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An Investigation of the Properties of Spacetime with Emphasis on the
Effects of a Cosmological constant
Ryan A. Carollo
Recent measurements indicate that the expansion of our universe is accelerating due to some unknown dark energy. The most likely candidate for this dark energy is a cosmological constant, Λ. We perform a calculation of the effects of Λ under a Newtonian approximation. Einstein and Straus [1] have calculated the relativistic effect of ordinary cosmic expansion on local geometry, but their calculation assumes Λ ≠ 0. We also recreate portions of their work under the assumption of Λ= 0 to examine the effects of this new discovery.
New Observations of Ultraviolet and H Solar Limb Spicules with the Transition Region and Coronal Explorer and the Swedish Solar Telescope
Kamen A. Kozarev
We present the methods of analysis and the first results from a new project on simultaneous observations of solar spicules with the Transition Region and Coronal Explorer (TRACE) instrument, the New Swedish Solar Telescope (SST), and the SUMER spectrograph on the SOHO spacecraft. We develop and expand a number of IDL routines for the alignment, reduction and analysis of the data from TRACE and SST, thus setting up a computational environment for the project. We examine 283 limb spicules in the ultraviolet at 1600 Å, and record their statistical morphological properties, namely maximum heights, widths, half-lifetimes, average velocities, and inclinations. From independent measurements of spicule height evolution above the limb over half-hour periods, we determine after wavelet analysis that many spicules recur periodically, with periods between three and five minutes, which confirms recent model predictions. We also examine the interesting dynamics of several prominent ultraviolet spicules, and show that they exhibit twisting motions around their axes. We present initial measurements of heights and widths of SST Hα frames.


Molecular Identification of Knockout Mutants in the Sphingolipid Metabolic Pathway
Jeffrey T. Dougherty
Sphingolipids are a class of lipids that have been implicated in a number of eukaryotic signaling functions. In order to carry out knockout studies within the sphingolipid metabolic pathway, we identified strains from a library of T-DNA insertional mutants that were disrupted in a series of genes related to sphingolipid metabolism. We then developed a PCR-based screen for individuals that were homozygous for the T-DNA insertional mutation and identified homozygotes in mutant lines corresponding all of our targeted genes. We also developed RT-PCR primers suitable for detecting mRNA from all of these genes and for the majority of them confirmed their function against wild-type RNA. We performed RT-PCR based mRNA expression studies on homozygotes from lines corresponding to long chain base-phosphate phosphatase and lyase enzymes, and carried out preliminary enzyme activity assays on the lyase knockouts. Our results for the phosphatase mutant line indicate that it is knocked out in its target gene, although results from other lab members indicate that the knocked out gene may not correspond to the phosphatase enzyme. Our results for the lyase mutant line indicate that individuals that are knocked out for the gene have a significant decrease in or total absence of lyase enzyme activity, confirming that the gene targeted by these lines is in fact the long chain base-phosphate lyase. Future directions for this work include additional work to confirm the information presented here as well as extension of this approach to the remainder of the sphingolipid metabolic pathway.
Reversible Cryptic Coloration Allows for Diet Mixing and Possible Host Shift in the Sawfly Larva, Empria obscurata
Christopher Eaton
Empria obscurata is a nearctic sawfly that is widespread in the northern United States and southern Canada (Smith 1979). Until a recent study by Kemper (2003), almost nothing was known of this cryptic species’ life history or feeding patterns. Larvae of the species are transparent, which exposes the contents of their guts. This cryptic coloration mechanism allows the larva to appear green after eating leaves of its host, Potentilla fruticosa, and yellow after eating the plant’s flowers, allowing it to remain cryptic on both. To our knowledge, this is the only report of an animal that is entirely transparent in order to expose its gut contents. The reversible cryptic coloration of E. obscurata allows it to mix its diet to obtain an optimal nutrient balance. We examined the sawfly’s life history more closely and investigated the importance of each food type (leaf and flower). We show that larvae fed a mixed diet exhibit a higher fitness than those fed only one item or the other. Another potential benefit of reversible cryptic coloration is that E. obscurata could remain cryptic on a new host plant, no matter what its color. Monophagous insects, such as E. obscurata, have made up the prime evidence for sympatric speciation by host shift. We studied the possibility for acceptance of four new rosaceous hosts by the sawfly larva: Fragaria vesca, Potentilla tridentata, Potentilla norvegica, and Rosa acicularis. All five hosts (four alternates and P. fruticosa) produced equal proportions of viable adults, suggesting that they are acceptable hosts for E. obscurata. If future studies can demonstrate host fidelity by the sawfly on these alternate hosts, then the possibility exists that a population of E. obscurata, could shift to one of them and develop into a new host race.
What Is the Effect of Ghrelin on Torpor in Mice? An Analysis of the Ghrelin Signaling Pathway and the Role Ghrelin Plays in the Initiation and Modulation of Torpor
Elizabeth F. Gluck
Torpor is a hypo-metabolic response in mice and other small rodents induced by low ambient temperature and food scarcity. This research analyzes the roles of ghrelin and the hypothalamic arcuate nucleus (ARC) in torpor. Body temperature of mice was measured telemetrically. The ARC was ablated by perinatal treatment of monosodium glutamate (MSG), while littermate controls received perinatal vehicle. Upon fasting at 16º C, the majority of the control mice entered torpor, whereas the majority of the MSG treated animals did not enter torpor, indicating the requirement of the ARC in mediating the onset of torpor. Fasted control mice had a torpor bout that was deeper when acutely injected with ghrelin. However, ghrelin did not induce torpor in MSG treated mice, suggesting that the effect of ghrelin on torpor is mediated through the ARC. One of the primary signaling pathways within the ARC is the melanocortin signaling pathway. To determine if ghrelin functions through this pathway, Agouti mice, in which the POMC pathway is constitutively blocked, were fasted and injected with saline or ghrelin. Although Agouti mice could initiate a decrease in body temperature, they were unable to enter a significant bout of torpor without acute ghrelin injection. Interestingly, ghrelin injected mice all entered torpor at approximately the same time. Unlike the Agouti mice, there was no significant difference between the minimum body temperatures achieved by the ghrelin injected and saline injected NPY -/- mice. NPY -/- mice were also able to initiate a decrease in body temperature, but do not appear to be able to control this decrease to the extent that arcuate intact animals can. Collectively, these data show that the ARC is required for both torpor and ghrelin’s influence on torpor. Further, ghrelin’s actions through the ARC appear to be independent of the melanocortin signaling pathway, and dependent on NPY neurons, although we hypothesize that both pathways must be intact for a normal bout of torpor.
Regulation and Function of the Core Components Mediating VirB-dependent Substrate Delivery by Agrobacterium tumefaciens
Meaghan Giuliano
Agrobacterium tumefaciens incites the formation of tumors in many species of plants through the use of a Type IV secretion system, comprised of eleven VirB proteins and VirD4. This membrane-spanning multi-protein complex, encoded on the tumor-inducing (Ti) plasmid, mediates the transfer of a segment of oncogenic DNA as well as several proteins into host plant cells. We have identified a putative promoter sequence between the end of virB6 and the translational start of virB7. It was previously demonstrated that this sequence from the A. tumefaciens pTiA6 can indeed function as a promoter. Cells (wild-type strain A348) carrying a reporter plasmid containing the promoter sequence cloned in front of a lacZ gene exhibit at least 20-fold more β-galactosidase activity than cells with the vector alone. This activity is observed in both vir-inducing and non-vir-inducing (LB) media, and in fact, promoter activity is reduced under vir-inducing conditions. By recombining a lacZ reporter gene into the Ti plasmid behind this promoter, we have created a strain engineered to report internal promoter activity from within the pTiA6 of strain A348. This strain exhibits significant levels of β-galactosidase activity, compared to negative controls. In addition, we have used RT-PCR to confirm the presence of a transcript of virB8 from a non-induced strain in which the main virB promoter is inactive. These findings support the hypothesis that this internal promoter is active in vivo under physiological, albeit pre-infection, conditions. Finally, the characterization of a bank of virB10 mutants was completed by measuring VirB-dependent conjugative transfer of a heterologous substrate. These virB10 mutant strains exhibited conjugation efficiencies that correlated well with their ability to incite tumors. The assays confirmed that none of these mutations conferred a substrate-specific phenotype.
