CY-ENCE Newsletter of the Interdepartmental Genetics Graduate Education and Research Training Program at Iowa State University

Confocal image of a double transgenic living zebrafish embryo, taken by Ying Wang, MCDB, Jeff Essner Lab. Green: Endothelial cells expressing a fusion of GFP and moesin. Red: Endothelial cells expressing RFP from a transposon insertion isolated from mutagenesis screen.

Philip Becraft, Chair, Interdepartmental Genetics

As IG trains students to be successful in scientific enterprises across the nation and around the world, the program has a long-term commitment to diversity. The IG program includes students from many countries, and we continue to

recruit students at meetings that attract outstanding minority students (such as MANRRS and SACNAS). Recent IG chair, Fred Janzen, and the current IG Associate Chair, Jo Anne Powell-Coffman, have key roles in the NSF-funded

ADVANCE program, which aims to increase recruitment and retention of women faculty in science, technology, engineering, and math fields at ISU. Faculty and students also mentor a diverse cadre of undergraduate and high

school summer interns working on research projects. Collectively and individually, IG faculty and students are working to expand the diversity of people, ideas, and cultures on campus, and this continues to enhance innovation and

education in the field of genetics.

Alumni Updates Kwang-Hun Baek (Ph.D./Ambrosio/Zoology and Genetics) is now a full professor at Pochon CHA University in Seoul, Korea. “I am now a vice director for the Cell and Gene Therapy Research Institute at Pochon CHA University. I have 8 students including 3 foreign students from India in my laboratory. Most of them (6 out of 8 students) are Ph.D. candidates. Regarding my family, I have a wife (Eulim Park) and two daughters (Sue Gene Baek and Sohjung Baek). These kids are 3 and 5 years old.” Matthew Abbott (Ph.D./Tuggle/Animal Science) is a full time instructor in biology for the DMACC Newton campus; this is his second year. Previously, he was a full time Biology Instructor at Iowa Lakes Community College in Estherville. Matt, his wife, and their son Alex, age 4, were joined in November by Scarlett Lucia Abbott, 8lbs 14oz, 19.5 inches. Anna Bennet (MS/Spurlock/Animal Science) is a PhD graduate student with Dr. Chris Elsik at Georgetown University in the Biology Department, majoring in Bioinformatics and Computational Biology. She is engaged to be married. Tyrell Carr (Ph.D./Whitham/Plant Pathology) received a 2 year NSF Minority Postdoctoral Fellowship. He is at the University of North Carolina at Chapel Hill working with Dr. Alan Jones in the Department of Biology. The Fellowship, which can be extended to a third year, includes full salary and research budget. Abstract of Planned General Research: “Biochemical and genetic characterization of a regulator protein of sugar signaling in Arabidopsis.” Plants require sugar as an energy source and as a chemical messenger to regulate growth. How plants sense and use sugars is important to a better understanding of the basic biology of plants and may lead to improved crops. This research investigates an encoded regulator of a G-protein signaling protein that has been identified as a D-glucose sugar sensor and that mediates plant growth in the plant model system Arabidopsis thaliana. Nicole Leahy (minor in Genetics/Mayfield/Zoology and Genetics/Ph.D. in BCB). I'm a postdoctoral fellow at the Jackson Laboratory doing what postdocs do; research in hopes that I get enough first author papers to have a career when this position ends. I'm divided across three projects. The most productive one is studying the properties of gene deserts. The other two are constructing a fine scale map of linkage disequilibrium in mice and identifying genomic features associated with recombination hot spots. Ruizhong Shen (Ph.D./Miller/Plant Path) after completion of a postdoc at University of Alabama - Birmingham (a top institution for virology research), he joined the Department of Medicine, University of Alabama at Birmingham, as an Instructor (2006) and is now an Assistant Professor (2008). He and his family often talk of Ames and the people they still know here. Jacqueline Jackson (Ph.D./Miller/Plant Pathology) accepted a faculty position (assistant professor) at Tuskegee University in Alabama and taught genetics to undergraduates this fall. This summer she went to Bangladesh visiting scientists at IIRD (The Institute of Integrated Rural Development) to teach them how to do sweet potato tissue culture and micropropagation. One of the IIRD goals is to eradicate poverty and the sweet potato will be used as a snack to feed children in the region. Liang Guo (Ph.D./Miller/Plant Path) is working for Monsanto in St. Louis as a bioinformaticist. Suqin Cai (Ph.D./Lashbrook/Horticulture) is working for Mendel Biotechnology, Inc. and is a member of group called Expression Profiling System Biology. This located in California. She is also completing a distance education degree in Statistics (MS) at Iowa State.

Greg Park (Ph.D./Carpenter/VMPM) and Cari (Steelman) Park (MS/Reecy/Animal Science) were married September 2007. Carrie started working, via computer from Minnesota, for Jim Reecy, Animal Science, this past October after almost 3 years at the University of Minnesota. She is now the curator for the AnimalQTL Database and she is working on the development of a trait ontology for livestock. Barbara Szlendakova (M.S./Henderson/Zoology and Genetics) sends good news. She and David Wilts are expecting their first child, a daughter, to be born on March 9, 2008. Oh, and they got a new puppy and bought their first home too in Milwaukee, WI! Kimberly (Petry) Hammer (Ph.D./Birt/FSHN) is now a post doc at the School of Pharmacy at the University of Wisconsin. Amanda Hemmingsen (MS/Serb/EEOB) is a Clinical Lab Scientist in Cytogenetics at the University of Minnesota Medical Center-Fairview.

