STUDENT ABSTRACTS
ASTROPHYSICS
h and
Persei: An Analysis of Cluster Membership
Rebecca T. Cover
I conducted CCD photometry of h and
Persei, the well-known pair of galactic clusters, and derived a
catalog of probable cluster members. I received the data from Scott
Wolk of the Harvard-Smithsonian Center for Astrophysics, who took
images of h and
Per
at the Fred Lawrence Whipple Observatory in Amado, AZ, in December
1998. I reduced the data with IRAF (Image Reduction and Analysis
Facility) between June and August 1999, obtaining U, B, V, R, and I
magnitudes (ultraviolet, blue, visual, red and infrared) with less
than 5% uncertainty. I then used IDL (Interactive Data Language) to
construct color-magnitude diagrams, contour plots, and graphs of
density as a function of distance from the cluster centers. Based on
the color-magnitude diagrams and the results of earlier studies, I
found h Persei to be more distant than
Persei. By analyzing the stars’ positions on the three types of
diagrams, I selected candidates for membership and identified their
membership probability.
Chapter 1 summarizes previous studies of h
and
Per, while Chapter 2 relates their properties and those of open
clusters in general. Chapter 3 explains the data reduction procedure,
and Chapter 4 describes the data analysis. Chapter 5 assesses
potential sources of error. Chapter 6 introduces the catalog, which
lists 11,000 stars.
Observations of Coronal Temperature and
Polarization from the 11 August 1999 Total Solar Eclipse
Sara Kate May
We present observations of the 11 August
1999 total solar eclipse from Rimnicu Vilcea, Romania. Addressing the
problem of coronal heating and using a theory first proposed by
Lawrence Cram (1976), we seek to measure the degree of Doppler
broadening in the K-coronal spectrum and thus infer the electron
temperature. Three sequences of data were successfully acquired
during totality through all combinations of three filters and four
polarizers (including an unpolarized glass position) and reduced
using standard techniques. As an intermediate step to the temperature
calculation, polarization measurements were made to separate the K
and F coronas. Our polarization data confirm the observations of
several other groups at this and earlier eclipses and agree with
calculated values of polarization suggested by some models. Though
our temperature measurements are not absolutely calibrated, a
relative temperature map was produced. Possibilities for future
improvements and observations are presented.
A Search for High-Frequency Coronal
Oscillations at the 1999 Total Solar Eclipse
Kevin D. Russell
We acquired CCD images of the solar corona
at 10 Hz at the total solar eclipse of August 11, 1999, from Rimnicu
Vilcea, Romania, to try to detect high-frequency waves along coronal
loops. The presence of magnetohydrodynamic waves in our frequency
domain is predicted by some theories to explain the energy transfer
that heats the corona to millions of kelvins. Only minor adjustments
to the procedure and apparatus of the 1998 experiment, described by
McConnochie ’98, were made. Fourier analysis of actual data and
Monte Carlo simulations using a computer model of the 1999 eclipse
indicate that we have the ability to detect oscillations with
amplitudes near 0.4% of total coronal intensity with widths near 0.2
Hz in frequency space. For the 1999 eclipse data, I carried out
Fourier analysis of every pixel, and also of every pixel binned 2x2
in both frequency and physical space. The results of this
comprehensive analysis were used to map where in our image the
highest peaks occurred. A strong correlation between high peaks and
coronal loop structure suggests that real oscillations in the 1 Hz
range are the source of increased power, though we cannot yet rule
out power introduced by image motion from frame to frame. Various
methods for resolving this question are presented, and a possible
method with the required precision to reach a conclusive answer is
outlined.
BIOLOGY
Characterization of the Role and Regulation
of the Hunchback Gap Gene Orthologue Lzf2 in Leech
Development
Stephanie J. Airoldi
This study aims to elucidate the role and
regulation of Leech Zinc Finger II (Lzf2) in
Helobdella triserialis and to isolate can characterize a leech
homologue to the Drosophila gene caudal. Lzf2 is
homologous to the Drosophila hunchback gene, which is critical
for the proper anterioposterior development of the fly embryo.
Functional studies using double stranded RNA interference (RNAi)
indicate that Lzf2 plays a role in directing the morphogenetic
movements of leech gastrulation. Regulation of Lzf2 was not
successfully characterized, but the presence of a Nanos Response
Element (NRE) like element in the 3’UTR of Lzf2 (Savage
and Shankland, 1996), as well as the presence of a nanos
homologue (HRO-NOS, Pilon and Weisblat, 1997) indicate that while the
function of Lzf2 may be different from that of
hunchback, the two homologues may be regulation similarly.
Elucidation of the function and regulation of Lzf2, as well as
characterization of other segmentation genes in the leech, will
reveal information about leech development as well as the
evolutionary conservation of homeotic genes.
The Dynamics of Temperate Forest
Fragmentation: An Examination of Susceptibility to Woody Invasive
Species
Lauren B. Buckley
Forest fragmentation and the invasion of
non-native species are two current threats to global biodiversity. We
investigate whether fragmentation increases the susceptibility to
woody invasive species in ten remnants (2 to 126 ha) of Eastern
deciduous forest. We counted all woody individuals in plots located
in belt transects at the edge and center of each fragment and midway
between. While 40% of edge individuals are invasive, interior regions
have fewer invasives (14%). Species richness, abundance of
individuals, and the percentage of invasive species decline
significantly from both the edges to the centers of the fragments and
with increasing fragment area. These patterns result from increased
susceptibility to invasive species in edge regions and in smaller
fragments. The increase in non-native species with decreasing
fragment area does not correspond to an equivalent decline in the
native species community, suggesting that non-native species may
colonize an empty habitat niche associated with the fragment edge.
However, the interiors of larger fragments had a richer community of
native species. Overall community diversity and evenness indices do
not vary with fragment size, which suggests their ineffectiveness in
assessing the integrity of fragmented forests. The diversity and
evenness indices do, however, reflect the expansion of the non-native
species community with decreasing fragment area. Our results provide
support for conservation efforts dedicated to preserving large tracts
of eastern deciduous forests in order to minimize the invasion and
dominance by non-native woody plants.
Characterization of the Plastic
Response of Pseudacris triseriata and Identification of a
Method to Elucidate the Molecular Components
Patrick M. Burton
Pseudacris triseriata tadpoles were
exposed to a natural predator, the Aeschna juncea dragonfly
nymph. Tadpoles underwent the characteristic plastic response.
Compared to controls, exposed tadpoles had larger tail fins, deeper
tail muscles, and tail-fin attachment points were closer to the head.
These changes were all significant (p<.05).
I compared expression patterns of these
tadpoles with controls using two different methods. Specific northern
hybridization of Xenopus laevis growth factors was used for
direct hypothesis testing, but failed to show significant changes in
gene expression. Restriction fragment differential display allowed
hypothesis building. Results from this method were readily obtained
and yielded reproducible products. Comparison between tadpoles
resulted in isolation of nine products, six of which were sequenced.
The final three products are currently being investigated.
Use of Zebra Finches for Refining DNA
and Song Comparison Methodology, In Order to Delve Into Transmission
of House Finch Song
Sadruddin K. Chandani
Transmission of birdsong in house finches
(Carpodacus mexicanus) is highly complex, not simply because
song is learned, but also because, in the particular case of house
finches, song learning occurs every season. New ways in which to
explore song transmission must be found, and the existing methodology
of analysis must be improved. Zebra finches (Taenopygia
guttata) and their song learning system can be used as a
simplified model of house finch song transmission; zebra finches are “simpler”
because they are “critical-period” learners, who form a
set song and stop learning relatively early in life, and also have a
less varied, less rich song. This study suggests that zebra finches
are also problematic as a tool of refinement for DNA analysis, since
extraction conditions seem to differ substantially between the two
species. However, using zebra finch song for quantitative comparison
purposes demonstrates that song comparison is a viable way to explore
transmission, especially by correlating trees that show relatedness
between individuals, and are derived from a variety of morphological
characteristics including song. Due to the complexity of house finch
song, a system for comparing house finch repertoires must be
developed that is comprehensive enough to accurately and reliably
score repertoire similarity. The revision of the classification
system of house finch songs in this study was a preliminary step
towards developing such a system. The ability to quantitatively
compare house finch song will greatly facilitate the investigation
into how song is transmitted and learned in this species. Revealing
how the complex system of song transmission in these birds operated
will not only be of importance for understanding general patterns of
learning in organisms, there may also be findings that can be applied
for speech and language development in human society.
Regulation of Vaccinia Virus dUTPase
Expression and Activity in vivo
Erin L. Davies
Vaccinia virus dUTPase, an enzyme encoded by
the nonessential, early phase gene ORF F2L, is a critical component
of the de novo pyridine biosynthetic pathway whose function is
also important to the maintenance of DNA replication fidelity.
DUTPase hydrolyzes dUTP to dUMP and pyrophosphate, a reaction which
simultaneously furnishes thymidylate synthetase with its substrate,
dUMP, and reduces the intracellular dUTP.dTTP ratio, thereby
preventing the misincorporation of dUTP into nascent DNA molecules.
Mutagenic U-DNA activates an interactive excision-repair process
catalyzed by uracil DNA-glycosylase, which ultimately leads to
chromosome fragmentation and cell death. An understanding of how
vaccinia virus dUTPase production and activity are regulated in
vivo will provide insight into the processes of DNA replication
and viral pathogenesis, and will aid in anti-viral drug design.
Therefore, profiles of vaccinia virus dUTPase expression, stability,
activity, and phosphorylation spanning the eight-hour viral
replication cycle in BSC40 cells were generated. Although
dUTPase is translated between two and five hours post-infection
(hpi), the enzyme is long-lived and does not undergo appreciable
turnover through 10 HPI. Once translated, the enzyme is
phosphorylated immediately, and shows basal levels of activity. A
dramatic increase in dUTPase phosphorylation levels is seen between
five and six hpi, which coincides with the steady rise in catalytic
activity seen late in infection must be the result of a positive
post-translational regulatory mechanism. It was proposed that
phosphorylation events allosterically active dUTPase, due to the
strong correlation between dUTPase activity and phosphorylation
levels throughout infection. In order to identify the phosphorylated
residues, phosphoamino acid analysis was performed on immunopurified
dUTPase using a 2D-TLC system. Preliminary experiments suggest that
vaccinia virus dUTPase is phosphorylated on tyrosine and threonine
residues in vivo.
Tidal Pulsing, Environmental
Variability, and Phytoplankton Dynamics in the Mystic River
Estuary
Joshua H. Goldstein
An ecosystems-level study of the Mystic
River estuary, CT, USA was performed to examine how short-term
environmental variability, induced by pulses such as tidal cycles and
storm events, influenced short-term variability in phytoplankton
dynamics. Salinity, temperature, dissolved oxygen, turbidity,
nutrients, fluorescence, chlorophyll a, and phytoplankton
counts were measured at a series of stations along the estuarine
gradient from mid-June through mid-August 1999. Vertical and
horizontal stratification throughout the study period was minimal due
to the severe drought conditions. Fluorescence levels throughout the
estuary pulsed on an approximately two-week cycle, with peak
magnitudes increasing as the summer progressed, and this fluorescence
pulsing appeared to be connected with the neap-spring tidal cycle.