The Physiological Response of the Marine Cyanobacterium Prochlorococcus to Thermal Stress
Elizabeth A. Hambleton
Marine cyanobacteria, including Prochlorococcus, contribute significantly to ocean production, which comprises nearly half of all global primary production. Prochlorococcus is the dominant phototroph in subtropical to tropical open oceans, and its global distribution, high density, and several-hundred-meter depth range make Prochlorococcus the most abundant photosynthetic organism in the oceans and, most likely, on the planet. In light of natural and anthropogenic warming of the world’s oceans, the physiological response of Prochlorococcus to thermal stress is an important factor in assessing future changes in global ocean ecology. Particularly relevant to phototrophs is the investigation of photosynthetic capacity changes during thermal stress.
The genomic organization of photosynthesis genes, as well as photosynthesis protein conservation through amino acid sequence identity, was investigated in and among five cyanobacterial strains – a freshwater strain, a marine Synechococcus strain, and three Prochlorococcus strains. Genomic organization of Photosystem I proteins was found to be highly conserved in all strains, though gene copy number and genome location of Photosystem II genes fluctuated among the strains. High amino acid sequence identities were found between high-light adapted Prochlorococcus MED4 and low-light adapted Prochlorococcus SS120, indicating a decoupling between photosynthesis gene conservation and light-adapted ecotype. Prochlorococcus MED4 has the smallest genome of any known oxygenic photosynthesizer, and possesses single copies of six key photosynthesis genes.
Two Prochlorococcus strains – MED4 and MIT9313 – were grown at increasing temperatures to assess the cellular morphological response, growth behavior, and photosynthesis protein expression of the strains under thermal stress. Cells of both strains were visualized with Scanning Electron Microscopy, and shown to have membrane and cell division disruptions at the highest temperature, 28°C. Both strains also had significantly larger cell sizes at higher temperatures. Average specific growth rates of both strains, assessed by changes in chlorophyll a fluorescence, changed significantly with temperature. MED4 was overall more sensitive than MIT9313 to abrupt temperature increases: MED4 growth rates always declined with increasing temperature, MED4 had complete and immediate loss of chlorophyll at 28°C, and MED4 cell sizes increased most drastically during the first of two temperature increases, from 21°C to 24°C.
Photosynthesis protein expression was assessed via Western blotting using antibodies to one protein each from Photosystem I and Photosystem II. Initial antibody tests on 21°C MED4 and MIT9313 cellular protein extracts indicated that the antibody to the Photosystem I protein is optimized, and therefore may be used in future protein expression studies of cells grown at 24°C and 28°C. The Photosystem II protein needs future optimization before use in detecting cellular proteins from Prochlorococcus grown at various temperatures. When optimized, photosynthesis protein expression will provide a third dimension, along with studies of cellular morphology and growth behavior, in analyzing how the environmentally realistic occurrence of thermal stress will affect this globally important marine cyanobacterium.
Environmental Stresses and the Photosynthetic Physiology of the Marine Cyanobacterium Prochlorococcus
Bryce Inman
Prochlorococcus is a marine cyanobacterium that accounts for a significant portion of the primary productivity in the world’s oceans. This cyanobacterium is abundant in subtropical and tropical oceanic regions and plays an important role in global carbon and oxygen cycles. Previous studies have indicated that Prochlorococcus has a narrower temperature range for growth and a smaller genome compared to other cyanobacteria. To better understand the impacts of environmental stress on the photosynthetic physiology of Prochlorococcus, I characterized the effects of temperature and light stress on the growth and pigment levels of two Prochlorococcus strains. Prochlorococcus MED is a high light-adapted strain - isolated at 5 m depth – that possesses the smallest genome of any known photosynthetic organism. Although it has about 20 High Light Inducible Proteins (HLIPs), it lacks PsbU and PsbV proteins, which are thought to stabilize the oxygen evolving complex during heat stress. Prochlorococcus MIT9313 is a low light-adapted strain - isolated from 135 m – that possesses PsbU and PsbV, but has about half the number of HLIPs. When transferred from 21°C to 28°C, both strains displayed reductions of ~50% or more in their growth rates, but MIT9313 exhibited greater (~45%) losses in Chl a concentrations. When shifted from irradiances of 20 mmol photons m-2s-1 to 110 mmol photons m-2s-1, MED4 displayed ~35% decreases in Chl a and 200% increases in growth rate, while MIT9313 showed ~80% losses in Chl a and decreased growth rate. These results suggest that although both strains are affected significantly by abrupt temperature upshifts, MED4 is better suited for acclimating to high light conditions. The amino acid sequences and genome organization of PsbO, PsbU, and PsbV were also investigated in a number of cyanobacteria. Sequence comparisons revealed a high degree of divergence within the Prochlorococcus genus and among other genera.
HSP27 Transgenesis in Zebrafish
Cameron Marshall
Regulation of the actin cytoskeleton through actin binding proteins is essential for cell motility. Actin and actin binding proteins are the final targets of signaling pathways involved in these processes. In non-neuronal motile cells, HSP27 has been implicated as a key component linking signaling pathways to organization of the actin cytoskeleton through its function as an actin binding protein. The phosphorylation and multimerization state of HSP27 determine its actin binding properties. Specifically, HSP27 behaves as a barbed-end actin capping protein in the non-phosphorylated monomeric state, and as an actin stabilizing protein in the phosphorylated dimeric and trimeric states. HSP27 is expressed in the mouse and rat during development of the nervous system. Furthermore, HSP27 is expressed during embryonic development and required for axon outgrowth in zebrafish. These data suggest that HSP27 may be involved in actin dynamics of the growth cone during axon extension. I have successfully used transgenic technology to misexpress HSP27 and a dominant negative variant in the nervous system. Preliminary analysis suggests that misexpression of these constructs has no effect on the gross morphology of VeMe spinal interneurons.
Costs of Phenotypic Plasticity in Chorus Frog Tadpoles
Daniel E. Runcie
Fitness costs paid by individuals that have the ability to alter their phenotypes in response to environmental variation feature prominently in models of the evolution of phenotypic plasticity. The observed limitations to the plasticity exhibited by a wide range of organisms supports this theory, but direct measures of energetic costs incurred by plastic species have found little evidence of their existence. In this study, I examine patterns of phenotypic variation in chorus frog (Pseudacris triseriata) tadpoles for evidence that their predator-induced changes in morphology and behavior are limited by energetic costs associated with their plasticity.
P. triseriata tadpoles live in pools on the shorelines of islands in Isle Royale National Park in Lake Superior and are known to alter their development in response to the presence of predators. In these experiments, tadpoles were hatched in artificial bins, and stimulated to produce alternative phenotypes by the addition of caged dragonfly larvae (Aeshna juncea). Detailed characterization of the induced phenotypes in young tadpoles revealed divergences in phenotypes similar to previous observations of more advanced tadpoles. But a distinct lack of additive genetic variation for the plastic phenotypes in comparison to phenotypes uncorrelated with the plastic response suggests that selective forces continue to be strongest in the direction of the plastic change. This result suggests that elements of tadpole phenotypes associated with the plastic response are less optimized for their environment than non-plastic characteristics, and provides evidence for the existence of costs limiting the evolution of predator-induced phenotypes in these tadpoles.
The Role of the Agrobacterium tumefaciens VirC1 Putative ATPase Motif in Virulence and Binding to Overdrive
Molly R. Sharlach
Agrobacterium tumefaciens is a gram-negative soil bacterium that causes crown gall tumor formation in eudicotyledonous plants.  Transfer of a segment of DNA (T-strand) from the bacterial tumor-inducing (Ti) plasmid into the plant genome incites the plant to form tumors and synthesize opines. We tested whether the putative ATPase motif in the VirC1 protein of A. tumefaciens is required for the function of the protein in T-strand production and transfer, using both in vitro and in vivo assays.  In vitro, we made progress toward obtaining pure wild-type and ATPase mutant VirC1 proteins, and plan to use gel retardation analysis to determine whether the ATPase motif is required for VirC1 to bind to the overdrive DNA sequence on the Ti plasmid.  In vivo, tumor assay results suggest that A. tumefaciens carrying VirC1 with an altered ATPase motif exhibits severely attenuated virulence on Nicotiana tabacum, meaning that the ATPase motif in VirC1 is required for virulence on this host plant.
