varanger estuary would have been exposed to the westerlies contributing to the development of a barrier bar system and the creation of an estuary environment. The integration of local environments, such as the monadnocks and their surrounding microenvironments, are part of understanding the larger systems at work on the planet during different periods in geologic time.

New geochronological data indicate the presence of Middle Proterozoic and Silurian felsic igneous rocks in the Berkshire massif. Ratcliffe (1984a, 1984b, 1985) mapped tabular, discontinuous bodies of alaskite and granite in the Berkshire massif, and he interpreted them as syn-tectonic anatectic melts that intruded Taconic thrust faults. There is great compositional diversity within the alaskite (from granite to trondhjemite), but the granite, here called the granite of Beckett Quarry, has a limited range of composition. Both the alaskite and granite of Beckett Quarry were derived from partial melting of basement gneisses, giving each an inherited volcanic arc geochemical character. The alaskite sills were derived from different sources with different degrees of partial melting and different degrees of melt segregation while the granite of Beckett Quarry was probably derived from a single source rock.

The alaskite sills are commonly found in the Middle Proterozoic Tyringham Gneiss. Eight 206Pb/238U SHRIMP analyses on cores of the Tyringham Gneiss yield a weighted average age of 1179 ± 9 Ma, and nine 206Pb/238U SHRIMP analyses of rims give a weighted average age of 1004 ± 9 Ma. The core ages represent crystallization of the Tyringham Gneiss whereas the rim ages record a high-grade metamorphic event coeval with anatexis. Zircons from three alaskite samples have xenocrystic cores with 206Pb/238U ages ranging from 1050 to 1200 Ma. Oscillatory zoned rims and oscillatory zoned grains without cores yield 206Pb/238U weighted average ages of 997 ± 10 Ma and 1004 ± 19 Ma and yield a 207Pb/206Pb weighted average age of 1003 ± 8 Ma, which are interpreted to be the crystallization age of the alaskite.

The granite of Beckett quarry also has inherited cores with 206Pb/238U ages ranging from 950-1250 Ma. Spot analyses on zircons with oscillatory zoned cores and on oscillatory zoned rims surrounding xenocrystic cores yield 206Pb/238U ages of 434 ± 5 Ma and 433 ± 3 Ma, which are interpreted as the crystallization age of the granite.

The alaskite sills formed during the waning stages of the Ottawan orogeny or during the newly proposed Rigolet phase (Rivers, 1997), and the granite of Beckett Quarry formed after the Taconic orogeny. The new age data indicate that the alaskite sills and granite of Beckett Quarry could not have intruded Taconic thrust faults during deformation. The alaskite sills may have intruded Middle Proterozoic fault zones or the fault interpretation may be incorrect. The granite of Beckett Quarry intruded Silurian faults on the east flank of the Berkshire massif, which are coeval with the extensional formation of the Connecticut Valley trough.

Garnets in Late Proterozoic to Devonian pelitic and mafic schist provide thermobarometric evidence for decompression in the core of the Chester dome of southeastern Vermont. Decompression was concentrated within and below the high strain zone, a zone of intense shearing and deformation located in Late Proterozoic to Ordovician metamorphic rocks that form an elongate ring around the core of the dome. Decompression is proposed to have taken place during low-angle normal faulting and extension along the high strain zone. The high strain zone is also characterized by extreme attenuation of lithological units; the rocks within it are substantially thinner than their stratigraphic equivalents elsewhere in Vermont. Up to 4.0 kbar of decompression are documented in sample RTD12A, a sample from Townshend Dam, located within the high strain zone on the southwestern flank of the dome. Decompression occurred during a 70ºC temperature increase and a subsequent 60ºC temperature decrease. At the southern tip of the dome, below the high strain zone, Sample 2745A records up to 2.4 kbar of decompression during a 10-75ºC temperature increase. In contrast, samples 3039A and 3041D, located along the eastern flank of the dome above the high strain zone, document isobaric to slightly increasing pressures during a 55-165ºC temperature increase. Rocks above the high strain zone record a different metamorphic history from those below and within it.

