Bill Hamilton
Robert Humston
Fred LaRiviere
Simon Levy
Tyler Lorig
David Marsh
Fiona Watson
Jack Wielgus
Research opportunities in the Hamilton lab for 2009: Soil
Biochemistry and Molecular Biology
The Hamilton lab in coordination with the Cabe lab conducts
research on soil microbial dynamics in soils from Yellowstone
National Park and from local agricultural fields. The
overarching goal is to elucidate the interactions between
grazers, grasses and microbes that contribute to the ability of
grassland systems to maintain primary productivity.
Methods: Spectrophotometric determinations of soil NH4+ and
NO3-,soil and root respirometry, soil DNA extraction, PCR,
quantitative PCR, Terminal Restriction Fragment Length
Polymorphism analysis, and DNA sequencing.
Projects:
Laboratory: Analysis of archived samples from Yellowstone
National Park experiments conducted in 2005-2008
Field: Local sampling of agricultural fields with the potential
to travel to YNP (depends on funding)
Modeling: Utilizing a database from over 350 soil samples I
would like to begin to model the processes of soil N-cycling in
relation to microbial abundance and diversity.
Two students may apply for these research opportunities.
Research opportunities in the Humston lab for 2009:
Dispersal and population genetics in stream fisheries. This
project will look at the genetic structure of fish populations
in stream-tributary networks to determine the relative strength
of connectivity and exchange between them. Two projects are
possible: one will consider dispersal and introgression of
hatchery stocks with putative native stocks of brook trout (Salvelinus
fontinalis), the other will examine basin-scale patterns of
connectivity and gene flow among smallmouth bass (Micropterus
dolomieu) stocks in the James River and tributaries. Selection
of study species to be determined in the near future. This
project will include field work for collection of specimens, lab
work for collection of genetic (microsatellite) data, and
statistical analyses of genetic data.
Designing optimal monitoring programs for highly variable river
fisheries. The populations of many important game fish species
in rivers of Virginia vary widely in abundance from year to
year. It is hypothesized that this is related to inter-annual
variability in regional climate conditions (precipitation,
temperature, etc.) State conservation and management agencies
monitor these fish populations through annual sampling programs
so that they can detect trends in abundance and project catch
rates for anglers. We will analyze past state monitoring data to
determine if a sampling approach can be optimized to reduce
effort (cost) without sacrificing accurate detection of trends
in abundance. This project will include statistical analyses of
state monitoring data and bio-economic simulation modeling of
monitoring approaches and objective functions to determine
optimal strategies.
Two to four students may apply for these research
opportunities.
LaRiviere research opportunities for 2009:
Research in the LaRiviere lab is aimed at understanding novel or
fundamental aspects of ribosome metabolism in eukaryotes. One
focus is to uncover the mechanistic details of non-functional
ribosomal RNA decay (NRD), a newly discovered ribosome quality
control pathway in yeast. NRD effectively removes
translationally defective ribosomes from the cell by specific
degradation of mature, yet, non-functional rRNAs. One of the
most important issues concerning the mechanism of NRD regards
the trans-acting factors involved in this process. In other
words, what factors are responsible for recognizing defective
ribosomes and what factors are responsible for the actual
degradation of the defective rRNA?
To this end, we are developing a synthetic lethal screen in
Saccharomyces cerevisiae to identify factors involved in NRD.
Once NRD factors are identified, we plan to study their role(s)
in NRD. A second focus is aimed at studying the molecular
interactions involved in the association of the large and small
ribosomal subunits during ribosome biogenesis and translation.
These interactions or intersubunit bridges (ISBs) have been
identified in bacterial ribosomes using in vitro structural
studies. However, relatively little is known about the
importance and the nature of these ISBs in vivo, especially in
eukaryotes. We are using two approaches to investigate ISBs in
yeast ribosomes. First, modification interference studies are
underway to identify regions of ribosomal RNA that are important
for subunit association. Second, a plasmid based rRNA expression
system is being used to study rRNAs with mutations that disrupt
the predicted RNA:RNA ISBs in yeast. We hope these studies will
help us to understand the structural and functional conservation
of ISBs, as well as their overall importance in ribosome
biogenesis.
Two students may apply for these research opportunities.
Research opportunities in the Levy lab for 2009:
Professor Levy works in the area of biologically-motivated
artificial intelligence, cognitive science, and robotics. His
current research includes two related projects: (1) using visual
map-seeking circuits to guide robot navigation; (2) using
replicator equations from theoretical/evolutionary biology to
model the process of analogy-making.
