Research Experiences for Undergraduates
(REU Program) June 13 - August 19, 2005
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 a 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.
Ten undergraduates will be accepted into the ten-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,
and confocal 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 of their choice. 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.
Back
to Top  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 U.S.A. Students are expected
to have completed one year of Chemistry and Biology in preparation for this program. Back
to Top For
More Information Students requesting information about the program
should contact Dr. Patricia Springer at (951) 827-5785 (patricia.springer@ucr.edu),
Dr. Julia Bailey-Serres (serres@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. Back to
Top Selection
of Applicants Completed — No Longer Accepting Applications for 2005 Once
again, the NSF-sponsored Research Experiences for Undergraduates (REU) Program
of the Center for Plant Cell Biology at UC Riverside received many applications
from undergraduates throughout the US. The review panel was very impressed by
the quality of the applicants, which included many students with a strong desire
to participate in plant cell biology research. The highly competitive pool of
applicants made the selection of only ten 2005 REU participants extremely difficult. Ten
students were finally selected by the panel and will start their internship positions
in June 2005. The CEPCEB REU Program Chair, Dr. Patricia Springer, would like
to thank everyone for their applications and interest in exploring the exciting
field of plant cell biology as a career option. CEPCEB will be advertising REU
internships in December of this year for the summer of 2006 and encourages students
to apply again. Back to Top Faculty The awardees will 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 | | Girke, Thomas | Bioinformatics |
| Huang, Anthony | Oils
in seeds; Role of the tapetum in flowers | | Jiang,
Tao | Computational molecular biology, design and analysis
of algorithms | | 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 |
| Springer,
Patricia S. | Organogenesis in plants | | Walling,
Linda L. | Role of aminopeptidases in defense and development |
| Yang, Zhenbiao | Signaling
networks in Arabidopsis |
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- Nine: Pursue individual research projects.
Attend weekly lab meetings with the other awardees. Attend weekly CEPCEB
research presentations. Week Ten: 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 2004 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 2004,
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 2004 research
programs in CEPCEB laboratories.
Marietta
P. Boisdoré
SOUTHERN UNIVERSITY AT NEW ORLEANS |
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| The Raikhel laboratory
is interested in understanding the role of vacuoles and the endomembrane system
in plant growth and development. Mutations leading to a loss of function of genes
encoding many of these components are either lethal because the genes are essential,
or they have no effect on plant phenotype due to the presence of multiple genes
with overlapping function. One new approach to identifying genes involved in endomembrane
biogenesis is chemical genomics, in which a library of diverse chemicals is screened
for compounds causing specific phenotypes. Using this approach the Raikhel laboratory
has identified several novel drugs, namely Sortins 1 and 2, which affect vacuole
biogenesis and root development of the weedy flowering plant Arabidopsis thaliana.
My participation in this on-going research is to conduct experiments to identify
the molecular targets of Sortin 1 using genetics. I will screen approximately
100,000 seedlings for those that are either resistant or hypersensitive to Sortin
1. As a convenient phenotype to detect mutants, I am working with a dose of Sortin
1 that inhibits root development. Thus, resistant mutants will have normal length
roots in the presence of a high dose of Sortin 1, whereas hypersensitive mutants
will have short roots in the presence of a non-inhibitory low dose of Sortin 1.
Putative mutants will be confirmed in two ways: 1) Seeds will be germinated with
and without Sortin 1 to confirm that the root phenotype is drug dependent; 2)
Seedlings will be viewed by confocal microscopy to examine directly their vacuole
morphologies. This is possible because the mutagenized plants also express a marker
protein (βTIP-GFP) that allows us to visualize the tonoplast in living cells.
Mutants that are confirmed will be backcrossed by the Raikhel team in order to
map and clone the genes responsible for resistance or hypersensitivity.
Back
to REU Students |
Michelle
Brown
MOUNT SAN JACINTA COMMUNITY COLLEGE, CA |
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|
B.
