Michigan Agricultural Experiment Station

New Technique Puts DNA Profiling of E. coli on Fast Track

Tom Whittam Using new genetic techniques, MAES scientists are unlocking the secrets of how E. coli bacteria contaminate food and make people sick.

MSU has developed a new technique to test the DNA of E. coli bacteria by examining very small genetic changes called single nucleotide polymorphisms or SNPs (pronounced “snips”). Using SNPs, scientists were able to genetically analyze 96 markers -- a rate never before accomplished in pathogenic bacteria.

"It used to take three months to score one gene individually," said Thomas Whittam, MAES scientist and Hannah distinguished professor at the National Food Safety and Toxicology Center at MSU. "Now, we are working on a new, more rapid system that can do thousands of genes per day."

In a new study released in the March 10 edition of the Proceedings of the National Academy of Sciences, "Variation in Virulence Among Clades of Escherichia coli O157:H7 Associated With Disease Outbreaks," Whittam and his co-authors looked at the DNA of more than 500 strains of a particularly dangerous member of the E. coli family, O157:H7. In collaboration with David Alland of the University of Medicine and Dentistry of New Jersey, Whittam discovered that individual bacteria could be separated into nine major groups, called clades.

E coli makes people sick because the bacteria produce toxins, called Shiga toxins, which block protein synthesis, an essential cellular function, particularly in the kidneys. What Whittam found was that the various clades produced different kinds of Shiga toxins in varying amounts on the basis of their DNA.

"For the first time, we know why some outbreaks cause serious infections and diseases and others don't," Whittam said. "The different E. coli groups produce different toxins."

Rapid genetic characterization also opens up a new world of possibilities for identifying the bacterial culprits in outbreaks and finding out where they originated.

E. coli bacteria usually come from animal waste contaminating sources of human food or water. Finding out how the bacteria entered the food source always has been a challenge, but now food safety experts can use DNA just as police use DNA at crime scenes. Scientists will be able to identify those bacteria making people sick, find out where they entered the food source and then use this information to reduce contamination.

"This is the first time anyone has been able to classify very closely related groups," Whittam said. "This is also the first time we can tell the differences in how they cause disease."

Whittam also has plans to use this methodology to study other bacterial strains, such as Shigella, a major cause of diarrhea around the world.

"This new equipment can be used to identify hundreds of thousands of pathogenic bacteria," Whittam said.

The research is supported by the National Institute of Allergy and Infectious Diseases of the National Institutes of Health through the Food and Waterborne Diseases Integrated Research Network.

Electronic Animal Health Record System Aims to Improve Management, Give Producers Marketing Edge

Dan Grooms Most Michigan livestock move through a number of operations and have several owners before arriving at their final destination. Mandatory radio frequency identification (RFID) tags on cattle allow animals to be traced back to their farm of origin. MAES researcher Dan Grooms wondered if the tags could be used to transport other kinds of information, such as an animal's health records.

"Medical records help producers make better decisions," Grooms said. "But because livestock move through many operations, an owner may have no knowledge of an animal's health history." An associate professor of large animal clinical sciences and a veterinarian, Grooms also heads up MSU's role in Vet Net, the Michigan Emergency Veterinary Network.

Using a $75,000 grant from the Michigan Agricultural Experiment Station, Grooms is heading a partnership of MSU scientists, private industry and the Michigan Department of Agriculture on a 3-year project to develop an easy-to-use, portable, electronic bovine medical record system.

Grooms envisions a system that will allow health information to be collected anywhere along the bovine production chain via laptop or handheld computer. The information would then be uploaded to a central database and could be viewed by anyone with access rights.

"Our goal is to demonstrate the feasibility of this type of system," Grooms explained. "This is a pilot project. We're going to demonstrate how the information can be collected and could flow and be used to make better management decisions."

The scientists will test the pilot system on two groups of cattle. MSU-owned cattle born at the Lake City Experiment Station and then moved to the on-campus Beef Teaching and Research Center are one group of about 200 cattle. Green Meadows Farms, Inc., a large dairy operation in Elsie, is allowing the researchers to upload the health records of bull calves born at the dairy -- about 1,500, Grooms estimated. The bull calves move from the dairy to a calf raiser operation to a feedlot.