Three students may apply for these research opportunities.
Research opportunities in the Lorig lab for 2009:
Dr. Lorig's current HHMI research concerns measuring brain
changes related to olfaction in humans. Since, during the
summer, a limited number of students are present on campus, I
tend to do most of my data collection during the academic year.
I use the summer to prepare the studies that will take place the
following academic year.
A major part of that preparation is devoted to writing the data
acquisition and analytic software that will be used later in the
year. We control data acquisition using software written in the
LabView language and this must present olfactory, auditory and
visual stimuli to subjects, detect breathing and encode a data
stream to another computer collecting physiological data. Over
the past few years I have developed several “basic” routines
that can be used in many programs – essentially creating a
library of programs that can be brought together to make a
useable data collection program. These “basic” programs need to
be expanded and formalized so that, eventually, students may
easily create their own programs for data collection.
In addition, we use public domain EEG analysis software (EEGLAB)
who’s development was supported by NIH. This software is written
in MATLAB and is rather generic. Over the past ten years, I have
modified this software for our specific system and needs. We
need to make a major overhaul to our modifications in response
to a recent update of this program. In addition, I want to
develop an additional application that will calculate brain
microstates (Pascual-Marqui et al. 1995) that can be added to
the EEGLAB package.
Segmentation of brain electrical activity into microstates:
model estimation and validation. Pascual-Marqui, R.D.; Michel,
C.M.; Lehmann, D. Biomedical Engineering, IEEE Transactions on
Volume 42, Issue 7, July 1995 Page(s):658 - 665
One student may apply for this research opportunity.
Research opportunities in the Marsh lab for 2009:
Dr. Marsh's current RE Lee research program focuses on the
ecology, genetics, and evolution of mountaintop salamanders in
Virginia. In particular, we are examining the population genetic
history of several of these species and the factors that
maintain their small geographic ranges. Students interested in
this project should plan on taking BIOL 242 (Field Herpetology)
during the spring term. Genetics Lab (BIOL 221) and GIS (GEOL
260) may also be helpful.
One to two students may apply for these research
opportunities.
Dr. Marsh's current HHMI research uses simulation models to
design programs for monitoring animal and plant populations in
the context of conservation or harvesting. The research involves
building simulation models that can compare different approaches
to monitoring, and using data on species’ characteristics to
optimize monitoring programs. CSCI 121 (winter term) is required
for eligibility.
One student may apply for this research opportunity.
Research opportunities in the Watson lab for 2009:
A current project in the lab is to understand how the electrical
activity of a neuron affects it’s morphology and development. In
particular, we are interested in the effects of electrical
activity on the shape of a neuron’s dendritic and axonal arbors.
Students in the lab will grow retinal ganglion cells from stage
28 Xenopus laevis in primary cultures. We will treat these cells
with tetrodotoxin (TTX), a neurotoxin that blocks action
potentials by binding to and blocking sodium channels, and
examine the effects of TTX on the number of primary neurites,
branches and spines on retinal ganglion cells grown in vitro.
Dr. Watson's research plans for the future will focus on
understanding the mechanisms underlying the wiring of the
central nervous system (CNS). Using the African clawed frog,
Xenopus laevis and the closely-related species, Xenopus
tropicalis, Dr. Watson plans to investigate the early
developmental mechanisms in glial-neuronal interactions. An
ongoing dialogue exists between neurons and glial cells, and
their survival is intimately linked. Recent evidence suggests
that in the peripheral nervous system (PNS), glial cell-derived
factors can modulate synaptic activities at developing
neuromuscular junctions. Likewise, in the CNS there is evidence
that glial cells can play a role in modulating synapse
formation. Development of glial cells occurs during the same
period when neurons are initiating axonal pathfinding and
establishing synapses with their targets. Dr. Watson and her
students will examine how glial-derived factors influence the
fundamental wiring of the brain and CNS.
Two students may apply for this research opportunity.
Research opportunities in the Wielgus lab for 2009:
Dr. Jack Wielgus investigates the role of nicotine in causing
hyperactivity disorders, using the development of the chick
embryo brain as a model system. This summer Dr. Wielgus will
work with two student assistants, examining the signal
transduction pathway by which nicotine suppresses programmed
cell death in the motor neurons in the oculomotor nucleus
(cranial nerve # 3).
Two students may apply for these research opportunities.
