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STUDENT ABSTRACTS


ASTROPHYSICS

Spiral Structure in the Galaxy M74

Christina L. Reynolds

Why are spiral galaxies spiral? This thesis is a response to that question. Rather than offering an explanation of the origin of spiral galaxies, I am presenting a description of the phenomenon observed. My case study is the galaxy M74, a beautiful face-on spiral in the constellation Pisces. I begin by considering the case of an M74 where no force is acting on the galactic disk to create spiral arms. I use this idealized, smoothed-out version of M74 as a base case to which to compare the actual M74. This comparison results in a description of the perturbation of the disk of M74 in terms of its luminosity relative to the base case.

Chapter 1 is an introduction to galaxies and the history of their observation. Spiral density wave theory is summarized in Chapter 2. Background information and past research are addressed in Chapter 3, while the observations necessary for the project are described in Chapter 4. Chapter 5 is an account of the processing and analysis of the data and contains the actual data in the form of azimuthal graphs of the galactic disk. Results and conclusions are found in Chapter 6.

BIOLOGY

An Investigation of Salt Dependent Inactivation of Antibiotic Peptides Found in Xenopus laevis Lung Tissue

Matthew R. Bachtold

Current research into the molecular mechanisms of the disease cystic fibrosis has suggested several new paths of study which may lead to the development of novel treatments. Studies on the concentration of NaCl in patients' airways show that the salt-dependent inactivation of natural antibiotic peptides may be a major cause of infection. This study performed antibiotic activity assays on Xenopus laevis lung tissue, and found no inactivation by NaCl. Peptides which are not susceptible to salt inactivation may be purified and used as a drug to treat cystic fibrosis.

Calcium Control of NPY mRNA Levels in PC12 Cells

Annaliese Beery

Neuropeptides, like neurotransmitters, are messenger molecules that are released in response to depolarization of a cell membrane and subsequent calcium influx. Different channel types have different activation kinetics, duration of activation, and/or cellular localization, and these differences may play an important role in the functioning of the cell. Neurotransmitter release in different developmental stages appears to be controlled by calcium influx through different channels, and neuropeptides may be similarly responsive. In this thesis, I begin to study how calcium influx affects genetic regulation of neuropeptide Y mRNA, to see whether this process is calcium regulated, and if the regulation is similar to regulation of neurotransmitter and neuropeptide release. Preliminary results were gathered and analyzed, and no significant response was found, however future normalization of the results may provide better resolution.

A Study of the Past and Present Ecology of the American Chestnut (Castanea dentata [Marsh.] Borkh.) in a Northern Hardwood Forest

Timothy J. Billo

This is a study of the past and present ecology of the American chestnut in the 2500 acre northern hardwood dominated Hopkins Memorial Forest (HMF) in Williamstown, MA, which lies on the extreme northern edge of the natural range of chestnut in this mountainous region. The study is based on a variety of different kinds of data including tree core increments, broad and fine scale mapping, historical observations, use of historical property and land used boundaries, and data from a permanent plot study in the HMF. The permanent plot data cover a wide range of physiographic variation and document almost 60 years of succession, the first complete survey being finished in 1937, and the last in 1996. The permanent plot study includes data on the herb/shrub layer, preblight chestnut logs, extensive tree core data, and live and dead stems of all standing trees 0.5 in, DBH.

In the presettlement forest, chestnut probably occupied as much as 60% of the canopy on well drained, south facing slopes below ridges which were prone to natural disturbances. In the postsettlement forests of Williamstown, in early to mid-successional stands (abandoned from agriculture in the 1870s and 1880s) on south facing slopes, especially bordering agricultural fields, chestnut occupied as much as 75% of the canopy. The persistence of chestnut sprouts in the understudy today, makes chestnut a good indicator of land which, at the peak of blight introduction, was adjacent to chestnut forests and abandoned from agriculture, particularly pasture, between 1890 and 1910.

Canopy openings caused by overstory defoliations in the late 1960s allowed for dramatic increases in chestnut sprout density in the 1970s. These defoliations may also have caused an increase in huckleberry cover. While in the 1970s chestnut basal area was concentrated in dense sprout colonies on land that was recently reclaimed pasture at the peak of blight damage, in the 1990s chestnut basal area was concentrated in large surviving trees on land that was mature chestnut forest at the peak of blight damage: On xeric, south facing slopes with open canopies, chestnut grows more rapidly than all other species, and it is not uncommon to find chestnuts which reach the canopy and bear fruit. The largest chestnuts are found on slightly more mesic sites, but are out competed by other species, and, as a result, do not bear fruit. The patchy distribution of sites suitable to chestnut growth in the northern hardwood forest may allow for the occurrence of relatively blight free "islands" of breeding trees. Three breeding populations have been identified in the HMF, including one population which may be a unique dwarf ecotype above 2000 ft. elevation.

The peak of blight damage in Williamstown was probably around 1920. Chestnut was replaced by beech which spread clonally into gaps left by chestnut. Today beech is generally the most important species on plots formerly occupied by chestnut although red oak is the most important species on plots prone to disturbance. Red oak most closely initiates the former role of chestnut, although chestnut probably responded (and still does) more quickly to increased light availability. On a few plots dominated by beech, oak actually occupies a slightly larger canopy percentage than beech due to the persistence of large canopy oaks. Neither species, however, has assumed the dominant canopy role which chestnut once played. Increment cores taken from preblight chestnut logs which were established on land that was once pastured show rapid and steady growth, whereas large trees in today's forest often exhibit up to two decades of relatively suppressed growth before showing strong release.

The role of insects as pollinators and blight dispersers is also studied and discussed.

Preliminary Purification of a Transcription Factor that Deactivates Interleukin-4 Expression in Murine Mast Cells

Eli Boritz

In mast cells, normal transcriptional regulation of the cytokine Interleukin-4 (IL-4) gene requires the activity of several upstream DNA sequences. One of these, the Neg-1 element, behaves like a negative regulator both in vivo and in vitro. Reporter gene experiments show that loss of Neg-1 from the IL-4 regulatory region causes more rapid transcription, and electrophoretic mobility shift analysis (EMSA) shows that the Neg-1 sequence forms a specific complex with nuclear proteins from mast cell nuclear extracts. To further investigate the regulatory functioning of this DNA sequence, we undertook to isolate the transcription factor with which it interacts. Accordingly, crude murine mast cell nuclear extracts were fractionated over a heparin-sepharose affinity resin. This method effectively separated the specific Neg-1 binding factor from the majority of nuclear proteins. In addition, partially purified binding factor retained the electrophoretic mobility and specific binding activity present in the crude extracts. To purify the Neg-1 binding factor further, partially purified samples were fractionated over a Neg-1-sepharose resin. Neg-1 binding proteins were eluted from the resin as a peak, but EMSA showed that relatively few of these proteins retained the electrophoretic mobility and specificity of the crude complex. Most binding proteins formed a Neg-1-unspecific complex of unexpectedly high electrophoretic mobility. This may mean that the Neg-1 complex contains several protein factors, and that the purification steps separate them somehow. Alternatively, the higher mobility complex observed with purified samples may be the result of a non-specific binding activity. These possibilities will be distinguished before work in this area continues.

Sphingoid Long-Chain Bases in Wounding Signal Transduction

Vy T. Bui

Sphingolipids and their derivatives have been implicated in animal signal transduction. The possibility of an analogous function for sphingolipids in plant signal transduction led to this research into the plant wounding response. Viral, bacterial, and herbivore damage initiate plant systemic acquired resistance which coordinates intracellular and extracellular processes to defend the plant from further damage. Phaseolus vulgaris leaves were pinched to mimic herbivore damage and the leaf long-chain bases were extracted after a time interval. Long-chain bases were identified and quantified using HPLC. Modified sphingoid bases, 4-hydroxysphinganine (phytosphingosine) and 8-sphingenine, consistently exhibited a transient increase 0.5 - 2.0 hours following wounding. Other long-chain bases, 4-hydroxy-8-sphingenine in response to wounding may indicate long-chain bases contribute to wounding signal transduction.

Site-Specific Mutagenesis of the Putative Magnesium Ion Binding Domain of Vaccinia Deoxyuridine Triphosphatase

Lauren Anne Burwell

The enzyme deoxyuridine triphosphatase (dUTPase) is involved in nucleotide metabolism and is important in maintaining DNA fidelity during replication. dUTPase activity is present in a variety of organisms, including prokaryotes, eukaryotes, and viruses. There are five highly conserved motifs in the amino acid sequences of organisms that encode this enzyme, and they may be essential for the activity of the enzyme.

Vaccinia virus encodes a 16.2 kD dUTPase that requires magnesium ions for activity. Motif 3 contains a Walter B sequence, a series of four hydrophobic amino acids followed by an aspartic acid residue. Walker B sequences have been implicated as the magnesium ion binding sites in enzymes that require this ion for activity. Using site-specific mutagenesis, the aspartic acid residue in the Walter B sequence of vaccinia virus dUTPase was altered in order to characterize the amino acid's contribution to the structure and function of the enzyme. Initially, this mutagenesis was attempted using a phagemid that unexpectedly expressed the vaccinia virus dUTPase gene. This vaccinia dUTPase activity interfered with the success of the Kunkel method of generating site-specific mutants. Therefore, another phagemid that did not express the vaccinia dUTPase gene was employed in order to generate mutants in the putative magnesium ion binding domain.

After the mutant enzymes have been purified, activity rests will be performed to determine the way in which the mutations affect the ability of dUTPase to bind and hydrolyze dUTP. Further studies will ascertain whether each mutant enzyme can associate as a homotrimer, the native configuration of the wild-type enzyme.

Bilateral Selective Axotomy of the Mauthner Neuron and its Effect on the Fast Startle Response of the Goldfish (Carassius auratus)

Walter W. Cheng

The Mauthner cells (M-cells) are thought to be involved in the C-start startle response in the goldfish, Carassius auratus. However, the exact role of these cells in this response has been the topic of debate for the past several decades. Studies have attempted to remove M-cell output through a variety of methods in order to see its contribution to the C-start response.

In this study, C-start response probability in goldfish undergoing bilateral selective axotomy of the Mauthner axon is not diminished when compared to controls. These results do not agree with previous selective axotomy results which have instead shown a significant decrease in C-start responsivity after double axotomy. Our results support the existence of a parallel neuronal circuit which can mediate the C-start response in the absence of M-cell output.

However, we believe that our results are not complete. Not all fish who went through this study could have their status as a double axotomy fish verified. The probability, though, is high that a number of surgically attempted double axotomy fish will turn out to be double axotomies after completion of morphological analysis. Inclusion of these putative double axotomy fish in data analysis does show a significant decline in C-start responsivity which leads us to speculate that the M-cell has an excitatory role over other neurons involved in the C-start. Further study will be needed to ascertain which conclusion is more accurate.

Differences in Morphology Imply Differences in Physiology for the Inputs to the Mauthner Cell Axon Cap

Elizabeth Helen Copanas

The Mauthner Cells (M-cells) are two large, identifiable, bilateral neurons in the goldfish, Carassius auratus, involved in the fast startle response. Surrounding the M-cell axon hillock and initial segment is the axon cap which consists of a central core and peripheral region surrounded by a glial cap wall (Bodian, 1937). The two inputs that terminate within the axon cap, namely the excitatory spiral fibers and the inhibitory interneurons, govern M-cell excitability. The PHP cells ensure that only one M-cell fires in response to an above threshold stimulus and that a given M-cell does so only once (Furukara & Furshpan, 1963; Faber and Korn, 1978; Kjorn & Fabver, 1983); Hackett & Faber, 1983; Faber et al., 1989). The inhibitory interneurons, known as PHP cells, can be divided into two groups, collateral and commissural, based on their physiology and morphology.

This study was designed to determine whether more inputs terminate within the axon cap than have been identified previously. The morphology of the cell bodies of the comissural and collateral cells projecting to the cap was also studied to examine whether these cells can be divided into different subclasses based on the number of processes originating from their cell bodies. In addition, immunohistochemistry using the rabbit KC polyclonal antibody was used to determine the presence and distribution of potassium channels within the axon cap.

We conclude that multipolar and bipolar collateral PHP cells exist that may participate in "feedforward" inhibition of the Mauthner Cell in response to visual stimuli. A separate group of unipolar cells was identified in this study that are located in the vicinity of the bipolar and multipolar collateral cells and that also project to the axon cap. In addition, unipolar and multipolar commissurant cells were identified that participate in "feedforward" inhibition of the Mauthner Cell. Therefore, differences in cell body morphology (unipolar, bipolar and multipolar) imply that each type of PHP cell plays a slightly different physiological role based on the types of inputs it receives. Finally, the Kv2.1 voltage gated potassium channel appears to be accumulated densely on the spiral fibers within the axon cap region.

