The finding upends conventional notions of how pathogens attack and could point the way to new approaches to fighting disease not only in plants but also in people, according to Stanford researchers. Corn smut is a plant cancer.

"This establishes a new principle in plant pathology, that a pathogen can tailor its attack to specifically exploit the tissue or organ properties where it is growing," said Virginia Walbot, professor of biology and senior author of a paper published inScience detailing the study. A summary of the study will be published in the May issue of Nature Cancer Reviews as a Research Highlight.

"It would be as if a pathogen of a human could recognize whether it is in muscle or kidney or skin, and activate different genes to exploit the host more effectively," she said.

Up until now, pathologists had always assumed that when a pathogen went on the attack, it used every weapon it had, no matter which part of an organism it was infecting. But Walbot's team found that only about 30 percent of the genes in the corn smut genome are always activated, or "expressed," regardless of whether it is in seedlings, adult leaves or the tassel.

The other 70 percent of the genome is what the fungus would pick and choose from, depending on the tissue it was infecting. Some of those genes were expressed in only one of the three organs the researchers studied; the others were activated in two of the three.

"This is a revolutionary finding," Walbot said.

Her team also discovered that different parts of the maize plant activated different genes in response to being attacked.

"We hope that other people working on pathogens of all types will go back now and ask, 'when the pathogen is found in different parts of the body, is it actually using different weapons?'" Walbot said. "We think this discovery will stimulate many new experiments with existing pathogens."

Pathologists generally collect their samples from the same, characteristic place on the organism they are studying. For a plant, that is typically the leaves or fruit, while in an animal, it is usually a spot where the pathogen of interest is clearly flourishing. But as a result, Walbot said, when researchers happen to find the pathogen in another place in the organism, they generally don't test whether the pathogen is doing different things.

"It may be just the specialization of modern pathology which has resulted in the 'whole organism' context being overlooked," she said.

Walbot hopes that her team's work on corn smut will also inspire new experiments on human disease such as cancer.

"Medicine has made the same assumption that pathogens use all of their weapons wherever they are attacking a human," Walbot said.

But it may be that human pathogens are also situationally selective, genetically modulating the nature of their attack to whatever part of the body they are infecting.

"If that is the case, then we could develop drugs that are specific for the particular organ or tissue where the pathogen is found," Walbot said. "I think that holds great promise for reducing the damage done to the patient in the course of drug treatment."

Walbot got interested in researching the possibility that pathogens might vary their attack while doing fieldwork on a different project for which she was evaluating some mutant strains of maize. She noticed that certain kinds of mutants were resistant to corn smut.

Through a series of experiments with different maize mutants, she determined that the key factor in determining whether -- or how intensely -- corn smut infected a given part of a plant was the potential for growth of that particular type of tissue. Greater potential for continued growth correlated with more intense infections of corn smut and bigger, more plentiful tumors.

The key aspect was the potential -- if a mutant grew only small leaves and then quickly stopped growing, the corn smut wasn't interested, even if there was sufficient area to host some tumors.

Walbot tested how various mutant strains of corn smut behaved when infecting normal maize plants. She discovered that a strain that was highly effective in causing tumors in, say, the tassels might be completely ineffective in triggering tumors in a seedling. That told her that different genes in the fungus were involved depending on which part of the maize the fungus was attacking.

"We found genetic evidence from both the pathogen and the host that depending on the growth potential, in an organ-specific way, of both the pathogen and the host, you could modulate the number of tumors," Walbot said.

The team then set to work with DNA microarrays, lab tools that can screen thousands of genes at a time and determine which ones are active and which are not. The microarray work confirmed and quantified the results of their earlier experiments -- corn smut was indeed situationally selective, to a high degree. Less than a third of its genes were consistently activated regardless of which organ of the maize plant it was infecting.

"We had proof from the microarray that paralleled the genetic proof; that is, that there is organ-specific expression by maize in response to corn smut, and corn smut expresses a specific suite of genes depending on where it is in the plant," Walbot said.

Corn smut, though a common pathogen, does not devastate maize crops and so relatively little work had been done by plant pathology researchers to study it. In Mexico, the fungus is called "huitlacoche," and the tumors, which are used in cooking, are sometimes purposely grown on ears of corn.

