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Summer 2004 Research Descriptions
| Biology |
Ann Auman |
| Molecular Analysis
of Natural Methanotrophic Communities using Culture-Independent
Techniques |
| The goal of this work
is to use molecular techniques to analyze natural populations
of methane-oxidizing bacteria, or methanotrophs. The genes
of interest to me are nifH, a gene found in all nitrogen-fixing
bacteria, and mmoX, a conserved subunit of the soluble
methane monooxygenase (sMMO). Both of these activities
have been shown to be important for the ability of some
methanotrophs to degrade the environmental contaminant
trichloroethylene (TCE). Although the experimental techniques
involved for analysis of each gene are quite similar,
I intend to have one summer student work to expand an
environmental clone bank of nifH gene fragments while
the other student works to begin making environmental
clone banks of mmoX. The techniques involved in both cases
will be extensive use of the polymerase chain reaction
(PCR), cloning of genes into Escherichia coli, restriction
analysis, agarose gel electrophoresis, plasmid purification,
preparation of samples for DNA sequencing, and sequence
analysis. As a partial nifH clone bank already exists,
the student working on this will likely be focusing on
the latter techniques. If time permits, this student may
also begin to make an environmental clone bank of nifH
fragments from a forest soil environment. The student
who works on the mmoX environmental clone bank will likely
need to troubleshoot getting the PCR to work using the
supplies we have available. |
| Biology |
Tom Carlson |
| Effects of Bisphenol
A on Development of Bombina orientalis Embryos |
Students will explore
the effects of the environmental contaminant bisphenol
A (BPA) on Bombina orientalis embryo development, focusing
particularly on gastrulation. Early embryos will be cultured
in different concentrations of BPA for various periods
of time to determine exposure levels to which animals
are sensitive. In order to ascertain the cellular nature
of gastrulation disruption, students will prepare microscope
slides of sectioned embryos collected at various stages
of gastrulation. Microscopic examination will be used
to characterize cell rearrangement patterns in treated
and control animals. Differences in patterns of cell rearrangement
will suggest alterations in cell behavior that might be
responsible for abnormal gastrulation in treated animals.
To further understand the molecular bases for BPA-induced
alterations in cell behavior during gastrulation, students
will use fluorescence in situ hybridization (FISH). Sections
of treated and control embryos will be screened with molecular
probes for signal molecules and cell surface proteins
known to contribute to gastrulation; differences in probe
binding patterns will suggest how alterations in gene
expression could account for abnormal gastrulation in
response to BPA. As an extension of in situ gene expression
studies, students will also do real time polymerase chain
reaction (RT-PCR) experiments using mRNA from control
and treated animals. These experiments will reveal BPA-related
alterations in expression patterns for a number of genes
whose products play roles in gastrulation. |
| Biology |
Mary Ellard-Ivey |
| Studies of the Expression
of a Calcium Dependent Protein Kinase Gene in Zucchini |
| I am interested in a class
of signaling molecules in plants called calcium dependent
protein kinases (CDPKs). Students will design experiments
to determine if the expression of this and other genes
is regulated in a developmental or tissue-specific fashion
in young plants. Students will use northern blot analysis
using radioactive nucleic acid probes to measure steady
state mRNA levels of CDPK and other genes of interest
in zucchini seedlings. |
| Biology |
Matt Smith |
| Role of Tachykinins
in Modulating Luteinizing Hormone Secretion in the Female
Rat |
| The goal of my research
is to further understand the mechanisms by which the brain
regulates reproductive function in the female rat and
how these mechanisms change with age. Specifically this
summer, we will examine the role that the tachykinins,
a family of neuropeptides, play in modulating gonadotropin-releasing
hormone neuronal activity in the female rat. Students
will be involved in all aspects of studies that utilize
several experimental approaches, including immunocytochemistry
and the local application of neuroactive agents into specific
regions of the rat brain. |
| Chemistry |
Valerie Burke |
| Investigation of Niacin
Biosynthesis in E. coli |
| This work focuses on the
characterization of quinolinate synthase, an enzyme involved
in the niacin biosynthetic pathway in E. coli. Specific
activities include the purification of quinolinate synthase;
the synthesis of substrate analogs; conducting enzyme
assays with substrate analogs to search for inhibitors
or dead-end substrates; and the analysis of enzyme reactions
with substrate analogs to identify abortive products that
may correspond to reaction intermediates. Students will
gain experience in organic synthesis as well as enzymology. |
| Chemistry |
Myriam Cotten |
| Investigating Molecular
Recognition and Biological Function at Interfaces Using
Antimicrobial Peptides |
This research studies
fundamental principles underlying biological functions
and molecular mechanisms of peptides active at interfaces.