The Influence of Testosterone on Song Plasticity in the Adult Male Zebra Finch

Jennifer W. Danforth

Zebra finches (Taeniopygia guttata), like other species of close-ended song learners, acquire their song during a restricted period in early development. Recent studies with zebra finches have shown that normal song development requires a period of low levels of circulating testosterone (T). A natural increase in T levels may contribute to the crystallization of song in young males by curtailing neural plasticity. Following the close of the critical period at 90 days of age, loss of plasticity allows the male zebra finch to retain one characteristic song for a lifetime. Under abnormal circumstances, however, such as deafness or damage to the tracheosyringeal (ts) nerve, changes to syllable syntax will occur in adulthood. This study investigates whether raising T levels in adult male zebra finches inhibits the type of vocal plasticity seen following ts nerve injury. Six pairs of adult male zebra finches were matched for song similarity and genetic relatedness. One bird from each pair received a testosterone silastic implant, the other received an implant filled with flutamide, a competitive inhibitor of testosterone. One month later, both groups underwent ts nerve surgery. The songs of all birds were recorded every two weeks thereafter for three and a half months and then analyzed. The flutamide treated group showed a significantly larger number of song alterations than did the testosterone treated group. The inhibitory influence of testosterone on song learning in the zebra finch thus extends beyond the close of the critical period. In addition, a novel type of song change occurred consisting of a reorganization of syllable order without an accompanying deletion or addition. Finally, flutamide was found to hasten addition of song syllables. While previous studies found that additions appeared at two weeks following surgery or later, 42.9% of additions in the songs of the flutamide group occurred one to three days after ts nerve injury. The ability of anti-androgens to promote syllable changes suggests that following ts nerve injury, T once again performs the plasticity-inhibiting role it does in juvenile finches. Since syntactical changes such as additions and deletions require the involvement of the recursive loop, a song pathway normally inactive during adulthood, the song nuclei of the recursive loop may once again become responsive to testosterone and its plasticity-inhibiting effects following tracheosyringeal nerve injury.

Pharmacologic Delay of Puberty: Effects on Song Learning in the Zebra Finch

Susan Elizabeth Gurgel

Zebra finch males learn their songs from a tutor in a process that culminates with song crystallization around 90 days of age, when syllables are fixed in a permanent order which the bird will sing for the rest of his life (Immelman, 1969). Many lines of evidence suggest that testosterone may play a role in song crystallization. The first major testosterone surge in zebra finch males occurs around day 75, and this, the hormonal event that marks puberty, is coincident with the onset of song stereotypy (Prove, 1983). Furthermore, castrated zebra finches add syllables to their songs at ages when learning is normally complete (Arnold, 1975), castration combined with antisteroid treatment blocks the production of mature, stereotyped song (Bottjer & Hewer, 1992), and males treated with testosterone early in life produce crystallized songs prematurely (Korsia & Bottjer, 1991). Thus, it appears that high plasma testosterone levels may close sensitive periods by curtailing the capacity for sensory learning.

The present study used steroid antagonists in an effort to prolong the period of neural plasticity and hold open the window during which sensorimotor learning can occur. Flutamide, a testosterone antagonist, and fadrozole, an aromatase inhibitor, were used to block the two pathways, direct and indirect (estradiol-mediated), by which testosterone affects the zebra finch brain at puberty. The songs of treated birds differed from those of controls in several respects. Most notably, 61.5% of treated birds added syllabes after 75 days of age, when songs are normally stable, whereas no control birds added syllables during this time. Additions were limited to the same few basic types of call-like notes in all treated birds that added syllables. Both the position of added syllables within the song and the age at which new syllables were added differed significantly with respect to the treatment group of the subject. Changes in syllable morphology and syllable deletions were also observed in treated birds. Thus, this study gave several indications that neural plasticity was prolonged in birds in which testosterone's actions had been blocked with antisteroid treatment.

Coordinated Regulation of Lipid Metabolism in Plants: Regulation of Microsomal Phosphatidate Phosphatase Activity in Zea Mays by Sphingoid Long-chain Bases

Trent Guthrie

Previous studies in animal model systems have established several mechanisms through which sphingolipids can act to regulate lipid biosynthesis, but there have been no investigations to date of similar effects in plants. This study showed that the presence of high intracellular concentrations of sphingoid long-chain bases induced by treatment of tissues with fumonisin can be correlated with down-regulation in the biosynthesis of both sterols, and phospholipids, specifically phosphatidylcholine and phosphatidylethanolamine. In addition, it was shown that the presence of D-sphingosine and DL-erythro-dihydrosphingosine, but not DL-threo-dihydrosphingosine or phytosphingosine, appears to significantly inhibit the enzymatic activity of microsomal phosphatidate phosphatase. These findings suggest that sphingoid long-chain bases may play a significant role in the regulation of lipid metabolism in sweet corn (Zea Mays).

The Distribution of Herbaceous Species in Primary and Secondary Woodlots in Williamstown

Susan M. Halbach

Following settlement of Williamstown, Massachusetts in 1753, the landscape was carved out for agricultural and industrial purposes, activities which had a profound effect on the native flora of the region's temperate forests, especially the herbaceous layer. Precolonial forests that have not been affected by agricultural practices are termed primary forests, while forests which have regrown on land that was previously cultivated, grazed or heavily logged are termed secondary. Many secondary woodlots have been recolonized with trees representing late-stage succession, showing that regeneration of a canopy resembling pre-colonial forest can happen in a relatively short amount of time. By contrast, the herbaceous layers differ greatly in primary and secondary woodlots, the latter having less diversity and species richness than the former. Myrmecochorous (ant-dispersed) species are virtually absent from secondary woodlots, suggesting that the limiting factor to colonization's dispersal mechanism. Past land use, however, is not the only factor that affects herbaceous communities. Herbaceous flora are also affected by tree-layer composition, with communities in hemlock-dominated woodlots extremely sparse even though the forest is primary. Limestone soils and rocky outcrops give way to richer herbaceous communities, and most species seem to flourish in very moist conditions. In a comparison between north and south-facing sites, the dry, acid soils of south-facing sites give rise to less rich herb layers.

Physical Mapping of the Tetrahymena thermophila Macronuclear Genome via Chromosomal Fragmentation

Kristen Eileen Hilty

The ciliated protozoan Tetrahymena thermophila contains two nuclei that have distinct morphologies. The somatic macronucleus is developed from the germ-line micronucleus shortly after conjugation by processes involving extensive DNA amplification, splicing, and sequence rearrangement. Although the mechanisms involved in the formation of the macronucleus from the micronucleus have recently been characterized, little is known of the arrangement of the genes themselves on the macronuclear chromosomes.

The goal of this project was two-fold. The first objective was to develop a system that will enable Tetrahymena DNA sequences to be mapped within individual macronuclear chromosomes in a relatively quick and easy manner, using a procedure that has been developed for use in Saccharomyces cerevisiae. The proposed procedure employs two vectors that will hold macronuclear sequences and will undergo homologous recombination with an endogenous macronuclear chromosome to produce two fragmented chromosomes upon linearization and transformation into Tetrahymena. The second objective was to develop two vectors that will enable a fragmented Tetrahymena macronuclear chromosome to be shuttled between Tetrahymena and Saccharomyces cerevisiae to allow for the study of macronuclear fragments in isolation from the rest of the genome. Progress has been made in the construction of both sets of vectors. While the Tetrahymena/yeast vectors have not been made, the plan for their construction has been developed. Also, the first set of vectors has been constructed and characterized. With these new fragmentation vectors, the main goal of transforming Tetrahymena with a macronuclear sequence can now be attempted.

A Quantitative and Molecular Population Genetics Study of Larval Chorus Frogs

David R. Jaskoski

This project studied the meta-population genetics of the Chorus Frog Pasudacris triseriata on North Government and South Government Islands off the NE tip of Isle Royale, MI. Clutches of eggs were collected from each island, hatched, and raised in controlled environments. Month-old tadpoles were photographed and frozen.

Quantitative morphometric analysis was conducted via the photographs. From this analysis, strong evidence for gene-pool variation between subships, between regions within islands, and between islands was found. Physical traits found to vary included the tail muscle height, and tailfin height--both of which may play a role in predator avoidance. The heritability for these two genetically controlled factors was calculated. This is the first rigorous examination of the population genetics of P. triseriata on Isle Royale, and the first quantification of heritability in wild chorus frogs.

Further analysis was done on survivorship, demonstrating that South Government tadpoles had higher mortality rates than tadpoles from North Government. This indicates that the south government population has a decreased fitness--perhaps due to inbreeding.

Qualitative genetic analysis was conducted on the frozen tissue using PCR technology. Polymorphisms were discovered and counted using RAPD markers. These data support the morphometric work in showing a significant amount of genetic variation within the metapopulation. Not enough markers were accumulated to perform statistical analyses of significant value.

Protein-DNA Interactions at the recA Operator in Bacillus subtilis: A Thermodynamic Approach to Understanding the Roles of DinR and ComK in Competence Development

Martha Browning Johnson

The RecA protein is required for induction of the SOS DNA repair system and general genetic recombination in Bacillus subtilis. In an uninduced cell, expression of the recA gene is repressed by the LexA protein. During SOS induction following DNA damage, a basal level of Rec A is activated to trigger the autocatalytic cleavage of LexA, which is then incapable of repressing recA. Evidence suggests that competence induction of recA proceeds in the absence of LexA cleavage (Lovett et all, 1989) through interaction of the competence transcription factor ComK with the recA promotor region (Hahn, 1994). This study investigates the binding of LexA and ComK to the recA promoter region in hopes of further elucidating the mechanism by which expression of recA is induced during competence development. Mobility shift assays were used to determine the dissociation constants (KD) for the interaction of both proteins with the recA promoter region. The KD was determined to be 4nM for LexA and 150nM for ComK. Based on these results and the expected intracellular concentration of ComK, it seems unlikely that induction of recA during competence is a result of the displacement of LexA by ComK alone. In conjunction with other experiments, this suggests that SOS induction and the cleavage of LexA may be necessary for efficient competence expression of recA.

Studies on Neuropeptide Y Release from PC12 Cells

Carter Jones

I have performed experiments to determine an effective method for harvesting and measuring Neuropeptide Y (NPY) from PC12 cell cultures. Several attempts were made to measure baseline levels of PC12 cellular neuropeptide Y. NPY from cell harvests were extracted with assay matrix and milliQ water to determine the effect of different extraction solvents on NPY detection. Enzyme immunoassay (EIA) of both assay matrix and milliQ water-extracted samples produced a detectable amount of NPY only once. Complete masking of NPY spikes added prior to extraction suggests possible degradation during the procedure.

EIA using HEPES-buffered saline (HBS) were also performed to determine the reliability of our experimental incubation medium as an assay solution. NPY standards prepared in HBS produced consistently larger absorbance values compared to those of assay matrix standards. Rehydration of HBS standards in assay matrix was demonstrated to transfer NPY effectively from HBS to assay matrix, although concentrating the standards interferes with NPY detection.

The Effects of Hindlimb Suspension on Phosphoglycerate Mutase Activity and Steady State mRNA Levels in Muscles of the Rat Hindlimb

Rachel A. Kell

Mammalian skeletal muscle fibers can be classified into several fiber types based on their physiological properties, biochemical composition and metabolic characteristics. Many muscle fibers have the capacity for long-term adaptation to changing work demands and exhibit plasticity under conditions which alter the weight-bearing stress imposed on the muscle. One such condition is hindlimb suspension, in which all weight-bearing stress is removed from the muscle. As a result of hindlimb suspension, muscle fiber type expression switches from fibers which utilize oxidative metabolism to fibers which rely on glycolytic metabolism. Phosphoglycerate mutase (PGAM-M) is an enzyme vital to the final stages of glycolysis. To study the effects of hindlimb suspension on this glycolytic enzyme, we analyzed the steady state mRNA levels and the enzymatic activity of PGAM-M in four hindlimb muscles of control rats and in rats which had undergone a month of hindlimb suspension. In the oxidative soleus muscle, PGAM-M mRNA was increased following suspension while three other glycolytic muscles showed no significant change in PGAM-M mRNA levels and PGAM-M specific activity following suspension. Activity levels decreased significantly in both the soleus and extensor digitorum longus (EDL). These results suggest the involvement of other mechanisms regulating PGAM-M gene expression. We also observed lower PGAM-M specific activity as well as lower PGAM-M mRNA levels in the oxidative control muscle (soleus) as compared with the glycolytic control muscles. This finding indicates that the increase in PGAM-M specific activity in the soleus is pretranslationally regulated.

