12/01/2010 Volume 1 Issue 2
If there's one summary about Itasca, it's that seven strangers became friends. We learned all sorts of useful and interesting things about plants from the various talks and mini-lab sessions we attended: from Dan Voytas, that high-precision zinc nucleotides are available that can modify specific nucleotides of a plant genome, from David Marks, about important fluorescent proteins and imaging technology to study cellular and sub- cellular behaviors of native or transgenic proteins, as well as many other details of faculty and student research. We also learned other important things: that when studying signaling pathways, it is very helpful to study pancake making; that cutting the same mushroom open again and again to watch it turn blue in an oxidation reaction is endlessly mesmerizing; that the floating bog peat at Itasca tastes rather grassy, and that Gail
The 2010 incoming class at their Itasca Orientation clockwise from left: is disturbingly good at (the card game) Mohamed Yakub, Rachel Hillmer, John Fankhauser, John Vincent, Apples to Apples. We returned home with Kevin Dorn, Xin Li, Amber Eule-Nashoba a better knowledge of wild fungi, information about how to get started with Contents MSI computing resources, and the Director’s notes friendships and resources that will help us walk confidently, and hopefully Meet the 2010 Students efficiently, through our graduate years. Student Achievements Phytograds -Rachel Hillmer Research:Students Research:Faculty Word from the Alumni Volume 1 Issue 2
Director’s notes
-Jane Glazebrook I am happy to introduce the second issue of the PBS Medium. Following the success of the inaugural issue, this issue is much larger, with lots of exciting reports about the PBS program! We are very happy to welcome a new class of seven first-year students, who all introduce themselves in the following pages. As you can see, they are a very interesting group with a wide range of interests. They are also ambitious and energetic! While explaining Jane’s Recommended Plan for Timely Ph.D. Completion during the Itasca Orientation, I was surprised to find that the most common questions were “How can I do it faster?”, and “Why do I have to wait for my second year to do my qualifying exams?” Luckily for me, I could assure them that they do not need to take qualifying exams earlier in order to finish earlier. Otherwise, I might have had to re-design the program on the spot!
Meanwhile, our other students have been making great progress. Recently, the success rate in preliminary examinations has been very high, which makes everyone happy. As Phytograds President Ye Sun explains, this may have a lot to do with teamwork and coaching from more advanced students. Many students have also received prestigious fellowships for support of their studies. This no doubt reflects the excellent quality of the students and their projects, and of course is most welcome in these days of budget- trimming everywhere. The research activities in PBS are lively and fascinating, as always. This issue features research highlights from students Tim Whitfeld, Suma Sreekanta and Ye Sun, as well as faculty member Nathan Springer. Somehow the PBS students manage to find time for fun amid their studies. The Phytograds have been very active recently, and are planning more fun events for the rest of this year (hint, DGSs love ice cream!).
We are glad to have reports from four PBS alumni in this issue. They have graduated from our program, but we have not forgotten them, and we love to hear about what they are doing now.
Upcoming Events...
PBS Open House January 27-29, 2011 Plant Biological Sciences Graduate Program Annual Retreat May 16, 2011 - visit http://www.cbs.umn.edu/plantbio/events/index.shtml
Transitions
Assistant Professor and Bell Museum Herbarium Curator Imke Schmitt returned to her home country, Germany, at the end of June 2010. She is a Professor in the Department of Ecology, Evolution and Biodiversity at Goethe University and holds a research position at the Biodiversity and Climate Research Centre, both in Frankfurt. Dr. Schmitt will remain an Adjunct Assistant Professor with the University of Minnesota’s Plant Biology Department.
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Meet the 2010 PBS Students!
