STUDENT ABSTRACTS

Laura W. Brenneman

The question of how spiral galaxies evolve over their lifetimes is a focal point in the modern study of cosmology. Given what we now know –that our own world resides within the delicate framework of such a galaxy—our pursuit of an answer to this query is personally relevant as well as scientifically compelling. Each year, more studies are conducted, searching for these solutions through a variety of different methods. Herein, I present the results of my own work on one such project, which I began involvement with during my internship at the Hubble Space Telescope Science Institute in the summer of 1998. Working with Dr. Paul Goudfrooij and using data obtained with the WFPC2 (Wide Field Planetary Camera 2) instrument on the Hubble, I examined the globular cluster populations (GCPs) in the halos of several edge-on spiral galaxies of varying Hubble types. The goal of this project is ultimately to find a relationship between the characteristics of the globular cluster populations and the type of central bulge in their parent galaxy. This technique, if successful in finding such a relationship, would prove useful in the future for gauging the age and stage of evolution of other nearby observable spiral galaxies. Chapter one is an introduction to galaxies and how we observe them. The next two chapters discuss how a spiral galaxy in particular is formed, and how we have arrived at our current theories of galactic evolution, also highlighting the ideas behind using globular cluster populations as a “smoking gun” to tell us more about changes in galactic morphology over time. Observations data reduction and analysis consume chapters four and five, and our most recent results and conclusions are presented in chapter six.

Kevin M. Bolduc

Vaccinia virus (VV) is a large double stranded pox virus that infects a wide range of mammalian species. The virus is unique in its relative autonomy from the host nucleus and the biochemical machinery of the infected cell. To a large extent, this phenomenon is due to the fact that within its large genome VV encodes many of the necessities of viral replication, including deoxyuridine 5’-triphosphate nucleotidohydrolase (dUTPase). This enzyme’s function in hydrolyzing dUTP to dUMP is necessary for the high fidelity of DNA replication associated with VV and also for ensuring the constant production of dUMP as a precursor for vaccinia’s de novo nucleotide synthetic pathway. VV dUTPase has been used as a potential model for the human enzyme because of its relatively high sequence homology with that enzyme.

DUTPase is a phosphorylated protein, although neither the functional significance of this modification nor the interacting kinase(s) have been identified. In this study, I attempted to discern whether the VV protein B1R kinase plays a role in the phosphorylation of dUTPase. This was investigated in cell culture through the use of a temperature sensitive mutant of B1R, ts2, and in vitro by production of soluble B1 kinase from a bacterial overexpression system. Although dUTPase proved to be a good in vitro substrate for B1 kinase, the physiological occurrence of this interaction was not demonstrable as dUTPase was shown to be phosphorylated in ts2 infected cells at the non-permissive temperature.

Julie L. Cantatore

The biosynthesis of glucosylceramide (GlcCer), a quantitatively significant sphingolipid located on the apoplastic (outer) layer of the plasma membrane in eukaryotic cells, involves a complex topological mechanism that has been reasonably well defined in animals but less understood in plant systems. Given that enzymes involved in the early steps of sphingolipid synthesis are on the cytoplasmic side of the endoplasmic reticulum membrane, the asymmetric distribution of GlcCer on the apoplastic side of the membrane must require a mechanism for establishing this topology that involves the transbilayer movement of either ceramide or GlcCer from the cytosolic to the apoplastic surface of the membrane compartment involved in biogenesis. Based on past evidence, a hypothetical model of GlcCer formation in plants was proposed where sterol glucosylation (as well as the subsequent step to form acylated sterol glucoside) occurs on the cytosolic side of the vesicle membrane, whereas GlcCer formation (via glucose transfer from sterol glucoside) occurs on the luminal side of the membrane. This study tested the proposed model through a number of means. Results from marker enzyme assays indicate that GlcCer synthesis tracks with sterol glucoside formation and is associated with Golgi and plasma membrane. Based on topological studies of the membranes, ceramide glucosylation in bean hypocotyls apparently occurs on the cytosolic surface of the vesicle membrane, requiring the translocation of sterol glucoside prior to glucose transfer to ceramide. At this point, the participation of acylated sterol glucoside in GlcCer synthesis appears unlikely, and the mechanism for sterol glucoside transport through the vesicle membrane remains to be defined.

Denise M. Connor

A male zebra finch (Taeniopygia guttatta) learns its song during a critical period that remains open until the bird is approximately 90 days old, the time at which it becomes sexually mature. Under normal conditions, the song is crystallized after that point, remaining unchanged for the remainder of the bird’s lifetime. However, Williams and McKibben (1992) showed that following damage to the bird’s tracheosyringeal nerve, changes to both the syllable syntax and temporal patterning can occur, demonstrating that some form of plasticity remains dormant and can be reawakened after the 90 day critical period has ended.

This experiment began the process of elucidating the physiological mechanisms behind the reappearance of plasticity. DAPI, a retrograde neural tracer, was used to map the ventralis muscle of the syrinx within nXIIts, the motor nucleus controlling the syrinx. Mapping was performed on birds in which the tracheosyringeal nerve had been cut unilaterally and allowed time to regenerate. The DAPI patterning within the nXIIts of experimental birds differed markedly from that of unaltered birds, with the defined compartmentalization of the somas in control of the ventralis muscle within the anterior “head” of the nXIIts of control birds being replaced by a more diffused pattern of DAPI staining in the experimental birds.

The appearance of DAPI-stained neurons within regions of nXIIts which had not previously been associated with the ventralis muscle indicated that cells which had previously synapsed with one of the other six syringeal muscles now innerbated the ventralis muscle.

Since the bird is able to reproduce a song very similar to that which it made prior to the surgery even with its motor nucleus sending out axons innerbating muscles which they had not innervated before the surgery, other song control and production nuclei in the bird’s song system must be compensating for the change. This research suggests a degree of plasticity in the higher level of song nuclei which was thought to be lost following the end of the critical period and provides a foundation on which further tracer studies may be built to study where and how the song system of the zebra finch regains its plasticity.

Edie DeNiro

This thesis tests the hypothesis that phenotypic plasticity is maintained in situations where the optimal phenotype differs between habitats so that selection operates in different directions in each habitat. We would thus predict that the phenotype expressed in each habitat would perform better than phenotypes expressed in other habitats. Chorus frog tadpoles (Pseudacris triseriata) in Isle Royale National Park live in pools of two habitat types: they either contain predaceous dragonfly larvae or are predator-free. Tadpoles develop different phenotypes in the two habitats. Taking overall size into account, dragonfly-exposed tadpoles acquire larger tail fin and tail muscle areas, smaller body lengths, and more anterior upper tail fin attachment positions relative to tadpoles in the absence of dragonflies.

My results indicate that this plastic response confers an adaptive benefit. In pools containing a feeding dragonfly larva, dragonfly-induced tadpoles survived longer relative to uninduced pool companions and a relatively large tail fin area was associated with increased survival. However, there are some downsides associated with a dragonfly-induced morphology: tadpoles with smaller body lengths and more anterior upper tail fin attachment positions grew more slowly. The overall agreement between the targets of selection and the traits showing plasticity suggests that the plastic response is maintained by divergent selection imposed by environments with or without predators. However, while tadpoles with a more posterior tail fin apex survived longer in dragonfly pools, dragonfly-induction had no effect on this trait. This incongruence between the traits exhibiting plasticity and those that are targets of selection is interesting since it suggests constraints that may affect the phenotype.

Leah E. Doret

The chromosomes of Tetrahyumena thermophila are largely uncharacterized. In order to obtain subtelomeric DNA from the macronuclear chromosomes, a PCR method was developed. Litmus 28 and the telomere cassette from YAC5 were combined to form two hybrid plasmids, one of 4130 bp (pLD1) AND ONE OF 4530 BP (PLD2). Using pLD1 as the template, Taq Extender, and two sequencing primers, a fragment of 1600 bp was obtained containing the entire telomeric repeat. When one of the sequencing primers was combined with a telomeric primer, the fragment preferentially amplified was the smallest possible size. Use of extraneous DNA in PCR that contained telomeres of known and unknown sizes that could not be amplified resulted in a substantial decrease in the amount of products obtained from the reaction when the amount of DNA in the reaction was large. These techniques can now be used to amplify subtelomeric DNA from hybrid Litmus 28/genomic DNA constructs.

Sylvia Englund

CDC14 is a gene required for exit from mitosis in Saccharomyces cerevisiae. Cdc14 mutants arrest in anaphase/telophase because of their inability to deactivate cycin dependent kinases (cdk’s). A recent model suggests that Cdc14, a phosphatase, positively regulates exit from mitosis through three mechanisms: stabilization of Sic1, a cdk inhibitor; allowing the nuclear entry of Swi5, a transcriptional activator ofSic1; and activating proteolysis of Clb cyclins through Cdh1/Hct1. Cellular localization experiments should determine whether Cdc14 ha the nuclear and cytoplasmic localizations implicated by this model. In this study, antibodies were obtained after purification of the Cdc14 protein through the use of a Gst-Cdc14 fusion construct. On a western blot, the purified antibodies recognized Cdc14 in wild-type and overproducing strains. Immunofluorescence of wild-type cells suggested the surprising result that Cdc14 is excluded from the nucleus. However, nuclear exclusion seen with pre-immune serum, inconsistencies in the Cdc14 antibody staining patterns, the lack of a negative control and the unreliability of the positive controls preclude a definitive conclusion that Cdc14 is nuclear-excluded. Further tests may show that cell-cycle-dependent localization of Cdc14 is fundamental to regulation of its activity, thereby regulating the exit from mitosis pathway.

