5/18/2012 Volume 3 Issue 2

Director’s Notes

By: George Weiblen

It has been an eventful year for the Plant Biological Sciences Graduate Program. We recognize the success of our

students in their diverse accomplishments. I invite you to take a moment and reflect on the awards received, papers

published, and dissertations defended as evidence that our program grows stronger. That eight of nine admitted

applicants accepted admission offers speaks to our competitiveness. And the careers of our distinguished alumni

continue to provide inspiration.

The reorganization of the Graduate School transferred the

operation of PBS to the College Biological Sciences in 2011

but our cross-collegiate faculty remains committed to a

program that transcends administrative boundaries. When

Gary Muehlbauer changed hats from Director of Graduate

Studies to Department Head of Plant Biology, I stepped into

his former role and Cindy Tong stepped up to serve as our

Associate DGS. I would like to thank Gail Kalli for her able

assistance to PBS during this transition and recognize her 25

years of outstanding service at the University.

As the plant biological sciences continue to change, perhaps faster now than ever before, it is timely to consider

our identity. At this years program retreat, I asked everyone in attendance to write down the names of three fields

that best describe their interests. The result was a “wordle” (word cloud) based on >50 responses where the size of

the field is proportional to the number of individuals identifying with it. If you did not attend the retreat but would

like to join in the exercise, please communicate your interests to Gail Kalli. Compared to how we defined plant

biological sciences in the past, it is interesting to observe how far we’ve come.

Plant Biology Head -Gary Muehlbauer

I have been a faculty member in the Department of Agronomy and Plant Genetics for almost 15 years. Throughout this

time I have been affiliated with the Plant Biological Sciences graduate program in various capacities. For example, from

July 2009 to July 2011, I was the Associate Director of Graduate Studies (ADGS) and in July 2011, I became the DGS for

the program. On March 1, 2012, I was appointed as Department Head of Plant Biology and I stepped down from the DGS

position. At that time Associate DGS George Weiblen graciously assumed the role of DGS. Needless to say, the program is

in excellent hands.

During my time as DGS and department head I have become increasingly impressed by the quality of the PBS graduate

students. Numerous awards and fellowships have recently been obtained including: Steve Eichten and Rosanne Healy were

awarded the Doctoral Dissertation Fellowships; Steve Eichten and Xing Liu were awarded the Hamm Scholarship; and

Kevin Dorn received an NSF predoctoral fellowship. These awards and fellowships attest to the strength of the graduate

students in the program. I am extremely happy and proud to be associated with such a strong graduate program.

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My laboratory works on a variety of topics including:

developing and utilizing genomics resources for barley

breeding and gene discovery; barley genome characterization,

Fusarium head blight of wheat and barley; examining the

genetic control of vegetative branching in barley; and

examining the genetic control of shoot apical meristem

architecture in maize. This is an exciting time for plant

biology as the genomics tools and resources available provide

the opportunity to conduct research on an unprecedented scale

and examine an array of questions that were previously

unattainable.

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Education:

Ph.D., Michigan State University, 1993

Research Interests: Ecological and evolutionary dynamics,

evolutionary genetics, microbial ecology and evolution.

Mike Travisano Associate Professor

Department of Ecology, Evolution and Behavior

Transitions: New Faculty

My long-term research goals are in understanding the causes of biological diversity and complexity. While natural

selection is the ultimate cause for both, that level of explanation is not sufficient to understand how the myriad forms of

life have come to exist. My research program is essentially a series of studies of increasingly more complicated biological

systems. By understanding more simple systems, we then work toward understanding more complicated, and realistic,

biological systems. My first projects were with a single species of free-living bacteria, one of the simplest living systems

that have biological complexity. Since those first experiments, my work has branched out to include simple eukaryotes,

predator-prey interactions, and microbial communities, all of which was possible because of the earlier work.

Volume 1 Issue 2

Transitions

Volume 3 Issue 2

Paul Boswell Research Assistant Professor

Department of Horticultural Science

Education:

Postdoctoral, University of Minnesota, 2010 (Metabolomics)

Ph.D., University of Minnesota, 2008 (Analytical Chemistry)

Research Interests: My interest lies at the intersection of Chemistry,

Biochemistry, and Software/Hardware Engineering.

HPLC and GC Retention Prediction:

High Performance Liquid Chromatography (HPLC) and Gas Chromatography (GC) are invaluable and widely used

tools for analytical separations of complex mixtures. They are ubiquitous in the chemical/biological sciences and are

routinely used to separate just about every imaginable compound - from small molecules to proteins, drugs to lipids,

gases to salts.