John Vincent I am a first year student in the Plant Biological Sciences Graduate Program at University of Minnesota working with Jeannine Cavender‐Bares. I’ve worked in forestry and physiological ecology in the Pacific Northwest and in Costa Rica. Broadly, my interests include community ecology, plant physiology and stable isotope biogeochemistry. Last year in December I finished my undergraduate degree (B.S. Biology) at Seattle University, after being born and raised in Billings, Montana. I spend my free time mountain biking, reading, listening to music and enjoying the great outdoors. Mohamed Yakub I completed my B.S in Microbiology and M.Sc. in Biology at the University of Wisconsin Oshkosh, where I worked on gene expression in Arabidopsis. I then spent a year working in Leonie Moyle's lab at Indiana; my work there was focused on fine-scale mapping pollen and ovule sterility QTL in tomatoes. I am very excited to be a student at the University of Minnesota; I have wanted to attend here since sophomore year in high school. Aside from courses and research, I enjoy teaching hands-on science to young kids and have been involved as a judge for Science Olympiad for 5 years (the MN State Science Olympiad will be held in March, and we always need volunteers!). I also love theatre, and finally had the opportunity to watch Wicked the Musical during their tour through MN; it was an amazing experience! Kevin Dorn I am originally from New Prague, Minnesota. I completed my undergrad here at the "U", where I graduated in 2008 with double major in plant biology and genetics. I then joined Teach For America, where I served in St. Louis, Missouri as a high school science teacher for two years. I am now back at the U for my PhD, where I will be working in David Marks' lab. Aside from my interests in science and education, I enjoy spending time with my new wife, Katie, and my cat, Bear. You'll often see me biking around campus, reading the Minnesota Daily, or drinking Diet Coke.
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Meet the 2010 PBS Students! Johnathon Fankhauser I have a Bachelor’s degree in microbiology from the University of Minnesota-Twin Cities. As an undergraduate, I studied lichen chemistry, biosynthetic genes (PKS’s), and also worked as a TA. This picture is from the spring of 2010 when I traveled to Papua New Guinea with Dr. Imke Schmitt to start field work on a project bio- prospecting endophytic fungi and will continue to work on this project in the coming years with Dr. Georgiana May; I will not, however, be hunting with a bow and arrow anytime soon. My interests are plant fungal interactions (especially metabolites), Keystone projects, chemical analysis of fungal metabolites, exploring the difference between endophytes and pathogens, and experimental evolution. I like to snowboard, paint, play video games, debate the intricacies of life’s existence, and spend time with friends- of course, sometimes, all at the same time. You will rarely find me without a Mountain Dew in hand except of course in the jungle where serious caffeine withdrawals and malaria keep me occupied. Amber Eule-Nashoba My master’s project examined differences and explanatory factors of seed size in lacustrine and riverine populations of Z. palustris (wild rice). Currently I am interested in plant ecological relationships on a medium to small scale. Particularly, I would like to apply these relationships to problem solving.
Rachel Hillmer
I grew up in sunny Atlanta, GA (Hotlanta as we call it) and finished my B.S. in Physics from the University of Illinois at Urbana-Champaign in 2007. I then completed a master's in Bioengineering from the Massachusetts Institute of Technology in 2010. I have joined the Katagiri lab, and will be doing my second rotation with Les Szabo. I am interested in plant biotechnology and the forward engineering of plant systems, especially with applications to crop plants. When not in the lab, I enjoy cooking.
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Meet the 2010 PBS Students!
Xin Li I am Xin Li, and I got my B.S. degree from Wuhan University in China in 2010. As a new Ph.D. student, I am currently on rotation. My interest in research is about molecular/genetic and genomic mechanisms of plant development and plant metabolism. I like playing badminton, cooking Chinese food and watching football games!
Student Achievements
Congratulations to the students passing their Preliminary Written Examination during Summer 2010!: Roseanne Healy, Advisor: Dave McLaughin/Imke Schmitt Jo Heuschele, Advisor: Florence Gleason Brendan Epstein, Advisors: Peter Tiffin/Mike Sadowsky Suma Sreekanta, Advisor: Jane Glazebrook Mike Wilson, Advisor: Jerry Cohen Mike Nelson, Advisor: Neil Anderson Jing Chen, Advisor: Adrian Hegeman Congratulations to the students who also passed their Preliminary Oral Examination: Jo Heuschele, Advisor: Florence Gleason Mike Nelson, Advisor: Neil Anderson Suma Sreekanta, Advisor: Jane Glazebrook Rosanne Healy, Advisor: David McLaughlin Mike Wilson, Advisor: Jerry Cohen
Great Accomplishments -- PBS students received an array of awards! Suma Sreekanta received a MPGI travel grant and GAPSA travel grant to present a poster at the American Society of Plant Biologist’s conference in Montreal this past August. Rachel Hillmer received an NIH Biotechnology Training Grant under the direction of Plant Biology faculty member Fumiaki Katagiri and Chemical Engineering faculty Wei-Shou Hu. Johnathon Fankhauser received a Diversity of Views and Experiences fellowship. Congratulations to Kevin Dorn who got married in September!