Tides deliver energy to an estuary, and the second-order fit between
tides and fluorescence suggested that photyplankton biomass was
maximized at intermediate levels of tidal energy. Nutrient
availability was a major factor driving variability in phytoplankton
biomass, and this suggested that the coupling between tidal energy
and phytoplankton dynamics was driven by resuspension of benthic
nutrients by tidal mixing. The high levels of phytoplankton biomass
observed in mid-August appeared to be caused by the synchronization
of a tidal pulse with a storm pulse. The strength of pulses dampened
going down the estuarine gradient, and the highest phytoplankton
biomass was found in the upper part of the river where environmental
variability was greatest. Tidal fluctuations induce periodic
short-term variability in physical and chemical conditions, and tidal
pulsing appears to be an important, regular, external pulse driving
short-term variability in phytoplankton dynamics in the Mystic River
estuary.
Injection of the Mauthner Cell with
Postulated LTP-Induction Enzyme, CaMKII, May Potentiate the C-Start
Reflex in Goldfish
Jason M. Langheier
Long-term potentiation (LTP), the NMDA
receptor (NMDAr) and Ca2+ dependent increase in synaptic
efficiency found neural pathways, has long been postulated as a
mechanism for memory and learning. This hypothesis has never directly
been proven in a vertebrate model.
CaMKII is involved at least in the induction
phase of rodent hippocampal LTP (Lledo, et al., 1995), and is also
active in response to the LTP-producing NMDAr-dependent
Ca2+ influx observed upon the delivery of a tetanus to the
goldfish posterior VIII nerve, which synapses on the Mauthner cell
(M-cell) lateral dendrite (Yang, et al., 1990). Direct injection of
the activated enzyme into the lateral dendrite has been shown to
potentiate both electrical and chemical synaptic conduction (Pereda,
et al, 1998). Gathering excitatory auditory and displacement input
from nerve VIII, the pair of M-cells of the medulla are also known to
initiate the C-start startle reflex, which can be measured by
high-speed cinematography.
Pressure injection of CaMKII into the left
M-cell of one animal caused it to only have C-starts to the right of
the controlled by that cell, at 1 and 2 hours post-injection, as
elicited by a suprathreshold vibratory stimulus. The fish also showed
spontaneous rightward jerks and a lowered threshold for sound evoked
rightward C-starts in that time period. Interestingly, at 4 hours and
thereafter, the fish only gave C-starts to the left.
That potentiation could give one cell a
competitive advantage during suprathreshold stimulation of both cells
might be explained by the theory that LTP at the excitatory synapses
of the M-cell lead to faster excitatory postsynaptic potentials
(reflected in larger slope), such that the cell which fires first
inhibits the other cell and initiates the C-start on the
contralateral side of the body. Among the possible explanations for
the loss of the rightward C-start are that the cell died due to
injection of CaM excitotoxicity, or that a late-phase potentiation of
inhibitory synapses occurred. If the last possibility is shown to be
true, one must question whether LTP may not be a memory mechanism,
but a means of cellular arousal which homeostatic mechanisms correct
for in eventually bringing synaptic efficiency back to baseline.
What Regulates the Regulator? A Study
of the in vivo Transcriptional Regulation of the
Muscle-Specific Transcription Factor MyoD
Randall L. Lindquist
Muscle fibers are generally specialized for
power or endurance; these specialized fibers are called fast and slow
muscle, respectively. The principal determinant of muscle fiber type
is the Myosin Heavy chain (MyHC) protein, which drives sarcomeric
contraction. Muscle fiber type is highly oastic; muscles can switch
their fiber type in response to mechanical, neural, or hormonal
stimuli. Such a change in muscle fiber type ultimately results in
corresponding changes in the cellular expression of MyHC isoforms and
in the velocity of muscle contraction. Previous work has suggested
that the muscle-specific transcription factor MyoD regulates muscle
fiber type and is involved in slow-fast fiber-type transitions;
MyoD had previously been shown to be pre-translationally
upregulated in fast muscle. Somatic cell gene transfer was used to
examine the in vivo transcriptional regulation of MyoD
in the tibialis anterior (TA) and the soleus, representative fast and
slow muscles of the rat hindlimb; it was shown that the
258-nucleotide MyoD distal enhancer is sufficient to confer
fiber-type specificity on a SV40 promoter-luciferase construct and
that a 25 base-pair region of this MyoD enhancer is required
for transcription in both the Ta and the soleus. There is a consensus
AP-1 site in this 25 base-pair region; it is proposed that fos and
jun bind to this AP-1 site in conjunction with one or more
trans-acting factors whose expression is fiber-type specific
to stimulate transcription at a higher level in the TA than in the
soleus.
Retinal Ganglion Cells Regenerate to a
Muscle Target
Melissa Motta
The Optic Nerve (ON) is comprised of Retinal
Ganglion Cells (TGCs), which have their soma in the retina and
project to the optic tectum in the brain. Unlike central neurons in
mammals and birds, neurons in the central nervous system (CNS) of
fish – such as RGCs – are capable of regenerating and
restoring vision. Though RGC show highly specific regeneration to the
optic tectum, it has been shown that they are capable of regenerating
to non-standard targets in the brain. Moreover, RGC can be redirected
through peripheral nerve implant to non-optic brain regions. In the
present study, the ON in Goldfish was transected and a section of
peripheral Lateral Line (pLL) nerve was used to redirect the RGC to a
peripheral muscle target. The RGCs regenerated through the pLL nerve
bridge and projected over the superior oblique, an extraoccular
muscle. After 60-90 days the neurons were stained with Neurobiotin
and could be raced leaving the ON, through the implant and onto the
superior oblique muscle. Some axons appeared to separate from the
nerve bundle projecting on the muscle and synapse on single muscle
fibers. This study validates the capacity of CNS neurons, which are
glutameric, to project to and synapse on a peripheral muscle target,
which is cholinergic.
Higher Cortical Reorganization in
Response to Peripheral Nerve Regeneration in the Zebra Finch
Charles N. Munyon
The zebra finch (Taeniopygia guttata)
is a songbird with a closed-ended learning period that ends at sexual
maturity, around ninety days of age. Transection of the right
tracheosyringeal nerve (NXIIts) in the adult male zebra finch results
in immediate perturbation of the frequency modulations which compose
that male’s song, but does not disrupt its temporal structure
(McKibben, 1989). Upon regeneration of the transected nerve, some of
the original song’s fidelity is restored in a manner that is
dependent on the lateral magnocellar anterior nucleus of the
neostriatum (LMAN) (Mehta, 1994). This recovery accompanies a
randomization of the topographic map of the tracheosyringeal motor
nucleus (nXIIts), which is responsible for controlling the muscles of
the syrinx, the bird’s vocal organ (Linck, 1999). The goal of
this study was to examine the effects of nerve transection on the
neuronal map of nucleus Robustus Arthistriatalis (RA), which
innervates nXIIts, in the hope of better understanding the mechanisms
by which some degree of plasticity is retained in crystallized song.
Injections of retrograde tracer into the syrinx and of anterograde
tracer into nucleus RA were administered in an attempt to visualize
any perturbations in the maps of both nXIIts and RA. Complications
with the experimental protocol prevented observation of the map of Ra
in a transected male, but this report offers suggestions for
continuation of the study which should alleviate these
difficulties.
Cytochrome C and Lipid Interactions in
the Mitochondrial Membrane
Jillian A. Pesin
Sphingolipids act as bioactive molecules
involved in signal transduction and cell regulation. Previous studies
have shown that, in animal cells, ceramide induces cytochrome c
release and the formation of reactive oxygen species in the
mitochondrial membrane, both hallmarks of apoptosis. No studies have
been done to investigate the possible role of ceramide in apoptosis
in plant cells. Phaseolus vulgaris mitochondria were used to
measure cytochrome c release from the mitochondrial membrane and the
formation of reactive oxygen species. The cytochrome c release assays
were inconclusive while the reactive oxygen species were induced by
incubations with sphingolipids. The physical interactions between
sphingolipids and cytochrome c were investigated using isothermal
microcalorimetry. Heat change was measured during interactions
between sphingolipids and cytochrome c, sphingolipids and liposomes,
and sphingolipids and liposomes containing cytochrome c. Ceramide
showed the strongest association with liposomes containing cytochrome
c, suggesting that it interacts directly with cytochrome c while the
protein is poised in the mitochondrial membrane.
Investigation into the Function of the
Hunchback Orthologue, LZF2, in Leech Development
Kerice A. Pinkney
A further investigation into the genes
controlling segment pattern formation in leeches has been the main
focus of this lab’s studies. Critical attention has been paid
to the Leech Zinc Finger II gene (LZF2), in an attempt to
characterize the role it may play in leech development. LZF2
is the leech orthologue of the Drosophila hunchback (hb) gene.
It appears as if translational repression, possibly mediated by a
nanos response element-like motif in the gene’s 3’UTR,
may be guiding protein expression. This hypothesis is given credence
by the recent finding of the nanos homologue, Hro-nos,
in leeches. Based on this theory, experiments designed to manipulate
the 3’UTR segment of the LZF2 gene were performed. While
the results of these experiments have not been conclusive, they do
provide us with some insight into the validity of this theory.
Interestingly, dsRNA experiments with LZF2 have indicated that
LZF2 plays a role in proper embryogenesis in the leech.
The Evolution of Plasticity and Local
Adaptation: Confronting a Computer Simulation with Empirical
Data
Ethan Plunkett
Almost all species encounter habitat
heterogeneity. Determining how species react to that heterogeneity is
an important evolutionary question. I used known life history factors
of an intensely studies natural population to simulate on a computer
the evolution of plasticity and local adaptations in response to a
heterogeneous habitat and predict the population structure and
genetic state of a natural population.
The simulation predicts that migration
between habitat types is necessary to maintain plasticity; that in
simple environments selection favors local adaptation over
plasticity; that fragmenting a population will increase drift and
that this drift will, in turn, drive migration between fragments; and
that increasing habitat uncertainty in the form of periodic storms
will maintain migration, maintain plasticity, and eliminate local
adaptation.
The Empirical findings, that there is
plasticity in the natural population and that there is no local
adaptation, support the predictions of the model; together they
suggest that habitat uncertainty maintains phenotypic plasticity and
prevents local adaptation in the North Government Island chorus frog
population.
An Analysis of CDC14 and SFP1
Interactions Using Temperature-Sensitive Mutants and the Yeast
2-Hybrid System
Kate D. Ramsayer
In order for a yeast cell to exit from
mitosis, the Cdc28/Clb2 complex that provides the main catalytic
mechanisms for mitosis must be degraded. This is achieved through
three different pathways in Saccharomyces cerevisiae that
involve Swi5, Sic1, and Hct1/Cdh1, each of which is regulated by the
dual-specificity phosphatase Cdc14. Cdc14 dephosphorylates and
activates these proteins, allowing Sic1 to inhibit Cdc28/Clb2, Swi5
to up-regulate the transcription of Sic1, and Hct1/Cdh1 to induce the
APC to degrade Clb2. Cdc14 itself is regulated by Net1, which tethers
Cdc14 in the nucleolus for the majority of the cell cycle until it is
released through the activity of TEM1.
In doing a search for suppressors of
temperature-sensitive cdc14 mutants arrested in late
telophase, it was discovered that there is an interaction between
CDC14 and SFP1, a zinc split finger protein (Sagasti,
1996; Paliulis, 1997). By sequencing the cdc14-8 allele, which
is the sole cdc14ts mutation not suppressed by
sfp1, the cdc14-8 mutation was found to be a change
from proline to serine at the 53rd amino acid residue of
the CDC14 gene. This is a significant change in amino acid
structure and probably significantly alters the conformation of the
cdc14-8 protein.