The Current Ecology of Eastern Hemlock (Tsuga Canadensis) in Williamstown, MA
Jasmine S. Smith
Eastern hemlock (Tsuga canadensis) is being decimated throughout the eastern coast of the United States by an exotic invasive insect pest known as the hemlock woolly adelgid (Adelges tsugae abbr. HWA). The insect has been expanding north from Virginia since the 1950s, and is currently present throughout most of Massachusetts. Williamstown, MA has not yet experienced any outbreaks of HWA, although an outbreak in the near future seems likely because the insect is already in southern Berkshire County and, by summer 2004, was as near to Williamstown as Stockbridge, MA (Ken Gooch, pers. comm.). The purpose of this study was to examine the current ecology of eastern hemlock in Williamstown prior to invasion by HWA.
Within Williamstown hemlock stands, hemlock exhibited a considerable degree of dominance, accounting for 60% of the total basal area and 45% of all trees present. This level of dominance creates the potential for a significant impact on forest community structure if stands are decimated by the HWA.
Hemlock stands were found at all topographic site types up to elevations of 600 m. Increasing elevation was negatively correlated with hemlock relative density, as other species such as beech (Fagus grandifolia) and red spruce (Picea rubens) became more frequent relative to hemlocks. Evidence was found for negative interactions between hemlock and several tree species including beech, red maple (Acer rubrum) and red oak (Quercus rubra). Hemlock growth exhibited a moderate positive correlation with growing season precipitation, but was insensitive to fluctuations in growing season temperature. Finally, historic land use appears to have had an impact on the current distribution of the species. 


Molecular Modeling on and Progress toward the Synthesis of New Discotic Liquid Crystalline Systems
Noah Bell
Mixtures of substituted triphenylene and triimide molecules have been shown to exhibit a discotic liquid crystalline phase in which the two molecules stack in an alternating fashion around a central axis due to donor/acceptor interactions. These mixtures exhibit a charge transfer band and could potentially serve as semiconducting nanowires. However, the band gap of the semiconducting system needs to be both tunable and controllable in order to give this system the flexibility it needs to be useful in a variety of applications. Previous work has focused on modulating the electron density in the donor/acceptor molecules through hydrogen bonding. The present work however, focuses on a proposed library of derivatives based on hexalkoxy triphenylene (HAT) and triimide molecules, which could allow control over the system due to the differing electronic properties of the derivatives. Additionally, molecular modeling is shown to be a useful and applicable tool toward the prediction of various columnar systems' properties. Modeling was used to predict the geometry and electronic configuration of several donor/acceptor mixtures. Although these calculations predicted electronic transitions relatively well, further work needs to be done to optimize and refine these values. Additionally, the syntheses of two of the derivatives - benzoquinone and triquinone - were started but not completed due to a variety of synthetic issues. Overall, the work presented in this thesis represents the first steps toward creating and characterizing a library of discotic liquid crystalline molecules whose differing electronic interactions could allow for the extraordinary control of properties and functionality in a nanowire system.
Single Molecule Studies of Dynamics in Polymer Glass
Noah Capurso
Single molecule fluorescence spectroscopy is used to observe the rotational diffusion of Rhodamine B probe molecules in poly(vinyl acetate). The data contained in these fluorescence intensity traces are used to calculate equilibrium environmental exchange constants at temperatures near the glass transition. Diffusion times are assigned to times on the fluorescence intensity trace by means of an autocorrelation function analysis. Computer simulations and statistical tests are used to find a method to quantify autocorrelation function decays. An integration analysis from 1>C(t)>(1/e) is chosen over linear, exponential, and Gaussian fit functions.
The setup was converted from using an N.A.=1.4 oil objective to an N.A.=0.9 air gap objective in order to minimize heat loss, and allowing for a wider temperature range and better temperature response at the sample. Temperatures as high as 60°C and cooling rates greater than -1.5°C/s are achievable, enabling us to quench cool samples and trap them high on the potential energy surface, allowing for non-equilibrium measurements to be done in the future.
Environmental exchange constants are calculated to be 654 s, 716 s, 683 s, 619 s, 614 s, 348 s, 175 s, and 138 s at 28.9°C, 29.4°C, 29.7°C, 30.2°C, 30.7°C, 34.7°C, 39.2°C, and 45.6°C respectively. The values are plotted on an Arrhenius type plot, which may provide experimental evidence for the computer simulation finding that barrier size on the potential energy surface becomes larger at a temperature between the glass transition and the onset of non-exponential relaxation behavior. Such a finding would draw a connection between dynamics and system defined potential energy surface features. While the data is not yet sufficient to draw any conclusions, a few more environmental exchange constants at higher temperatures may be all that is needed to find evidence of this connection.
Lead in the Soils of Pittsfield, Massachusetts: Chemical Analyses and Community Questions
Kathleen Carroll
In the urban west side district of Pittsfield, Massachusetts, human activities over the past century have contributed to a buildup of lead (Pb) in the soils of residential areas. Sediments at several properties in the area have been contaminated by old leaded house paint, which has seeped into the ground. This problem merited investigation because the city of Pittsfield has considered turning some of these sites into community gardens, a project which could expose local citizens to harmful amounts of Pb.
Soils from 7 west side lots were collected and analyzed for Pb, and of these, 5 had soils with elevated levels of Pb. The lot at 98 John Street was sampled more extensively, which showed that several parts of this property had more than 400 mg Pb/kg dry soil, the level considered hazardous by the U.S. Environmental Protection Agency.
Soil from 98 John Street was then collected for use in a greenhouse vegetable garden, in which broccoli, radish, lettuce, pea and tomato plants were grown in the soil and then analyzed for lead. Both soils and plants were analyzed using Atomic Absorption and Laser-Induced Breakdown Spectroscopies (AAS and LIBS). While most of the vegetables had less than 3 mg Pb/ kg dried vegetable, the roots of vegetables grown in contaminated soil contained as much as 25 mg kg-1 Pb.
LIBS was established as a satisfactory method for positive, qualitative identification of Pb in contaminated soils. With the current apparatus, however, LIBS is not sensitive enough to detect trace amounts of Pb in vegetables.
Individuals working in a garden at 98 John Street would be at risk, predominantly from inhalation and ingestion of Pb-contaminated soil. Since Pb in the human body is known to have serious adverse health effects, this particular Pittsfield lot is not a suitable place for a community garden to be established.
Asymmetric Synthesis of (R)-Goniothalamin
Pamela Choi
Goniothalamin is a naturally occurring α, β-unsaturated δ-lactone. It is isolated from various species of the Goniothalamus plant and also possesses anticancer properties. The α,β-unsaturated δ-lactone ring is a common target of organic synthesis and there have been a number of groups who have reported the synthesis of both naturally occurring (R)-goniothalamin as well as its (S) enantiomer.
We attempted to establish a unique asymmetric synthesis of (R)-goniothalamin by adapting reactions that have been developed by our research group. The stereocenter was established through an auxiliary directed aldol and the auxiliary was displaced with a monoethyl malonate group to form the δ-hydroxy-β-ketoester. Both of these steps were used directly from a protocol developed by Smith group for the synthesis of the kavalactones, and were repeated with high fidelity to Smith’s reported success.
A pathway was developed to lead to the desired natural product by lactonizing the δ-hydroxy-β-ketoester and reducing the β-ketolactone into an alcohol with an ammonia-borane complex in citric acid, followed by acetylation and elimination to yield goniothalamin. While this procedure proved successful with high crude yields, we have had difficulty achieving complete conversion on large scale reactions with our current protocol. We are also unable to provide complete yield information as well as spectroscopic analysis. However, we have made great strides in our project, and our synthesis shows promise as a highly efficient and short pathway to goniothalamin.