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Recent Publications:
Swanson-Wagner, R.A., Eichten, S.R., Kumari, S., Tiffin, P., Stein, J.C., Ware, D., Springer, N.M.. 2010. Pervasive gene content variation and copy number variation in maize and its undomesticated progenitor. Genome Research, In press. doi:10.1101/gr.109165.110
Lusk, C.H., Sendall, K., and Kooyman, R. 2010. Latitude, solar elevation angles and gap-regenerating forest pioneers. Journal of Ecology, in press.
Grotheer, S. Hood, R., and Eule-Nashoba, A. 2007, Biomass SOP / Custom Proposal NAQWA 2172: U.S. Geological Survey, National Water Quality Laboratory standard operating procedure BIOB 0333.1B
Ballhorn, D.J., Schmitt, I., Fankhauser, J.D., Katagiri, F. & Pfanz, H. CO2 mediated changes of plant traits and their effects on herbivores are determined by leaf age. 2010. Ecological Entomology (in press).
Halici, M.G., Kocakaya, M., Sweeney, K., Fankhauser, J.D., Schmitt, I. 2010. Pertusaria paramerae (Pertusariales, Ascomycota), a species with variable secondary chemistry, and a new lichen record for Turkey. Nova Hedwigia. 91-1-2.
Schmitt, I., Fankhauser, J.D., Sweeney, K., Spribille, T., Kalb, K. & Lumbsch, H.T. 2010. Gyalectoid Pertusaria species form a sister-clade to Coccotrema (Ostropomycetidae, Ascomycota) and comprise the new lichen genus Gylectaria. Mycology: an International Journal of Fungal Biology 1:75-83. Recent Graduates CONGRATULATIONS!! Nick Deacon (adv. Jeannine Cavender-Bares) earned his Ph.D. degree in August 2010. Nick is an adjunct faculty at the Art Institutes International Minnesota. Ryoko Oono (adv. Ford Denison) earned her Ph.D. degree in August 2010. Also, she recently got married. Keunsub Lee (adv. Georgiana May) earned his Ph.D. degree in August 2010. He is currently working as a postdoctoral research associate in Dr. Kan Wang’s lab at the University of Iowa. Jessica Savage (adv. Jeannine Cavender-Bares) earned her Ph.D. degree in May 2010. She is currently working as a postdoc in the Ecology, Evolution, and Behavior department of the University of Minnesota. Sajeet Haridas (adv. Steve Gantt) earned his Ph.D. degree in August 2010. He is working as a postdoctoral research associate at the University of British Columbia, Vancouver.
