MAES News
January 1, 2005
- Chicken Genome Analysis Will Benefit Human Health and Agriculture
- MAES Scientists Honored at Great Lakes Expo
- Canola Study Solves Seed Oil Mystery
- Peers Rate MAES Hort Scientist's Nature Paper as No. 1
- MAES Researchers Study Users of Lansing River Trail
- McPherson Honored by Farm Bureau
- Entomology Grad Student Honored by ESA
Chicken
Genome Analysis Will Benefit Human Health and Agriculture
We may soon be thanking Michigan State University chicken
No. 256 for better treatments or even new vaccines for the flu and other
human ailments.
As the first bird and the first agricultural animal to have its genome sequenced, the chicken is paving the way for research on human diseases, as well as studies on chicken breeding to benefit agriculture. An international consortium of scientists that includes an MAES researcher analyzed the chicken genome and published a paper in the Dec. 9 issue of the British science journal Nature.
The first draft of the chicken genome was placed into free public databases for use by researchers around the world in March 2004.
The bird whose genome was sequenced, a red jungle fowl (Gallus gallus) known by her wing band number, 256, still lives on the MSU campus in a facility that serves the lab of Jerry Dodgson, MAES microbiology and molecular genetics researcher, who has worked on mapping the chicken genome for the past 17 years. At 7, she’s quite old for a chicken and is oblivious to the importance of her contributions to science.
No. 256 was chosen as the genome model because she’s from an inbred line; this makes her genome more uniform than that of non-inbred chickens. Also, red jungle fowl represents the wild type species from which all domestic chickens came. A female was chosen because female birds contain a sex chromosome (called W) that male birds lack. She also provided DNA used to create recombinant DNA clone maps of the chicken genome. Those maps provided the framework for the much more detailed genome sequence assembly.
“Chickens and humans are, in some cases, infected by the same viruses, bacteria and parasites,” said Dodgson, one of the coordinators of the International Chicken Genome Sequencing Consortium, which sequenced and analyzed the red jungle fowl genome. “The research shows that chickens and humans share more than half of their genes. The chicken genome sequence is expected to help us uncover genes that enhance natural disease resistance in birds. Then we can see if those same genes are in humans.”
Widely used in biomedical research, the chicken is an important model for vaccine production and the study of embryology and development, as well as for research into the connection between viruses and some types of cancer.
Dodgson said the sequenced genome may someday allow poultry producers to know why certain chickens lay more eggs than others or why certain broiler chickens may have less fat. They then can identify commercial chickens with the same genetic predisposition to these desirable traits.
“If we know the genes that influence these traits, we can select for chickens that better meet consumer demand and, at the same time, are healthier themselves,” he said.
“The chicken genome fills a crucial gap in our scientific knowledge,” said Francis S. Collins, director of the National Human Genome Research Institute, which is part of the National Institutes of Health, which funded the chicken genome sequencing project. “Located between mammals and fish on the tree of life, the chicken is well positioned to provide us with new insights into genome evolution and human biology. By comparing the genomes of a wide range of animals, we can better understand the structure and function of human genes and, ultimately, develop new strategies to improve human health.”
“Having the chicken genome sequenced is a fundamental tool for doing research in chicken genetics,” Dodgson explained. “Now, whatever trait we want to look at – whether it’s resistance to a virus or how the bird responds to a new type of feed – we can home in on the genetic component.”
He compared biologists’ knowing the genome sequence to a sociologist’s wanting to study the population of New York City and using a telephone directory.
“How useful is the phone book for that?” he asked. “It doesn’t provide answers on its own, but it does give you a summary of who’s there and how to reach them. It’s a starting point for asking and answering all the more complex questions. That’s what sequencing the genome does for us – now we know where all the genes are, and we can analyze them and find out what they do.”
Researchers estimate that the chicken has between 20,000 and 23,000 genes in its 1 billion DNA base pairs. The human count is 20,000 to 25,000 genes in 2.8 billion DNA base pairs.
Like all birds, chickens are thought to have descended from dinosaurs in the middle of the Mesozoic period and have evolved separately from mammals for at least 310 million years. Chickens were first domesticated in Asia, perhaps as early as 8000 B.C.
The consortium was made up of more than 175 scientists from China, Denmark, France, Germany, Japan, Poland, Singapore, Spain, Sweden, Switzerland, the United Kingdom and the United States.
MAES Scientists Honored at Great Lakes Expo
MAES researchers Ed Grafius and David Epstein were honored at the 2004 Great Lakes Fruit, Vegetable and Farm Market Expo in Grand Rapids in December.
Grafius, an entomologist, received the Master Farmer Associate Award from the Michigan Vegetable Council. Grafius was recognized for his research on insecticide resistance monitoring and management and his development of various on-farm kits to test Colorado potato beetles for resistance to insecticides. He has also been a strong advocate for vegetable integrated pest management (IPM) education and support. For several years he has organized the winter Vegetable IPM School and has written many IPM educational materials.