Synthesis toward Novel Aminomethyl Oxazoline Platinum Complexes for
Use As Anti-Tumor Agents
James Enterkin
Since its discovery, cisplatin has played a crucial role in treating certain types of cancers. Its toxic effect on certain types of cancer stems from its ability to bind the tumor’s DNA. Many attempts have been made to improve upon cisplatin by synthesizing new platinum based drugs which are better able to bind DNA and less likely to be deactivated by binding other cellular products. With this goal in mind, a series of chiral aminomethyl oxazoline ligands with methyl, phenyl, and benzyl groups attached to the oxazoline ring at the 4 position were synthesized in both enantiomers. The product of the reaction coordinating these ligands to platinum was insoluble in every solvent tried. To increase the solubility of the complex, a dicarboxylate leaving group was chosen to replace the chloride leaving groups. Such a substitution was tested first on previously synthesized chiral platinum bioxazoline complexes. The platinum bioxazoline complexes had previously been shown to bind DNA nucleotides, with low solubility being their major drawback. The substitution was successful, and vastly increased the solubility of the platinum bioxazoline complexes. It is believed that when the synthesis of the aminomethyl oxazoline platinum complexes with dicarboxylate leaving groups is complete, they too will be soluble and will demonstrate the ability to bind DNA.
Progress toward the Asymmetric Total Synthesis of (+)-Ratjadone:
A Potent Cytotoxic Metabolite from the Myxobacterium, Sorangium cellulosum
Salem Fevrier
The highly cytotoxic polyketide, (+)-ratjadone, isolated from the myxobacterium, Sorangium cellulosum, exhibits potent in vitro antifungal activity. The recently discovered antitumor behavior of ratjadone at startlingly low concentrations (40−50 pg/mL) has drawn substantial attention from the scientific community. Ratjadone is structurally similar to several antitumor antibiotics. Its total synthesis is of significance because it may suggest a synthetic route to other therapeutically valuable natural compounds. Prior to our efforts, two total syntheses of ratjadone had been published.
The initial proposal for the convergent synthesis of ratjadone entailed joining three subunits together via a sulfone anion addition to an aldehyde and a palladium catalyzed cross-coupling. Our work commenced with efforts to synthesize the C17−C24 tetrahydropyranyl fragment. Difficulty with silylation and reduction the β-hydroxy-δ-lactone precursor hindered progress toward the synthesis of the C17−C24 sulfone fragment and led us to an alternative coupling strategy involving a dithiane anion addition to a carbonyl electrophile. After model studies using a cinnamyl dithiane with a lactone proved problematic, we considered constructing this C16−C17 linkage prior to lactonization. Model coupling experiments with an aldehyde helped established a reasonable route to achieve connection between the C17−C24 tetrahydropyranyl unit and C8−C16 bifunctional polyene fragment.
Characterization of an Essential Early Sporulation Protein in Streptomyces coelicolor
Renee Kontnik
Streptomyces coelicolor is a model representative of a group of soil-dwelling bacteria characterized by a complex life cycle involving mycelial growth and spore formation. This investigation is devoted to the characterization of a vital developmental protein implicated in the sporulation process of this microbe. The whiJ gene cluster of S. coelicolor, consisting of three open reading frames (orf1, orf3, and orf5), is known to be involved in the early stages of sporulation. Previous analyses have revealed that the Orf3 protein is likely to contain a helix-turn-helix motif, suggestive of a probable DNA-binding domain. A series of analyses were therefore performed to investigate this supposition.
Overexpression of this protein in an Escherichia coli host yielded insoluble inclusion bodies which were solubilized, followed by Orf3 purification and refolding. DNA affinity chromatography and electrophoretic mobility shift assays were performed to investigate the potential function of Orf3 as a DNA-binding protein. DNA affinity chromatography assays indicated the ability of Orf3 to interact with a DNA-cellulose resin. Electrophoretic mobility shift assays further suggested the interaction of Orf3 with DNA, although in a weak, nonspecific manner. A gel mobility shift-PCR technique has been initiated to determine the DNA sequence to which Orf3 specifically binds. Examination of the binding activity of Orf3 in the presence of Orf5 suggested that this latter protein might function to facilitate DNA-binding by Orf3. Additionally, renaturation of the protein in the presence of DNA may facilitate proper refolding.
Developing Templates for the Alignment of Liquid Crystalline Materials
Elizabeth Landis
Discotic liquid crystalline systems are of interest because of their potential as molecular wires. Several systems of discotic liquid crystals consisting of rigid cores with alkyl chains around the periphery have previously been developed in the Park Lab. It was thought that porous templates might be used for the alignment of these molecules, a necessary precursor to measuring their charge transport properties. Studies of the interactions of our discotic liquid crystals with silica chromatography beads with varying pore sizes showed that the ideal pore size for alignment of our molecules was around 300 Å. Aluminum disks can be anodized to form pores in the desired size range. Experiments were successful in producing pores of 40 nm, 20 nm and several sizes in between, although some work to clean the surfaces of the disks remains. These anodized disks can be derivatized with C18 chains in order to promote more favorable interactions with the peripheral alkyl chains of our molecules. The derivatization happens quickly and seems to coat at least the surface and possibly the interior walls of the pores within thirty minutes.
The Binding of Chicken Linker Histone H5 to Chromatin
Joanna Lloyd
The purpose of this investigation was to determine a protocol for efficient, reliable extraction and purification of avian linker histone H5. Changes in the linker histone complement of mature avian erythrocytes correlate with a change in transcriptional competency. The role of histones in higher order chromatin structures and their effect on transcription in cells is an active area of research. The goal of this investigation was to analyze the interaction of linker histone H5 with chromatin through a variety of thermodynamic parameters. Significant problems prevented the completion of this pursuit.
Reaction-Diffusion Equations Applied to Predator-Prey Systems
Edward McGehee
Researchers have begun to explore the possibility that spatial patterns in predator-prey ecological systems are generated by Turing instabilities, whereby large differences in species population dispersal rates cause heterogeneous population distributions to become stable. In this project, we extend those hypotheses to the Bazykin model, a two-species predator prey model represented by a system of partial differential equations that accounts for fighting among predators. Our analysis of the Bazykin system dynamics reveals the coexistence of multiple Turing attractors and the coexistence of a Turing attractor and a stable limit cycle in the system. We conclude this project with a brief, introductory look at how spatial and non-spatial attractors interact with one another to affect system dynamics, a topic that has not yet been considered in the field of population dynamics.
The Synthesis of Self-Aggregating Copolymers
Katherine Rutledge
Poly(ethylene glycol) (PEG)-peptide copolymers are composite macromolecules formed from linking peptide blocks to a PEG backbone. Copolymers were investigated for their self-assembling properties as potential drug delivery vehicles. PEG-peptide conjugates were synthesized using DCC-activated coupling and base catalyzed deprotection reactions, and copolymer composition was varied by modifying the peptide sequence, the type of linker, or the molecular weight of PEG. The library of PEG-peptide conjugates synthesized included PEG-Valine5 (MW 10 kDa, ester linkage), PEG-Gly-Val-Gly-Pro-Val-Fmoc (PEG-elastin) (MW 10 kDa, ester), PEG-elastin (MW 10 kDa, amide), PEG-Valine5 (MW 4.6 kDa, ester), and PEG-elastin (MW 4.6 kDa, ester) in 10%, 22%, 1.25%, 17%, and 20% yield, respectively. The self-aggregating properties of PEG-Valine5 (MW 10 kDa, ester) and PEG-elastin (MW 10 kDa, amide) were investigated using fluorimetry studies with the probe Nile Red. Studies indicate both copolymers aggregate, however, PEG-Valine5 aggregates more effectively than PEG-Elastin.
Vibrational Overtone Spectroscopy and Weak Intramolecular Forces in Hydrofluorocarbons
Brian Saar
We have recorded the CH-stretching fundamental and overtone spectra of three hydrofluorocarbons: pentafluoroethane, 1H-heptafluoropropane and 1H-nonafluorobutane with up to 6 quanta of stretching. Hydrofluorocarbons are of atmospheric interest and provide the opportunity to study in detail the vibrational motion of an isolated CH-chromophore. In this study we make use of conventional spectroscopy and well as cavity ringdown spectroscopy and measure absorbances as small as a few parts per million. We model our spectra using a one-dimensional local mode model that considers uncoupled CH-stretching. We calculate potential energy parameters and dipole moment functions ab initio using density functional theory and triple-zeta-quality basis sets.