David M. Finkelstein

The SOS system in E. coli consists of a set of genes that are activated when there is DNA damage in the cell and that code for proteins that participate in DNA repair. One protein expressed by an SOS gene is UmuD, which participates in mutagenesis, or error-prone repair. Mutagenesis consists of DNA replication with reduced fidelity and may allow a cell to avoid death at the expense of mutation. Another protein coded for by an SOS gene is RecA. Among its many other roles in DNA repair, RecA interacts with UmuD and promotes it to autocleave its 24 N-terminal amino acids. The removal of the N-terminus allows the rest of UmuD to play its role in mutagenesis. UmuD cleaves in the absence of RecA under high pH conditions. Cleavage occurs between the Cys24-Gly25 bond. Ser60 performs a nucleophilic attack on the carbonyl group of this bond, and Lys97 acts as a general base, removing a proton from Ser60. RecA most likely promotes UmuD autocleavage at physiological pH by causing a drop in the pKa of Lys97, which emulates high pH conditions. We are interested in finding our how RecA interacts with UmuD to cause this drop in the pKa of Lys97 and thus promote UmuD cleavage.

To study the interaction of RecA with UmuD, various amino acid residues were mutated in UmuD. I constructed three UmuD mutants: K98R, T95K, AND T95V. To do this, the wild-type UmuD gene was altered by the side-directed mutagenesis. Mutant proteins were expressed from these mutated genes, isolated from cells, and purified. Many RecA-mediated UmuD cleavage assays were performed. These consist of incubating a mixture of RecA, UmuD, (DNA, ATP(S,DTT, and pH 8 cleavage buffer at 37C) and analyzing the reactions by SDS-PAGE. The amount of cleavage in different assays was quantified by densitometric analysis. The original goal was to develop a Michaelis-Menten curve for the reaction with wild-type UmuD. First-order (with UmuD concentration) rate constants were calculated for assays, as well as decay constants (for the disappearance of UmuD). Since these constants were equal, this strongly suggests that the concentrations of UmuD and RecA used in these assays were resulting in values in the low, linear part of a Michaelis-Menten curve. Values of Km and kcat were also calculated for wild-type UmuD. The UmuD mutants were assayed in comparison to wild-type. K98R behaves similarly to wild-type. The T95K mutant resulted in a total absence of cleavage, probably because the lysine alters the conformation of the active site. T95V appears to cleave at a lower rate than wild-type UmuD, although more assays need to be done with T95V. This suggests that threonine 95 may be important, perhaps for hydrogen bonding to RecA or to the other UmuD molecule in a UmuD dimer. Computer models of UmuD based on its crystal structure suggest that UmuD undergoes intermolecular cleavage.

Elissa A. Hallem

Interleukin-4 (IL-4) is an immunoregulatory cytokine produced by the Th2 subset of T cells and cells of the mast/basophil lineage. In both cell types, expression of IL-4 is under tight transcriptional control. In mast cells, IL-4 is expressed at significant levels only in response to either cross-linkage of the high affinity RFc,RI receptor in vivo, or stimulation with the calcium ionophore ionomycin in vitro. In CFTL-15 murine mast cells, maximum levels of IL-4 are produced at 30 minutes post-stimulation, and by 6 hours, expression has returned to basal levels. This pattern of expression is under the control of both positive and negative DNA regulatory elements which lie upstream, or 5’, of the structural gene. The present study focuses on one of these negative DNA regulatory elements: NEG-1 (-402 to -302 relative to the start of transcription). Previous research has identified one DNA-protein interaction within the NEG-1 region, implying the existence of at least one transcription factor which binds specifically to this DNA regulatory element. This transcription factor has been designated the Neg-1 protein. For this work, studies were carried out to identify the specific base pairs which are required for Neg-1 binding, as well as the specific base pairs which are required for the negative regulatory function of NEG-1. In addition, the concentration of the Neg-1 protein found in crude nuclear protein extracts was estimated. Based on this concentration, the dissociation constant (K_d) of the Neg-1 DNA binding event was then approximated using nuclear proteins isolated from both stimulated and unstimulated murine mast cells.

John C. Haney

Skeletal muscle displays a high degree of plasticity, altering contractile proteins in response to mechanical, hormonal, or neural signals. Myosin heavy chain (MGC) exists in adult mammalian skeletal muscle in one of four isoforms, Types I, IIa, IIx, and IIb. In controlling the expression of the various isoforms, basic helix-loop-helix (bHLH) transcription factors of the myogenic regulatory family (MRF) have been implicated in regulating transcription of the NHC isoforms. For the MHC Iib isoform, the transcription factor MyoD has been hypothesized to play a causal role in transcription activation. This thesis examines the role of MyoD by utilizing a line of MyoD-/- mice. Significant differences in Iib expression were not detected in either locomotive or weight-bearing muscles. In the diaphragm, the absense of MyoD was found to be associated with a lack of IIB expression. In response to hindlimb suspension, we report an induction of Iib mRNA in the unweighted soleus of wild-type animals, but found no such induction in MyoD -/- animals. In response to thyroid hormone (T3) treatment, we report an induction of IIB mRNA in the soleus, but again found no Iib induction in the MyoD -/- treatment group. In the diaphragm muscles of wild-type T3-treated animals, we observed an increase in IIb expression, while this increase was absent from the MyoD -/- T3 group. From these results we conclude that, while not required for IIb expression, MyoD does play a causal role in activating transcription of the MHC Iib gene and is required for induction of IIb in response to unweighting or hyperthyroidism in the soleus and diaphragm muscles. These results are consistent with a model of activation in which MyoD enhances basal transcription activators to induce Iib transcription.

Inna Hughes

In this project the methods of electroporation, CHEF gel electrophoresis, and Southern blotting and hybridization are tested in the hopes of creating a comprehensive and accurate protocol for the analysis of Tetrahymena transformed with chromosome fragmentation factors. Though Tetrahymena transformation efficiency has been traditionally low for our laboratory, it has been possible to determine some of the factors that greatly affect the efficiency of transformation and the viability of cells; these factors include percentage of conjugating cells at the time of transformation, molarity of electroporation buffer used, and quality of DNA used for transformation. Once transformed cells are obtained, reliable methods for DNA preparation, pulsed field gel electrophoresis, Southern blot and hybridization, and DNA detection must be in place for accurate analysis of chromosome fragmentation events. It has been the goal of this project to attempt to optimize these techniques.

Janet Iwasa

The Drosophila segmentation gene hunchback (hb) is critical for the proper anteroposterior development of the fly embryo, but its function outside the insecta is currently unknown. Savage and Shankland (1996) described the RNA expression of Leech Zinc Finger II (Lzf2), the leech orthologue of hb. Here, the development of an antibody that specifically recognizes Lzf2 protein and the pattern of protein expression of Lzf2 during leech embryogenesis is described. Unlike hunchback protein in Drosophila, Lzf2 is not expressed in segmental tissues during segment pattern formation and thus does not appear to play an analogous role in leech segmentation to that of the hunchback protein in the fly. In early embryogenesis, Lzf2 protein is expressed in a subset of micromeres and is later expressed in the epithelium of the provisional integument and prostomium, structures that are micromere-derived. Lzf2 protein is later detected in the leech CNS during organogenesis.

Emily D. King

A Biotic Index (B.I.) is a system used to determine the water quality of a river or stream based on the faunal communities living in the water that is based on the diversity of the community as well as the ability of organisms within that community to withstand pollution. Algae, fish, and aquatic insects are biota that can be used to indicate the health of an ecosystem. In 1977, Hilsenhoff proposed a Biotic Index based on an extensive study of 53 streams in Wisconsin designed to evaluate the water quality of all streams in Wisconsin based on their aquatic insect communities. The biotic index is an average of pollution tolerance values and measures of the rate of organic decomposition (Hilsenhoff 1982). Most biotic indices used in North America are based on the Hilsenhoff (1977) Biotic Index.

The Hilsenhoff (1977) Biotic Index has never been tested for accuracy in Northern Berkshire County though a version of it is frequently used by Williams College students and local water quality groups to assess water quality in the area. Hilsenhoff (1977) proposes in his methods that future samples of insects should include between five and fifteen minutes of collecting in the field. Hilsenhoff (1977) is also unclear as to whether or not the biotic index will work for insects collected from pool habitats as well as for insects collected from riffle habitats.

In this study, the Biotic Index proposed by Hilsenhoff (1977) has been tested and modified to be specific to streams and rivers in Northern Berkshire County, Massachusetts. The methods for sampling as described in Hilsenhoff (1977) were also tested to determine the amount of time needed for sampling and which habitat, pools or riffles, bests describes the water quality of the river as a whole.

Eleven sites of known, differing water quality were chosen on the Hoosic and Green Rivers. Aquatic insects were sampled from pool and riffle habitats from each of the sites for five and fifteen minutes. Pollution tolerance values were determined for all aquatic insects commonly found in Northern Berkshire County. It was found that the pollution tolerances given in Hilsenhoff (1977) are accurate for insects in this part of the country.

There is a significant difference between the insect populations in pools and riffles. Samples taken from riffles give a better indication of the health of a river than those taken from pools. There is no significant difference between the samples of insects collected for three repetitions of five minutes and those collected for three repetitions of fifteen. Future studies in this area should sample aquatic insects for three repetitions of five minutes from riffle habitats to determine the quality of the water.