In applications requiring the identification of large numbers of compounds from complex mixtures, mass spectrometry

(MS) has become the detector of choice, following separation by either GC or HPLC, because of its high sensitivity

and high resolution. It also provides an additional dimension of chemical information. While GC and HPLC separate

compounds based on their unique chemical interactions, MS essentially separates compounds based on their molecular

mass. Therefore, the two modes of separation should complement each other extremely well as separate means to

identify compounds.

Yet in the vast majority of GC-MS and LC-MS analyses, only the mass spectral information is used to identify

compounds - the chromatographic information, though readily available, is ignored! This is because there is still no

practical, reliable way to harness retention information for compound identification because there are so many

experimental factors that influence observed retention times. This is especially prominent in temperature programmed

(in GC) and gradient elution (in HPLC) modes, where even small differences between makes/models of GC and HPLC

instruments significantly affect retention.

We recently discovered a new way to predict retention that is extremely accurate, easy-to-use, and works under a range

of experimental conditions. To learn more about our approach and see a demonstration of our retention prediction

software, you can visit www.retentionprediction.org.

HPLC Simulation Software:

We recently developed new simulation software to help educators teach the fundamentals of HPLC. The open-source

software features controls and indicators for a very wide range of experimental parameters and updates a graphical

chromatogram. See it at www.hplcsimulator.org.

Student Achievements Congratulations to the PBS students for receiving the following fellowships, scholarships, and grants:

NSF Fellowship: Kevin Dorn

Doctoral Dissertation Fellowships: Steven Eichten and Rosanne Healy

UNCF/Merck Science Initiative Fellowship: Amanda (Cece) Martin

Interdisciplinary Doctoral Dissertation Fellowship: Moana McClellan

Hamm Scholarship: Steven Eichten and Xing Liu

Phinney Fellowship: Steven Eichten

Charles J. Brand Fellowship: Michael Wilson

Dayton Wilke Bell Museum Fellowship: Stephanie Erlandson and John Vincent

Carolyn Crosby Fellowship: Elizabeth Fallon

Outstanding CBS TA Award: Kevin Dorn

Outstanding Student Presentation Award, American Bee Research Conference: Michael Wilson

Student Delegate Award: 2012 7th International association of lichenology symposium (IAL7): Bangkok, Thailand:

Johnathon Fankhauser

Walter M. Fitch Award Finalist: Society for Molecular Biology and Evolution (Upcoming SMBE Conference

Presentation June 2012): Dublin Ireland: Johnathon Fankhauser

Congratulations for passing their Preliminary Written Examination: Kevin Dorn, Margaret Taylor and John Vincent

and to Alyson Center for passing her Preliminary Oral Examination this past year.

Volume 3 Issue 2

Christopher Pinahs, advisors Reich and Montgomery, earned his M.S. degree jointly with a University of Minnesota Law

degree in January 2012. He is the first student to earn a dual degree from PBS with the law school. “Experimental Warning:

How Temperature Affects Germination and Survival of Minnesota Tree Species”

Xing Liu, advisors Cohen and Gardner, earned her Ph.D. degree in April 2012. She started her postdoc appointment with

Professor Ray Deshaies at California Institute of Technology. “Roles of Multiple Mechanisms in Regulating Auxin Levels

during Plant Growth and Development”.

Heather Whittington, advisor Powers, earned her Ph.D. in May 2012. “Consequences of Elevated Temperatures on Prairie

Plants: Legumes, Nitrogen, and Phenology”.

Timothy Whitfeld, advisor Weiblen, earned his Ph.D. in May of 2011. Tim is working in the Dept. of Forest Resources at the

University of Minnesota as a Research Associate. . “Phylogenic Diversity and Functional Traits in Plant Community Assembly

across a Lowland Rainforest Light Gradient”.

Sumitha Nallu, advisors VandenBosch and Silverstein, earned her Ph.D. in May of 2011. Sumitha is a Postdoc at the

University of Chicago. “Expression, Regulation and Evolutionary Patterns of a large Family of Defensin-Like Genes found in

the Nodules of Medicago Truncatula”.

Xiaodong Sun, advisor Ni, earned his Ph.D. in July of 2011. Xiaodong is a Postdoc at the University of California-Davis.

“Regulation of De-etiolation and Stomatal Opening Responses by Hyposensitive to Light and Hypersensitive to Red and Blue

1”.

