Students will
work on a concise project as part of ongoing projects within the research
laboratory of their choice. Students are expected to give their full time commitment
to this program. Housing is provided in excellent facilities adjacent to the
research laboratories, so that students have ready access to laboratory,
computer facilities, library, etc at all hours. Frequent special events will be
arranged to reinforce informal student-student and student-faculty interaction;
these events will include dinners at faculty homes and trips to the surrounding
countryside. The
Students may work with any faculty within the Department of Biological Sciences however preference is given to students interested in working with one of the faculty listed below.
Students will work in chosen laboratories, on projects relevant to both evolutionary biology and the central theme of the laboratory. Participating faculty and some possible project areas of potential interest can be found below. Interested students are encouraged to contact participating faculty directly in addition to Dr. Ely (Program Director). Make sure you tell them that you are applying to the REU program.
Erin Connolly
Phenotypic and molecular adaptation in the freshwater crustacean Daphnia
Jeff Dudycha
Bert Ely
Robert Friedman
How important are nonconsumptive effects of predators when the threat of predation is transitory?
Effects of climate change on the physiology and ecology of
marine organisms
Brian Helmuth
Jerry Hilbish
Austin L. Hughes
Functional characterization of AIL genes in Arabidopsis development
Beth Krizek
Richard Long
Rick Lovell
Timothy A. Mousseau
Spatiotemporal distributions of Benthic Microalgae in North
Inlet Estuary
Jay Pinckney
Joe Quattro
Richard Showman
Johannes Stratmann
Research in the Phytoplankton Ecology Laboratory
Tammi Richardson
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For
the past several years, Dr. Ely’s laboratory has been studying bacterial and
bacteriophage genome evolution. We are in the process of sequencing the genomes
of a family of 14 closely related bacteriophages that
infect Caulobacter crescentus.
Results to date have demonstrated considerable variation among these genomes,
both in terms of nucleotide sequence and gene order. To determine how
differences in gene order might impact genome recombination, REU students will
have the opportunity to design mixed infection experiments with phage that have
varying numbers of differences in gene order. The products of these mixed
infections will be purified as single plaques and grown to high titer. DNA will
be isolated from the resulting lysates, digested with
restriction enzymes, and subjected to pulsed field electrophoresis to
characterize genome rearrangements. The resulting data will contribute to an
understanding how genome rearrangements impact phage genome recombination
during mixed infections.
Undergraduate students in my laboratory start by working with an experienced researcher and eventually work independently on their own project. Many of these undergraduates do publishable research and end up as co-authors of papers published in top journals. For a listing of our recent papers, click on my name at the top of this section.
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Research in the Connolly lab focuses on mineral nutrition in plants. We
study iron metabolism and are particularly interested in understanding the
regulatory networks that control iron uptake, distribution and storage in
plants. Although iron is an essential micronutrient, it is toxic if accumulated
at high levels within cells. Thus, iron uptake and sequestration are controlled
by complex regulatory mechanisms. Strategy I plants, including the dicots and non-grass monocots, induce expression of a set
of genes in response to iron deprivation. Our studies have focused on the iron
uptake response in the model plant Arabidopsis
thaliana, a Strategy I species. The Arabidopsis
FRO2 (Ferric Reductase
Oxidase) gene encodes the inducible ferric chelate reductase responsible for
reduction of iron at the root surface. IRT1 (Iron Regulated Transporter) is the
major high affinity iron transporter responsible for iron uptake from the soil
in Arabidopsis. Thus, IRT1 and FRO2
serve as two major components of the iron uptake machinery.
At present, work in the laboratory is focused in three areas. The first project aims to elucidate the molecular basis of post-transcriptional control of the iron uptake responses (FRO2 and IRT1). The second project centers around uncovering the precise functions and evolution of a family of ferric chelate reductase enzymes in Arabidopsis. Third, we are working with Dr. Tammi Richardson’s lab to elucidate mechanisms of iron uptake in a marine diatom (T. pseudonana). We use a combination of genetics, molecular biology, physiology, biochemistry, cell biology and genomic approaches in our studies.
Our work should enable the development of crop plants that contain elevated levels of iron and other micronutrients. The production of nutritionally-enhanced crop plants is widely-considered to be one important potential solution to widespread nutrient deficiency in humans. The WHO estimates that 3 billion people worldwide suffer from iron deficiency, so the development of plants that contain elevated levels of bio-available iron should help alleviate this enormous problem.
