Interdepartmental Genetics Holiday Newsletter 2007 Philip W. Becraft, associate professor in the department of genetics, development and cell biology - for insights into the developmental biology of cereal endosperm—named American Association for the Advancement of Science (AAAS) Fellow. Marit Nilsen-Hamilton, professor the department of biochemistry, biophysics and molecular biology - for distinguished contributions to the fields of biochemistry, cell biology and mathematical biology—named AAAS Fellow. The College of Agriculture and Life Sciences fall semester convocation on Wednesday, Sept. 12, included a medallion ceremony for newly endowed chairs and professors, presented by President Geoffroy and Dean Wintersteen. Four faculty holding endowed positions will be honored: William Beavis, George F. Sprague Endowed Chair in Agronomy; Matt Liebman, Henry A. Wallace Endowed Chair for Sustainable Agriculture; Thomas Lubberstedt, Kenneth J. Frey Endowed Chair in Agronomy; and Max Rothschild, Marion Eugene and Audrey H. Ensminger Chair in Animal Science. At the College of Veterinary Medicine fall convocation held on Wed August 29, Dr. Anumantha Kanthasamy, Professor, Biomedical Sciences, was presented with a medallion to recognize his promotion to an endowed CHAIR in Neurotoxicology: The W. Eugene & Linda Lloyd Chair in Neurotoxicology

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The American Phytopathological Society (APS) named Allen Miller, plant pathology, a fellow in recognition of his contributions to plant pathology and the society. Dan Voytas, Professor, GDCB, has accepted a position as Director of the Arnold and Mabel Bechman Center for Transposon Research at the University of Minnesota beginning in January 2008. At its August meeting, the Regents approved the university's request to change the name of one of its centers from the Center for Designer Crops (created in 1999 as part of the Plant Sciences Institute) to the Center for Metabolic Biology. College faculty member Basil Nikolau, biochemistry, biophysics and molecular biology, is director of the center. The change reflects a desire to expand the scope of the center to support needed research in the area of metabolic networks and systems. The goal of the center is a better understanding of metabolism in order to improve the nutritional quality of agricultural products and discover new biorenewable industrial feeds. Jonathan Wendel, chair of the ecology, evolution and organismal biology department, is featured in a 23-minute, MTV-style movie about plant genomics for high school and grade school students. The "Secrets of Plant Genomes Revealed!" features three scientists who are experts studying the genomics of cotton, corn and potatoes. Wendel's segment on cotton starts out in a corn field and jumps to the largest cotton field in Iowa -- Wendel's research plants in the greenhouse on top of Bessey Hall. The National Science Foundation commissioned Minnesota Public Television to produce the video, which will soon be available on the web to schools and teachers nationwide.

Why sweet corn is sweet and other good fortunes by Teddi Barron, News Service

Associate scientist Martha James, BBMB, wraps a corn tassel

in a paper bag to capture the pollen for a very controlled pollination process (photo by Bob Elbert).

"It was on this campus as a student, June

1873, that I found myself..." When she walks by the commemorative

plaque on the boulder near LeBaron Hall, Martha James nods in agreement with the inscription that honors ISU alumnus W.T. Hornaday. A leading wildlife conservationist, Hornaday was the first director of the Bronx Zoo and a cousin of James' grandfather.

"It's probably true for me and many others at the university. It's a place where people can find themselves," James said. "And I've been lucky here in that respect."

For the past 20 years, James has created a successful scientific career at Iowa State as an associate scientist in biochemistry, biophysics and molecular biology. In the laboratory and in the cornfield, she researches how plants make starch. James was not always a scientist. Nor is she only a scientist.

Recognized as the outstanding senior woman of 1968, James graduated from the University of Colorado - with a degree in economics. She returned to her hometown of Des Moines and had three children "very close together." For the next several years, she was a stay-home mom and a community volunteer.

"When my youngest was eight, I started classes at Drake. And I knew I didn't want a master's in economics," she said.

James fell in love with the sciences. In fact, when she talks about biology, her voice drops to a hushed tone of reverence.

"Biology is fascinating. There's a wonder about it," she said. "There are so many interesting questions. So much is being discovered everyday and remains to be discovered. It's just ripe with opportunity."

She earned a master's in biology at Drake, and then came to ISU for her doctoral degree in genetics. "I'm really fortunate that it was all available for me here in central Iowa," she said.

James has built her successful career on that love of science, studying the genes that contribute to starch production and structure. Her lab group has cloned many of the genes in the starch biosynthesis pathway and helped determine their specific functions in starch production. And even though she can tell you what makes sweet corn sweet and why the Peaches and Cream variety is extra sweet (more on that later), that's not her reason for studying starch. "It's more to figure out how plants make starch," she said. "Plants produce starch and then break it down when they need more energy. It's a mechanism for plants to manage their growth and development - by the amount of energy they store. We want to understand how they do it."

In their work, James and her research partner, Alan Myers, professor and chair of biochemistry, biophysics and molecular biology, have successfully modified the biosynthetic pathway of starch to produce two different starches. One type is more slowly digested by humans. It could be useful in foods for people suffering from diabetes, and could possibly help control obesity. The other type is just the opposite - a starch that is more rapidly digestible. "The second starch has more potential benefit for industry. For example, before either ethanol or high fructose corn syrup can be produced, the starch needs to be broken down to glucose," she said. "That process requires high heat for long periods of time and adds to production costs." To develop and commercialize the two new starches, James and Myers started a biotech company, Starch Design, in the Plant Sciences Institute's Carver Co-Laboratory.