Pardalis, Inc., an Oklahoma-based information technology company, is developing the database.

"Producers initially will have to enter more data," Grooms said, "but I think down the road this could be a marketing advantage for Michigan cattle. I could see processors wanting to have the health information of cattle before slaughter and offering to pay a premium for that information. Michigan is the only state right now that has mandatory RFID tags on cattle, and we're trying to help producers take advantage of that and set our cattle apart from the others."

Once developed, the system also could help protect food safety and quality.

"Having a system that keeps records of all health events in the life of a food-producing animal gives us an opportunity to intervene if we identify issues that are potentially harmful to food safety and quality," Groom explained.

Others working on the project are Dan Buskirk, MAES animal science researcher; Kenny Wells, animal science outreach specialist; Ken Metz, Beef Teaching and Research Center farm manager; Lou Neuder, associate professor of large animal clinical sciences; Glynn Tonsor, MAES agricultural, food and resource economics researcher; Steve Holcomb, Pardalis, Inc., founder and CEO; and Kevin Kirk, Michigan Department of Agriculture electronic identification coordinator.

Chicken Genome Leads to New Vaccine to Fight Poultry Disease

Jerry Dodgson Researchers in Michigan, Delaware and Texas are using the chicken genome sequence to develop vaccines to combat Marek's disease, a highly contagious, cancer-causing viral disease that costs the poultry industry $1 billion a year worldwide.

MAES scientist Jerry Dodgson and colleagues at MSU, the USDA Agricultural Research Service Avian Disease and Oncology Lab, the University of Delaware and Texas A&M University began by assembling the physical map of the chicken genome using DNA clones that describe all or nearly all of the genes in the chicken. The researchers then began to identify individual genes whose levels went up or down after infection by Marek's disease virus (MDV). To do this, they used a "gene chip" with approximately 13,000 gene sequences (about half the chicken genes) to test levels of gene products before and after MDV infection, and in chicken lines that were highly susceptible versus lines that were more resistant.

In the field, MDV spreads from bird to bird via inhaled feather dander. Any infected tissue is a mixture of uninfected and infected cells that are closely intermingled, making it difficult to distinguish differences between them. Using a laser to microdissect a clump of infected cells from uninfected ones, the group discovered a suite of genes in the chicken genome that influence the course of viral infection. This new understanding of the interaction between the virus and the genes was used to develop new ways to identify genes in the chicken that are turned on or modified by MDV infection.

A new recombinant vaccine was developed by cloning one of the identified genes, called chicken MIP-1, into the vaccine strain of the virus. The protection this vaccine provides is comparable to that afforded by the best commercially available vaccines.

The chicken genome sequence developed during this project is now available to scientists working on MDV worldwide. The data generated by this project are also available on two Web sites, the U.S. Poultry Genome Project Web site at Michigan State and the U.D. Chick EST Database Web site at the University of Deleware, to provide other scientists instantaneous access to the data prior to publication.

The project was funded by the U.S. Department of Agriculture Cooperative State Research, Education and Extension Service through the Initiative for Future Agricultural and Food Systems program.

MAES Scientists Finding Solutions to Rising Greenhouse Energy Costs

MAES scientists are traveling the globe and compiling Web sites of information to help Michigan greenhouse growers reduce their energy costs.

Escalating energy costs have strapped greenhouse growers searching for innovative strategies to reduce this monthly expense. Thanks to a new online resource developed by MAES horticultural researchers, growers now have access to a variety of useful information in one convenient location.

The Greenhouse Energy Cost Reduction Strategies Web site was developed by MAES horticulture scientist Erik Runkle and horticulture graduate student Matthew Blanchard to help improve the profitability and sustainability of the state’s greenhouse industry.

Runkle noted that since 2004, energy costs have escalated by 30 to 50 percent. Increased energy costs reduced the profitability of Michigan’s greenhouse industry by more than $20 million in 2005.

"Energy is usually one of the greenhouse industry’s top two highest priorities because, on average, it accounts for between 8 and 12 percent of a producer’s total expenses," Runkle said. "Because there is not one single best way to reduce energy costs that’s right for everyone, growers have several options to choose from."