Updates: Phytograd Corner It has been quite the social year already for the Phytograds! In July we indulged our sweet tooth with an Ice Cream Social in Cargill, sampling many of the University’s own Food Science frozen creations. So many graduate students, lab technicians, and professors came out that a repeat of the event can certainly be expected. The middle of August brought the yearly retreat at Itasca, an orientation for the incoming graduate students and a fun break for current students. Besides the daytime mini labs and evening seminars, the new students enjoyed biking, kayaking, and swimming. Volume 1 Issue 2
Not to mention the always memorable late evening games of Apples to Apples and Gail Kalli’s specialty: Guesstures. The last afternoon of the retreat was the Phytograds’ barbeque to welcome the new students, where all manner of grilled things and food was enjoyed. In the end the new students were able to meet all sorts of fellow grad students and professors and some went away with the unconscious ability to find fungi everywhere, even when they didn’t want to. The start of the fall semester brought the annual Greenhouse Party and an experiment in meeting new plant-based people. As we thought about the fact that there are several other departments who study similar things (Applied Plant Science, Plant Pathology), we realized that often we have no contact with those graduate students. So we decided to begin inviting APS and Plant Path students to the social events that we hosted. A host of APS students attended our Greenhouse Party which had a rather astounding turnout of grad students, professors, etc. And with the wonderful sunny weather partially to blame, people really enjoyed themselves. Will there be another Greenhouse Party in the spring? Oh there just might be! At present Phytograds has a Friday evening gathering every other week and plans to host a Game Night sometime this semester, probably with our new APS and Plant Path fellows. Be on the lookout for many opportunities for socializing in the future, we hope to see you there! -Alicia Knudson From the Phytograd President: Summer is a wonderful season for outside plants, and also an exciting period for the Phytograds, the official organization of PBS graduate students. Near the end of the spring semester, we elected new office members: President- Ye Sun, Vice President- Mike Wilson, Treasurer- Rosanne Healy, Officers- Cece Martin, Peng Yu and Jo Heuschele. After that, we started with a bunch of new and exciting activities. The first thing we would like to advertise here is that the Phytograds are on Facebook. Just search for “Phytograds” under “Groups” and you will find it. Not only current students but also Plant Biology alumni, postdocs, faculty, technicians, and staff are welcome to join the group. You will notice that photos of many previous events are already there. Have a look, and maybe you will find yourself there. We hope to make this web page a space to post group photos, to announce events, to discuss questions, and to keep in touch with new and old friends. It would be very much appreciated if PBS alumni could share information on job openings and other opportunities here. “Let’s celebrate summer in Minnesota!” The Phytograds hosted an Ice Cream Social on a sunny afternoon in July. Alicia, Rosanne and Ye brought various flavors of ice cream from the Food Sciences dairy store to the Cargill lobby, and attracted over fifty Plant Biology friends to participate. You can hardly imagine how sweet and cool we felt when the lobby was filled, when the cones and plates ran short, and when everyone got a chance to get together in a usually no-event summer. Phytograds as a program-based student organization should be about more than just having fun. And it is! Jessica and Ye hosted an Oral Prelim Preparation Workshop to help junior graduate students to cope with the toughest exam towards their degrees. In this workshop, we introduced the format of the Oral Prelim Exam, selection of date and room, interaction with the committee, sample questions from the faculty, benefits of mock exam, coverage of knowledge, and stress management. Jessica and Ye also mentioned some common tricks, like “make sure you understand the question before answering it”, “admit not knowing something then make a reasonable guess”, and so on.
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Most first- and second-year students attended in this event, and we have been hearing good news from every participant who took the exam after the workshop. Coincidence? In late August, Cece, Peng, Rosanne, Alicia, Zhou and Carrie headed to Itasca to welcome the new students. It was as exciting as in previous years to have a barbeque and to take part in outdoor sports. It was a little special because we celebrated Rosanne’s birthday by the lake. Back on campus the Phytograds held a semi- annual meeting, during which various student committee positions were quickly assigned. At the end of September, a Greenhouse Party successfully took place. Chief organizer Alicia invited students from Applied Plant Sciences and Plant Pathology to create a broader network within the plant sciences circle. Many other events, including Happy Hour, Game Night, Soup Lunch, Open House, Winter Itasca, Plant Sale, Bake Sale and so on are planned for the future. We are sincerely anticipating your participation, feedback and suggestions. -Ye Sun
Research Highlights-Current Students