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Animal science faculty and students brought home several awards from the Joint Annual Meeting of the American Dairy Science Association (ADSA), Poultry Science Association (PSA), Asociacio Mexicana de Produccio Animal (AMPA) and the American Society of Animal Science (ASAS) held last week in San Antonio. Max Rothschild, Charles F. Curtiss Distinguished Professor in Agriculture and Life Sciences and M.E. Ensminger International Chair, was honored as an ASAS Fellow. Elisabeth Huff-Lonergan, associate professor, was given the ASAS Meats Research Award. Jack Dekkers, professor, received the Rockefeller Prentice

Memorial Award in Animal Breeding and Genetics. During the PSA meeting Sue Lamont, Charles F. Curtiss Distinguished Professor in Agriculture and Life Sciences, received the Merck Award for Achievement. The College of Agriculture and Life Sciences Newsletter, July 16, 2007 No. 460

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BioForce Nanosciences in Ames was named to the “Class of 2006” list of nanotech stocks to watch by Forbes magazine. It names BioForce among 20 nano-related companies to keep an eye on, while cautioning that inclusion isn’t a recommendation. Company founder and Chief Executive Officer is Eric Henderson, GDCB.Des Moines Register. BioForce Nanosciences, Inc., is the leading developer of nanoarray technology for biomolecular analysis. They have created innovative, proprietary methods and instrumentation for ultra-sensitive, ultra-miniaturized analysis of proteins, nucleic acids, and other biological material. Their technology is embodied in the NanoPro™ system.

Allen Miller, Plant Pathology, ran in the 111th running of the Boston Marathon on Monday, April 16, 2007. “During the run itself, we just got sprinklers now and then and we’d get gusts of wind, but I was telling a friend I thought it compared to running around Ada Haden or running up to Gilbert in February or March.”

Miller finished the 26 mile 385 yard race in 3 hours, 42.15 minutes, not his personal best, but an enjoyed experience. He said he didn’t get much sleep the night before the race. He was staying in his nephew’s apartment and the roof began leaking during the night. “It was the most fun I’ve ever had in a run,” said Miller, adding that he may try qualifying for the Boston race again. “It was sort of a dream since I was 16 years old and it was kind of a neat thing to do and it was really fun.” The temperatures were in the 40’s when the run began.

Miller qualified for the Boston Marathon at the Des Moines Marathon last October. Ames Tribune, Saturday, April 21, 2007, By Dick Kelly, Staff Writer Thomas Baum, plant pathology, was honored with the Ruth Allen Award for Innovative Research by the American Phytopathological Society. Along with two other researchers he has identified more than 100 secretions nematodes use to infect plants. The long-term goal of the research is to devise new mechanisms against these pathogens. Plant Sciences Institute Update October 2006, volume 7, Number 1. Fredric Janzen II, ecology, evolution and organismal biology, received the ISU Award for Outstanding Achievement in Teaching The International Journal of Biological Sciences has launched a special issue on Swine Genome Science to celebrate the year of the pig, which began Feb. 18. It is edited by Max Rothschild, animal science, and Zhihua Jiang, Washington State University and will cover topics including swine genome sequencing, mapping and evolution; swine whole genome linkage disequilibrium; swine biomedical model genomics; and the U.S. Department of Agriculture's efforts in agricultural animal genomics.

One Iowa State scientist is hoping to strike oil—but not by drilling wells. David Oliver, a member of the Center for Designer Crops, is researching an untapped source in plant leaves.

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“Any good plant biologist will tell you that plants produce oils primarily in the seeds,” said Oliver. “Some oil is also produced in the pollen and in the

meat around the seed.” (Photo: Bessey Hall Greenhouse. David stands over plants that have been genetically modified to have altered

oil synthesis. Photo by Bob Elbert.) But, he added, tell a plant scientist there is oil

in the leaves and they’ll likely disagree. Oliver disagreed, too, at first, with Nels Lersten, professor emeritus of botany. Lersten discovered early references to oil bodies in leaves and had also observed leaf oils in hundreds of plants himself, the old fashioned way—a slice of plant in a drop of water on a slide, under the microscope. Lersten believed a change in lab procedure caused a shift away from leaf oil observations. Around 1920, botanist stared to embed plant samples in wax, first treating them with alcohol fixatives, which dissolve plant oils.

Oliver’s first objective of the research, which is funded by a Plant Sciences Institute Innovative grant, is to prove conclusively that oils exist in the leaves of the boxwood plant. Preliminary data using three different methods show biochemical evidence of oil in boxwood leaves. To back that data up, leaf samples will be tested with high-performance liquid chromatography—mass spectrometry (HPLC-MS), at the Iowa State W.M. Keck Metabolomics Laboratory. Tests will also be confirmed in other laboratories.

If the tests prove oils exist in the leaves of boxwood, the next step is to find out how much. Oliver will also test the leaves of different species to see if some plants might produce more leaf oils than others. If it all proves true, Oliver said, the results could lead to a whole new field of research. Plant Sciences Institute Update October 2006, Volume 7, Number 1.

Coralie Lashbrook, an assistant professor of horticulture and an affiliate of the Center for Plant Responses to Environmental Stresses, studies abscission: the shedding of plant organs. Her lab takes multiple approaches to determine how plants become competent to abscise in response to environmental or developmental cues. In the case of trees, some species respond to autumn abscission signals, while others like oaks shed old leaves in spring. “We’d like to know how plants make such different decisions to shed or retain organs,” Lashbrook said.

One lab project focuses on revealing molecular events that occur in specialized cell layers called abscission zones (AZs). Upon receiving an abscission signal, cells in these rows release enzymes that digest cell walls connecting neighboring cells. Because AZs are located at the base of plant parts, AZ cell separation leads to organ detachment. “If we can capture just those abscission zone cells that separate in response to abscission signals, we can identify the molecular machinery that is causing that separation. Modifying parts of that machinery should let us improve abscission behavior in economically important plants,” said Lashbrook.