Jamie A. O'Rourke (Ph.D./Shoemaker/Genetics) is a postdoc for the Agricultural Research Service, USDA at the University of Minnesota working with Debby Samac. She has a 2 year appointment with the option of extended funding for two additional years. Her main research focus is to identify transcription factors involved in remodeling cell wall composition of Medicago truncatula and Medicago sativa. She is also characterizing gene expression profiles of plants infected with Powdery Mildew and continuing collaborative projects established while working at Iowa State.

Corinne Nielsen (M.S./Ambrosio/Zoology & Genetics) is currently in the Ph.D. program at Harvard Medical School and is studying brain development in the Genetics department. She and her husband Andrew are expecting their first baby (a girl!) in January. Ruying Chang (Ph.D./Peterson, P/Agronomy) is teaching school in Washington D.C. and says to “Say hello to all old friends there (Ames) and best wishes to all in the Genetics program.” Nguyen Phan (Ph.D./Bassham/GDCB) is a postdoctoral fellow in the Jones lab in the Biology Department at University of North Carolina - Chapel Hill. He writes: “I recently started here so not much to report. However much is missed in terms of Ames and Iowa State University. Aside from the area which you already know, the accessibility of resources involved in research and interaction with people provided at ISU rivals that of bigger named universities. You never know what you are missing until you realize you don’t have it. The atmosphere and interdepartmental programs ISU provides a great place to further science as a whole. Somebody has to say it, might as well be me.” Kim Hammer (Ph.D./Birt/FSHN) is a postdoc in Dr. Paul Marker's laboratory at the University of Wisconsin-Madison in the School of Pharmacy. Her research involves a candidate prostate cancer oncogene identified in her mentor's laboratory using the Sleeping Beauty transposon system in mice. She is also developing a high-throughput model of prostate cancer that will be used to test prostate cancer oncogenes and tumor suppressor genes alone or in combination. Megan Harvey (M.S./Scott/Agronomy) is working for Monsanto and is a member of the Insect Control Discovery team located in Chesterfield, MO.

Lisa Haney (M.S./Scott/Agronomy) is an Associate Scientist for Syngenta Seeds, Inc. in Bloomington, IL. She works on maize traits in the Product Development Division. Her group plans and evaluates all of the field trials for all new input traits for corn in addition to a few output traits as well. On a personal note, she is getting married in February 2009. Milan Joksimovic (Ph.D./Tuggle/Animal Science) is a postdoctoral fellow at the Northwestern University, Department of Neurology, Feinberg School of Medicine in Chicago, IL, in the laboratory of Dr. Raj Awatramani. His work is related to a question on how the neuronal cell fates are specified in the midbrain and hindbrain during development. Basically, he is continuing work on development of the central nervous system that he initially started at Iowa State University in the laboratory of Dr. Chris Tuggle. Milan has a six year old son Luka and a wife Aleksandra (who is also a postdoc at Northwestern University).

ISU ALUMNI CENTER

The ISU Alumni Center is the realization of a 30-year dream, recently built at 420 Beach Avenue near the Iowa State Center in Ames. https://www.isualum.org/en/alumni_center/ The $11.2 million, 34,500-square foot facility is the new home of Iowa State University's alumni, students, and friends and offices for the staff and programs of the ISU Alumni Association. The Center serves as an enhancement to student life, alumni homecomings, and community and alumni engagement. It is made possible thanks solely to the generous support of Iowa State University's alumni and friends, especially lead donors Roy ('57 AG JL) and Bobbi ('06 Honorary Alumna) Reiman. The ISU Alumni Center includes a library, ballroom, offices, meeting rooms, and a multipurpose office and activity space for the Student Alumni Leadership Council. IG Students who graduated during 2008 Xiaomin Bao (Ph.D/Johansen/GDCB), Jacquelyn Jackson (Ph.D./Miller/Plant Pathology), Benny Mote (Ph.D./Rothschild/Animal Science), Nguyen Phan (Ph.D./Bassham/GDCB), Shengqiang Zhong (Ph.D./ Jannick & Dekkers/Agronomy), Brian Campbell (MS/Hannapel/Horticulture), Amanda Hemmingsen (M.S./Serb/EEOB), Qiaohui Lin (M.S./James & Myers/BBMB), Kimberly (Petry) Hammer (Ph.D./Birt/FSHN), Pingsha Hu (Ph.D./Wise/Plant Pathology), Jamie O’Rourke (Ph.D./Shoemaker/ Agronomy), James Peterson (Ph.D./Phillips/Vet Micro & Preventive Medicine, (Keri (Andersen) Davis (MS/Coffman/GDCB), and Ramesh Koukuntla (Ph.D./Link/GDCB).

