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MAES Researcher Helps in First Decoding of Tree Genome

Chalk up another species -- Populus trichocarpa, a poplar tree -- that’s had its DNA laid bare for all to see online.

An international team of scientists, including Kyung-Hwan Han, MAES forestry researcher, made the announcement in September. It is the first time a tree’s genome has been decoded, an accomplishment that may help wean the United States from imported oil, better predict the possible effects of global warming and perhaps even help remove carbon dioxide, a greenhouse gas, from the atmosphere.

"It’s exciting to have the entire gene set available," Han said. “We can use the information to pinpoint which genes cause the tree to go dormant in winter and become active in the spring, and to explore how global warming might affect this process.”

Sequencing the genome is like creating a dictionary full of words without definitions. Han’s lab has identified functions for several thousand of the tree’s genes -- in effect, writing in definitions for entries in the poplar’s DNA dictionary.

Scientists published the genome’s raw information online at http://www.jgi.doe.gov/poplar and will update the free Web-based poplar database as Han’s and other researchers’ work continues.

The first draft of the human genome was published in 2001 to much fanfare. But, in fact, several species -- including yeast -- a nematode, the mouse and dozens of kinds of bacteria -- have given up their ancient genetic secrets to the tools of modern microbiology.

Scientists are interested in learning more about the fast-growing poplar tree partly because of the promise of alternative energy production, including the possibility of swapping biomass for oil. By 2050, improvements to plant productivity and conversion efficiency could allow the United States to replace 25 percent of its oil imports with energy from plantation-grown trees, the U.S. Department of Energy estimates.

This poplar tree, which grows over a dozen feet per year until reaching its maximum height of 200 feet, might be a good candidate for these plantations. Learning the function of the tens of thousands of genes in the poplar genome might help foresters breed trees for better yield, quality and pest resistance.

"Michigan has a dynamic, $9 billion per year forest products industry that provides high-paying manufacturing jobs throughout the state," said Daniel Keathley, chairperson of the MSU Department of Forestry, who collaborated with Han on the poplar research. "This project provides fundamental knowledge needed to enable a better understanding of tree growth, which is critical to maintaining the broad array of goods provided by our forests, ranging from wildlife habitat and recreational areas to watershed protection, and including the wood products, housing materials, furniture and paper needed by our citizens."

The poplar species studied by the international team is native to Washington state. Several of the tree’s cousins, including the eastern cottonwood and trembling aspen, are found in Michigan.

In addition to boosting trees’ economic benefits, altering genes of poplars and other trees might make it possible to remove more climate-altering carbon dioxide from the atmosphere.

Forests account for 90 percent of the biomass on Earth’s dry land and naturally consume carbon dioxide, storing it in leaves, branches, stems and roots. This carbon dioxide is released back into the atmosphere when forests are harvested and burned. Tweaking the genes so that trees store increased amounts of the gas belowground in their roots might scrub carbon dioxide from the skies for longer stretches of time.

“How difficult that would be is hard to say,” said Gerald Tuskan, a plant geneticist at Oak Ridge National Laboratory, who was part of the international poplar sequencing team. “But it is certainly a testable hypothesis with high probably of success.”

For all the potential practical applications of the research, it’s questions of basic science that most interest Han and Keathley.

With lifespans stretching into the hundreds or thousands of years, trees have traditionally been difficult study subjects. It might take generations of researchers to learn how a particular stand of trees responds to environmental change over time.

Han and his MSU colleagues are now making month-by-month measurements of poplar gene expression, a task made vastly easier by having a complete picture of the tree’s DNA.

“This opens up a whole new field of biology that’s little understood,” Keathley said.

For more information on Han’s research, visit his lab’s Web site.

37 Trained in Blueberry IPM Program at Trevor Nichols

There was no reason to be blue Sept. 29 at the Trevor Nichols Research Complex. That afternoon, the Fennville-area MAES field research station celebrated the second annual graduating class from MSU’s blueberry integrated pest management (IPM) training program.

The graduates included Eugenio Alemán Jr., Rosalío Rojas and María Flores from Pullman, Jamie Ochoa from West Olive, and Melinda Jackson, the first African American to receive a certificate, from Allegan. In all, 37 west Michiganders received certificates. They join the 22 graduates from 2003 in hoping to translate training into economic success growing the state’s most profitable fruit crop.

The blueberry IPM program offers courses for limited-resource growers and farm workers who want to expand their technical knowledge and skills for career advancement. It consists of a combination of classroom and laboratory instruction and hands-on field practice.

Beyond support from the MAES, the certificate program is funded by the USDA Risk Management Agency; MSU Extension (Ottawa County), the Michigan Works! service center for Allegan and Kent counties, and Project GREEEN (Generating Research and Extension to meet Economic and Environmental Needs), the state’s plant agriculture initiative at MSU.