Tim Whitfeld George Weiblen, Advisor Tropical rainforests are the most productive and diverse terrestrial ecosystems in the world. They cover less than 10% of the world’s land surface yet contain close to half of all the world’s species. The island of New Guinea is recognized as one of the world’s five most important tropical wilderness areas because of its endemic plants, high biological diversity, and extent of undisturbed primary forest. New Guinea contains the third largest remaining area of tropical wilderness after the Amazon and Congo basins and as such is a vital part of the tropical rainforest biome. A basic question asked by ecologists is how high species diversity, at small and large scales, can be maintained in communities such as tropical rainforests. For example, in 1 hectare (2.47 acre) of lowland rainforest in northern Papua New Guinea up to 250 species of woody plants can coexist. By contrast, in the equivalent area of the most diverse North America forest there would rarely be more than one tenth the number of coexisting trees, shrubs, and vines. High diversity at small scales is a conundrum because competition theory predicts that ecologically similar, closely related species cannot coexist over the long term. The goal of my dissertation project is to investigate the ecological processes driving the high plant diversity in tropical rainforests. I am using the evolutionary history of woody plants to investigate changes in the patterns of species coexistence as forests age. I also use traits of these plants to analyze the morphological and physiological similarity (or dissimilarity) of coexisting species. Results so far indicate that trees in young forests are more closely related to one another than would be expected by chance whereas in older forests trees are less closely related than expected. These patterns hint at a process of environmental filtering in the younger forests drawing closely related, ecologically similar species together while in the older forest, competitive exclusion is pushing close relatives apart. Volume 1 Issue 2
Suma Sreekanta Jane Glazebrook, Advisor Plants are continuously challenged by a variety of pathogens such as bacteria, fungi, nematodes, and viruses. Plants have both constitutive as well as inducible defense responses against these pathogens. Arabidopsis thaliana, the model plant, has been used to study plant pathogen interactions for some time now. In the Glazebrook lab, we use this system to understand the defense responses of plants to bacterial pathogens such as Pseudomonas syringae. We are especially interested in studying the role of Arabidopsis genes involved in defense signaling pathways triggered by the defense signaling hormone salicylic acid (SA). My thesis focuses on an Arabidopsis gene PAD4-Co expressed Kinase (PCK). This gene belongs to the Receptor like cytoplasmic kinase (RLCK) family. The expression of PCK is induced by the phytopathogen Pseudomonas syringae strain Psm ES4326. Plants with mutations in this gene show enhanced susceptibility to growth of Psm ES4326 relative to wild-type plants, suggesting that the function of this gene is important for defense against Psm ES4326 (see figure 1). Higher bacterial growth in mutant plants could be due to reduced levels of SA in mutant plants. However, the levels of SA in the mutant plants were similar to wild-type. This suggested that SA signaling in pck mutants may be compromised while not affecting the SA levels. A Fig1: A: Plants are infiltrated with PsmES4326. B: Bacterial growth was assayed three days after infection. Enhanced growth of Psm ES4326 in pck1-1 and pck1-2 was observed compared to wild type Col-0 plants. Highly-susceptible pad4-1 was used as a positive control.
Additionally, the mutant plants showed upregulation of several genes induced by other defense signaling molecules, jasmonic acid (JA) and ethylene (ET), suggesting that PCK may be involved in JA, SA and ET crosstalk. To test this hypothesis, bacterial growth in double mutants homozygous for pck and mutations in genes blocking SA synthesis or JA responses was examined. The results of this experiment suggested that PCK may be partially independent of SA and JA. Currently, an in vitro phosphorylation assay to test the kinase activity of PCK is being conducted. Further a “kinase dead” version of the gene PCK (K118E) has been generated by replacing a critical amino acid in the kinase domain of the gene. PCK (K118E) will be introduced into pck mutant plants to check if it complements PCK activity by restoring the resistance of the mutant lines. Failure to complement PCK activity will show that the kinase activity of PCK is important for its defense function. Lines expressing PCK coupled to a green fluorescent protein (GFP) have also been created and will be used to study the sub- cellular localization of PCK. Ye Sun John Ward, Advisor As a fourth year graduate student in the PBS program, I am studying the structure and function relationship of plant sucrose transporters (SUTs). We built a 3D structural model of SUTs by homolog modeling using crystallized structures of related bacteria proteins as templates. I mutated conserved, charged amino acids in putative trans- membrane spans and analyzed transport activity of the mutants in oocytes and in yeast. Single substitutions of five amino acids resulted in remarkable decrease or complete loss of activity, indicating their importance for protein function. I am thinking about measuring efflux, exchange and counterflow by the mutants in oocytes. I am also considering using tryptophan fluorescence quenching to test substrate binding of mutants. Different roles of the key amino acids might be revealed based on these experiments. If you have any good ideas or suggestions, please do let me know ([email protected]). Thank you!!
