NSF Research Experiences for Undergraduates
(REU Program)
June 19 - August 18, 2006
Overview
The Center for Plant Cell Biology (CEPCEB) in association with
the Institute for Integrative
Genome Biology (IIGB) at the University of California, Riverside is committed
to providing rewarding research experiences to undergraduate students. As an NSF Research
Experience for Undergraduates (REU) Site, CEPCEB brings research experiences to
students of two- and four-year colleges who have limited opportunity to learn
about the excitement and career options that research in plant cell biology offers.
Eight to twelve students are accepted into the nine-week residential program. The
program will begin with a one-week workshop, in which students will be introduced
to techniques and approaches used for analysis of plant and plant fungal pathogen
cell function, including basic molecular biology, genomic and bioinformatic analyses,
as well as microscopy methods used to study live cells. Students will then spend
nine weeks working with a faculty mentor and a graduate or postgraduate mentor
on a research project. Students will also participate in workshops
to enhance learning skills and professional development, and to discuss ethics
in science.
Students will live on campus and be given an allowance for meals
and a stipend of $3600 for the summer.
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Eligibility:
Undergraduates Interested
in Discovering Research
Undergraduate students enrolled in a
two- or four-year college are eligible for the program. In addition, students
must be citizens or permanent residents of the USA. Students are expected
to have completed one year of Chemistry and Biology in preparation for this program. Back
to Top Application Deadline March 1, 2006
Please download the application form [printable pdf (for mailing hard copy), or electronic MS Word]. Please fill in the application and mail it to:
Dr. Thomas Eulgem
The Center for Plant Cell Biology
Department of Botany and Plant Sciences
University of California
Riverside, CA 92521
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For
More Information
Students requesting information about the program should contact Dr. Thomas Eulgem at (951) 827-7740, thomas.eulgem@ucr.edu or the Center for Plant Cell Biology at (951) 827-2152.
For information about related-graduate studies at UC Riverside, please visit: Opportunities for Graduate Training.
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Top Faculty
The awardees have the opportunity
to work with the following members of the Center for Plant Cell Biology.
The area of research in each laboratory is indicated. Please follow the
links to the members' web pages to further explore their research areas.
| Raikhel,
Natasha | Processing
of proteins in the secretory system; Organization of the plant cell wall |
| Bailey-Serres,
Julia | Selective
mRNA translation in response to plant stress | | Borkovich,
Katherine | Signal
transduction pathways used by fungi to respond to their environment |
| Bray,
Elizabeth | Regulation
of gene expression in response to water-deficit stress | | Carter,
David | Microscopy |
| Ding,
Shou-Wei | Post-transcriptional
gene silencing in plant viruses | | Eulgem,
Thomas | Regulation
of the plant defense transcriptome | | Girke,
Thomas | Bioinformatics |
| Huang,
Anthony | Oils
in seeds; Role of the tapetum in flowers | | Jiang,
Tao | Computational
molecular biology, design and analysis of algorithms | | Jin,
Hailing | Signal
transduction of plant-microbial interaction | | Judelson,
Howard | Developmental
biology of spores in the plant pathogenic fungi | | Lonardi,
Stefano | Computational
molecular biology, data mining | | Lord,
Elizabeth | Mechanisms
of pollination | | Nothnagel,
Eugene A. | Structure
and functions of arabinogalactan-proteins (AGPs) | | Nugent,
Connie | Fundamental
cellular processes responsible for maintaining telomeres |
| Ozkan,
Cengiz | Micro-
and nano- electromechanical systems for biosensing, nanotechnology |
| Ozkan,
Mihri | Development
of novel biomedical microdevices | | Pirrung,
Michael | Chemical
genomics; ethylene action | | Smith,
Harley | Regulation
of inflorescence architecture | | Springer,
Patricia S. | Organogenesis
in plants | | Walling,
Linda L. | Role
of aminopeptidases in defense and development | | Yang,
Zhenbiao |
Signaling
networks in Arabidopsis. Cell polarity and shape formation. Hormonal signaling. |
| Zhu,
Jian-Kang | Genetic
analysis of abiotic stress sensing and signal transduction; mechanisms of gene
silencing; role of miRNAs and siRNAs in gene regulation and abiotic stress response |
Back to Top Schedule
of Events Week One: Attend a week of lecture/labs
to become oriented to the program and to pick a research project for in-depth
study.