Lashbrook’s lab is currently using technology called laser capture microdissection (LCM) to get at AZ cells of Arabidopsis flowers. First developed for isolating cancer cells, LCM can pluck out individual cells or cell types from sectioned plant tissue.

Graduate student Suqin Cai optimized LCM to isolate AZ cells from flower stamens abscissing in response to pollination. From those cells Cai isolated RNA of sufficient quality and quantity to support gene chip studies of thousands of genes at a time. “The data identifies genes with potentially important roles in controlling abscission,” said Lashbrook. “We’re testing the impact of modifying their expression on post-pollination abscission. Practical applications for abscission research are plentiful.” Plant Sciences Institute UPDATE January 2007, Volume 7, Number 2.

A broad-reaching team of scientific colleagues including plant molecular biologists, immunologists, agricultural engineers, animal scientists, agronomists, risk-assessment experts and agricultural economists is conducting what in many ways is becoming the textbook example for producing biopharmaceuticals in plants.

Assembled by Kan Wang, leader of the Biopharmaceuticals Research Initiative, as well as director of the Center for Plant Transformation and professor in the Department of Agronomy and Department of Genetics, Development and Cell Biology, along with Manjit Misra, co leader of the research initiative, director of the Seed Science Center and the Biosafety Institute for Genetically Modified Agricultural Products (BIGMAP) and professor in the Department of Agricultural and Biosystems Engineering, the interdisciplinary team has successfully developed a very powerful technology and put in place a system for evaluating potential risks.

Spawned in 2001 by Wang’s former graduate student Rachel Chikwamba, now a research project director in South Africa working on methods to produce an HIV vaccine in corn, the project is loaded with biotechnology challenges, logistical, regulatory and biosafety hurdles and public opinion issues.

The present project takes the nontoxic portion of an E.coli strain responsible for causing diarrhea in humans and animals and places it into corn plants. The plant then manufactures the product and deposits it only in the seed. Once ingested, it provokes an immune response, protecting the individual from the bacterium’s harmful effects.

As the project progressed from Petri dish to test plot, Wang helped develop previously nonexistent regulatory guidelines with the USDA’s Animal and Plant Health Inspection Service (APHIS) for this type of experiment.

This year’s crop was a technological advancement in that the biopharmaceutical was produced in a male sterile corn line—essentially no pollen is produced—which reduces many safety concerns. It was grown and harvested at an Iowa State farm plot. “This is what Iowa State has been fostering,” says Wang. “They do not shy away from potentially sensitive issues; they say let’s do the science to improve the technology.”

Several College of Agriculture faculty and staff were recognized for their support of students honored at the March 25 Student Scholars and Leaders Recognition Ceremony. Students listed the following for special recognition: Don Beitz, animal science/biochemistry, biophysics and molecular biology; Adam Bodganove, plant pathology; Nancy Boury, George Brant, Joan Cunnick, Matthew Ellinwood, Doug Kenealy, Lee Kilmer, Brad Skaar and Curtis Youngs, animal science; Tom Brumm and Raj Raman, agricultural and biosystems engineering; Dermot Hayes, economics; Rita Knight, agriculture administration; Patrick Schnable and Andrew Manu, agronomy; Steve Padgitt, sociology; Lisa Schulte, natural resource ecology and management; and Lester Wilson, food science and human nutrition. Service A team of Iowa State University plant scientists and materials chemists have successfully used nanotechnology to penetrate plant cell walls and simultaneously deliver a gene and a chemical that triggers its expression with controlled precision. Their breakthrough brings nanotechnology to plant biology and agricultural biotechnology, creating a powerful new tool for targeted delivery into plant cells.

Iowa State scientists (from left) Brian Trewyn, Francois Torney, Kan Wang and Victor Lin are the first to use nanotechnology to penetrate rigid plant cell walls and deliver DNA and chemicals with precise control. (Photo by Bob Elbert)

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Gwyn Beattie (left) and graduate student Amarjyoti Sandhu..Photo by Bob Elbert.

The experiment started with a giant pickle jar. "We put several maize leaves in a jar, introduced a phenol gas and let it sit for a while. We tested the air in the jar and the phenol was all gone. There was none left," said Gwyn Beattie, professor of plant pathology.

That was good news. Phenol is a gas that causes the foul odors found in automobile exhaust, cigarette smoke, decomposing manure and emissions from burning wood, coal and municipal waste. In her experiment with the pickle jars, Beattie needed to find a measurable amount of phenol in order to test how the leaves remove it from the air. So, she began reducing the number of leaves in the jar. Holding her thumb and finger two inches apart, Beattie said, "We put three little leaves about this big in the jar and we finally had a measurable amount of phenol at the end of 24 hours. The plants really took it up."

To a microbe, a leaf is a vast landscape. To Beattie, those leaf-dwelling microbes are the basis of her research. In 1995, she came to Iowa State to study leaf-associated bacteria, including how they can be used to reduce air pollutants and odors. "The leaf surface is considered a nutrient-limited environment and I'm researching whether bacteria on a leaf can utilize the organic compounds that are air pollutants," said Beattie, who was named the Robert Earle Buchanan Distinguished Professor of Bacteriology for Research and Nomenclature in 2006.