To determine if there is a direct,
protein-protein interaction between SFP1 and Cdc14, a plasmid with
the SFP1 gene inserted into a 2-hybrid expression vector was
constructed using PCR mutagenesis, restriction enzyme digestions, and
ligation reactions. PWR1084, the pGAD/SFP1 vector, was then
transformed with pGBDu/CDC14 into the yeast host strain PJ69-4A in a
2-hybrid test. While initial results were positive, implying that
there is a protein-protein association of Cdc14 and Sfp1, additional
controls gave questionable results; thus additional experiments need
to be run to confirm this interaction.
Influences on Distribution of Spring
Ephemerals on the Mount Greylock Reservation, Williamstown,
MA
Aya E. Reiss
Spring ephemeral distribution in
Williamstown has been significantly linked to influences of past land
use (Nash 1994; Grossmann, 1996; Halbach, 1997). Alterations to the
landscape of the Mount Greylock Reservation have been varied
throughout the history of Williamstown. Disturbances through
agriculture, logging and landslides have changed the forests, and
most especially the herbaceous layer. Forests which have been cleared
are termed secondary woods, whereas those which remain in the old
growth state or were used with minimal disturbance, such as woodlots,
are termed primary woods. The herbaceous layer recolonization
patterns of secondary forests are strongly influenced by seed
dispersal mechanisms. Ant dispersed species are much slower to return
to a secondary woods than wind or vertebrate dispersed species (Nash,
1994). While land use does remove an existing seed source and
therefore deplete a forest of its herbaceous species, the Mount
Greylock Reservation has more significant limitations to growth.
Distribution patterns of spring ephemerals on the Mount Greylock
Reservation are largely controlled by elevational influences. Changes
with increasing elevation include increasing acidity, decreasing
nutrient availability and changes associated with shifts from
deciduous to coniferous forests. In addition to the impacts of past
land use, climate and forest extremes dictate the areas for potential
growth on the Reservation, limiting many herbaceous species to the
lower elevational ranges. Therefore, in areas above 1500 feet, the
physical environment overwhelmingly influences spring ephemeral
distribution, unlike other parts of Williamstown where land use
appears to be the primary factor controlling wildflower abundance and
dispersal.
Exploring Regulation of CDC14 in
Exit from Mitosis: Characterization of a cdc14 Mutation and a
Search for the Mechanism of Inhibition by SFP1
Daniel J. Richter
In eukaryotic organisms, major cell cycle
events are induced by the activity of cyclin dependent kinases
(Cdks). Exit from mitosis is one of the two key cell cycle
transitions that govern the switch between high and low states of Cdk
activity. CDC14, a protein phosphatase, is the farthest
downstream of any single gene required for mitotic exit in budding
yeast, Saccharomyces cerevisiae. A series of genes including
TEM1, LTE1, CDC15, DBF2/DBF20, CDC5, MOB1 and NET1 are
involved in the regulation of CDC14, a significant component
of which is nucleolar sequestratin via Net1 and the RENT complex. Two
cdc14 temperature-sensitive mutant alleles were previously
identified: c14-2 and cdc14-8. SFP1 is a split
zinc finger protein whose mutation or deletion is capable of
partially suppressing the cdc14-2 mutant allele, but is
incapable of suppressing cdc14-8. Sequence data show that
cdc14-2 has a point mutation near the active site, and that
cdc14-8 has a point mutation in an unrelated part of the
protein. I examined the consequences of these mutations in light of
the differential suppression by sfp1 mutants and will suggest
possible modes of action for SFP1. Furthermore, I will propose
and partially implement two novel ways to investigate the
relationship between CDC14 and SFP1; polymerase chain
reaction epitope tagging (PET) of SFP1 to detect
protein-protein interaction and electrophoretic mobility shift assays
(EMSAs) of SFP1 with possible CDC14 promoter sequences to test
for transcriptional regulation.
A Kinetic Examination of the Vaccinia
Virus Deoxyuridine Triphosphatase (dUTPase)
Jeffrey D. Roizen
Deoxyuridine triphosphate pyrophosphatase
(dUTPase, EC 3.6.1.23) is a ubiquitous enzyme which catalyzes the
cleavage of deoxyuridine triphosphate (dUTP) to deoxyuridine
monophosphate (dUMP) and pyrophosphate (PPI). The dUMP
product of this reaction is an intermediate in the pathway towards
synthesis of deoxythymidine triphosphate (dTTP). As this enzyme is
necessary for DNA replication, it is a tempting target for cancer
treatment and antiviral chemotherapy. In addition to the practical
interest in this enzyme, it has several unique enzymatic
characteristics, including active sites formed by portions of all
three subunits of the active trimer, which make it an intriguing
focus for research. Preliminary data from crosslinking experiments
suggests that this enzyme may exhibit some kind of cooperativity.
To examine the cooperativity of this enzyme,
kinetic studies were undertaken over a large range of substrate
concentrations (0.05 μM to 200 μM) to generate a Hill
Curve. In order to perform these studies, dUTPase was overexpressed
in a T7 RNA polymerase overexpression system, and then subsequently
purified using affinity chromatography and then ion exchange
chromatography. From these kinetic studies, it was learned that the
vaccinia virus dUTPase is negatively cooperative, with a Hill
coefficient (nH) equal to 0.63155 (in units of log μM).
It was found that the dUTPase has three distinct apparent
KmS (in increasing order: –0.07 μM,
-0/47 μM and ~3.6 μM) and that the overall Vmax
for the enzyme is ~8.7*10-9 μmoles/sec [with the
VmaxS equal to (in increasing order) ~2.5*10-9 μmoles/sec
and ~6.2*10-9 μmoles/sec.] We are thus the first
lab studying dUTPase to report such a result, which only adds to the
rich uniqueness and intellectual intrigue of this enzyme. This
negative cooperativity may be due to enzymatic or systemic
evolutionary pressures.
The Role of MyoD in Muscle Fiber-Type
Maintenance: A Tissue Specific Phenomenon
David J. Seward
In this study, we endeavored to characterize
the role of MyoD, a myogenic transcription factor, in muscle
fiber-type maintenance. Previously it has been proposed that MyoD
plays a causal role in the transcriptional activation of the type Iib
myosin heavy chain (MHC) gene. Using MyoD -/- mice in concert with
hindlimb unweighting we obtained data linking MyoD to Iib MHC gene
induction in the soleus and diaphragm muscle of wild-type (WT) mice.
MyoD -/- mice do not express MHC protein in their diaphragm. In
response to unweighting, the MyoD -/- soleus does activate expression
of the MHC Iib gene, but to a lesser degree compared with the WT
unweighted soleus. Significant variations in the MHC protein
composition between the diaphragm, biceps, and masseter of WT and
MyoD -/- mice support the view that in certain muscles MyoD is in
fact required to maintain a WT-like MHC protein profile. Together
these data suggest MyoD is a tissue specific enhancer molecule able
to mediate Iib expression when the necessary basal transcriptional
machinery is in place. However, it is clear that MyoD should no
longer be thought of as playing a causal role in Iib MHC expression
as MyoD -/- mice are able to express Iib MHC protein in several
muscle tissues. It would appear that MyoD’s role can be altered
in a given muscle tissue depending upon external stimuli and the
presence of tissue depending upon external stimuli and the presence
of tissue specific cofactors.
Factors Affecting the Distribution of
Spring Ephemerals on the Taconic Range
Emily L. Simpson
During the initial settlement of
Williamstown, much of the Taconic Range on the western boundary of
town was divided into lots and cleared for farms, removing the native
flora of the temperate deciduous forests. While farming was
extensive, reaching slopes higher than 1500 ft in elevation, it only
lasted generally less than a century and by the mid-1800s most of the
farmland on the Taconics had been abandoned leaving the land to
recover its native forests. Forests that returned to these
agricultural areas are considered secondary, while forests that were
not cleared are considered primary and represent the undisturbed
flora. The herbaceous communities of these secondary and primary
forests are considerably different due to their divergent land-use
history. Primary forest tend to have a richer and more diverse
herbaceous population, while secondary forests are less rich and
diverse, due mostly to the absence of myrmemecochorous
(ant-dispersed) species which are slow to re-colonize past
agricultural areas. Past land-use is only one of many factors
affecting herbaceous distribution above 1500 ft however. Elevation
also tends to limit species. Lower elevation sites have richer more
diverse populations while areas above 2300 ft contain species not
found at lower elevations. Another important factor is the aspect or
topographic position of an area, with dry south-facing slopes and
ridge-tops having lower richness and diversity than moister valley
bottom and north-facing slopes. The difference in herbaceous
distribution within these three factors of past land-use, elevation,
and aspect are linked to characteristic soil nutrients and canopy
compositions.
Development of an In Vitro
Vaccinia dUTPase Phosphorylation System
Lauren M. Singer
Vaccinia Poxviridae is a double stranded DNA
virus that infects a wide range of mammalian hosts. The virus
replicates in the cytoplasm of the host cell. Independence from the
host cell nucleus requires vaccinia to encode its own DNA replication
machinery. One enzyme important in maintaining vaccinia’s
nucleotide pol is deoxyuridine 5'-triphosphate nucleotidohydrolase
(dUTPase). DUTPase hydrolyses dUTP to dUMP, which increases levels of
dUMP, a precursor in thymidine synthesis, and decreases levels of
dUTP, thereby reducing risk of inappropriate incorporation of uracil
into the DNA. Thus, dUTPase is important in DNA replication
fidelity.
Mechanisms of regulation of dUTPase activity
are currently unknown. DUTPase is a phosphoprotein; however, the
significance of this modification, the involved kinases, and the
phosphorylated residues have not been determined. Previous studies
have shown that while neither of the known vaccinia encoded protein
kinases, F10L and B1R, are individually responsible for
phosphorylating dUTPase in vivo, both are capable of
phosphorylating dUTPase in vitro. This study aimed to use
these viral kinases and other commercially available protein kinases
to develop an in vitro system of dUTPase phosphorylation with
the long-term intent of using this system to elucidate the effects of
phosphorylation on the activity of dUTPase. F10L and PKA were used to
phosphorylate dUTPase and attempts were made to identify the
phosphorylated residues by phosphoamino acid analysis.
The Translocation of
Inositolphosphorylceramide across the Lipid Bilayer
Carolin E. Spiegel
Inositolphosphorylceramides, or InsPCers,
are a class sphingolipids present in the plasma membranes of plants,
fungi, and protozoa. It appears that IPC synthase, the enzyme that
catalyzes the formation of inositolphosphorylceramide, or IPC, is
located on the cytosolic side of the Golgi membrane. The ultimate
destination of IPC is presumably on the exterior of the plasma
membrane. Using these two hypotheses as a framework, this thesis
explores the translocation of IPC across the lipid bilayer using
microsomal and plasma membranes isolated from the golden butterwax
bean plant. This was the first reported study of IPC translocation in
any organism.
The translocation of IPC is not simultaneous
with its synthesis, as demonstrated in assays with phospholipase C, a
membrane impermeable, phosphatidylinositol-specific lipase. However,
it does seem to occur soon after formation. An exogenous energy
source, GTP, enhanced the rate of translocation by 33.3%; ATP was
less effective in facilitating translocation. Concentrations as low
as 0.2 mM GTP were shown to effectively increase the rate of
translocation. It is clear that other translocation mechanisms exist;
perhaps these depend on an endogenous energy source or an
energy-independent pathway.
Experiments were begun to localize IPC with
certainty on the exterior of the plasma membrane. The prepared plasma
membrane vesicles were 92% right side out, permitting their use in
investigating and quantification of IPC content. Because there is
such a small amount of IPC in the plasma membrane, very sensitive
methods of detection are necessary. Studies were initiated with one
such possibility, phenylisothiocyanate derivative.