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Evolution of insect life history and
behavior, Timothy Mousseau
My
laboratory studies the evolution of life history and behavior. There are
currently two projects that are suitable for REU student involvement:
1)
The Genetic and
Evolutionary Consequences of Environmental Mutagens. Since 1999, Dr.
Mousseau’s lab has been investigating the effects of
low-level radioactive contaminants stemming from the Chernobyl disaster of 1986
on wild populations of insects, birds and plants. Students will have the
opportunity to participate in a number of sub-projects including studies aimed
at estimating the amount of genetic damage to somatic and germ (sperm) cells
caused by radiation using comet assays in birds and insects. Additional studies
are being conducted using both laboratory and wild populations to examine the
impact of radioactive mutagens on immune system function and reproductive
performance in first and second generation offspring.
2)
Ecological and
Human Impacts on Reptile and Amphibian Ecology and Reproduction. Students will
have the opportunity to participate in field studies of snake, turtle and
amphibian populations in coastal and sandhills areas
of South Carolina. Target species include the eastern diamondback rattlesnake
and the gopher tortoise among many others.
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Our laboratory has studied the molecular evolution of marine
mussels in a species complex that hybridizes in various locations throughout
the world. As part of this study, we used PCR to amplify and sequence the 5'
and 3' untranslated regions of the gene encoding a polyphenolic adhesive protein. We then constructed species-specific
genetic markers for both the 5' and 3' UTRs of this gene. During this study, we
identified numerous alleles of the polyphenolic
adhesive gene that are the product of intragenic
recombination. This study comprised parts of undergraduate projects for Ms
Karen Joyner and Mr. Keith Meetze. An ongoing
undergraduate project by Ms Lisa Weaver has demonstrated that the recombinant
alleles are restricted to the hybrid zone between two of these species.
Intragenic recombination has often been implicated
as an important mechanism for generating genetic variation, particularly in
hybrid zones, as well as a potentially important defect that forms the basis
for some genetic diseases. An undergraduate student project to continue the
study of intragenic recombination within this hybrid
zone is planned. The student(s) will learn methods for DNA isolation, PCR,
cloning and DNA sequencing. The student(s) will first characterize the
frequency of recombinant alleles in hybrid population using PCR and restriction
analysis. Recombinant alleles are uncommon and thus far have only been found in
the heterozygous state so the student(s) will use a combination of PCR and
cloning to isolated recombinant alleles. These alleles will then be
characterized by DNA sequencing to determine the genetic diversity of
recombinant alleles. This project will provide the student(s) with an
outstanding opportunity to learn basic molecular biological techniques as well
as address an important question in evolutionary genetics.
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As the primary organelle responsible for production of ATP,
mitochondria play an essential role in the survival of all eukaryotes. While most mitochondria are inherited from
their mothers, a few organisms in the order Mytilidae have evolved a doubly uniparental inheritance (DUI) of mtDNA in which a paternal
mitochondrial haplotype is inherited from the father
and a maternal from the mother. A highly
positive selection coefficient for DUI clearly indicates that this otherwise
unique mechanism of mitochondrial inheritance offers a significant selective
advantage to these organisms. Students
in this laboratory are using this M versus F haplotype
difference to determine the selective advantage each haplotype
confers to the embryo and how this advantage is manifested at the cellular and
molecular level. Past students have
determined the difference in molecular organization of the control region of
different Mytilids, using the variation to identify
common conserved elements and the evolutionary timing of reversals and
reinitiating of DUI. Other planned
projects include the identification and determination of the role of haplotype-specific elements of the control region and the
role of timing and cellular localization of evolved mitochondrial haplotypes in
regulating mtDNA synthesis.
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After
perception of stress signals, the signals must be amplified and relayed via a
signal transduction pathway. A critical component of many signaling pathways is
an enzyme, called a MAP kinase (MAPK). This kinase is activated as a consequence of stress signal
perception and relays the signal to downstream factors such as transcription
factors that finally lead to the activation of defense genes. We have characterized three MAPKs
from tomato (Solanum lycopersicum).
In Arabidopsis thaliana (Brassicaceae), a
model plant for which the entire genome has been sequenced, there is an
additional MAPK, AtMPK4, which is involved in stress responses. We would
like to know whether the tomato homolog of AtMPK4 serves a similar function.