Beattie said the process is called phylloremediation, a natural cleaning process that uses the leaves and its microflora to clean the air. "Phylloremediation is similar to rhizoremediation, which works because plants draw water to the roots

and bring soil pollutants into the area where large numbers of bacteria live. Rhizoremediation has been studied extensively and works, but phylloremediation is relatively uncharted territory," Beattie said. Beattie and Janice Seibel, now a research associate in veterinary microbiology at Iowa State, began looking at how plants filter phenol out of the air eight years ago. They used phenol as an indicator compound because it's nontoxic and a component of the odor emitted from livestock facilities. It's also a compound that is easily degraded by most microorganisms. Phenol is common in the air but usually is at low levels, Beattie said. When you are near a source - such as a livestock facility - and you can smell an odor, it's often an indication of higher levels of phenol.

"Your nose is a great test of air pollutants like phenol," Beattie said. "In Iowa, it's commonly emitted from livestock and municipal waste facilities, but in other parts of the world, it's produced from burning coal or chemical industries."

"One mystery we wanted to solve was whether the bacteria could find the phenol that attached to the leaf because bacteria are not found everywhere on the leaf," Beattie said. To track the phenol, Amarjyoti Sandhu, a graduate student in microbiology, used a biological reporter that turned the microbes fluorescent green when they came in contact with phenol. That produced some interesting results.

"The plant was like a sponge. It held the phenol until the bacteria could detect it," Beattie said. "A plant could be harmed by high levels of this stuff, thus the bacterial degradation of phenol could help protect a plant."

Beattie said researchers are just beginning to understand the potential of phylloremediation. Studies like this could provide tools to help eliminate air pollutants near livestock and industrial facilities. "It may mean that the more plants growing around a facility, the better. They influence the aerodynamics and act as a filter for particulates and airborne molecules," Beattie said.

"I can also envision an air outtake system that would filter through a whole canopy of leaves," she added. "We recently found that phenol-degrading microbes are part of the natural flora on leaves, so it's conceivable that we can find ways to increase natural populations of these microbes, such as planting species that favor them." by Barbara McBreen, Ag Comm.

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Arabidopsis has been Diane Bassham's plant of choice for a number of years. Her fundamental research looks at how plants respond to nutrient stresses. Recently Diane has started a new research project that is a total switch. Now she is switching to a more applied research method, investigating ways to store therapeutic proteins made in the seeds of soybean plants engineered to produce biopharmaceuticals. "It's exciting to work on a project that's economically important. Instead of saying ‘someone in the future will use this,' now I can be involved in that process myself."

Atop Bessey Hall sits Iowa's largest cotton crop. It's also the home of the nation's leading research being conducted on the crop better suited for Alabama and Mississippi than Ames, Iowa. "I would be hard pressed to find a better place to do this than here.Cotton is the classical botanical mystery," Jonathan Wendel says. "I've always enjoyed studying speciation and evolution, and cotton is a fascinating model to study the evolutionary process." Jonathan has been awarded numerous grants for his research, including a five-year, $4.2 million grant to study the comparative evolutionary genomics of cotton. "No one else in the world is doing this technically challenging research with cotton. We think we can develop resources and tools that will benefit the entire cotton research and breeding communities."

Dr. Srinivas Aluru, along with ISU plant scientist Patrick Schnable are in the process of cracking the corn genome. "We've been able to do science that nobody has been able to do," Schnable said. It's science that's advancing agricultural production capabilities, improving nutrition, and uncovering new opportunities in biofuels production.

How do plant leaves talk to roots and vice versa? Not a trivial question—it’s a matter of how a plant coordinates what’s happening above ground to what’s happening underground. Plant leaves sense the environment and having perceived appropriate conditions, transmit signals underground to roots, stolons and rhizomes.

ISU professor David Hannapel has found in his studies that the signal is an RNA, a messenger RNA. That would have been unheard of ten years ago. Messenger RNA was thought to stay within a cell slavishly carrying information from the nucleus to cytoplasm.

Using the potato as a model, Hannapel has shown that shorter days cue leaves to export RNA down the vascular system of the plant, signaling stolens to tuberize. The results of this study are described in The Plant Cell, “Dynamics of a Mobile

RNA of Potato Involved in a Long-Distance Signaling Pathway,” December 22, 2006.

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Hannapel’s study showed that a particular RNA that encodes a protein called BEL 5 is signaled to move by short days. This was demonstrated by growing plants under both long-day and short-day conditions and measuring the accumulation of BEL 5 throughout the plant. Under short days, higher levels of BEL 5 RNA were found at base than at the top of the plant, and concentrations increased through the stem to the stolon tip indicating that the BEL 5 RNA had traveled. The concentration levels were the reverse for plants grown under long day conditions Experiments also showed the untranslated ends of the BEL 5 RNAs contain the travel information. What Hannapel calls “chaperone” proteins bind to

untranslated regions of the RNA and carry it to other regions of the plant.

“When we looked at plants with just the coding sequence, the BEL 5 RNA wouldn’t move in response to short days. But when we looked at them with the untranslated regions, it did move in response to short days,” Hannapel said. He added that the photoperiod seems to regulate the process. Increased movements of BEL 5 RNA toward the bottom of the plant were correlated with enhanced tuber production—overexpression of BEL 5 consistently resulted in shorter growing periods and higher yields. A higher yielding potato could be a future application of this work and would be particularly useful in developing countries. In the meantime, Hannapel said, this model system will help scientists to better understand the process of tuberization and the role of mobile RNAs in development. Hannapel’s research has been supported by the Plant Sciences Institute and the National Science Foundation From PSI UPDATE April 2007.

Ravindra Singh received the 2006 Presidential Early Career Award for Scientists and Engineers. Singh was appointed associate professor of biomedical sciences at the ISU's College of Veterinary Medicine on July 1, 2007. His award-winning research focused on correcting the spinal muscular atrophy (SMA) gene while he was at the University of Massachusetts Medical School. Singh will continue his research on SMA at Iowa State University.