Overall, we find that our one-dimensional model does a good job of reproducing the total overtone intensities in each region, though it often fails to predict the detailed structure of the overtone polyad regions. Based on calculations and on the structure of the measured spectra, we conclude that the overtone spectrum of 1H-nonafluorobutane may be interpreted using contributions from three conformational isomers, including a six-membered ring that contains a blue-shifting hydrogen bond. We also analyze the overall widths of the measured vibrational transitions to find evidence for intramolecular vibrational redistribution from a CH-stretching bright state, through a CCH bending doorway state and into the bath of states nearby in energy.
Toward a Novel Synthesis of the Oxoaporphines and 3-Arylisoxazoles
Marie-Adele Sorel
I. Oxoaporphines
The naturally occurring oxoaporphines are of interest for their biological activity. The work of this thesis was to develop a new, versatile synthesis of the oxoaporphines. The methodology was based upon previous syntheses of the oxoaporphines and their analogs and upon previous work in the Markgraf lab applying a radical-induced ring closure. The methodology developed for the oxoaporphines would then permit the synthesis of the analogous sampangine alkaloids. Several routes to oxoaporphines from commercially-available starting materials were developed which involved three, four, or five steps. In each case, the synthesis of the key intermediate was achieved, but the final cyclization step could not be effected.
II. 3-Arylisoxazoles
A series of 3-arylisoxazoles was synthesized, and 13C and 15N nuclear magnetic resonance (NMR) spectra were used to measure the correlation with the Hammett substituent constants. This correlation demonstrated that the high magnitude electronic effects on N(2) were dominated by electron-withdrawing effects.


Artificially Intelligent Animation Generation
Marina Lifshin
This interdisciplinary project explores one area in the growing space where the visual arts and computer science intersect. It introduces an original, specialized knowledge representation scheme and generative algorithm for ANGE, an Animated Narrative Generation Engine that creates silent, moving art for projection or internet display. ANGE generates a specific genre of this moving art, which expresses my own creative and aesthetic goals, as well as my perspectives on interesting, emotive storytelling. ANGE focuses on the interaction between the formal qualities and subject matter of the moving image as inscribed in simple, loose narrative structures, on the way these interactions create visual experiences, and on the best way to computationally represent the creation of these works.
Hidden Markov Models in the Analysis of Time Series Data
Alexandra Constantin
Hidden Markov Models (HMMs) are probabilistic models over a finite set of states. Each state transition generates an observation symbol or output, which we would like to predict. HMMs are useful for many applications, including speech recognition and computational biology. In general, they can be applied in the analysis of a large number of time series data. My winter study project consisted of applying HMMs to anomaly detection, specifically detecting intruders to an account based on their patterns in using the system. In this talk, I will give an overview of HMMs and describe my results for the intruder detection application.


Monsoon-Induced Changes in Coccolithophorid Primary Productivity in the Bay of Bengal
Alicia L. Arevalos
The Bay of Bengal represents an ideal location to test marine productivity changes in response to monsoon-driven fluctuations in riverine nutrient input. The productivity of marine primary producers may represent an important feedback in the climate system. Using the new productivity indicator, the Sr/Ca ratio of coccolith calcite, we tested recent sediment from the Bay of Bengal collected in traps over a one-year period and monsoon cycle (1994-1995). Data from sediment trap sites NBBT-N (N 17.5 E 89.5; trap depth 684 m), NBBT-S (N 15.5 E 89.2; trap depth 731 m) and SBBT (0.05 N 86.75 E; trap depth 1919 m) shows the flux of total coccolith carbonate and the component coccolith fractions does increase in response to monsoon-induced nutrient fluxes. Sr/Ca data, however, do not necessarily track changes in flux, highlighting the need to better understand mechanisms behind how coccolithophores utilize nutrients and what regulates Sr/Ca variations in coccolith carbonate. Chemical weathering from the Himalayan and Indo-Burman ranges and wind-induced mixing of surface waters play important key roles in understanding coccolithophore species fluxes.
Characterization of Chemical Weathering in the Middle Boulder Creek Catchment: A Step toward Understanding Front Range Evolution
Jennifer E. Campbell
Thin section observations and weathered rock and water chemistry analyses from the Middle Boulder Creek catchment provide a detailed qualification and quantification of the chemical weathering processes driving the formation of the thick regolith that mantles this part of the Front Range. Two rock types, Boulder Creek Granodiorite and Silver Plume Granite, dominate the area and follow a similar pattern of weathering.
Thin section observations show that plagioclase is the main mineral undergoing alteration. Isherwood and Street’s research (1976) focused on the role of biotite as the primary driver of grussification. In thin section, biotite does show slight bleaching and expansion along cleavage planes, but its alteration is not as complete as that of plagioclase. The other primary minerals, microcline and quartz, show minimal alteration. These observations correspond with the sequence of weathering derived from laboratory dissolution rates, plagioclase>biotite>microcline>quartz.
Mass balance analyses of the weathered rock and sample stream water chemistry confirm the significance of plagioclase and biotite in the weathering process. Mass balance analyses show loss of the main cations up through the weathering profile, Ca>Mg>>Na>Si>K, with Ca and Mg exhibiting the greatest loss. Water chemistry from the area likewise shows significant losses of Ca and Mg, in addition to SiO2 and Na (SiO2>Ca>Mg, Na).
The one peculiarity in the water chemistry is the excessive loss of Ca over Na. Ca flux values average 1.34 g m-2yr-1 for valley samples and 0.91 g m-2yr-1 for alpine samples, while Na flux values average 0.28 g m-2yr-1 for valley samples and 0.35 g m-2yr-1 for alpine samples. Similarly, the molar Ca/Na values for the weathered rock chemistry decrease up through the weathering profile, from 0.66 to about 0.33 in Boulder Creek Granodiorite and from 0.23 to about 0.18 in Silver Plume Granite. Plagioclase in the only primary mineral containing both Ca and Na, and thus the cations should be leached out in the proportions in which they are present in plagioclase. The molar Ca/Na is 0.61 in Boulder Creek and 0.33 in Silver Plume. It appears that excess Ca in drainage water originates from weathering of minor calcic phases. Both rock types contain trace amounts of calcite and apatite, and the Boulder Creek rocks additionally contain traces of epidote and hornblende in amounts up to 23.3% in selected samples. Excess Ca in the Silver Plume must be originating from calcite and apatite, whereas up to 45% of the excess Ca in Boulder Creek may be originating from hornblende with some additional Ca from epidote. Laboratory dissolution rates for calcite and hornblende are much faster than those of the primary minerals, consistent with the idea that significant amounts of Ca are leached from these additional calcic phases.
My analyses can be used to help constrain weathering rates using a box model approach. Dethier and Lazarus (2005) made a first approximation of denudation rates in the Front Range using this approach and determined that formation of about 7 m of weathered rock material would take from 230 to over 1340 kyr. Dethier and Lazarus’s box model is limited by elemental flux rates based solely on alpine stream samples as well as an inability to assess the percent of density reduction due to chemical flux versus physical weathering. The weathered rock and water chemical data in the following report will allow the adjustment of their model to depict erosion more accurately.
Kinematics and Chronology of Faulting in the Western Berkshire Massif, Massachusetts
Ryan P. Gordon
The Berkshire massif in western Massachusetts and Connecticut is composed of Middle Proterozoic rocks that were thrust over Cambrian to Ordovician continental shelf deposits. It has been traditionally accepted that westward-directed thrusting occurred during the Ordovician Taconic orogeny, yet the kinematics and age of deformation have not been well constrained. Ratcliffe and Harwood (1975) described zones of cataclasis and recrystallization in “blastomylonitic seams” along the western edge of the massif, but sense of shear indicators and microstructures have not been described in these rocks since their work.
