Download 1-2. REU Site - Heritage University

DESCRIPTION OF POTENTIAL HOST LABS
HERITAGE UNIVERSITY REU SITE
1-2. REU Site: University of Puget Sound. Biology Dept. Tacoma, WA.
1. Dr. Andreas Madlung Laboratory
There are two major projects currently ongoing in the Madlung lab. The first addresses the role of
polyploidy in plant evolution. Autopolyploidy (the doubling of the chromosome complement within
a species), and allopolyploidy (genome doubling and hybridization of two different species) may
have implications for rapid evolution. Polyploids are often more vigorous than diploids and
therefore are found frequently among agriculturally important crop species. Using the model genus
Arabidopsis, the lab focuses on molecular mechanisms that underlie the transition from polyploidy
to establishment of a new and stable species. In collaboration with other labs, students in the
Madlung lab have used this system to study the genomic effects of polyploidization on
transcriptional activity, genome structure, transposon activation, epigenetic changes, and cell
division. They have also characterized a new floral phenotype in the allopolyploid A. suecica, which
results in the reversion of flowering to an earlier developmental phase in a day-length dependent
manner. Dr. Madlung’s research team is using scanning electron microscopy and investigating the
underlying molecular mechanisms of this floral phenotype, as well as quantitative PCR, and whole
genome RNA sequencing (RNA-seq) to address these questions. The second project examines the
role of light perception and the transduction of the light signal inside the plant. Plants need light not
only for photosynthesis but also to direct their three-dimensional growth to achieve plant
architecture that is optimally adjusted for light and nutrient capture and attraction of pollinators.
They use tomato as a genetic model system for these studies because fruit development can be
studied well in this plant. This project aims to understand the function of 5 genes, which are
members of a gene family of the photoreceptor phytochrome. They are currently attempting to
knock out these genes to produce mutants and study the effect of the mutation on the transcriptome
and proteome of the plant. Students on these projects are involved in gene cloning, plant
transformation, phenotypic analysis of mutants, transcriptome and proteome analysis, and
verification of transcriptome results using qPCR. Bioinformatics plays an increasingly larger role in
these projects as well and students with an interest in computational work are welcome. Typically
REU students interact with the PI, 2-6 undergraduates, a technician and/or postdoc (in addition to
other research labs at UPS). For more information go to:
http://www.pugetsound.edu/academics/departments-andprograms/undergraduate/biology/research/faculty-research/andreas-madlung/
2. Dr. Alice DeMarais Laboratory
There are two potential projects at DeMarais Lab. Liver bearing fish, such as guppies, retain their
embryos in the ovary as the young fish develop. We are interested in investigating how the mothers
may transfer nutrients to their young during gestation. The amount of nutrients transferred may
depend on the environment of the female fish in good environmental conditions, the female may
transfer more nutrients, while poor environmental conditions may result in reduced nutrient transfer.
A project addressing this nutrient transfer would involve identifying the mechanisms of nutrient
transfer in response to environmental conditions. Female fish would be exposed to different
1
environments and transfer of small molecules would be identified using confocal microscopy. The
ovary tissue would then be used to identify proteins involved in nutrient transfer. Development of
viable eggs is necessary for successful reproduction. Using zebrafish as a model species, we
investigate the mechanisms resulting in the production of eggs that are ready for fertilization. One
area that needs study is the effect of environmental conditions on the production of viable eggs.
Female zebrafish would be exposed to different environments and the ovaries and eggs assayed for
the presence of apoptosis (programmed cell death). The expression of proteins involved in cell
death can be determined and the localization of dying cells can be identified through confocal
microscopy.For more detailed information go to:
http://www.pugetsound.edu/academics/departments-andprograms/undergraduate/biology/research/faculty-research/alyce-demarais/
3. REU Site. Washington State University. Department of Plant Pathology. IAREC. Prosser,
WA. Dr. Naidu Rayapati’s laboratory.