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Roseanne Healy David McLaughlin, Advisor The origin of truffles has fascinated people since the first century A.D., when Romans thought them products of thunder. Since then, we have learned that truffles 1) are unrelated fungi with closed underground fruiting bodies, 2) lack forcible spore discharge, and 3) are dispersed by animals that eat them. Their morphologies make them appear more similar to each other than to their above ground relatives. Molecular phylogenetic research suggests that truffles evolved independently in at least 15 Ascomycete lineages from ancestors with open, cup-shaped fruiting bodies (cup fungi) and forcible spore discharge. Nearly half of ectomycorrhizal (EM) lineages across fungi have members that are truffles or truffle-like, implying a correlation between the truffle form and EM trophic status. The EM truffle genus Pachyphloeus (eg. Fig. A) is interesting because there is evidence that it includes an EM cup fungus (eg. Fig. C), which could be indicative of recent evolution to a truffle form in this genus. Preliminary phylogenetic analyses of nuclear ribosomal DNA sequences support previous similar published results interpreted to show that Pachyphloeus has evolved to a truffle form several times within the lineage. Reconstruction of the Pachyphloeus phylogeny will aid in inference of where and when the intra-generic lineages spun off truffles. This basic information can then be used to formulate hypotheses on the more interesting questions regarding “how” and “why” truffles evolved in the genus. Pachyphloeus includes 13 described species with a worldwide distribution in temperate, mostly oak- beech woodlands. The genus is currently paraphyletic, and species concepts are confused. I hope to sort this genus out using molecular and morphological data. A) Pachyphloeus thysellii truffle (sexual fruiting form) B) P. thysellii asexual fruiting form C) Scabropezia flavovirens cup fungus (sexual fruiting form) D) S. flavovirens asexual fruiting A B form. Scabropezia sequences nest within the genus Pachyphloeus, and are likely achyphloeus. Figure C possibly displays the ancestral form of at least one lineage within Pachyphloeus. Since Scabropezia also produces asexual fruiting forms, the production of an asexual form may be an C D ancestral trait. This work will aid mycorrhizal research, since many sequences deposited in GenBank from ectomycorrhizal root tips BLAST to Pachyphloeus, with no knowledge of the species involved. It is known that an asexual form of Pachyphloeus from New York exists, but an exciting part of my project is the discovery that the asexual form (eg. Fig. B and D) is far more common and diverse than previously thought. Preliminary sequence data from the variable ITS portion of nuclear ribosomal DNA of sexual fruiting bodies and asexual fruiting forms has linked at least 6 sexual forms to their asexual forms. The fact that asexual forms fruit on the soil surface, and appear to be conspecific with individuals that make sexual fruiting bodies and form mycorrhizae considerably facilitates work on this cryptic genus. While looking for diversity of asexual forms among Pachyphloeus species, I and my collaborators at Duke University discovered another truffle genus that produces an asexual form, and a lineage of cup fungi for which there is no sexual form known. Some of the implications of a predominant asexual form fruiting on the soil surface are that 1) dispersal of these species may be through multiple avenues (wind, water, mammals, insects), 2) sexual reproduction may be facilitated by above-ground propagules of compatible mating types, and 3) asexual fruiting, which is completed over a matter of days as opposed to the weeks necessary for truffle maturation, may be an alternate strategy for survival and propagation during suboptimal periods for these fungi. The most exciting aspects of this research are the discovery of “hidden” fungal diversity, the satisfaction of linking asexual forms with their sexual forms, linking sexual forms with the mycorrhizal roots they have been detected on, and piecing together the relationships within this genus.
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PBS Faculty Research
Nathan Springer As a geneticist I am interested in the mechanisms of heritable variation within a species. Selecting upon this natural variation is the basis of breeding efforts and the combination of natural variation from two parents can result in heterosis or hybrid vigor. My lab uses a variety of approaches to study different levels of variation among different inbred lines of maize. One area of research has focused on profiling gene expression in different inbred and hybrid lines. Studies began by Robert Stupar, a former post-doc, identified numerous gene expression differences in maize inbreds and characterized how these genes were expressed in hybrid off-spring. One subset of differentially expressed genes includes those that are expressed in some lines but completely absent in others. Moumita Chakravartty, who just finished her Master’s degree, characterized the prevalence of genes that exhibit these present-absent expression patterns and explored the types of genes that are subject to this unusual pattern. A second area of research has focused on structural variation in the genomes of different maize inbreds. Comparative genomic hybridization (CGH) has been used to compare the copy number of sequences in different inbreds and to identify many examples of copy number variation (CNV) and presence-absence variation (PAV) in the genomes of two maize lines, B73 and Mo17. A study recently published at Genome Research by Ruth Swanson-Wagner (a post-doc) and Steve Eichten (a graduate student) extended this analysis to look at how CNV and PAV have affected gene content in diverse maize genotypes. They found evidence that 3% of genes exhibit altered copy number and nearly 9% of genes that are present in the reference genome are missing from the genome of some other genotypes. The analysis of variation in genome structure and gene expression has provided evidence for severe types of variation among individuals of the same species. Current research efforts are focused on profiling patterns of DNA methylation in different maize inbreds to allow us to compare the epigenome of different individuals within a species. A long-term goal of my research is to understand how different forms of genetic and epigenetic variation contribute to phenotypic differences within a species and heterosis.