Monazite ages from two samples from Townshend Dam (384 ± 5 Ma and 380 ± 3 Ma) suggest that extension occurred at ca. 380 Ma. Monazite from sample 2739P, structurally below the high strain zone, has a bimodal age population with peaks at 380 and 350 Ma. This is interpreted as documenting two metamorphic events and confirms the 380 Ma age of extension within the high strain zone. The age of decompressional deformation is further supported by monazite dated at 384 ± 5 Ma located in a sample whose silicate mineral chemistry documents decompression. The occurrence of both monazite age data and thermobarometric data in the sample suggests that they document the same deformational event. Thus, it is proposed that the high strain zone reflects Acadian extension rather than Taconic thrusting.

There is evidence that a meteorite impacted the earth in the modern-day Catskill Mountains sometime between the Late Silurian and Late Devonian Periods (Isachsen et al., 1994). This interpretation of the anomalous circular structure at Panther Mountain sparked the initial interest for this study. Marker beds within the Manlius Formation, historically placed in the Lower Devonian Period, were studied in an effort to determine their origin. After initial investigations, the waterlime at Thacher State Park and Cedar Park Cemetery in Hudson, the marker bed in Cherry Valley and the Clark Reservation Member (CRM) in Jamesville became the focus of the study.

With stratigraphic columns and investigations of polished slabs from these marker beds, fining upwards material, escape burrows, swaley beds and liquefaction structures were found as partial evidence indicating event deposition. Through thin section analysis, spherical micritic thingies (SMTs) were found that were distinctly different from nearby ooids, but contained similarities to accretionary lapilli and dolomite spherules found in known impact-related material around the world. The element compositions of the samples, obtained using Inductively Coupled Plasma (ICP) spectroscopy and Instrumental Neutron Activation Analysis (INAA), showed trace element anomalies, indicating that the marker beds from Cherry Valley to the east were distinctly different from average carbonate as well as from the CRM in Jamesville.

Though much research is still needed to confidently make any conclusions, the marker beds were determined to be event deposits, the origin of which is still unknown. The beds from Cherry Valley to the east vary greatly from average carbonate and are more likely than the CRM to be of impact origin.

Few examples of ultramafic magmas younger than the Archean exist in the rock record, but a highly unusual thin sill-like body of ultramafic rock, the only such occurrence known in the southern Front Range, occurs within the Early Proterozoic rocks in the Badger Flats region of south-central Colorado. The host sequence is dominated by metamorphosed pelitic schists interlayered with amphibolites, which are mostly metabasalts.

This is a study of the ultramafic rock and the nearby ortho-amphibolites. Petrographically the amphibolites are mostly granoblastic and are composed of plagioclase and hornblende. The ultramafic samples contain primary olivine, orthopyroxene, and spinel, along with two distinct types of metamorphic amphibole: an orthoamphibole close to anthophyllite and a clinoamphibole that is a magnesio-hornblende. The hornblende forms large (>1 cm) oikocrysts in some samples, making the rock distinctly coarse-grained in hand specimen.

Geochemically the amphibolites are tholeiitic metabasalts, and the ultramafic rock is a peridotite. The peridotite is low in SiO2 (41-44 wt%) but high in MgO (19-25 wt%), Cr (800-1600 ppm), and Ni (400-1100 ppm), with a Mg # averaging 65. The geochemistry of the peridotite is close to that of Early Proterozoic metamorphosed ultramafic volcanic rocks near Mt. Ouray, 80 km to the southwest, which have been called komatiites and komatiitic basalts (Boardman, in preparation). However, since the peridotites of Badger Flats appear to be intrusive, they cannot be termed komatiites.

The major regional metamorphic event in the Badger Flats region occurred at around 1,700 Ma and was concurrent with emplacement of Boulder Creek granitic plutons. Metamorphic conditions are well constrained by mineral assemblages in the ultramafic rocks and adjacent metasedimentary layers. Metamorphic temperatures reached a peak of 650 to 750ºC and pressures were between 3.5 to 6.5 kbar, consistent with metamorphic conditions generally found in the southern Front Range.

The peridotite and the amphibolites predate regional metamorphism, but they need not have formed at the same time. However, they may have formed in related environments. The metabasalts are interpreted as products of a primitive arc setting, matching results from previous studies of metavolcanic rocks in the area. The peridotite may have formed from a higher degree of partial melting of the mantle in an extensional area behind a volcanic arc (back-arc basin). It could even represent a feeder to overlying ultramafic flows (komatiites) that have subsequently been eroded.