Anumantha Kanthasamy Biomedical Sciences, (middle) speaks with Nobel Prize winner Stanley Pruisner (right), 2007 Workshop IG speaker.

A collaboration spawned from a journal club discussion and supported in its infancy by the Plant Sciences Institute has united insect physiologist Bryony Bonning (Entomology) and molecular Virologist Allen Miller (Plant Pathology) in a quest

to control crop damage brought about by aphid infestations. Bonning and Miller are on their way to genetically engineer plants for aphid resistance in

an effort to cut billion dollar losses to U.S. farmers due to aphid damage. Their approach could offer an alternative to pricy and environmentally unfriendly chemical pesticides.

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Be it backyard asparagus, acres of cotton, the prize rose bush or this year’s soybean crop, all are on an aphid’s preferred menu. They do not eat roots, leaves or seeds but rather feed on the phloem or plant sap, slowly robbing the plant of its hard-earned nutrition.

Ladybugs, a natural predator of aphids simply cannot eat them fast enough, explains Miller, director of the Center for Plant Responses to Environmental Stresses and professor of plant pathology. Aphids reproduce asexually. “They are born pregnant, essentially carrying their own grandchildren,” says Miller. To sum up, they reproduce a lot in a very short period of time. Aphids are also responsible for the transmission of more than 200 viruses from plant to plant, many of which bring about additional crop loss. In the case of luteoviruses, aphids are the sole mode of transmission.

Capitalizing on this uniqueness, Bonning and Miller are working to combine a gene encoding an insect-specific toxin with that of a luteovirus coat protein.

One such insect-specific toxin is found I the venom of the North African scorpion. Bonning and Miller have attached the toxin to a viral coat protein

molecule—one of 1800 copies of this molecule that can form a wrapper around the luteovirus.

The researchers anticipate that when the toxin-coat protein complex is ingested by the aphid, the coat protein will deliver the toxin into the body cavity where it will break down cells inside the aphid gut, reducing it to a gelatinous mass, killing the aphid.

Preliminary data with the coat protein fused to a fluorescent marker protein confirms that the coat protein does usher the toxin into the aphid body cavity.

“It is a novel idea and it works,” says Bonning, an expert in insect physiology. The next step is to generate transgenic plants that can express the coat protein-toxin-fusion product. Then, when an aphid taps into the phloem, it will eat up the toxin.

“Viruses are not always bad,” points out Miller. ”They are extremely useful tools for problems such as insect control.”

The insect families Lepidoptera (caterpillars, moths) and Coleoptera (beetles) feed o the external structures of the plant and have been successfully controlled in an environmentally friendly manner with insect-specific Bt toxins. Because Bt toxin is typically applied as a topical insecticide or expressed on external structures in genetically engineered plants, aphids tape the sap and feast unscathed.

“Transgenic plant approaches haven’t worked as well in controlling pests from the Hemiptera (the insect order that includes plant bugs and aphids) that feed on the xylem and phloem, and in some cases these insects now compromise the success of Bt technology,” says Bonning.

Because aphid crop damage is not immediate, anything that slow the aphid population until harvest, even if it does not eradicate them is enough to offer significant relief to farmers. “Our approach started as fundamental high-risk research with a clear applied goal,” says Miller. “Someone has to do it and companies generally want universities to do this basic research. Plant Sciences Institute seed money for our basic research allowed us to make enough progress to secure USDA funding.” 2006 Annual Report Plant Sciences Institute.

The Plant Sciences Institute and the Department of Agronomy have teamed up to help quantitative geneticists peer into the black box of the genome, to illuminate specific genes that bring about defined phenotypic traits.

Identification of genes and deciphering their function is an essential component of crop breeding today. In the past, plant breeders used traditional selection techniques to generate better crops. But a more sophisticated approach is needed to meet the demands of a food-and fuel-hungry society.

The Sequenom MassARRAY® system acquired by the institute in partnership with the Department of Agronomy makes rapid gene identification and genotyping possible. Desirable crop traits include “robust stalks that can withstand strong winds or weak stalks that can more easily be broken down for biofuel production,” explains Patrick Schnable, the Plant Sciences Institute’s associate director, director of the Center for Plant Genomics, and professor in the Department

of Agronomy and the Department of Genetics Development and Cell Biology. “Or improving productivity simply to reduce the footprint agriculture is making on the world, in favor of more wild landscape.”

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Technologies such as gene chips or real-time RT-PCR inform researchers how much RNA is produced at a given time or under different conditions.

But the Sequenom® allows researchers to scan through plant genomes rapidly, accurately identifying very subtle differences in DNA. Using mass spectrometer technology, it sifts through thousands of bits of DNA, identifying single nucleotide p0olymorphisms (SNPs), which direct

researchers to specific chromosomal regions where important genes can be clustered.

Schnable is looking for the genetic basis of hybrid vigor in corn, the unexplained phenomenon whereby certain progeny outperform both inbred parents.

“We are retrospectively looking to see which regions of the genome have been altered, which genes breeders are changing,” says Schnable. “We know the genes are behaving in unusual ways and we’re looking for mater regulators, if you will.” “It is similar to an epidemiological study,” Schnable says. This means churning through huge numbers of samples from diverse sets, linking phenotype to genotype. Student Updates Supraja Puttamreddy is in her third year of graduate (PhD) study in the Interdepartmental Genetics program. Her research in the Minion lab focuses on genetic analysis of Escherichia coli O157:H7 biofilm formation. Escherichia coli O157:H7 is a food borne pathogen that causes gastrointestinal infections in humans. It is causing several outbreaks associated with ground beef, municipal and swimming water, green leafy vegetables, un-pasteurized milk etc. Symptoms range from mild diarrhea to severe hemorrhagic colitis with hemolytic uremic syndrome (HUS), which is one of the leading causes of acute renal failure in children. This organism forms biofilms on various surfaces such as stainless steel, glass, spinach and lettuce. Microbes in biofilms are highly resistant to heat, desiccation, sanitizers, household cleaners as well as to antibiotics. The ability to form biofilms on a wide range of food and food processing surfaces together with its very low infectious dose (~100 organisms) makes E. coli O57:H7 one of the most feared emerging food borne pathogens.