Walter Evans
UNIVERSITY OF ALABAMA |
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| My project
in Dr. Borkovich's laboratory involves the mutational analysis of two of the eleven
putative hybrid histidine kinase genes of the ascomycete fungus, Neurospora
crassa. Dr. Borkovich is conducting an on-going project to study the role
of two-component regulatory systems in this multicellular fungus. These cascades
regulate a diverse array of functions, ranging from responses to nutritional stress
or chemical signals to multicellular development, chemotaxis and light sensing.
Two-component systems consist of proteins containing histidine kinase and/or response
regulator domains. The "knockout" gene constructs that I am using have
already been made by Dr. Borkovich's team. My goal is to transform these constructs
into the yeast, Saccharomyces cerevisiae, then into the bactierum Escherichia
coli, and finally, into Neurospora crassa. As these transformations
progress through a series of electroporations and analyses using PCR and Southern
hybridization, my job is to identify and isolate the mutants for the putative
histidine kinases, NCU 01823.1 and NCU 048341.1. By the end of the summer I hope
to analyze the fungal mutants for cellular and developmental phenotypes, and their
defects compared to those of the response regulator and histidine phosphotransferase
protein. Back to REU Students | It
has been my good fortune to be able to work in the Ding lab for the summer. The
focus for this lab is on RNA interference (RNAi). RNAi is a conserved mechanism
in which genes are silenced by mRNA degradation in a sequence specific manner.
RNAi has been found to contribute to antiviral responses, development, and chromatin
regulation in many different types of organisms. RNAi has also proven to be an
important experimental tool for selected inhibition of expression of genes. My
project is to determine if certain factors of a known mRNA degradation mechanism
contribute to RNAi in fruit fly (Drosophila melanogaster) cells. For this
project, I have been able to learn many knew ideas and techniques due to, in large
part, the patience and kindness of my postdoctoral mentor, Dr. Saba Aliyari. I
am very grateful for the chance to have these experiences and friendships received
in this lab. Back
to REU Students
| In the Bachant lab, I am testing
the idea that mutant strains of S. cerevisiae, that lack both the S phase
and spindle assembly checkpoints, will be able to initiate and complete mitosis.
RAD53 is a protein kinase that is the key regulator of the S phase checkpoint,
which prevents mitosis when DNA synthesis is perturbed. rad53 mutants lack
the arrest of mitosis, and the mutants move on through the cell cycle with unreplicated
DNA. Our lab has observed that although rad53 mutants initiate mitosis,
they do not complete it. Our hypothesis to explain this observation is that another
checkpoint, the spindle assembly checkpoint, compensates for the loss of the S
phase checkpoint. If so, we predict that cells containing mutations that cause
both checkpoints to malfunction will start and complete mitosis even though DNA
is not replicated. To test this I will generate and test two different mutant
strains. (1) The first is a rad53 ipl1 mutant. IPL1 (Increase in PLoidy)
is a protein kinase that is responsible for preventing chromosome segregation
at the spindle assembly checkpoint in the event that the kinetochores are not
properly attached to spindle poles. An ipl1 mutant is defective for this
checkpoint and is thus unable to prevent chromosome segregation following spindle
damage. (2) The second is a rad53 mad2 mutant. MAD2 (Mitotic-Arrest-Deficient)
protein detects unoccupied kinetochores and arrests chromosome segregation if
microtubules are not properly attached to the kinetochores. mad2 mutants
are defective for this response, allowing chromosome segregation to continue even
if chromosomes are not properly attached to the spindle. I will test these two
double mutants to determine if they initiate and complete mitosis when DNA replication
is perturbed.
Back to REU Students
|
Candida
S. Fielding
FORT VALLEY STATE UNIVERSITY, GA |
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|
Ivann
Martinez
CALIFORNIA STATE UNIVERSITY, LONG BEACH |
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|
Veronique
Matthews
FORT VALLEY STATE UNIVERSITY, GA |
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| | This summer I
will participate in a project to determine the roles of four genes that each encode
a protein of no known function that is highly up-regulated in response to low
oxygen stress (hypoxia) in Arabidopsis thaliana seedlings. I will be learn
how to grow Arabidopsis, perform stress treatments, extract and analyze
DNA and mRNA, and evaluate data available from a number of web-based resources.