Because ultramafic outcrops can only be brought to the surface of the Earth’s crust in a limited number of ways, this unique unit provides valuable information regarding the geologic and tectonic history of the Badger Flats region.

This paper presents results from a set of parameter optimizations on a simple model of the terrestrial carbon cycle using ten years of hourly CO2 flux data collected from a tower in Harvard Forest. The results were not sensitive to changes in the starting point of the optimization or to the step sizes used to search the parameter space, but that they did depend on whether or not the model’s output was compared with gap-filled as well as measured data. The research demonstrates (1) how parameter optimization can be used to determine correlations between the model’s parameters, and (2) how the parameter optimization can be used to test the importance of different aspects of the model’s structure.

Sediment Core 0203 from Sharpeye Swamp, Darke County, Ohio contains a sedimentologic shift from laminated to bioturbated sediment at 470 cm depth corresponding with increases in Sr, Ca, Sr/Ca, and organic content and with decreases in Mn, magnetic susceptibility, grain size, and carbonate content. Mg and Fe concentrations do not shift at this interval. The transition observed through multiple proxies indicates a change in the fractions of sediment entering the basin resulting from ice sheet retreat. The core is believed to consist of sediment aged 17,900-13,800 14C yrs BP and the transition at 470 cm depth to occur ~15,400 (+690 / -736) 14C yrs BP.

Sedimentologic and geochemical data, which show evidence of one ice sheet retreat, support the theory that the southern margin of the Laurentide Ice Sheet advanced through Ohio 22,000 BP, reached its maximum extent at 17,000 14C yrs BP, and remained there until retreating around 15,000 14C yrs BP. None of the nine Keck 2002 cores from western and eastern Ohio shows evidence of the Erie Interstade, a proposed large-scale ice sheet retreat from Ohio ~16,500-15,000 14C yrs BP, indicating that further research is necessary to address the discrepancy between recent findings and decades of research in a variety of geologic disciplines that indicates the presence of such an interstade.

Using triangle sequences, a multi-dimensional continued fraction algorithm, this paper develops a higher-dimensional version of the Pell Equation. The set of solutions to this Pell-Analog has the same structure as the solution set to the original Pell Equation. Further, this paper explores the connection both Pells share with the units of particular fields.

In this paper, we prove the following characterization of the completion of a domain with given generic formal fiber: Let (T,M) be a complete local ring, G ⊂ SpecT such that G is nonempty and the number of maximal elements in G is finite. Then there exists a local domain A such that the completion of A is T and the generic formal fiber of A is exactly G if and only if T is a field (and G = {(0)}) or the following conditions hold:

From this theorem and its proof, we will also derive some more specific theorems, including a characterization of completions of excellent domains with semi-local generic formal fiber in the characteristic zero case.

Tight closure is one of the most active areas in current algebra research. It is conjectured that tight closure and completion will commute for excellent rings, finally providing ring theorists with a sufficiently strong condition to study the relationship between a ring and its completion. I constructed two local rings, a unique factorization domain and an "almost excellent" domain (all fibers are geometrically regular except the generic one), for which tight closure and completion do not commute.

This thesis briefly reviews basic concepts of statistical mechanics. A detailed exposition of the Farey Number-Theoretical Chain (FNTC) model is provided. Critical phenomenon of this statistical-mechanic model is further discussed. The Knauf Number-Theoretical Chain (KNTC) model is revisited, and an elegant new proof of exact phase transition location is provided.

A couple of new two-dimensional number sequence models that assume Knauf-like, denominator interactions are proposed. The first one is based on a triangle sequence introduced by Von Rudolf Monkemeyer and D. Grabiner. The existence of the model's phase transition is verified.

To construct the remaining models, a couple of new continued fraction Re2 algorithm-generalizations are proposed, and their properties analyzed. The existence of respective phase transitions is proved.