Present Students News

Tonia Schwartz (Bronikowski/Powell-Coffman/EEOB) took part in the Computational Phylogenetics Course at the National Evolutionary Synthesis Center. From this intensive course/hands-on workshop, Schwartz gained a more thorough understanding of the programming languages (Perl and SQL), which are necessary skills needed to complete her PhD dissertation. Schwartz's PhD research is based in comparative genomics and population genomics focusing on the evolution of gene networks and particularly the evolutionary role of 1) gene duplication events, 2) regulatory elements, and 3) alternative splicing mechanisms. This course has provided Schwartz with alternative methods to analyze her data through scripts rather than limiting herself to the available package methods and

furthermore is allowing her to develop new methods for data analysis. Melissa Hillwig, Nicole Lebrasseur, Pamela Green, and Gustavo MacIntosh were featured on the cover of the Molecular Genetics and Genomics journal, Volume 280, Number 3, September 2008, pp. 249-261(13). GUS staining of a flower from a transgenic Arabidopsis plant carrying an RNS1promoter-GUS construct (B-glucuronidase gene). RNS1 is a secreted ribonuclease, and in normal conditions (no stress), it is only expressed in flowers. With this assay they were able to determine that the expression is limited to anthers, which was unexpected. "Impact of transcriptional, ABA-dependent, and ABA-independent pathways on wounding regulation of RNS1 expression" (MGG 280/3), Figure 7e. Wendy Woods Sparks (Bonning/Entomology) and Michael Sparks had a baby girl, Brynn Olissa Sparks (the BOS!) on Saturday, September 6.

Becky Weeks took genetics when she was a junior in high school and was hooked. So hooked, in fact, that she repeated the class her senior year, just for fun. Then she came to Iowa State to learn more. “I wasn’t sure if I wanted to go into plant or human genetics, but I wanted something that kept me in the Midwest. I knew if I went into a health-related field, I’d probably have to go to a coast to get a job,” says Weeks, who is a graduate student in genetics researching ear and tassel development in corn.

Weeks began researching corn genetics as an ISU junior when Erik Vollbrecht, GDCB, gave her the chance to do hands-on research. She continued the research in the college’s Science with Practice program, a course that links faculty mentors with students and provides research experience, credits and a paycheck. “Science

with Practice was great because it allowed me to become more autonomous,” Weeks says. “I learned how to look at my results and decide the next step.” It didn’t take long for Weeks to decide to continue her research as a graduate student. “I graduated on May 5 and started graduate school on May 7. I wanted to get started right away,” Weeks says. “This isn’t work to me – it’s what I want to do.” “The key for succeeding in this field is to make things easier and more profitable for the farmer,” Weeks says. Reprinted with permission and editing from STORIES in Agriculture and Life Sciences at Iowa State University, Fall 2007 By Barbara McBreen

Selected IG Student Publications

Schwartz, Tonia S, and Stephen a Karl. 2008. Population Genetic Assignment of Confiscated Gopher Tortoises. Journal of Wildlife Management 72: 254-259.

Flagel, Lex E., Ryan A. Rapp, Corrinne E.Grover, Mark P. Widrlechner, Jennifer Hawkins, Jessie L. Grafenberg, Inés Álvarez, Gyu Young Chung, and Jonathan F. Wendel. Phylogenetic, morphological, and chemotaxonomic incongruence in the North American endemic genus Echinacea. American Journal of Botany, In Press.

McGaugh, S. E. 2008. Color variation among habitat types in the spiny softshell turtles (Trionychidae: Apalone) of Cuatrocienegas, Coahuila, Mexico. Journal of Herpetology 42:347-353.

Martinez, P., Ezaz T., Valenzuela, N., Georges, A., and Graves J.A.M. 2008. An XX/XY heteromorphic sex chromosome system in the Australian chelid turtle Emydura macquarii, a new piece in the puzzle of sex chromosome evolution in turtles. Chromosome Research

Lawrence M., D. Cook, E-K Lee, HL Babka, ES Wurtele. (2008) Explorase: Multivariate exploratory analysis and visualization for systems biology. Journal of Statistical Software. 25 (9).

Flint-Garcia Sa, Bodnar AL, Scott MP. Wide Variability in Kernel Composition, Seed Characteristics, and Zein Profiles Among Diverse Maize Inbreds, Landraces, and Teosinte. (Submitted to Theoretical and Applied Genetics in October 2008).

Gorbach, DM, Hu Z-L, Du Z-Q and Rothschild MF (2008). SNP discovery in Litopenaeus vannamei with a new computational pipeline. Animal Genetics. Published online: Sept 26, 2008

Campbell, BA, Hallengren, J. Hannapel DJ. 2008. Accumulation of BEL1-like transcripts in solanaceous species. Planta 2008 Nov; 228(6):897-906. Epub. 2008 Aug 27.

Cheeseman, JH, Kaiser MG, Ciraci C, Kaiser P, Lamont SJ. Breed effect on early cytokine mRNA expression in spleen and cecum of chickens with and without Salmonella enteritidis infection. Deve Comp Immunol. 2007; 31(1): 52-60.

Hillwig MS, LeBrasseur ND, Green PJ and MacIntosh GC (2008) Impact of transcriptional, ABA-dependent, and ABA-independent pathways on wounding regulation of RNS1 expression. Molecular Genetics and Genomics 280: 249-261, June 2008.

Haen, K.M., F.B. Lang, SA Pomponi & D.V. Lavrov. 2007. Glass Sponges and Bilaterian Animals Share Derived Mitochondrial Genomic Features: A Common Ancestry or Parallel Evolution? Mol Biol Evol 24: 1518-1527.

Yu XF, Li L, Li L, Chory J. and Yin YH (2008). Modulate of Brassinosteroid-Regulated Gene Expression by Jumonji Domain-Containing Proteins ELF6 and REF6 in Arabidopsis. Proc Natl Acad Sci USA 105:7618-7623.