"If you order a mushroom omelet in Mexico, the fungus that you are eating is Ustilago maydis, or corn smut," Walbot said.

Though the new findings may not have much impact on those who savor corn smut for its culinary delights, Walbot said researchers are likely to take note.

"That is just a prediction," she said, "but I think pathologists will be quick to pounce on this."

Coauthors of the paper include David Skibbe, a postdoctoral fellow in biology, and John Fernandes, a bioinformaticist and research assistant in biology, both at Stanford. Coauthor Gunther Doehlemann is a research group leader in terrestrial microbiology at the Max Planck Institute for Terrestrial Microbiology, Marburg, Germany

The findings, recently reported in the journal Cell, hint at an unimagined complexity of the genome and may open a new avenue of investigation regarding the mysterious causes of the human genetic disease known as ATR-X syndrome.

"Our work shows that the regulation of histone variant localization -- the shape of the so-called epigenetic landscape at different regions of the genome -- is more complex than previously thought," says first author Aaron Goldberg, an M.D.-Ph.D. student in the Laboratory of Chromatin Biology and Epigenetics at Rockefeller.

Cells use a number of mechanisms to establish and maintain the activation or silencing of specific genes. Among these is the chemical modification of histones. But in addition, histone variants, which differ from other histone proteins by just a handful of amino acids, can be inserted at specific locations in the genome to provide a cell with another mechanism for fine-tuning gene regulation.

Previous work had identified a number of histone variants, including one known as H3.3. Studies in fruit flies established that histone H3.3 is prevalent in regions of the genome where active genes are found as well as at the ends of chromosomes, in telomeres.

To track histone H3.3 and distinguish it from other histone proteins, Goldberg and C. David Allis, Joy and Jack Fishman Professor and head of the Laboratory of Chromatin Biology and Epigenetics, collaborated with researchers at Sangamo Biosciences. Together, they designed and used a DNA-cutting enzyme called a zinc finger nuclease to chemically tag histone H3.3 and distinguish it from other histone proteins in mouse embryonic stem cells. They then used a technique called ChIP sequencing to produce the first genome-wide maps of H3.3 localization first in mammalian embryonic stem cells and then again after the cells had differentiated to become neurons. In collaboration with bioinformatics experts at the Albert Einstein College of Medicine, they found that the location of histone H3.3 throughout the genome changed with stem cell differentiation.

Most scientists in the field believed that a factor known as HIRA was responsible for controlling the localization of histone H3.3. To test this idea, Goldberg and Allis used ChIP sequencing to track H3.3 in normal embryonic stem cells and in genetically modified embryonic stem cells that lack HIRA, generated by colleagues in the United Kingdom. The researchers compared the genome-wide localization of H3.3 in the presence and absence of HIRA and, as expected, found that HIRA is required for H3.3 localization at genes. Without HIRA, H3.3 was mostly gone from genes.

But that wasn't the whole story. Even without HIRA, H3.3 was still present in many other specific areas of the genome. The researchers went on to identify several additional proteins associated with H3.3.

Two of them, ATRX and Daxx, had never before been linked to H3.3. ATRX is particularly interesting, because mutations in the gene that codes for this protein in humans causes a genetic disease known as the α-thalassemia and X-linked mental retardation (ATR-X) syndrome.

"Instead of one universal factor for a particular histone variant, different factors are used to localize the same histone variant (H3.3) to different regions of the genome," says Allis. "We now know that genes, transcription factor binding sites and telomeres all have their own dedicated series of proteins to properly localize histone H3.3."

"Our work also demonstrates an important new function of the ATRX protein: the proper localization of histone H3.3 to telomeres," says Goldberg. "This finding may provide a clue as to how mutations in the ATRX gene lead to the human genetic disease of α-thalassemia and X-linked mental retardation."

"They process fat differently," said Randall Johnson, professor of biology at the University of California, San Diego, who directed the research, which is published in the April 15 issue of the journal Cell Metabolism. While their normal littermates gain weight, develop fatty livers and become resistant to insulin on a high fat diet, just like overweight humans do, the mutant mice suffered none of these ill effects.

The protein, an enzyme called FIH, plays a key role in the physiological response to low levels of oxygen and could be a new target for drugs to help people who struggle with weight gain. "The enzyme is easily inhibited by drugs," Johnson said.