Kian Peng Koh

The ciliated protozoan Tetrahymena thermophila contains a germinal micronucleus and a somatic macronucleus. While the micronucleus contains five pairs of chromosomes involved in faithful gene transmission, the macronucleus contains fragmented pieces of chromosomes that have been replicated to about 45 copies (and the ribosomal DNA minichromosome which is amplified to 104 copies) by a mechanism that is still not well understood. Replication origins have been mapped on the palindromic rDNA minichromosome using two-dimensional agarose gel electrophoresis (MacAlpine et al., 1997). To gain insight into the mechanism of replication of non-rDNA chromosomes, we begin an attempt to map replication origins on a non-rDNA macronuclear chromosome using 2D gel electrophoresis. Using cloned probes, we identified two distinct non-rDNA macronuclear chromosomes -- mac2-8 and mac2-16 of approximate sizes 780 kb and 230 kb respectively. A 2D gel study of two restriction fragments from mac2-16 failed to show any pattern of replication intermediates. However, a subsequent 2D gel study of a 4.2-kb HindIII-fragment of the palindromic rDNA, with the aim of reproducing the result of MacAlpine et al (1997), was successful. Furthermore, we demonstrated that chemiluminescent detection can potentially substitute for conventional radioactive detection methods in 2D gel studies.

Katherine P. Liao

A basic principle in conservation biology is that loss of genetic diversity can result in the extinction of a species. This study focuses on two disjunct populations of the arctic plant, Sagina nodosa –one in Isle Royale National Park, Michigan and the other in Acadia National Park, Maine. Comparisons of natural and experimentally pollinated flowers show that self-pollination occurs freely and can result in successful seed set. However self-pollinated plants set fewer seeds and also have significantly more “streaks” (long sections of callose) in their pollen tubes. These “streaks” suggest the possibility of cryptic self-incompatibility since they are associated with decreased seed set.

We used the Amplified Fragment Length Polymorphisms (AFLP) technique to assess genetic diversity among individual plants from Little Moose Island in Acadia, and four islands (Edwards, Split, South Government Islands and the South Government Islet) in Isle Royale. Analysis of Molecular Variance (AMOVA) reveals significant population structuring at all levels: among the Isle Royale and Acadia populations (p<0.001) and among islands of Isle Royale (p<0.00001). Cluster analysis showed that geography was associated with genetic relatedness only on closely neighboring islands in Isle Royale. This suggests that although some gene flow occurs among islands in close proximity, most islands remain relatively isolated from one another. Bootstrap analysis indicates that the Isle Royale population of S. nodosa has lost much of its genetic variance in comparison to the Acadia population.

These studies illustrate an outcome of inbreeding, genetic drift, and isolation ongenetic diversity in small populations. Overall, the genetic profile of S. nodosa shows that subpopulation structuring dominates variation among the islands of Isle Royale. Implications of these findings suggest that conservation strategies aimed at maintaining genetic diversity in highly structured populations should focus on preserving a variety of subpopulations rather than one large population.

Brett E. Linck

A male zebra finch (Taeniopygia guttatta) learns its song during a critical period that remains open until the bird is approximately 90 days old, the time at which it becomes sexually mature. Under normal conditions, the song is crystallized after that point, remaining unchanged for the remainder of the bird’s lifetime. However, Williams and McKibben (1992) showed that, following damage to the bird’s tracheosyringeal nerve, changes to both the syllable syntax and temporal patterning can occur, demonstrating that some form of plasticity remains dormant and can be reawakened after the 90 day critical period has ended.

This experiment began the process of elucidating the physiological mechanisms behind the reappearance of plasticity. DAPI, a retrograde neural tracer, was used to map the ventralis muscle of the syrinx within nXIIts, the motor nucleus controlling the syrinx. Mapping was performed on birds in which the tracheosyringeal nerve had been cut unilaterally and allowed time to regenerate. The DAPI patterning within the nXIIts of experimental birds differed markedly from that of unaltered birds, with the defined compartmentalization of the somas in control of the ventralis muscle within the anterior “head” of the nXIIts of control birds being replaced by a more diffused pattern of DAPI staining in the experimental birds.

The appearance of DAPI-stained neurons within regions of nXIIts which had not previously been associated with the ventralis muscle indicated that cells which had previously synapsed with one of the other six syringeal muscles now innervated the ventralis muscle.

Since the bird is able to reproduce a song very similar to that which it made prior to the surgery even with its motor nucleus sending out axons innervating muscles which they had not innervated before the surgery, other song control and production nuclei in the bird’s song system must be compensating for the change. This research suggests a degree of plasticity in the higher level song nuclei which was thought to be lost following the end of the critical period and provides a foundation on which further tracer studies may be built to study where and how the song system of the zebra finch regains its plasticity.

Sarah A. Moline

The landscape of western New England has been drastically altered by the historical agricultural use of the land. Much of this region was cleared during the 1700s for farming and has since been owned by a series of proprietors and used for a wide range of purposes. In areas where agriculture has been abandoned, relatively simple, successional forests have replaced the previous undisturbed old-growth stands. Thus, human use of the land leaves its mark on the landscape even a century after land abandonment.

The purpose of this study is to examine the specific ways in which land use effects the current ecosystem and to develop a model that can be used to predict the patterns of forest succession associated with various land uses. This study was conducted in a 250-acre area located in Hopkins Memorial Forest, which is a northern hardwood forest that was formerly used for agriculture, located in Williamstown, Massachusetts. In this area, as with much of New England, the main land uses were for cultivation (121 acres), pasture (2 acres), wood lot (42 acres) or for cultivation and then pasture (87 acres). The physical properties of the land, including the slope of the land and the underlying bedrock composition, had significant impacts on the way the land was used. The reforestation of the land was significantly impacted by the human use of the land, with each different land use resulting in a unique forest composition and pattern of succession. Based on these trends, a successional model for the area was developed which can be used to predict the patterns of succession within this research site and can also be applied to other northern hardwood forests in the western New England region.

Andrew A. Nguyen

The ciliated protozoan, Tetrahymena thermophila, contains two types of nuclei: a diploid, transcriptionally inert, germinal micronucleus and a polyploid, transcriptionally active, somatic macronucleus.

The process of macronuclear genome formation from a copy of the micronuclear genome has been well-studied, but there is little understanding of the arrangement of the genes on individual macronuclear chromosomes. One technique that could aid macronuclear genome mapping is chromosome fragmentation, a procedure originally developed for use in Saccharomyces cerevisiae, the budding yeast (Vollrath et al., 1988).

In Tetrahymena the process would involve introducing into cells a linear piece of DNA with a telomere at one end and some cloned Tetrahymena DNA on the other. Recombination between the Tetrahymena DNA and its homologous sequence in a macronuclear chromosome will produce a fragmented chromosomes whose size will reveal the physical location of the cloned DNA within the chromosome.

Essential to this work is the development of a highly efficient protocol for introducing DNA into Tetrahymena cells. This thesis describes experiments designed to determine optimal conditions for transformation of conjugating Tetrahymena using electroporation (Gaertig and Gorovsky, 1992). Transformants were obtained by introducing replicative transformation vectors pH4T2 and pH4a-11 into conjugating Tetrahymena cells between 10 and 11 hours into the mating. However, the transformation efficiency is still too low to yield transformants using integrative vectors such as chromosome fragmentation vectors. Also, a previously constructed fragmentation vector (pAL-1, Hilty 1997) was modified to contain a polylinker and a fragment of macronuclear DNA from Tetrahymena and is ready for testing in the chromosome fragmentation procedure.

Kim X. Nguyen

Auxin is known to affect lateral root development in Arabidopsis, but its exact role has not yet been revealed. Lateral root development has been characterized as a two-step process involving the initiation of a primordium through divisions in the pericycle cell layer, followed by transformation of the primordium into a secondary meristem. Auxin appears to play a role in both steps (Laskowski et al., 1995; Celenza et al., 1995).

Two lines of experimentation were used to explore the role of auxin in lateral root development. Root section culture experiments were designed to examine the stage at which lateral root primordia become functional as meristems and whether that stage is affected by auxin. Preliminary results found here indicate that root sections are very vulnerable to mechanical damage and that the initiation of lateral roots is sensitive to extremely low concentrations of auxin. These results will help refine root section culture methods for further experimentation.

Immunolocalization experiments were designed to examine the auxin content in lateral root primordia of various stages. Although the use of a fluorescent tag proved unsuccessful, with the use of an alkaline phosphatase-conjugated antibody was developed as an effective method of auxin immunolocalization for Arabidopsis root sections. Preliminary results seem to indicate that auxin is present in primordia of several stages in greater amounts than in surrounding tissue. Further experimentation is needed to confirm this and to determine if a change in the amount of auxin present occurs very early in lateral root development. Further experiments using this immunolocalization protocol along with root section cultures may reveal if a change in auxin content is correlated to the stage at which lateral root primordia are transformed into functioning secondary meristems.

