The 2011 incoming class at the Itasca Orientation clockwise from bottom left:
Beth Fallon, Vai Lor, Erin Treiber, Stephanie Erlandson, Yuan Xu, Margaret Taylor
Top: Amanda Waters and Nagendra Palani
12/09/2011 Volume 1 Issue 4
Contents
Director’s notes
Meet the 2011 Students
Student Achievements
Phytograds
Research:Students
Upcoming Events...
PBS Prospective Student Open House Feb. 2-4, 2012
Retreat-Como Park May 14, 2012
Itasca Orientation Aug. 14-19, 2012
- visit http://www.cbs.umn.edu/plantbio/events/index.shtml
Volume 1 Issue 4
Director’s notes
-Gary Muehlbauer
Welcome to the Fall 2011 issue of the PBS medium. The PBS program has eight new students that
entered the program this fall. Each of the students attended the Itasca orientation and had great fun and
learned a lot at the labs, lectures, and field studies. In addition, they got to know each other and become
familiar with some of the faculty that participated. As a bonus, they got to step into a hornet’s nest on the
floating bog walk! On page three of this newsletter the new students introduce themselves. Please
make a point to say hello to them when you see them on campus. The current students are progressing
nicely through the program and three (Peng Yu, Zhou Fang and You Lu) of them have just recently passed
their oral preliminary examination. Congratulations! Several of the current students have published their
research. Make sure to check out these recent publications (see page five for citations).
Dr. Kathryn VandenBosch, head of the Department of Plant Biology, has been named dean of the College
of Agriculture and Life Sciences (CALS) at the University of Wisconsin, Madison. Kate has made
extraordinary contributions to the Graduate Program in Plant Biological Sciences since she arrived in
2000. Kate strengthened the PBS program through her tireless engagement of faculty and departments
across the Colleges of Biological Science, the College of Food, Agriculture, and Natural Resources
Sciences, and predecessors. She transformed her department and our program by recruiting talented new
faculty with expertise in plant molecular biology, genomics, and evolution who, in turn, have attracted and
mentored outstanding graduate students. The national standing of our program for excellence in
scholarship is due, in part, to her vision and leadership. Kate has played an active role in university
governance as a member and chair of the Faculty and Senate Consultative Committee. And, in 2006, she
served as interim dean of the College of Food, Agricultural and Natural Resource Sciences. It comes as no
surprise that a peer institution should seek someone of her standing.
CALS enrolls approximately 2,600 undergraduate and 1,000 graduate students. The dean oversees the
college's 19 academic departments, which span environmental, social, and basic life sciences and
production agriculture, as well as numerous research centers and a range of outreach and university
extension activities. The dean also coordinates Cooperative Extension Service programs within the college
and serves as director of the Wisconsin Agricultural Experiment Station.
We will dearly miss Kate as a leader and colleague, and we wish her success in the Badger state.
TRANSITIONS: by George Weiblen- PBS; Associate Director of Graduate Studies
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A native Minnesotan, I earned my undergraduate degree at Gustavus Adolphus college,
majoring in Biology and Environmental Studies. While there, I studied abroad for a semester
in Panama, and spent about a month of that time chasing quetzals (a tropical bird) around
the cloud forests of Chiriquí for my research project. After college I spent a year teaching
environmental education in northern Minnesota. With breathtaking views of Lake Superior,
wolf tracks right outside my door, and plenty of adventures to be had, it was a hard place to
leave. Yet I am excited for the adventures to come; I’ll be joining David Moeller’s lab and my
research interests include plant ecological speciation and phylogeography.
I am from the city of eternal summer - Chennai, India. I graduated with a BS in Biotechnology from
Anna University, India in 2007. I worked as a software engineer for a Fortune 500 company
before the grad school bug bit me. In Fall 2009, I joined the department of Bioproducts &
Biosystems Engineering here at the U for a Master's degree, which I received early this Fall
working on bacterial molecular biology. Now, I have joined the PBS program for my PhD.
I am interested in understanding how complex functions arise in organisms from the interactions
of their molecular components. I hope to use such systems-level information to rationally
engineer organisms for biotechnological purposes.
Hello! My name is Mandy Waters. I graduated from the University of Minnesota in December of
2010 with a Bachelor of Science degree in Biology. I have been working in Nathan Springer’s
lab for the past year and half as a lab tech. I absolutely love genetics, which is one of the many
reasons that I will be joining the Springer Lab after this semester to work on epigenetic
phenomena. As an undergrad I also worked as a TA in Zoology and Human Biology. Being a TA
helped me realize one of my true passions is teaching. I hope to one day teach at the college
level and help create a universal understanding of basic biological concepts.