“Isolation from mainstream culture and minimal educational background are often limiting factors for limited-resource farmers and workers who want to further their education,” said Anamaría Gómez-Rodas, agricultural and Extension educator and MAES program coordinator. “The blueberry IPM program provides these growers and farm workers with an opportunity to learn valuable technical and social skills to help them advance their careers, and it provides the Michigan fruit industry with IPM-trained growers and workers.”

MAES Scientists Excited about New Diagnostic Center

New Diagnostic Center

MAES scientists in MSU’s sprawling new Diagnostic Center for Population and Animal Health (DCPAH) say that a little extra space goes a long way.

Steve Bolin, MAES veterinary pathologist, has a compact second-story DCPAH office with room for his desk, a small table and chair, and not much else.

“Our old lab was just two times the size of this office,” said Bolin, who studies West Nile virus. “Sometimes we’d have to say, ‘We can’t accommodate this sample this week, maybe next week.’”

The new facility at the corner of Forest and Beaumont roads, formally dedicated Sept. 30, combines 10 labs that had been spread across the MSU campus. Clinical pathology, parasitology, bacteriology, toxicology and virology labs are now consolidated at the 152,000-square-foot building.

The facility also has several biosafety level III (BL-3) spaces for handling dangerous infectious pathogens. Large BL-3 rooms allow for postmortem examinations of large animals, supporting Michigan’s efforts to eliminate bovine TB. BL-3 microbiology labs are equipped for work on West Nile virus, multidrug-resistant Salmonella and other pathogens that threaten animal and human health. Bolin conducts research in these BL-3 labs.

Other MAES scientists affiliated with the DCPAH include pathologists Richard Fulton and Jon Patterson, microbiologist Carole Bolin and virologist Roger Maes.

“With pathogens, a quicker diagnosis means reduced economic loss and reduced risk to human health,” said Willie Reed, DCPAH director.

Just how much a speedy diagnosis matters was illustrated a few years ago in the American Journal of Veterinary Research.

Researchers from the University of California, Davis, created a mathematical model to simulate an outbreak of foot-and-mouth disease in a three-county region of California. According to the simulation, each hour the diagnosis of the first case, or index case, was delayed meant an additional $2 million to $3 million in economic losses.

“Now, if that were extended to California or the United States, the cost would escalate dramatically,” wrote Tim Carpenter, one of the study’s authors, in an e-mail interview.

The DCPAH is also home to technicians and scientists from the Michigan departments of Agriculture and Natural Resources. This makes it dramatically easier for the two agencies to collaborate with MSU.

“I am looking forward to observing classes, particularly anatomy classes, held in the building,” said Jean Fierke, MDNR lab scientist. “It’s great to be able to have such easy access to other animal disease researchers.”

For the first time, the MDNR scientists will be doing DNA analysis, made possible by the DCPAH’s clean spaces for lab work and ultralow-temperature freezer, complete with a backup energy system. DNA analysis might someday allow the MDNR to determine relationships between animals infected with TB or other disease agents and to identify particular strains of TB bacteria found in harvested animals.

Other DNA projects will include analyzing feathers of nestling woodcocks, small birds in the sandpiper family. The data will allow MDNR researchers to determine the male-to-female ratio of nest clutches. The sex ratio will be used as part of a population health index.

Bear hair identification will be done, too, as part of the MDNR’s work to determine population and harvest sizes for Michigan bears.

“There’s room enough in our new Wildlife Surveys Lab for larger microscopes that can be attached to computers, so we’ll be able to more easily digitize microscopic images,” Fierke said. “This will be particularly helpful when we age teeth – determining an animal’s age by counting rings, much like counting rings in a tree – of bears and other animals.”

With reports of a particularly nasty strain of avian influenza in Southeast Asia and fears that terrorists might target U.S. agriculture with microbial pathogens, people in Michigan and around the world are increasingly counting on facilities such as the DCPAH.

“The agency coordination – MSU, MDNR and MDA – serves Michigan residents well,” Bolin said. “Because we’ve already got experience working together on bovine TB, chronic wasting disease and West Nile virus, we’re well prepared to take on a big project, if necessary.”

MAES-affiliated Scientist Launches Book on Latinos in the Justice System at D.C. Briefing

A sobering portrait of U.S. Latinos hides in the dry reams of federal and state data on the justice system.

Nationwide, Latinos represent 13 percent of the U.S. population but 31 percent of all incarcerated adults. Latinos face a one-in-six chance of spending time in jail during their lifetimes, compared with a one-in-13 chance for non-Latinos. And though Latinos are no more likely than members of any other ethnic group to use illegal drugs or alcohol, they’re far more likely to be arrested and detained for drug-related offenses.