Kim W-I, Cho Y-I, Liu S. Kinyon J, Yook-J 2008. Multiplex real-time PCR test to aid the diagnosis of calf diarrhea. Proceedings, Annual Meeting of American Association of Veterinary Laboratory Diagnostians, page 69.

Yu F, Liu X, Alsheikh M, Park S, Rodermel S. (2008). Mutations in Suppressor of Variegation1, a factor required for normal chloroplast translation, suppress var2-mediated leaf variegation in Arabidopsis. Plant Cell 20, 1786-804.

Birt, DF, Widrlechner M, LaLone CA, Wu L, Bae J, Solco Avery, Kraus, GA, Murphy PA, Wurtele, ES, Leng Q, Hebert, SC, Maury W, and Price J. Echinacea in infection. The American Journal of Clinical Nutrition 2008, 87, (2), 488S-292S.

Puttamreddy, S., M.D. Carruthers, M. L. Madsen, and F.C. Minion 2008. Transcriptome analysis of organisms with food safety relevance. Foodborne Pathog Dis 5:517-29.

Ru Y, Wang B, and Brendel V. 2008. Book Chapter: Spliceosomal proteins in plants. In Nuclear pre-mRNA processing in plants. Reddy & Golovkin (eds.). Current Topics in Microbiology and Immunology 326, 1-15.

X Zhao, ZQ Du, MF Rothschild. Comparative Gene Discovery for canine cryptorchidism in Siberian Huskies. Plant and Animal Genome XVII Conference, January 10-14, 2009. Abstract.

Anantharam V, Kaul S, Song C, Kanthasamy A, Kanthasamy AG. Pharmacological inhibition of neuronal NADPH oxidase protects against 1-methyl-4-phenylpyridinium (MPP+)-induced oxidative stress and apoptosis in meencephalic dopaminergic neuronal cells. NeuroToxicology, Volume 28, Issue 5, September 2007, pages 988-997.

Uthe JJ, Royaee A, Lunney JK, Stabel TJ, Zhao SH, Tuggle CK, Bearson SM. Porcine differential gene expression in response to Salmonella enterica serovars Chloeraesuis and Typhimurium. Mol Immunol. 2007, 44-2900-14.

Swanson-Wagner RA, Y Jia, R DeCook, LA Borsuk, D Nettleton, PS Schnable (2006). All possible modes of gene action are observed in a global comparison of gene expression in a maize F1 hybrid and its inbred parents. Proceedings of the National Academy of Sciences, 103: 6805-6810.

Wang X and Lavrov D. (2007). Mitochondrial genome of the Homoscleromorph Oscarella carmela (Porifera, Demospongiae) reveals unexpected complexity in the common ancestor of sponges and other animals. Mol. Biol. Evol. 24: 363-373.

X Zhao, Z-Q Du, MF Rothschild, et al. Biological Candidate Gene Analyses identify that HOXA10, ZFPM2 and MMP2 are associated with scrotal hernias in pigs. American Journal of Veterinary Research, in press.

Jennifer Young (Animal Science/Dekkers). My research pertains to the residual feed intake selection project in swine. Residual feed intake is a measurement of feed efficiency in which you measure a pig's actual feed intake using electronic feeders and subtract the estimated feed intake based on a curve that accounts for growth and backfat depth. In regards to this selection project, I am looking specifically at feeding behavior traits, sow performance, and scale behavior and how they are related to selection for residual feed intake. Greg Peiffer (Agronomy/Shoemaker). My studies have been focused on the molecular basis of abiotic stress of soybean, specifically Iron Deficiency Chlorosis (IDC) and the regulatory characteristics of genes potentially associated with IDC. IDC is a major problem for soybean growers in the Mid-west and the effects are felt worldwide. I feel that controlling diseases in local crop species will result in higher economic strength of Iowa farm families.

Charles Kanobe (BBMB/MacIntosh) My project is about Fatty acid signaling in soybean under multiple biotic stresses. I specifically look at fatty acid changes in foliar and storage tissues of low and normal linolenic acid soybeans to gain an understanding of effects of microsomal Fatty Acid Desaturase (FAD) mutations on plant fitness, since linolenic acid plays a key role in plant defenses. Mutations in the microsomal FAD resulted in the development of the low linolenic acid soybean lines.

Read more about IG students at: http://www.genetics.iastate.edu/newslet.html

IG Faculty in the News Exploring the Mechanisms of Cancer Metastasis Clark Coffman, GDCB, received funding from the Roy J. Carver Charitable Trust based in Muscatine, Iowa, to explore the mechanisms of cancer metastasis. (Photo credit: Dave Gieseke, ISU). Relatively little is known about how cancer cells become metastatic. Yet, it is the migration of tumor cells away from the primary tumor and their colonization of secondary sites such as the brain, lungs, bone, liver, and lymph nodes that are the cause of 90% of cancer deaths. This is why metastasis is the most feared and life-threatening aspect of cancer. The award will fund investigations into how cells sense and respond to environmental cues, initiate migratory movements, and home in on distant locations. It will also investigate mechanisms of programmed cell death that are also disrupted in cancer cells. Clark uses the germ cells of the fruit fly, Drosophila, as a model for these developmental genetic studies. During normal development, the primordial germ cells transition from a non-motile to a migratory state, move across epithelial layers and through multiple tissues to locate and colonize the somatic cells of the forming gonads. The similarities between the behaviors of cancer cells and developing primordial germ cells are more than superficial. Germ cells and cancer cells both use cell surface G protein-coupled receptors to sense the environment around them. Also, the target tissues release attractive signals that result in the germ cells or cancer cells migrating towards the source of the ligand. It is this release of attractive ligand that partially explains why secondary sites of tumor formation are not random. In addition, current thinking about the etiology of cancer metastasis is that it involves the abnormal reactivation of latent cellular migration programs that are part of normal animal development. Therefore, a better understanding of what controls transitions to migratory states, the molecular mechanisms of cell migration, and the regulation of programmed cell death in normal development will provide information relevant to the metastatic behaviors of cancer cells. $18.5 Million Grant for Biorenewable Chemicals Research Center