Because the protein influences a wide range of genes involved in development, the scientists were surprised that its deletion improved health.

"We expected them to die as embryos," said Na Zhang, a graduate student in Johnson's lab and lead author of the study. "Then we saw they can survive for a long time."

"From the beginning I noticed that these mice are smaller, but not sick. These mice seem to be healthy," Zhang said. The lean mice have a high metabolism, and a common check for insulin resistance, a symptom of diabetes, revealed a super sensitivity to insulin.

"We fed the mice with a very high fat diet -- 60 percent fat -- just to see how they would respond," Zhang said. "Mutants can eat a lot, but they didn't gain a lot of weight. They are less fatty around their middles compared with their littermates."

Obese people develop a "fatty liver," and so did the wild type littermates. The fat mice also developed high blood cholesterol with elevated levels of the "bad" type, LDL. In lean mutants, LDL increased much less.

"All of these observations support that the modified mice have better metabolic profiles," Zhang said.

The genetic manipulations disabled the FIH gene entirely. "In every tissue, in every cell, the protein is gone," Zhang said. But the scientists wanted to know what part of the mouse physiology was responsible for the changes, so they created new mice in which the FIH protein was deleted only in specific tissues: the nervous system or the liver.

Mice that were missing FIH only from their nervous system showed most of the same effects. "But if it was only deleted in the liver, then no." Zhang said.

Though smaller, the mutant mice eat and drink 30 to 40 percent more than wild-type mice.

"Where do those calories go? To heat generation and an increased heart rate." Johnson said. They also breathe heavily compared with normal mice, taking in 20 to 40% more air. "This deep breathing is like exercise for them."

The FIH protein is part of a wide system that responds to low levels of oxygen. The mice behave as if they are breathing thin air. When people travel to higher altitudes, they breathe heavily for a few days, then adjust by producing more oxygen-carrying blood cells. "These mice never adjust to the apparent low oxygen," Johnson said. "They stay in this acute phase of hypoxic response their whole lives."

Their findings, which will be published in the April 16th issue of the journal Science, provide the first empirical support for a model of the evolution of two different sexes whereby expansion of a sex-determining region creates genetic diversity followed by genes taking on new functions related to the production of male and female reproductive cells termed gametes.

"Until now, sex-determining chromosomes had generally been viewed as regions of decay, steadily losing genes that are not involved in sexual reproduction," explains James Umen, Ph.D., assistant professor in the Plant Molecular and Cellular Biology Laboratory at the Salk Institute, who led the team conducting the study. "Our study shows the opposite-that such regions can expand and generate new genetic material much more rapidly than the rest of the genome."

Most multicellular organisms such as plants and animals have two distinct sexes with females producing large immotile eggs and males producing small motile sperm. While unicellular organisms can also reproduce sexually, the two sexes of single-celled species are typically indistinguishable from each other and are thought to represent an ancestral or early evolutionary state. However, the large distances that separate plants or animals from their closest unicellular relatives have precluded understanding the evolutionary transition to male-female dimorphism.

"In unicellular organisms like Chlamydomonas, the gametes look the same. In contrast, multicellular organisms, includingVolvox, produce eggs and sperm-they are distinctly male and female. Yet no one really has any idea how the evolution of males and females occurs or what genetic changes were required to achieve it," explains Umen.

Although the genomes of Chlamydomonas and Volvox are similar in most ways, there is one glaring exception that provided the Salk researchers with an entrée into the origin of male and female sexes-the so-called mating locus that functions in much the same way as human X and Y chromosomes to determine gender.

When Umen and his colleagues examined the mating locus genes in Chlamydomonas and Volvox they found that they shared some of the same genes, as you would expect from closely related species. However, Volvox also now possessed a surprising variety of new genes that were added to its expanded mating locus, and expression of many of these genes had come under the control of the male or female differentiation programs.

"We found that the Volvox mating locus is about five times bigger than that of Chlamydomonas," says postdoctoral researcher and co-first author Patrick Ferris, Ph.D. "We wanted to understand the evolutionary basis of this. How did it happen? And where did these new genes come from?"