Alicia Knudson, advisor McLaughlin, earned her MS degree in August of 2011. Alicia is currently an instructor at the

University of Wisconsin-Platteville. “The Diversity of the Coral Fungi Genus Ramaria in Minnesota”

Graduates – Congrats!

Waters AJ*, Makarevitch I*, Eichten SR*, Swanson-Wagner RA, Yeh C, Xu W, Schnable P, Vaughn M, Gehring M, Springer

NM. 2011. Parent-of-Origin Effects on Gene Expression and DNA Methylation in the Maize Endosperm. Plant Cell. 7 (1)

4221-4233.

Eichten SR*, Swanson-Wagner RA*, Schnable J, Waters A, Hermanson P, Liu S, Yeh C, Jia Y, Gendler K, Freeling M,

Schnable P, Vaughn M, Springer NM. 2011. Heritable epigenetic variation among maize inbreds. PLoS Genetics. 7 (11):

e1002372. doi:10.1371/journal.pgen.1002372

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. 156 (4): 1679-1690.

Zhou Fang, Tanja Pyhäjärvi, Allison L. Weber, R. Kelly Dawe, Jeffrey C. Glaubitz, José de Jesus Sánchez González, Claudia

Ross-Ibarra, John Doebley, Peter L. Morrell, Jeffrey Ross-Ibarra. Megabase-scale Inversion Polymorphism in the Wild

Ancestor of Maize. Genetics (accepted).

Asplen MK, Bruns E, David AS, Denison RF, Epstein B, Kaiser MC, Kaser JM, Lacroix C, Mohl EK, Quiram G, Prestcott K,

Stanton-Geddes J, Vincent JB, Wragg PD, May G. 2012. Do trade‐offs have explanatory power for the evolution of organismal

interactions? Evolution (in press).

Epstein B, Branca A, Mudge J, Bharti AK, Briskine R, Farmer A, Sugawara M, Young ND, Sadowsky MJ, Tiffin P.

Population genomic evidence for widespread selection on symbiosis-related genes in the mutualistic rhizobia Sinorhizobium

meliloti and S. medicae. PLoS Genetics (in revision).

Sun, Y., Lin Z., Reinders, A., and Ward, J. (2012). Functionally important amino acids in rice sucrose transporter OsSUT1.

Biochemistry. 51: 3284-3291.

Reinders, A., Sun, Y., Karvonen, K., and Ward, J. (2012). Identification of amino acids important for substrate specificity in

sucrose transporters using gene shuffling. Journal of Biological Chemistry (in revision).

Wagenius S, Dykstra AB, Ridley CE, Shaw RG. 2012. Seedling recruitment in the long-lived perennial, Echinacea

angustifolia: a ten year experiment. Restoration Ecology. 20: 352-359.

Koehler, K, AE Center, J Cavender-Bares. 2011. Evidence for a freezing tolerance – growth rate trade-off in the live oaks

(Quercus series Virentes) across the tropical-temperature divide. New Phytologist.

Eberle, C., B.M. Clasen, N.O. Anderson, A.G. Smith. 2011. A novel pollen tube growth assay utilizing a transmitting tract-

ablated Nicotiana tabacum style. Sex Plant Rep 25: 27-37.

Gillitzer P, Martin AC, Kantar M, Kauppi KL, Dahlberg S, Lis D, Kurle J, Wyse D (2012). Optimization of screening of

native and naturalized plants from Minnesota for antimicrobial activity. Journal of Medicinal Plants Research. 6 (6): 938-949.

Eule-Nashoba, A., Biesboer, D., and Newman, R. 2012. Seed Size in Lacustrine and Riverine Populations of Wild Rice

(Zizania palustris L.) in Minnesota and Wisconsin. Botany. 90: (1) 27-33.

Kumar, TK, RA Healy, JW Spatafora, M Blackwell, and DJ McLaughlin. 2012 Orbilia ultrastructure, character evolution and

phylogeny of Pezizomycotina. Mycologia. 104: 462-476.

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.

Van Den Boom P., Giralt, M., Fankhauser J.D., Moberg R. Lichens of Panama, biodiversity in Physciaceae (Ascomycota).

2012 Submitted to Glalia. Bálint M., Fankhauser, J.D., Tiffin, P., Hallström B., O’Hara R.B., Schmitt, I. 2011. Assessing

diversity of leaf-associated fungal communities

on balsam poplar by 454 pyrosequencing. Inoculum, Vol. 62, No. 3. (2011), pp. 8-8.