Rayapati’s lab at the Irrigated Agriculture Research and Extension Center (IAREC) is conducting
strategic and applied research on virus and other graft-transmissible diseases affecting wine grapes
(Vitis vinifera). The program is aligned with the Washington State grape industry’s research priority
“Management of viruses that impact fruit quality and vine health for achieving the central goal of
tripling the economic value of the wine and juice industry by 2020.” His applied research has
generated ecologically relevant information on epidemiology and impacts of grapevine viruses for
developing strategies for mitigating negative impacts of viruses on grapevine health and berry
quality. Rayapati’s strategic research integrates traditional virology with cutting-edge molecular
biology technologies to generate new knowledge on grapevine viruses. Cross-disciplinary and transinstitutional collaborative research has been the cornerstone of his research program, since
multidisciplinary team-based research is often the most effective strategy in deploying solutions to
complex virus diseases affecting sustainability of Washington State’s wine grape industry that
contributes annually an estimated $3.5 billion to the State’s economy and $4.7 billion to the US
economy. In addition, Rayapati is also working on virus diseases affecting vegetables crops in the
US and developing countries. This work involves detection of viruses by molecular diagnostic
methods and characterization of virus genomes by cloning and sequencing. Rayapati has been
providing an individualized program of study in grape virology for undergraduate
students. Undergraduate students will participate in research projects on (i) genetic diversity of
viruses, (ii) diagnosis of viruses by serological and molecular assays, and (iii) epidemiology of
grapevine virus diseases. In these projects, students will conduct independent research with welldefined objectives and work with Rayapati, graduate students and post-doctoral research associates.
The internship opportunities will provide avenues for undergraduate students to connect classroom
learning with on-site hands-on experiences and offer the necessary intellectual foundation for
achieving success in college in STEM fields. For more information visit:
http://plantpath.wsu.edu/people/faculty/Rayapati.html; http://wine.wsu.edu/virology/
4-6. REU Site. USDA, ARS. Wapato WA.
4. Dr. Rodney Cooper’s Laboratory
Research in the Cooper laboratory emphasizes: 1) host-plant defenses against insect pests of
vegetable crops and tree fruits, 2) acquisition and transmission of plant pathogens by their insect
vectors, and 3) ecological interactions among host-plants, insects and bacterial symbionts of
2
insects. The students will be working as team members with two full-time research technicians, 2-3
part-time biological science aids, and the PI. The goals for student apprentices in this REU include:
1) become familiar with experimental design and analysis, 2) become efficient with basic laboratory
techniques including the conduct of biological assays or basic molecular techniques including PCR,
fluorescence in situ hybridization (FISH), and molecular cloning/sequencing, and 3) gain real-world
experience working in a government research laboratory. Studies on host-plant defenses focus on
identification of constitutive defenses against potato psyllid and aphids among germplasm of wild
potatoes, and identification of mechanisms of both acquired and constitutive defenses against pear
psylla on pear. Techniques used in these studies include greenhouse bioassays, field studies, PCR
and FISH. Studies on the acquisition and transmission of plant pathogens by their insect vectors
focus on the epidemiology of “Candidatus Liberibacter solanacearum”, a pathogen of Solanaceous
crops that is transmitted by the potato psyllid. Conventional and quantitative PCR are used to
diagnose Liberibacter infection of plants and psyllids, and FISH is used to track the infection of
specific psyllid organs by Liberibacter. Studies on bacterial symbionts of insects focus on the 1)
identification of bacterial endosymbionts of potato psyllid and pear psylla, 2) potential role of plant
defenses in reducing obligate bacterial symbionts of psyllids, and 3) the potential role of the
bacterial symbiont, Wolbachia, in limiting gene flow among distinct haplotypes of potato
psyllid. Techniques used for these projects include conventional and quantitative PCR, FISH, gene
cloning and sequencing, and greenhouse-based biological assays. For more information go to:
http://www.ars.usda.gov/pandp/people/people.htm?personid=43467
5. Dr. Joe Munyaneza’s Laboratory.
Dr Munyaneza major research area is the integrated pest management of insect pests and diseases of
potato and other vegetable crops, with emphasis on insects vectoring potato diseases. Current
research includes biology and management of psyllids, leafhoppers, aphids, and their associated
pathogens and diseases. Of particular interest, is his research on Zebra Chip (ZC), a new and
economically important disease of potato in the United States and several other countries. The
disease has caused millions of dollars in losses to the potato industry, including in the Pacific
Northwest, where over 50% of U.S. potato production is threatened. ZC is characterized by severe
dark striped symptoms in raw and fried chips and fries processed from infected potatoes, affecting
their taste and making them commercially unacceptable. ZC is caused by the new bacterium
“Candidatus Liberibacter solanacearum” (Lso), transmitted by the potato psyllid, Bactericera
cockerelli. This phloem-limited bacterium also severely affects other solanaceous crops. Lso is
unculturable and currently, the only means of detection is by polymerase chain reaction (PCR). Dr
Munyaneza research team was the first to discover the association between ZC and potato psyllid
and has played a leading role in elucidating the disease and developing effective management
strategies to reduce its damage. Currently, the only effective means to manage ZC is by targeting
the potato psyllid, its insect vector. Therefore, increasing the understanding of the psyllid biology
and its interactions with Lso and its host plants is essential to developing effective management
strategies for ZC. The students will work in a team composed of two postdocs, a PhD student, and
several technicians and undergraduate students. Also, the students will have access to other labs at
the ARS Wapato facility and interact with several scientists and students. Following are two
examples describing activities in which the students will be involved:
1)
Potato psyllids acquire Lso by feeding on infected plants (horizontal transmission). Also, the
bacterium is transmitted from mother to offspring (vertical transmission). ZC spread depends on the
3
dispersal of infected psyllids. However, little is known on how important vertical transmission in
ZC spread is. A project will be designed in the laboratory to address this issue. Students will set up
mating pairs of infected psyllids, monitor egg oviposition and hatching, nymph development, and
adult emergence. The offspring and different life stages will be tested for Lso using PCR to estimate
transmission rate of the bacterium in the psyllid populations. The student will also investigate
potential transmission of Lso to healthy females by infected males. This research will provide
information on the role of Lso transovarial transmission in ZC spread.
2)
Very little is known about mechanisms by which potato psyllid transmits Lso to its host
plants. Based on the persistent and circulative nature of the phloem-limited Lso, two main probing
behaviors of the psyllid control its acquisition and inoculation. These are: 1) phloem sap ingestion,
during which Lso is acquired from a host plant, and 2) salivation into a phloem sieve element,
during which inoculation occurs. Characteristics waveforms representing potato psyllid probing
behaviors were recently identified by Dr Munyaneza research team using Electrical Penetration
Graph (EPG) technology. This system makes the insect part of an electrical circuit, allowing for the
measurement of resistance changes that occur during probing events. Students will use EPG and
PCR to assess transmission of Lso by potato psyllid to selected solanaceous crops. This research
will provide information on how the pyllid acquire and transmit Lso, leading to development of pest
management strategies that would impede the insect’s probing behavior and reduce its efficacy as a
vector. For more information go to:
http://www.ars.usda.gov/pandp/people/people.htm?personid=34267
8. Dr. Jennifer Nemhauser Laboratory.
Life is hard. Among the many challenges of life at the cellular scale is how to gather and respond to
information about an ever-shifting environment. One solution to this challenge is the evolution of
mechanisms to convert information gathered by cellular receptors—which act like antennae to
monitor the environment—into chemical signals. These chemical signals can then be translated by
networks of interacting molecular factors into changes in cell growth or identity. The Nemhauser
Lab investigates how the architecture and dynamics of signaling networks allow for the effective
processing of information, and how plants tune these networks to optimize their morphology for a
given environment. Our recent work has drawn from molecular genetics, genomics, physiology and
synthetic biology to build new tools to study signaling dynamics and to apply these tools to a
variety of fundamental questions in cell and developmental biology. Specifically, we are:
a) Building tools yo study signaling dynamics; b) Integrating metabolic status into growth control
networks; and c) Evaluating the impact of evolution on signaling networks. For more information
go to: http://depts.washington.edu/nemlab/research.htm
9. Dr. Barbara Wakimoto’s Laboratory.
Broad range interests in the Wakimoto laboratory center around chromosome organization and its
relationship to gene expression and chromosome maintenance. Two different projects are being
pursued to address these issues. The first involves studies of the heterochromatin of Drosophila.