A Word from our Alumni: Please let us know if you change positions, so we can keep the alumni database current. If you would like to be included in the next PBS Medium, email a short description of your current position (including pics) to [email protected]
Steven Cannon PhD., 2003 Nevin Young, Advisor I graduated from the PBS program in 2003, and then worked as a postdoc on the Medicago truncatula genome sequencing project with Nevin Young through 2005. In 2006, I took a job as a geneticist with the USDA Agricultural Research Service at Iowa State University. There I worked on assembling and analyzing the soybean genome sequence (published early this year in Nature). I also worked with two teams to make websites for accessing genomic data: SoyBase for soybean data, and the Legume Information System for numerous crop and forage legumes. I am interested in species diversity and evolution, especially in the legumes. My wife Ethy and I maintain a large home garden in Ames, and also manage a community garden, where we grow several dozen legume varieties -- among other things. One unusual species is a North American bean relative, named Apios americana -- sometimes called "potato bean", since it produces edible tubers. Several researchers believe this has promise as a potential new crop. Volume 1 Issue 2
Peter Avis Ph.D., 2003 David McLaughlin, Advisor Fungi are diverse organisms responsible for globally important ecological processes such as decomposition, nutrient cycling and disease. Recently, the challenges in identifying fungi and their activities have been surmounted with molecular technology. I fuse approaches in mycology, ecosystem ecology and molecular diagnostics to predict how fungi respond to a changing environment and to document fungal diversity. More specifically, undergraduate researchers and I use DNA identification techniques such as PCR, fragment analysis, cloning, and sequencing 1-5; and I link these to field studies designed to determine the effects of pollution on fungi in natural ecosystems and to enumerate fungal diversity especially in threatened habitats. I conduct four key studies: (I) A > 6 year long manipulative ecosystem experiment that adds simulated pollution to replicate mature forest plots at the Indiana Dunes National Park and where fungal communities are now less diverse with simulated pollution6 and current tests examine how shifts in fungal communities impact ecosystem activity; (II) A molecular, morphological and functional study of a group of mycorrhizal fungi that respond positively to high nitrogen pollution and can be considered “epidemic” and potentially parasitic to host plants7,8; (III) A pollution gradient study conducted in a globally threatened biome, a temperate oak savanna also in the National Park but adjacent to a major steel mill; (IV) A detailed documentation of the fungal diversity of oak savannas in the Indiana Dunes region and elsewhere7 by using systematic field surveys of macrofungi, total soil environmental DNA approaches and selective PCR to target specific fungi like a member of the species group commonly referred to as “porcini,” highly edible fungi indicative of pristine oak savanna. In addition to these studies, a number of additional, collaborative projects including the Northwest Indiana Restoration Monitoring Inventory (NIRMI) are in progress.Overall, my research at IUN over the last three years has been a productive and rewarding endeavor. During this time, I have authored or co-authored five research papers published in leading journals in my field. In addition, I have submitted ten external grant proposals (requesting over $2 million). To date, two of these have been selected for funding ($120,000) and the others are pending.