To trace the origin of the added genes, the team looked to see if they could also find them in Chlamydomonas. "We found that although some of the mating locus genes in Volvox are completely new, many of them have counterparts inChlamydomonas that are near the mating locus," explains co-first author Bradley Olson, Ph.D. "So Volvox has taken these genes that initially had nothing to do with sex, incorporated them into its mating locus, and started using some of them in its sexual reproductive cycle."

The team is now studying these new mating locus genes to understand their individual roles in sex determination and sexual development.

They have already identified a Volvox mating locus gene named MAT3 that appears to have evolved a new role in sexual differentiation. MAT3 is related to a human gene called the retinoblastoma tumor suppressor that controls cell division and is frequently mutated in cancer cells. In Volvox, MAT3 probably has a role in controlling cell division as it does in animals and plants, but has also acquired intriguing gender-specific differences in its sequence and expression pattern that correlate with differences in male/female reproductive development. Umen's laboratory is following up on this finding to determine the newly evolved role of MAT3 in Volvox gender specification.

"This study shows that Volvox and its relatives are a powerful model in which to study the evolution of sex," says Umen. "It provides us with a system in which we can retrace evolutionary history to ask questions about the origin of gender and other traits that are difficult to approach in groups such as plants and animals."

The team is also working with collaborators to examine the mating locus of an evolutionary intermediate betweenChlamydomonas and Volvox called Gonium,which has between four and 16 cells. "Gonium allows us to look at the evolutionary steps between Chlamydomonas and Volvox to better understand how the evolutionary process happened," says Ferris.

In addition to Ferris, Olson and Umen, contributors to this work were Peter L. De Hoff, Ph.D., and Sa Geng, Ph.D. at the Salk Institute; Stephen Douglass, David Casero and Matteo Pellegrini at UCLA; Simon Prochnik at the U.S. Department of Energy (DOE) Joint Genome Institute (JGI), Rhitu Rai at the Salk Institute and the Indian Agricultural Research Institute, New Delhi; Jane Grimwood and Jeremy Schmutz at Hudson Alpha Institute for Biotechnology, Alabama; Ichiro Nishii at Nara Women's University, Nara, Japan; and Takashi Hamaji and Hisayoshi Nozaki at the University of Tokyo, Japan.

"The antioxidant and antimicrobial properties of the flavonoids of the raw onion make it a good candidate for use in food preservation," says researcher Jonathan Santas from the Department of Nutrition and Bromatology at UB and co-author of a project carried out in the Department of Agrifood Engineering and Biotechnology at UPC.

The study, that has just been published by the International Journal of Food Science and Technology, shows that the flavonoids of onion, in addition to having beneficial properties for health, increase the life of foods, and so "they are a natural alternative to artificial additives used in the food industry." Flavonoids are phenolic compounds (with the phenol group) which are synthesized by plants.

The results confirm that, especially the yellow variety, is "a good source of these types of substances, and there is a positive correlation between the presence of flavonoids and their antioxidant capacity."

"The onion can be effective for delaying lipid oxidation in emulsions of oil and water -a model system of foods like margarines and mayonnaises-, and it also inhibits the growth of microorganisms that alter foods," Santas indicates.

The scientific team analysed onions of the White varieties "Fuentes de Ebro" and "Calçot de Valls" and the yellow variety "Grano de Oro." Using them the researchers demonstrated that phenolic compounds in the onion prevent the development of bacteria such as Bacillus cereus, Staphylococcus aureus,Micrococcus luteus and Listeria monocytogenes, microorganisms typically associated with the deterioration of foods.

Previous studies indicate that flavonoids have beneficial effects for health due to their antioxidant, anti-inflammatory, cardioprotective, vasodilatory and anti-carcinogenic properties, making it of special interest in the prevention of chronic illnesses, such as cardiovascular illnesses, and some types of cancer.

The flavonoids of the onion are more stable than some of its other components, such as sulphur compounds. Traditionally it was indicated that these sulphuric compounds are good for the health, as they are responsible for the characteristic taste, aroma and lacrimogenic effects of the plant. These substances, which are very volatile and unstable, are released when the onion is damaged or cut.

The onion (Allium cepa) is one of the most cultivated and consumed vegetables on the planet (around 66 million tonnes in 2008, of which 1.1 million were produced in Spain, especially in Castilla-La Mancha), and one of the main ingredients of the Mediterranean diet.