Isolation of Two sfp1
Suppressors and Partial Cloning of Three cdc14
Alleles
Elizabeth Wells
CDC14 is a key effector of exit from
mitosis in Saccharomyces cerevisiae, and studying the
regulation of this dual-specificity phosphatase is crucial to
understanding how cells exit from mitosis. Cdc14 mutants
display a temperature-sensitive phenotype at 340C,
arresting at late anaphase with mitotic spindles extended. Some of
Cdc14’s substrates, such as Swi1, Sic1, and Cdh1, are already
known. However, the upstream regulation of Cdc14 is still not fully
understood. Localization in the nucleolus by the RENT complex is
known to be important, as is Cdc10/APC activity. Previous work in the
Raymond lab has shown that mutations in the SPF1 gene,
encoding a split zinc-finger protein, can suppress the cdc14
allele-specific, which suggests a number of possible models for
SPF1/CDEC14 interaction rather than bypass mutations of
CDC14 function. While little is known about the
regulation of SPF1, it is our belief that study of this novel
regulatory element may prove to shed light on regulation of
CDC14.
In this study, I rescued three cdc14
alleles into the gapped plasmid gpWR1069 (cdc14-1, cdc14-4,
and cdc14-7, from WR148, WR030, and WR024, respectively). The
portion of these rescued plasmids containing the cdc14 ORF
will, in future research, be made chimeric by restriction enzyme
digestion and ligation, and the site of mutations in each allele will
be localized. The mutant segments of each CDC14 insert may
then be sequenced, and the sequence of each allele compared to its
level of sfp1 suppression. In addition, two putative dominant
suppressing mutations of afp1-1 and sfp1-2 were found
through a mutant hunt for suppressors of sfp1 cold-sensitive
phenotype. These mutations may be revertants, but it is possible that
they encode bona fide double mutants, whose wild-type function
in vivo may be relevant to CDC14
Characterization of a Polychaete
Hunchback Homologue
Andrew H. Werbrock
In this study, we attempted to determine
whether the function of hunchback orthologues are conserved
throughout the annelid phylum. In Drosophila, the gap gene
hunchback (hb) encodes a transcription factor possessing a
highly conserved N-terminal zinc-finger DNA-binding motifs. Hb
is involved in the earliest stages of segmentation and AP pattern
formation. In the leech, Helobdella triserialis, an orthologue
of hb, LZF2 (Leech Zinc Finger 2), is
functionally very different from its insect counterpart and is not
involved in segmentation. In order to ascertain whether the function
of LSF2 in leeches is shared throughout the annelid phylum we
analyzed the protein expression pattern of a putative hunchback
homologue, Caphb, in the polychaete Capitella capitata
sp. 1, a basal annelid, with a cross-species antibody designed to
LSF2. We found that, on a Western blot, the LZF2 antibody binds the
N-terminal domains of both Caphb and LZF2, verifying that the
antibody is cross-species reactive to Caphb. In early leech and
Capitella embryos, the LZF2 antibody is localized to the
micromeres, suggesting a common function for Caphb and
LZF2 early in annelid development.
Dragonfly Labial Attack and Tadpole
Startle Response: A Study with Aeshnidae Larvae and Rana
pipiens
David T.O. Walfish
This thesis studies various parameters of
the dragonfly labial strike and investigates the factors that
influence a tadpole’s chances of escape from predation by
dragonfly larvae. The organisms used in this study were dragonflies
of the Aeshnidae family and Rana pipiens tadpoles. The
strike of the Aeshnid larvae was explored under a variety of
circumstances: we tethered the dragonfly and presented inanimate
metal probes; we tethered the dragonfly and presented live
free-moving tadpoles, and we let the dragonfly hunt tadpoles
unimpeded.
Study of the tethered-dragonfly/probe trials
yielded important findings about the duration of the forward thrust
of the labial attack. We found that the maximum duration of the
forward thrust in our trials was less than the published value for
maximum duration of the forward thrust. In the free-moving
dragonfly/free-moving tadpole trials, we discovered that the duration
of the forward thrust in unimpeded interactions with tadpoles is far
less than the maximum duration time we calculated, and far less than
the minimum estimated latency of the tadpole startle response. This
led us to conclude that, contrary to what we had originally thought;
the innate startle response possessed by tadpoles does not enable
them to avoid being struck by the labial
attack.
CHEMISTRY
Determining the Absolute Stereochemistry of
Sugar Moieties in Toxicariosides A, B, and C
Karelle S. Aiken
The structures of Toxicariosides A, B and C
were determined in the lab of Professor David Richardson, at Williams
College. The Richardson group was able to determine the absolute
stereochemistry of substituents on the aglycone moieties of these
cardenolides. However, with respect to the monosaccharide moieties,
the group was only able to resolve the relative stereochemistry of
these sugars: A: 6-deoxy-2-O-methylgalactose; B:
6-deoxy-2-O-methylglucose; C: 6-deoxy-2-O-methylgulose. In an attempt
to determine the absolute stereochemistry of the sugar moieties,
diastereomers of the sugars were synthesized with a chiral and
optically active molecule, and then subjected to gas chromatographic
analysis. The absolute stereochemistry of toxicarioside sugars can be
determined from a comparison of the retention times of these
diastereomers to the retention times of diastereomers derived from
similar sugars of known stereochemistry. Reactions involved in the
synthetic preparation of the sugars for gas chromatography consisted
of cleavage of the monosaccharides from the aglycone structure,
isolation and butylation with optically pure sec-butanol, followed by
permethylation. In this study, these reactions have been developed to
give unambiguous and conclusive results. In addition, new approaches
to the synthetic preparation of sugars were considered in order to
determine if the reactions could be more accommodating of the most
probable conditions under which the toxicariosides will be
investigated.
The Synthesis and Characterization of
Novel Mesogenic Compounds
Michelle B. Dunn
This work focuses on the synthesis and
characterization of novel metal-chain complexes in search of
metallomesogenic compounds. Using a Co(II) system with ester and
amide derivatized pyridine ligands, metal-chain complexes were
synthesized, but they converted to tetrahedral, individual molecules
upon heating. Both the Mn(II) and Ni(II) systems investigated were
generally thermally unstable, decomposing before melting. However,
both the MnL2Br2 C10 amide and the
NiL2Br2 C10 amide showed mesogenic
behavior. Preliminary work a Fe(II) system revealed the facility with
which Fe(II) oxidizes to Fe(III). In the future, these complexes must
be synthesized and stored under an inert atmosphere for successful
synthesis and characterization to occur.
Structural Analysis of SOS
Regulation
Biniam T. Gebre
In order to avoid the disastrous affects of
DNA damage cells have evolved elaborate machinery tailored to helping
them survive this damage. Specifically, cells have evolved
strategies, known as DNA damage tolerance mechanisms, which play an
important role in allowing them to deal with the consequences of
unrepaired damage to their genomes. The SOS regulatory network is a
complex system of over twenty genes that, when induced by DNA damage
or inhibition of DNA replication, results in the elaboration of these
DNA damage tolerance mechanisms. The SOS system, found both in
Escherichia coli and Bacillus subtilis, modulates
between these two states, which is ultimately either gene expression
or gene repression. The LexA protein regulates the toggle between
these two states.
LexA's repressor activity has two parts to
its functionality; this includes autocleavage (which allows SOS gene
expression) and DNA binding (which represses the SOS genes). The LexA
activity is realized structurally by the division of the LexA protein
into two parts: the carboxyl-terminal autocleavage/dimerization
domain and the amino-terminal DNA binding domain. Studying these
structural features and the molecular details of LexA's activity
should provide further clues as to how the SOS response is regulated.
Furthermore, the study of another SOS protein known as UmuD, which
shares high sequence homology and presumably similar cleavage
activity, should also provide further insight into the LexA
autocleavage process.
Molecular modeling and computational methods
are employed heavily in this study to extract information about these
two proteins in order to gain insight into both the autocleavage
process of E. coli UmuD and B. subtilis LexA and the
binding of the B. subtilis LexA to the B. subtilis SOS
operator consensus sequence. To this end, a structural analysis of
UmuD was performed using Molecular Simulation's Insight II modeling
suite. Where it was found that UmuD most likely undergoes
autocleavage in an intermolecular reaction as a molecular dimer. The
structure of UmuD also suggests that RecA might cause a
conformational change at Lys98 on UmuD, causing it to push into the
active site to catalyze the autocleavage reaction. All the residues
in the active site of UmuD and their potential significance have been
outlined. Moreover, a model for the B. subtilis N-terminal DNA
binding domain was built and then docked on the B. subtilis
SOS operator consensus sequence, which provides information about how
LexA binds to this sequence and represses SOS gene activation.
Similarly, the dimerization domain of the B. subtilis LexA
protein was also built using homology techniques and further analyzed
for any structural significance that might lend information about the
autocleavage process.
Fishing for RNA
Michael D. Hurwitz
Recent discoveries have determined that
there are RNA molecules other than transfer RNA that are capable of
being aminoacylated in prokaryotes. An ultimate goal in this project
is to discover novel RNA structures that may be charged by
aminoacyl-tRNA synthetases. In order to commence these studies, it is
vital to create a system through which aminoacylated RNA can be
extracted from a large RNA pool and identified. Reverse transcription
and polymerase chain reactions are utilized to produce large amounts
of DNA that correspond to isolated RNA. Successful polymerase chain
reaction requires knowing the 3 and 5 ends of a nucleotide sequence.
This thesis presents techniques for polyadenylation of the 3 end of
tRNA, reverse transcription of RNA with considerable secondary
structure, and finally, ligation of a T7 promoter sequence to the 3
end of the resulting cDNA.
A Study of Building a Thin Film of
Sulfuric Acid on n-Hexane Soot
Bevan P. Londergan
Heterogeneous chemistry has seen an
explosion of interest in the last few decades due to the discovery of
the participation of heterogeneous reactions in the mechanisms of
some important reactions, such as ozone depletion. Elevated levels of
sulfuric acid and depressed levels of sulfur dioxide in jet aircraft
exhaust contrails, relative to the levels predicted by the currently
characterized reaction mechanisms, have prompted some researchers to
hypothesize that the oxidation of SO2 may be facilitated
by a heterogeneous reaction involving the soot, a solid aerosol. The
adsorption of SO2 onto a dry soot surface has been
characterized through previous research in this laboratory. It is now
appropriate to study the question of how SO2 interacts
with a soot surface on which trace amounts of sulfuric acid are
present.
In preparation for the study of this
interaction, I have concentrated my efforts on devising an
experimental process for creating a thin film of
H2SO4 on a cooled soot surface inside a vacuum
chamber designed for the infrared spectrographic analysis of
surfaces. The formation of a film of H2SO4 on
soot is carried out by reacting SO3 and H2O on
the soot surface, and this year’s study focused on determining
appropriate experimental conditions for the generation of a monolayer
acid layer. We use an FTIR and mass spectrometer to monitor the
experiments, which range in temperature from –140oC
to –65oC. Calibrations have been carried out for
determining the thickness of a layer of SO3 through the
integration of a characteristic infrared peak. We have succeeded in
creating thin layers of acid on soot surfaces, possibly of near
monolayer thickness by rough calculations, and we are near to
beginning the methodical study of the interaction between
SO2 and a sulfuric acid-coated soot surface.
Our relocation to a new laboratory gave us
an opportunity to improve upon our extensive experimental apparatus.