Publications

Volume 3 Issue 2

Updates: Phytograd Corner

The end of 2011 and start of 2012 has been great for the Phytograds, the

Plant Biological Science Graduate Program student group. This winter,

Brendan, Mandy, Erin, and Mohamed organized the Phytograd Soup

Lunch, which was held in November in Cargill Atrium. Phytograds, staff,

and faculty came through with some delicious soups, breads, and desserts.

It was well attended and enjoyed by all. Rachel and Beth helped to

organize the winter holiday party, complete with festive hats for the

current and former department heads (see picture right)! Hope they

appreciated it. The annual white elephant gift exchange was entertaining.

as usual. The fact that a box of tea was the most prized “gift” speaks

volumes.

By: Rosanne Healy and Kevin Dorn

Winter Itasca was a big success, despite the lack of snow (for the

first time in memory!). Thanks to Stephanie and Steve for

organizing this event. About a dozen students tore themselves away

from their lab experiments to attend. In January, the Phytograds

also wrote and signed letters to legislators in support of a bonding

bill to rebuild the University Research Station at Lake Itasca

Biological (for which most of us have great memories from PBS

orientation, winter trips, and for some of us, active research sites).

The bill recently funded ~4 million to Itasca.

The jointly held annual plant sale and bake sale were a big success in April. Johnathon Fankhauser organized this

event, getting volunteers to plant a large variety of peppers and other vegetables on a snowy day in February (see

picture above). Mike Nelson brought a variety of woodland native plants, which was a new and popular offering this

year. Zhou rounded up volunteers to man the registers, and Suma and Vai helped with planting and advertising.

Margaret took on the task of organizing a very successful bake sale, and with the help of many other overly tasked

students, nearly sold out all of the goods on the first day and had to resupply.

Mohamed organized the recruitment weekend activities where

prospective and current students dined at Stub and Herbs on the

Minneapolis campus, which had a better-than-usual turnout for a

Friday night Phytograd gathering. Many stayed late shooting pool

and playing darts, with the program providing funds for food!

Mike Nelson, You Lu, Yuan, and Stephanie organized the annual PBS Retreat. This year, featured two alumni

speakers (Victoria Ranua-Moses, an environmental scientist with the Shakopee Mdewakanton Sioux Community; and

Yiping Qi, a research associate in Microbial and Plant Genomics), and two student speakers, Suma and Jo. We are

bringing back the legendary lab Olympics, which we hope will bring a fitting close to another year of intense

research, teaching, writing, and rewriting, and rewriting….

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I feel privileged to be a member of a department which supports a winter retreat to Itasca. Not only did I get to experience

the awesomeness of Itasca State Park and immerse myself in winter activities, but the retreat let me deepen my connections

with other students in the program, and gave me a change of pace from the business of the semester. To me, the retreat was

well worth the time and the drive.

The first thing the group (of six) and I did upon arrival (besides making breakfast) was to hike on the lake. There, we

encountered fox tracks crisscrossing the ice, ravens cackling to each other, and a brilliant blue sky. We challenged each

other to races and to an ice-breaking contest at the source of the river (I think Mandy won). We then climbed up on

Schoolcraft Island for a better view of the surrounding pine forests. After lunch we hiked down the southeastern arm of the

lake and bonded over a game of Dominion. Finally, that night, we lay down on the ice to watch the stars and tell stories.

The only thing missing to the retreat this year was enough snow to go cross-country skiing! I guess I’ll have to wait until

next year. Overall, the retreat was a great way to see more of northern Minnesota, to bond with other students in the

program, and just to relax. I will definitely go again next year, hoping for lots of snow and the chance to ski.

Winter Itasca

By: Stephanie Erlandson

The Council of Graduate Students (COGS) is the student organization that represents, advocates for, informs, facilitates

communications among, and supports graduate students. As the COGS representative for the Phytograds this year I have

had the opportunity to attend the monthly general assembly meetings bringing ideas and concerns of PBS graduate

students to the attention of this organization. Furthermore, I have had the unique role of serving as the collegiate

delegation lead for all of the graduate students in CBS. In this role I represent my fellow graduate students in meetings to

discuss the graduate school reformation. Additionally, in meetings with the dean’s office I have brought forth the student

voice for issues including: the GSWU/UAW vote, the plant biology department head transition, allowing graduate

students to register for classes while on 1-credit status, the Itasca initiative, transparency of graduate student fees in

award letters, and uniting CBS graduate programs from both campuses. We have been able to plan events such as the

graduate student appreciation week ice-cream social, the CBS social hour at Sally’s, and new this fall a joint orientation

for all new CBS graduate students. Finally, COGS helps us to recognize our wonderful PBS faculty this year both

Adrian Hegeman and Ruth Shaw won COGS outstanding faculty awards, so congratulations! COGS is a great

organization that is “there for us” as graduate students, their general assembly meetings are open to all students.