The goal of Supraja’s work is to understand the process of biofilm formation in E. coli O157:H7 in depth, which later helps in devising methods to control its dissemination.

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Student Updates James Koltes' next job is a post doc in Belgium at the Medical School of the University of Liege. He received two fellowships: a Fulbright and Belgian

American Educational Foundation fellowships. James graduates Fall 2007.

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The College of Agriculture's Agricultural Entrepreneurship Initiative has named Colin Shepherd, a Fellow. The fellowship is a year-long program designed to expand participants' knowledge of business and technology transfer. Shepherd received a bachelor's of science degree in agricultural biotechnology from the University of Kentucky and

received his doctorate in August from Iowa State in genetics. The Agri-Sciences Commercialization Fellowship is funded through the Agricultural Entrepreneurship Initiative and the PappaJohn Center for Entrepreneurship.

Suqin Cai, Horticulture/Lashbrook Lab, received a Research Excellence Award. She receives her Ph.D. Fall 2007. Dana Awwad (GDCB/Link) completes her M.S. in genetics this fall and plans to stay in Ames for a few more months and work for NewLink.

Graduates 2007: Zhiyan Liu (Ph.D./Bonning/Entomology), Gang Ren (Ph.D./Thornburg/BBMB), Ying Liu (M.S./Nilsen-Hamilton/BBMB), Lacey Luense (M.S./Komar, Reecy/Animal Science), and Lei Zhu (M.S./Johansen/GDCB). Robert Dick (M.S./Voytas/GDCB), Li Fan (M.S./Schnable/GDCB), Mayumi Fukuda (M.S./Zhang/VMPM), Jason Hasenstein (Ph.D./Lamont/Animal Science), Jodi McKay (Ph.D./Buss/BBMB), Colin Shepherd (Ph.D./Scott/Agronomy). Dana Awwad (M.S./Link, Ellinwood/GDCB), Lisa Haney (M.S./Scott/Agronomy), Megan Harvey (M.S./Scott/Agronomy), Marie Hasenstein (M.S./Scott/Agronomy), Justin Schares (M.S./Vollbrecht/GDCB), Suqin Cai (Ph.D./Lashbrook/Horticulture), Jun Cao (Ph.D./Schnable/GDCB), Tyrell Carr (Ph.D./Whitham/Plant Pathology), Corrinne Osborne Grover (Ph.D./Wendel/EEOB), James Koltes (Ph.D./Reecy/Animal Science), Rebecca Dahlin Laborde (Ph.D./Beetham/Entomology); James Peterson (Ph.D./Phillips/VMPM); Chunling Yang (Ph.D./Whitham/Plant Pathology). Anastasia Bodnar (Scott Lab/Agronomy) is researching maize endosperm as an attractive location for transgene expression. Applications include biopharming and crop improvement. However, high levels of transgene expression in the endosperm could cause changes in the amounts of native proteins, specifically the zein storage proteins. This could have negative consequences; for example, decreased zein content in opaque2 mutants have decreased kernel hardness and poor field traits. These changes must be investigated before the endosperm can be fully exploited as a location for protein expression. We hypothesize that high expression levels of a protein of interest

controlled by the endosperm specific 27kD gamma zein promoter will have an effect on the relative levels of native zein proteins. New Students for 2007. IG recruited 19 new students during 2007; 15 in rotations and 4 directly into labs. Domestic students are from Iowa State, Cornell College (IA), Truman State (MO), North Caroline State, Michigan State, St. Cloud State (MN), University of South Florida, University of Wisconsin-Madison and Virginia Commonwealth. International students are from Egypt, Argentina, Uganda, and China (Peking University, China Agricultural University, Sichuan University, Huazhong Agricultural University and Nankai University). Three students received USDA National Needs Fellowships in Statistical Genetics; one student received a USDA National Needs Fellowship in Animal Biotechnology; one student received a Plant Sciences Institute Fellowship; one student received a MILLER Fellowship; and one student received an IGERT Fellowship in Computational Biology. If you have contacts with good potential students, send them our way! A Few Alumni Updates Barbara Szlendakova (MS/Henderson) joined the Medical College of Wisconsin, Milwaukee in June 2005. She has been working as a prenatal genetic counselor in the High Risk Obstetric Clinic at the Froedtert Hospital. She sees patients for advanced maternal age, family history of a genetic disorder, abnormal maternal serum screening and ultrasound. Recently, she passed the genetic counseling board certification. For Zhiyan Liu's Ph.D. research on regulation of development in the vinegar fly, Drosophila melanogaster, she demonstrated that overproduction of the juvenile hormone esterase (JHE) binding protein DmP29, resulted in a plethora of anti-juvenile hormone effects including reduced longevity, fecundity, and reduced abundance of aggregation and courtship pheromones. Without the appropriate pheromones, males cannot tell males from females and exhibit male-male courtship behavior with long lines of males each attempting to court the male in front. Unexpectedly, both sexes were also

hyperactive. Work is now underway to elucidate the physiological basis for the observed phenotypes and specifically what role DmP29 plays in the biology of JHE to facilitate degradation of juvenile hormone..