We collected samples of deformed basement and cover rocks near thrust faults in the western part of the massif. Rocks within a few meters of faults are mylonites with a strong planar foliation; however, strain decreases dramatically with distance from faults, based on the appearance of deformation fabrics. Basement rocks approximately 20 m away from faults generally preserve their Proterozoic gneissic fabric, which is crosscut by distinct mica-rich shear bands with recrystallized feldspar and quartz. Biotite seams, quartz ribbons, and regions of fine-grained recrystallized feldspar define a sub-planar fabric that wraps around feldspar porphyroclasts. Porphyroclasts have short tails and theta- or sigma-type shapes, suggesting that recrystallization was rapid compared to the strain rate. Asymmetric porphyroclasts, S-C fabrics, and extensional shear bands locally show east over west displacement. Elongate quartz ribbons are composed of equant subgrains that are commonly recovered and strain-free, whereas the interiors of most feldspar porphyroclasts preserve evidence of deformation by grain-size reduction. Such grains are highly strained and show undulose extinction, suggesting that deformation was controlled by dislocation creep at temperatures above 500 degrees C. No evidence for cataclasis or other brittle mechanisms is preserved in these rocks.
Monazite grains in rocks from three locations were dated using the U-Th-Pb electron microprobe method. Two samples of sheared Cheshire Quartzite from a fault zone at Dry Hill were dated at 392 ± 14 Ma. One sample of graphitic schist from below the fault zone at Benton Hill was dated at 436 ± 8 Ma. One sample of sheared Dalton Formation from a complex fault zone at Umpachene Falls yielded four age peaks at approximately 530 Ma, 435 Ma, 380 Ma, and 290 Ma. Based on shear-sense indicators, this fault zone may have experienced low-angle normal faulting.
Surficial Deposits: Digital Mapping, Classification, and GIS Analysis
Robert S. Hahn
Data from a GIS-based map of surficial deposits in the 294 km2 Boulder Creek catchment compare favorably with classified images calculated from a 14-band, 15-m ASTER image collected by the Earth Observing System’s satellite, Terra. The catchment heads in the alpine Indian Peaks area and extends east past the late Pleistocene glacial limit. Surficial deposits reflect local bedrock geology, weathering, and erosion and transport by glaciers, mass movements and other surface processes. Calculations of long-term weathering and erosion rates for the Front Range require measurements for area and thickness of these surface deposits.
Weathered bedrock and colluvium covered with forest (~52%) dominates the digitized map, particularly east of the glacial limit. Glacial drift covers 18% of the mapped area and extends in tongues from the larger alpine catchments down U-shaped valleys between about 3400 and 2700 m. Bedrock and talus (9% and 8% of mapped area, respectively) are generally but not exclusively confined to the U-shaped valley (glacier-carved) system. The spatial distribution of bedrock is more diverse than talus—the former occurring anywhere from valley floors to sharp arêtes as high as 4,110 m, whereas the latter mainly occurs along steep valley walls, beneath large bedrock outcrops, and in association with nivation hollows. Alpine colluvium (8% of mapped area) and patterned ground (5% of mapped area) are almost exclusively confined to interfluves between glaciated valleys. Field data also show that patterned ground (of periglacial origin) has the highest elevation of the alpine units, followed by talus, bedrock, and then alpine colluvium. Approximately 11% of the overall bedrock area and 1.5% of the talus area occurs below the glacial limit, mainly in steep, narrow canyons along the Middle Fork of the Boulder Creek; talus also occurs adjacent to isolated bedrock tors.
Satellite-based classifications varied in degree of user input from minimal (K-means classifier) to entirely user input (decision tree); the latter corresponding to the most versatile classifier. The decision tree captured many features associated with the field map, although the range and similarity of spectral properties in some cases foiled even a field-guided attempt at classification. Shadows were eliminated from the ASTER image using band ratios calculated from a DEM hill-shade image. The parameterization of slope, aspect, and elevation in the decision tree classifier prevented large-scale misclassification of terrain distinguishable to the human eye on a satellite image, but unrecognized by the computer.
All of the classifications show high precision (up to 15-m); however the boundary accuracy varies based upon the effectiveness of the class calibration. Field classifications are extremely effective in the high-country of Colorado, where the exposure is excellent. However, the Boulder Creek catchment is about the largest area that could be readily mapped using the digitization approach. Thus, the decision tree classification of an ASTER image offers a reliable and viable alternative, although field experience remains a pre-requisite. Overall statistical and visual similarity between the ASTER and field-based classifications suggests that in this environment, field-based mapping helps improve and validate classification using satellite imagery alone.
Carbonate Dunes on the Gulf Coast of Baja California, Mexico
Paul A. Skudder
Unique oceanographic conditions cause the Gulf of California to have unusually high biological productivity. Winds from the north prevail during winter and subject north-facing shores in the gulf to high wave energy. Bivalve shells that wash onto the beach are broken down and blown into dune systems. This study characterizes the sedimentology of three previously unstudied dunes, analyzes the changes in volume undergone by shells of Megapitaria squalida, develops a model for determining the amount of shell material present in dunes, and assesses the role of remote sensing in future work on this system.
Effects of Nutrient Limitation on the Productivity of Coccolithophore Algae and the Paleoclimatic Implications
Susanna M. Theroux
Three strains of Emiliania huxleyi coccolithophore algae (NAP4, G284, G320) were cultured to investigate the effects of nutrient limitation on coccolith chemistry and cell physiology. Batch and continuous culture chemostat experiments were performed for a duration of one to two weeks utilizing either full nutrient or nutrient-depleted media. Cultures were grown in a continuous chemostat with a peristaltic pump delivering nitrate-limited media at pre-determined slow, medium, and fast rates. Rate of nutrient input dictated cell division rates and cells were kept in exponential growth phase for the duration of the experiment. Daily overflow collections determined cell density, growth rate, inorganic calcium/cell, and Sr/Ca ratios of coccoliths. Cells were also grown in full and nitrate-limited batch cultures, wherein a fixed volume of media was depleted of nutrients over time as cells approached stationary phase. SEM image analysis provided information on coccolith morphology over time.
Both chemostat and batch culture experiment results indicate that as nutrient input increases, calcification decreases substantially. Fast chemostat experiment samples were below detection for calcium measurements, as were the majority of medium chemostat samples. These samples are believed to have entered a naked, or non-calcifying, stage. Sr/Ca values for overflow samples may have been influenced by barite formation or the accumulation of organic matter with higher Sr/Ca ratios, and are therefore erroneously high. Rinsed final harvest samples are minimally-effected by this contamination and demonstrate a clear, positive relationship between Sr/Ca and growth rate. Coccolith morphology results of individual experiments suggest changes over time in calcification habits, but further analyses of these images is required to establish statistical validity. Evidence that calcification rates are influenced by nutrient concentrations is of importance in the development of climatic models of environmental conditions and algal productivity response.


Helical Structures
Stephen Savinar Moseley
We explore the structural properties of a class of stable structures resembling triple helices. We assume a simplified physics model, and observe an ideal system as it settles. By changing the relative sizes of elements and varying the properties of the rules that define the system's dynamics, we identify which systems assume regular, stable configurations. We further test stability by applying Brownian perturbations and stretching settled configurations to observe how quickly they resettle. Given the final range of variables that yield stable systems, we compare our structures to the ideal physical characteristics of the collagen protein (which forms a regular triple helix) and hypothesize how the differences between the rules of our simulation and those in nature cause our stable systems to differ from collagen.
Juggling Braids, Links, and Artin Groups
John Mugno
We study the SITESWAP notation used by jugglers and mathematicians for denoting juggling patterns. We construct a map from the space of juggling patterns to links, and prove that this map is onto. In other words, all links can be juggled. We extend this to other juggling patterns that arise from alternate Artin groups.
On Diophantine Approximation along Algebraic Curves
Ashok Pillai
Building on the previous work of Carsten Elsner from 2001, here we discover a method for approximating almost all positive real numbers by integer points that lie on homogeneous algebraic curves of degree two. We first examine circles and ellipses as special cases before generalizing our work to produce a result for all symmetric homogeneous quadratic curves. Next, we extend this generalization to all homogeneous quadratic curves. Finally we employ our methods to approximate certain U-numbers by rational points on singular cubic curves.