Zachary E. Niman

The ecology of exotic invading species has received substantial attention in recent years since these species are clear competitors with native flora and fauna and have caused significant disruptions of native ecosystems. Plants which have been introduced into ecosystems they have not previously occupied can be placed into two categories. Plants that enter an unoccupied habitat and initiate succession are referred to as colonizers, while plants that enter relatively intact vegetation and strongly dominate it or replace it entirely are called invaders (Bazzaz 1986, as cited in Anderson et al. 1996). Alliaria petiolata (Cavers et al. 1979; Nuzzo 1991), is a cool-season, shade-tolerant, obligate biennial herb that invades forested natural communities in the Midwestern and northeastern United States and adjacent Canada. Alliaria invades shaded communities, habitat essentially unoccupied by other invasive alien herbs. Alliaria threatens the floristic structure of invaded natural communities, particularly the herbaceous layer. By sampling comparable areas of woods and trail at two sites, Hopkins Memorial Forest and Cole Field in Williamstown, MA, comparisons of densities of Alliaria in the two different sub-environments showed the plant was significantly more dense along the trails than in the woods (p=.0013; p=.0050). At Cole Field, where the population is more established, Alliaria is significantly more numerous than at Hopkins Memorial Forest (p<.0001). Alliaria has shown an ability to reach equally high densities in both the woods and on the trail (>16 plants per .1 m2). Therefore, it appears that the disparity in overall density is the result of more than environmental differences seen on the trails, such as an increased ability for seed dispersal through adhesion along these avenues. Willson (1993), in a general study of seed shadow, used three categories in describing dispersal ability of a variety of plant species: wind dispersed, ballistic mechanism, or no specific dispersal mechanism. In addition to no physiological aspects which might place Alliaria in either the wind or ballistically dispersed categories, the combined seed shadow of three plants (shown as a proportion in order to weight each replicate equally) fits in the category of unknown dispersal mechanism due to its mode,<.4 m from the base of the plant, and its maxima ( 3 m). The maxima were the same for each direction sampled, but significantly more seeds were recovered in the direction in line with the lean of the plant. Three categories were manipulated to be wet or dry 2 x 2 x 2 study) in an attempt to determine how seeds of Alliaria are able to travel in the absence of any obvious dispersal mechanisms. The results clearly indicate that moisture is a pivotal component of this ability; more importantly, however, is which components are wet. If the soil is wet and the shoes are dry, the seeds tend to adhere to the soil. If the shoes are wet, and the soil is dry, the seeds tend to adhere to the shoes. There is a significant (p<.0021) three-way interaction involving seeds which adhere to the test surface for more than ten seconds, meaning all three categories (soil, seeds, and shoes) play a critical role, but clearly wet shoes have an ability to transport seeds under certain conditions. This potential transport system agrees well with the finding of Alliaria more commonly along the trails. A regression analysis of the densities of transects at Hopkins Memorial Forest in relation to their respective densities from the origin of the trail, the Rosenburg Center, show a significant decline in densities as the transects get further away (p<.0001). This implies a source population at the Rosenburg Center that is spreading into the forest, primarily along the trails, and secondarily from the trails onto the forest floor. It is our contention that this primary spread is the result of seeds adhering to the shoes of people who use the trails.

Christine R. Whitcraft

Mortality determination, tree diameter at breast height, tree height, historical observations, disease states of certain tree species, and aerial photographs were analyzed for United States Forest Service genetics plantations in the Hopkins Memorial Forest, Williamstown, MA. The majority of the trees were planted by the USFS between the years of 1949-1960, and the height, dbh, vigor, disease state, and foliage state of the trees were observed throughout this period. The plots were divided into three types: hardhack conversion plots, genetics plantations, and hybrid poplar clonal tests.

The hardhack conversion plots examined the effect of different treatment combinations on randomized blocks containing four species: red pine, European larch, Norway spruce, and red oak. The treatment method had a significant effect on the long-term mortality in red pine, European larch, and red oak. The block effect was also significant on red pine, European larch, and red oak. Neither treatment effect nor block effect were significant effects on the Norway spruce.

The genetics plantations contained plots of white pine, sugar and red maples, birch, white and green ash, larch, and spruce. The effect of clone type varied from plot to plot and from species to species. Generally, plantations of trees with relatively short life spans, such as birch, showed greater mortality, above 60% while other plots of trees with longer life spans, such as sugar maple, had mortality rates lower than 50%.

Due to their fast-growing, early successional nature, the hybrid poplar plantations experienced extremely high mortality (average 97.7 %). Early data, from four to fifteen years after planting from these plantations indicated that clone type had a significant effect on the diameter at breast height (dbh) and on vigor, but as the tree grew older, average 45 years after planting, the clonal effects on dbh and vigor were no longer significant. 1998 data demonstrated some clonal effects on vigor in the crop-tree tests, but clonal effect had no significance on dbh.

The successional relationships since plantation abandonment were also studied. The majority of plantations had great ingrowth of sugar maples of small dbh, average 2 inches. The ingrowth varied from plot to plot depending on the neighboring vegetation.

Ernesto Andrianantoandro

The damage inducible genes dinB and dinC are part of the B. subtilis SOS DNA repair system. They each contain a binding site for LexA, the repressor protein involved in the SOS DNA repair system, and are induced by DNA damage. It is hypothesized, then, that these genes encode proteins that are DNA repair enzymes or involved with regulating DNA repair. Comparisons of genetic sequences between B. subtilis and E. coli (where the SOS system was first characterized) have shown that there are no homologs for the dinB and dinC genes in the E. coli genome. This would imply that the DinB and DinC proteins might be involved in an entirely novel mechanism of DNA repair. In order to characterize and ascertain the function of these proteins, appreciable amounts of protein must be produced.

PCR with Pfu DNA Polymerase was used to amplify the sequences of the dinB and dinC genes. Attempts at ligation of these genes into pET21A vector proved unsuccessful. Success in cloning was achieved by using Invitrogen’s Zero Blunt TOPO PCR Cloning Kit. The blunt-end PCR products were each ligated into pCR-Blunt II-TOPO vector, and the vector containing the insert was purified. The orientation of the inserted genes within each vector was determined, and the vectors containing correctly oriented inserts were used to transform BL21(DE3) cells. Protein expression was induced by the addition of IPTG, and the results were monitored by SDS PAGE.

The preliminary results of the protein induction suggest that further studies should be done. This would require that difficulties in ligation of inserts into the pET21A vector be overcome, or that conditions for protein induction from the pCR-Blunt II-TOPO vector be optimized. Successful cloning of dinB and dinC constitutes an important first step in the eventual characterization of the proteins they encode.

Geoffrey R. Hutchison

This work centers on the preparation and characterization of platinum(II) bipyridine-based metal chain compounds. Liquid crystalline properties have been observed in the family of square-planar dicyano-platinum(II) bipyridines through substitution of amide functionality on the bipyridine ligand. A first example of a bipyridine-based metallomesogen is observed in the 4,4’-octyldiamide-2,2’-bipyridine compound, though similar 5,5’-substituted bis-amide ligands and 4,4’ and 5,5’ substituted diester ligands do not show mesophases. This opens the door to further exploration of square-planar group VIII metal chain liquid crystalline compounds.

Annabel H. Muenter

Heterogeneous reactions between gases and solid or liquid aerosols in the upper troposphere have the potential to explain observations irreconcilable with expected gas-phase chemical reaction schemes. Examples include the role of polar stratospheric ice crystals in ozone depletion and the suspected role of soot particles in aircraft exhaust plume formation. For gaseous species to undergo heterogeneous reaction with an atmospheric aerosol, the gas molecules must first stick to the solid or liquid surface. A better understanding of trace gas adsorption onto atmospheric aerosols will contribute to the pool of information needed to predict how heterogeneous reactions affect the overall chemistry of the atmosphere.

In this laboratory study, I investigated the adsorption of ammonia onto n-hexane soot between -100°C and -158°C. While these temperatures are colder than the temperatures where ammonia would be found in the atmosphere, this study gives an initial understanding of ammonia adsorption and better understanding of the n-hexane soot surface. Ammonia was studied because of its atmospheric importance and n-hexane soot was used to model atmospheric soot particles. The ammonia-soot interactions studied took place in a vacuum chamber in our lab and were monitored by infrared transmission spectroscopy and mass spectrometry.

Ammonia adsorbs to n-hexane soot at temperatures at least as warm as -100°C but ammonia adsorption could only be quantitatively studied in our system at temperatures colder than -120°C. Ammonia initially adsorbs to the surface rapidly (fast adsorption) and then the adsorption rate shows a marked decrease (slow adsorption). More ammonia adsorbs at colder soot temperatures and at higher ammonia pressures. Ammonia appears to partially passivate the soot layer and all ammonia does not desorb from the surface unless the surface is heated. At pressures above 5 x 10^-6 torr and at temperatures above -140°C, more ammonia rapidly desorbs than rapidly adsorbs. This indicates that ammonia slow adsorption is not diffusion limited but is likely the result of ammonia-ammonia interactions on the soot surface. Under the assumption that on a soot-coated germanium wafer ammonia adsorbs to only the soot surface, the enthalpy of desorption for rapidly adsorbed ammonia is 24 ± 5 kJ/mole and the saturated local surface coverage for fast adsorption is 0.12 ±0.6 ML. These values were found using Langmuir adsorption isotherms for experiments at or above -150°C.

James P. Sieradzki

Development of stereoselective methods for the synthesis of kavalactones and other natural products. The method takes advantage of the regioselectivity and stereofacial selectivity of the Heck reaction.

