News Release

Wednesday, April 12, 2006

 MSU researchers shake out basis for rice domestication

Contact: Michael Steger: (517) 432-4561, stegerm@msu.edu; Sue Nichols: (517) 353-8942, nichols@msu.edu; or Tao Sang: (517) 355-4689, sang@msu.edu

EAST LANSING, Mich.  Michigan State University scientists have identified the genetic mutation that reduces grain shattering during rice domestication – research that will improve production of the crop that feeds more than half of the world’s population. In an article on the cover of  the March 31 edition of Science Magazine, MSU scientists, led by Tao Sang, associate professor of plant biology, identify for the first time the genetic mutation for the reduction of shattering, a key step in the domestication of all cereal crops including corn and wheat.

The researchers were able to pinpoint and confirm that a single base pair mutation in DNA causing an amino acid change in a protein led to non-shattering rice varieties. This slight change in DNA prevented mature rice grains from easily falling from stalks to allow a more effective field harvest. In essence, humans several thousand years ago unknowingly practiced de facto gene selection by planting varieties with this trait.

Shattering in cereal crops refers to grains easily falling off of plants.  The shattering trait of the wild forerunners of rice and cereals prevents effective field harvest and is undesirable for cultivation.

“What we can learn from historical plant domestication will benefit our ongoing and future effort to domesticate energy crops that will be equally important to the long-term sustainability of our society,” Sang said. “It is remarkable how the earliest farmers could have selected a single mutation in DNA to develop a major food crop of the world.”

The researchers first determined which chromosomal regions contained the mutations selected for rice domestication. Chromosome 4 was pegged as being responsible primarily for the reduction of shattering.

“Several hundred hours were spent in the greenhouses where we had to shake the plants and record the various degrees of shattering,” Sang said. “Even with all the advances in technology, a careful firsthand observation proves to be essential for biological research.”

The researchers then developed a new method for rapid and cost-effective DNA isolation to clone a gene from the chromosomal region. Changbao Li, research associate in plant biology, invented a process that increased the speed of DNA isolation and allowed researchers to efficiently complete the screening of 12,000 seedlings.

“This technical innovation will greatly speed up genetic research for plants since it saved us time and money, yet delivered accurate results,” Sang said.

“By tracing the breeding of rice and identifying the genetic mutations, the researchers have opened new doors to the science community that benefit the world through a more effective use of the land and water used to grow rice,” said Rich Triemer, chairperson of the Department of Plant Biology.

“These findings will improve yields to a crop that is the staple food for more than half of the world’s population. Our scientists are continuing the legacy started by William Beal more than one hundred years ago of using plant research to benefit the world,” he said.

The article, “Rice Domestication by Reducing Shattering,” was published today in Science Express – an electronic publication designed to get important papers quickly in front of the scientific community prior to being published in Science. Science is the world's leading journal of original scientific research, global news, and commentary and is published by the American Association for the Advancement of Science.

The research is funded in part by the Michigan Agricultural Experiment Station at MSU. Other Department of Plant Biology researchers involved in this project include Changbao Li, research associate, and Ailing Zhou, graduate student. For more information visit the plant biology Web site at http://www.plantbiology.msu.edu/ or Science Express at http://www.sciencemag.org/sciencexpress/recent.dtl. 

Source: Scripps Research Institute

Posted: March 18, 2006

Minor Mutations In Avian Flu Virus Increase Chances Of Human Infection

Scientists at The Scripps Research Institute, the Centers for Disease Control, and the Armed Forces Institute of Pathology have identified what the researchers described as a possible pathway for a particularly virulent strain of the avian flu virus H5N1 "to gain a foothold in the human population."

 The H5N1 avian influenza virus, commonly known as "bird flu," is a highly contagious and deadly disease in poultry. So far, its spread to humans has been limited, with 177 documented severe infections, and nearly 100 deaths in Indonesia, Vietnam, Thailand, Cambodia, China, Iraq, and Turkey as of March 14, 2006, according to the World Health Organization (www.who.int).

"With continued outbreaks of the H5N1 virus in poultry and wild birds, further human cases are likely," said Ian Wilson, a Scripps Research professor of molecular biology and head of the laboratory that conducted the recent study. "The potential for the emergence of a human-adapted H5 virus, either by re-assortment or mutation, is a clear threat to public health worldwide."

Of the H5N1 strains isolated to date, the researchers looked at A/Vietnam/1203/2004 (Viet04), one of the most pathogenic H5N1 viruses studied so far. The virus was originally isolated from a 10-year-old Vietnamese boy who died from the infection in 2004. The hemagglutinin (HA) structure from the Viet04 virus was found to be closely related to the 1918 virus HA, which caused some 50 million deaths worldwide.

Using a recently developed microarray technology—hundreds of microscopic assay sites on a single small surface—the study showed that relatively small mutations can result in switching the binding site preference of the avian virus from receptors in the intestinal tract of birds to the respiratory tract of humans.These mutations, the study noted, were already "known in [some human influenza] viruses to increase binding for these receptors."

The study was published on March 16, 2006 by ScienceXpress, the advance online version of the journal Science.

Receptor specificity for the influenza virus is controlled by the glycoprotein hemagglutinin (HA) on the virus surface. These viral HAs bind to host cell receptors containing complex glycans—carbohydrates—that in turn contain terminal sialic acids. Avian viruses prefer binding to a2-3-linked sialic acids on receptors of intestinal epithelial cells, while human viruses are usually specific for the a2-6 linkage on epithelial cells of the lungs and upper respiratory tract. Such interactions allow the virus membrane to fuse with the membrane of the host cell so that viral genetic material can be transferred to the cell.