The Translational Genomics Research Institute (TGen) and the Van Andel Research Institute (VARI) have created the Canine Hereditary Cancer Consortium, a program designed to study naturally occurring cancers in dogs to better understand why both pets and people get sick.

"Rare diseases in humans also show up in dogs. By studying the DNA of canines, we expect to more quickly discover the genomic causes of disease and more quickly find ways to better treat dogs, and people,'' said Dr. Mark Neff, director of the new TGen-VARI Program for Canine Health and Performance.

Using voluntarily donated saliva, blood and tumor samples from many breeds of privately owned dogs, researchers hope that by studying canine cancers they can pinpoint the causes of human cancers. The goal is to translate that knowledge into therapeutics useful to both veterinarians and clinical oncologists.

No dogs will be harmed and many should be helped. Nearly half of all dogs 10 years and older die from cancer. Dogs will be treated as patients at veterinary clinics nationwide. The research is endorsed by the American Kennel Club and by the Morris Animal Foundation. Samples will be gathered with the consent of owners and veterinarians.

In addition to cancer, TGen and VARI eventually will study neurological and behavioral disorders as well as hearing loss and other debilitative conditions in dogs that could relate to people.

The cancer research will be supported by the recent approval of a 2-year, $4.3 million federal stimulus grant to the Canine Hereditary Cancer Consortium, which includes TGen and VARI in partnership with the National Cancer Institute (NCI), the University of Pennsylvania, Michigan State University, dog breeders and veterinarians.

The public-private program also is funded by $1 million in grants from businesses involved in pet care -- $500,000 from PetSmart, and $500,000 from Hill's Pet Nutrition.

"We're proud to be part of such an innovative approach that fully supports our mission of providing total lifetime care for pets, and one that will offer hope to people and dogs who are suffering from these illnesses," said Phil Francis, Executive Chairman of PetSmart.

Neil Thompson, President and CEO of Hill's Pet Nutrition, said support of cancer research in dogs "goes hand-in-hand with the company's mission of enriching and lengthening the special relationships between people and their pets. Maintaining the health of dogs goes beyond good nutrition. We support this research and the hope it provides, which will ultimately benefit dogs and dog lovers everywhere."

Through the federal grant, researchers also will draw on experts at the National Cancer Institute's Pediatric and Genetics Branches and Comparative Oncology program, including Dr. Paul Meltzer, Chief of NCI's Genetics Branch. Dr. Meltzer and his colleagues will use gene expression profiling to identify genes involved in osteosarcoma to determine if the same genetic markers, alterations, and targets found are also found in human osteosarcoma, and in dogs. Comparing data between humans and dogs has the potential to significantly advance understanding of this cancer.

Dr. Meltzer indicated he is hopeful the study will pinpoint the genetic causes of osteosarcoma, as well as identify individualized treatment options.

The program's "bark-to-bedside" approach represents an unprecedented alliance of veterinarians, basic scientists and private practice clinicians, non-profit research institutes, universities, industry and government. The project also will involve TGen Drug Development Services (TD2), a subsidiary of TGen, which will seek partnerships with pharmaceutical companies.

Dr. Jeffrey Trent, President and Research Director for TGen and VARI, said that it is difficult to study rare cancers in people, because there is insufficient data. But by studying similar types of cancers more prevalent in dogs, researchers should be better able to help those who currently have little hope.

"There's no question that you are doubly-cursed if you get a rare cancer. You may have a very difficult disease course, and you have very little information about how to guide the physician, and what treatment would be best. For some of these rare cancers, we don't even have consensus on what the best treatments might be,'' Dr. Trent said.

For example, children with osteosarcoma, a rare bone cancer, still often results in the loss of limbs.

"Many rare human cancers are very common in dogs. We're excited about the idea that we may be able to identify areas that could be mutually beneficial -- that could help the canine patient and can help the human patient with these various cancers," Dr. Trent said. "The unique and exciting aspect of this is that it's a rare occasion where industry, academia, government and the private sector are joined together in a common goal of obtaining information to advance both pet and human health."

The study is focused on sarcomas, those cancers that originate in the connective tissues such as bone, cartilage and fat.

"The sad reality of sarcoma, because it is such a rare human disease, is that very few scientists take the time to do any research on it because it is not possible to get the number of samples you need for those kinds of studies," said Dr. Nick Duesbery, co-director of VARI's Center for Comparative Biology and Genetics.