When I am not in school I love to be outside biking or swimming. I am currently in the beginning
stages of training for an olympic distance triathlon. Here is for hoping I survive the run! When I
am not running, biking or swimming I also love making pottery. I have been making pieces for
about ten years and have loved every minute of it.
Meet the 2011 PBS Students!
Volume 1 Issue 4
I earned my B.S. in Botany and Biology from the University of Wisconsin-Madison. Then I
moved to the southwest where I've been since, spending some time in the California
coastal chaparral and several years in the Sonoran Desert in Arizona. I'm joining
Jeannine the Cavender-Bares lab, and I'm interested in plant community evolution and
ecology.
I now spend part of my free time looking for a good local Mexican food restaurant (with
unlimited chips and salsa!) and would appreciate suggestions!
Volume 1 Issue 4
Nagendra Palani
Stephanie Erlandson
Beth Fallon
Mandy Waters
Meet the 2011 PBS Students!
Student Achievements Congratulations to the students passing their Preliminary Written Examination 2011:
Peng Yu, Zhou Fang, You Lu, and Alyson Center
Congratulations to the students who also passed their Preliminary Oral Examination 2011:
Peng Yu, Zhou Fang and You Lu
I completed my B.S. and M.Sc. at the University of Wisconsin Oshkosh, where I studied the
effects of plant-environment interactions on gene expression. Currently, I am rotating with
Dr. Marks and Dr. Olszewski. I am excited to attend the U of M since the program and the
location of the campus were perfect for me. Besides academics, I enjoy spending time with
my wife and 11 month old daughter Lyra (if you know Arabidopsis, you can figure where her
name came from). Being a father to a baby and a graduate student can be hard so you will
see my with a can of energy drink somewhere on me at all times.
I’m a first year graduate student in the Plant Biological Sciences Graduate Program working
with George Weiblen. I completed my B.S. in Plant Biology and Ecology, Evolution, and
Behavior at the University of Minnesota in 2009. My research interests involve plant-insect
interactions. I love plants and have been lucky enough to supplement my lack of a garden with
a great population of Ficus plants at the Bell Museum (which is open to the public, so check
them out sometime). When I’m not in lab, I enjoy spending time with friends and family,
reading, and spending time outdoors.
I grew up in China, Beijing. I completed my undergrad from Peking University in
Biotechnology and participated in two projects of ABA signaling and MAPK cascades. I'm
especially interested in plant defenses and signaling. I'm now doing my first rotation in
Gary Muehlbauer's lab, participating in projects on FHB and tillering in wheat and barley.
Then I'll do my second rotation in Fumiaki Katagiri's lab, and participate in interaction
study between PTI and ETI. I love playing violin, listening to music, reading and traveling.
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I'm originally from Southern California. I moved to Minnesota to study at Carleton College, where
I earned a B.A. in Biology in 2010. My research interests include plant cell and molecular
biology. At the U, I work in John Ward's lab on a family of amino acid transporters in rice.
In my free time, I love writing science fiction and fantasy and trying out new and interesting
veggies from the Hampden Park Co-op.
Vai Lor
Erin Treiber
Margaret Taylor
Yuan Xu
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Recent Graduates CONGRATULATIONS!! Alicia Knudson (adv. David McLaughlin) earned her M.S. degree in September 2011. Alicia is now an
assistant professor teaching at the University of Wisconsin, Platteville.
Xiaodong Sun (adv. Min Ni) earned his Ph.D. degree in May 2011. Xiaodong is now doing a post doc at the
University of California-Davis.
Student Publications:
Liu X, Cohen JD, Gardner G (2011) Low-fluence red light increases the transport and biosynthesis of auxin. Plant
Physiology 157: 891-904. Epub 2011 Aug 1
Eichten SR, Foerster J, de Leon N, Kai Y, Yeh C, Liu S, Jeddeloh J, Schnable P, Kaeppler S, Springer N. 2011.
Genetic architecture of maize B73-Mo17 near isogenic lines (NILs). Plant Physiology.
Kumar, TKA, R Healy, JW Spatafora, M Blackwell, DJ McLaughlin. Orbilia ultrastructure, character evolution and
phylogeny of Pezizomycotina. Mycologia (in press).
Kovács, GM, JM Trappe, AM Alsheikh, K Hansen, RA Healy, P Vági 2011. Terfezia disappears from the North
American truffle mycota as two new genera and Mattirolomyces species emerge. Mycologia 103: 831-
840.
Steve R. Eichten, Ruth A. Swanson-Wagner, James C. Schnable, Amanda J. Waters, Peter J.Hermanson, Sanzhen
Liu, Cheng-Ting “Eddy” Yeh, Yi Jia, Michael Freeling, Patrick S. Schnable, Nathan M. Springer, Matthew W.