Among the additions to the lab are a new gas line in a hood, a
separate pump room, a new corrosive-gas turbomolecular pump, and a
new corrosive-gas mechanical pump to back it up.
Regulation of the Bacillus
subtilis SOS System Dual Regulation of recA and Novel SOS
Genes with Multiple LexA Binding Sites
Veena Mandava
Expression of the Bacillus subtilis
recA gene can be induced by two signals: DNA damage and
competence development. The DNA damage pathway has been
well-characterized, but the induction of recA during
competence development is still not understood. The major competence
transcription factor, ComK, interacts in undefined ways with RNA
polymerase and LexA on the upstream regulatory region of recA,
resulting in transcriptional activation of the recA gene
during competence development. To study this interaction, we proposed
to perform hydroxyl radical footprinting of recA with the
three proteins involved in its induction - ComK, LexA, and RNA
polymerase. First, we purified RNA polymerase on a nickel-NTA column
using a B. subtilis strain engineered with a His tag attached
to the β' subunit. RNA polymerase was unable to bind to the
recA promoter, however, because the à subunit was
absent from the preparation. Footprinting was attempted with just
LexA, but could not be continued without active RNA polymerase.
Novel B. subtilis SOS genes with
multiple LexA binding sites were identified in a computer search and
were shown to compete with recA for binding of LexA. Four
novel genes, yqjW, yqzH, yozL, and yozM,
have two SOS boxes, and a third gene, lexA, has three SOS
boxes. Band shift assays were performed with these genes to show that
each binding site was capable of binding LexA. Results of the band
shift experiments suggest that three genes, lexA, yqjW,
and yozL, have multiple, active SOS sites. The KDs
for lexA and yqjW were found to be 11 nM and 34 nM,
respectively.
Finally, we attempted to clone three SOS
genes, dinB, dinC, and recA, into an
Escherichia coli expression system in order to obtain their
protein products. Both dinB and dinC were successfully
cloned, but only the DinB protein was produced.
Selective Lithiation of Aromatic
Systems
Michelle S. Mourad
The deprotonation of aromatic species often
results in a mixture of isomers, and thus poor regioselectivity upon
reaction with electrophiles. Lithium diethylamine was used to
facilitate an equilibrium between the two anions formed that might
favor the more thermodynamically stable anion and thus improve
regioselectivity. The compounds 3-methyl-2-thiophene-carboxylic acid
and 1-methyl pyrazole were most extensively studied. In their
alkylation with methyl iodide, acetone and benzaldehyde,
deprotonation with lithium diethyl amine as compared to n-butyl
lithium or lithium diisopropylamide gave improved regioselectivity
for these two systems.
The Synthesis and Study of Models for
the Active Site of Liver Alcohol Dehydrogenase
Megumi Onishi
The mechanism of catalysis by Liver Alcohol
Dehydrogenase (LADH) has not been completely elucidated. Furthermore,
the importance of zinc(II) in the active site, as well as the
possible significance of the two cysteine and one histidine ligands
coordinated to the metal have not been well defined. Synthetic models
whose ligands bind in a distorted tetrahedral geometry will allow for
studies into the role of zinc(II) at the active site of LADH. Steps
toward the synthesis of bi- and tri-dentate ligands to model the
active site are described, utilizing
2-methyl-4-tert-butyloxazole, as well as organic and inorganic
linker molecules, including benzophenone,
2,2'-dicholoro-4,4',5,5'-tetramethylbenzophenone, and
phenyldichloroborane. Molecular modeling studies suggest that the
target ligands will bind to zinc(II) with structural parameters
similar to the active site of LADH.
The Role of RNA Structure in tRNA
Interactions with Aminoacyl-tRNA Synthetases
Michelle Pacholec
In contrast to the uniformity observed in
cytoplasmic tRNAs, there is a great deal of structural variation in
animal mitochondrial tRNAs. The most extreme cases are observed in
the nematodes C. elegans and A. suum, where 19/20 of
the tRNAs have their entire T-stem/loop and variable loop deleted and
replaced with a short 6-12 nucleotide TV-replacement loop. In order
to study these truncated tRNAs, hybrids that mixed and matched
elements from both the cytoplasmic E coli tRNAAla system and
the C. elegans mitochondrial tRNAAla system, were
created. Determination and comparison of the rates of aminoacylation
of these chimeras by both E. coli and C. elegans
mitochondrial alanyl-tRNA synthetase, both of which have been
expressed in a plasmid vector, would allow one to determine what
structural elements are important for charging. In this thesis, all
of the chimeras were tested for aminoacylation by E. coli
AlaRS. As expected, this enzyme aminoacylated neither C.
elegans mt-tRNAAla nor any of the hybrid constructs
containing the C. elegans acceptor stem. Surprisingly,
however, hybrids that preserved the E. coli acceptor stem, but
contained other C. elegans structural elements were not
aminoacylated by E. coli AlaRS. These results indicate that
deletion of the T-stem/loop and its replacement with the TV-loop
negatively effects charging. Two possible reasons for this lack of
aminoacylation are discussed, including the possibility that these
chimeric tRNAs are adopting non-canonical tertiary structures that
inhibit E. coli AlaRS from accessing and hence charging the
acceptor stem.
Cloning and Purification of Bacillus
subtilis ComK, and Expression Profiling of Unknown SOS
Genes
Amish A. Shah
Exposure of Bacillus subtilis to a
variety of DNA-damaging agents results in the induction of the global
“SOS response.” Expression of the genes in the SOS
regulon are controlled by the LexA protein. LexA acts as a
transcriptional repressor of these unlinked genes by binding to
specific sequences (SOS boxes) located within the promoter region of
each LexA-regulated gene. Alignment of known LexA binding sites found
in the B. subtilis chromosome reveals a consensus of
5'-GAACN4GTTC-3'. By using this consensus sequence as a
search criterion, Lovett, et al. has recently performed computational
searches of the entire B. subtilis genome to identify novel
LexA-regulated genes. These searches identified a total of 33
potential LexA-regulated genes, including some previously
characterized LexA-regulated genes. Using electrophoretic mobility
shift assays, 18 of the 33 were found to bind LexA. This study used
gene macroarrays and expression profiling to investigate whether
these 18 putative SOS genes were expressed during a SOS response.
Results suggest that these 18 genes are, in fact, expressed at
significant levels during SOS response, thereby allowing us to
identify 18 novel LexA-regulated genes. The potential function of
each newly identified LexA-regulated gene is discussed.
ComK is a 23 kD competence transcription
factor which drives the development of competence in B.
subtilis, yet also activates the transcription of recA. The RecA
protein is required for induction of the SOS DNA repair system and
general recombination in B. subtilis. In order to investigate
the relationship between LexA, which functions as the repressor of
SOS regulon, and ComK, which acts as the transcriptional activator of
recA during competence-development, large quantities of highly
purified ComK protein are needed. ComK was amplified from chromosomal
B. subtilis DNA and cloned into an Escherichia coli
expression vector. Preliminary results of the protein induction
indicate successful cloning, although further investigations must be
performed to optimize a purification protocol.
Progress toward the Synthesis of
(+)-Pacifigorgiol:
Formation of the Tetrahydroindene Skeleton
Carolyn A. Stickney
(+)-Pacifigorgiol is a sesquiterpenoid
compound that has been isolated from the gorgonian soft coral
Pacifigorgia adamsii; its enantiomer, (–)-pacifigorgiol,
has been isolated from the essential oil of the plant
Valeriana
officinalis. As the former has shown evidence of ichthyotoxicity,
it is posited to be a defense mechanism for the coral from which it
was isolated. In 1982, an 11-step racemic synthesis of pacifigorgiol
was completed by the Clardy group; shortly thereafter, an asymmetric
synthesis of (–)-pacifigorgiol was accomplished in the same
group; the yield for their sixteen-step synthesis was 15%. In this
research we propose a twelve-step asymmetric synthetic scheme
applicable to the construction of either (+)-pacifigorgiol or (–)-pacifigorgiol
wherein the key step is a transition metal-catalyzed [4+2]
cycloaddition. This step, which is the focus of this work, forms the
tetrahydroperindene skeleton of the pacifigorgiol molecule in a
single step from an acyclic precursor, resulting in the directed
establishment of two stereogenic centers. The following research
describes the successful optimization of many of the reactions
leading to formation of the substrate for the key cycloaddition step.
In addition, a viable catalyst system,
Ni(acac)
2/Et
2AlOEt, has been found for the
cycloaddition reaction, and evidence has begun to be gathered in
support of the accomplishment of the
cycloaddition.
COMPUTER SCIENCE
Automatic Generation of Penrose
Empires
Jason B. Healy
Penrose Tilings are infinite tilings that
cannot tile the plane in a periodic manner. They are of interest to
researchers because they may model a new type of matter called “quasicrystals.”
Being able to manipulate and study Penrose Tilings easily is
important, and that is the primary goal of this research. Although
Penrose Tilings are infinite, we would like to be able to store them
in a finite device, such as a computer, so that they may be more
easily studied. The primary aim of this research is to attempt to
discover some of the underlying structure of Penrose Tilings, so that
the tilings can be reduced and stored in an efficient, finite
manner.
In addition to being able to store tilings,
this research also aims to learn more about constructing the tilings
themselves. Because we are reducing an infinite amount of data to a
finite amount of information, there will necessarily be some
computation required to reconstruct the information that is not
explicitly stored. This research will also investigate methods of
constructing Penrose Tilings from a small amount of initial
information. The algorithms developed and discussed in this work
allow us to represent Penrose Tilings as a small set of finite
variables and then compute any arbitrary information about the tiling
on demand. In this way, we can reconstruct as much of any tiling that
we desire, without needing to store the entire tiling. It is hoped
that the methods used will allow a more detailed study of Penrose
Tilings to take place in future research.
Co-circular Point Sets and the Minimum
Weight Triangulation
Reed L. Townsend
We investigate the minimum weight
triangulation of co-circular point sets and demonstrate a large
subset for which the minimum weight triangulation can be found in O(n
log n) time. Generalizing our approach, we present strong evidence
that the general problem of finding the minimum weight triangulation
of co-circular points is a more difficult problem and that our
previous technique of searching for improving moves on the dual tree
may not be the best approach.
GEOSCIENCES
Petrogenesis and Correlation of the
Mid-Tertiary Upper Bonanza Tuff, Central Colorado
Rebecca K. Atkinson
The mid-Tertiary upper Bonanza tuff of south
central Colorado is the only rhyolitic unit associated with the
intermediate volcanic units of the Bonanza caldera: the Rawley
andesite, the lower Bonanza tuff (a dacite), and the upper andesite.
Two other rhyolitic units are also associated with the caldera: the
Spring Creek pluton and the Porphyry Peak rhyolite, the latter an
exogenous dome on a ring fracture of the caldera. The Bonanza caldera
is located between the two major mid-Tertiary volcanic fields of
central Colorado—the San Juan and Thirty-nine Mile—and
has previously been considered a part of the San Juan volcanic field.
However, its geographic separation and greater age suggest that it is
more closely related to the Mt. Aetna and Grizzly Peak calderas,
which are aligned with the Bonanza caldera along the western edge of
the Rio Grande rift. These calderas are the probable sources of some
of the ash-flow tuffs of the Thirty-nine Mile volcanic field, which
lies to the east.