Every real number α has a continued fraction expansion which can be developed in several ways. We will examine some of the properties of continued fractions in order to work on generalizing them. Contained in Sections 1, and 3, this work is well known. An introduction to the Geometry of Numbers developed by Minkowski can be found in [4], while a slightly different, but still geometric approach to continued fractions is presented in [5]. Section 2 is also an introduction to well-known background material. Continued fractions are closely tied to distinguishing quadratic irrationals and determining properties of the algebraic fields that they determine. The generalized continued fractions we develop and investigate will follow the approach of Minkowski by using convex bodies in R3, namely parallelepipeds, to approximate certain vectors and planes. These methods will resemble the geometric development of continued fractions from Section 3, and we will demonstrate that some of the results from continued fractions generalize as a result of this method. Two approaches will be given: the first, contained in Section 4, is not original; the same approach is contained in [2] under the title A Criterion for Algebraic Numbers. The second generalization, in Section 5, is original in the choice of parallelepipeds, but employs methods from The Theory of Continued Fractions in [2]. We will also examine the connection between the two generalizations.

It is conjectured that the meridian length for any alternating knot complement is bounded above by 2, though the best known upper bound approaches 3 for high crossing knots. We show that the bound of 2 is held for ``almost all" alternating knots, and indeed almost all alternating links as well. Moreover, we show that any knot complement, and indeed any link complement, can be realized as Dehn surgery on a special type of link with meridian length exactly 2.

When eukaryotic genes are edited by the spliceosome, the first step in intron recognition is the binding of a U1 snRNA with the 5’ (donor) splice site. To identify splice sites, we model this interaction physically. Our thermodynamic model is applied to a set of 65 annotated genes, with 338 splice sites and 16961 other false potential sites. A significant separation of true and false splice sites is achieved, demonstrating the potential of physical modeling as an approach to the problem of gene finding.

The discrete Wigner function provides an alternative to the Schrodinger wave function for describing discrete quantum systems. While the discrete Wigner function has many potential applications in areas of physics such as quantum computation and truncated quantum optics, many of the basic properties of this function remain to be discovered. This thesis pursues the formalism for the discrete Wigner function originally developed by Wootters [18], in which a system with a prime N number of orthogonal states is described on an N x N array of points. We extend this formalism to systems where N can be a power of a prime, and have pursued the question as to how one determines the number of truly distinct ways of defining a Wigner function for a given N. We have answered this question for the N = 2, N = 3, and N = 4 cases, and have made progress on the N = 5 case. Our methods remain to be extended to further values of N.

We present progress towards the first direct measurements of the isotope shift, Stark shift and Stark induced amplitudes in the 6P1/2  6P3/2 transition in thallium. The weak nature of this “forbidden” M1 and E2 transition requires a new RF detection technique called “two-tone” spectroscopy, which we describe here. Using a vapor cell, we demonstrate that our detection apparatus has adequate sensitivity for measurements in the atomic beam. Precision measurements of atomic structure, such as these, provide strict tests of wave function calculations and electroweak physics, important steps in the ongoing efforts to refine the Standard Model and understanding of atomic properties.

We propose a new model polymer physics model, the “Stacked or Freely Jointed Chain” (SFJC). This model addresses the observed tendency for single-stranded nucleic acids to align with their nearest neighbors, forming “stacks.” It builds on the Freely Jointed chain by not only allowing nucleotides to freely rotate but also allowing them to rigidly align. This thesis is a theoretical and conceptual exposition of the SFJC. We report on experimental evidence regarding stacking. In addition, we consider the SFJC in terms of recent DNA stretching experiments and propose the stretching of poly(T) and poly(A) as a potential application of the SFJC.

In this thesis, we explain how a MOT works, covering both Doppler cooling and Zeeman trapping. We also describe how one can apply the theory to a gas of real atoms, and the techniques we used to accelerate and optimize the setting of the optical elements required. A MOT will bring the temperature of a gas of atoms down to the 10-7K range, and it will increase the density in the cloud to at least 1012 atoms/cm3.

The MOT was applied to a gas of 87 Rubidium atoms, inside a steel vacuum chamber. To create the laser beams required, three diode lasers were used, two of which we set at the same frequency through the means of injection locking. Frequency was controlled through the means of an external cavity, and it was monitored and stabilized, “locked” to within 10 MHz of the desired frequency, using Saturated Absorption Spectroscopy.

In November 2002, we trapped our first cloud of atoms. Our MOT slowed and confined between 108 and 109 atoms, making clouds that were up to 5 millimeters in diameter in between 3 to 5 seconds.