The site includes a compilation of studies on how to reduce energy costs conducted by researchers from MSU and other universities. Though the site is targeted at Michigan growers, the information is applicable to many other regions of the northern United States with similar climate patterns.

Visitors to the Web site can locate timely information on a variety of topics, such as greenhouse lighting, temperature and scheduling, energy-saving technologies, alternative fuels, and energy grant and loan programs.

Runkle also traveled to Europe with MAES agricultural, food and resource economics scientist Stephen Harsh to gather information on how to curb rising energy costs for greenhouse growers. Runkle and Harsh are spearheading a project to identify alternative energy sources and innovative strategies for reducing energy costs and help the state’s floriculture industry regain its competitive edge.

Harsh and Runkle decided to study how greenhouse operators were dealing with similar situations in other areas of the world. The quest took them to the Netherlands, the top-ranking country in greenhouse crop production, to survey how growers there responded to a government-imposed mandate to reduce climate-warming gases by 40 percent.

Because the climate of the Netherlands is similar to Michigan’s, they were interested in studying the practices that operators there were using to help reduce greenhouse energy costs. The most interesting method that Harsh came across during his weeklong trip was cogeneration, a technique used to produce heat and carbon dioxide for the greenhouses and electricity for the town at the same time.

Steve Harsh "The trip to the Netherlands really opened our eyes to how many opportunities exist for generating alternative energy," Harsh said. "The government of the Netherlands has implemented important regulatory policies to encourage greenhouses to commit to conserving natural resources."

Although cogeneration systems aren't used in the United States, Harsh came across other promising methods worth further study. For example, during the warm months, greenhouses in the Netherlands capture solar energy by using heat exchangers in the greenhouses and store it in an aquifer. During the cool months, the stored energy is used to heat the greenhouses. Other alternative energy technologies used include wind energy, biomass (wood pellets), other alternative fuels and different types of glass or plastic.

Runkle is hoping to come up with methods to reduce greenhouse energy costs by developing a better understanding of how crops respond to temperature. The temperature in a greenhouse dictates how long it will take for a crop to reach maturity. Plants grown in cooler temperatures take longer to develop; plants grow much faster in warmer temperatures. Runkle and Blanchard are trying to identify the optimum temperature that would permit energy costs to be lowered without jeopardizing plant growth rate.

"We predict that growers may be able to save up to 10 to 30 percent on energy costs by managing greenhouse temperature," Runkle said.

Because each plant responds differently to varying temperatures, Runkle is partnering with the U.S. Department of Agriculture to build a user-friendly computer program to generate mathematical models to forecast how well various crops can be expected to grow at specific temperatures. Runkle said the computer program, which is still under development, will allow users to select the type of crop they wish to grow and recommend the most profitable temperature at which to grow the plants.

"We hope to contribute to helping Michigan’s greenhouse industry remain a competitive and dominant player," Harsh said. "Our ultimate goal is to learn how the industry can become more efficient and competitive, and identify the role it can play in reducing carbon emissions."

This research also is supported by Project GREEEN (Generating Research and Extension to meet Economic and Environmental Needs), Michigan’s plant agriculture initiative at MSU, and the Michigan Floriculture Council.

MSU Wheat Wins Best in Show

An MSU line of soft, white wheat earned the highest ratings of its class in the 2007 quality evaluation by the Soft Wheat Quality Council.

According to the Quality Evaluation Committee report, the wheat line (D8006W) scored higher than those of the other three institutions in the category because of its moderate resistance to viruses such as stripe rust and wheat spindle streak mosaic virus and its superior milling and baking properties. It was also praised for its low water absorption and gluten strength.

Soft wheats are used to make cookies, crackers, flatbreads and pastries, and are distinguished from hard wheats (used to make bread) by lower gluten content and lower resistance to water and mixing. There is a growing demand for white wheats within the industry, said MAES crop and soil sciences researcher and wheat breeder Janet Lewis.

"Industry is interested in having more white wheat available because of consumer interest in having high-fiber foods," Lewis said. "There is a high concentration of wheat fiber in the wheat bran, and the bran of white wheat is more palatable -- less bitter --to consumers than the bran of red wheat.