References 1.Avis P.G., Branco S., Tang Y., Mueller, G. 2009. Pooled samples bias fungal community descriptions. Molecular Ecology Resources 10:135-141. 2.Avis P.G., I.A. Dickie, and G.M. Mueller. 2006. A “dirty” business: Testing the limitations of terminal restriction fragment length polymorphism (TRFLP) analysis of soil fungi. Molecular Ecology 15:873-882. 3.Avis P.G. and Feldheim K. A. 2005. A method to size DNA fragments from 50 to 800 base pairs on a DNA analyzer. Molecular Ecology Notes 5:969–970. 4.Dickie I.D., Avis P.G., Reich P.B, and McLaughlin D.J. 2003. GERM: Good Enough RFLP Matching Program. Mycorrhiza 13:171-172. 5.Avis P.G., G.M. Mueller and J. Lussenhop.2008. Ectomycorrhizal fungal communities in two North American oak forests respond to nitrogen addition. New Phytologist 179:472-483. 6.Avis P.G. 2009 “Causes and consequences of epidemic growth in mycorrhizal fungi and their role in structuring plant communities in response to global change events.” Invited presentation at the Mycological Society of America Annual meeting’s symposium “Phylogenetic and functional patterns of host plants and their associated fungi: implications for symbiotic co-evolution, community interactions, and ecosystem processes” Snowbird, Utah.
Editors: Jane Glazebrook, Gail Kalli, Kelsey Morovic and Johnathon Fankhauser Questions or comments contact Gail Kalli at [email protected] Wendy Clement Ph.D., 2008 George Weiblen, Advisor Since finishing my Ph.D. in 2008, I have been a Post-doctoral Associate with Michael Donoghue in the Ecology and Evolutionary Biology Department at Yale University. My research, broadly focused on describing the evolutionary history of plant biodiversity, recently has concentrated on the phylogeny and biogeography of Viburnum and the Dipsacales, the honeysuckles and relatives. My work on the Viburnum phylogeny has suggested that while Viburnum is most diverse in temperate forests, it may have its evolutionary roots in the tropics of Southeast Asia. I have also been involved in a project that examines the utility of recently proposed plant DNA barcodes among closely related species in a phylogenetic context using Viburnum as a test case. During the summer of 2009, I was part of a team from Yale that went on an expedition to collect Viburnum along the Andes in Ecuador (http://www.yale.edu/yibs/yen_backissues.html, Vol. 15). I am now using those collections to answer questions concerning the species status and phylogeography of Viburnum in Ecuador. I have also continued research I began as a Ph.D. student at UMN on the mulberry family, Moraceae. Together with collaborators at the Field Museum of Natural History and the University of Dar es Salaam, we are investigating the pollination biology of Mesogyne insignis (Moraceae), a common understory shrub that is endemic to the Usambara Mountains of Tanzania. The goals of this work are to identify the likely insect pollinator of the plant, as well as study the effects of forest fragmentation on pollination. This fall I have been accepted to the Women Evolving the Biological Sciences (WEBS) conference in Seattle to take part in a discussion of issues concerning women in science. Currently I am a Lecturer at Yale and teach “Diversity of Life” and “Evolution of Plant Diversity.” Divya Chandran Ph.D., 2006 Deborah A Samac, Advisor Upon completion of my graduate work, I moved to the west coast to pursue a postdoctoral career in the Plant and Microbial Biology Department at the University of California, Berkeley. My first project involved using laser microdissection and global expression profiling to investigate powdery mildew infection site-specific processes and regulators in Arabidopsis. This study enabled me to identify novel host genes and processes with altered expression during the growth and reproductive phase of the fungus and provided strong support for host cell cycle modulation at the infection site. I then showed for the first time that host endoreduplication was induced in mesophyll cells at the powdery mildew infection site and identified MYB3R4 as a novel regulator of this process. myb3r4 mutants were compromised in the induced host endoreduplication response and supported reduced growth and reproduction of powdery mildew, suggesting that localized induced host endoreduplication is required for the sustained growth and reproduction of powdery mildew on Arabidopsis Chandran D et al. Laser microdissection of Arabidopsis cells at the powdery mildew infection site reveals site-specific processes and regulators. PNAS 107: 460-5. 2009). Currently, with the help of two undergraduate mentees, I am studying how MYB3R4 function is regulated and working on uncovering additional regulators of this localized induced host endo- reduplication response. When I am not in the lab, I enjoy spending time with my one year old baby girl, Sana.