Scott A. Snyder

A concise and efficient synthesis of 6H-indolo[3,2,1-de][1,5]naphthyridine (isocanthin-6-one, 26) was achieved in 43% overall yield over four steps starting from indole-3-carboxaldehyde; the key step was an intramolecular hetero Diels-Alder reaction of a 1-aza-1,3-diene with an acetylene dienophile. An analogous synthesis of 1-methylisocanthin-6-one (31) was successful in 52% overall yield starting from 3-acetylindole. Attempts to synthesize 5,6-dihydro-4H-indolo[3,2,1-ij][1,6]naphthyridine (isocanthine, 21) via similar methodology in three steps was successful with an 8% overall synthetic yield; unfortunately, similar efforts to prepare the 1-methylisocanthine (32) congener failed. An alternative pathway to both isocanthine (21) and 1-methylisocanthine (32) was obtained in two steps from 4,5-dihydroisocanthin-6-one (25) and 4,5-dihydro-1-methylisocanthin-6-one (36), increasing the overall synthetic yield of 21 and 32 to 10% and 12%, respectively. Syntheses of the 5-oxa derivative of isocanthin-6-one (39) and the benzo[4,5]isocanthin-6-one analog (40) were attempted, but Diels-Alder cycloaddition could not be effected in either case. Preliminary pursuit of a five-step synthesis of eburnamonine (29) via an intramolecular hetero Diels-Alder reaction starting from 3,4-dihydro-β-carboline and 2-furylacetic acid was undertaken, as was an attempt to generate γ-carboline (33) via intermolecular hetero Diels-Alder cycloadditions.

Matthew K. Whalin

Immunologic challenge elicits a set of physiological and behavioral adaptations. The physiological adaptations include activation of the immune system and increased body temperature. The behavioral adaptations include decreased activity, decreased consumption of food and water, and increased sleep. All of these effects are mediated in part by the action of messenger molecules called cytokines. The sickness behavior produced by immunologic challenge has been proposed as a model of depression, and the action of the proinflammatory cytokines interleukin (IL)-1b, IL-6, and tumor necrosis factor (TNF)-a in the brain has been implicated in these behavioral changes. This study examined the central expression of these cytokines following immunologic challenge in a genetic animal model of depression. The Flinders Sensitive Line (FSL) rat exhibits several depressed behaviors that are normalized by treatment with human antidepressants. The central cytokine response to immunologic challenge in these animals was compared to a control strain over a twelve-hour time course using quantitative competitive reverse transcriptase-polymerase chain reaction (RT-PCR). To control for variations in the preparation of tissues and efficiencies of enzymes, an internal RNA standard was used and results were normalized to the expression of a housekeeping gene.

Christina P. Williams

The SOS response in Esterichia coli bacteria induces multiple proteins involved in DNA repair. It is initiated by the RecA protein which is activated when bound to single stranded DNA and ATP. UmuD is one of the proteins induced in this system and it functions in error prone DNA repair, one of the SOS repair mechanisms. UmuD is thought mediate error prone repair by lowering the fidelity of DNA polymerase thereby allowing DNA polymerase to make more errors. In order for UmuD to be active, a 24 amino acid peptide chain must be removed from the amino terminus. This process occurs in the absence of any other proteins in the pH range of 10 to 11, but requires of the allosteric effector RecA for cleavage in the physiological pH range between 6 and 8. In order to study the interaction between RecA and UmuD a mutant was made in which threonine 95 of the UmuD protein was altered to a cysteine. The site mutated is at one of the potential contact points between the active site of UmuD and the RecA protein. The cysteine residue contains a sulfhydryl that can be used for crosslinking UmuD and RecA with selective crosslinking agents. The mutant was purified using a hydroxy apatite column. The cleavage rates of mutated UmuD at biological pH only varied slightly from those of the wild type reaction. The rate constant, k, for wild type UmuD was around 0.019 min^-1, while k for mutant UmuD was around 0.036 min^-1. Because the UmuD mutant appears to cleave in a similar manner to wild type UmuD, it should provide a good model for cleavage of wild type UmuD by RecA. By crosslinking UmuD and RecA through the cysteine 95 sulfhydryl, the active site on RecA can be located.

Marc S. Blackstein

The minimum weight triangulation (MWT) of a point set S is the triangulation that minimizes the sum of the Euclidean lengths of its edges. While finding the MWT of an arbitrary S is still an open problem, Dickerson et al provide a powerful algorithm that, in the expected case, finds a large subgraph of the MWT in polynomial time. Using this result, implementations have been able to find MWTs of thousands of points, where only a few years ago, this would not have even been conceivable. However, in practice, this “Extended LMT” algorithm is rather slow, with an expected case of O(n^3) and a worst case of O(n^6). I present modifications to this algorithm that speed the expected case to O(n^2), and the worst case to O(n^4). It is the hope that these optimizations will lead to a better understanding of the MWT problem, both through the techniques used, and the creation of faster implementations.

Neelay N. Shah

The increasing size of the Internet has provided millions of users with access to various forms of digital information including images, video, and music. Perhaps more importantly, the properties of digital media allow users to copy, modify, and distribute what they find with relative ease. The desire of content providers to use the Internet and its resources to distribute their material while retaining some control over its subsequent use has raised significant issues in the area of content protection. There has been a great deal of research focused on providing both technological and system-level solutions to this problem. One proposed technological solution is called digital watermarking and consists of adding material to digital media in order to later identify it. The goal is to embed a signal within the distributed material that can be detected to help identify its possible misuse. The bulk of digital watermarking research has focused on the development of new algorithms and on the description of watermarking tasks. What has been lacking is a systematic exploration of how different algorithms relate to one another and to the desirable properties of watermarking applications. This research focuses on three goals: 1) providing a categorization of watermarking algorithms based on the types of image properties they rely on, 2) discussing the issues involved with developing an experimental comparison of watermarking algorithms, and 3) presenting the results of a specific experiment comparing the robustness of two watermarking algorithms based in the spatial domain.

Joseph C. Vanderwaart

In the past few years a large body of work has developed on the use of typed intermediate languages in compilers. It has become apparent that the retention of type information in the intermediate representation of a program is useful for ensuring compiled correctness and facilitating optimizations. The use of intermediate languages resembling typed lambda-calculus in the compilation of functional languages like ML and Haskell has been particularly successful, but not much has been done on using this kind of intermediate format for non-functional languages.

Meanwhile, TOOPL, TOIL and LOOM have been developed as object-oriented programming languages with static type-safety and semantic foundations firmly in mind. Encodings for the object and class constructs of these languages in lambda-calculus are known, and consideration of these encodings has proved fruitful in their design and implementation.

In this thesis, our intention is to exploit the work on the semantic foundations of object-oriented languages and on typed intermediate languages for compilation, in an attempt to design a compiler for LOOM. Our translation makes use of two intermediate languages, each based on aversion of polymorphic typed lambda-calculus and similar enough to the intermediate formats of other compilers to make the use of a previously developed back-end possible in principle. We outline the design of our intermediate languages and the translations involved in our proposed compilation strategy, and we discuss our prototype implementation, which compiles a subset of LOOM into lambda-calculus for subsequent interpretation.

Jana C. Comstock

This project is a petrographic and geochronologic study of the Mazatzal Group and related rocks in central Arizona. The Mazatzal Group consists of the Deadman Quartzite, Maverick Shale, and Mazatzal Quartzite, and overlies the Red Rock Rhyolite. Outcrops of similar quartzite units and underlying and interbedded rhyolites occur at Tonto Bridge. The Del Rio Quartzite, which outcrops in Paulden, Arizona, is similar in bedding and deformation to the Mazatzal Group Quartzites. These units have been tentatively correlated, but the stratigraphic relations are not confirmed. In addition, the tectonic setting in which these quartzites were deposited is not understood.

Previous work has interpreted the Mazatzal Quartzite, the Deadman Quartzite, the Del Rio Quartzite, and related quartzites as pure quartz arenites (Trevena, 1979; Bayne, 1987). Dickinson’s (1985) QFL analysis of sandstone composition correlates quartz arenites with stable craton deposition. While the tectonic setting of central Arizona at 1.7 Ga may be debated, all interpretations show that it was tectonically active. There is no modern analog for deposition of pure quartz arenites in a tectonically active setting, and for this reason, the Mazatzal Quartzite has never been fully understood. Therefore this study tests the hypothesis that quartzites of the Mazatzal Group were deposited as immature sediments, and that diagenetic processes have skewed their provenance interpretation. To this end, I have used a combination of petrographic and chemical data to reconstruct a normative depositional mineralogy. The reconstructed composition yields provenance information that is more appropriate to the active tectonic setting in which these rocks are known to have been deposited.

The grain size, degree of sorting, and abundance of subaqueous traction structures indicate that these quartzites were waterlain. Sandstones deposited by traction mechanisms generally have less than 5% depositional matrix (Visher, 1969). Thus, if these sandstones have significantly higher amounts of matrix and framework grains are well sorted, it can be inferred that much of this matrix is secondary. Since the framework grains that were converted into matrix are no longer available for point counting, production of pseudomatrix introduces a significant source of error into provenance analysis through petrographic study.

Framework grains are primarily quartz, but interstitial material includes considerable amounts of sericite, iron oxide, and micas, and the amount of matrix in the thin sections is considerably higher than is expected in a traction-deposited sandstone. The proportion of matrix ranges from zero to thirty-eight percent, with a median of twelve percent. Thus I infer that most of these samples contain secondary matrix, indicating that a significant percentage of framework grains have been altered beyond mineralogical recognition. The chemical analysis data allows me to reconstruct normative compositional values for the eleven samples. These fall in the recycled orogen field on a Dickinson QFL plot. This new provenance interpretation makes a contribution to the debate on tectonic setting. The recycled orogen interpretation, combined with the predominance of rhyolitic volcanic clasts and k-feldspar, and the dearth of mafic volcanic clasts and plagioclase, suggest that this region has a continental origin; and the composition of associated rhyolites, in addition to the regional geology, indicates that the tectonic setting was a continental margin arc.