Construction of EXM1 and EXM2 Gene Deletions in S. Cerevisiae

Karen Sisi Lee

EXM1 and EXM2 (Exit from Mitosis) are two novel Saccharomyces cerevisiae genes putatively identified to be involved in a checkpoint regulatory mechanism that monitors cellular exit from mitosis. In order to characterize more completely the roles of these genes in this checkpoint system, two different gene deletion techniques were employed in an attempt to disrupt the function these genes in vivo. Because an EXM2 plasmid construct with amenable restriction sites was available, simple cloning steps were used to generate successfully an 84% deletion of the open reading frame of EXM2. To create this gene disruption, 684 base pairs (BPS) of the 786 bp EXM2 open reading frame was replaced with a hisG-URA3-hisG construct that can undergo mitotic recombination to eliminate the URA3 marker. Unlike EXM2, none of the existing plasmid constructs containing EXM1 had convenient restriction sites suitable for the conventional cloning procedure used to generate the EXM2 deletion. Thus, the creation of an EXM1 null allele was attempted through the use of double fusion PCR, a technique that completely and precisely eliminates the open reading frame of the gene. Double fusion PCR was successful in generating a genetic construct suitable for transformation into yeast that contained the LEU2 selectable marker flanked by the 3' and 5' adjacent regions of the EXM1 gene. Because this complete fusion product could not be amplified by PCR, however, this EXM1 null construct could not be integrated into yeast due to the low concentration of DNA used in the transformation. These results suggest that the conventional cloning procedure employed to make the EXM2 gene deletion is more efficient and reliable than the double PCR fusion technique used for the EXM1 null allele. Once the EXM1 and EXM2 gene disruptions have been completely constructed and integrated into diploid yeast, the phenotypes of these deletion mutants can further clarify the in vivo functions of these genes.

The Vaccinia Virus dUTPase Gene: Disruption in Tissue Culture and Site-Specific Mutagenesis of a Conserved Motif

Elizabeth J. Maxwell

Vaccinia virus is a large double-stranded DNA virus that replicates in a host cell's cytoplasm. The virus relies little on host functions and encodes many of the enzymes involved in DNA metabolism and synthesis. One such enzyme is dUTPase. Found in a variety of organisms, dUTPase is thought to play a role in nucleotide precursor metabolism and in the prevention of uracil incorporation in DNA. Studies of the vaccinia dUTPase protein has shown that it requires a Mg2+ cofactor for catalysis. It is thought that Mg2+may associate with the third of five highly conserved motifs in the enzyme. This motif resembles a Walker B sequence, implicated as a Mg2+ binding site in a variety of NTPases.

The present study had two objectives. The first goal was to alter the conserved aspartic acid residue located at position 82 in the third motif, the putative Walter B sequence. Using site-specific mutagenesis, this aspartic acid residue was successfully changed to an asparagine and to a glutamate. Mutant proteins possessing these changes lacked dUTPase activity. Pre-incubation with excess Mg2+ failed to restore activity to the mutants. Thus, the aspartic acid residue at position 82 was shown to be essential for the enzyme's activity.

The second objective was to disrupt the dUTPase gene within the vaccinia genome using a dominant selectable marker. The failure of a previous attempt to disrupt the dUTPase gene suggested that the gene was essential, although it had been eliminated in large scale genomic deletions. One such deletion mutant possessed a small plaque phenotype that was not screened for in the previous attempt to disrupt the dUTPase gene. In this study, recombinant virus was produced and formed plaques with an unusually small size. However, technical difficulties delayed the isolation of recombinant virus from live monolayers, which was eventually accomplished by switching cell lines. Once this recombinant virus is purified, it will be analyzed by southern blot to determine if the dUTPase gene has been disrupted.

Detour Ahead: Retinal Ganglion Cells Directed to a Foreign Muscle Target

Jason Robert Meyers

Retinal ganglion cells (RCGs) are the group of central interneurons that form the sole output of the retina to the brain. They are capable of highly specific regeneration into the optic tectum in lower vertebrates, which can lead to functional recovery of vision. Though RGCs show a particularly strong affinity for the optic tectum, they can be surgically directed to non-optic regions of the brain where they are capable of forming functional synapses. In the present study, RGCs of goldfish were axotomized by transection of the optic nerve, and their regeneration was redirected to the superior oblique muscle with a nerve bridge made from the posterior lateral line nerve of the fish. After allowing 60-90 days for regeneration, numerous RGC axons could be traced into the lateral line implant and the superior oblique muscle, where they appeared to form synapses. This is the first report of vertebrate central interneurons forming synapses on a peripheral muscle target. following stimulation of the implant, long-latency EMG responses were recorded in the superior oblique muscle, indicating that the synapses formed are functional. These EMG responses have a light-sensitivity, for after a period of 30-60 minutes of almost complete darkness, some EMG responses increased in amplitude by up to 167%. However, RGCs are glutamatergic, whereas acetylcholine is the neurotransmitter at the vertebrate neuromuscular junction. Hence, these results imply a phenotypic change of neurotransmitter for either the pre-synaptic or post-synaptic cells in this novel neuromuscular junction.

Addition by Subtraction: Early Catecholaminergic Lesion of the Zebra Finch Area X Leads to Increased Number of Notes in Song

Franklin M. Mullins

The male zebra finch (Taeniopygia guttata) learns its song from adult tutors during a sensitive period spanning days 25 to 90 post-hatch. Around day 90, song "crystallizes," or stops changing.

The zebra finch forebrain nucleus Area X is necessary for normal song development but not for normal maintenance of adult song (Scharff & Nottebohm, 1991). A developmental trend in which the catecholaminergic innervation of Area X increases throughout the sensitive period has recently been characterized (Soha et al., 1996). This experiment determined the effects of depleting catecholamines in Area X during the sensitive period on song acquisition.

Juvenile zebra finches aged 30 to 45 days were given stereotaxic microinjections of either the catecholaminergic neurotoxin 6-OHDA or a saline (vehicle) solution. compared to birds receiving saline injections, birds treated with 6-OHDA had greater numbers of notes in their songs and had more variable songs according to the sequence linearity measure. The greater variability reflected by 6-OHDA-treated birds' lower sequence linearity scores arose from their singing more atypical internal transition types than sham birds.

There were no significant differences in catecholamine histofluorescence in brain sections from sham-operated and 6-OHDA-treated birds sacrificed at six months post-surgery. This finding verified Soha's result that significant ingrowth of catecholaminergic terminals into Area X can continue until late in the sensitive period.

Because the trend of increasing catecholaminergic innervation in Area X continues at least up to and perhaps past the time of crystallization, it is unclear whether catecholamines in Area X facilitate song plasticity or contribute to closing down the sensitive period. This study's results could be interpreted as consistent with a model in which catecholamines help end the sensitive period.

On the Way to Cellular Localization of EXM2

Sheyda Namazie

Fidelity of the eukaryotic cell cycle, a highly regulated sequence of temporal events, is critical for survival of the eukaryotic organism; an error occurring at any stage of the cell cycle could result in cell death and severe genetic damage to the organism (Allen et al., 1994). Because of the importance of the cell cycle, it is logical that the cell exercises tight control over the ordering of the cell cycle events.

One manner in which control over the cell cycle is exercised is through the check point mechanism. A number of regulatory checkpoints exist throughout the cell cycle at points such as entry-into and exit-from mitosis (Agarwal et al., 1995, Weinert et al., 1994). At these checkpoints, the cell cycle pauses to verify that all prior events were successfully completed. If the events were not successfully completed, the cell cycle engine would pause until necessary repairs of damage or completion of upstream events were ensured (Enoch and Norbury, 1995, Hartwell and Kastan, 1994).

Therefore, a careful study of checkpoint control mechanisms of the genes involved in checkpoints is critical. Two genes called EXM1 and EXM2 isolated from the organism S. cerevisiae have been implicated in the exit-from-mitosis checkpoint (Raymond, 1996). This work begins the examination of the cellular localization of EXM2. A pET21-a(+)-EXM2 plasmid was prepared through the subcloning of EXM 2 from the pWR1054 plasmid into the pET21-a(+) vector. Subcloning was accomplished through the creation of restriction sites flanking the EXM2 gene. These sites were used in the excision of the EXM2 and subsequent ligation into the pET21 vector between corresponding restriction sites. The EXM2 ORF is located downstream of the pET vector's T7 promotor and upstream of the pET vector's His-6 tag. Future work will involve overexpression and purification of the Exm2 protein, followed by preparation of antibodies to the protein. These antibodies can then be used in a variety of manners, including indirect immunofluorescence experimentation. This can lead to the cellular localization of the Exm2 protein and thus, will further the characterization of a potentially important checkpoint gene.

SPF1, A Cold-Sensitive Suppressor of cdc14-7, Regulates Exit from Mitosis

Leocadia Victoria Paliulis

Proper cell cycle progression is necessary for maintenance of an organism. One essential component of the yeast (Saccharomyces cerevisiae) cell cycle is CDC14. CDC14 encodes a protein tyrosine phosphatase which contains other functional domains (Wan et al., 1991, Shirayama et al., 1996). The goal of this work was to study two extragenic suppressors of temperature-sensitivity of cdc14-7, sup1-15 and sup9-13. In this study, it was determined that sup1-15 and sup9-13 are two alleles of the same gene, SFP1 (Split Finger Protein 1). SFP1 has a nuclear localization sequence and two Cys2 His2 zinc-finger domains split by approximately 40 amino acids (Blumberg and Silver 1991). It was determined that sup1-15 cannot suppress lethality of a cdc14-disruption mutant, indicating that suppression is not through a complete bypass of CDC14 function. An sfp1-null mutant was created, found to be cold-sensitive, and found to suppress temperature-sensitivity of cdc14-7. Results found from creation of the sfp1-null indicate that suppression of temperature-sensitivity of cdc14-7 does not involve restoration of a protein-protein interaction between sfp1 and cdc14. Microscopic observations show random bud polarity in sup1-15 cells. cdc14-7, sup1-15 double mutants had abnormal mitotic spindles. Compared to wild type, sfp1-null mutants display an altered reaction to treatment with nocodazole, showing a delay in cell cycle arrest. These data suggest that sfp1 may interact, not only with CDC14, but with many other members of the exit-from-mitosis machinery in controlling an exit-from-mitosis checkpoint through one of a number of possible models.

Using Random Amplified Polymorphic DNA Markers to Study the Genetics of Tetrahymena thermophila

Sylvia Y. Park

Tetrahymena thermophila, a ciliated protozoan, has two nuclei: the macronucleus and the micronucleus. During conjugation, the macronuclear genome is created by extensive DNA rearrangement and deletion of a copy of the micronuclear genome. To investigate macronuclear development, polymorphic markers (occurring between two inbred strains B and C3) on chromosome 5 were obtained through RAPD PCR methods (outlined in Brickner et al., 1996) and used as probes. Probes were hybridized to target DNA on Southern blots made from pulsed field gel electrophoreses of Tetrahymena's macronuclear genome. With some exceptions, obtaining micronuclear probes through RAPD PCR proved to be an expedient and reliable method. The results give some clues into macronuclear genome processing and development.

Analysis of Plant Sphingolipids: Relevance to the Cancer-Preventative Effects of Dietary Fruits and Vegetables

Jessica Wege

Sphingolipids are involved in a number of signaling pathways including ion transport and cell growth. Recently, sphingolipid involvement in cell growth has been examined with respect to possible cancer-preventative properties. It was discovered that milk sphingolipids and glycosphingolipids inhibit the formation of colonic cysts. The interest in dietary sphingolipids has led to our research on the composition of glucosylceramide long-chain bases in plants, given that plant-rich diets are associated with decrease incidence of cancer, and studies aimed at testing plant sphingolipids as cancer-preventative agents are planned. Glucosylceramides are the prevalent glycosphingolipid in plant cells. Our results show similar long-chain base profiles for apple, tomato and summer squash which contained a large amount of cis- and trans-double bonds. Potato was predominantly di-hydroxy long chain bases with equal amounts of both cis- and trans-double bonds. Broccoli proved to be an anomaly with 30% of the long-chain bases as 4-hydroxysphinganine (t18:0) which does not appear in any other type of plant published to date. These results are a first step in more comprehensive studies examining the effects of plant sphingolipids as cancer-preventative agents.