The upper Bonanza tuff is petrographically a
phenocryst-poor rock with sanidine as its dominant mineral; notably
it contains no quartz phenocrysts. While these features distinguish
it from the other units of the Bonanza caldera, it is similar to
rhyolitic ash-flow units of the Thirty-nine Mile volcanic field,
especially the Wall Mountain and Gribbles Park tuffs. Geochemically,
the upper Bonanza tuff is also distinct from the other intermediate
units of the caldera, but it closely resembles, in both major and
trace element composition, the Spring Creek pluton and Porphyry Peak
rhyolite of the caldera.
The petrogenesis of the upper Bonanza tuff
magma is still problematic, as it overlies a dacitic unit, the lower
Bonanza tuff, contradictory to the expected stratigraphy produced
from a zoned magma chamber. One possible origin of the upper Bonanza
tuff magma is by pure fractionation of a less evolved magma, such as
the lower Bonanza tuff. However, the distinct separation of trace
element ratios in the lower and upper Bonanza tuff argues against
this possibility, as does a petrogenetic model which postulates the
lower Bonanza tuff as a parental magma. When used to recalculate the
major element chemistry of the upper Bonanza tuff, this model
produced a daughter liquid of a dacitic-rhyodacitic composition,
proving that the upper Bonanza tuff is not derived by pure
fractionation of the lower tuff and implying that direct partial
melting of the crust may be involved in the generation of the upper
tuff.
In a regional perspective, the upper Bonanza
tuff is petrographically and geochemically similar to the Wall
Mountain and Gribbles Park tuffs of the Thirty-nine Mile volcanic
field. However, because it differs in age and paleomagnetic signature
from the Wall Mountain tuff, only the Gribbles Park tuff may be
actually correlative with the Bonanza tuff. This suggests the
possibility that the Bonanza caldera is actually the source of the
Gribbles Park tuff as well as the upper Bonanza tuffs and that late
explosive activity that produced the tuffs also produced the
rhyolites of the Spring Creek pluton and Porphyry Peak dome.
Geochronologic, Structural, and
Tectonic Analysis of the Itremo Group, Central Madagascar: A Look at
Deformed Metasediments and Paleo-Reconstructions from 800-500
MA
Carla B. Chokel
The Itremo Group of central Madagascar is
composed of metamorphosed and deformed quartzites, pelites, and
marbles that exhibit a strong north-south structural trend. This
study applies geochronology and structural techniques to interpret
the tectonic history of the Itremo Group and paleoposition of
Madagascar prior to Gondwana formation. Results from U-Pb SHRIMP
dating indicate that deposition of the sediments began no earlier
than 1722 Ma. U-Pb data from igneous rocks intrusive into the
metasediments (Handke, et al., 1999) indicate that deposition of the
Itremo Group was complete by 790 Ma. U-Pb SHRIMP analysis of detrital
zircons suggests a major lead-loss event at or around 600 Ma which is
interpreted to coincide with the major metamorphic event.
Structural analysis of lithologic maps and
satellite images highlights steeply dipping structures that are a
result of ductile deformation. Based on structural trends seen in
SPOT and Landsat images of the Itremo region, the degree of
deformation diminishes to the east of these structures, where several
dissected nappes are located. Also present in the Itremo region are a
series of large-scale sigma-type complexes (tectonic fish) and shear
zones, all of which indicate sinistral movement. Structural analysis
indicates that metamorphism and deformation occurred as a consequence
of a westward-directed continental collision, possibly between
Madagascar and India. If this is the case, then Madagascar may have
been contiguous with Africa during the Proterozoic before the
amalgamation of Gondwana.
Petrological and Mathematical Analysis
of Polymict Conglomerates
Patricia G. Hines
There are two main types of conglomerates:
those that contain polymict material and those composed of quartz
pebbles. Currently, there are no means to quantify the amount of
pressure solution and diagenesis in conglomerates (Cant and Ethier,
1984), but Gutmann’s (1999) thesis on quartz pebble
conglomerates and this study on polymict conglomerates are first
attempts to quantify diagenesis and pressure solution. Quartz pebble
conglomerates may form either by breakdown of weaker clasts during
transport, or post-depositionally by preferential breakdown of weaker
clasts during diagenesis. If polymict conglomerates generally
demonstrate low levels of diagenesis relative to high levels seen in
quartz pebble conglomerates (Gutmann, 1999), it is reasonable to
assume that diagenesis may play a significant role in the formation
of quartz pebble conglomerates. On the other hand, if polymict
conglomerates demonstrate higher or comparable levels of diagenesis,
we would infer that the differences between quartz pebble
conglomerates and polymict conglomerates are not due to diagenetic
processes, and that quartz pebble conglomerates form at
deposition.
In this study on polymict conglomerates from
Ireland and Norway, techniques and methods established by Gutmann
(1999) were applied. This includes line counting of thin section,
point counting in the field, fourier and fractal analysis, and
application and renovation of the Pressure Solution Index (PSI).
Textural differences between the two sets of
conglomerate types (Gutmann 1999) suggest that the quartz pebble
conglomerates have undergone more mass transport. In addition, the
polymict conglomerates have relatively lower levels of
interpenetrating and nested contacts than the quartz pebble
conglomerates, indicating that the polymict conglomerates are less
pressure solved and less diagenetically altered. The results of my
research do not, however, conclusively support a diagenetic origin
for quartz pebble conglomerates. Grain behavior (rheology), rather
than diagenetic processes may be responsible for the significant
textural differences between polymict conglomerates and quartz pebble
conglomerates.
Paleoecology of Upper Pleistocene Coral
Reefs Based on Morphology and Fossil Assemblages, Baja California
Sur, Mexico
Cordelia R. Ransom
During the last interglacial, oxygen isotope
substage 5e, eustatic sea level was 6 ± 2 m higher than the
present (Ashby, Ku, and Minch, 1987). Upper Pleistocene carbonate
terrace deposits associated with substage 5e are widespread along the
current Gulf of California coastline in Baja California Sur, Mexico.
Coral reef colonies, composed primarily of Porites
californica, dominate three carbonate localities (117.9-125 ka)
in the eastern central coastal region at Punta Chivato, Punta San
Antonio, and Punta El Bajo. Each of these localities is unique based
on the cardinal orientation of the preserved reef and morphology of
Porites californica. Morphospace analysis, coral dating, and
comparison of associated fossil assemblages are used to reconstruct
the paleoecology of the coral reefs. Factors affecting upper
Pleistocene coral reef ecology include the semi-monsoonal wind
pattern of the gulf (Bray and Robles, 1991), storm events, and the
interglacial climate.
Uranium-series dating provides a date of
117.9 ± 0.6 ka for coral colonies from Punta Chivato. In order
to record coral morphologies and associated fossil assemblages at
Punta Chivato, 22 census grids were surveyed along the baseline. The
reef boundaries were determined by setting up three 360-375 m-long
transects that perpendicularly bisect the baseline. At total of 51
pits (ave. 0.25 m-deep) were excavated along these transects in order
to map parts of the buried reef. Living non-reef coral colonies were
recorded offshore Punta Chivato using mask and snorkel and census
grids. Eight census grids were taken from Punta San Antonio and a
total of 36 census grids were employed at Punta El Bajo. Panel
diagrams were constructed based on stratigraphic relationships and
census grids for the reef exposures at Punta Chivato and Punta El
Bajo.
The coral reef at Punta Chivato sits in a
topographic bay opening to the south on the south side of the Punta
Chivato promontory. Bordered to the north, east, and west by Pliocene
and Miocene ridges, the reef facies visibly overlies Miocene volcanic
breccia and adjacent Pliocene conglomerate. The head of the bay is
bordered by lagoonal deposits extending approximately 100 m to the
north. Within the reef itself are 3-4 generations of bouquet-shaped
Porites californica, in various states of preservation ranging
from in situ to jumbled. The coral heads average 12 cm in height,
reflecting relatively young coral colonies. The reef contains a rich
associated fossil assemblage representing 78% of the total 68
recorded marine invertebrate species from the three localities. Coral
generations are divided by terrestrial sediments and rhodolith algae
indicative of periods of heavy run-off or storm generated bottom
currents resulting in successive kill-off of coral colonies.
Punta San Antonio features an abandoned
Upper Pleistocene embayment that opens to the Gulf of California from
east to west. The embayment margins are defined by stratified
Pliocene limestone and/or Miocene tuff overlain by a 1-m thick
boulder deposit, which is extensively encrusted by coralline algae. A
small cove occurs at the eastern termination of this bay and contains
a single generation of Porites californica, comparable in
height to the coral colonies at Punta Chivato, but with a
distinctively rotund morphology. Single finger-shaped coral colonies
appear in growth position in the larger embayment outside the cove.
The variation in morphology reflects the subdued waves that are
refracted around the points, into the cove. The cove deposit contains
an associated fossil assemblage of moderate diversity representing
21% of total recorded species.
At Punta El Bajo, a 2-m high north-facing
exposure, with coral reef deposits runs discontinuously for 290 m
along the present high tide line and is bordered to the east and west
by higher topography extending into the subtidal. The deposit
contains moderate numbers of marine invertebrates (31% of total
recorded species) and a single generation of high arborescent
Porites californica ~1.6 m tall, indicating longer-lived
corals than seen at the other two localities. Another coral reef
deposit, >100 m long, is located on the east side of the eastern
point. This community is capped by a massive andesite boulder bed
reflective of a severe rain storm event or a transition to a
prolonged wetter climate. The coral in the eastern reef are much more
robust with branches at least twice as thick and the associated biota
twice as large as found among and along the neighboring western
ridge. The fossil assemblage associated with the east reef is minimal
representing 18% of the total recorded species. The more robust coral
community developed on a distal spur from the main N-S coastline in a
setting fully exposed to northerly winds, whereas the arboral
community developed in a more protected, proximal environment.
Observed interfingering of carbonate reef deposits and massive
conglomerates suggest transitions between dryer and wetter climates
related to glacial cycles. Notably, no living Porites
californica reefs appear offshore these Upper Pleistocene
deposits. Therefore, climate during the last interglacial in the Gulf
of California appears to have been significantly different than the
present and can provide insight into current trends in global climate
change and the health of living coral reefs.
Fire and Ice: The Geomorphic History of
Middle Boulder Creek as Determined by Isotopic Dating Techniques,
Colorado Front Range
Taylor F. Schildgen
Cosmogenic 26Al, 10Be,
14C, and 36Cl dating of fluvial fill terraces
and other geomorphic surfaces along steep canyons of the Colorado
Front Range provides a temporal framework for analyzing fluvial
response to sediment budget perturbations. Fluvial terraces > 4 m
above the Middle Boulder Creek channel (grade) record activity during
late Pleistocene time. Terraces < 4 m above grade and alluvial
fans preserve evidence for system responses to Holocene climate
change. The fluvial processes that these surfaces record contributes
to a comprehensive understanding of the long-term evolution of Front
Range canyons.
Cosmogenic exposure ages of boulders on
glacial moraines near Boulder Canyon are consistent with glacial
chronologies derived from nearby regions. Samples from Bull Lake
moraines have minimum average 10Be and 26Al
ages of 101 ± 21 ka and 122 ± 26 ka, comparable to other
age estimates of 150 to 100 ka for moraines at sites in Wyoming,
southwest Montana, and other regions of Colorado. Pinedale moraines
near Nederland have average model 10Be and 26Al
ages of 16.9 ± 3.5 and 17.5 ± 3.6 ka, consistent with other
cosmogenic exposure ages and 14C estimates of 35 to 15 ka
reported elsewhere in the Rocky Mountains. These new age estimates,
considered together with field relationships, suggest that late
Pinedale glaciers were nearly as extensive as those active during
earlier Pinedale and Bull Lake advances.