The second part of this study examines the proposed stratigraphic correlation between two rhyolitic layers which are interbedded with these quartzites. U-Pb zircon geochronology was used to date these rhyolites and the underlying Red Rock Rhyolite. The geochronologic data provide support for this hypothesis by establishing dates of approximately 1.7 Ga for both of the two rhyolites. Further, since these dates are identical within error to that of the Red Rock Rhyolite, the geochronology data also constrains the ages of the quartzite unit at Tonto Natural Bridge and the Lower Deadman Quartzite to 1.7 Ga, proving the correlation of these two units.

Ethan D. Gutmann

Methodology for quantifying the degree of diagenetic influence on conglomerates is weak to non-existent. Workers have shown that diagenesis can exert a significant effect on sandstone composition, and if these processes can have significant effects on conglomerates, then they are important to consider in the provenance, climatic, or economic analysis of conglomerates. This study attempts to show that diagenesis can have a significant effect on the clast population of a conglomerate, and present methods are useful in determining the potential extent of this effect in different conglomerates.

Qualitative analysis in the field and in thin sections show that diagenesis can have a significant effect on conglomerates. Studies of clast abrasion show that it is difficult to completely remove any specific clast composition from a population, even after long periods of transport and mechanical abrasion. Alteration of labile clasts in the Tertiary Whitetail Conglomerate by low temperature ground water reveals that it is possible to selectively weaken specific clast compositions before diagenesis begins, and pseudomatrix in ancient rocks, both in thin-section and in outcrop shows that significant alteration has occurred in many ancient rocks. Macroscopic and microscopic evidence also shows that it is possible to transport large quantities of material during diagenesis. The chemical alteration of clasts before and during diagenesis, combined with the possibility of removing large quantities of material during diagenesis shows that it is possible to significantly alter the clast population of a conglomerate by post-depositional processes.

Several methodologies are considered for analyzing the degree of diagenesis in conglomerates. Point-counting, fourier analysis, and fractal analysis have been shown to be useful in determining diagenetic effects on sandstones. Intergrain contacts evolve during diagenesis as pressure solution between grains increases, and therefore they can be a useful indicator of the degree of diagenesis. Line-counting, similar to point-counting, can be used to determine an approximation of the quantities of contact types in sediments. Grain-shape also evolves during diagenesis, both in small-scale complexity and large-scale shape changes. Closed-form fourier analysis of grain-shape can yield information about many variations in grain-shape, and has even been used to separate provenance of quartz sand grains in sandstones. Analysis of the fractal dimension has been noted as a good indicator of the complexity of shapes on many scales and may be a useful indicator of diagenetic effects.

Ten samples were arranged according to a qualitative estimate of the diagenetic effects on each, and then analyzed with each of these techniques to analyze the effectiveness of each. Data collected from these samples support the use of line counting and fourier analysis in the quantification of diagenesis. Analysis of the fractal dimension of grain shape appears to give little useful information, though a larger number of samples analyzed in more detail may yield more useful results. More data is necessary to quantify the relationship between diagenesis and closed-form fourier analysis, or intergrain contact types, however this study shows that quantification of the degree of diagenesis is possible by either of these methods.

Erik W. Klemetti

The Vinalhaven “Diabase” (VHD) is located at the northwest corner of Vinalhaven Island in Penobscot Bay, ME, where it is underlain by the Thorofare Andesite and overlain by the Vinalhaven Rhyolite. It is a massive mafic to intermediate volcanic to subvolcanic unit of probable Siluro-Devonian age, with associated breccias and vesicular rocks. The VHD is remarkably homogenous in outcrop, entirely dark grey, fine grained, and containing <1 cm quartz “eyes” distributed throughout the unit at 5-10 cm intervals. In all locations (except the point just north of Leadbetter Narrows) the VHD is associated with a breccia of volcanic and sedimentary clasts. At two locations (Brown’s Head and Hopkins Point) the VHD is associated with a vesicular flow rock. Although the contact between the VHD and the Silurian Seal Cove formation is exposed in a number of sites, no evidence for contact metamorphism of the mudstones of the Seal Cove formation could be found, and the nature of the contact remains enigmatic.

In thin section, the VHD is homogenous; it is predominantly aphanitic but is characterized by <1 cm quartz “eyes” (xenocrysts) with ocellar rims, and by spongy cellular plagioclase. The groundmass consists of fine-grained plagioclase, with minor clinopyroxene. The quartz xenocrysts usually show pervasive cracking, while their ocellar rims contain pyroxene and amphiboles, opaques, epidote, muscovite, and chlorite.

Eighteen samples were selected for geochemical analysis on the basis of relative freshness of the sample and to provide geographic coverage. Seven samples were sent to Oregon State University for Instrumental Neutron Activation Analysis (INAA) to obtain trace element data. Major and minor elements, along with additional trace elements, were analyzed by X-ray fluorescence (XRF) at the University of Massachusetts at Amherst. According to the Zr/TiO2 vs. Nb/Y classification of Winchester and Floyd (1977), all samples plot as either basaltic andesite or andesite. Spider diagrams of trace elements normalized to MORB show relative enrichment in LILEs (10-40x MORB), while REE diagrams show a moderate Eu anomaly and some enrichment in LREEs (Lan/Lun approx. 4). When plotted on the Pearce (1983), Pearce and Cann (1977) and Wood (1980) tectonic discriminant diagrams, the VHD plots as calc-alkaline basalt, indicating continental margin arc or mature island arc affinities (Condie, K.C., pers. comm., 1999 and Condie, 1986.)

The Vinalhaven “Diabase” thus shows characteristics that are inconsistent with its name. Petrographic analysis shows little to none of the ophitic texture of a true diabase, and geochemical data show that the VHD plots as an andesite or basaltic andesite. The presence of the small quartz xenocrysts in the VHD indicates that there must have been some hybridization of the original basaltic magma with more felsic magma before the emplacement of the unit. The intermediate composition of the VHD also decreases the possibility that this unit and the felsic volcanics of Vinalhaven represent an example of typical back-arc bimodal volcanism, as found at the Cranberry Island-Cadillac Mt. Complex (Seaman, et al., 1995). Discriminant diagrams show that the VHD may instead be the result of continental margin arc volcanism, presumably along the leading edge of Avalonia during the closing of the Iapetus Ocean.

Jennifer L. Newton

The northern section of Vinalhaven Island in Penobscot Bay, Maine, is dominated by a volcanic complex of probable Silurian age consisting of a rhyolitic dome and associated pyroclastic rocks which are underlain and flanked by various breccia units and by one or more mafic to intermediate sills and flows of the Vinalhaven Diabase (Klemetti, 1999). The felsic units consist of the Vinalhaven Rhyolite (Smith, 1907) and the Perry Creek Formation (Gates, in preparation).

This project incorporates a description and stratigraphic study of the Perry Creek Formation, a unit which has not previously been discussed in detail, as well as providing new geochemical analyses for the Vinalhaven Rhyolite. This information leads to conclusions about the eruptive history of this dome and its relationship to the granitic pluton in the southern portion of the island. The field and lab work conducted for this project may also serve to give a better understanding of the regional tectonic picture by complementing similar studies, such as that of the Cranberry Island Volcanic Series in and near Acadia National Park (Seaman et al., 1995).

Field investigation of the lower layers of the Perry Creek Formation west of Hopkins Point revealed samples of the trace fossil Chondrites in a matrix of maroon siltstone. They were filled with different sediment that was reactive to a weak acid solution, indicating an interval of carbonate deposition. Thus an erosional unconformity of unknown duration exists either between the Seal Cove and Perry Creek Formations or as an interval within the Perry Creek Formation.

The upper units of the Perry Creek Formation are breccia layers with pebble-sized clasts of flow-banded rhyolite and sparse lithic fragments of mafic to intermediate composition. Layers show variation in thickness from several centimeters to as much as 4.7 meters; they are variably matrix- or clast-supported and show evidence of mild to moderate reworking.

The exposures on the Vinalhaven Rhyolite on the western coast of Crockett Point show some of the best-developed devitrification textures ranging from flow-banding to a spherulites. There are also incredibly well preserved layers of tephra in several locations. Medium bedded layers of ash (some containing accretionary lapilli) and breccia form a sequence roughly 10m in thickness. Thinly bedded (1-2 cm) layers of ash and tuff form a package roughly 15m in total thickness. The stratigraphic spacing between successive ash, welded tuff, and flow horizons indicates that several pulses of explosive volcanism in fairly rapid succession produced the Vinalhaven Rhyolite and the volcaniclastic rocks of the Perry Creek Formation.

Geochemical analysis shows that most of the samples lie within the rhyolite field, although all three ash samples and the Vinalhaven Granite plot as rhyodacites. MORB-normalized spider diagrams of the rhyolites and granites show similar patterns, with those of the granites most closely resembling the ash layers of the volcanic units. Both the Vinalhaven Rhyolite and the Vinalhaven Granite plot along the boundary between the “within-plate” and the “volcanic arc” fields on tectonic discriminant diagrams, a pattern consistent with other volcanic and plutonic rocks of similar age along the Maine coast. This signature may indicate that the series of volcanic arcs composing the Coastal Volcanic Belt had already been amalgamated by the time of felsic volcanism.