Quantum dots and quantum wells, as two classifications of quantum-confined semiconductors, offer a variety of possible applications in such fields as opto-electronic communications. However, they cannot be put to best use until their optical characteristics are quantitatively measured and modeled. This thesis continues the work of past Bolton lab members in examining exciton dynamics in In0,04Ga0.96As quantum wells and PbS quantum dots. Exciton dynamics in InGaAs wells are affected by inhomogeneous broadening, local field effects, and excitation-induced dephasing, as well as by exciton-phonon interactions. Results are numerically confirmed by computer simulations, and suggestions to quantify the effects mentioned above as a function of well width are made. These data will be used in the design of technological applications of these materials.

The present study is designed to examine one of many possible links between religion and Teen Adjustment. I hypothesized that the positive a relationship between religion and teen adjustment would be mediated by positive familial interactions, specifically adolescents’ perceptions of their mother’s interactive behavior in general and mother’s and teens’ actual behaviors during interactions. I focused on three important characteristics that are important in both religion and interpersonal interactions: hopefulness, patience, and forgiveness. Twenty-seven African-American and Caucasian-American mother-teen pairs visited a neutral location, participated in a brief interaction and completed measures of religiosity, teen perceptions of their mother’s hopefulness patience, and forgiveness during interactions in general, and teen adjustment. Results did not support the hypothesized mediation model, although teen’s religiosity was significantly correlated with the "Deviant Behaviors" subscale of the teen adjustment measure. Moderation models were posited, also but not supported. Secondary exploratory analyses revealed interesting suggestive positive relationships between mother’s religiosity and their attributions about the causes of their negative teen’s behavior, and between mother’s religiosity and teens’ perceptions of their mother’s hopefulness, patience and forgiveness. Limitations of the present study as well as suggestions for continued research are discussed.

The Flinders Sensitive Line is a genetic animals model of depression that has been shown to have similar behavioral, neurological and immunological abnormalities as depressed humans. The main objective of this study was to determine if the FSL genetic condition affects maternal behavior, and if the lifetime trajectory of the rat can be altered by differences in the quality of maternal care. In this experiment, the quality of the early environment was equated with the quality of maternal care since all other factors were controlled for in the laboratory setting. We hypothesized that strain differences in these animals are not completely transmitted genetically, and that early rearing experience has an impact on adult expression of behavioral and immunological traits. Specifically, we hypothesized that immobility during forced swimming and KLH-specific antibody and cytokine production in the FSL rats would be modulated in animals reared by FRL dams. In addition, we hypothesized that the same variables in FRL pups reared by FSL dams would begin to resemble those of FSL pups. The first part of this experiment was designed to determine if there is a detectable difference in the way that the FRL and FSL Dams treat and respond to their litters. This was done by cross-fostering FRL and FSL litters within 3 days of birth so that FSL and FRL litters were raised by both FSL and FRL dams. This procedure included control groups. Maternal behavior was assessed on postnatal days 5 and 8 in the pup retrieval test. Pup emotionality was measured by recording ultrasonic vocalizations following a period of maternal separation (20 minutes) on postnatal day 5. The second part of this study was designed to determine whether differences in maternal behavior can alter the lifetime trajectory of the FSL and FRL rat pups as evidenced by the swim testing, cytokine and antibody analysis. Depressive symptomology, specifically behavioral despair, of the litters was measured in adulthood by the forced swim test on postnatal day 60. Cytokine and antibody production were assessed using enzyme linked immunosorbent assay kits following immunization with KLH antigen. The data from this study offer partial support for our hypotheses. Rearing experience clearly influenced depression-like behavior in the FST. Our results partially confirmed our main hypothesis that maternal behavior, as seen in FSL and FRL rats, is hampered by the effects of depression and has long-term consequences for offspring when they are genetically vulnerable (FSL offspring). At 15 days old, there was an apparent maternal effect on both FSL and FRL pups, as evidenced in USV production. However, in adulthood only FSL dams appear to be affected by their rearing conditions. Results from the FST showed that FSL raised by FRL dams had decreased symptoms of "psychomotor retardation", a hallmark of depressive disorder. This does not mean that the FRL pups were not affected by the rearing conditions, only that our tests could not show that they were affected. Further research is needed to elucidate the underlying mechanisms, as they cannot be determined from this study