Week Two- Eight : Pursue individual research projects.
Attend weekly lab meetings with the other awardees. Attend weekly CEPCEB
research presentations.
Week Nine : Complete a write-up of the
laboratory project. Present a 15-minute talk detailing the results of the
project. Back to Top Contributions
of CEPCEB REU Students to Published Works CEPCEB REU
2003 Student Involved in Published Work Using Chemical Genomics A paper
recently published in the Proceedings
of the National Academy of Sciences involves the contribution of co-author
and CEPCEB 2003 REU student Jacob
Vasquez. The article titled "The Power of Chemical Genomics to Study
the Link between Endomembrane System Components and Gravitropic Response"
uses a chemical genomics approach that focuses on the use of small molecules to
modify or disrupt the functions of specific genes or proteins. In this significant
paper, chemical genomics was used to identify novel compounds affecting gravitropism.
Jacob remained in Natasha Raikhel's
lab after his REU experience and has contributed to the lab's research efforts
while pursuing studies at UCR. In addition to Jacob and Natasha Raikhel, this
paper was also authored by the following CEPCEB researchers: Marci Surpin, Marcela
Pierce-Rojas, Clay Carter, Glenn Hicks. For more information regarding this
paper, please see the UCR
press release (March 14, 2005). CEPCEB REU 2003 Student Involved
in Published Work Utilizing Quantum Dots Work performed by CEPCEB REU
student Rebecca Martin and researchers from
the departments of Chemical and Environmental Engineering, Mechanical Engineering
and Botany and Plant Sciences has just been published in the January 2005 issue
of Nanotechnology. The work utilizes Quantum Dot bio-conjugates to uncover new
knowledge about the binding of a protein at the growing pollen tube tip. In addition
to Rebecca, the interdisciplinary research team includes the following CEPCEB
members: Sathyajith Ravindran of the Chemical and Environmental Engineering Department;
Sunran Kim and Elizabeth Lord of the Botany
and Plant Sciences Department; and Cengiz Ozkan
of the Mechanical Engineering Department. For more information regarding
this paper, please see the UCR
press release (January 26, 2005). Back
to Top REU
Students and their Summer 2005 Research Programs
Undergraduate
students were invited to apply to the Center for Plant Cell Biology (CEPCEB) to
pursue individual research projects in the area of plant cell biology. In 2005,
the following ten students were accepted from over seventy applicants who applied
to this ongoing 10-week residential summer program. Please click on the
following student links to see photos and read about their Summer 2005 research
programs in CEPCEB laboratories. | REU
Student | College/University | CEPCEB
Faculty Mentor | | Benjamin
Becerra | California State
Polytechnic University, Pomona, CA | Smith
Lab | | Michelle
Brown | Mount
San Jacinto Community College, CA | Springer
Lab | | Hilary
Christensen | Carleton
College, MN | Pirrung
Lab | | Robert
Dick | Iowa State University,
IA | Zhu Lab | | Candida
Fielding | Fort Valley State
University, GA | Bachant Lab | | Janet
Lee | University of California, Los Angeles, CA | Jin
Lab | | Noelle
Oas | Saint Mary's University,
MN | Eulgem Lab | | Amy
Sainski | University of Wisconsin,
Parkside | Raikhel Lab | | Ricardo
Sayegh | Chaffey Community
College, CA | Girke Lab | | Quynh
Vu | University of Houston,
TX | Borkovich Lab | | Naa-Darkua
Wellington | Xavier
University, LA | Gallie
Lab |
Benjamin
Becerra
CAL STATE POLYTECHNIC
UNIV., POMONA, CA |  |
| Dr.