Two additional white wheats entered by MSU to be evaluated -- Crystal (MSU line E0027) and Jewel (MSU line E1007W) -- also received favorable marks from the judges.

"This wheat is not only good for the farmers because of its disease resistance and high yield," said Randy Judd of the Michigan Crop Improvement Association, "but it also has the high quality the milling industry is looking for to meet its extensive standards. The Michigan Crop Improvement Association’s relationship with Michigan State certifies us to sell the breed," Judd added, "and we’re very excited to market wheat of such quality."

Pot-in-Pot Offers Alternative Growing System for Christmas Tree Farms, Nurseries

Bert Cregg Potted evergreen trees are the hottest trend going in the Christmas tree market, and nurseries and Christmas tree farms are poised to take advantage of this budding niche market.

Potted evergreens are ideal for consumers looking for an environmentally friendly alternative to artificial trees, and container-grown table-top evergreens provide Christmas tree growers and nurseries with a profitable specialty line. They’re also the tree of choice for those who prefer a live tree but don’t have room in their home or apartment for a large tree, or for those who like the option of planting their tree after the holidays.

"Consumers can purchase a live potted conifer between 2 and 4 feet tall, use the small tree for their holiday celebrations, and then plant the tree in their yard to watch it grow and enjoy for years to come," said Bert Cregg, MAES horticulture and forestry scientist.

Cregg and graduate student Wendy Klooster are in the second year of a project to refine a production system for container-grown trees known as pot-in-pot. In pot-in-pot production, growers first place a “socket pot” in the ground. A second pot, containing the crop tree, is then placed inside the socket pot.

"Pot-in-pot production combines the benefits of container growing with standard field production techniques," Klooster said.

"The system eliminates problems with trees blowing over in the wind, and placing the tree container in the socket pot in the ground insulates the roots and prevents cold damage during the winter," Cregg said.

Cregg and Klooster’s research is focused on improving fertilization practices for conifers used for living Christmas trees and for deciduous shade trees.

"Identifying the types and amounts of soil, nutrients and other resources that various tree species need to thrive when they’re grown in the pot-in-pot system will help us develop management guidelines to help growers avoid common missteps such as overfertilizing or over- or underwatering," Cregg said.

Christmas tree farms and nurseries across Michigan are already experimenting with pot-in-pot growing. Cregg said he has received a good response from growers who have seen the system in operation and producers who are interested in expanding their markets to include living trees.

The largest barriers for growers interested in the pot-in-pot system are the start-up costs and the need for a suitable production site. The costs of installing socket pots and irrigation occur up front, though these can be used for multiple crop cycles. If the production area does not drain well naturally, growers must install drainage, which adds to growers’ initial costs.

Despite the initial costs, Cregg expects the use of pot-in-pot production to continue to increase for both nursery stock and living Christmas trees.

"The general trend in the nursery industry is toward container production," he said, "but for Michigan growing conditions, pot-in-pot is a great option to produce high-quality container-grown trees."

This research is supported by Project GREEEN, J. Frank Schmidt and Sons Nursery, Boring, Ore.; Nursery Supplies, Inc., Chambersburg, Pa.; Renewed Earth, Inc., Kalamazoo, Mich.; Peterson's Riverview Nursery, Allegan, Mich.; Fairplains Nursery, Greenville, Mich.; Scotts, Inc., Marysville, Ohio; the Michigan Nursery and Landscape Association; the Michigan Department of Agriculture; the Michigan Christmas Tree Association; and the Michigan Forestry and Parks Association.

Delfosse Named Entomology Chair

Ernest Delfosse, senior national program leader with the U. S. Department of Agriculture (USDA) Agricultural Research Service (ARS), has been named chairperson of the MSU Department of Entomology. His appointment was approved by the MSU Board of Trustees at its Feb. 22 meeting and becomes effective May 1.

Delfosse succeeds Rich Merritt, who has been chairperson of the department since 2004 after having served in the position on an interim basis beginning in 2002. Merritt will return to his faculty position within the departments of Entomology and Fisheries and Wildlife.