Several researchers will be involved in the National Science Foundation award to Iowa State and its research partners of a five-year, $18.5 million grant to establish the NSF Engineering Research Center for Biorenewable Chemicals based at Iowa State.

Basil Nikolau, the Frances M. Craig Professor in the departments of biochemistry, biophysics and molecular biology and food science and human nutrition, will be the deputy director.

The leadership team of the new facility includes, front row, left to right, Tonia McCarley, Adah Leshem-Ackerman, Basil Nikolau, Jackie Shanks and, back row, Derrick Rollins, David Oliver, Brent Shanks and Raj Raman.

Photo by Bob Elbert. Article by Mike Krapfl, News Service

Turtles alter nesting dates due to temperature change

Fred Janzen, a professor in ecology, evolution and organismal biology, has studied turtle nesting habits and also accumulated research going back decades in order to track the habits of the turtles to find out when they make nests and lay eggs. "The results have been astonishing," says Janzen. "In some cases such as regional populations of red-eared sliders, they are now nesting three weeks earlier than they did in the early 1990s. That is the fastest response to climate change of any species that I know of."

The turtles that changed their nesting habits were not only young turtles that are nesting for the first time, said Janzen, but were also older turtles that were changing their habits. This trait, called plasticity, helps animals alter their behavior in the short term until inherited behavior takes over. "What we found was that in the late 1980s, painted turtles started nesting in early June, now it is on the order of 10 days or more earlier," said Janzen. "These behaviors are showing how the plasticity of the species is helping them survive, but we are wondering what the limit is to their ability to adapt."

Janzen's research took a broad look at the entire species and not just turtle populations that are on the fringe of where the animals can live. Janzen feels this aspect of the collaborative study gives the results added credibility. Janzen and his collaborators studied mud turtles, sliders, snapping turtles and painted turtles that live in South Carolina, Nebraska, and along the Mississippi River between Iowa and Illinois. An aspect of the study that surprised Janzen was the gender of the offspring. The gender of turtle offspring, as with many reptiles, is typically determined by the temperature of the ground where they lay their eggs. Dan Kuester, ISU News Service, November 6, 2008

The Promise of Gene Silencing to Fight SCN-Soybean Cyst Nematode

"The beauty is we know what some of these proteins are doing and are now able to apply the knowledge to make plants more resistant. We're able to make educated guesses at how to kill the worm. Gene silencing appears promising. We know which genes to target; we target the genes that secrete specific essential proteins into the plant." --Thomas Baum, chair and professor of plant pathology, quoted in the October 2008 issue of the USB Issues newsletter, a monthly report of the United Soybean Board on issues affecting the soybean checkoff. Baum and collaborators at other universities form the USB-funded SCN Parasitism Gene Group that is studying the mechanism the soybean cyst nematode uses to infect and establish a feeding

site in the soybean root.

Studying contagious diseases from many different angles.

Lisa K. Nolan, Professor and Associate Dean of Academic and Student Affairs, and Nancy Cornick, an associate professor in VMPM, focus on bacterial diseases of production animals, including their effects on animal and human health and food safety. The long term goals of their research are to establish the molecular basis of virulence and antimicrobial resistance of different types of Escherichia coli and to apply this knowledge to disease control. Nolan’s research team seeks to understand how extraintestinal pathogenic E. coli (ExPEC) causes diseases such as peritonitis, colispeticemia, air sacculitis, and cellulites of poultry and urinary tract infection, septicemia, and neonatal meningitis in human beings. ISU Biotechnology Update May 2008

New Research Video on the Web: Harvesting Wood as a Biofuel

Rick Hall, forestry professor and new interim chair of the natural resource ecology and management department (NREM), researches the selection of genetically improved cottonwoods, aspens and other tree species for use in the biofuels and new products. More: http://www.ag.iastate.edu/research/videos/?id=3.