Smith's laboratory is focused on understanding the molecular mechanisms that control
the specification of flowers during inflorescence development in the shoot apical
meristem (SAM) of Arabidopsis plants. As simple as it may sound, flowering is
actually one of the most dramatic and important developmental events that occurs
during the lifetime of a flowering plant. However, very little is known about
the cellular and molecular events associated with flowering. Previous research
by Dr. Smith and his colleagues has demonstrated that the two BEL1-like (BELL)
homeodomain transcription factors PENNYWISE (PNY) and POUNDFOOLISH (PNF) interact
with another transcription factor SHOOTMERISTEMLESS (STM) to form a heterodimer.
Genetic studies suggest that inflorescence development requires the redundant
activities of PNY-STM and PNF-STM heterodimers, which function to specify flowers,
regulate early internode patterning events and maintain the boundary between initiating
floral primordia and the inflorescence meristem. Currently, Dr. Smith's laboratory
is focused on understanding the molecular mechanisms by which these homeobox transcription
factors specify floral cell fate in response to environmental and endogenous cues. My
goal as an REU student is to characterize the expression patterns of genes regulated
by PNY-STM and PNF-STM heterodimers, identify and characterize mutations in pny
pnf plants to suppress the non-flowering phenotype and map the genomic positions
of these mutants. The laboratory methods I will be utilizing throughout this summer
include molecular techniques such as activation tagging, DNA extraction, PCR,
gel electrophoresis, and DNA sequencing. I will use histological approaches to
localize promoter GUS expression patterns in the SAM and quantitate developmental
phenotypes that disrupt flowering and inflorescence architecture in Arabidopsis. Back
to REU Students | The
summer project in the Springer lab is to investigate whether there is a connection
between the LATERAL ORGAN BOUNDARIES (LOB) gene and brassinosteroid signaling
in Arabidopsis thaliana. The LOB gene is expressed in the boundary between
the meristem and the lateral organs. While the exact function of the LOB
gene is unknown, LOB is known to interact with a subset of transcription
factors. Some of these transcription factors are regulated by brassinosteroids
(BR). Brassinosteroid signaling is associated with many developmental and physiological
processes, such as germination, hypocotyl elongation, and wound response.
Interestingly,
when LOB is over expressed, the dwarf phenotype that results is very similar
to the phenotype of an Arabidopsis thaliana plant that is brassinosteroid
deficient. Since root and hypocotyl elongation are indicators of the BR response,
precise measurements of both will be taken when plants that over express LOB are
exposed to varying concentrations of brassinolide (BL), the most biologically
active of the brassinosteroids. In addition, assays to examine molecular responses
to BR will be done following BL application in over expressed LOB plants
and in wild type plants. These experiments will help to clarify the connection
between the LOB gene and brassinosteroid signaling. Back
to REU Students
|
Michelle
Brown
MOUNT SAN JACINTO COMMUNITY
COLLEGE, CA |  |
|
Hilary
Christensen
CARLETON COLLEGE,
MN |  |
| Small
RNAs in Arabidopsis play important roles in gene expression regulation.
They consist of two main classification groups: Micro RNAs, which originate from
RNA hairpins, and Short Interfering RNAs, which are cut from longer sections of
double-stranded RNA. Current methods for detecting these small RNAs are not very
effective, so the goal of this study is to develop a method of small RNA detection
using a microarray analysis. Consisting of complementary surface-bound primers
that fluoresce when they hybridize to their target RNAs (or cDNAs), microarrays
are already widely used. However, the small size in the case of microRNAs or siRNAs
(20-23 nucleotides) can result in problems such as weaker hybridization between
primer and target. The Pirrung lab has developed a technique called APEX (Arrayed
Primer EXtension) to specifically analyze RNAs. The microarrays are prepared with
complementary primers that hybridize to the RNAs of interest, after which reverse
transcriptase adds a fluorescent dideoxy nucleotide. Previous studies have shown
that chemically modified primers have a higher affinity for RNA, specifically
a 2' O-Methyl group or a 2' Fluorine. 2'F is more suitable for high-density microarrays
since the extra methyl group on the primer renders it unrecognizable by the enzymes.