The Genetic Structure of Arctic Disjunct Populations of Sagina nodosa (Caryophyllaceae), Isle Royale, Michigan

Jason A. Wilder

On the islands at the northeastern end of Isle Royale National Park, Michigan there exist populations of arctic plant species that are completely disjunct from their main home ranges in the arctic. In this project I mapped the disjunct ranges of six of these arctic species on 27 different islands at the NE end of Isle Royale. Tissue samples were taken from two species, Sagina nodosa (Caryophyllaceae) and Saxifraga tricuspidata (Saxifragaceae), and a variety of different protocols were used to attempt to extract genomic DNA from these samples. Using random amplified polymorphic DNA (RAPD) analysis, I examined the population structure of Sagina nodosa. This analysis revealed 40 different polymorphic loci (based on four 10 oligonucleotide primers). These variable loci showed that 90.2% of the genetic diversity was partitioned within populations, while 9.8% occurred among populations. Further, the island populations were highly differentiated, with an FST value of 0.546 (indicating extensive population subdivision). Internal structure of the island populations was not based on relatedness of geographically close individuals, as there was no correlation between increasing genetic distance with increasing geographic separation between individuals. Cluster analysis revealed that there may be some within population genetic structuring based on distance above the average water-line. Data from the North Government Island population suggest that individuals that grow close to the water are more closely related to each other than to individuals from higher on the shore. The pattern shown by the Isle Royale arctic disjuncts, where island populations are highly differentiated, but still retain extensive genetic diversity within populations, is probably maintained by a balance of genetic drift, genetic structuring within populations mediated by differential selection, and rare gene flow events between populations.

Photoaffinity Labeling and Proteolytic Cleavage of Vaccinia Virus dUTPase

Jane Yoo

Deoxyuridine triphosphatase (dUTPase) plays a critical role in the growth cycle of cells and thus serves as a possible target for gene therapy. Characterization of dUTPase's active site may facilitate the development of chemotherapeutic agents and is therefore an important step in this process. The experiments performed in the present study were directed towards the specific goal of characterizing the dUTP binding site in vaccinia dUTPase via a procedure that is generally used to identify nucleotide binding sites on proteins. This technique is based on a combination of photoaffinity labeling, which covalently links the protein and a radiolabeled target nucleotide at the protein's active site, and proteolytic cleavage, which subsequently digests the labeled protein at specific and characteristic sites. Separation and identification of labeled products by SDS-PAGE and autoradiography reveal peptide domains that are likely involved in nucleotide binding. Before proceeding with this technique, it was first necessary I) to demonstrate successful cleavage of dUTPase by our selected proteolytic reagents and ii) to show that our chosen nucleotide substrate, ATP, covalently crosslinks to dUTPase in a manner that is specific, competitive, and dependent on UV exposure, thereby demonstrating its utility for photoaffinity labeling. Here, we report the derivation of protocols for digestion of dUTPase by hydroxylamine, cyanogen bromide, and endoproteinase Lys-C; and we report unsuccessful initial attempts at demonstrating the utility of ATP as a cross-linking substrate analog for future photoaffinity labeling experiments.

CHEMISTRY

Kinetic Studies of the LexA Repressor Autodigestion: Determination of Temperature Dependence and Thermodynamic Parameters

Darci A. Gaiotti

The Bacillus subtilis SOS DNA-repair system is comprised of approximately 20 din (damage inducible) genes which are constitutively repressed by the 22.7-Kd protein, B. subtilis LexA. When DNA damage occurs in a B. subtilis bacterial cell, the LexA repressor undergoes cleavage to allow for the expression of the din genes and thereby activate the full SOS response.

Repressor cleavage is mediated by a second protein, RecA, activated by a single-stranded DNA signal generated by the damaging agent. The cleavage has been characterized as an intramolecular general base-catalyzed hydrolysis of the peptide bond between the alanine-91 and glycine-92 residues of the protein. In the proposed cleavage model, an ionized lysine residue abstracts a proton from the oxygen of a serine residue and thereby activates the serine oxygen towards nucleophilic attack of the carbonyl carbon of the peptide bond.

This work investigates the autodigestion of the repressor in vitro in order to further elucidate the mechanism of B. subtilis LexA cleavage. The thermodynamic parameters of the reaction were determined by examining the pH dependence of the reaction rate at two different temperatures, 37[ring]C and 47[ring]C. The rate assays were done in high pH boric acid buffers to effect ionization of the catalytic lysine residue and thereby cleavage in vitro.

A pKa of 9.52 and a kmax of .91/hour were determined for the 37[ring]C autodigestion of B. subtilis LexA; at 47[ring]C, a pKa of 9.12 and kmax of 1.41 were determined. Using these results, the thermodynamic parameters of the reaction with wild-type repressor were calculated. For the ionization step, the following were found: [Delta]G=13.5 kcal/mol, [Delta]S=14.9 cal/K
*mol, and [Delta]H=18.1 kcal/mol. For the activation step, [Delta]G=23.3 kcal/mol, [Delta]S=49.4 cal/K
*mol and [Delta]H=8.0 kcal/mol.

Synthesis and Partial Characterization of Ruthenium Lewis Acid-Urea
and Ruthenium Lewis Acid-Amide Complexes

Jin W. Kwon

Transition metal Lewis acid complexes with carbonyls are applicable for a number of fields, including organic synthesis, and can sometimes provide a simpler model for biological systems. The carbonyl groups of ureas and amides were examined. The urea ligands used in this analysis were urea, 1,1-dimethylurea and1,3-dimethylurea. Mass spectral analyses, conducted in lieu of combustion analyses, provide evidence for coordination between the urea ligands to the ruthenium. The amide ligands used in this analysis included acetamide, 2-pyrrolidinone, and dimethylformamide. Dynamic behavior may be occurring within the dimethylformamide complex because of steric considerations, such as E vs. Z isomerization. Spectroscopic characterization of the ruthenium-urea and ruthenium-amide complexes provides evidence for [sigma] coordination between the lone pair of electrons on the oxygen of the ligand to the ruthenium.

Complex Dynamics in a Modeled System of Two Coupled Oscillators

Casey H. Londergan

Most hormone concentrations in the body are regulated by negative feedback mechanisms in which the production and release of hormones are regulated according to the concentration of related species. Many hormones are released in a pulsatile manner. A wide range of pulsatile release patterns have been observed in different hormonal systems. The mechanism driving these complex release patterns is not known in most cases. The mechanistic complexity needed to sustain complex hormonal release patterns is a matter of much recent conjecture.

A simple six-species, ten-parameter model of two chemical oscillators coupled through their external products is analyzed to investigate the possibility of a simple system's ability to sustain complex dynamical behaviors like the release patterns observed for hormones in vivo. Although analytical methods for measuring hormone concentrations in vivo have improved greatly in recent years, it remains very expedient to observe the behavior of models similar to the physiological systems in question to answer questions about mechanisms and reasons behind hormone release.

The simple model of two coupled oscillators coupled through negative feedback to their external products sustains a wide range of different periodic, chaotic and other dynamical behaviors. The coupling between the two oscillators is the element responsible for the appearance of these behaviors. The range of dynamical behaviors observed in the model demonstrates that something as simple as a physiological feedback loop with similar coupling between circulatory concentrations of hormones and production centers could be the source of complex hormone release patterns observed in vivo.

Synthesis of Organic Electrochromic Materials based on Benzoquinone Centers and Attempted Synthesis of an Anthraquinone Ligand for a Ruthenium-Polypyridine Complex

Benjamin W. Partan

The synthesis of the potentially useful electrochromic compound 2,5-bis--(4,4-dipyridyl)-3,6-dioxy-1,4-benzoquinone (1) was attempted in a variety of solvents and conditions. Using 2,3,5,6-tetrachloro-1,4-benzoquinone and six equivalents of 4,4-dipyridyl in refluxing acetonitrile for 12 hours resulted in a 58% yield of 2-(4,4-dipyridyl)-3-oxy-5,6-dichloro-1,4-benzoquinone (2) as determined by 1H-NMR, 13C-NMR, and FT-IR. The yield was increased to 78% in refluxing o-dichlorobenzene. Using 2,3,5,6-tetrafluoro-1,4-benzoquinone and six equivalents of 4,4-dipyridyl in chloroform at room temperature resulted in a 66% yield of 2. Using 2,3,5,6-tetrafluoro-1,4-benzoquinone and one equivalent of 4,4-dipyridyl in chloroform at room temperature resulted in a mixture of products that contained 2 as well as an unidentified compound which could not be isolated that could be 1.

Synthesis of a Chiral Benzene-Ruthenium (II) Catalyst for Use
in Hydrogenation Reactions

Natalia Raoof

The goal of this project was to synthesize a chiral catalyst with a ruthenium center for use in hydrogenation reactions. Attempts at synthesizing the catalyst involved coordinating various chiral phosphine ligands to a benzene-ruthenium molecule by cleaving the dimer, [(u6-C6H6)RuCl2]2. Preliminary procedures entailed synthesizing the catalyst by allowing the dimer to react with the ligand directly. However, low yields necessitated producing a precursor molecule, [(u6-C6H6)RuCl(CH3CN)2]+PF6-, to the catalyst. Reactions between the dimer and NH4PF6 in CH3CN resulted in the production of this precursor which, when reacted with the phosphine ligand bis(diphenylphosphino)butane (CHIRAPHOS), resulted in the production of the catalyst in high yield. A determination of the effectiveness of the catalyst in the chiral hydrogenation of 3-methyl-2-cyclohexen-1-one resulted in 100% conversion to 3-methylcyclohexanone. The optical activity of this product was not determined at this time.

Preparation and Electrochemical Investigation of Mono- and
Bis-Pyridinium Anthraquinones

Jean L. Raphael

The goal of this research has been the preparation and electrochemical investigation of a series of mono- and bis- pyridinium anthraquinones in order to determine the effects of pyridinium substituent position and number on reduction potentials. The 2-(4-dimethylaminopyridinium) anthraquinone and 1,8-(4-dimethylaminopyridinium)anthraquinone were readily prepared in respective yields of 48.2% and 39.8%. The 1,5-(4-dimethylamino-pyridinium)anthraquinone was prepared in 68.6% yield by isolation and purification of the mono-pyridinium product of the 1,5-dichloro-anthraquinone and subsequent reaction with 4-dimethylaminopyridine. Electrochemical characterization of the prepared pyridinium anthraquinones shows that pyridinium substituent position and number can be used to modestly modify the reduction potentials of anthraquinones. In order to expand upon this work, the preparation of mixed pyridinium anthraquinones was also attempted. Although no successful preparations were carried out, mixed pyridinium anthraquinones may be synthesized by the isolation of the mono-pyridinium product of the 1,5-dichloroanthraquinone and subsequent reaction with a different pyridine. The preparation of pyridinium hydroanthraquinones was also attempted in order to more fully characterize the pyridinium anthraquinones. Unfortunately, this reaction was unsuccessful under a variety of conditions

An FT-IR Study of the Interactions of Sulfur Dioxide and Soot
from -100deg.C to -150deg.C Abstract

Henry G. Roe

The realization in the last 10 to 20 years that heterogeneous reactions in the atmosphere play an important role in atmospheric chemistry has led to increased interest in studying atmospherically relevant gas-solid and gas-liquid reactions in a laboratory setting. One current puzzle in atmospheric chemistry is that in some situations, such as in contrails of high altitude jets or industrial plumes, there is an observed overabundance of sulfuric acid and underabundance of sulfur dioxide compared to what is expected from models based on known chemical reactions. Some researchers have suggested that SO2 conversion to H2SO4 on the surface of soot particles may explain these observations.

Using a vacuum system designed for the infrared spectroscopic study of atmospherically relevant surface reactions, I investigated the interactions of SO2 and soot over the temperature range of -100deg.C to -150deg.C and the pressure range of 10-7 to 10-4 Torr. I observed and quantified sub-bulk rapid adsorption of SO2 to soot and a slower adsorption on, or diffusion into, soot by SO2. Developing a kinetic model to explain the rapid adsorption, I estimated the initial sticking coefficient of SO2 on soot to be 0.01 (0.004 to 0.05) at -135deg.C. When soot is exposed to SO2 under sub-bulk growth conditions, one or more reaction products that absorb in the 1050 to 1200 cm-1 region form on the soot. This reaction product or products desorb with heating to -80deg.C. Other reaction products absorbing at below 1000 cm-1 form on soot when exposed to SO2 and higher trace concentrations of H2O. These reaction products absorbing below 1000 cm-1 form a non-volatile residue believed to be H2SO4.

Future work will continue this investigation of SO2 and soot attempting to quantify what I observed and also moving to warmer, more atmospherically relevant, temperatures.