The fluvial response to glaciation in the
Front Range can be analyzed using regional and local late Pleistocene
glacial chronology and cosmogenic exposure age estimates for fill
terraces in Boulder Canyon. Results from Boulder Canyon show that
terrace heights above grade can be divided into (1) Bull Lake (>
~100 ka) at 15 to 20 m above grade; (2) Pinedale (30 to10 ka) at 4
to15 m above grade; and (3) Holocene age at < 4 m above grade.
Better-preserved terraces of latest Pleistocene age suggest that
variations of height above grade reflect short-term fluctuations in
the river profile during periods of rapidly changing stream load and
power. Net river incision apparently occurred during transitions to
interglacial periods. Soil development and stratigraphic position,
used with limited cosmogenic and 14C dating suggests that
~ 130 ka terraces in Boulder Canyon correlate with the Louviers or
Slocum Alluviums, and that 32 to 10 ka fills in the Canyon correlate
with the Broadway Alluvium on the High Plains east of the Front
Range. Middle to late Pleistocene incision rates represented by high
terraces in Boulder Canyon are higher than early Pleistocene rates,
possibly as a result of east to west migration of a knickpoint on
Middle Boulder Creek.
Low terraces (< 4 m above grade) and
alluvial fans in Boulder Canyon record Holocene deposition resulting
from forest fires related to climate change. Forest fires
destabilized small (0.5-1.0 km
2) tributary catchments
within the canyon during the early and late Holocene, producing
episodes of alluvial deposition. Alluvial fans accumulated at rates
between 0.2 and 95 Mgha-1yr-1 depending on whether we assume constant
or episodic sediment accumulation rates. Alluvial deposition and
associated forest fire occurrence in Boulder Canyon correlate with a
late Holocene climate characterized by conditions drier than at
present. Fire and deposition is also correlated with the warm and wet
early Holocene climate which likely induced widespread vegetation
growth to fuel extensive fires during occasional dry periods.
Alluvial fans and fluvial terraces appear to be effective in
preserving evidence of past climate change, and of processes that
have contributed to the evolution of the Colorado Front
Range.
MATHEMATICS
Uniqueness in m-Dimensional Triangle
Sequences
Tegan Cheslack-Postava
In the generalization of continued fractions
introduced by Garrity, each point in an m-dimensional simplex is
represented by a sequence of nonnegative integers. After introducing
the algorithm for generating these sequences, we show that the
representation map is in general not injective. We use the notions of
partition simplices and associated dimension to investigate the set
of points identified by an m-triangle sequence.
Strict Minimality of Alternating Knots
in S x I
Thomas Fleming
In the late 1800’s Tait conjectured
that for knots that lie in the plane, a reduced alternating
projection has the smallest possible number of crossings for any
projection of that knot, and that any non-alternating projection must
have more crossings. This fact was proven in 1984 by Kaufmann,
Murasugi, and Thistlethwaite. In the summer of 1999, the Colin Adams
directed Knot Theory SMALL group of Fleming, Levin and Turner was
able to prove that if the knot projection lies on a surface (such as
a torus) and the knot lies in a layer around that surface (the
surface cross an interval), then a reduced alternating projection has
the smallest possible number of crossings for any projection of that
knot. We will extend this work to prove that for a knot in a surface
cross an interval, a reduced alternating projection of the knot must
have strictly fewer crossings than a non-alternating projection. We
will use arguments based on a generalized Kauffman bracket
polynomial, Menasco-type geometric arguments, and covering space
techniques.
Applying a Bayesian Hierarchical Model
to a Data Set Consisting of Hospital Mortality Rates
Cory Heilmann
Bayesian hierarchical modeling is often
applicable to data sets where the data originate from many different
entities, each of which measures a similar quantity. Examples of
these data sets are students’ test scores from different
schools and mortality rates from different hospitals. This sort of
modeling is particularly useful when we wish to estimate means and
variances of each entity, but some of the entities have low numbers
of observations, and thus the maximum likelihood estimator is
unreliable. This thesis uses a Bayesian hierarchical model on a data
set consisting of the mortality rates from organ transplants in 131
hospitals. We will rank the hospitals according to their predicted
mortality rate, and also decide whether the mortality rates of small
hospitals appear to be larger than the mortality rates of large
hospitals.
A Structural Analysis of the Triangle
Iteration
Adam Schuyler
Classically, it is know that the continued
fraction sequence for a real number
±
is eventually periodic if and only if
±
is a quadratic irrational. In response to this, Hermite posed
the general question which asks for ways of representing numbers that
reflect special algebraic properties. Specifically, he was inquiring
about possible generalizations of the continued fraction. In this
paper, we will study the triangle iteration, a two-dimensional
analogue of the continued fraction. We will take a primarily
geometric approach and look at the probabilities of the occurrences
of certain sequences.
PHYSICS
An Investigation of Non-Linear Dynamics in
a Modelocked Ti: Sapphire Laser
Mark R. Acton
We present research into the non-linear
dynamics of a modelocked Ti:Sapphire laser. We employ non-linear
analytic tools to describe and characterize non-linear dynamics. We
present the first known demonstration of single transverse mode chaos
in the laser. We also hypothesize a possible mechanism for generating
the non-linear transition associated with this chaotic regime. A
computer model is presented that can test the validity of this
hypothesized mechanism.
Hyperfine and Rotational Structure in
Sodium Dimers: Ultracold Photassociation to the Molecular State
Na2 1g (3S + 3P3/2)
Ginel C. Hill
Ultra-cold photoassociation spectroscopy was
used to investigate the transition between rotation-dominated
structure and hyperfine-dominated structure in spectra of a specific
Na2 molecular state, the 1g (3S +
3P3/2). High-resolution spectra of representative
vibrational levels from ν = 50 to
ν = 75 displayed distinct rotational
levels with increasing hyperfine splittings over this range. A novel
experimental technique was used to distinguish between odd and even
I hyperfine lines in the 1g spectra by employing a
doubly-excited 0u state as the ionization pathway. The
observed hyperfine lines were fit with Wigner threshold law
lineshapes to extract the natural line positions, which revealed a
breakdown of the Wigner threshold law for Á-wave
collisions at temperatures T≥250μK.
Finally, a simple model for the competition between hyperfine and
rotational structure presented by Wang, et. al., Phys. Rev. A
57, (1998) was used to construct a theoretical spectrum for
the data. This model matched spectral line positions within 3-4 MHz
and labeled each line with quantum numbers consistent with the
experimental odd and even I designations.
Quantum Mechanics and Phase
Space
Anthony M. Ndirango
Phase space, whose axes represent position
and momentum variables, is a concept from classical physics that is
not normally included in formulations of quantum mechanics. This is
because the position and momentum of a quantum particle cannot
simultaneously take definite values. Nevertheless, there are a number
of interesting issues concerning the relationship between quantum
mechanics and phase space, some of which are explored in this thesis.
In particular, we prove the “trace-area theorem,” which
relates a geometrical quantity from quantum mechanics (the trace of a
product of operators) to a geometrical quantity in classical physics,
namely, the area enclosed by a path in phase space. We show that this
theorem can be used to generalize some of the features of phase space
to discrete quantum variables such as spin.
Entangled Chains & Rings
Kevin M. O’Connor
Entanglement is the resource underlying many
potentially useful technologies including quantum cryptography,
quantum teleportation, and quantum computation. In this thesis we
explore how this resource can be shared “optimally” in
entangled chains and rings of particles. We define an “optimally-entangled”
chain or ring state to be one in which the minimum nearest-neighbor
entanglement in the chain or ring is maximized. Using certain
strategies that we conjecture are useful for finding
optimally-entangled states, we present our findings for several
finite chains and rings as well as what we believe to be formulas for
the optimal concurrence of two classes of ring states. We conclude by
considering the entanglement sharing properties of
physically-realizable rings of spin-1/2 and spin-1 particles and
showing that these are, under certain restrictions,
optimally-entangled.
Measuring the Stark Shift in the
Thallium 6P1/2
7S1/2 378 nm Transition
Andrew J. Speck
This thesis details the apparatus, which
includes electric field plates, an atomic beam, and an ultraviolet
laser system, and procedures necessary to measure the Stark shift in
the 6P
1/2
7S
1/2 transition in atomic thallium. The operation of the
experimental apparatus needed to make this measurement is discussed
and results from simulating the proposed experiment are given.
Details of a method to frequency stabilize a diode laser using a
Fabry-Perot cavity to transfer frequency stability from a stabilized
laser are described.
PSYCHOLOGY
What Video Games May Do: An Empirical
Examination of the Effects of Violence and Sexist Content in Video
Games
Emily Eustis
The present research examined the effects of
violent and sexist content in video games on the attitudes and
beliefs of male college students (N = 93). Previous research has
shown that media violence and pornography can negatively impact an
individual. The sparse available research on the effects of
electronic games has indicated that violent video games may increase
aggression in the short term for younger boys, but beyond this
immediate effect, little else is known. The goals of this experiment
were to confirm previous findings that violent video games increase
state hostility, and to determine whether sexist video games
influence an individual’s sexist beliefs. Participants came to
the laboratory and played one of four video games: a sexist game, a
violent game, a sexist and violent game, or a non-sexist/non-violent
game. Approximately every 6 minutes, they paused the game and
completed a number of measures related to hostility and sexism.
Results indicated that highly violent video games increased state
hostility and arousal and that participants’ trail hostility
predicts participants’ state hostility, preference for sexual
material, sexism, and attitudes towards women. Participants who
played games with sexist content exhibited more sexism on the Mate
Preference Questionnaire and the Modern Sexism Scale. They also had
more sympathy for an individual who committed a murder of passion.
The effects of the sexist game tended to be more pronounced among
participants who were high in trait hostility. Therefore, the results
suggest that not only do violent video games tend to increase
hostility, but also that sexist video games tend to increase sexist
attitudes and judgements, particularly among people who are high in
trait hostility.
Postnatal Stress and Hippocampal
Plasticity: Implications for Learning and Memory
Deborah F. Frisone
This study examined the effects of early
stress on the development of learning and memory in a spatial
navigation task. Long Evans hooded rats were socially isolated (SI)
for six hours daily at postnatal (PN) days 15-21 to determine the
effects of early stress on hippocampal function. Blood samples were
collected one hour after separation on PN 18 and plasma
corticosterone (CORT) was assayed. The Morris water maze (MWM) was
used to test spatial learning and memory at PN 22-24 and in adulthood
(mean age PN 92-94). SI subjects weighed significantly less than
controls at PN 22, but not at PN 15, 25, or 100 indicating that any
weight loss due to SI was not of an inherent or permanent nature and
most likely did not affect performance on the MWM. SI subjects showed
impairments on the MWM at PN 22-24, with mean latency to the platform
differing significantly from controls on the first day of testing. In
adults, there was a significant interaction between test day, trial
number, sex, and condition. SI subjects tended to show significant
enhancements on the MWM, as compared to controls. These results are
discussed in light of previous findings related to the study of
neural development, stress, and hippocampal morphology and
function.
Male Emotional Expression: When Sadness
Becomes Anger
Stephen M. Gray
This study examined 1) the influence of
social context on males’ expression of sadness and 2) the
relationship between expressed sadness and subsequent anger
expression. Sadness was induced in 94 college males, who were then
brought into a room with two confederates (2 males or 2 females) and
asked to talk about their sadness following either expression of
sadness by one confederate (while the second confederate either
listened in a manner accepting of emotional expression or in a
neutral manner) or withholding of sadness expression by the speaking
confederate. Participants were then issued an anger manipulation.