The Master Farmer Associate Award is presented to an individual who, though not directly involved in vegetable production, has had a significant impact on the well-being of the Michigan vegetable industry.
Epstein, MSU IPM specialist in tree fruit, received the Distinguished Service Award from the Michigan State Horticultural Society. He was honored for his participation in a number of research projects on topics including mating disruption for control of fruit pests, new monitoring systems for plum curculio and fruit flies, and biological controls for codling moth. He also coordinated the Michigan Apple IPM Implementation Project and helped develop educational materials that foster IPM adoption, including an apple scouting DVD, IPM pocket guides for stone fruit and apples, and a tart cherry pest guide calendar.
Canola Study Solves Seed Oil Mystery
Scientists from Michigan State University have uncovered a previously unknown metabolic mechanism used by plants to create seed oil.
The results, described in the Dec. 9 issue of Nature, the British science journal, address a longstanding question in plant biology – why do oilseed plants rely on a seemingly inefficient metabolic process to produce such prodigious amounts of energy-rich oil? The answer, according to the MSU team, is that plant seeds are more efficient than anyone thought.
“Seeds achieve this high efficiency by using long-known biochemical reactions that are combined in an unconventional way, which had not been expected by biochemists,” said Jorg Schwender, MSU plant biology professor and lead author of the study. MAES plant biologist and university distinguished professor John Ohlrogge was one of the paper’s co-authors.
The researchers studied canola, an annual crop in the mustard family that is widely cultivated throughout the Upper Midwest, Canada, Europe and Asia. The oil extracted from the seeds of this plant is used to make everything from margarine to industrial lubricants.
Seeds store large oil reserves to use as energy when the time comes to germinate and grow. In canola, for example, oil can make up half of the seed’s weight.
People have long exploited these oil-rich plants. People in India and China have processed canola seeds into oil for cooking and lamps for 4,000 years.
In more recent history, the rise of modern biochemistry over the past few decades has increased interest in making quantitative descriptions of plants and animals’ biochemical reactions.
With canola, the biochemical balance sheet just didn’t add up. As far as researchers could tell, the seeds were relying on an inefficient pathway to produce their sought-after oil.
All plants use carbon from carbon dioxide, a basic part of Earth’s atmosphere, to make compounds such as sugars, oils and proteins in stems, leaves and flowers. To harvest carbon from the air, plants go to a lot of trouble to convert carbon dioxide into simple sugars. When canola then transformed these sugars into oils, the plants appeared to give off large amounts of carbon dioxide.
In its research, the MSU team tagged carbon atoms and tracked how they were processed by developing canola seeds.
During the conversion of sugars to oils, researchers expected to see the tagged carbon go through a step-by-step series of chemical reactions known as glycolysis, used by all plants and animals to turn sugar into energy and cellular building blocks. This energy, in turn, is used to link the carbon building blocks into molecules of oil.
Instead, the scientists observed an enzyme called rubisco providing a more efficient pathway to convert sugar to carbon chains for oil. And the pathway involved much less carbon dioxide emission than researchers expected.
Scientists have long known that in the process of photosynthesis, rubisco is the key enzyme that captures atmospheric carbon dioxide for conversion into sugars.
However, the MSU team was surprised to see rubisco – the enzyme’s shorthand stands for ribulose bisphosphate carboxylase/oxygenase – also acting as a key agent producing oil in the seed.
In fact, in terms of metabolic heavy-lifting, rubisco appeared to be much more efficient than glycolysis. The newly uncovered rubisco bypass pathway produced 20 percent more of the carbon chain building blocks to make oil while losing 40 percent less carbon dioxide than is lost during glycolysis.
The results cast new light on the seemingly well-understood protein rubisco, which accounts for 50 percent of a plant’s total protein content and is likely the mostly abundant protein on Earth.
Through its role in grabbing carbon atoms from atmospheric carbon dioxide, rubisco has been recognized as the main chemical gateway for carbon to enter the biosphere. The new findings suggest that rubisco also gives plants a way to greatly reduce losses back to the atmosphere while they’re synthesizing oil.
In addition to enzymes, plants need energy for all this carbon-culling. They capture it using chlorophyll, a molecule responsible for plants’ green coloring. Chlorophyll uses energy from sunlight to make sugars and other compounds in plants.
It takes lots of light energy to capture carbon dioxide. This is why plants have broad canopies of light-catching leaves. The rubisco pathway that operates in seeds also requires light energy, but only a fraction of the energy needed by leaves.
In fact, the small amounts of chlorophyll in a canola seed, which has a diameter of about 1/8 inch, may grab enough sun energy to switch on the rubisco-only reaction.
“Understanding the pathways plants use to make oil will help us to develop new crop varieties with greater oil content,” said Ohlrogge. “And this becomes especially important as the world depletes its supplies of petroleum.”
Peers Rate MAES Hort Scientist's Nature Paper as No. 1
MAES-affiliated horticulture professor Ning Jiang achieved the scientific equivalent of a Billboard Top 40 song in October.