Preliminary Characterization of Two Interacting Sequences Within the
Interleukin-4 NEG-1 Negative Regulatory Element in Murine Mast Cells

Stacey E. Rutledge

A Negative Regulatory Element termed NEG-1 which functions in mast cells has been previously identified in the murine Interleukin-4 promoter. (Weiss, unpublished results) Reporter gene assays identified two subregions, termed Neg 1A and Neg 1B, which are critical to NEG-1 function. Mutation of either region in reporter gene constructs led to significant increases in reporter gene activity, which demonstrates that Neg 1A and Neg 1B do not function independently. An oligonucleotide which spans NEG-1 was used as probe in Electrophoretic Mobility Shift Assays (EMSAs) with nuclear extracts from murine mast cells to determine which bases are critical for protein binding to this region. Cold competition experiments, using molar excesses of Neg 1A and Neg 1B, indicated that Neg 1A, but not Neg 1B is critical for protein binding to NEG-1. The NEG-1 oligonucleotide, however, extends only two base pairs past the Neg 1B site, and for protein to be able to bind this site, more of the 3' flanking region is likely needed. In this study, oligonucleotides spanning Neg 1B only, termed Neg 1B, and the entire NEG-1 region (with more of the Neg 1B 3' flanking region), termed Neg 1A+B as well as a mutant version of the Neg 1A+B oligonucleotide were used as probe in EMSAs. Neg 1B was unable to form a specific DNA-nuclear protein complex under a variety of binding conditions. Neg 1A+B forms a complex of higher mobility than the complex formed with Neg 1A. These results support a cooperative model of protein binding to Neg 1A and Neg 1B.

The Menschutkin Reaction of Strained Heterocyclic Systems

Poorab K. Sangani

The pseudo first order rate constants for the Menschutkin reaction of 2,3-dimethylquinoline 7, 2,3-dihydro-1H-cyclopenta[b]quinoline 8, 1,2-dihydrocyclobuta[b]quinoline 9, 2-benzylpyridine 10, 2-benzhydrylpyridine 11, and 1-azatriptycene 12 with iodomethane in acetonitrile-d3 at 50 [ring]C were measured by proton NMR spectrometry. Duplicate kinetic runs gave precise (<= +/- 2.8%) linear (R coefficient >= 0.993) rate constants. Ring strain effects on basicity were not correlated with the observed rate constants. Ring strain effects on molecular geometry and steric interference were applied to explain the trends in relative reaction rates across compounds 7-9 and 10-12.

A Concise Route to Isocanthine Alkaloids

David A. Vosburg

A concise synthesis of 5,6-dihydro-4H-indolo[3,2,1-ij][1,6]naphthyridine (6), an isomer of canthine (3), was attempted in three steps from indole-3-carboxaldehyde (9). The key step, an intramolecular hetero Diels-Alder reaction, gave the desired isocanthine only as a minor product. An analogous synthesis of 1-methyl-isocanthine (14) was likewise unsuccessful. A concise four-step synthesis of isocanthin-6-one (8) was attempted. 4,5-Dihydro-isocanthin-6-one (11), the direct precursor of 8, was synthesized in three steps in 45% overall yield. Preliminary attempts to oxidize 11 to 8 with DDQ were unsuccessful.

Low Temperature Collisional Electronic Quenching of Nitric Oxide
Laser-Induced Fluorescence (A2[Sigma]+, v'= 0)

Frederick C. Winston

Following single photon excitation (A2[Sigma]+, v'= 0 <- X2[Pi], v" = 0) of nitric oxide (NO), we study the behavior of the fluorescence transition (A2[Sigma]+, v'= 0 -> X2[Pi], v" = 3) in the presence of NO, argon, methanol, benzene, thiophene, toluene, and cyclohexane between 215 K and 300 K. By examining the fluorescence decay lifetime of a gas mixture containing NO and a collision partner as a function of the partial pressure of the collision partner, we determine the quenching cross section ([sigma]) of the collider, a term reflecting the electronic collisional quenching effect of the collider on the fluorescence quantum yield of the gas mixture. The temperature dependence of s reveals information about the transfer of energy between the excited NO molecule and the quenching species.

The argon and cyclohexane room temperature and low temperature quenching cross sections are negligible, reflecting their non-existent dipole moments and non-aromatic structures. Impurities in the gas sample, in particular water, account for an insignificant increase in the quenching cross sections of these colliders with increasing temperatures.

NO, methanol, benzene, thiophene, and toluene are efficient quenchers with quenching cross sections significantly larger than gas kinetic cross sections. As the temperature decreases the quenching efficiency of these five molecules increases. Using the Parmenter attractive force model, the cross-sectional temperature dependence of the five molecules is analyzed . The potential well depths of NO, methanol, benzene, thiophene, and toluene are 49 cm-1, 112 cm-1, 118 cm-1, 105 cm-1, and 126 cm-1, respectively. Based on the dipole moments, polarizabilities, and electron affinities of each molecule, the calculated potential well-depths support the hypothesized dominance of collision complex formation and near-resonant electronic energy transfer at low temperatures. There is no conclusive evidence, however, that the near-resonant energy transfer accounts for the observed increase in quenching cross sections at low temperatures.

COMPUTER SCIENCE

Phil-Tor: Natural Language Preprocessing in Filtering Techniques

Jeffrey G. Bolas

As the size of on-line information resources increases exponentially, new tools are becoming necessary to navigate the informational glut. Recently, information retrieval has turned to artificial intelligence as one method for counteracting the low signal-to-noise ratios that plague most search queries. This thesis applies machine learning to the task of content-based filtering, with a specific examination of how natural language preprocessing affects filtering performance. It is hypothesized that a vocabulary consisting of adjacency bigrams will facilitate improved learning, as opposed to a vocabulary consisting of word tokens. We collect a data set suitable for document rating research. We will show that natural language analysis in the form of adjacency bigrams does not improve performance. We will also describe a learning algorithm that outperforms similar filters on small training sets.

Adding Concurrency to LOOM

Hilary K. Browne

Over the past decade, both object-oriented and concurrent programming languages have become popular tools for solving complex problems, and language designers have recognized that combining these two paradigms can be useful. Concurrency allows object-oriented languages to address more types of problems and potentially speed up execution. Object-oriented features can improve the organization of concurrent programs and potentially remove some of the low-level process control by encapsulating it in object structure. In this thesis, we explore the addition of concurrency to the object-oriented language LOOM, focusing on providing a safe, easy to use language for programmers familiar with object-oriented programming but not necessarily with concurrency. We introduce a large grain of concurrency by identifying processes with objects, and allow these objects to communicate both synchronously and asynchronously using the existing message structure. Special semantics for self-inflicted messages prevent deadlock when processes send messages to themselves, but mutually referential objects can cause deadlock. Conditional synchronization of message reception is handled with separately inheritable pre- and post-condition sections in classes, avoiding extensive redefinitions of synchronization constraints in subclasses and most forms of inheritance anomaly.

GEOSCIENCES

Sackung on Dead Indian Hill, Park County, Wyoming

Molly B. Barrett

Sackung, or gravitational spreading of the ridge-top of Dead Indian Hill (elevation, 2644 m) has resulted in a summit trench approximately 70 m wide and 400 m long as well as uphill-facing scarps and small linear trenches. Dead Indian Hill, a cuesta located just south of the mouth of the canyon of Clarks Fork of the Yellowstone River, is part of a monocline of Paleozoic and Mesozoic sedimentary rocks with an east dip ranging from 6 to 15 degrees. The summit trench trends 015o, the primary joint set is oriented at 020-030o, and a secondary set trends 120-130o. Talus mantles both the east and west slopes, and a block slope and block stream extend beyond the talus on the east side. The blocks of the taluses, block slope, block stream, and bedrock at the summit trench are competent sandstone of the Pennsylvanian Tensleep Formation. Beneath are the shales and limestones of the incompetent Upper Mississippian/Lower Pennsylvanian Amsden Formation.

Field observations are used to determine how this summit trench fits existing theories of sackung initiation. Potential weaknesses include the dipping bedding planes which could accommodate slippage of sandstone over shale, and the joints which are subparallel to the main trench. Furthermore, solution cavities in the limestones of the Madison and Amsden Formations include a sink in nearby Sunlight Basin as well as several caverns in the US 296 roadcuts near the top of Dead Indian Pass. The shales have locally failed numerous times, including landslides in Cambrian to Cretaceous shales throughout the area and a large landslide in the Cambrian Gros Ventre formation on the west side of Dead Indian Hill. These shales could contain one or more failure surfaces. Removal of lateral support has resulted from downcutting by the Clarks Fork and the creek along Dead Indian Gulch; this has destabilized the slopes, especially on the east side where Dead Indian Gulch has removed the toe of the dip slope of the Tensleep and Amsden Formations. Other potential factors include seismic shaking, which could trigger slope failure, and the structure at the site, which includes several steep faults. Furthermore, a former wetter and/or colder climate could facilitate rock falls and movement of joint blocks by increasing fluid pressure and periglacial activity.

It is most likely that the sackung at Dead Indian Hill was caused by the removal of the toe of the dip slope by fluvial erosion to the east of the summit, with probable seismic triggering. Failure is hypothesized along the contact of the Tensleep and Amsden Formations, or slightly below it, with elevated pore pressure reducing the friction along the plane to permit sliding. Stress analysis suggests failure along planes dipping at 60o; these planes are most likely joints.

The Shores of Wyoming: Depositional Environments of the Middle Cambrian Flathead Sandstone, Park County, Wyoming

Robin A. Beebee

The Flathead Sandstone of northwestern Wyoming and Montana is a quartz-rich sheet sandstone overlying the Archean igneous and metamorphic basement rocks of the area. It represents the first cycle of deposition as the Cambrian sea transgressed over the craton, and is Middle Cambrian in age. Little detailed work has been done on the Flathead Sandstone, and its provenance and environment of deposition are poorly understood.

This project uses petrographic analysis and stratigraphic evidence to distinguish the various marine and continental environments present during the deposition of the formation in the Clarks Fork area. The purpose of this study is not only to learn more of the Flathead Sandstone in its manifold variations, but also to contribute to the understanding of ancient transgressive deposits in general.

Internal structures, textures, and mineralogic composition point to both marine and fluvial facies in the Flathead Sandstone. Fluvial facies are distinguished by pebble lag deposits, submature textures, and feldspathic composition. Structures evident within the fluvial facies are trough cross-stratification, cut-and-fill structures, and thin horizontal bedding. Marine facies are on average medium-grained, texturally mature quartz arenites, some of which display horizontal feeding traces or vertical burrows. Sedimentary structures include thick horizontal bedding, low-angle planar and trough cross-bedding, and hummocky cross-stratification.

Point-count data indicate a craton interior provenance with some evidence for basement uplift. The composition of the sandstone is consistent with derivation from the underlying granitic rocks. However, a portion of the samples contains detrital chert and metamorphic quartz, suggesting contribution from a metamorphic source.

The Quaternary Evolution of Waldron Island, Northern Puget Lowland, Washington

William H. Crane

Thick deposits of unconsolidated sediments on Waldron Island and in the adjacent channels of the northern Puget Lowland record the advance and retreat of the Cordilleran ice sheets most recently between 18,000 and 13,500 14C years before present. I mapped beach cliff exposures on Walron Island along Cowlitz Bay, North Bay, and at Point Hammond. I collected striation data and made measurements of preserved channel orientation in order to establish paleoflow directions. In addition, I conducted marine seismic surveys along a trackline west from Cowlitz Bay around Waldron Island to Mail Bay. The data from these surveys was used to correlate submarine sediments with onshore exposures.

Reconnaissance mapping and seismic surveys and well log data demonstrate that much of Waldron Island is blanketed with unconsolidated sediment that in places reaches >160 m in thickness. Basal crossbedded sands and gravels are probably the Esperance Sand member of the Vashon drift and provide an excellent basis for correlation with the regional stratigraphy of Armstrong and Easterbrook. The absence of major preserved thickness of Vashon till on Waldron suggests that erosional processes at the glacier bed were active throughout the glaciation. As ice retreat accelarated after 14.0 ka, the development of extensive subglacial drainage contributed to continued erosion. The bulk of the deposits filling channels in the Esperance Sand appear to be related to meltwater erosion beneath the glacier and deposition at the glacial terminus. In addition, the high pressure subglacial meltwater streams probably contributed to the deep scour observed in the channels around Waldron Island.

Seismic reflection profiles offshore of beach cliff exposures provide data critical to a three dimensional reconstruction of the sedimentation processes in operation at Waldron at the close of the last glaciation. Major bedrock channels exposed in seismic surveys cross-cut the regional structural grain indicating minimal structural control on sedimentation.