Complementary solid-state Nuclear Magnetic Resonance (ssNMR)
techniques will be used on site-specific isotopically
labeled peptides bound at interfaces to better understand
structure/dynamics/function relationships at the molecular
level. This summer’s research will focus on a class
of antimicrobial peptides that work through as-yet-unknown
interactions with biological membranes and that serve
as models for the study of membrane proteins and the design
of broad-spectrum drugs. More precisely, we will study
piscidins from fish mast cells (immune cells).
We will 1) prepare isotopically labeled amino acid derivatives
using blocking chemistry, 2) synthesize isotopically labeled
peptides by solid phase peptide synthesis, 2) purify (HPLC)
and characterize (mass spectroscopy) these peptides, 3)
prepare NMR samples by incorporating the peptides in hydrated
lipid bilayers under various conditions (lipid types,
hydration level, pH); and 4) perform well-established
ssNMR experiments and analyze the results to get structural
and dynamic information. A significant part of the work
will be done at PLU but we will also work at the University
of Washington and I hope at the Pacific Northwest National
Laboratory in Richland, Washington. |
| Chemistry |
Dean Waldow |
1) Laser Light Scattering
Studies of Polymer Blends and Polymer/Liquid
Crystal Blends
2) Monte Carlo Computer Simulations of Polymer Blends
using a Linux Beowulf Cluster |
| Project 1: Students will
study the effect of various additives on a polymer blend
system. The techniques employed will include laser-based
instrumentation such as cloud point instruments, static
birefringence, wide-angle light scattering, and dynamic
light scattering. The research may include some work at
a national neutron scattering facility to supplement the
data obtained at PLU. There are opportunities for the
use of sophisticated air-sensitive synthetic procedures
as well as new hybrid polymerization techniques such as
atom transfer radical polymerization and ring opening
metathesis polymerization. Special analytical techniques
to study synthesized molecules will also be used. Project
2: This is a computer simulation project in which many
of the same aspects of the experiment work are studied
with Monte Carlo simulation techniques using a modern
10-node Linux Beowulf Cluster as the computational engine. |
| Geosciences |
Rose McKenney |
| Snow Melt Timing and
its Hydro-Geomorphic Influences in Heterogeneous Terrain,
Upper Yukon River Basin |
| This project will investigate
the effect of snowmelt volume and timing on stream processes
in the upper Yukon Basin. Specific goals of the project
include determining to what extent the melt onset, melt
progression, and monitored discharge affect the sediment
loads, channel morphology, and vegetation patterns in
a range of types of streams. The work will be carried
out in summer field seasons, focusing on initial mapping
of the riparian corridor followed by repeat monitoring
of suspended sediment concentration, channel, and vegetation
systems. Field work will be supplemented by multi-temporal
observations with aerial photographs and high resolution
satellite data. |
| Math |
Dane Wu |
| A Quantitative Study
of Student Retention by Both Statistical and Probabilistic
Approaches |
| Students will search literature,
collect and organize data, formulate and test statistical
hypotheses, compute conditional probabilities, and estimate
various risks. Students are expected to present their
research findings in mid-August. Students may coauthor
a paper on the research findings for submission to a peer-reviewed
journal. |
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