National Science Foundation Funds $2.1 Million Soybean Disease Project Identifying genes essential for the soybean plant’s defense against three major diseases will be the aim of a new $2.1 million research project led by Iowa State University. “We expect that information resulting from the research will help improve soybean cultivars for disease resistance by accelerating plant breeding programs and by enabling the engineering of new disease resistance traits,” said Steve Whitham, associate professor of plant pathology. Whitham leads the four-year project that earned a $2.1 million National Science Foundation grant. The research is important for the state of Iowa, which leads the nation in soybean production. Nationally, soybean yield losses linked to diseases are estimated to cost farmers more than 400 million bushels every year. Even though soybean is the nation’s second most economically important crop (behind corn), scientists know little about specific genes in charge of defending the soybean plant against diseases. The ISU project will focus on genetic resistance against three important soybean pathogens: soybean mosaic virus, Asian soybean rust and soybean cyst nematode. To help study gene function, the scientists will use an approach called virus-induced gene silencing (VIGS). The technology uses a virus equipped with a small segment of genetic material matching a soybean gene of interest. When the virus infects the soybean plant, the plant recognizes the invader and begins defending itself. In the process, the plant is tricked into destroying its own genetic material, but only the part that matches what is carried by the virus. This prevents the gene of interest from making its intended product—in effect, silencing it. When a gene is silenced, scientists can see how well the plant fares against a certain disease without the gene’s help. Brian Meyer, Agriculture and Life Sciences Communications

Animal Scientist Part of Bioinformatics Standardization Effort

James Reecy, Animal Science, is part of an international effort to harmonize standards for high-throughput biology. More than 20 grass-roots standardization groups have combined to form the "Minimum Information about a Biomedical or Biological Investigation" (MIBBI) initiative. The scientists' methodology for the initiative was described in an article published Aug. 7 in the journal Nature Biotechnology. More: http://www.mibbi.org. The Nature Biotechnology article can be found at: http://www.nature.com/nbt/journal/v26/n8/full/nbt.1411.html.

Iowa State Crop Genomics Lab Largest in Nation

The largest cluster of plant databases in the nation has a new home, the Crop Genome Informatics Laboratory, a USDA-Agricultural Research Service (USDA-ARS) and Iowa State University facility. The building housing the center was recently renovated and formerly known as the Agronomy Laboratory. The center houses 25 researchers from both Iowa State and the USDA-ARS Corn Insects and Crop Genetics Research Unit under one roof. Previously the scientists were scattered in different offices across campus. The 8,000 square-foot building now includes the MaizeGDB (Maize Genetics and Genomics Database), PlantGDB (Plant Genome Database), Soybase and the Soybean Breeder's Toolbox and the PLEXdb (Plant Expression Database). Each database is a tool that provides biological information as well as gene data about specific agronomic traits. The databases are available to researchers on campus and around the world. The goal of the center is to enhance communication and collaboration among scientists says Carolyn Lawrence, a USDA-ARS research geneticist and assistant professor in genetics, development and cell biology in the College of Agriculture and Life Sciences. Lawrence, who coordinates the facility, said there are advantages to having scientists studying similar topics under one roof. “Things are happening a little faster,” Lawrence said. “There's something to be said about using technology to communicate but it's easier to communicate now that we are all in one building.” Barbara McBreen, Communications Service News Release October 30, 2008 Carolyn Lawrence (left) Randy Shoemaker (right)

Tiny Gene Discovered Hiding in a Major Family of Plant Viruses

In an international collaboration, researchers in Allen Miller's lab in the Department of Plant Pathology have shown a tiny gene exists in all members of the largest family of plant viruses. Without this gene, the virus is harmless. The discovery was published recently in the Proceedings of the National Academy of Sciences. The work was based on a prediction made in the lab of John Atkins of University College Cork, in Cork, Ireland. Atkins is a world-renowned expert in the field of "recoding" - genetic decoding events that don't follow the normal rules. A researcher in Atkins' lab, Andrew Firth, turned to computers to discover tiny genes hidden in the sequences of viruses. Firth set his program to work crunching through the genome sequences of the largest and most devastating family of plant viruses - potyviruses. The computer output soon revealed what appeared to be a new gene that overlaps with a much larger and well-known gene in these viruses. At this stage the possible gene was identified simply as a stretch of nucleotide bases in the viral RNA uninterrupted by a "stop" signal and hence known as an open reading frame or ORF. Firth said he thought this was a "pretty interesting potyvirus ORF" so he called it by the acronym pipo and the name stuck. This is where Iowa State entered the picture. Firth temporarily joined the lab of Allen Miller, who is an expert on plant virus recoding, to obtain the necessary materials and expertise needed to investigate plant viruses. This Irish-Iowa State team used a potyvirus called Turnip mosaic virus (TuMV) that had been engineered to express a protein that turns infected plant parts fluorescent green. It was brought to Iowa State previously by Steve Whitham, associate professor of plant pathology. The researchers altered the sequence of the virus genome so the protein synthesis machinery of the plant cell could not make any protein from the predicted pipo minigene, while all the well-known large genes it overlaps with still could be translated normally. These small mutations "killed" the virus.

Jack Girton, BBMB, was promoted to University Professor. Girton’s many contributions in his 23-year career at Iowa State have helped shape the university’s academic structure and redefine how the university deals with complex issues of faculty conduct, academic organization and research management. He is an award-winning teacher and successful research scientist and helped develop the undergraduate genetics major into a program that attracts students from around the globe. Inside Iowa State September 12, 2008

Great Ames Adventure Race Gustavo MacIntosh, Alan Myers, and Phil Becraft win in their division the GAAR: Great Ames Adventure Race. Phil ran the 5K, Alan kayaked two figure 8’s at Ada Haden Heritage Park, and Gustavo biked 15 miles. The race was held Sunday, August 31. Individuals could participate in all three legs of the event or participate as part of a team. Proceeds benefited the Skunk River Paddlers, Ames Area Running Club and the Friends of Central Iowa Biking. Jonathan Wendel, IG graduate students Corrinne Grover and Lex Flagel, and their research on the cotton genome were featured in an NSF movie describing the benefits gained by plant genomics research. http://www.plantgenomesecrets.org/