Previous DNA microarray experiments in the JBS lab that compared wild type control
and hypoxia treated Arabidopsis seedlings led to the identification of a group
of gene transcripts that have increased abundance under hypoxia stress. Clustering
of the DNA microarray data revealed a group of 216 genes that are induced under
hypoxia stress; 109 of these genes encode proteins of unknown function. My project
aims to identify the importance of four of these genes. My objectives involve:
(1) The confirmation of data obtained by the DNA microarray experiment, by studying
the changes in mRNA levels and their ribosome association after several time points
of hypoxia treatment; (2) The identification of Salk T-DNA insertion alleles for
each of these genes, to study whether a loss of each of these genes affects survival
of the stress. This will involve the identification of individual plants that
are homozygous for the T-DNA insertion allele, from a family of plants that are
segregating for the insertion mutation. Screening and genotyping will be done
by use of PCR; (3) The compilation of publicly available data on these four genes.
Hypoxia stress treatments on wild type and mutant lines will be used in order
to compare their response phenotypes. Back
to REU Students | Our
lab focuses on the role of Rop GTPase signaling networks in the establishment
of cell polarity. I will investigate mechanisms for cell morphogenesis in the
epidermal cells of the Arabidopsis thaliana leaf. These epidermis cells have a
puzzle-like shape. The formation of the epidermis cells requires coordination
and communication between adjoining cells. For this reason, Arabidopsis leaf cells
serve as a model system to investigate the mechanism of interdigitated cell formation
in a multicellular organ. Dr. Yang's lab identified 11 Arabidopsis genes that
belong to the RIC family (Rop-interacting CRIB-motif containing proteins) that
interact with ROP GTPase in the process that interconnects epidermal cells. ROP
activates RIC4, which promotes cortical fine F-actin required for outgrowth of
lobes. At the same time ROP inactivates RIC1, which promotes transverse microtubules
that inhibit outgrowth in the indentation region of the cell. The goal is to figure
out how RIC1 proteins promote microtubule assembly. To investigate which domains
of the protein are important for microtubule binding and promoting activity, I
will perform the polymerase chain reaction (PCR) and plasmid cloning to generate
deletion mutants. Next, I will use the gene-gun method to transfer the plasmid
DNA into the leaf cells. Then, I will use confocal microscopy to observe how the
protein localizes within the cell and function in microtubule assembly. These
along with other techniques of molecular biology, biochemistry, and cell biology
will be involved in this investigation.
Back
to REU Students |
Judy
Ann Melendez
UNIVERSIDAD METROPOLITANA,
PUERTO RICO | .jpg) |
| In Dr. Linda Walling's
lab I am screening a combinatorial chemical library to identify molecules that
specifically inhibit or activate leucine aminopeptidases (LAPs), which catalyze
the hydrolysis of amino acid residues from the amino terminus of proteins. LAPs
are hexameric metallopeptidases that have alkaline pH optima and are inhibited
by the potent aminopeptidase inhibitors amastatin and bestatin. The tomato LAP-A
is the best biochemically characterized aminopeptidase in plants. LAP-A is highly
expressed at the RNA and protein level in response to wounding, various biotic
and abiotic stresses and during both floral and fruit development. The plant model
organism, Arabidopsis thaliana, has three LAP enzymes, but the roles of
these enzymes are unknown. Last summer an NSF-REU student developed a chemical
genetics procedure to identify small molecules that inhibit or enhance the activity
of tomato LAP-A and Arabidopsis LAP-1. This summer I hope to further characterize
tomato LAP-A and Arabidopsis LAP inhibitors and continue to screen the
chemical library for new inhibitors and activators. The goal is to find small
molecules that specifically inhibit and activate LAPs and not other classes of
aminopeptidases. This will provide the Walling lab with tools to better understand
the function and importance of LAPs in plants.