Zhiyan Liu graduated in May 2007(Ph.D./ Bonning lab/Entomology) and her postdoc research uses Drosophila as a model organism for the study of eye development Chris (Dongying) Wu(Ph.D./1999/Rodermel) is presenting a scientist at the Genome Center of UC Davis. His research is in the field of bioinfomatics and metagenomics. He and his partner Peter live in Berkeley, CA. Kemba Kelly (M.S./Rothschild) is working as a Senior Research Specialist at the University of Illinois-Chicago investigating novel approaches to bupivicaine toxicity. Mythreyi Shastry (Ph.D./Girton) is working as a Senior Research Associate in a consulting company called Technology Catalsysts, Intl. (Virginia) with the drug delivery group. Mythreyi had a daughter in 2005, Lakshmi Shastry. Axel Elling (Ph.D./Baum) is at Yale University in the Department of Molecular, Cellular and Developmental Biology. Jun Cao (Ph.D./Schnable/F07) has just arrived (November) at the Max-Planck Institute in Tubingen, Germany. He is working with natural variation in Arabidopsis.

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A Selection of Recent Student Publications (bold = present students; underline = genetics alumni; italic = genetics faculty). Bao, Xiaomin, Girton J. Johansen J, Johansen KM. the lamin Dm(0) allele Ari3 acts as an enhancer of position effect variegation of the w (m4) allele in Drosophila. Lerach S., Zhang W. Bao Xiaomin, Deng H. Girton J. Johansen J, Johansen KM. Loss-of-function alleles of the JIL-1 kinase are strong suppressors of position effect variegation of the wm4 allele in Drosophila. Genetics 2006 (Aug; 173(4): 2403-6. Cai, Suqin. and Lashbrook, CC (2006). Technical Advance. Laser capture microdissection of plant cells from tape-transferred paraffin sections promotes recovery of structurally intact RNA for global gene profiling. Plant Journal 48: 628-637. Carr, Tyrell. and Whitham, S.A. (2007). An Emerging Model System: Arabidopsis as a Viral Host Plant. Plant Cell Monographs: Viral transport in plants, 159-183. Yang, Chunying., Guo R., Jie F., Nettleton D., Peng J., Carr, Tyrell., Yeakley, J., Fan, J-B. and Whitham, S.A. (2007). Spatial analysis of host gene expression in response to viral infection. Molecular Plant-Microbe Interactions 20, 358-370. Morrone D., Jin Y, Xu M, Choi Suh Yeon, Coates RM, Peters RJ. An unexpected diterpene cyclase from rice; functional identification of a stemodene synthase. Arch Biochem Biophys. 2006 Apr 15; 448 (1-2): 133-40. Udall, J.A., Lex E. Flagel, F. Cheung, A.W. Woodward, R. Hovav, Ryan.A. Rapp, J. M. Swanson J.J. Lee, A.R. Gingle, D. Nettleton, C.D. Town, Z.J. Chen, and J.F. Wendel. 2007. Spotted cotton oligonucleotide microarrays for gene expression analysis. BMC Genomics 8:81. McGaugh, Suzanne.E. and F. J. Janzen, 2006. The status of Apalone ater populations in Cuatro Cienegas, Coahuila, Mexico, preliminary data. Accepted to Chelonian Conservation and Biology. O’Rourke, Jamie A., MA Graham, L Vodkin, DO Gonzalez, SR Cianzio, RC Shoemaker. Recovering from Iron Deficiency Chlorosis in Near Isogenic Soybean Lines: A Microarray Study. Plant Physiology and Biochemistry 45 (2007) 287-292. Carlie Peck LaLone, Hammer, KDP, Wu L, Bae J, Leyva N, Liu Y, Solco AKS, Kraus GA, Murphy PA, Wurtele ES, Kim O-K, Seo K, Widrlechner MP, Birt

D.F. (2007) Echinaceas species and alkamides inhibit Prostaglandin E2 production in RAW 264.7 mouse macrophage cells. Journal of Agriculture and Food Chemistry (2007) 55 (18): 7314-7322 Hammer Kimberly Petry, Hillwig ML, Solco AKS, Dixon PM, Delate K, Murphy PA, Wurtele ES, Birt DF (2007) Inhibition of PGE2 by anti-inflammatory Hypericum perforatum extracts and constituents in RAW 264.7 macrophage cells. Accepted in the Journal of Agriculture and Food Chemistry. Xiong Y, Contento AL, Phan, Nguyen Q, and DC Bassham. 2007. Degradation of Oxidized Proteins by Autophagy during Oxidative Stress in Arabidopsis. Plant Physiology 143: 291-299. V. Anantharam, S Kaul, Chunjuan Song, Arthi Kanthasamy, AG Kanthasamy. “Pharmacological inhibition of neuronal NADPH oxidase protects against 1-methyl-r-phenylpyridinium (MPP+)-induced oxidative stress and apoptosis in mesencephalic dopaminergic neuronal cells”, accepted by Neurotoxicology, 2007. Vollbrecht E., and Brandi Sigmon. 2005. Amazing grass: developmental genetics of maize domestication. Biochemical Society Transaction 33:1502-1506. Shen C. Shao, Zhiyong, Powell-Coffman JA (2006). The Caenorhabditis elegans rhy-1 gene inhibits HIF-1 hypoxia-inducible factor activity in a negative feedback loop that does not include vhl-1. Genetics 174 (3) 1205-14. Jolita Janutenaite Uthe, Royaee A, Lunney JK, Stabel TJ, Zhao SH, Tuggle CK, Bearson SM. Porcine differential gene expression in response to Salmonella enterica serovars Choleraesuis and Typhimurium. Mol. Immunology. 2007, 44: 2900-14. JJ Uthe, Stabel TJ, Zhao SH, Tuggle CK, Bearson SM. Analysis of porcine differential gene expression following challenge with Salmonella enterica serovar Chloleraesuis using suppression subtractive hybridization. Vet Microbiology 2006; 114: 60-71. Xiujuan Wang and D. Lavrov. 2007. Mitochondrial genome of the demosponge Oscarolla carmela (Porifera, Demospongiae) reveals unexpected complexity in the common ancestor of sponges and other animals. Mol. Biol Evol. 24: 363-373. Skibbe D., X Wang, X Zhao, LA Borsuk, D. Nettleton, PS Schnable (2006). Scanning microarrays at multiple intensities enhances