Vaughn (2011) Heritable Epigenetic Variation Among Maize Inbreds. Accepted to PloS Genetics
Amanda Waters*, Irina Makarevitch*, Steve R. Eichten*, Ruth A. Swanson-Wagner, Mary Gehring, Cheng-Ting
Yeh, Patrick S. Schnable, Matthew W. Vaughn, Nathan M. Springer (2011) Prevalent Parent-of-Origin
Effects on Gene Expression and DNA Methylation in the Maize Endosperm. Resubmitted to Plant Cell.
*authors contributed equally
PBS graduate students
hold a festive barbeque
at the end of the Itasca
orientation as a way to
build new friendships
and reconnect with old
friends.
Updates: Phytograd Corner
Welcome to a new year of graduate education in the PBS program! The phytograds (you
and me) are here to support one another as well as helping out with the program.
2010-11 was a great year for Phytograds under the able and cheerful leadership of Ye
Sun. Among a number of quiet accomplishments: she started a facebook page for
Phytograds (log on to Facebook, put “Phytograd” into the search window), and shared
useful information from senior grad students about the best classes to take as a first
year and how to prepare for oral prelims. At the annual PBS retreat in May, she shared
Volume 1 Issue 4
When I heard that the PBS program required a weeklong orientation in
Itasca I was, to say the very least skeptical. I went to Itasca for an
undergraduate orientation as an incoming freshman at the U of MN. I
can say whole heartily that the second time around was 1x106 times
better. Excluding the mutant floating bog hornet/wasps and drowsy
side affects of Benadryl of course. Other than that the seven other
members of my cohort have completely changed my once negative
attitude toward Itasca. Each one of us has unique experiences and
distinct areas of expertise. Instead of shaming one another for not knowing something we praised each other for
our diverse backgrounds, while taking the opportunity to learn something about a topic that we have little (or some
cases no) knowledge. Some of us excelled at plant identification out in the field while others appreciated not
getting poison ivy. Others of us excelled at laboratory techniques, while others enjoyed the fact that their project will
not require an immense amount of bench work. One thing we all excelled at was gestures. If this whole grad school
thing doesn’t work out we can at least fall back on our ability to act out random words under pressure, and not to
mention have a fabulous time doing it. I can honestly say that I could have not asked for a better group of people to
spend my next four to five years with. Overall, Itasca was a successful trip and start to my graduate career.
answers to an interesting Phytograd survey of opinions about required classes for the PBS program. She and
Jessica started what we hope will become an annual prelim preparation event hosted by students who have gone
through this fun and relaxing process.
New phytograd officers were elected at the end of June: President- Rosanne Healy, Vice President-Kevin Dorn,
Treasurer Zhou Fang, Officers-Johnathon Fankhauser and Rachel Hilmer. After an eventless summer, several of us
(Cece, Mo, Carrie, Jessica, and Rosanne) spent a weekend at Itasca in late August to welcome the incoming PBS
students. Johnathon and Kevin kicked off the fall semester with a well-attended greenhouse party. The weather
was perfect, Johnathon’s special-sauce chicken wings were delicious (so I am told…), and the guests sociable. This
year, the EEB students were invited to join us, which was a great way to meet some of the other students we will
see at seminars. We were pleased to see the faculty who attended as well.
Carrying on the tradition (see paragraph above), Cece organized a prelim exam workshop that was held on Oct.
24th where candidate panelists discussed their strategies and answered questions. Mo, Brendan, Erin, and Mandy
planned a fun soup lunch, complete with fabulous prizes for the best soup donations. Other activities in the works
are a winter weekend at Itasca, where students have a chance to spend the weekend in a cozy cabin, do some
cross-country skiing, play games or just relax before spring semester starts. A bake sale and a plant sale are slated
for spring; and an end-of-the-term student-run retreat is scheduled for May 14th. We will also participate in the PBS
Recruitment Open House on Feb 2-4. Please plan to attend all of these events to make 2011-12 a great year!
From the Phytograd President : Roseanne Healy
By: Mandy Waters
UV-B radiation (280-320 nm) is a natural component of sunlight, and
plants have evolved specific responses to this type of light. Plant
responses to UV-B are often thought of as either photomorphogenic
(non-damaging) or damaging. This distinction is usually dependent
on wavelength and total fluence of UV-B. Photomorphogenic
responses are those that are mediated by a photoreceptor at lower
UV fluences or longer wavelengths (>300 nm), and such responses
include hypocotyl growth inhibition, change in gene expression or
accumulation of UV-absorbing compounds. Damage responses are
typically caused by the direct absorption of UV-B by macromolecules
such as DNA or proteins and disruption of electron transport in
photosystem II. These types of responses usually occur after high UV
fluences or from shorter wavelengths (<300nm). .