Results showed that participants expressed the most sadness in the
presence of expressive and accepting males. Their anger expression
was recorded and coded and was found to be negatively correlated with
the amount of sadness expressed during the group interaction.
Clinical and research implications are discussed.
Ah Who Yuh Dey Call Mad Man? Young
Jamaican’s Attitudes toward Mental Illness
Dahra N. Jackson
Two studies were carried out to assess young
Jamaicans’ attitudes and opinions about mental illness. Study 1
presented male and female high school students (N = 1223) with a
video interview of a male or female confederate seeking a job. The
job candidate was presented as either 1) a normal person or as 2)
having had a history of mental illness resulting from a “chemical
imbalance” or as 3) a result of a “dysfunctional family
life”. Subjects completed a 9-item social distance scale. As
predicted, subjects desired more social distance from the job
candidate who was presented as having illness vs. not, and the most
social distance from the job candidate who was presented as having
mental illness resulting from a dysfunctional family life. Contrary
to hypotheses, neither the gender of the “job candidate”
nor of the subject had and effect on desired social distance. In
study 2, the same subjects completed the Opinions about Mental
Illness Scale; half of them completed the standard scale and half
completed it with the wording “mentally/mental illness”
replaced by the more colloquial “mad/madness” in each
item, in order to examine the effects of such language. Subjects in
the “mad/madness” conditioned expressed more socially
restrictive attitudes than did those in the “mentally
ill/mental illness” condition. Females expressed more
authoritarian attitudes than did males, and were more benevolent
towards the mentally ill than were males. There was no gender
difference in socially restrictive attitudes. Exploratory analyses of
the effects of other demographic variables revealed much more
authoritarian, socially restrictive, and less benevolent opinions
about mental illness among lower socioeconomic class students and
less authoritarian, and less benevolent attitudes among urban vs.
rural students, with interesting interactions of gender and these
variables. Comparison of the Jamaican sample to US samples in the
literature revealed more authoritarian, more socially restrictive,
but also more benevolent attitudes in the former. Implications for
public education and further research are discussed.
The Effect of Expert Testimony on
Confession Evidence in the Courtroom
Lisa D. Knappen
The present research studied the effect of
expert testimony on confession evidence in the courtroom.
Specifically, it aimed to determine whether expert testimony would
help jurors be more sensitive to police interrogation techniques that
increase the risk of false confessions, or if the testimony would
overwhelm jurors, causing them to discount confessions that were not
unreasonably coerced. Two studies were conducted that were conceptual
replications of each other. In both experiments, mock jurors were
randomly assigned to one of seven groups: voluntary confession
condition with or without an expert (in these conditions, the
defendant signed the confession voluntarily); physically coerced
confession condition with or without an expert (in these conditions,
the defendant initially denied the charges, but eventually signed the
confession after he was physically coerced); psychologically coerced
confession condition with or without an expert (in these conditions,
the defendant initially denied the charges, but eventually signed the
confession after he was psychologically coerced); and a control,
no-confession group. Mock jurors viewed a videotaped summary of an
actual trial and afterward completed a case-related questionnaire.
The results in both studies confirmed previous findings that
confession evidence is extremely influential in determining a
defendant’s guilt. The results from Experiment 1 did not
confirm the hypothesis that the presence of an expert would sensitize
mock jurors to psychologically coercive interrogation techniques.
However, results from Experiment 2 indicated that expert testimony
sensitized jurors to psychological interrogation pressure, but that
the testimony did not overwhelm mock jurors in the other conditions.
The findings support the notion that expert testimony should be
admitted in cases involving disputable confessions.
The Effects of Pre-Weaning Social
Environment on Learning, Locomotor Activity, and Play Behavior in
Juvenile Rats
Meghan N. Moscati
This study examined the role of early social
environment on the learning, activity, and play behavior of juvenile
rats. Pregnant Long Evans hooded female rats were housed in one of
four housing conditions throughout gestation until weaning at
postnatal day 25: “Sire” (biological father), “Aunt”
(unrelated, nulliparous, adult female), Large Cage (larger cage also
used in Sire and Aunt to accommodate two adults), or Small Cage
(standard breeding cage). At post-natal day (PN) 32, sixty-eight
subjects began training in the Morris Water Maze where the latency to
find the platform was recorded. The remaining 74 subjects were tested
singly for activity levels for three consecutive days and then on the
fourth day were placed in the activity chamber with a stimulus
playmate and observed for quantifiable play and social behaviors (no
contact, sniffing or following, grooming self, dorsal contact,
crossovers, wrestling, pinning, and getting pinned). Significant
effects across condition were not found for the Morris Water Maze
learning task or in activity levels. There were significant effects
across condition for some of the observed play behaviors. Subjects
raised in the Sire condition spent significantly less time sniffing
and following the stimulus playmate than did subjects raised without
an additional adult, regardless of cage size. There was a sex effect
for crossovers where females made significantly more crossovers than
males across all four conditions. The data suggest that the early
social environment may not be as important for later learning and
activity levels, although a different learning task may be able to
pick up more subtle differences. The early social environment did
appear to be of minor importance in later social behaviors, and
further research might investigate hormonal changes that could be
resulting from differences in socialization as well as alterations in
adult social behaviors.
The Phenomenology of Custody
Jason C. R. Oraker
The present study investigated perceived
freedom in custody-like situations. In the Preliminary Study, 44
participants read 20 vignettes, varying indicia of custody (as ruled
on by the courts), and made subsequent judgments about the freedom of
individuals, in each, to leave. While results indicate that people
are sensitive to factors signifying custodial situations, in all
situations, they see others as more free to leave than they see
themselves. In Study 1, 81 participants watched either a low,
moderate, or high custody videotaped interrogation and subsequently
made objective and subjective judgments concerning the actor’s
freedom to leave. In the moderate custody condition, judgments of
whether the actor was free to leave and whether he thought he,
himself, was free to leave, differed, with people seeing him as free
to leave, but unaware of that objective reality. Even in the high
custody condition, where people believed that the actor did not
perceive freedom to leave, 40% of participants still saw him as free
to leave. In Study 2, 81 participants watched either a low or high
custody videotaped interrogation and, in addition to the same
judgments from Study 1, made reasonable person judgments –
assessing custody as though they, themselves, were suspects. The
reasonable person judgments provided a new outcome to the custody
question. These results suggest that how one asks the question
concerning whether an individual is in custody greatly affects the
answer, and that judges and jurors, who are ultimately ruling on
these decisions, should be adequately informed.
The Magnitude Effect in Intertemporal
and Risky Decision Making: Fact or Artifact?
Jennifer C. Page
Existing data do not tell us why we observe
a magnitude effect in intertemporal or probabilistic decision making.
Three studies tested the possible explanations of rounding artifacts,
a ceiling or floor effect, and a constant-difference effect. In
Experiment 1, we used a second-bid auction procedure in which
participants “bid” their subjective value of the delayed
reward for four reward amounts: $11, $14, $21 and $24. All bids were
for real monetary rewards. In Experiment 2, we also looked at the
magnitude effect in intertemporal decision making but used a
different paradigm known as the staircase procedure. Participants
were asked to make choices between a smaller, immediately obtainable
reward and a larger, but delayed reward for three reward amounts: $9,
$18 and $36. The value of the smaller reward increased or decreased
in incremental steps of 50 while the delay to both rewards was fixed,
thereby establishing patterns favoring delayed reward choices when
the immediately obtainable rewards were small. Again all rewards were
real. Experiment 3 paralleled Experiment 2 except that we had
participants make choices between a smaller, sure-thing reward and a
larger, but risky reward in order to look at the magnitude effect in
probabilistic decision making. We also looked at one additional
possible theoretical explanation for the magnitude effect in
Experiment 3 known as the peanuts effect. This study is the first to
examine the magnitude effect in probabilistic decision making using
real rewards. In all three experiments, we found no evidence that any
of the possible artifactual explanations of rounding artifacts or a
ceiling or floor effect could account for the observed magnitude
effects. We also found no evidence that the constant-difference
hypothesis or the peanuts effect could explain the magnitude effect.
The data suggest that the magnitude effect is indeed a real
phenomenon that remains in need of explanation.
The Nuanced Self: A New Accuracy
Measure in Interpersonal Perception
Maria Gabriela D. Pereira
This thesis examines three different types
of interpersonal perception: self-perception, social perception and
metaperception. Self perceptions are peoples’ perceptions of
themselves; social perceptions are their perceptions of other people,
and metaperceptions are how they think others will perceive them.
This research focuses on the links between these three types of
perception. Previous research in this area has documented both error
and accuracy in these types of perceptions uncovering significant
differences between mean ratings for each type of perception
alongside strong correlations between the three. In this paper, we
argue that mean differences and correlations are not sufficient to
assess the accuracy of interpersonal perception. We propose a new
additional accuracy measure: the accuracy of variability. This
measure does not examine mean differences of ratings themselves, but
the standard deviations across ratings. The results of three studies
show that there are significant differences between the variability
of self and both social and metaperceptions; participants rate
themselves as being more “nuanced” than others rate them,
and rate themselves as more nuanced than they expect others rate
them. Although there is no apparent overall difference in variability
for social and metaperceptions, the results in at least one study
yield significant interaction between the variability of social and
metaperceptions when the relationship between individuals is
considered. Participants expect friends to rate them as more nuanced
than friends actually do. With strangers, on the other hand,
participants expect less nuanced ratings than is actually the case.
Throughout this thesis, we argue that a measure of variability across
traits is useful for assessing both error and accuracy in
interpersonal perception. Discussion focuses on avenues for future
research.
The Plot Thickens: Children’s
Autobiographies and Parents’ Biographies of Their
Children
Amy L. Sprengelmeyer
The present study attempted to address two
questions: 1) what are the autobiographies of pre-adolescents and
adolescents like? and 2) along what lines do children’s
autobiographies converge or diverge with their mothers‚
accounts of the same life? Children of ages 8, 11, and 14 and their
mothers, 15 in each age group, participated in this study. The
children in the pairs were asked to write their own life story; the
mothers were asked to write the life story of their child.
The study shows that as children get older,
they are more likely to agree with their parents; however, they are
also more likely to disagree on specific pieces of information. As
children age, their narratives come to resemble the narratives of
adults: they include turning points, elaborate on events, and include
more references to emotion. These findings support Bruner’s
argument that narrative structure guides autobiographical memory
(1993).
Gender differences were also observed.
Females wrote more emotionally, made more references to other people,
and included more detail in their autobiographies than males did.
Males, on the other hand, had a higher convergence with their mothers
about mentioning specific events than females did.
Socio-economic status and presence or
absence of siblings emerged as mediating factors in the narrative
process. The overall tone of the narratives was measured by reader’s
response. This analysis showed that mothers and children communicate
their lives as being happy overall, even when they mentioned specific
negative events.
When the Group Does Less than the Sum
of Its Members: Unpacking Effects in Allocations of
Responsibility
Wayne M. Wight
Three studies test an extension of support
theory and overclaiming research. Participants tend to rate the
productivity of a group as greater when the group is broken down
(unpacked) into individual members as opposed to when the group is
considered (packed) as a whole. This phenomenon occurs whether
participants are members of the group that they are evaluating or
uninvolved outside observers. When participants are members of the
groups that are under evaluation, unpacking the group reduces
overclaiming - participants become less likely to self-allocate more
responsibility than they are due. Alternative hypotheses based on
numerosity and artifactual effects are considered and tested in Study
3.