IG Faculty Holding Endowed Professorships and Chairs Dorian Garrick: Jay Lush Endowed Chair in Animal Breeding and Genetics Anumantha Kanthasamy: W. E. Lloyd Chair in Neurotoxicology Thomas Lubberstedt: K. J. Frey Chair in Agronomy Basil Nikolau: Frances M. Craig Professorship Max Rothschild: Ensminger Chair Patrick Schnable: Baker Professorship in Agronomy Ravindra Singh: John G. Salsbury Endowed Chair in Veterinary Medicine Thomas Peterson: Pioneer Hi-Bred Chair in Molecular Biology of Maize. New IG Faculty member: Thomas Lubberstedt, Agronomy, is using molecular approaches to better understand complex characteristics such as forage quality, disease resistance and bioenergy-related traits in crop plants. These activities aim at development and application of molecular markers to more efficiently exploit genetic diversity in breeding new crop varieties. (ISU Biotechnology Update, January 2008). New IG Faculty member: Ravindra Singh, Biomedical Sciences, is conducting research on alternative splicing, a process that allows synthesis of multiple proteins from a single gene. The process of alternative splicing is associated with spinal muscular atrophy, Alzheimer’s disease, Parkinson’s disease and other neuronal and mental disorders. Alternative splicing has been linked to various cancers, cardiovascular disease, obesity and diabetes. Singh’s research could lead to a better understanding of these diseases and provide novel targets for therapies. (ISU Biotechnology Update, January 2008). A recent article: Nucleic Acid Research (NAR) publication from Singh Group in collaboration with the Australian group. The article describes the identification and characterization of a novel isoform of a housekeeping protein that makes all selenium proteins in the cell. http://nar.oxfordjournals.org/cgi/reprint/gkn829v1

2007-2008 IG Teaching Excellence Award Interdepartmental Genetics first year graduate students nominated Dr. Yanhai Yin, GDCB, for the 2007-2008 IG Teaching Excellence award. Twenty-one instructors from six different departments teach IG core courses and seminars. This award is significant because IG strives to provide a positive first year experience for our new graduate students. Dr. Yin teaches in both GDCB 510 (Transmission Genetics) and GDCB 511 (Molecular Genetics). Eight faculty were nominated by the students; Dr. Yin received the highest number of nominations. One student best summed up their interactions with Dr. Yin: “He was my favorite lecturer … because he

expressed a genuine care for the students’ understanding of the material. He assigned homework that stretched our minds and understanding, but always helped in studying for the exams. I had the same rewarding experience in both (of the classes).” Dr. Yin was presented with a framed certificate and a Laser pointer. Max Rothschild, Animal Science, received the Bouffault International Animal Agriculture award from the American Society of Animal Science. The award recognizes ASAS members who have made meritorious scientific contributions through the teaching, research, or other service to animal agriculture in at least one developing area of the world over the past 5 years.

Anumantha Kanthasamy, Biomedical Sciences, has been awarded the Clarence Hartley Covault Distinguished Professor in Veterinary Medicine award. An internationally renowned neuroscientist, Kanthasamy’s research focus is the cellular and molecular mechanisms of Parkinson’s disease and other neurodegenerative disorders, and the development of novel therapeutic agents to treat such disorders. He also studies mechanisms underlying prion diseases such as Kuru and Jacobs/Kreutzfelt disease. His laboratory has become a major site for training of Ph.D. students in the field of neurotoxicology. Basil Nikolau, professor in the Department of Biochemistry, Biophysics and Molecular Biology and in the Department of Food Science and Human Nutrition, was presented with the Frances M. Craig Professorship. Nikolau's research has focused on biochemical and genetic regulation of plant metabolism, and plant metabolic engineering. His work explores the future of metabolic biology to improve oils, starches and proteins from crops for bioenergy, food and feed uses. He also leads advances in improving production of bio-based lubricants made from soybeans. He serves as the director of the Center for Metabolic Biology. The Frances M. Craig Professorship was established through the Craig Family Fund. The Craig Family Fund allows the president to place special emphasis on faculty support. It provides faculty with funds for research and honors outstanding individuals. The fund was established through a bequest from Frances M. Craig, combined with past gifts from other family members. Roger Wise, plant pathology and USDA collaborator, and former graduate student Brent Kronmiller developed software called TEnest, a computer software tool to identify the location and history of troublesome transposable elements in a plant’s genome. To date, the tool has been applied to four agriculturally important grains -- maize, barley, wheat and rice. The work was funded by USDA's National Research Initiative.

Maize Research Leaps Ahead with Early Jumping Gene Discoveries Two premier researchers serving on the faculty at Iowa State University for 50 years are pioneering contributors to the field of maize cytogenetics. Research discoveries through the course of their careers in the area of transposon biology by Peter A. Peterson, professor in the Department of Agronomy and Donald S. Robertson, emeritus professor in the Department of Genetics, Development and Cellular Biology have helped to usher in the genomics era to plant biology.