While plants have photoreceptors for red light (phytochromes) or
blue and UV-A light (cryptochromes and phototropins), one such
molecule has not been fully characterized for UV-B. I’m interested in
how plants perceive and respond to UV-B. Specifically, I am
interested in determining whether DNA absorption of UV-B induces
responses that are typically thought of as “photomorphogenic”.
Research in the Gardner laboratory has shown that DNA repair
mutants of Arabidopsis, uvr1-1 and xpf-3, are hypersensitive to UV-B,
even at the lowest UV fluences tested (Fig. 1). This suggests that an
accumulation of DNA damage, specifically photodimers produced
through direct UV-B photon absorption by DNA, may result in the
increase in hypocotyl inhibition seen in the repair mutants. One goal
of my research is to determine if increased photodimer
accumulation is triggering cell-cycle arrest, and/or if it is related to
downstream responses such as the induction of chalcone synthase
(CHS), a UV-B responsive gene.
Research Highlights-Current Students
Volume 1 Issue 4
Jessica Biever Advisor: Gary Gardner
Figure 1. Fluence response curves for
inhibition of hypocotyl growth by UV light
in nucleotide excision repair (NER)
mutants of Arabidopsis. Two-day-old
etiolated seedlings were irradiated with
the total fluence indicated and returned
to the dark for two additional days. Data
are expressed as percent of the
unirradiated dark control of the same
genotype (± S.E.).
Pre-zygotic interspecific incompatibility is the active recognition and
rejection of pollen or pollen tubes from interspecific crosses. Successful
interspecific pollinations result in hybrid plants with unique gene
combinations. However, interspecific fertilization frequently wastes parental
resources due to seed abortion or unfit hybrid offspring. The ability of plants
to identify and prevent interspecific pollinations preserves reproductive
resources for successful intra-specific pollinations. Mechanisms of
interspecific incompatibility are diverse and the factors regulating them have
not been fully identified. The goal of my thesis project is to identify
interspecific incompatibility mechanisms that result in Nicotiana obtusifolia
pollen being rejected by the N. tabacum style.
The transmitting tract (TT) is a highly secretory, specialized tissue of the
style. Pollen tubes grow through the extracellular matrix secreted by the TT
cells. Despite the TT being considered essential for pollen tube growth a
transgenic N. tabacum plant, with no mature TT cells (TT-ablated), supports
self-compatible pollen tube growth. Additionally, pollen tube growth of N.
obtusifolia, which is incompatible with N. tabacum, is compatible in TT-
ablated style (Fig 1). This reversal of incompatibility demonstrates that the
mature TT is required for interspecific incompatibility but is not essential for
pollen tube growth.
We were able to purify and identify the proteins from the N. tabacum TT that
regulate the interspecific incompatibility interaction. The major protein
identified is a class III pistil extensin-like protein (PELPIII). While the
expression and biochemistry of PELPIII is well characterized in the literature,
the function was unknown. We were able to show that a protein solution
comprised primarily of PELPIII specifically inhibited N. obtusifolia pollen tube
growth. Additionally, PELPIII antisense N. tabacum plants were tested for
compatibility with N. obtusifolia pollen. It was found that for plants with
undetectable PELPIII protein, the growth of N. obtusifolia was compatible,
whereas plants that had detectable PELPIII protein showed incompatible
pollen tube growth. The loss of interspecific inhibition in PELPIII antisense
styles supports the conclusion that PELPIII is involved in the interspecific
inhibition of N. obtusifolia pollen tube growth in the N. tabacum style.
Peter Morrell (waiting for his article)
Figure 1: Normal (A, C) and TT-
ablated (B, D) N. tabacum styles
pollinated with N. obtusifolia. A) and
B) show pollen tube growth at the
upper end of the style surface. The
styles were pollinated after stigma
removal and addition of a drop of
trilinolein to the cut style. C) and D)
show the front of pollen tube growth
after 40 hrs. Pollen tube growth is
quantified by measuring the average
distance of the tips of the pollen
tubes from the upper end of the style.
Dashed lines indicate measurement
of the pollen tube growth front,
hollow arrows indicated pollen tubes,
and the line arrows indicate vascular
bundles. N. obtusifolia pollen grows
significantly longer in the TT-ablated
style and eventually reaches the
ovules.
Alumni – we would love to hear about your research. Please send articles to Gail Kalli at
[email protected] for the next newsletter. Pictures are always welcome!
Carrie Eberle Advisors: Alan Smith and Neil Anderson
Volume 1 Issue 4
Editors: Gail Kalli and Johnathon Fankhauser Questions or comments contact Gail Kalli at [email protected]