The project began with the study of hemangiosarcoma -- angiosarcoma in humans -- a cancer for which there are currently no effective treatments. These tumors start in the lining of blood vessels and in the spleen. They are highly malignant and can be found most anywhere in the body.

Although rare in humans, these tumors are relatively common in certain breeds of dogs, such as Golden Retrievers, German Shepherds and Clumber Spaniels. After as many as 150 years of breeding, there are few genetic variations in these dogs, making it easier to identify the few genetic differences that can affect cancer susceptibility and response to drugs.

With the support of the American Kennel Club and the Clumber Spaniel Health Foundation, VARI in February 2008 began to study hemangiosarcoma in Clumber Spaniels. Researchers are using new genetic technologies developed at VARI to create genetic screens, diagnostic tests and treatments for hereditary canine cancers. VARI is analyzing the DNA and RNA of Clumber Spaniels, looking for genetic patterns that eventually could indicate if a particular dog is a carrier of a defective gene that could cause cancer.

With the addition of TGen and federal and private funding, the program is expanding to study four other cancers among as many as 20 breeds of dogs.

In the first two years, the project also will study osteosarcoma, oral melanoma, malignant histiocytosis, and non-Hodgkin lymphoma. Information from these studies will be used to develop diagnostic DNA tests for larger groups of dogs, enabling researchers to look for genes that influence cancer.

"We've got an incredible advantage here with the dogs, because these diseases are much more common in dogs than they are in humans. We can get some insight into the biology. Our strongest hope and desire is that we can translate that into therapies we can use for people,'' Dr. Duesbery said.

Dr. Gefen's research into fat cells, published in a recent issue of Tissue Engineering, has led him to conclude that the necessary tissue can be produced from fat, skin, bone and muscle cells. His breakthrough study could have hundreds of applications in the pharmaceutical and medical world.

"Drugs make our lives better, and basic science is needed to push new drugs through clinical trials. But there is no doubt that an untold number of animals are sacrificed in the laboratory setting -- both in basic research and in applied conditions when testing particular molecules," says Prof. Gefen, who heads TAU's Teaching Laboratory for Cell and Tissue Engineering. As a medical researcher himself, he was dependent on animal trials for testing new hypotheses he developed for living systems -- until recently.

Bridging the worlds of biology and engineering, Prof. Gefen is now using adult rat stem cells -- cells that can be stimulated to create skin, bone, fat and muscle tissue from an animal in a laboratory setting. In his own work on studying the mechanical properties of pressure ulcers, many tissue replications were needed. His new approach no longer requires the sacrifice of large numbers of animals. When an experiment is over, not one animal life has been lost.

The use of engineered tissues, says Prof. Gefen, may also be more scientifically efficient than using those from a living source. "The model we've created offers a very reliable method for researchers asking questions about basic science, and those investigating new drugs. We can injure tissue in a very controlled environment and grow muscle tissue without blood vessels, thereby neutralizing certain variables that often cloud what's happening in an experiment."

Though Prof. Gefen's method may not completely eliminate the need for animal testing, as few as 5% of the animals used today will need to be sacrificed in future tests, he predicts.

"It's a matter of proportion. Our tools spare an enormous number of lives," Prof. Gefen says. He is currently bringing together a number of discrete research directions from the separate fields of mechanics, tissue engineering and biology. He is also developing a new tool for researchers to investigate fat accumulation in cells (an important question for diabetes researchers) and weight loss drugs. Among his devices is one that can tell doctors how much mechanical stress is being placed on a person's foot, buttocks or other soft tissues. Another measures how much sensation is left in a diabetic limb. For all these approaches, Prof. Gefen has adopted tissue engineering methods to use fewer animals in his trials.

"We are now able to build a number of 'simplified' living tissues quite readily, and we're able to keep them 'alive,'" Prof. Gefen says. "They're genetically similar to the biological tissue of the animal, so we can factor out irrelevant physiological elements such as bleeding and pain response in an experiment. The fact that this tissue is genetically identical and the environmental factors are so well-controlled means that we can obtain far more experimental reproducibility than with experiments done on live animals."

In the future, Prof. Gefen hopes that similar models can be based on live human tissue, but that could be a number of years down the road.