Due to the fact that only the pyrimidines (C and U) are available commercially
in fluorinated forms, our targed RNAs will be A and G rich in order to allow the
presence of as many fluorinated bases in the complementary primer as possible. Back
to REU Students
| I'm
working in Jian-Kang Zhu's lab to understand how plants respond to environmental
stress. By identifying mutant phenotypes in Arabidopsis and what genes are responsible
for the observed mutant phenotypes we can generate hypotheses about what roles
these genes play in the plant stress response. The Zhu lab has isolated mutants
with altered expression of the NCED3 gene, which encodes a key enzyme in
abscisic acid (ABA) synthesis. I am working with the NCED3 deregulated1 (ced1)
mutant, which has increased ABA accumulation and reduced growth under stress
conditions. By constructing a double mutant of ced1 with the ABA-deficient
mutant (aba2-1), I will assess whether the increased ABA content of ced1
is required for the stress-sensitive phenotype. I will also undertake additional
physiological characterization of the ced1 mutant.
I am also working
to identify the mutated gene in the repression of silencing2 (ros2) mutant.
In ros2, a normally active RD:29A:LUC transgene construct as well
as the endogenous RD29A gene are silenced. Mapping of ros2 has narrowed
the location of the mutation to a defined interval. I will sequence ros2 candidate
genes in this interval in order to locate the mutation. My work this summer will
be under the direction of Dr. Verslues in Dr. Zhu's lab.
Back
to REU Students |
Robert
Dick
IOWA STATE UNIVERSITY, IA |
 |
|
Candida
Fielding
FORT VALLEY STATE UNIVERSITY,
GA |  |
| In
the Bachant lab, I am trying to understand a possible role for SUMO modification
in histone acetylation, DNA replication, and genome stability. SUMO is a small
protein belonging to the ubiquitin family of protein modifiers. The addition of
SUMO can modulate the ability of proteins to interact with their partners, alter
their patterns of subcellular localization and control their stability. SUMO is
synthesized as a precursor and processed by hydrolases to make the carboxy-terminal
diglycine motif available for conjugation. It is then conjugated to proteins by
means of E1 activating, E2 conjugating, and E3 ligating enzymes. Yet after conjugation,
SUMO can be removed by a class of enzymes known as SUMO isopeptidases. The main
isopeptidase in budding yeast is Smt4. Smt4 is required for budding yeast cells
to be able to withstand conditions where hydroxyurea, an inhibitor of DNA replication,
is present. This observation suggests that when SUMO modification is misregulated,
DNA replication errors arise at a high frequency and must be appropriately processed
by the repair machinery in order for the cell to survive. A dosage suppressor
screen performed on a Δsmt4 strain has shown that elevated levels
of HOS3, which is a gene encoding histone deacetylase, has the ability
to suppress smt4 mutant's sensitivity to hydroxyurea. Histone acetylation
itself is very important to the experiment being conducted because this process
correlates with transcriptional activity in many genes, including those involved
in origin of replication firing. The knowledge of the relationship between SUMO
modification, and histone acetylation/chromatin structure brings us to the project
of understanding how HOS3 suppresses the hydroxyurea sensitivity of smt4
mutants. The questions that we are addressing to help us further our understanding
are as follows: Does HOS3 suppress other smt4 mutant phenotypes,
are acetylated histone levels affected by the loss of Smt4 function, and is origin
firing altered in smt4 mutants. Back
to REU Students | Dr.