Generally, it is assumed that a high homology correlates with a similar function.
Therefore, a comparison of the function of the tomato and Arabidopsis MAPKs
provides an excellent model system to study whether a high structural homology
correlates with functional homology.
To study the function of MPK4 in tomato, students will
silence the gene for MPK4 using virus-induced gene silencing (VIGS). The
silencing will be verified by measuring MPK4 mRNA and protein levels. The
plants will then be exposed to caterpillars to find out whether the
MPK4-silenced plants are more susceptible to insect attack. Pathogen-related
stress signals will also be tested. The results will be compared with data
published by other groups on MPK4 homologs in Arabidopsis and other plant species.
Thus, the project will provide REU students with a well-rounded introduction to
molecular techniques and the ability to test concepts of molecular evolution.
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Spatiotemporal distributions of Benthic
Microalgae in North Inlet Estuary, Jay Pinckney
The project will involve the collection of benthic microalgae
inhabiting the upper 2 mm of sediments in a variety of habitats in the North
Inlet estuary. These samples will be analyzed using high performance
liquid chromatography to determine benthic microalgal
biomass and community composition. The purpose of the project will be to
document the short-term (over 24h period) changes in the spatial distribution
of benthic microalgae. The REU student will be trained in sampling and
analytical techniques. Field sampling may involve some overnight trips to
the Baruch Marine Field Lab in
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Functional characterization of
AINTEGUMENTA-LIKE (AIL) genes in Arabidopsis development, Beth Krizek
The Arabidopsis transcription factor
AINTEGUMENTA (ANT) is an important regulator of lateral organ growth in plants.
Reduced ANT activity results in smaller than normal organs while increased ANT
activity results in larger than normal organs. ANT is a member of the AP2
subfamily of the AP2/ERF family of transcription factors, members of which play
important roles in plant development and stress responses. Seven closely
related AINTEGUMENTA-like (AIL) genes in the Arabidopsis genome
have partially overlapping expression domains within shoots and roots.
Furthermore, we and others are finding complex genetic interactions among these
AIL genes. Students will help to
dissect the functions of AIL proteins during meristem
and flower development. Possible projects include the characterization of
triple and quadruple mutant plants, characterization of transgenic plants that misexpress AILs,
and identification of downstream targets of AIL regulation. These projects will
involve genetics, molecular biology and biochemistry. ANT-like genes have been identified in the moss Physcomitrella and lycophyte Selaginella genomes revealing that these genes were present
during the early evolution of land plants. A better understanding of the
function of AIL genes in Arabidopsis
will provide insight into how gene duplication and diversification within this
gene family may have contributed to the evolution of increasingly more complex
plant body plans.
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Mutualistic interactions between bacteria and plants,
Rick Lovell
Bacteria enter into numerous interactions
with plants, some detrimental, some neutral, and some beneficial. In all
of these interactions, the bacteria benefit by obtaining nutrients, mainly
carbon and energy sources, from the plant host. In mutualistic
interactions, the plant may also gain benefits from the bacteria. These
can include a degree of protection from potentially damaging microorganisms
(microbial antagonism), provision of inorganic nutrients, such as nitrogen,
phosphorus, and/or iron to the plant, and stimulation of plant growth by
bacterial production of auxins, such as indole acetic acid (IAA). We have identified numerous
species of bacteria that can reduce (fix) atmospheric nitrogen to ammonia,
potentially providing some of this resource to the plant host. These include
several species of the genera Vibrio and Shewanella. We would now like to 1) determine the
conditions under which these bacteria fix nitrogen, 2) examine the
distributions of these bacteria in association with plant roots, and 3) examine
the degree of plant growth stimulation by nitrogen fixing bacteria. The
student will be introduced to strategies
for bacterial identification, quantification of nitrogen fixation activity and other relevant activities, and interpretation of the mechanistic underpinnings of this mutualistic interaction.
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Various projects are available where students can use molecular biology techniques to compare aquatic bacterial community "fingerprints" based upon temporal population succession, response to stimulus, or perturbation. Bacterial systems afford themselves to short research projects due to their rapid response and relatively short generation times. Students will work with the PI and graduate students to develop a hypothesis based environmental sampling scheme or experimental system to examine short term evolution of bacterial communities. These changes will be assessed by applying both classical and modern techniques, i.e. plate counts, epi-fluorescent cell counts of bacteria and molecular biology.