Two-Cycles in Three-Dimensional Space
Jordan Rodu
Two-Cycles are approximations of stationary trajectories of flows under probabilistic control, formed when two flows are anti-parallel at a particular point. We know what these two-cycles look like in two dimensional space. In this paper, we will investigate the structure and conditions of two-cycles in three dimensional space. Specifically, we show that locally the locus of points in which flows are anti-parallel is a curve, and that two cycles that approximate these points form a two parameter family of curves.
Class Groups of Function Fields and the Decomposition of Irreducibles in Field Extensions
Matthew P. Spencer
Let n be an integer greater than 2 and suppose S, T and U are pairwise disjoint finite sets of monic irreducible polynomials in Fq [T]. We construct infinitely many quadratic function fields K of degree m such that n divides the size of the class group of K, and such that polynomials in S split completely, polynomials in T remain inert, and polynomials in U are totally ramified in K. We present further results concerning higher degree extensions and class groups of high n-rank.


Derivation and Analysis of Bounds in Dirac Leptogenesis
John A. BackusMayes
Progress toward BEC: Detecting and Measuring Dipole-Trapped Clouds
Justin M. Brown
This thesis describes progress toward creating a Bose-Einstein condensate (BEC) in a dilute 87Rb vapor. One creates a BEC by trapping and cooling atoms to extremely low temperatures and high densities to achieve a phase space density on order of unity. Prior work included a magneto-optical trap (MOT) containing ~109 atoms at 300 µK. We have successfully transferred ~106 atoms from the MOT into an optical dipole trap where they may be further cooled to the BEC transition temperature. We have crated an absorption imaging system to detect dipole-trapped clouds. Through absorption images, we measure key cloud properties, the number, the temperature, and the phase space density of the atoms. In our initial experiments, we created clouds with a measured phase space density of 2 x 10-5.
Phase Shift Spectroscopy in the Study of the 6P1/2—>6P3/2 M1 Transition in a
Thallium Atomic Beam
Colin D. Bruzewicz
A phase sensitive method of high precision atomic spectroscopy is presented. Due to the intrinsic weakness of the M1 transition, previous spectroscopic techniques based on the direct absorption of laser light are untenable in the reduced atomic density thallium beam unit. A feasibility study and results of bench top testing of a newly constructed high finesse Fabry-Perot cavity capable of resolving atomically induced phase shifts are described here. The future high precision measurements afforded by this technique will provide general tests of atomic wavefunction calculations of relevance to the refinement of the Standard Model of Electroweak Interactions.
The Second Law of Thermodynamics in a Timeless Universe
Joshua H. Cooperman
I approach the origin of the second law of thermodynamics within the timeless theoretical framework. This framework asserts that evolution derives from the correlations within the zero-energy stationary state vector of the universe. In this picture the existence of the second law is reduced to a property of the universal state vector. First I reformulate the second law in the timeless framework: observers witness positive correlations in entropy between independent object systems. I then study two model universes, each consisting entirely of spin one-half particles, both of which exhibit the second law of thermodynamics. I begin to analyze the characteristics of these universes that might give rise to the second law.
Toward the Measurement of a T-odd P-even Interaction in the 6P1/2 —>6P3/2 1283nm Transition in Atomic Thallium
Joseph A. Kerckhoff
We have begun several preliminary steps necessary for a future experiment that has the potential to set new limits on fundamental T-odd P-even (TOPE) forces, which will help to further characterize and constrain the Standard Model. This future experiment is an adaptation of an experiment proposal by [KOZ89] and will look for evidence of a TOPE interaction in the 6P1/2—>6P3/2 1283nm M1 transition in atomic thallium. To prepare for this high precision measurement, we have investigated the potential phase resolution of a length stabilized Fabry-Perot ring cavity that will eventually be used to detect minute atomically-induced optical phase shifts, developed a new laser frequency stabilization technique that utilizes low-field Faraday polarimetry and has achieved frequency locking of our 1283nm laser to within an uncertainty of .3MHz, and begun the analysis of potential systematic errors of the proposed experiment that will assist in interpreting future experimental results.
Effects of Polarization in a Fiber Laser with a Nonlinear Optical Loop Mirror
Aubryn Murray
This thesis presents work conducted with an erbium-ytterbium doped optical fiber laser. The laser employs a nonlinear optical loop mirror (NOLM) as a mode-locking device to create pulses of single picosecond duration. The development of an effective mathematical model of polarization in the NOLM is reported. Finally, the thesis examines the effects of polarization on the laser’s production of pulses.
Efficiency of Dirac Leptogenesis
Sean P. O’Brien
Effects of Excitation Bandwidth on Quantum-Confined Excitons
Jennifer E. Simmons
Despite the prevalence of quantum confined semiconductors in present technology, many of the dynamics involved in signal transmission are not fully understood. In this thesis, we are extending work previously done in the Bolton lab that focused on the effects of confinement on four-wave mixing measurements of the ultrafast exciton dynamics in the In0.04Ga0.96As quantum well samples. We present data gathered using the newly implemented grating system that allows narrower bandwidth excitation spectra than previously available in Bolton lab. The preliminary data indicates that we have successfully implemented a system that will allow the excitation of a selected type of exciton, and even sub-populations of the excitons. This grating system will enable the comparison of pump-probe data to the four-wave mixing results gathered in the past to further determine the effects of confinement on interactions in the semiconductor sample.


The Evolutionary Psychology of Jealousy in Romantic Relationships: Evidence for a Sexually Dimorphic Response Mechanism in Humans
Rebecca M. Allen
Evolutionary psychologists have proposed that men and women differ in their relative responses to sexual vs. emotional infidelity in a romantic relationship, a proposal based upon the presumption of evolved sex differences in mating strategies. Because sexual infidelity signals the possibility of being cuckolded and emotional infidelity signals the possible withdrawal of resources, men are expected to be relatively more jealous over the former whereas women are expected to be relatively more jealous over the latter. Although past research has demonstrated robust support for the evolutionary hypothesis, this support has been called into question on both empirical and conceptual grounds. In this thesis, I test the claims of the evolutionary hypothesis using a novel experimental paradigm designed to address previous methodological concerns. In two studies, participants (college students in Study 1; married adults in Study 2) were asked to consider a series of hypothetical scenarios depicting cues to either sexual or emotional infidelity and to rate their responses on a variety of continuous measures. Across both studies, as expected, women were found to be significantly more bothered by emotional cues than were men. Contrary to expectations, however, women and men displayed similar responses to sexual cues, with women having a slight tendency to be more bothered than men. The latter effect was less consistent than the former, however, giving rise to a reliable two-way interaction between sex and infidelity type (sexual vs. emotional). Although these findings were only partly supportive of my predictions, they nonetheless demonstrate that humans do display a sexually dimorphic jealousy response, and provide support for the contention that this is an evolved mechanism. Discussion addresses a number of additional findings, as well as avenues for future research.
Knowledge Is Power: Educating about Stereotype Threat as a Means to Reduce Its Debilitating Effect
Emily M. Bloomenthal
We hypothesized that we could reduce the effects of stereotype threat by making people more aware of the phenomenon itself. Participants took a math test after learning about either research on stereotype threat or an unrelated research finding, or after receiving a self-affirmation induction. We found a three-way interaction among participants‚ gender, ethnicity, and our manipulation. Men and Asian women performed worse when informed about stereotype threat than in the alternate conditions, whereas non-Asian women showed the reverse pattern, suggesting that stereotype threat education can reduce performance gaps between members of stigmatized groups and those in non-stigmatized groups by decreasing both stereotype lift and stereotype threat. We also found that men who learned about stereotype threat were less likely to consider the test fair than men in the control condition.