Jin's lab is interested in the mechanisms of plant pathogen resistance. Plant
diseases cause significant crop losses each year. The pathogen P. infestans
causes late blight, a disease affecting potato and other Solanaceous plants. The
RB gene provides a broad-spectrum resistance to late blight and has recently
been isolated. EDS1, NDR1, SIPK, and WIPK are genes that are important
signaling components in the R gene-mediated disease resistance pathways. In order
to determine if these four genes also play important roles in the RB resistance
pathway, my project this summer is to study these genes using virus-induced gene
silencing. The silencing construct containing the gene of interest is first transformed
into A. tumefaciens. I will then inoculate N. benthamiana with the
agroinoculum. The virus carrying the silencing gene fragment is extracted from
the infiltrated leaves after eight days post silence induction. The extract sap
is then used to inoculate wild potato plants that carry the RB resistance
genes. After the gene of interest has been silenced, I will use a detached leaf
assay to test for resistance. My project will contribute to a better understanding
of the RB-mediated resistance signaling pathway, which will hopefully one
day lead to crops with improved pathogen resistance traits. Back
to REU Students |
Janet
Lee
UNIVERSITY OF CALIFORNIA,
LOS ANGELES |  |
|
Noelle
Oas
SAINT MARY'S UNIVERSITY,
MN |  |
| One
of the largest threats to the agricultural industry is disease susceptibility
of many crop species. Over the past decades, a comprehensive research effort has
been conducted to understand the means by which plants defend themselves against
pathogens. Major advancements have been made in this area, such as the identification
of resistance genes (R-genes) and components of defense signaling pathways. However,
mechanisms of transcriptional regulation associated with these pathways are not
well understood. The Eulgem lab is interested in the molecular mechanisms which
control transcriptional reprogramming triggered during the immune response of
plants. For this purpose the model system Arabidopsis thaliana Peronospora
parasitica is used.
This summer, I
will be working with several short-conserved promoter motifs of co-regulated defense
genes previously identified in the lab. These conserved motifs may constitute
cis-elements important to coordinate expression of defense genes. The ability
of these motifs to bind with nuclear proteins present in Arabidopsis thaliana
will be tested using Electrophoretic Mobility Shift Assays (EMSA). For the EMSA,
the motifs will be labeled with radioactive phosphate (32P) and incubated with
nuclear protein extracts before being subjected to gel electrophoresis. If the
motif is able to bind to the nuclear proteins, the migration of the complex will
be slowed during electrophoresis, and there will be a shift in the position of
the band. If a shift in band location is observed, a yeast one-hybrid system can
be used to identify cDNAs encoding transcription factors that interact with the
respective conserved promoter motif.
Back
to REU Students | This
summer I am privileged to be working in Dr. Raikhel's lab using chemical genomics
to study vacuolar biogenesis of Arabidopsis cells. There are three main experiments
I will be contributing to this summer, all involving chemicals previously screened
and found to have varying effects on the Arabidopsis endomembrane system. The
first experiment involves isolating mutant plants based on their sensitivity to
the chemicals. I will be screening an EMS-mutagenized population to identify plants
that are hypersensitive to the chemical 247 (ID number from Chem Library 5850247).
Once hypersensitive mutants have been identified, the lab can use map-based cloning
to discover where the mutation exists and what pathways the chemical affects.
The second experiment also tries to find what pathways are influenced by the chemicals.
Here we will be treating wild type seedlings with chemicals for short periods
of time. We will then extract RNA and analyze the accumulation levels of different
transcripts using RT-PCR. The genes to be monitored were chosen from previous
micro array experiments. Finally, the goal of the third experiment involves the
characterization of the effects of the chemical on several florescent markers
using a confocal microscope. The markers will label plant proteins that, under
normal conditions, are targeted to specific organelles, such as the nucleus, ER,
golgi body, and tonoplast. Back
to REU Students |
Amy
Sainski
UNIVERSITY OF WISCONSIN,
PARKSIDE |  |
|
Ricardo
Sayegh
CHAFFEY COMMUNITY COLLEGE,
CA |  |
| The
Girke lab is interested in improving the current models of genes with unknown
function that are encoded in entirely sequenced plant genomes. Those annotation
improvements can often provide important leads for the functional identification
of unknown genes on the molecular and biological levels. In this project I will
use a comparative genome analysis approach to identify incomplete and new genes
in the genome sequences from Arabidopsis and rice. The following three approaches
will be used to achieve this goal: 1) Assuming there is a low degree of
gene order similarity between rice and Arabidopsis (synteny), the identification
of identical gene pairs can indicate that the current genome annotation has falsely
annotated one longer gene as two separate ones. In those instances the two truncated
genes will be merged into one and the correctness of the resulting protein sequence
will be confirmed by comparisons against the UniProt databases.