Dates obtained by 14C dating of preserved marine invertebrates at Point Hammond combined with previously reported data demonstrate a trend of declining age as one moves northward through the San Juan Islands, consistent with backwasting of the Vashon ice sheet and subsequent isostatic rebound as proposed by Dethier et al. (1995). Rapid shallowing of local sea level at Waldron Island is demonstrated by the juxtaposition of deep marine species (Clinocardium ciliatum. ) with shallow intertidal species (Saxidomus gigantea ). Dating of the faunal succession at Point Hammond indicates an isostatic rebound rate of at least 16 cm yr -1 during the first 500 years after glacial retreat.

Geochemistry and Tectonic Setting of Proterozoic Amphibolites From the Southern Front Range and Northern Wet Mountains, Central Colorado

Martha J. Folley

Most of the Early Proterozoic supracrustal rocks of south-central Colorado are complexly interlayered pelitic schists, felsic gneisses, and amphibolites which have experienced a regional amphibolite-grade metamorphic event at about 1700 Ma and multiple intrusive and deformational events. Amphibolites from the southern Front Range, Arkansas River Canyon, and northern Wet Mountains are found concordantly interlayered with, or as pods or xenoliths within biotite-quartz-plagioclase gneiss and gneissic granites. Amphibolites are closely associated with pelitic schists and calc-silicates in the southern Front Range and are interlayered with felsic volcanics in the Arkansas River Canyon. An age of ~1720 Ma for a granitoid that intrudes the layered gneiss sequence provides a minimum age for the wall-rock package in this area.

Amphibolite samples collected from twenty-nine localities throughout the field area were petrographically and geochemically analyzed in order to determine their origins and tectonic settings. Modal analysis identifies most of the samples as ortho-amphibolites containing relatively equal amounts of amphibole and plagioclase, and minor quartz and biotite. The high grade of metamorphism and deformation has erased any primary structures or textures which might positively identify their protoliths. Most samples display a crystalloblastic fabric, although a few have retained what could be relict sedimentary layering or relict igneous textures. Geochemical analyses of major elements by XRF and trace elements by XRF and INAA makes it possible to identify the origin and tectonic setting for amphibolites from the southern Front Range and northern Wet Mountains. When plotted on N-MORB-normalized spider diagrams and REE plots all display trends similar to volcanic arc basalts, with an enrichment of LILEs and LREEs and a depletion of HFSEs and HREEs. When plotted on various tectonic discriminant diagrams for basalts, all cluster in the volcanic arc field. On the diagrams, a distinction can be made between amphibolites from the southern Front Range and northern Wet Mountains. Rocks from the northern Wet Mountains have a relatively higher enrichment in LILEs and LREEs than those from the southern Front Range. Samples from the northern Wet Mountains also consistently plot as calc-alkaline basalts, while those from the southern Front Range plot as volcanic arc tholeiites. Because samples from the northern Wet Mountains have a relatively high alkali enrichment and plot as calc-alkaline basalts, they are part of a more evolved "continental"-like arc system. Samples from the southern Front Range, with their lower alkali enrichment and identification as volcanic arc tholeiites, are part of a more primitive, less evolved arc system.

Because the geochemical trends shown by rocks from each of the two regions are so distinct, they may represent two separate arc systems. These two arc systems presumably developed independently and collided with one another and with the North American Craton sometime late in the Early Proterozoic, though the nature of their collision can not be determined from this study. The results of this investigation were compared with those from studies done in Arizona where the boundary between the Yavapai and Mazatzal provinces was defined. The geochronologic, lithologic, and structural characteristics of the units found in the southern Front Range and northern Wet Mountains, as well as the geochemical data obtained for the amphibolites of this study, would characterize this region as a component of the Yavapai province. However, the position of the province boundary in this part of Colorado is still unresolved.

Quaternary History and Evolution of Submarine Banks, Northern Puget Lowland, Washington

Joanna K. Holbert

The Cordilleran ice sheet, which last retreated through the northern Puget Lowland about 14.0 14C yr BP (13.5 ka), left a thick mantle of glacial deposits in its wake. Submarine banks up to 12 km in length with volumes of at least 1.5 km3 line the seafloor in this region; marine seismic surveys show that these banks are composed of Quaternary sediments as thick as 300 m. This report examines the glacial history of five of these marine banks: Alden, Middle, Hein, Smith, and Eastern Bank.

We collected seismic reflection data throughout the Puget Lowland during the summers of 1995 and 1996; seismic tracklines included profiles of seven marine banks. Based on previous studies of submarine glacial deposits, I used seven seismic facies associations for analysis of our data, including bedrock, till, glaciomarine sediments, glaciomarine diamict, sand and gravel, silt and sand, and marine fill. My interpretation of glacial history for each bank depended upon two primary considerations: (1) the relative distribution, thicknesses, and stratigraphic relationships of these facies as indicated in the seismic record, and (2) bank morphology and orientation relative to paleoflow.

The morphology and internal sedimentary composition of the marine banks reflect local conditions at the ice margin during deposition. As the Cordilleran ice front approached the San Juan Islands during retreat, the calving rate at the terminus decreased. Ice grounded on the substrate, reaching a temporary stillstand in several locations. Where terminus stability lasted for decades, sediment flowing through meltwater channels beneath the ice accumulated at the margin in the form of ice-contact submarine fans, deltas, and moraines, with paleoflow typically to the south-southwest. Alden Bank formed as a terminal moraine at the margin of an ice lobe grounded east of Alden. Middle, Hein, and Eastern Banks formed as ice-contact submarine fans along an ice margin that gradually retreated to the northeast, moving from one bedrock high to the next. Ice lay along the northern and eastern margins of Smith Bank during its deposition, forming a curved terminus around the bank; the combination of deposition from both sides created a composite bank feature with characteristics of both a moraine and an ice-contact submarine fan. Each of these banks accumulated over a period of tens of years and no more than 200 years.

The interaction between rising sea level and isostatic rebound through the Holocene has modified the bank forms we see today. Surficial sediment has been eroded up to 20 m from the bank tops and accumulated in thicknesses of less than 50 m along the bank margins. Waves have been eroding those bank surfaces exposed above sea level, such as Smith Island, at rates of 0.2-1.0 m/yr since about 5 ka. Glacial processes have been a dominant force as the landscape of the Puget Lowland has evolved through the late Quaternary.

Evidence of Seasonality and Climatic Cycles From the Upper Cretaceous El Gallo Formation of Baja California

Alison H. Kopelman

Like the climate of almost all other west coasts around the latitude of 30o north and south of the equator, Baja California has a dry heat, deserts, and sparse vegetation. Almost no research has focused on the climate of Baja California during the Late Cretaceous, when the terrestrial El Gallo Formation was deposited along the Pacific Coast of this area. The paleolatitude of the El Rosario area was only about 4o farther south than it is today, based on paleomagnetic data (Filmer and Kirshvink, 1989; Renne et al., 1996; Bohnel, 1997). The El Gallo Formation was deposited in a fore-arc basin during a period of rapid tectonic uplift of the Alisitos Formation and the Peninsular Ranges Batholith. The overall architectural sedimentary structure of the El Gallo Formation represents a major transverse river system that is associated with orogenic highlands. The field site for this study is El Jabon Canyon, on the northwest side of El Rosario. A thick sedimentary package of 15 alternating sandstone and siltstone cycles of the upper El Disecado Member of the El Gallo Formation, capped by a basal conglomerate belonging to the overlying Rosario Formation, is well exposed. Levels of cyclicity and seasonality are indicated through a) sedimentary cycles within the stratigraphy; b) small scale cyclicity apparent in color variegations in paleosols; c) synthesis of all previous research regarding the biota and climate of Late Cretaceous Baja California. During Late Cretaceous time, the El Rosario area supported a diverse biota, including abundant gymnosperm, angiosperm and palm trees, and a fauna including dinosaurs, amphibians, and therian mammals (Cevallos-Ferriz, 1997; Lillegrave, 1976; Morris, 1974; and Kilmer, 1963). These data are used to test the hypothesis of Weaver (1990) that a poleward flowing current, not unlike the anomalous Leeuwin Current off Western Australia today, modified the climate of Cretaceous Baja California.

Dynamic Coastal Facies of the Alisitos Formation At Punta San Isidro, Baja California, Mexico

Jonathan L. Payne

Exposures of the Lower Cretaceous (Aptian-Albian) Alisitos Formation at Punta San Isidro, Baja California, Mexico, include a series of pyroclastic, conglomerate, and sandstone units interbedded with limestone (biohermal beds composed of the rudist Caprinuloidea perfecta). These lithologies are exhibited within a stratigraphic thickness of less than 125 m. A sandstone unit contains abundant fossil wood with tree limbs up to 55 cm long and 5 cm in diameter, testifying to the close proximity of the shoreline. Two conglomeratic units bear andesite cobbles encrusted by oysters (Arcostrea sp.?). This relationship implies a rocky shoreline of late Early Cretaceous age, which predates the well-preserved rocky shorelines of Late Cretaceous and Pleistocene ages also exposed on the present coast. The interlayering of pyroclastic and reworked clastic units with nearly pristine limestones presents a scenario of marine life attempting to establish itself along a coastline subject to nearly continuous explosive volcanic activity. In one case, bivalves were incorporated into a pyroclastic deposit, as debris swept into a lahar of terrestrial origin or in a mass flow resulting from a hydromagmatic explosion. Proximal volcanic activity to Punta San Isidro is demonstrated by a series of andesitic dikes, feeding the 10 m-thick andesite flow locally forming the uppermost stratigraphic unit of the Alisitos Formation.

The fossils preserved at Punta San Isidro conform to the back reef facies of the model provided by Coogan et al. (1972) of Cretaceous rudist reefs. The interlayering of limestone and volcaniclastic units demonstrates that during periods of rapid volcanogenic sedimentation, the marine fauna was temporarily eliminated from the local sea bottom. This is consistent with the model of Heikoop et al. (1996), who relate substrate and water depth to the effects of proximal volcanism.

The Alisitos succession is often structurally complex, i.e. tightly folded, faulted, and intruded by Late Cretaceous igneous rocks. Inland exposures of bedrock are deeply weathered, further complicating the interpretation of faults and folds. The constant wave action on the Pacific coastal cliffs around Punta San Isidro provides the advantage of fresh Alisitos exposures. The fault structures on these exposures are quite apparent and are not significant impediments to stratigraphic interpretation. The advantages of coastal exposure apply also to bedding structures and fossils, especially trace fossils.

Pliocene to Recent Carbonate Dunes at Punta Chivato, Baja California Sur, Mexico

Patrick S. Russell

Studies of modern and lithified dunes on the gulf coast of Baja California are scarce. Anderson (1950) observed a calcareous eolianite on Isla Carmen, and Walker and Thompson (1968) mention dunes in the interfingering of ancient coastal facies at San Filipe. Ives (1959) identifies sediment source and mechanism of formation of a carbonate dune field in Sonora. None approaches the depth or extent of this study in drawing inferences about regional atmospheric circulation conditions and their continuity over time, or the effects of the wind field on carbonate sedimentation with implications for sustained upwelling-induced biological productivity in the Gulf of California.

The carbonate sedimentary environment in the Gulf of California is closely controlled by prevailing seasonal winds. Distribution and growth orientations of krummholz, especially leatherplant (Jatropha cuneata) and copal (Bursera hindsinia) trees, illustrate the predominance of strong winter winds from the north at Punta Chivato. Modern sediments developed in this windward setting are described in terms of distribution and composition. Extensive dune deposits stretch up to 1.2 km inland and attain elevations of 60 m along the north coast of the promontory. Sediment composition of beaches and dunes determined by point-counting is 40% - 80% calcium carbonate, indicative of high marine productivity in surrounding waters. Lithics derived from the surrounding volcanic bedrock are a secondary constituent. Shelly fauna indicative of a high wave-energy environment, such as molluscs, dominate the bioclast fraction. The low amount of red algae debris reflects the absence of rhodolith fields along the north shore. Rhodoliths are currently forming offshore to the east and are subsequently transported south to a protected bay. This rough biological zonation is a direct result of the windward/leeward dichotomy that exists across the promontory of Punta Chivato.