Martin Wong

Precambrian Mazatzal Group rocks in the Mazatzal Mountains, Arizona, consist of a quartzite-shale-quartzite sequence; the basal Deadman Quartzite, the Maverick Shale, and the Mazatzal Peak Quartzite. This sequence was subject to widespread thrusting and folding during the Mazatzal orogeny (1.66-1.65 Ga). Thrusting was generally towards the northwest and fold axes trend northeast–southwest. Composite quartz/chlorite and hematite veins are present throughout the mountain range and record the stress field during the time of vein formation. Veins may form as either tension or shear fractures, both of which form with known orientations to a stress field. Tension and shear veins are distinguished by the presence of quartz fibers which are perpendicular to the vein wall in tension veins and parallel to the wall in shear veins.

Tension veins predominantly strike northwest in the estimated thrusting direction and are steeply dipping. Less commonly, tension veins form perpendicular to this main set and parallel to most fold axes. Shear veins form at 30° to the thrust direction. Both tension and shear veins indicate a s1 direction which is similar the thrusting direction, suggesting that tension and shear vein formation was contemporaneous with thrusting. Tension veins that are perpendicular to the main set form parallel to fold axes in extensional stress fields near the crests of folds.

Analysis of syn-tectonic tension and shear veins is significant because it provides insights into the deformation of thrust sheets during transport. Both tension and steeply dipping shear veins indicate that thrust sheets expand perpendicular to the transport direction. Locally, thrust sheets extend parallel to the transport direction when moving over such obstructions as ramps. Shallowly dipping shear veins accommodate crustal shortening in the transport direction.

Crosscutting relationships suggest that long planar veins striking north-south and east-west with a blocky texture formed after tension and shear vein formation. These veins most likely accommodated crustal extension during Tertiary uplift or Basin and Range faulting.

The source of the fluids and cations necessary for vein formation is most likely metamorphic reactions in the Maverick Shale and shale interbeds in the quartzite units. Fluid pressure built up in the shale until it fractured the quartzite above it. Pressure solution in the quartzites was a secondary source for cations. Proximity to the fluid source greatly increases vein density in the quartzites. Vein density is also higher near the contact between the Maverick Shale and the Mazatzal Peak Quartzite because of the rheologic contrast between the two units. Bedding thickness is a significant secondary control on vein density with massive beds inhibiting vein formation.

Veins may form through a multi-stage process. Fluid inclusion trails are often found parallel to veins in the host rock and some veins are formed entirely from fluid inclusion trails. This suggests that the formation of fluid inclusion trails is an initial step towards vein formation. Thin veinlets of quartz also typically run parallel to and merge with larger veins. Some and perhaps all veins are composed of a number of closely spaced veinlets. This suggests that veins form episodically, opening in small increments. This interpretation supports Ramsay’s (1980) proposed crack seal mechanism of vein formation.

Zachary J. Grossman

The goal of invariant theory is to describe the algebra of invariants for a vector space under a given group action. After introducing invariant theory and its two main problems, we will prove the Second Fundamental Theorem for vector-valued bilinear forms, which describes the basis relations between invariants of vector-valued bilinear forms.

Davina Kunvipusilkul

In this thesis, we give an overview of some of the optimization problems that arise in computing orthogonal and hexagonal drawings of graphs. We then employ the concepts of spine and spirality to develop a polynomial-time algorithm that, given a biconnected, 6-planar, series parallel graph, computes a hexagonal drawing having the minimum number of bends over all possible embeddings. The algorithm runs in O(n^⁸) time. This work extends similar results by Di Battista, Liotta, and Vargiu on bend minimization for orthogonal graph drawings.

Sang Pahk

One of the oldest invariants utilized for the study of knots is the crossing number of a knot, which is the least number of crossings in any projection of the knot. In this thesis, the supercrossing number of knots, a variation on crossing number, is investigated. It is proved that the supercrossing number is always at least 3 greater than the crossing number. The trefoil knot is shown to have supercrossing number 6 or 7. The crossing map is then investigated as a tool to understand the supercrossing number.

Scott B. Reynolds
A hyperbolic 3-manifold is defined as the quotient of hyperbolic 3-space by a discrete group of fixed point-free isometries. It is known that the set of volumes of all noncompact (cusped) hyperbolic 3-manifolds is well-ordered, and in 1987, Professor Adams proved that the hyperbolic manifold of smallest volume (V=1.0149...) is the Gieseking manifold. Working in the upper-half space model of hyperbolic 3-space, the Gieseking manifold is obtained by taking a regular ideal (vertices at infinity) tetrahedron and identifying its edges with each other. This paper provides background on these types of problems and then proves that, for a large class of cusped hyperbolic 3-manifolds, the manifold of second-smallest volume is the non-orientable one obtained by gluing two 45-45-90 (angles between vertical faces, measured in degrees) ideal tetrahedra together. This manifold has volume approximately equal to 1.83.

Aaron D. Weinberg

Let (T, M) be a complete regular local ring of dimension at least two containing the rationals, such that the cardinality of the residue field T/M is at least the cardinality of the real numbers. Suppose p is a nonmaximal prime ideal of T and L is a set of prime ideals of T[[X₁, ..., X_n]] (where X₁, ..., X_n are indeterminates) such that the cardinality of L is strictly less than the cardinality of T/M, Q intersected with T is a subset of p for each Q in L, and if Π is the prime subring of T, then Pi[X₁, ..., X_n] intersected with Q is the zero ideal for each Q in L. Then there exists an excellent regular local ring A such that the completion of A is T, the generic formal fiber of A is local (this means that the ring Τ⊗_ΑΚ is a local ring where K is the quotient field of A) with p⊗_AK its maximal ideal, and Q intersected with A[X₁, ..., X_n] is the zero ideal for each Q in L.

Craig C. Westerland

For smooth four-dimensional manifolds M we explore the representation of classes in H₂(M) as smooth embeddings of two-spheres into M. For simply connected manifolds, it is known that such a representation is always possible for continuous embeddings, but the smooth case is in general mostly unknown. Given a class that can be represented in this manner, we determine several bounds on the self-intersection of the class. Additionally, we demonstrate a relationship between the occurrence of certain types of these homology classes that can be represented as smooth spheres in a manifold and the smooth structure on that manifold. Finally, we present an abortive attempt to determine a class of manifolds whose second homology contains no non-characteristic classes that are representable as smooth spheres. To introduce the appropriate background to complete the work herein, we also include several chapters on differential topology, algebraic topology, and four-manifold theory.

Alexandre Wolfe

This thesis discusses techniques and results in the study of necessary conditions for representability of second homology classes of compact, orientable, simply connected 4-manifolds by smooth 2-spheres.

Brian F. Gerke

Photoisomerizations are light-induced shape-changing reactions. They occur with striking speed in many conjugated polyenes. Although many theoretical studies of conjugated polyenes have been undertaken, a theory that satisfactorily describes these striking dynamical behaviors has remained elusive. We present a model aimed at illuminating the mechanism behind ultrafast photoisomerization. We find that competition between electronic and steric interactions, as well as the quantum mechanical correlations of the electrons are both important contributors to these reactions. As a test of the model, we present a complete calculation for the simple case of ethylene, where we find that the molecule’s shape-change reaction proceeds within approximately 30 fs, in good agreement with experiment. We also present preliminary calculations for longer molecules, which also look promising.

Robert N. Lyman

We have undertaken a measurement of the excited state hyperfine splitting and isotope shift of the 6P_1/2 → 7S_1/2 transition in atomic thallium using a frequency-doubled diode laser. The operation of the experimental apparatus is explained and current preliminary experimental results are presented. Continuing work on an atomic beam, which offers dramatically reduced linewidth and enables a measurement of the Stark shift on this transition, is described.

Kelly A. Becker

The Flinders Sensitive Line rat is a genetic animal model of human depression that has been shown to have a number of immunological abnormalities characteristic of those seen in depressed patients. Recently, clinical depressed human subjects were shown to mount a diminished virus specific cellular immune response to immunization against varicella zoster virus (Irwin et al., 1998). The aim of the present study was to determine whether the in vivo antibody response to primary immunization would be similarly impaired in FSL rats. FSL (n=10) and control R+FRL (n=8) rats were immunized interperitoneally with keyhole limpet hemocyanin and blood samples drawn from tail veins before, 3,5,7,11 and 14 days after immunization. Serum samples were then analyzed for KLH-specific antibody levels by ELISA. Statistical analysis showed that the FSL rats had significantly lower IgM responses than the RFL rats [F(1,16)=5.17,p<.05] and that the difference between the strains were particularly marked after Day 3[F(5,80)=4.48,p,.01]. In contrast, IgG responses were similar between the two strains at all time points. A second set of experiments focused on the IgG response. Since previous research suggested that IgG2a more than IgG1 would be affected in the FSL rats, we hypothesized that IgG2a levels would be reduced in the FSL rats as compared to the FRL animals. Samples from the above experiment were analyzed by ELISA for the production of KLH-specific IgG1 and IgG2a levels. Statistical analysis showed a trend (p=0.1) toward reduced IgG2a levels in the S=FSL rats and no differences in IgG1 levels in the FSL rats and no differences in IgG1 levels between the two strains. However, the addition of more samples to the analysis did result in a significant difference between the strains in IgG2a (F(1,25)=5.41, p<.05)]. Furthermore, we examined the levels of cytokines in the rats which control differential production of IgG1 and IgG2a. Specifically we measured levels of Il-2, IFN-y, and IL-10 from splenocytes cultured for 72 hours with 25 μg/ml of SEB. We hypothesized that the FSL rats would show lower levels of the Th-1 cytokines IL-2 and IFN-y since Th-1 activity had been shown to be reduced in the IgG2a assay. Alternatively, though, we suggested that the FSL rats would show higher levels of IL-10, due to its negative influence on Th-1 cells. Taken together, these data suggest that the FSL rats may be physiologically less responsive to a primary immunization than control animals. Moreover, these results agree with the clinical observation that depressed humans show an impaired response to immunization, suggesting that the FSL rat could be an important and valid animal model with which to study depression.