Writing in the April 15 edition ofNature, scientists led by Leonid Kruglyak, a professor in Princeton's Department of Ecology and Evolutionary Biology and Lewis-Sigler Institute for Integrative Genomics, report that they developed a straightforward method for studying millions of yeast cells at the same time.

Their method allows them to identify regions of the genome that cause a specific trait in the offspring of two yeast strains that have been mated. In using such a large group, the scientists have been able to identify subtle patterns that could not be detected before.

"One of the important insights gained from research enabled by the sequencing of the human genome is that, rather than being obvious, the connections between genes and most traits are very complicated," Kruglyak said. "Our results show, however, that it is possible to identify many of the factors underlying complex traits using straightforward techniques."

The Princeton team's finding could help illuminate the answers to the current difficulties inherent in tying traits to genes, known as the "missing heritability problem," Kruglyak said.

There are some cases, he said, where scientists have identified mutations in single genes that produce a specific trait, such as a susceptibility to cystic fibrosis or Huntington's disease. In most cases, however, scientists believe that large numbers of genes working in concert produce trait variation. Some genes play a major role while others are more "quiet" but still are important. Scientists want to know all of the genes involved in producing a given complex trait, but they have not been able to find these groupings, leading to the "missing" problem.

Kruglyak was part of an expert panel the National Human Genome Research Institute convened last year on the missing heritability problem. When the Human Genome Project was completed in 2003, it provided an entire sequence of human DNA. The panel discussions centered upon the idea that, despite major technology advances made possible by the project and studies of tens of thousands of individuals, the great majority of the genetic factors responsible for differences between individuals have not yet been found.

"In many cases, the effects of genes are so small that detecting them is extremely difficult," said Ian Ehrenreich, a postdoctoral research fellow who is the first author on the Nature paper. "Under conventional methods, we just don't have the power to identify many of these genes. We knew we had to find a different way."

The method described in the paper is "a creative adaptation of existing family-based, genome-wide methodology," said Yin Yao, who is chief of the molecular and genetic epidemiology program in the division of neuroscience and basic behavioral science at the National Institute of Mental Health. She and Thomas Lehner, chief of the genomic research branch at the institute, said Kruglyak's work is highly valued and described him as a pioneer in the field of statistical genomics.

Scientists in Kruglyak's lab conduct experiments on organisms like yeast, as well as perform computational analyses, aimed at understanding how changes in DNA are shaped by molecular and evolutionary forces. They also study how these changes lead to the observable differences among individuals within a species. For this research project, the team looked to develop a process that would identify genetic associations with observable traits.

"We know in the human genome there are 20,000 genes, but I can't ask someone to point out to me which genes account for most of the variation in human height, for example, because we just don't know," Kruglyak said. "The underlying goal of what we are trying to do is both understand how complicated these patterns are and try to come up with some concrete examples where we can take some traits and nail down most of the variations, as opposed to only finding a small percentage."

Studies in model organisms like yeast -- just as in humans -- have failed to detect a large fraction of the genes believed to underlie most complex traits. So Kruglyak and his team developed a method using a sample size of yeast that went beyond the scale of any human studies. They crossed two strains of yeast, generating about 10 million offspring. Each of these progeny was genetically distinct as opposed to being a clone.

To find a subset offspring that shared a trait, the scientists grew the progeny on a chemical that causes breaks in DNA, killing most of them. They then sequenced the genomes of the few thousand yeast that survived, looking to see what genes they inherited from each parent.

Mendel's laws, which explain the principles of heredity, state that most of the genetic material should be randomly inherited from one or the other parent in a manner equivalent to a coin flip --half of the cells should have one parent's genes and half the other parent's. But, at the locations of the genes that protect yeast from the chemical, most of the cells should have genetic material from the parent with the version of the gene that produces greater resistance.

The surviving yeast cells' genomes were placed on tiny chips and scanned on automated laboratory machines, a process known as genotyping. The machines surveyed each yeast cell's genome for strategically selected markers of genetic variation. They found certain genetic variations to be significantly more frequent in the surviving yeast, serving as a powerful pointer to the regions of the genome where the genes underlying the trait resided.