Post-Mid-Pliocene karst deposits scattered on the north shore of Punta Chivato are investigated for evidence of continuity in the windward environment. Weakly to well-consolidated outcrops occur between 11 m above sea level (close to the coast) and 50 m above sea level, set inland on slopes of arroyos. The similar distribution of paleobeaches and paleodunes along the north shore, and their overwhelming, mollusc-dominated bioclast content, establishes the windward setting of the north shore through the Pleistocene and possibly back to the Middle Pliocene. Previous study has shown current conditions to have existed at Punta Chivato during the Lower and Middle Pliocene (Simian and Johnson, 1997). In addition, Libbey and Johnson (1997) show that Pleistocene 5e sediment composition on the southern shores of the promontory are 80% - 90% rhodolith-derived red algae hash. This study, then, completes the model of persistent windward/leeward shores at Punta Chivato from Pliocene times through today. The continuity in wind field and sustained high levels of marine productivity recorded in the geological record argue for consistent upwelling circulation in the Gulf of California over the last 3-4 Ma.

MATHEMATICS

A Hybrid Systems Approach to the Problem of Balancing an Inverted Pendulum

Sandeep Bhatt

This thesis is a brief introduction to modern control theory and an introduction to the hybrid systems approach to problems in control theory. We consider the classic nonlinear control problem of balancing an inverted pendulum as a function minimization problem from the point of view of optimal control theory and as a dynamical system from the point of view of the hybrid systems approach developed by Guckenheimer and Johnson. We demonstrate the usefulness of the hybrid systems approach for considering questions of both stability and optimality in balancing the inverted pendulum, and we delineate some of the questions that need to be considered if the hybrid systems approach is to be applied to control problems of stability and optimality in general.

Comparison of Ordinary Differential Equation Models of HIV Infection

Laura Louise Christensen

Many ordinary differential equation models have been bused in research on HIV to test treatment effectiveness and to define and describe the dynamics between HIV and the immune system. In this thesis three such models (presented by McLean et al., Perelson et al. and Hraba et al.) are compared with and without treatment incorporated. The conclusions of this comparison are as follows. The McLean model, which is very similar to the Perelson model, but designed to model dynamics during treatment, is robust only for initial conditions which reflect an infected steady-state and not for infection dynamics from initial inflection or after the completion of a treatment course. Treatment dynamics are compared between the Perelson and McLean models. Particular treatments were implemented on both the Hraba and Perelson models yielding the conclusion that, though the models are quite different, they give similar predictions of relative treatment effectiveness.

Cost Minimizing Networks Separating Immiscible Fluids in R2

Brian Elieson

Cost minimizing networks model certain behavior of immiscible fluids in the plane. This paper proves the existences of minimizers of straight lines with an upper bound on the number of nodes, closely following the work of Alfaro. It provides some basic examples of minimizers. The paper also gives sufficient conditions for an upper bound on the number of regions meeting around a point.

Characterization of Completions of Integral Domains

Deborah L. Greilsheimer

Christer Lech characterized the complete local (Noetherian) rings that are completions of domains. We reprove Lech's result showing that a complete local ring T is the completion of a local domain if and only if no integer of T is a zero divisor, and, unless equal to (0), the maximal ideal of T does not belong to (0) as an associate prime ideal. Moreover, suppose p != M is a prime ideal of T such that Q is an associated prime of T implies Q [Atilde] p, and suppose that |{q Œ Spec T | q À p}| [sterling] | T/M2| and p intersected with the prime subring of T is the zero ideal. In this case, we construct a local domain A such that = T and the generic formal fiber ring of A is local with p*AK the maximal ideal where K is the quotient field of A.

Weak Mixing, III0 Staircase Zd Actions

Erich Muehlegger

This thesis presents two new examples of staircase Zd actions, functions mapping points from Zd x R to R. Expanding on the work of Silva/Adams and Touloumtzis, the first construction is shown to be an infinite measure preserving action with weakly mixing basis transformations. The second and more interesting example is a type III0 action with weakly mixing basis transformations. In addition, the several concepts and criteria applying to Z2 actions are generalized to their Zd counterpart.

Bayesian Prediction Intervals for Symmetric Shrinking Linear Smoothers

Jason Ross Schweinsberg

In many statistical problems, it is important to estimate the relationship between a dependent variable y and some independent variables, so that given values for the independent variables, a 95 percent prediction interval for y can be computed. Here we describe how Bayesian methods can be used to calculate prediction intervals for a class of modeling methods called symmetric shrinking linear smoothers. We show that how well these "Bayesian prediction intervals" perform can be related to simple properties of the smoother. When one "smoothing parameter" is chosen optimally, we show that Bayesian prediction intervals perform well asymptotically for generalized ridge regression. For other smoothers, the asymptotic performance of Bayesian prediction intervals is conjectured to depend on the eigenvalues of a linear operator called the covariance operator.

Outer-crossing Numbers: A New Parameter for Graphs

Alexander Woo

Outer-crossing numbers of graphs are defined and basic properties are given. The outer-crossing numbers of complete bipartite graphs are found. Some conjectures and a generalization to surfaces other than the plane are discussed.

PHYSICS

Efficient Transmission of Quantum Mixed States

Jennifer A. Drake

The amount of information contained in a quantum pure state is well defined and there exists a known method of transmitting pure state information in the most efficient manner possible. In this thesis we attempt to attain a similar understanding of quantum mixed states. We propose a likely value for the information content of mixed states and show that under certain conditions this value characterizes the efficiency with which a sequence of mixed states can be transmitted. Also, we find a simple way of characterizing certain coding strategies ("cluster codes") and obtain a formula for their efficiency. Finally, we outline an algorithm which we believe will bring about maximally efficient mixed state information transmission in the limit of large messages.

Nonlinear Dynamics in a Mode-Locked Ti:Sapphire Laser

Sarah W. Dugan

This thesis presents research done on the non-linear dynamics of a Ti:sapphire laser. The appearance of higher periodicities in the pulse train was examined in depth, period two, period three and quasi-periodicity were seen. The spatial properties of these higher periodicities were also studied and the relative pulse heights were found to vary across the laser beam. Double pulsing was also observed. A computer model of the laser was begun; at this point only the first order cw beam is modeled.

Entanglement

Scott A. Hill

Entanglement is a type of correlation between particles that is much stronger than any correlation that could exist in classical physics. Originally studied in the context of the quantum theory and its interpretation, entanglement has come into its own recently in the study of quantum information. In this thesis we explore some of the history of this notion of entanglement and then present a formula that quantifies the amount of entanglement present for a certain subclass of states in the simplest correlatable system: a pair of two-level particles. We conclude by discussing how this expression might be made correct for all states of this system.

Stability of Pulsar Radiation Mechanisms

Ruth OGorman

Despite repeated attempts to describe the pulsar magnetosphere in general physical terms, none of the current models of the pulsar radiation mechanism has yet achieved either internal self-consistency or complete general acceptance. However, since the models differ primarily in their placement of the radio emitting region, it is possible to use observations of the long-term stability of the pulse profile to place constraints on the likelihood of certain mechanisms. Since the pulsar magnetic field can be treated as approximately dipolar and since a dipole field drops off as 1/r3, those regions of the magnetosphere that are farther from the pulsar are less tightly bound to the magnetic field, and are likewise less tightly bound to the pulsar. Emission mechanisms located in these regions farther from the pulsar are therefore more sensitive to local field perturbations that could affect the long-term stability of the pulse profile.

We conducted observations of the pulsars PSR 0329+54 and PSR 1933+16 in two groups, one in August and September of 1996 and the other in January of 1997, for the purpose of analyzing the stability of each of the pulse profiles over the course of a few months. We reduced each of the observations and extracted the Full Width at Half-Maximum (FWHM) for the main peak of each profile. A comparison of the median FWHM for each pulsar for the earlier sample against that from the later sample yielded no statistically significant traces of instability of aberration. Since the sample size was smaller than we would have liked and time constraints required that the comparison was drawn across only a few months, a more thorough study would be necessary in order to make a conclusive statement about the nature of the pulsar emission mechanism. However, even though it is not currently possible to rule out one of the models completely, our results support the polar cap model of radio emission over the outer magnetosphere gap (relativistic beaming) model.

The Design, Construction, and Application of an Atomic Beam Apparatus

Julie R. Rapoport

This thesis will describe the design, construction, and application of an atomic beam apparatus. Experiments to measure the Stark shift and Stark mixing effect on the 6P1/2 -> 6P3/2 transition in thallium will be described. The final portion of the thesis will consider future experiments.

Highly precise parity non-conserving effects in thallium have been measured. However, theoretical thallium wavefunctions are not so precise as the experimental measurements. Thus, if the predictions and measurements do not agree, it is not evident whether the disagreement is due to imprecision in the wavefunctions, or possible inaccuracies in the Standard Model. In order to ameliorate this problem, we have devised several experiments (such as measuring the Stark effect) that will check the accuracy of the thallium wavefunctions independent of the parity non-conserving effects.

PSYCHOLOGY

Effects of Directed Forgetting on Implicit Memory Tasks

Michelle Adams

The directed forgetting effect refers to the enhanced performance on a free-recall test and on a yes/no recognition test of items followed by "remember" cues relative to items followed by "forget" cues. Two explanations have been proposed to account for the directed forgetting effect observed on explicity memory tests. Three experiments were conducted to test the selective encoding account and the selective retrieval account of the directed forgetting effect by investigating whether a directed forgetting effect can be observed on implicit memory tests. A significant directed forgetting effect was observed for the implicity memory tests, word-fragment completion (Experiment 1), category production (Experiment 2), and general knowledge questions (Experiment 3). Overall, the pattern of findings reported here indicate that the directed forgetting effect reported on explicity memory tests using a mixed-list presentation design is due to differential encoding of items followed by remember relative to forget cues rather than due to retrieval inhibition.

The Effect of Anxiety on the Central Executive Function.

Lori Chelius

One of the major theories proposed to account for the pattern of findings related the effect of anxiety on cognitive performance is the working memory capacity theory, articulated by Eysenck (1979). According to this theory, high levels of state anxiety lead to deficits in cognitive performance by creating task-irrelevant processing, resulting in a restriction in functional capacity of the working memory system. The purpose of this study was to directly investigate the effect of anxiety on the central executive function, the system responsible for the allocation of working memory resources. Five experiments were conducted to investigate this question. Results indicate that in four of the five experiments conducted, the anxiety manipulation failed to significantly increase self-reported state anxiety in the experimental group relative to the control group. In the five experiments reported, there was no observable difference in performance between the experimental and control groups on either the central executive tasks or the digit span and Stroop tasks, two tasks previously shown to be influenced by state anxiety. This current set of findings is inconclusive regarding whether the central executive function is influenced by anxiety. Implications for future research in this area are discussed.

The Development of Preschool Children's Understanding of False Belief in Fairy Tales

Faith Cinquegrana

Two studies explored preschool children's understanding of the false beliefs in fairy tales. In the first study, groups of 3-, 4-, and 5-year-olds listened to tape-recorded versions of a familiar and unfamiliar fairy tale read in either a dramatic or an ordinary tone of voice. Children were also tested on standard measures of false belief. Three-year-olds performed below chance on both their understanding of the protagonist's mental state and on false belief, whereas the two older groups performed above chance on both measures. Neither story familiarity nor voice influenced children's understanding of the protagonist's beliefs. In the second study, 3- and 4-year-olds listened to a familiar fairy tale presented in either traditional form or in a form that made the protagonist's beliefs more salient. Four-year-olds performed better when mental states were more explicit, but 3-year-olds remained below chance. Results were discussed in terms of changes in representational thought occurring around 4 years.

Genetic Influences on Anxiety: Differential Neurosteroid Responsivity in Selectively-bred Rats

C. Dana Critchell

Roman High Avoidance (RHA) and Roman Low Avoidance (RLA) rats were selectively bred from Wistar rats using an active-avoidance paradigm; this breeding has resulted in an increased "emotionality" in RLA rats, as evidenced by, for example, increased grooming and defecation rates. RLA rats also have decreased 3H-diazepam binding as well as decreased GABA-stimulated Cl- uptake in cortex. This experiment investigated whether response to the neuroactive steroid allopregnanolone (AP), a positive modulator of the GABAA receptor, would also differ in these two lines. Rats were tested as neonates (one week) and as adults using measures of both emotional behavior and activity. In neonates, AP, as previously reported by this laboratory, decreased the number of ultrasonic vocalizations after maternal separation. RHA pups vocalized more and were more active than RLA pups and, on both measures, they had a greater responsivity to AP. As adults, RHA rats had a greater anxiolytic response to AP on the plus maze test compared to RLA rats. Furthermore, adult RHA rats were more active than RLA rats, with RHA activity significantly decreased in response to the highest AP dose. RLA rats also had increased plasma levels of AP after swim stress compared to RHA rats. These results suggest that behavioral differences in these two psychogenetically bred lines may be due to divergent functioning of the neuromodulatory neurosteroid system.