Francisco Villarruel, MAES-affiliated family and human ecology researcher and University Outreach and Engagement fellow, distilled information from a variety of sources, including the 2000 U.S. census, in a new book, Lost Opportunities: The Reality of Latinos in the U.S. Criminal Justice System. The book was released Oct. 14 at a congressional briefing in Washington, D.C., followed by a reception at the Open Society Institute, a nonprofit organization founded by billionaire George Soros.

Lost Opportunities was commissioned by the National Council of La Raza (NCLR), the largest national Hispanic organization in the United States. The 150-page monograph supports NCLR’s mission “to reduce poverty and discrimination and improve life opportunities for Hispanic Americans.”

The book provides the first comprehensive look at the topic, with analysis of the special problems associated with the prosecution and treatment of Latinos with substance abuse issues and recommendations for reversing Latinos’ downward spiral of incarceration and recidivism.

Villarruel was on hand for the release, along with his co-authors: Nancy Walker, associate director of MSU’s Institute for Children, Youth and Families; J. Michael Senger, senior staff attorney for the Center for Youth Policy Research in Traverse City, Mich.; and Angela Arboleda, civil rights policy analyst at NCLR in Washington, D.C. The book builds on themes from Villarruel’s 2002 report, ¿Dónde Está la Justicia? A Call to Action on Behalf of Latino and Latina Youth in the U.S. Justice System, which showed that Latino youth receive disparate and more punitive treatment than their Caucasian peers charged with the same types of offenses.

Key findings from Lost Opportunities are available on the NCLR Web site.

MSU Land Policy Program Receives Grants to Support Research And Outreach Projects

Land use challenges are not limited to cities that are losing residents or rural areas that are losing farmland -- they have implications for all Michigan citizens. To help meet these challenges, the MSU Land Policy Program has received funding to conduct research and outreach at the state and local levels.

The initiative, titled “Research and Outreach to Support Short-term Policy Innovation and Development in Michigan: Implementing Recommendations of the Michigan Land Use Leadership Council,” was awarded $200,000 from the W.K. Kellogg Foundation of Battle Creek, Mich., with $190,000 in matching funds from MSU.

It will feature six short-term projects that were developed on the basis of recommendations of the Michigan Land Use Leadership Council (MLULC), discussions with Gov. Granholm’s office, and exploration of public and private sector concerns.

The projects focus on developing commerce centers for Michigan cities; evaluating how alternative housing densities may affect infrastructure costs; exploring the potential for an innovation fund for Michigan agriculture; examining alternative funding sources for farmland preservation; developing a framework to identify farmland for preservation; and analyzing alternative land preservation tools, including equity insurance and equity mortgage programs.

Results of the studies will inform land use policy decision makers at the local and state levels, as well as land use stakeholders. The studies will be completed within one year.

“This funding from the Kellogg Foundation allows us to implement research projects that we believe will shape state policy choices regarding important land use issues,” says Soji Adelaja, John A. Hannah distinguished professor in land policy and MAES-affiliated scientist. “By developing teams of experts across colleges and programs at MSU, we are focusing our scientific energy on critical issues in Michigan.”

Michigan Growers Have New Tool for Making Insect, Disease Control Decisions

Fruit growers confronted by crop-damaging insects or diseases now have a readily available resource to help them eliminate the guesswork from making weather-related management decisions.

PESTNET, a real-time pest prediction system designed by MSU researchers, provides Michigan fruit growers with the weather and climate information essential to making key pest and disease control decisions.

Through PESTNET, growers can access one of 30 weather stations located across Michigan’s fruit belt to get current rainfall data, length of wetting period and average temperature during the wetting period. Reports are sent for every wetting event, either daily or twice a day, depending on the length of the event. Typically, the colder the temperature, the longer the wetting period needed to generate disease.

“The advantage to the PESTNET system is that it is accessible 24 hours a day,” said Jim Nugent, research coordinator at the Northwest Michigan Horticultural Research Station and MAES scientist. “A farmer can consult PESTNET at six in the morning and, based on the information provided, make his spray application management decisions for the day.”

The PESTNET system utilizes detailed weather information from the Michigan Automated Weather Network (MAWN). MAWN, a network of weather stations located across the state, provides detailed weather data to aid Michigan’s agricultural industry in making pest management and other weather-dependent management decisions.

PESTNET provides farmers with weather information and crop management advice reports specific to fruit production.

“PESTNET deals only with fruit,” said Jeff Andresen, MAES-affiliated scientist and MSU agricultural meteorologist. “There is another Web site that offers similar information for vegetable and field crops, except that it provides models and methods requiring the user to enter some information the program needs to provide advice specific to the crop, problem and location.”