The purpose of this study was to investigate the role of a tricyclic antidepressant on the in vivo antibody response of FSL rats. FSL, control FSL, and SD rats received chronic infusion of a well-known antidepressant, desipramine hydrochloride (DMI; 5mg/kg/day) or saline treatments through an implanted osmotic mini-pump (OMP) that continuously pumped for 3-4 weeks. After 3 weeks of treatment, Porsolt’s forced swim test (FST) paradigm was used as a behavioral measure to evaluate the effects of treatment. One week after the FST, animals were immunized intraperitoneally with keyhole limpet hemocyanin (KLH; 300µg/kg) and KLH-specific immunoglobulin (Ig)M, IgG, IgG1, and IgG2a responses were measured 7, 14, 21, and 28 days after immunization. Another group of animals were used to examine the effects of DMI treatment on T-helper 1 (Th-1) and Th-2 cell response through the production of cytokines, interferon-gamma (IFN-g) and interleukin-10 (IL-10).

To our knowledge, this was the first study to examine the effects of chronic treatment with antidepressants on the immune response of the Flinders’ genetic animal model of depression. Since previous research suggests that depressive behavior in rats is greatly reduced by antidepressants, we hypothesized that FSL rats treated with DMI would express less immobility than the FSL saline-treated group. DMI was not expected to effect the FRL or SD controls. Dependent upon effective antidepressant treatment, DMI-treated FSL rats were expected to produce similar IgM, IgG, IgG1, and IgG2a titers as the FRL and SD saline-treated controls. Additionally, it was hypothesized that DMI-treated FSL rats would exhibit higher levels of IFN-g than saline-treated FSL rats that have been shown to produce diminished Th-1 cytokine response. Due to the negative immunoregulatory nature of Th-2 response, it was predicted that FSL rats treated with DMI would produce lower levels of IL-10 compared to FSL saline-treated rats.

Statistical analyses showed that FSL rats in both treatment conditions had significantly greater immobility than FRL and SD controls. Contrary to previous findings, DMI had a significant effect on all strains by increasing immobility, while treatment had no significant effect on KLH-specific antibody response. FSL rats showed greater anti-KLH IgM antibody production than the FRL and SD rats, which had no strain differences. The FSL IgG response was significantly less than FRL and SD antibody production, while the FSL anti-KLH IgG1 antibody production was greater than FRL and SD rats. There were no significant strain differences between FSL and SD production of IgG2a..

This study found inconclusive results regarding the suggest immunoregulatory effects of antidepressants. From this study, we conclude that the association between depression and altered immune function remains complex. We propose future research using the Flinders model in order to elucidate further the significant dysregulation of immunological activity in human depressives.

Previous studies that examine the shape of utility functions are confounded by nonlinearities in the function relating people's decision weights to objective probabilities. In three experiments using real monetary payoffs, we eliminated this confounding by setting all probabilities equal, so that they did not bias utility estimates. We tested the predictions of three possible models of utility: power, hyperbolic, and negative exponential. In Experiments 1 (n = 15) and 2 (n = 25) hyperbolic utility was ruled out, and the power function fit marginally better than did the negative exponential. Experiment 3 (n = 23) replicated these results, and also showed that taking concavity of the utility function into account improves the fit of delay-discounting functions for delayed rewards. Although a power utility function performed better than the other two functional forms, across the three experiments even the power function could only be fit to 59% of the participants' data.

Children aged 25- to 30-months were tested in four symbolic domains to assess the interrelationships that may exist among pretense production, pretense comprehension, pictorial representation, and language as discrete symbol systems. The pretense production phase measured children's ability to engage in free play with their mothers for fifteen minutes using a designated toy set. The pretense comprehension phase measured the child's ability to follow another person's pretend play actions. The pictorial representation phase investigated children's ability to understand that pictures can represent the objects they portray. Finally, language was measured using the toddler MacArthur Communicative Development Inventory: Words and Sentences. All of these domains were positively correlated with each other, though only some correlations were significant. It was concluded that some symbolic relationships are stronger than others, and that pictorial representation may be the purest measure available of overall symbolic competence.