"Dr. Delfosse is a widely recognized researcher and brings strong scientific leadership to MSU," said R. James Kirkpatrick, dean of the MSU College of Natural Science. "His expertise will connect with many faculty members and students across the university and throughout the state."

Delfosse will provide leadership for the MSU Department of Entomology and work closely with other university units to build interdisciplinary partnerships with public, private and government research groups. He will be a jointly tenured professor in the College of Agriculture and Natural Resources and the College of Natural Science and will contribute to the academic, research and outreach programs of both colleges.

"Dr. Delfosse has a distinguished record in research and technology transfer in an extensive range of entomology and weed science issues," said Jeffrey D. Armstrong, dean of the MSU College of Agriculture and Natural Resources. "Through his leadership, the department will continue to build upon its 100-year legacy as a national leader in entomological education, research and Extension that are relevant to the needs of our constituents."

At the ARS, Delfosse has been responsible for managing research scientists in 55 locations throughout the United States and six ARS overseas biological control laboratories. He also served as a the director of the USDA National Biological Control Institute (NBCI) from 1991 to 1997, and he was a research scientist and research leader with the Division of Entomology of the Commonwealth Scientific and Industrial Research Organization (CSIRO) in Australia from 1979 to 1991.

Delfosse is an active member of many professional societies, including the American Association for the Advancement of Science, the Ecological Society of America, Gamma Sigma Delta and the International Organization of Biological Control. He is also a 30-year member of the Entomological Society of America. His accolades include numerous USDA ARS citations for superior service, several White House commendations and acknowledgements from various sections of the Entomological Society of America. He was named 1994 Entomologist of the Year by the Florida Entomological Society.

Delfosse has authored or co-authored more than 100 publications and been a guest lecturer for more than 40 university courses. He also served as an adjunct faculty member at the Australian National University in its Department of Entomology.

Delfosse received his doctoral degree in entomology from the University of Florida (1975), his master’s degree in entomology from South Dakota State University (1972) and his bachelor’s degree in biology from the University of Louisville, Kentucky (1971).

Gibbs and Rood Receive Distinguished Service to Agriculture and Natural Resources Awards at ANR Week

Two Michigan agriculture leaders were honored March 4 with MSU Distinguished Service to Agriculture and Natural Resources awards during the annual Agriculture and Natural Resources (ANR) Week luncheon.

Lou Anna Simon, MSU president, and Jeffrey Armstrong, dean of the College of Agriculture and Natural Resources, presented the awards.

Donald Gibbs, of Onondaga, Mich., and Paul J. Rood, Jr., of Covert, Mich., were recognized for their successful agribusiness enterprises and their commitment to leadership in community, state and national activities.

2008 Distinguished Service Award Winners

Paul J. Rood, Jr., of Covert, Mich., and Donald Gibbs, of Onondaga, Mich., received MSU Distinguished Service to Agriculture and Natural Resources awards March 4 during the ANR Week Luncheon. Shown above are (left to right) Steve Lovejoy, MSU Extension associate director; Rood; Gibbs; and Jeffrey Armstrong, dean of the MSU College of Agriculture and Natural Resources.

Gibbs owns Gibbs Berry Farm, a 284-acre operation that grows strawberries for U-pick buyers and farmers’ markets, as well as asparagus, apples, blackberries and black raspberries. Gibbs also supplies raspberries and strawberries to Sandhill Crane Winery in Jackson, Mich.

He is a staunch supporter of the Michigan Agricultural Experiment Station and MSU Extension and has participated in MSU field research as a grower cooperator for more than 20 years. Gibbs, who plans to retire this year, has provided numerous plots for horticulture, plant pathology and entomology research, taking crop losses in stride in the service of advancing knowledge.

Rood owns Paul Rood Orchards, a centennial farm specializing in tree fruits. A major producer of pears in the eastern United States, Rood also produces and markets plums and apples. He has supported the Michigan Agricultural Experiment Station and MSU Extension in local educational and research programs and as an advocate for industry support.

Through his agribusiness operation, he has participated in dozens of field research trials. Rood was appointed to the Michigan Plum Advisory Board by Gov. Granholm in 2005 and is a member of the Michigan State Horticultural Society, the Michigan Pear Research Association and the Michigan Apple Research Committee.