Castration Affects Spatial Working Memory in Male Rats: The Role of Testosterone
Ju Kim
Although much research has examined the effects of ovarian hormones (e.g., estradiol and progesterone) on learning and memory processes, the effects of testicular hormones are not as well understood. The present studies examine the effect of castration on spatial learning and memory. In Experiment 1, castrated and intact rats were trained on a standard Morris water maze task. Castration had no effect on performance during acquisition and had no effect on performance during a probe trial. In Experiment 2, the effects of castration and subsequent testosterone replacement were examined using a twelve-arm radial maze with all arms baited. Early in training, castrated rats made more working memory errors and committed the first working memory error earlier in the trial than intact rats. To examine the effect of castration on working memory retention, a 1 or 15 min delay was interpolated after either the animal’s fourth or eighth arm choice. Performance on this version of the task did not differ between the castrated and intact animals, suggesting that castration does not affect memory retention. Finally, the effect of replacement testosterone was evaluated by implanting the castrated rats with either testosterone or placebo capsules followed by testing on the standard radial maze. Interestingly, there was no significant effect of testosterone replacement on performance of castrated rats. Furthermore, performance of these groups did not differ from intact males. This pattern of results may be due to a ceiling effect in performance on the maze. Together these findings suggest that castration may have a transient negative effect on working memory in rats.
Trait-Focused Spin in Presidential Debates: Surviving the Kisses of Death
Matthew Kugler
This study examined the effects of trait-focused pre-debate spin on college student assessments of Presidential Debate outcomes. Also of interest were differences between high and low need for cognition subjects. In two experiments, participants consistently showed favorable reactions to trait-focused spin, especially for high need for cognition subjects. Study 1, employing Dole’s aggressive performance in the 1976 Vice Presidential Debate, showed high need for cognition subjects responding better to trait-focused spin than to a spin with a favorable prediction and low need for cognition subjects producing equivalent outcomes in those conditions. Study 2, employing Dukakis’s intelligent but detached performance in the second Presidential Debate of 1988, used a similar design but also incorporated negative predictive spin. High need for cognition subjects rated the target candidate more positively in the trait-focused spin conditions, even when the trait was described in negative terms. Low need for cognition subjects contrasted positive trait-focused spin and, in a non-significant trend, reacted negatively to trait-focused spin overall. Results are consistent with the debate and need for cognition literature and indicate the influence of framing on subject perceptions.
Does Priming of Teenager Stereotypes Affect Cognitive and Social Judgment Processes?
Rui Nie
Modern American culture includes the prevalent stereotype of adolescence as a very difficult period of time, including risky sexual behavior, drug abuse, and high conflict with parents. Although parent-adolescent conflict does exist, it is less frequent and extreme than implied by the stereotypes, yet those stereotypes may still influence attributions and help promote subsequent conflicts. The broad goals of the present project were to study cognitive processes that may be operative in close family relationships. Specifically, we examined the role of primed teenager stereotypes on judgment processes. In Experiment 1, we utilized supraliminal priming of college students, in the form of scrambled sentences, to ascertain the effects of stereotype activation on basic cognitive processes in a lexical decision task. Experiment 2, with college students, investigated the effects of the scrambled sentences prime on an impression formation task in which participants rated the target of an ambiguous vignette. Experiment 3, with a broader sample that included college students, parents, and other adults used the same impression formation task to examine effects of subliminal priming via a lexical decision task. In Experiment 1, primed college students had slightly faster response times than neutral participants in judging stereotypic words than neutral words on the lexical decision task, although the difference among groups was not significant. In Experiments 2 and 3, primed college students and adults made slightly higher ratings of stereotypic traits on the impression formation task than did neutral participants, although the difference between groups was not significant. Implications of the experiments are discussed in relation to parent-adolescent relationships, as well as suggestions for future research.
Popularity, Likeability and Influence: The Effect of Social Status on Peer Conformity
Lydia Romano
This study explored the impact of peer popularity and likeability on children’s tendency to conform. Children in the 4th and 5th grades (N=111) completed a baseline questionnaire assessing preferences and behavioral responses to hypothetical vignettes. Participants later participated in a simulated internet chat in which they believed that they were talking with a peer of the same age and gender. This “e-buddy” (who was described as exhibiting either high or low popularity, and high or low likeability) provided answers on target preference and hypothetical vignette questions that were diametrically opposite to those given by participants on the original questionnaire. After viewing responses of the e-buddy, participants were given the opportunity to answer these questions once again. Children’s degree of conformity was defined as the extent to which their original answers shifted toward those of the e-buddy after being exposed to an alternative view. Results suggest that neither gender of the participant nor status of the e-buddy had a significant effect on children’s tendency to conform on matters of preference. However, both gender of the participant and status of the e-buddy did have a significant effect on children’s tendency to conform in their responses to hypothetical vignettes. Specifically, boys showed more conformity than girls, and participants were more likely to conform to a peer’s hypothetical behavioral choice when the peer was portrayed as both popular and likeable. These effects remained significant even after controlling for certain key personal characteristics of the participants (e.g., self esteem, social status).
Basolateral Amygdala Modulation of Consolidation and Reconsolidation of Inhibitory Avoidance Memories
John Rudoy
The present studies examine the role of the basolateral amygdala (BLA) in the consolidation process following inhibitory avoidance training and the reconsolidation processes following reactivation. In Experiment 1, adult male rats received a single training trial on an inhibitory avoidance task. Immediately after conditioning, they received bilateral infusions of saline or the GABA agonist, muscimol, directed to the BLA. When tested 24 hr later, rats that received muscimol exhibited significantly shorter cross-over latencies than rats that received saline. In Experiment 2, rats were trained on the inhibitory avoidance task. Twenty-four hours later, they received a 1-min exposure to either the bright side of the conditioning apparatus (Reactivation) or a novel environment (No Reactivation) after which they received bilateral infusions of saline or muscimol. Animals infused with muscimol after reactivation had lower latencies than animals infused with muscimol after no reactivation. However, animals infused with saline after either treatment had low latencies as well. The findings from this study were difficult to interpret, and we hypothesize that the aversive nature of the drug infusions resulted in the pattern of behavior we observed. Specific suggestions are given for future experiments that will eliminate the source of this problem and allow for a more accurate investigation of the role of the BLA in memory reconsolidation.
Incorrect Correction for the Self-Interest Bias: How Naïve Theories of Bias Can Contribute to Poor Decision-Making
Amy Shelton
The present research was designed to test the hypothesis that when people are placed in a situation in which their preference for an outcome aligns with their self-interest in that outcome, they may be unable to determine to what extent their preference is due to their self-interest. People’s general inability to determine the cause of their feelings through introspection, combined with their naïve theories about the effects of self-interest, may result in people shifting away from their initial preference to correct for the assumed biasing qualities of their self-interest. This desire to be fair may lead, ironically, to reducing the quality of their decision. In Study 1, participants judged two essays, one of which was superior in quality to the other. All participants were given a reward incentive to prefer the essay written by someone from their in-group. Some participants were led to believe that the superior essay was written by someone from their in-group, and the inferior essay was written by someone from their out-group. The other participants were unaware of the authors’ supposed group affiliation. Additionally, some participants were primed with the concept of fairness, whereas others were not. Study 2 was designed to replicate and strengthen the results of Study 1, with some slight changes to the procedure. Overall, across the two studies, the results revealed that participants who knew which essay was in their self-interest and who had been primed with fairness tended to judge the inferior essay more positively than participants in the other conditions. These results suggest that people cannot accurately detect the times that self-interest is actually biasing their decisions, so they will tend to correct for it when the appearance of a self-interest bias is present and salient. The implications of this finding, as well as suggestions for future research, are discussed.
Are Gamblers Rational? Examining the Impact of Indivisible Goods on Individuals’ Risk Preferences
Noam Yuchtman ’05
In this thesis, I model and experimentally test the impact of indivisible goods—goods that can only be purchased in large, expensive “chunks”—on individuals’ risk preferences. I first prove that the existence of an indivisible good results in greater risk-taking by an individual in a simple, model economy. To test this theory, I designed two experimental economies that differ only in the divisibility of one good, and elicit subjects’ risk preferences in these two economies. My model’s prediction is strongly supported: subjects are significantly more willing to take risky gambles, and gambles with lower expected values, when these gambles provide the only means of obtaining an indivisible good.