Heterochromatin is generally regarded as transcriptionally silent and capable of inducing gene
repression. However, several genes are located within the heterochromatin and when these genes
are displaced from heterochromatin by chromosome rearrangements, they show abnormal
4
expression. In order to understand this phenomenon known as position effect variegation, and the
function of heterochromatin in general, Dr. Wakimoto's group is combining genetic, cytogenetic,
and molecular tools to understand the structure and regulatory requirements of heterochromatic
genes.
A second major research goal is to understand the regulation of events from chromosome
condensation during spermiogenesis through sperm decondensation that occurs in the egg
cytoplasm. This chain of events occurs in nearly all animal species and results in a dramatic change
in chromatin packaging of an entire nucleus. Several paternal effect mutations of Drosophila have
been identified that promise to provide insight into the molecules involved in this process. These
mutations are being studied genetically and molecularly with the goal of identifying components
that normally act to ensure sperm decondensation, the formation of the male pronucleus and stable
maintenance of the paternal chromosomes during embryogenesis. For more information go to:
http://www.gs.washington.edu/faculty/wakimoto.htm
10. Heritage University. Biology Program. Dr. Michael Parra’s Laboratory.
Dr. Parra’s Lab focus on understanding the role of histone variants in chromosomal dynamics.
Specifically, the functionally important residues on the histone H2A variant H2A.Z and the
understanding of the role that posttranslational modifications (PTMs) play in H2A.Z function. This
work utilizes the single cell eukaryote Saccharomyces cerevisiae (baker’s yeast). Understanding the
structure and function of chromatin will provide insights into the regulation of many DNAtemplated processes including: DNA damage response and repair, transcription, and DNA
replication. Student projects will focus on understanding the function(s) of H2A.Z SUMOylation in
yeast. The goal of this project is to elucidate the function of a recently described H2A.Z
posttranslational modification: SUMOylation. This PTM is known to be found on lysine residues
that lie in the motif: ψKxE (where ψ is a hydrophobic residue and x is any residue). When found on
other proteins, this PTM has a well described role in DNA repair and transcription. However, the
mechanisms underlying these roles are not well understood. Dr. Parra recently found that mutation
of a potential SUMOylation site on yeast H2A.Z renders cells susceptible to DNA double-strand
break-inducing agents. To date, this one of only a handful of single amino acid changes that
dramatically alter H2A.Z function. The goal of this project is threefold: 1) identify the site(s) on
yeast H2A.Z that is/are SUMOylated, 2) identify the enzyme(s) that place the SUMO group onto
H2A.Z, and 3) identify the function(s) of SUMOylation. Students will use site-directed mutagenesis
to determine the site(s) of SUMOYlation. A plasmid bearing a tagged version H2A.Z will be used
as a template for site-directed mutagenesis to produce unSUMOylatable versions of H2A.Z (e.g.
mutating residues that lie in the SUMO motif-see above). These plasmids will be placed in a strain
lacking endogenous H2A.Z. The sites of SUMOylation will be confirmed by purification of H2A.Z
from strains bearing a wild-type H2A.Z or H2A.Z mutants. This will be followed by Western Blot
analysis using an antibody raised against the SUMO mark. To determine the enzymes responsible
for the addition of the SUMO mark, the plasmid bearing the tagged H2A.Z will be placed in a strain
that lacks endogenous H2A.Z as well as deletions of enzymes suspected to function in
SUMOylating other proteins (e.g. the SUMO ligase SIZ1). H2A.Z SUMOylation will be assessed as
above. In addition, the function(s) of SUMOylation will be ascertained using spotting assays.
Essentially, wild-type and mutant strains will be grown, serially diluted, and spotted onto solid
media containing a variety of agents used to assess fitness or viability of the cells.
5
.
6