An online tool to point scientists around the world to the most significant new research in biology gave ultra-high marks to a paper Jiang co-authored for the Sept. 30 edition of the British science journal Nature.
The tool, Faculty of 1000, is maintained by open access publisher BioMed Central. F1000 is available free on the Web and relies on recommendations of 1,600 scientists in fields from biochemistry to structural biology to rate the current research.
Jiang’s paper explores how transposable elements or so-called “jumping genes” influence evolution. The paper’s "exceptional" rating is reserved for "a landmark paper representing the top 5 percent of publications each year," according to the F1000 Web site. The F1000 list changes as new papers are published and reviewed, but in mid-October, Jiang’s paper was ranked first in impact and importance among all of the papers recently published in biology.
“Dr. Jiang's contribution, picking up on the Nobel Prize-winning work of Barbara McClintock that discovered transposable elements, shows that these transposable elements are common and provides some new insights into how they work in genome evolution,” said Wayne Loescher, MAES horticulture professor and one of Jiang’s faculty mentors.
The Nature article, “Pack-MULEs: transposable elements mediate gene evolution in plants,” is featured in the Oct. 1 edition of MSU Today.
MAES Researchers Study Users of Lansing River Trail
MAES scientists have found that most people using the Lansing River Trail (LRT), an 8-mile path that follows the Grand and Red Cedar rivers, are bikers and walkers/runners who live along the trail.
Christine Vogt and Charles Nelson, MAES scientists in the Department of Community, Agriculture, Recreation and Resource Studies, worked with the Mid-Michigan Environmental Action Council (Mid-MEAC), the Lansing Parks and Recreation Department and the Rails-to-Trails Conservancy on the survey.
During the summer and early fall of 2004, the MAES researchers studied users of the LRT to provide a current estimate of the number of trail users and to profile users by activity, access points, time on the trail and satisfaction with the trail experience.
“This was a good first step toward determining where the Lansing River Trail as a main spine might eventually go,” said Murdock Jemerson, the director of parks and recreation for the city of Lansing.
The survey was the community’s first major effort to learn who uses the LRT. From more than 350 completed surveys and more than 140 hours of observing trail users, the researchers compiled the following results:
- The LRT was used about 72,040 times between May 1 and Sept. 30. The trail was used more on weekdays (64 percent) than on weekends (36 percent).
- Adults (18 and older) made up 86 percent of the users; children, 14 percent. When adults used the trail, 49 percent were bicycling, 46 percent were walking/running and 5 percent were inline skating. For children, 62 percent were bicycling, 34 percent were walking/running and 4 percent were inline skating.
- A majority (56 percent) of the people using the LRT were Lansing residents. Fifteen percent were from East Lansing and 29 percent were from elsewhere.
- Men made up 57 percent of the adult trail users. One-third of the adult users were age 50 and older, 39 percent were 35-49, and 28 percent were 18-34.
- More than half (55 percent) of the people using the LRT did so without driving a vehicle to it. About half (48 percent) of the users were people who lived 2 miles or less from the trail.
- Most of the time (84 percent) the trail was used for two hours or less. Almost everyone (93 percent) rated their experience as satisfactory.
- On average, visitors used the LRT 10 times per year, with about half their visits taking place from June to August.
- Five percent of users were disabled (had an impairment that seriously limits their participation in work or recreation).
The project was funded by a grant to Mid-MEAC from the Dick Allen Lansing to Mackinac (DALMAC) bike tour to improve the environment and quality of life in the greater Lansing area.
McPherson Honored by Farm Bureau
MSU President Peter McPherson has received the Distinguished Service to Agriculture Award, one of the top honors given by the Michigan Farm Bureau (MFB).
MFB, the state’s largest general farming organization, presented the award to McPherson and Rick Johnson, speaker of the Michigan House of Representatives, at the organization’s 85th annual meeting, Dec. 2 at the Grand Traverse Resort near Traverse City.
The award honors individuals who have made exceptional contributions to Michigan’s agriculture industry.
"Speaker Johnson and President McPherson fit the DSA qualifications to a 'T'," said MFB President Wayne H. Wood. "In their respective roles, presiding over the Michigan House of Representatives and Michigan State University, neither has lost sight of where he came from. To the contrary, both men have applied their understanding of agriculture to their influential positions and led efforts to improve Michigan's agriculture industry."
Entomology Grad Student Honored by ESA
Julianna Tuell, a doctoral student of MAES entomologist Rufus Isaacs in the Small Fruit Entomology Lab, received first place for her poster presentation, “Use of Pan Traps to Monitor the Pollinator Community in and around Highbush Blueberry Fields,” from the Behavior and Ecology Section of the Entomological Society of America at the group’s annual meeting in Salt Lake City in November.
Tuell worked with Isaacs on the project. Her research focuses on how the surrounding landscape affects the abundance and diversity of wild bees in blueberry fields.