The scientists repeated this experiment with other chemicals that were toxic to most of the yeast, looking again and again for skewed genetic patterns of inheritance. Each time, they were able to locate gene regions pointing to specific traits, confirming that the method worked.

Viewing their success, Ehrenreich said, "It's really been a combination of having the technology to do this genotyping precisely and also being able to survey such a large number of individuals simultaneously."

From here, the team intends to use the information it has on gene regions and markers to fine tune the method and identify the specific genes associated with each trait, and to extend the method to many other yeast strains.

Detlef Weigel, director of the Max Planck Institute for Developmental Biology in Germany, already sees additional applications for the technique. "The new work by Dr. Kruglyak and colleagues beautifully showcases how new sequencing technologies are revolutionizing genetics," he said. "While the work was carried out with yeast, I am convinced that it can be easily extended to any other genetically tractable organism, including crop plants."

Other Princeton scientists on the paper were: Noorossadat Torabi, a graduate student; Amy Caudy, a Lewis-Sigler fellow; Joshua Shapiro, a postdoctoral research fellow; Yue Jia, a research specialist; and Jonathan Kent and Stephen Martis, undergraduate students. Another author, David Gresham, who participated in the effort as a postdoctoral research fellow, is now at the Center for Genomics and Systems Biology at New York University.

The research was supported by the National Institutes of Health, a James S. McDonnell Centennial Fellowship and the Howard Hughes Medical Institute.

A team of Agricultural Research Service (ARS) researchers has found a way to speed things up by developing a way to identify genetic markers in the grapevine's genome that can be linked with specific traits, such as fruit quality, environmental adaptation, and disease and pest resistance.

The research is published in theProceedings of the National Academy of Sciences.

In order for a gene to create a protein, the gene's DNA must first be converted into what's known as messenger RNA. These RNA molecules are the instruction manuals that show the ribosomes -- the cell's protein factories -- how to build a protein. A few years ago, scientists studying bacterial cells discovered sections in certain messenger RNAs that metabolic products (metabolites) can bind to. In doing so, they induce the RNA molecule to change its spatial structure and make it possible to switch protein production on or off. For the bacteria, these sections -- the riboswitches -- provide a fast and efficient way of controlling protein synthesis. Unsurprisingly, it had previously been impossible to demonstrate the presence of such riboswitches in the chloroplasts of plant cells.

Max Planck scientists based in Golm near Potsdam were recently the first to modify and insert riboswitches into the genetic material of the chloroplast in order to control the formation of certain chloroplast proteins. The scientists smuggled a gene into the chloroplast DNA and equipped it with a riboswitch. Theophylline, a substance found in the tea plant, was used as the "switch": it has the capacity to bind to the riboswitch on the messenger RNA, thereby enabling the chloroplast ribosomes to read the RNA. "When we spray the tobacco plants with theophylline, we find that the chloroplasts form the corresponding protein. In the absence of theophylline, no protein is produced. So the theophylline riboswitch allows us to switch a gene on or off at will and see what effects result," explains Ralph Bock from the Max Planck Institute of Molecular Plant Physiology. This had previously been a difficult thing to achieve, given that the chloroplast genome contains numerous genes which are essential for survival. Switching one of these genes off permanently would result in the death of the cell, rendering it useless for further investigation.

However, studying the way chloroplasts work in more specific detail is not the only thing that can be done with the theophylline riboswitch. Riboswitches could also play an important role in the biotechnology of the future, given that chloroplasts are well-suited to the production of potential drugs. That's because each tobacco cell contains as many as 100 chloroplasts. The chloroplast genome is therefore present in many copies. As a result, it is capable of building more proteins than the DNA in the cell nucleus. By way of example, the Potsdam-based scientists modified the genes of the tobacco plant such that it was able to produce large quantities of an antibiotic in its leaves.

Proteins could be produced in much larger quantities in genetically modified chloroplasts. In many cases, however, these foreign proteins damage cellular metabolism or photosynthesis if the cells produce them continuously. Consequently, the growth of such plants is often inhibited or extremely slow. Riboswitches could prevent that. They could be used to switch on the corresponding genes when the plant is already fully formed and about to be harvested. Foreign genes have another advantage in the chloroplasts besides this: they are inherited almost without exception through the female egg cell. It is therefore extremely rare for foreign genes to spread through the pollen of the tobacco plants.