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My laboratory uses
bioinformatic approaches to study evolutionary processes using nucleotide
sequence information from public databases. Each student designs and completes
a project during the course of a summer research experience. For example, the
neutral theory of molecular evolution predicts that most sequence polymorphism
is maintained by genetic drift, and that therefore effective population size is
the most important predictor of genetic diversity. Some recent papers have
questioned the truth of this prediction. In summer of 2010, Christine O’Connor
tested the prediction using nucleotide sequence polymorphism data from a large
number of vertebrate and invertebrate animal species. The results showed that
effective population size is indeed the major factor predicting levels of
sequence polymorphism in both mitochondrial and nuclear protein-coding genes of
animals.
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Phenotypic
& Molecular Adaptation in the Freshwater Crustacean Daphnia, Jeff Dudycha
We address questions in
evolutionary ecology and genetics with the freshwater crustacean Daphnia.
Currently the lab is working on projects in speciation, life history
evolution (particularly growth and aging), and trade-offs associated with
consumer-resource interactions. Daphnia present unique opportunities for
study since they reproduce clonally and sexually, and we now have access to the
complete genome sequence. In the
upcoming summer, REU participants most likely will develop a project on
phenotypic plasticity, examining life history responses to variation in food
level, temperature and/or photoperiod. A previous undergraduate project
involved an investigation of the population genetics of Daphnia in the ponds of an old-growth floodplain forest at Congaree National Park.
Different parts of the park are subjected to flooding at different
frequencies, and the student tested the hypothesis that populations in areas
with more frequent flooding will be genetically more similar to each other than
populations in the infrequently flooded region.
A second project involved a study of differential gene expression in
alternate ecotypes of Daphnia. An initial experiment identified ~100 genes
whose expression may differ between pond-adapted and lake-adapted
populations. Subsequently, a combination
of bioinformatic approaches were used to define key domains of three of these
genes, DNA sequencing to determine whether the structure of the genes has
differed and qPCR used to confirm differential
expression under a variety of condition.
Future students could test whether particular ecological conditions
alter expression of one or more of these genes.
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Research
in the Phytoplankton Ecology Laboratory, Tammi
Richardson
Research in my laboratory focuses on the role of light, nutrients, and temperature in the growth of marine phytoplankton. These tiny algae are responsible for 90% of the primary production in the ocean, and thus, they form the base of aquatic food webs. Current projects examine: 1) the role of underwater spectral irradiance (water color) in determining phytoplankton community composition in blackwater estuaries, 2) effects of iron supply on iron transport in the marine diatom Thalassiosira pseudonana, and 3) the development of spectral fluorescence approaches for the in-water detection of different phytoplankton taxa. REU student projects could stem from any of these lines of research.
Back to Projects This project is not available in 2009.
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Effects of climate
change on the physiology and ecology of marine organisms, Brain Helmuth
Research in the Helmuth lab explores the effects of climate and climate change on the physiology and ecology of marine organisms. Specifically, Dr. Helmuth and his students use thermal engineering techniques, including a combination of field work, remote sensing and mathematical modeling, to forecast the impacts of climate change on coastal marine animals such as mussels and seastars. A major goal of this approach is to predict where the effects of climate change are likely to be the most severe, a method of “ecological triage”. Students in the past have examined how body temperature affects physiology and behavior of organisms, or have developed methods for predicting patterns of stress in the field that are likely to emerge under different climate change scenarios.
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How important are nonconsumptive
effects of predators when the threat of predation is transitory? Blaine Griffen
Predators often have strong impacts
on ecological communities through both direct consumption of prey and through
intimidation, or nonconsumptive effects. However, most studies on the nonconsumptive effects of predators have used experiments
where predator cues have been present throughout the duration of the
experiment. In reality, predators are
often highly mobile so that the threat that they impose is likely variable both
spatially and temporally. Large nonconsumptive predator effects that have been repeatedly
demonstrated under experimental conditions may become less important under more
natural conditions where the threat imposed by predators comes and goes. This project will use laboratory experiments
on prey foraging behavior to examine the influence of nonconsumptive
predator effects when the threat of predation is temporally variable. I anticipate that the study will focus on
blue crabs (Callinectes sapidus), an
important predator in local systems, and one of its primary prey,
the suspension/deposit feeding bivalve, Macoma
balthica.