Back
to REU Students |
Jonathan
Ringler
AQUINAS COLLEGE,
GRAND RAPIDS, MI | .jpg) |
|
Carrie
Thurber
FRAMINGHAM STATE COLLEGE, MA |
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| My lab project
involves one of the largest factors in natural selection, the ability of a species
to overcome pathogens. Plants are no exception to this rule, though it may seem
as if they are at a disadvantage. The immunities of the plant cell ultimately
work off of two basic principles. The first recognizes that a pathogen that cannot
enter cannot infect; ergo the utilization of complex cell walls and membranes.
The second maintains that a pathogen cannot grow in a toxic habitat. When a plant
cell senses a pathogenic breech, it initiates a doomsday sequence; the cell becomes
poisoned and cannot support the invading threat. The genetic mechanisms
controlling the suicide are currently the subject of research in the Eulgem lab.
Two genetic families have been targeted for investigation. One consists of genes
that code for calcium-binding proteins (CaBPs) and appear to be thrown into full
gear during invasions. The other, known as the WRKY group, seems to be integral
in many functions, including immunities. Examining members of both families may
expose an individual cell death sequence. The investigation of these functions
involves inserting a piece of foreign "T-DNA" by a plant infecting bacterium
into a targeted gene sequences, thereby nullifying previous wild-type functions.
Another method involves reporter genes, specialized sequences that are inserted
at the end of particular gene codes and made manifest when the gene is transcribed.
My mentor and I are using these tools to observe the functions of the aforementioned
gene families, which may be involved in the plant immune system. Back
to REU Students | Dr.
Judelson's lab studies the genetics of the spore-producing oomycete Phytophthora
infestans. P. infestans is a fungus-like organism that produces spores
(sporangia) that are uncharacteristic of most true fungi. For example, the Phytophthora
sporangia are undesiccated and release zoospores. These zoospores are the main
mechanism by which P. infestans spreads disease among plants. Potatoes
infected with P. infestans, a condition termed potato late blight, die
quickly and spread the disease across large regions in a short period of time.
This disease was the major cause of the 1845 potato famine in Ireland and has
since resurfaced in potato crops worldwide. I will initially use bioinformatic
tools to study genes previously found to be up-regulated during sporulation in
this oomycete. These genes include P. infestans cleavage genes, termed
Pic genes, and P. infestans sporangia genes, termed Pisp genes. BLAST,
or Basic Local Alignment Search Tool, will be used to compare the P. infestans
genes to those of related Phytophthora species; P. sojae, the cause of
soybean root rot, and P. ramorum, the cause of sudden oak death. By comparison
of the conserved regions of these genes it is my goal to determine the functionally
important regions of promoters of selected genes. These regions will be amplified
using PCR and clone into a plasmid vector. If time permits, this vector will be
attached to a GUS reporter gene and tested in P. infestans.
| The LATERAL
ORGAN BOUNDARIES (LOB) gene is expressed in the boundary found
between lateral organs and shoot apical meristems of plants. LOB is a member
of a large gene family called the LATERAL ORGAN BOUNDARIES
DOMAIN (LBD), which consists of forty-three similar genes that are found only
in plant species. My research will focus on the functional analysis of members
of the LBD gene family in Arabidopsis thaliana. To understand the
function of these genes, three approaches will be used. (1) The expression pattern
of LBD25, one member of the LBD gene family, will be studied. I will analyze
transgenic plants that contain a GUS reporter gene under the control of
the LBD25 promoter to determine the developmental expression pattern of
LBD25 in plants and plant tissue sections. (2) Loss-of-function mutants
will be analyzed. We already know that the lbd25 single mutant displays
no visible phenotype. This suggests that the function of LBD25 may be redundant
to other LBD genes. To test this, plants are mutant for both lbd25
and the related gene ASYMMETRIC LEAVES2 (as2) will be examined.
I will use PCR to identify the double mutant plants (lbd25, as2) from a
segregating population. The double homozygotes will be examined for phenotypes
not present in either single mutant. (3) Publicly-available microarray data will
be analyzed to obtain information about LBD gene expression and the processes
in which LBD genes may control. Back
to REU Students |
Justin
D. Wood
SAN BERNANDINO VALLEY COLLEGE, CA |
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|
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