Christine J. Caveney

The present study investigated whether the pervasive phenomenon of behavioral confirmation is relevant to police interrogations. In Phase I, 52 participants were guilty or innocent of committing a mock crime and 52 participants interrogated these suspects. Results demonstrated that interrogators with guilty expectations planned to ask more guilt-presumptive questions and were marginally more likely to see their suspects as guilty. Interrogators also exerted more pressure on truly innocent suspects than on guilty suspects. In Phase II, 78 observers listened to the mock interrogations and answered a series of questions about the interrogators and suspects. Observers rated interrogators with guilty expectations as presuming guilt more and using more pressure on suspects than interrogators with innocent expectations. They also perceived suspects questioned by interrogators with guilty expectations as being more defensive. Observers’ judgments were influenced not only by actual guilt but by interrogator expectations. These results suggest that an interrogator’s expectations have the power to influence questioning, behavior, and judgments.

Amanda M. DiMauro

This study examined the influence of dietary restraint, hunger and negative affect on food consumption We were interested in better understanding the concept of disinhibition and what factors result in a loss of dietary control for restrained eaters. We also explored the relationship between restraint, hunger and mood on the number of food references that subjects projects into stories. Subjects were classified as restrained or unrestrained eaters using the Restrained Eating Scale. They were instructed to either eat one or four hours before the study, placing them in one of two hunger conditions. Subjects were either induced into a negative or a neutral mood condition using the Velten Mood Induction Procedure (1968). Subject’s food consumption was measured by the amount of candy they consumed in a taste-test. We found a marginally significant interaction between restraint and hunger on food consumption, with restrained, hungry subjects consuming more than unrestrained, hungry subjects and more than restrained subjects who were not hungry, although the latter effect was marginal. We found no interaction between dietary restraint and negative affect on the amount of candy consumed by subjects. We did not find a three-way interaction for restraint, hunger and mood on food consumption. We did, however, find a marginally significant three-way interaction for these variables with respect to the number of food references that subjects projected into their stores. Post-hoc analysis revealed that restrained subjects who received the negative mood induction and were not hungry included significantly fewer food references in their stories than unrestrained eaters who were also not hungry and had been induced into a negative mood state. We concluded that hunger is a variable that deserves further exploration in future studies of restraint. The findings with respect to the food references that subjects expressed in their stories indicate that there is much more to be explored to understand the different cognitions and means of control that restrained eaters employ to inhibit their food intake.

Melissa Brilliant

The study sought to determine the relation between children’s understanding of Denial and Projection and their use of Denial and Projection. Responses to the Thematic Apperception Test (TAT), scored for Denial, Projection, and Identification using Cramer’s Defense Mechanisms Manual (1991), and responses to a Defense Understanding task were collected from 122 students in first, second, fourth and fifth grades. Defense use findings showed that relative use of Denial decreases and relative use of Identification increases as a function of grade level. Defense understanding results showed that understanding of both Denial and Projection increases as a function of grade level, and that Denial is better understood than Projection across all grade levels. A relation was found between Denial Understanding and Denial use for younger children, such that children who showed understanding of Denial used Denial less than children who showed understanding of Denial used Denial less than children who showed no understanding. A similar finding emerged in the older group between Projection Understanding and Projection use. The findings suggest a developmental progression from the use of a defense to the understanding of that defense and the decreased use of it in favor of a more mature defense.

Jennifer Hendi

The goal of the present study was to evaluate the effectiveness of the Alzheimer’s Disease Caregiver Questionnaire (ADCQ) in screening for Alzheimer’s Disease (AD). In 1998, Sarah Lurding, developed this screening battery for AD to be used by primary care physicians. It was designed to be brief, inexpensive, and easy to administer. This questionnaire is composed of 56 yes/no/not applicable questions that are to be answered by an informant at his/her own pace. The ADCQ is composed of six types of questions: (1) memory; (2) confusion and disorientation; (3) geographic confusion; (4) aphasia; (5) apraxia; and (6) personality change. The categories are not delineated on the questionnaire. Subjects were community dwelling individuals over the age of 60(n=35), as well as referrals to the Vermont Memory Clinic in Bennington, Vermont (n=51). Through the use of CART analysis, the Lurding model was evaluated. The original model consisted of Questions #4, 1, and 12 (in that order). We found this model to have a sensitivity of 90% and a specificity of 77% when the JMH Data Set was applied. Further studies are necessary to assess the ADCQ in a primary care setting.

Phillipa Marie Johnson

This study examined the ways in which Jamaicans living in Jamaica, Jamaican immigrants in the United States, and Americans living in the United States perceive and attribute causality about psychological disorders. One of the main goals of this thesis was to inform clinicians of the types of attributions culturally diverse clients might make about ehe cause of their psychological problems, as these attributions have implications for psychotherapy process and outcome. A review of related studies in anthropology, psychology and sociology is presented. In the present study, 136 adults, aged 18 to 71, from Jamaica and the United States read one of three vignettes about a person with the characteristic symptoms of schizophrenia, depression or ADHD. They then answered free from questions about their initial thoughts about the cause and severity of the person’s problem and completed the Levels of Attribution and Change Scale (LAC; Norcross, Prochaska & Hambrecht, 1985). The LAC is a 60-item, 10 subscale measure of attributions about the causes of psychological problems. Subscales include Interpersonal Conflicts, Insufficient Effort and Biological Inadequacies. Specific hypotheses about the effects of culture and “condition” (i.e. type of disorder) on attribution were tested in analyses which controlled for the effects of age, education, and socio-economic status. Overall, the results indicate that, culturally, participants were not as quantitatively different in their attributions as were expected, though they differed in what they believed to be the most salient causes of different psychological disorders. Content analysis of the qualitative data suggested cultural differences that the LAC did not capture. The results indicate that clinicians should not assume that all clients have the same casual beliefs about problems, regardless of culture. Limitations of the present study and suggestions for future research are discussed. For example, future studies could investigate the influence of level of acculturation on attributions.

Kate Niederhoffer

The primary objective of the present study was to determine the prevalence of Alzheimers disease (AD) in a nursing home, a setting for which only impressionistic data exist on the prevalence of AD. The secondary objective was to determine the sensitivity and specificity of the 7 Minute Screen in identifying AD in this setting, as a comparison of its accuracy in other settings.

One hundred thirteen residents at the Willowood Nursing Home in Williamstown, Massachusetts with no confirmed diagnosis of Alzheimers Disease or other dementia were screened using the 7 Minute Screen and the MMSE. Seven residents refused testing and 7 died prior to screening. Of the 64 patients that completed the 7 Minute Screen, 87.5% were evaluated as having a high probability of dementia (HPD), 10.89% were evaluated as having a low probability of dementia (LPD) and 1.6% was evaluated as having a moderate probability (MPD). Thirsty-five patients with a Global Deterioration Scale (GDS) score of 7 were unable to complete the screen; they were also considered to have HPD. Determining how many patients in such a setting have AD or other forms of dementia will increase the publics awareness of the significant toll of this disease. Understanding the epidemiology of AD in the nursing home setting will be the first step in overcoming the obstacles to early diagnosis and point towards a solution to the under-recognition of the disease.

Alex Wong

Neurosteroids are steroids synthesized in glial cells that have direct effects on membrane channels, as compared to the classic genomic effects of peripherally-derived circulating steroids. The neurosteroid allopregnanolone (3_-hydroxy-5_-pregnanolone-20-one), which is released during stress, has been shown to act via positive allosteric modulation of the GABAa receptor complex. This experiment explored the changes in biogenic amines in stress sensitive areas of the brain due to the administration of exogenous allopregnanolone. Neonatal and adults rats were tested behaviorally and assessed neurochemically. In neonates, allopregnanolone, as previously reported in this laboratory, decreased the production of ultrasonic distress vocalizations after maternal separation. In the adult subjects, allopregnanolone increased the exploration of the open arms of an elevated plus maze. Thus the administration of allopregnanolone resulted in anxiolytic behavior in both neonates and adults. In addition, sedation was observed at the highest dose in the adults. The neurochemical analyses of the neonates did not yield any significant changes in biogenic amines. In the adults, the administration of allopregnanolone resulted in an increased concentration of norepinephrine in the hypothalamus. This suggests that allopregnanolone inhibited the release of norepinephrine. Because of the role norepinephrine in the hypothalamus plays in activating the hypothalamic-pituitary adrenal (HPA) axis, allopregnanolone may exert its effect by mediating the HPA axis. Additionally, allopregnanolone administration increased the dopamine and epinephrine concentrations in the hypothalamus. These results will help in the understanding and treatment of anxiety disorders.