Gender Issues and Identity Development

Susan Costanzo

The Extended Measure of Ego Identity Status-2 (EOM-EIS-2), Narcissistic Personality Inventory (NPI), Rosenberg Self Esteem scale (RSE), and Social definition measure using the Thematic Apperception Test (TAT) were administered to 33 male and 60 female senior Williams College students who had also participated in a similar study when they were entering college (Cramer, 1995). The present study was partially a follow up o these subjects to determine their developmental pathways and to study sex differences in Identity Development. The study also sought to investigate links between Social definition and Ego Identity Status, Narcissism and Self Esteem. No sex differences emerged in the Ego Identity Statuses, Social definition scores, or Self Esteem, but males scored higher than females on measures of Narcissism, with higher scores on Maladaptive Narcissism and subscales of Vanity, Exhibitionism and Entitlement. Subscales of Social definition revealed that females were more socially focused and perceived more causality in the world. Self Esteem was significantly correlated with the Achieved status for both sexes, and Self Esteem was significantly correlated with Narcissism and all three subscales which comprise Adaptive Narcissism. Vanity was significantly positively correlated with the Social definition measure of individual focus. Overall the study implies that sex differences do not exist in the Ego Identity Statuses, but that females have a tendency to be more socially focused and to perceive more causality.

The Relationships Between the Dimensions of Impulsivity and Delay and Probability Discounting

Julia Finch

The multi-dimensional structure of impulsivity was investigated by factor analysis of 95 self-report items from various psychometric inventories. Measures of delay and probability discounting were also obtained to determine their association with the dimensions of impulsivity. A questionnaire containing the I-7 Questionnaire, other impulsiveness-related items, and a series of monetary choice items allowing estimation of delay and probability discounting rates, was administered to 407 participants at three colleges. Exploratory principal components analysis identified six factors: Cognitive Impulsiveness/Carelessness, Planning/Seriousness, Venturesomeness, Attention/Distraction, Carefree/Happy-Go-Lucky, and Impatience. The delay discounting measure loaded on the impatience factor and correlated with both scales from the I-7. The probability discounting measure failed to load on any of the factors, although it did correlate with the I-7 Venturesomeness scale.

Motivating Self-control by Linking Future Rewards

Barbarose Guastello

Two experiments were conducted to test the effect of linking future rewards on motivating self-control (Ainslie, 1975, 1992). Participants were offered choices between smaller immediate rewards and larger rewards at different delays until delays at which the participants made impulsive choices of the smaller rewards were found. These same rewards were then embedded in a linked series of identical future choice pairs and participants would reverse their previous impulsive choice and instead choose the larger rewards in the series. In Exp. 1 (n=60) participants made choices between monetary rewards and the reward linking effect was significant in all conditions, all ps < .05. In Exp. 2 (n=34) participants made choices between different quantities of pizza. Linking occurred only in a condition in which the participants had to make a one time choice between al of the larger rewards and all of the smaller rewards, p < .05.

Attributions in Saudi Arabia and Israel: The Presence of the Correspondence Bias and the Effects of Suspicion

Andrea L. Lieberman

Previous research has shown that individuals tend to think more in trait terms than do collectivists which means they might be more inclined to make the correspondence bias. Past research on attributions found that suspicion is an antidote to the correspondence bias among Americans. The present research employed two different paradigms to examine attributions among Saudi Arabian office workers and Israeli high school students, and measured their levels of individualism/collectivism. The results of this study (1) showed that both the Saudi Arabians, who tended to be collectivist, and the Israelis, who straddled individualism and collectivism, made correspondent inferences when making attributions about a person's behavior, (2) revealed that both Saudi Arabians and Israelis who had not been asked to make previous attributions made fewer correspondence inferences when describing their friends' behaviors, and (3) suggested that ulterior-motive information effects Saudis' and Israelis' inference processes, making them less vulnerable to the correspondence bias.

Self Regulating Processes for Enhanced Performance in Athletic and Academic Domains Under Pressure

Bradley A. Maron

This research examined the effects of self-regulating processes on performance under pressure, both in athletic and in academic domains. Three experiments manipulated the pressure under which participants were asked to perform a task. Study 1 examined the effects of visualization, distraction, and self-affirmation on participant's performance under pressure in an athletic setting, and the results indicated that only self-affirmation was effective in reducing the debilitating effects of the pressure. Study 2 found that self-affirmation was effective in reducing the negative effects of pressure on participants' performance on math problems. Study 3 found that under conditions of pressure, women did significantly worse than men on a series of math problems, but that self-affirmation eliminated this difference. Study 4 involved a survey of basketball players from the Italian National ... and from a small college in the U.S. to assess players' intuitions and behaviors relevant to performance under pressure and self-regulation processes. The implications of this research for performance under pressure, and of the viability of several self-regulating processes, are discussed.

The Levels-of-Processing Effect in Implicit Memory Tasks: It's Not an Artifact

Stephanie Anne Nelson

In recent years, a distinction has been made between explicit and implicit memory. Two explanations (the separate system account and the transfer appropriate processing account) have been proposed to account for the pattern of dissociations observed between explicit and implicit memory measures. The transfer appropriate processing account (TAP) predicts that a levels-of-processing effect will be observed in conceptually-driven implicit memory measures but not in data-driven implicit memory measures. Researchers have recently reported a levels-of-processing effect in data-driven implicit memory measures when processing is manipulated using a between-subjects design or in a within-subjects blocked list design (Challis & Brodbeck, 1992; Thapar & Greene, 1994.) The current study tests the hypothesis that the levels-of-processing effect previously reported in data-driven implicit memory measures is the result of non-lexical processing of the study items in the shallow encoding condition. Lexical processing of the words were manipulated by instructing subjects to read each word aloud prior to making the encoding judgment. Results reveal a significant levels-of-processing effect in anagram solution, a data-driven implicit memory task. These findings suggest that the levels-of-processing effect previously reported in data-driven implicit memory measures is not an artifact of truncated processing of the blocked list items. Implications for the transfer appropriate processing account and the separate systems account of the explicit/implicit memory distinction are discussed.

Political Debate Strategies

Michael Norton

Political campaigns often set a low percentage-of-the-vote expectation for their candidates (a "low pitch") in primary campaigns and caucuses, so that they may claim that their candidates have done "better than expected." It is often the case that the surprising candidate receives more media attention and exposure than the actual winner. When campaigns apply the same strategy to political debates, however, complications arise, since there is no clear measure of performance in debates (as total votes provides in primaries). Some research has shown that the sue of a low pitch in political debates simply lowers viewer's expectations and their subsequent performance ratings; they assimilate the low pitch. The present study attempts to discover if a positive post-debate "spin" of performance could lead to contrast effects, boosting ratings of a candidate's performance even higher, while also examining all other combinations of high, low and no pitches and high and no spins. In an effort to simulate actual network debate coverage, the present study also includes a source manipulation; the pitches and spins come from either the media or the campaigns themselves. Results show that a low pitch followed by a high spin is deadly when used by a campaign for its own candidate, while it works quite effectively when presented by the media. It is likely that communicator credibility accounts for this difference. Discussion of other secondary findings is also included.

Cross Cultural and Developmental Differences in Suspicion and the Fundamental Attribution Error

Archana J. Pandey

This research tries to determine if the fundamental attribution error is truly fundamental by testing for the appearance of the correspondence bias in Indian subjects using the essay paradigm. It also examines the effects of suspicion to determine if it can reduce the occurrence of the correspondence bias in Indian subjects as it has been shown to occur in the American subjects tested in most other studies. A second aspect considered by this study was a developmental approach that used the essay paradigm to examine the emergence of the correspondence bias and the effects of suspicion on second and fifth graders. Results indicate a very strong tendency for the Indian subjects in the first study to make correspondence inferences regardless of the presence of ulterior motives. Results from the developmental study indicate a tendency for the fifth graders to discount more than the second graders. The second graders were not significantly affected by the suspicion condition whereas the fifth graders were affected by the ulterior motives and showed more thinking. Implications and possible reasons for these reasons for these results are discussed.

Delay Discounting and the Time Course of Regret

Maria-Teresa Plantilla

Two experiments were conducted to test the predictions of a discounting theory of the time course of regret. In Experiment 1 (n=16), participants were induced to make an impulsive decision of a smaller, earlier reward over a larger, later reward. They were then contacted by telephone on 5 subsequent days and asked to rate their satisfaction with their decision. As predicted, satisfaction with the choice of the smaller reward decreased up until the day that the larger reward would have been available, then increased slightly, p<.0001. In Experiment 2 (n=61), a discounting explanation of the difference in the time course of regret over actions and inactions was examined. As is usually found with hypothetical scenarios, regret for a single action was greater than for a single inaction when both led to the same outcome, shown here for the first time with real rewards. However, due to a failure of one of the manipulations, it was impossible to test the prediction that multiple inactions would be regretted more than single actions over time.

Transaction Costs, Risk and Practice in Myopic Decision-making

Mariana Santiesteban

Normative economic models assume that individuals discount delayed rewards at constant rates over time (exponentially), but recent studies using real rewards indicate that discounting rates decrease with delay, consistent with hyperbolic model (Kirby, 1997). However, the effects of transaction costs, risk and practice have remained unexplored in studies using real rewards to assess the fits of different discounting models. Participants (N=102) bid in a series of second-bid auctions for real delayed monetary rewards. Their bids represented their present discounted value of the delayed rewards. The predicted effects of transaction costs and risk were disconfirmed, and there were no effects of practice. In all conditions the hyperbolic model outperformed the exponential model. In addition, a significant correlation (r = -0.37) between participants' discounting rates and college GPAs supported the external validity of discounting rate as a measure of impulsivity.

Diagnosing Dementia in Parkinson's Disease: A Cognitive Screening Battery

Marilyn L. Samuels

Primary neurodegenerative dementia is under diagnosed in the United States. Because of this, considerable effort has been put forth to develop brief diagnostic techniques suitable for use in primary care practices. One such technique is the `7-Minute Screen.' This neurocognitive instrument has been shown to be both highly sensitive and specific to Alzheimer's Disease (AD). There are, however, other diseases which produce dementia. The purpose of the present study was to determine if the `7-Minute Screen' would also be useful in diagnosing dementia due to Parkinson's Disease (PD). To accomplish this, 21 patients with PD recruited from the Movement Disorders Clinic (n = 16) at the Brigham and Women's Hospital in Boston and a local neurology practice (n = 15) and 19 age and education matched controls recruited from the community underwent the `7-Minute Screen.' Patients and controls subsequently underwent a comprehensive neuropsychological battery. The clinical standard of diagnosis for Parkinson's Disease dementia (PDD) indicated that 3 of the PD patients were demented. The `7-Minute Screen' detected all 3 patients for a sensitivity of 100%. Of control patients, none were demented. The `7-Minute Screen' detected 1 of 19 controls as demented, for a specificity of 95%. Additionally, non-demented PD patients performed worse than controls on all neuropsychological tests in the comprehensive battery. We conclude that the `7-Minute Screen' may be useful in primary care settings for discriminating between demented and non-demented PD patients. The data from this study also suggest that PD patients who do not meet clinical criteria for PDD, have subtle cognitive deficits.

Inadmissible Evidence and Juror Noncompliance: A Further Investigation of the Just Verdict Motivation

Samuel R. Sommers

The present experiments investigated the role of the need for cognition (NC) in two aspects of the juror decision-making process: (1) selective compliance with a judicial admonishment to disregard, and (2) the tendency to overcorrect against the perceived biasing influence of unreliable evidence. In Experiment 1, 105 mock jurors read a criminal trial summary in which an incriminating wiretap was ruled admissible, inadmissible because it was illegally obtained, or inadmissible because it was unreliable (participants in a control group never heard the wiretap evidence). As expected, mock jurors were more likely to disregard unreliable evidence than reliable evidence regardless of its admissibility, and this selective compliance was found to be the result of their overt motivation to render a "just" verdict. This selective compliance was found only in high NC mock jurors, who, compared to low NC mock jurors were more likely to arrive at such a "just" verdict. High NC mock jurors also exhibited some overcorrection in the inadmissible-unreliable condition, estimating the probability of the defendant's guilt to be significantly lower than control participants did. Experiment 2 further investigated the just verdict motivation by presenting participants with trial scenarios involving different types of evidence and different grounds for inadmissibility. As expected, mock jurors recognized that legal guidelines of admissibility are based on a due process model, even though their own perceptions of the strength of the evidence were influenced by reliability concerns.


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