discovery of differentially expressed genes. Bioinformatics 22(15): 1863-1870. Sponseller, B.A., Wendy Wood Sparks, Y Wannemuehler, Y Li, AK Antons, JL Oaks, and S. Carpenter (2007). Immune selection of equine infectious anemia virus env variants during the long-term unapparent stage of disease. Virology. 363: 156-65. Sparks, WO, L. Bartholomay, and BC Bonning. (2008) Insect Immunity to Viruses. In Insect Immunology, N.E. Beckage, Ed. Academic Press. (in press). Shengqiang Zhong and Jean-Luc Jannink. 2007. Using QTL results to discriminate among crosses based on their progeny mean and variance. Genetics 177: 567-576. Sholpan Davletova, L Rizhsky, H. Liang, S Zhong, David Oliver, J Coutu, V Shulaev, K Schlauch, and Ron Mittler. 2005. Cytosolic Ascorbate Peroxidase 1 is a central component of the reactive oxygen gene network of Arabidopsis. Plant Cell 17 (1): 268-281. Wang, Qu Uthe, Barson, Kuhar, Lunney, Oliver Couture, Nettleton, Dekkers, Tuggle, 2007. Global transcriptional response of porcine mesenteric lymph nodes to Salmonella enterica serovar Typhimurium. Genomics; 90(1): 72-84.

Iowa State University 150th cake

Sesquicentennial kickoff and Veishea weekend April 20-21.

VEISHEA parade float Ames has a New Super Walmart on Duff Avenue.

The hole where a new $9.5 million Ames Aquatic Center on 13th Street near Squaw Creek in the pastures just north of the area where Iowa State University keeps its horses. It is expected to be completed in Spring 2009.

Elwood Drive becomes University Boulevard. The name change, which was approved by the city council in April, will apply to the stretch of road currently known as Elwood Drive.

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It rained a lot in August. (Aerial photo provided by Jordan Birkholz/Haps Air Service).

It snowed a lot during February 2007. (with permission Photo by C. Bensend, www.bennyvision.com).

Oh, and we had some ice too. (Photo by C. Bensend)

Mother Nature did some pruning. (Photo by C. Bensend).

We had some good weather too! Oh, okay, this was taken in Moloka’i Hawaii.☺ in January 2007. Ruth Swanson-Wagner (Schnable Lab) spent 3 weeks on Moloka'i making controlled corn crosses in the winter nursery. An interdisciplinary undergraduate degree in bioinformatics and computational biology was approved by the Board of Regents at Iowa State University.

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The College of Agriculture is now the College of Agriculture and Life Sciences.

New Farms of the Future

“As we enter the 21st century, mainstream agriculture faces many challenges that may propel agriculture in … new directions. As fossil fuels are depleted, the ratio of energy produced to energy required to produce it continues to diminish, making that source of energy increasingly costly. So agriculture will have to find an alternative energy source to sustain its productivity. Agro-ecologists increasingly are convinced that the most viable alternative technology will spring from the biological synergies inherent in multispecies systems and that additional research might make such systems the next new technology. It would appear that these new farms of the future will operate on the basis of at least eight principles that are almost diametrically opposed to the assumptions industrial agriculture has taken for granted. Postmodern farms will likely need to: be energy conserving; feature both biological and genetic diversity; be largely self-regulating and self-renewing; be knowledge intensive; operate on biological synergies; employ adaptive management; feature ecological restoration rather than choosing between extraction and preservation; and achieve optimum productivity by featuring multiproduct, nutrient-dense, synergistic production on limited acreage.”

A closer photo. (Photo: ISU Alumni News Flash) More Alumni updates: Olivier Fedrigo (Ph.D./Naylor) is doing a postdoc with Greg Wray at Duke University. He is working on cis-regulation evolution in human and more particularly he is interested in detection signature of positive selection by comparing human genome to other great apes. His work is both bioinformatics and wet-lab. A recent publication: Haygood, R., O. Fedrigo,B. Hanson, K.-D. Yokoyama, and G. A. Wray. (2007) Promoter regions of many neural- and nutrition-related genes have experienced positive selection during human evolution. Nature Genetics. 39(9): 1140:1144. These authors contributed equally to this research

---Frederick Kirschenmann, “Potential for a New Generation of Biodiversity in Agroecosystems of the Future” (Agronomy Journal, Feb 6, http://agron.scijournals,org/cgi/content/full/99/2/373

New entry way on University Boulevard (formerly Ellwood Drive) coming in from Highway 30 towards Linda got a new dog this year—a small Australian

Shepherd named Bella. She is about 1 ½ years old and came from the Marshalltown Animal Rescue League shelter. She wasn’t very good about sitting still for her picture, but she enjoys her toys.

Campus. (Photo: ISU Alumni News Flash) The Interdepartmental Genetics program wishes you and your families an enjoyable holiday season. Stay warm!

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