Attending them is an easy way to meet students from all over campus, stay informed about topics relating to graduate

education at the U, and get involved to make the PBS graduate experience the best that it can be.

COGS and You By: Amanda (Cece) Martin

Volume 3 Issue 2

PBS Retreat: May 2012

On Monday, May 14, the Plant Biological Sciences graduate program held its annual retreat at the Como

Conservatory. The day began with a welcome from the Director of Graduate Studies, George Weiblen, followed by

an update on the Phytograd happenings by Phytograds president Rosanne Healy and introductions by the the first-

year students. The day also included two successful poster sessions in which students presented their research to

fellow students and faculty. The poster sessions generated many interesting discussions and interactions between

students and faculty.

Also included in the agenda were four presentations by current and former PBS students. First, Suma Sreekanta,

currently a student in Jane Glazebrook’s lab, presented her research on plant defense responses. Jo Heuschle, a

student in Florence Gleason’s lab, then presented a talk about her research of the hormolan control of Potamogeton

crispus turions. This year’s presenters featured two PBS alumni. Yiping Qu, currently a post-doc in the Dan Voytas

lab, described his post-doc research on modification of the Arabidposis genome using zinc finger nucleases. Finally

Victoria Rauna, manager of the Shakopee Mdewakanton Sioux Community’s Wozupi (organic farm), shared her

story of how her experience as a PBS student helped her to find her path to her current position.

Following lunch on the Conservatory’s green roof space, there was a game of people bingo, in which people were

asked to match names to facts about their peers. The game was both fun and revealing! The Lab Olympics 2012

comprised three rounds. The first was an equation trivia game, followed by a plant identification round (complete

with Gleason and Cronquist dichotomous keys), and finally a faculty author/paper title matching game. The retreat

concluded with a tour of the Como Conservatory led by DGS George Weiblen. Overall the retreat provided an

excellent opportunity for team building among students and faculty, as well as a chance to find out about current

research within the program.

Alumni – we would love to hear about your research or updates on your career. Please send

articles to Gail Kalli at desha001@umn.edu for the next newsletter. Pictures are always

welcome!

In the future, PBS will only issue one newsletter every year in the fall.

Volume 3 Issue 2

Editors: Gail Kalli and Whitney Burger

Questions or comments contact Gail Kalli at desha001@umn.edu

Current Student Research Highlights

Margaret Taylor

Advisor: John Ward

In plants, cell-cell amino acid transport is important for long distance transport to sink tissues such as seeds. Amino

acid transport is crucial for proper seed development and nutritional quality. We don't fully understand how plant

amino acid transport works, but we know that a family of transporters, the Amino Acid Permeases (AAPs), is involved.

Though AAPs are conserved in both the monocots and the dicots, they have only been studied in detail in Arabidopsis

and legumes. I'm interested in characterizing a family of AAPs found in a monocot, rice. The Ward lab has done a

phylogenetic analysis of AAPs from several species, and found some groups of rice AAPs that do not have a direct

homolog in Arabidopsis (Tegeder and Ward 2012; Figure 1). I'm interested in learning whether the sequence

differences that have accumulated between rice AAPs and dicot AAPs translate to differences in function.

So far, to address this question, I've been studying the kinetic properties of the rice AAPs. Transport reactions can be

studied using similar methods to those that are used to study enzyme reactions. I am currently doing experiments to

measure the specificity and affinity that rice AAPs have for different amino acid substrates. In the future, I will

correlate rice AAP functions to differences in their sequence to predict amino acid positions that are important for

transporter function.

References:

Tegeder, M., and Ward, J.M. (2012). Molecular evolution of plant AAP and LHT amino acid transporters. Frontiers in

Plant Science 3.

Upcoming Events:

Itasca Orientation…………………………………………………………………………Aug. 14-19, 2012

Upcoming Seminars- visit http://www.cbs.umn.edu/plantbio/events/index.s.html