2) Completely
unidentified genes will be detected by searching for similarities between the
intergenic regions and the UniProt databases. Significant similarities in this
analysis will result in the discovery of new genes in the annotations of the two
genomes.
3) Incomplete genes will be identified by comparing the similarities
of the intergenic and protein coding regions from the two organisms with the UniProt
database. If intergenic and coding segments of the same gene show similarity to
one protein then this indicates a truncated gene model that may be correctable
with the generated similarity information. The following computational tools
will be used to automate the required searches and analysis steps for this project.
Large scale sequence similarity searches of ten thousands of sequences will be
performed with the BLAST program on the command-line. Perl scripts will be written
to parse and analyze the results. Statistical analysis will be performed with
the R program and the final results will be uploaded into an existing web-based
database. Back to REU Students
| Dr. Borkovich's
lab is part of an NIH-funded project along with labs from UCLA and Dartmouth to
understand more about functional genomics in Neurospora crassa. Approximately
10,600 N. crassa genes are present in the genome, but their functions have
yet been studied. My objective for this summer project is to find putative transcription
factor(s) that can be regulated by G proteins and other upstream factors. This
will be done by analysis of phenotypes exhibited by G protein mutants, and genetic
and molecular analysis to verify their epistatic relationships. Under my mentor,
Gyungsoon, I will test the phenotypes of 99 transcription factors and G-protein
mutants for growth, female fertility, and conidiation. For this, several tests
will be conducted. First, fresh transcription factor mutants will be grown in
various types of media for analysis. Then, phenotypes of each will be studied
and compared. Thirdly, candidates from 99 transcription mutants will be screened
and further examined against G-protein mutants. Lastly, epistatic relationships
will be determined using data gathered from above experiments as well as molecular
data taken from Northern analysis or RT-PCR. By the end of this project my goal
is to find the downstream transcription factor(s) of G-protein signaling in Neurospora
crassa.
Back
to REU Students |
Quynh
Vu
UNIVERSITY OF HOUSTON, TX |
 |
|
Naa-Darkua
Wellington
XAVIER UNIVERSITY, LA |
 |
| Excessive
light in plants leads to the augmented production of reactive oxygen species.
This activity results in oxidative stress and the damage of many of the cellular
components in plants. Plants are able to deal with the stress through an oxygen
radical scavenging system in which ascorbic acid plays a key role. Asc is also
known as vitamin c and it is the most abundant antioxidant found in plant chloroplasts.
Asc works by reducing hydrogen peroxide either directly or through ascorbate peroxidase
(APX). The product monodehydroascorbate (MDHA), a very unstable molecule then
dissociates instantly to either Asc and dehydroascorbate (DHA) or is reduced to
Asc by the enzyme MDHAR. DHA is either reduced to Asc by the enzyme dehydroascorbate
reductase (DHAR) or undergoes irreversible hydrolysis to 2,3-diketogulonic acid.
Plants with increased expression of DHAR have more Asc and are resistant to oxidative
stress.
For this project I will be determining the functions Asc plays
in plant photosynthesis and photoprotection using transgenic tobacco plants that
have altered DHAR expression. The western-blot method will be used to screen DHAR
overexpression and DHAR RNAi plants. I will analyze the photosynthetic performance
such as carbon dioxide assimilation rate and transpiration rate of control, DHAR
overexpression and DHAR RNAi plants using Li-Cor Gas Analyzer. Finally I will
study the light and carbon dioxide response combined with chlorophyll fluorescence
measurements to investigate the efficiency of light and CO2 of these transgenic
plants.
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