The goal of PESTNET is to help growers and managers make better, more informed pest management decisions, Andresen said.

“We are a public service, and we want to apply new technology to help producers make profitable, environmentally sound pest management decisions,” he said.

Agricultural economists estimate that the PESTNET weather management system could help save tart cherry growers one spray a year. Environmentally, this would mean 3.25 fewer pounds of pesticides used per acre per year. One less spray per year would equal a savings of $18.96 per acre for farmers.

“There are approximately 17,000 acres of tart cherries grown in northeastern lower Michigan,” Nugent said. “If every producer were to take advantage of PESTNET, the cherry industry could save $320,000 in pesticide costs.”

Growers can subscribe to PESTNET by calling the Northwest Michigan Horticultural Research Station at 231-946-1510. The e-mail version is free; the fax version costs $25 for the season. Growers can also access the disease reports via phone toll free at 877-763-3300. A touch-tone phone is required.

The project was also supported by Project GREEEN (Generating Research and Extension to meet Economic and Environmental Needs), the state’s plant agriculture initiative at Michigan State University; and Bayer CropScience, Hamilton Farm Bureau, Wilbur Ellis, the Gowan Company, UAP Great Lakes, Great Lakes Packing Co., North Bay Produce, Inc., Graceland Fruit, Inc., and the Gerber Products Company.

Beverage Popular in Colonial Times Could Benefit Apple Industry, Entice Consumers

Renewing an old custom may lead Michigan apple growers to a lucrative new market and consumers to a tasty alternative to traditional beer and wine.

Hard apple cider is attracting renewed interest among connoisseurs of brewed products. This drink was the beverage of choice in colonial times, but its popularity fizzled out soon after industrialists realized that brewing beer from grain harvested in the Plains states was less expensive than producing hard cider.

Hard cider -- fermented apple juice -- is expected to appeal to both wine and beer drinkers because parallels exist between the beverages. Like wine, hard cider is fermented from fruit and captures the fruit’s distinct flavor. Hard cider’s alcohol content is similar to that of beer.

Hard cider produced from Michigan-grown apples could provide the state’s growers with a unique product for marketing their fruit. This is welcome news for the state’s apple growers, who have survived several years of low apple prices brought on by a surplus of fresh apple imports from China, Chile, Argentina and Poland.

Suzanne Thornsbury, MAES agricultural economist, said the apple industry is adapting to consumer needs and wants.

“Increasingly, growers are concentrating more heavily on value-added processed products such as hard apple cider or fresh sliced apples, which are now offered as a substitute for french fries in McDonald’s Happy Meals,” she said. “Developing differentiated products has become the target.”

Michigan is one of the nation’s leading producers of apples, so most of the infrastructure needed to create a hard cider industry already exists. Michigan had 40,000 acres of apple orchards in 2003, and apple production was valued at nearly $100 million. Growers harvest between 20 million and 25 million bushels of apples annually.

“Michigan has the apple trees, the growers and cider makers, the storage and processing facilities, and the knowledge to grow apples,” said Patrick O’Connor, MSU doctoral student and research associate. “Developing a Michigan hard apple cider industry makes all the sense in the world.

“We have a strong Michigan and Midwest consumer base seeking alternative and interesting products,” he continued. “If one looks at the trends in the wine and microbrewery industries, you can see that locally produced, high quality products are being accepted and sought after by consumers.”

With this in mind, numerous cider mills and microbreweries across the state are entering the hard cider business. The local hard cider market has been small but growing. Nationally, consumer interest in hard cider has been up and down.

“Consumer research may determine that folks in the Midwest prefer a sweeter taste,” he said. “Michigan apple producers may find that the best strategy will be to target their products to locals and not the nation as a whole.”

“Mapping consumer preferences is important for identifying a potential market niche and designing a successful product,” explained Janice Harte, MSU visiting associate professor of food science and human nutrition. “We can take the information we gather from beer and wine drinkers to help determine their likes and dislikes. This will help us decide what attributes we want to include in a Michigan hard cider.”

Researchers’ current focus is on developing an appropriate fermentation process and marketing strategies.

“Based on attendance and interest levels at meetings, I expect that there will be substantial growth in hard cider as the industry learns the fermentation process and adopts strong marketing strategies,” O’Connor said.

MAES Considers Unmoderated Mail Group for Faculty

MAES administrators are considering creating an unmoderated mail group for MAES faculty members. This would allow all MAES faculty members to post directly to the group about upcoming conferences, discuss research issues and share information.

Currently, the MAES faculty list server is moderated and all messages must be sent to the MAES office and approved by MAES directors.

Please let us know what you think. Would you like an unmoderated mail group? Would you use it?

Send your comments to Jamie DePolo by Nov. 22.
Last Updated: January 16, 2007
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