Their ground-breaking research on these genetic elements that can hop around the genome, reshape it and alter specific gene activity has spurred a new understanding about genomes and offered up some extremely valuable genomic tools. Peterson and Robertson were contemporaries and in the case of Peterson, a colleague of Barbara McClintock whose discovery of the transposable elements Dissociator (Ds) and Activator (Ac) in maize in 1947 earned her the Nobel Prize in Physiology or Medicine in 1983. Transposons, or jumping genes are segments of either DNA—classical transposons or RNA-based retrotransposons that are highly mobile within and between chromosomes. They have captured the attention of geneticists in every sub-discipline from molecular to evolutionary genetics. “Seventy-five percent of the corn genome is mobile,” says Peterson “and fifty percent of the human genome.” The rice genome is made up of twenty percent transposable elements. Regardless of percentages, transposons appear to be ubiquitous, found in eukaryotes and prokaryotes to varying degrees.

Geneticists Donald S. Robertson and Peter A Peterson

Jay Lush Endowed Chair in Animal Breeding and Genetics

Dorian Garrick, Animal Science, was named the first Jay Lush Endowed Chair. Garrick’s past research exposed him to the genetic improvement of a range of animal species and a variety of traits. “Animal breeding is using knowledge of genetics to improve populations,” he says. “There is a tremendous amount of work being done in animal genomics, and knowledge being generated, that needs to be transferred into animal breeding.” At Iowa State, Garrick sees the greatest opportunity in beef cattle. He is a director of the National Beef Cattle Evaluation Consortium, which is responsible for the development of selection tools. “The critical mass of universities

working on beef cattle has declined,” Garrick says. “That’s sad, given the value of the beef industry. I feel an obligation for Iowa State to pick up the reins and assist with beef cattle improvements.” In particular, Garrick says he hopes to establish a closer relationship with the American Angus Association. “Iowa State has a long history of research and collaboration with Angus breeders,” he says. “We have a herd of 450 registered Angus cows and I look forward to making use of these animals in my research.” (By Susan Thompson, Fall 2007, Stories; the ornate desk above was originally a piano that belonged to Jay Lush)

Does the Spindle Matrix Exist? Two Iowa State researchers are making headway in convincing others that the "spindle matrix" exists. Kristen and Jorgen Johansen, both professors of biochemistry, biophysics and molecular biology, have identified four "matrix protein candidates" and are using mutant fruit flies to confirm the proteins' function in cell division. It's basic science with far-reaching applications into human health. "Cell division is at the fundamental crossroads of life," Kristen said. Jorgen added that most types of cancer and some birth defects occur because "something had gone wrong

with cell division." For decades scientists have known about the spindle, so called because of its shape. A spindle is an arrangement of protein filaments that are needed to segregate a dividing cell's two sets of chromosomes. Some 40 years ago it was proposed the spindle needed a matrix in order to move the chromosomes. However, not all cell biologists concurred. The Johansens' matrix research, which has received National Science Foundation funding, was highlighted in a Nov. 30, 2007 article in the journal Science. "We have the proteins identified by virtue of where they go and the dynamics of their distribution," Kristen said. "The real key will be to get down to the function of these molecules." "We have enough molecules - more than we can handle," Jorgen said. "So the idea now is to show that this matrix does what it's supposed to do, which is to stabilize the spindle and be involved in generating the forces behind chromosome movement." Jorgen added that scientists are curious to know how the chromosomes are pushed apart. "How the proteins actually exert the force, nobody really knows. Using higher-resolution instrumentation, they saw a "spindle-like structure" forming in the nucleus. It surprised them. "It was all strange," said Jorgen, "because there was nothing in the literature about things that reorganized in the nucleus to form a spindle." "It's a good illustration of the value of basic research," Kristen noted. "You can find interesting things and follow them and make some significant advances." Around LAS

Biological video game “Meta!Blast" the new educational 3D video game being created by a research team headed by Eve Syrkin Wurtele, GDCB. The team also includes Diane Bassham, GDCB, Julie Dickenson, ISU computer engineer , Steve Hernstadt, artist and game designer, and graduate students and undergraduate students from a variety of academic disciplines. Meta!Blast" is designed to give high school and college students an interactive approach to understand the inner workings of a

plant cell. The game will be distributed as DVDs to universities and high schools. It will also be utilized with introductory college biological courses at Iowa State.

Iowa State University and Ames The university has added new signage to welcome Iowa Staters and guests to Jack Trice Field. The new

athletics logo has been placed on the back side of the stadium's scoreboard facing University Blvd. (below) Ames took part in RAGBRAI this summer and bike riders rode into Ames on Stange Avenue. Photo by Bob Elbert (photo is looking north out of campus)

(below) Campus colors near Agronomy Hall

Greene: Science is Greatest Adventure

"Science is the greatest of all adventure stories, one that's been unfolding for thousands of years as we have sought to understand ourselves and our surroundings. Science needs to be taught to the young and communicated to the mature in a manner that captures this drama. We must embark on a cultural shift that places science in its rightful place alongside music, art and literature as an indispensable part of what makes life worth living." --Brian Greene, professor of physics at Columbia University and author of "The Elegant Universe" and "The Fabric of the Cosmos" (New York Times, June 2)

A note from Linda Best wishes to all of you this holiday season from the IG graduate program. I did a little bike riding this past summer and took a couple of exercise classes at ISU this fall along with neurobiology. I have not yet graduated in biology because I am avoiding the 2nd semester of organic chemistry. We have another option now so I plan to complete the degree next fall—maybe ☺. The best part of the summer was that I took all Wednesday’s off; it was wonderful. I think I can handle retirement—5.5 years to go!