The switch from a2-3 to a2-6 receptor specificity is a critical step in the adaptation of avian viruses to a human host and appears to be one of the reasons why most avian influenza viruses, including current avian H5 strains, are not easily transmitted from human-to-human following avian-to-human infection. However, the report did suggest that "once a foothold in a new host species is made, the virus HA can optimize its specificity to the new host."

"Our recombinant approach to the structural analysis of the Viet04 virus showed that when we inserted HA mutations that had already been shown to shift receptor preference in H3 HAs to the human respiratory tract, the mutations increased receptor preference of the Viet04 HA towards specific human glycans that could serve as receptors on lung epithelial cells," Wilson said. "The effect of these mutations on the Viet04 HA increases the likelihood of binding to and infection of susceptible epithelial cells." The study was careful to note that these results reveal only one possible route for virus adaptation. The study concluded that other, as yet "unidentified mutations" could emerge, allowing the avian virus to switch receptor specificity and make the jump to human-to-human transmission.

The glycan microarray technology, which was used to identify the mutations which could enable adaptation of H5N1 into the human population in the laboratory, could also be used to help identify new active virus strains in the field by monitoring changes in the receptor binding preference profile where infection is active, according to according to Jeremy M. Berg, the director of the National Institute of General Medical Sciences (NIGMS), part of the National Institutes of Health (NIH). The glycan microarray was developed by The Consortium for Functional Glycomics, an international group led by Scripps Research scientists and supported by the NIGMS.

"This technology allows researchers to assay hundreds of carbohydrate varieties in a single experiment," Berg said. "The glycan microarray offers a detailed picture of viral receptor specificity that can be used to map the evolution of new human pathogenic strains, such as the H5N1 avian influenza, and could prove invaluable in the early identification of emerging viruses that could cause new epidemics."

Other authors of the study include James Stevens of Scripps Research; Ola Blixt of Scripps Research and Glycan Array Synthesis Core-D, Consortium for Functional Glycomics; Terrence M. Tumpey, Influenza Branch, Division of Viral and Rickettsial Diseases, Centers for Disease Control and Prevention; Jeffery K. Taubenberger, Department of Molecular Pathology, Armed Forces Institute of Pathology, and; James C. Paulson, Scripps Research and Glycan Array Synthesis Core-D, Consortium for Functional Glycomics. The work was supported by the National Institute of Allergy and Infectious Disease, the National Institute of General Medical Sciences and the National Institutes of Health.

Press Release 06-035
Doodle Search

New software can hunt through online catalogs using only a sketch

Working with support from the National Science Foundation's Small Business Innovation Research (SBIR) program, Imaginestics, a company located in West Lafayette, Ind., has created 3D-Seek: a new kind of search engine that lets users find items in an online catalog without ever needing to know the items' names, part numbers or keywords.

Thanks to a major advance in practical pattern recognition, all the user needs is a freehand sketch--a doodle.

The Purdue Research Park-based company developed 3D-Seek and its associated catalog mainly for manufacturing firms, which are constantly looking for hinges, bolts, conveyor belts, motors and a host of other products. For those firms, notes Errol Arkilic, the NSF officer overseeing the SBIR awards, "this search engine can help find the proverbial needle in the haystack. By allowing manufacturers to re-deploy and re-purpose parts from existing catalogs, the tool can make it easier for businesses to design complex mechanical systems."

Eventually, however, the basic search engine could prove equally useful for ordinary shoppers: instead of having to go to the hardware store lugging, say, a specific plumbing joint, a customer could just sketch what he or she needed to find an exact match.

The 3D-Seek software was built on top of technology created by Karthik Ramani and his colleagues at the NSF-supported Purdue Research and Education Center for Information Systems in Engineering (PRECISE) at Purdue University. Ramani, who is an NSF CAREER Awardee, the director of PRECISE and the chief scientist of Imaginestics, had led the way toward search algorithms that ranked among the world's fastest for a certain application: comparing the computer-aided design files and other 3-D images that are ubiquitous in industry.

From there, further collaboration between university and company researchers resulted in a system that required only critical shape characteristics, not entire image files. This allowed even faster search speeds and protected the proprietary information held by parts suppliers loading their products to the online database. And as a bonus, the refined search could now glean important information from quick sketches, a favorite means of communication for engineers and designers.

The public can try the freehand-search online at the 3D-Seek portal.

"In order to make such a search engine commercially viable we had to overcome the challenge of matching something as rudimentary as a doodle to a 3-D object - in seconds," said Nainesh Rathod, co-founder and President of Imaginestics. "This is important, as Web users have become accustomed to retrieving information instantaneously. Our shape-search engine processes data that are far more complex then those handled by the leading Internet search engines, and yet still finds results quickly."

While researchers have been working for several years on software that can compare industry-standard 3-D image files to each other, the new method is faster than most and permits search "terms" that are far outside the norm. With the new tool, users can find in seconds what once took weeks of warehouse searches or even a complete part redesign. "It's the difference between describing a part over the phone and seeing it in person," added Rathod. "You can look at it visually instead of explaining it in words."

The 3D-Seek catalog currently contains more than 6,000 parts and continues to grow as suppliers manually upload their files or as the system's i-crawler web spider discovers parts online. A related technology, i-prowler, hunts for image files on a user's computer and merges them with either the online database or an internal company catalog - critical for large companies that may not have simple mechanisms to search internal inventories.

Even global corporations can have difficulty tracking supplies internally. According to Rathod, a Fortune 100 manufacturer recently estimated that lack of a proper search technology resulted in duplicate purchases for 10 to 16 percent of parts.

One reason is that factories creating the same product, yet located continents apart, will go to different suppliers for the same component. Those suppliers may have to independently engineer the components from scratch, which can be costly. With an easily searchable company-wide database, even metric conversion would not stand in the way of a part search.

-NSF-