Searching for the gene: MU scientist works to find link to nutrient content of seeds

David Mendoza-Cozatl uses Arabidopsis plants like these as a model to understand how plants transport nutrients from soil to seeds and leaves.

David Mendoza-Cozatl uses Arabidopsis plants like these as a model to understand how plants transport nutrients from soil to seeds and leaves.
Courtesy Randy Mertens/CAFNR

Forget fruits and vegetables, seeds provide a critical part of the average person’s diet. From beans to cereal grains, understanding how genes and soil types impact nutrition could one day help produce more nutritious food.

One University of Missouri researcher wants to know which genes control the elements in these nutrient-rich packages.

“Iron and zinc deficiencies are considered two major nutritional disorders in the world, so there’s a lot of interest in developing plants with enhanced amounts of these micronutrients,” said David Mendoza-Cozatl, a Bond Life Sciences Center plant scientist. “The question for labs like mine is how can you convince a plant to accumulate more of these metals even though high concentrations can be toxic to plants?”

In a five-year collaboration with researchers at the University of Nevada and UC San Diego, the group measured the amounts of 14 elements in both plant seeds and leaves of mutant Arabidopsis thaliana plants planted in different soil types (salty, alkali, heavy metal and normal).

These mutants were special. Each plant had a different gene disabled, allowing researchers to tell if the disabled gene  affected uptake of minerals into the seeds or leaves.

The teams found that 11 percent of genes influence proteins relevant to the nutritional content in seeds. Soil types also played a role in the significance each gene’s impact.

The approach could be likened to understanding how a car works.

“What we are doing here is we have a car with different parts missing, and the question we are asking is what happens to the car without each of these parts,” Mendoza-Cozatl said. “In plants we ask how more or less elements or nutrients can accumulate without each of these parts, these genes. That’s how we are trying to assign the function of a gene to nutrient homeostasis.”

Mendoza-Cozatl’s work with the group focused on soil laced with non-essential heavy metals (e.g. cadmium and arsenic). They grew mutant plants from seeds and compared nutrient content of those plants’ leaves and seeds to a baseline. To do this, researchers “digested” leaves and seeds, separately, then quantified the amounts of elements.

“We turn everything into basic elements by putting the seeds or leaves in a tube, adding nitric acid and boiling them,” Mendoza Cozatl said. “We found that the mineral makeup of the seed and leaves can be different.”

This surprised him since nutrients in seeds come through the leaves via the phloem. The phloem is living tissue that transports nutrients throughout a plant.

Nutrition isn’t the only area that could benefit from knowing what controls the transport of minerals in plants.

A newly engineered plant could be made to use less fertilizer or move particular types of minerals, like toxic heavy metals.

“Many former industrial areas contain fields contaminated with heavy metals like cadmium and arsenic,” Mendoza-Cozatl said. “Understanding genes important to nutrient transport could help both with bioremediation in soil and bio fortification in food.”

Genes identified through this study will lead to new research in the Mendoza lab as well as other labs involved in this large project.

“The mechanism underlying these changes in nutrient seed composition are not known, so we still need to find how these genes are affecting the seed composition,” Mendoza said. “That’s where the advance will be more significant, and we’re not there quite yet.”

A grant from the National Science Foundation funded this research. Mendoza-Cozatl is an assistant professor of plant sciences in MU’s College of Agriculture, Food and Natural Resources and a member of MU’s Interdisciplinary Plant Group.

Read details about the research in the science journal PLOS ONE.

MU team narrows search for parasite that destroys soybean yields

MU team narrows search for parasite that destroys soybean yields

Henry Nguyen‘s progress to identify the genes responsible for root-knot nematode is garnering some attention. The Bond LSC and CAFNR plant scientist helps find genetic candidates for the disease, as explained in this recent CAFNR story by Randy Mertens.

——-

A team of scientists from the University of Missouri, the University of Georgia and the Beijing Genome Institute have used next-generation sequencing to identify two genes — out of approximately 50,000 possibilities — that defend soybeans from damage caused by the root-knot nematode (RKN) parasite.  This parasite causes millions of dollars in yield losses each year in the United States.

This is the first time the process has been used in soybean research. Using another genetic technique, the team is now working to identify the specific gene that prevents RKN from infecting the soybean. With this knowledge, resistant soybean varieties or cultivars can be bred for farmers.

RKN-infected roots are stunted and darker in color than healthy roots and have fewer nitrogen-fixing nodules. Attached SCN females may be visible as shiny white or yellow spherical bodies on the roots. Courtesy Fisher Delta Research Center, Missouri Agricultural Experiment Station.

RKN-infected roots are stunted and darker in color than healthy roots and have fewer nitrogen-fixing nodules. Attached SCN females may be visible as shiny white or yellow spherical bodies on the roots. Courtesy Fisher Delta Research Center, Missouri Agricultural Experiment Station.

Researchers believe that this process also can be applied to other crops to map genes important for traits, such as yield and stress responses, said Henry Nguyen, director of the National Center for Soybean Biotechnology (NCSB), housed at the MU College of Agriculture, Food and Natural Resources.

The discovery was recently published in theProceedings of the National Academy of Sciences. The research was funded by the Missouri Soybean Merchandising Council.

A Silent Killer of Profits

The root-knot nematode is a microscopic roundworm that can become a parasite on an enormous variety of crop species including the soybean, potato, sugar beet, rice, coconut palm, banana, pepper, tobacco, watermelon, tomato and peanut. It is one of the three most economically damaging plant parasites worldwide, causing an average worldwide yield loss of 5 percent, Nguyen said.

J. Grover Shannon.

J. Grover Shannon.

J. Grover Shannon, associate director of the NCSB and David M. Haggard Endowed Chair of Soybean Breeding at MU, estimates that RKN and other nematodes (excluding soybean cyst nematode) accounts for annual losses of more than $50 million in soybean yield in the United States. The U.S. is the world’s largest producer of soybeans, growing more than 3 billion bushels, or 33 percent of the world’s production.  The value of the 2011 U.S. soybean crop exceeded $35.7 billion. U.S. soybean and soy product exports exceeded $21.5 billion in 2011.

Jinrong Wan, MU research scientist, said RKN larvae infect plant roots, causing the formation of root-knot galls that drain the plant’s photosynthate and other nutrients. Infection of young plants may be lethal, while infection of mature plants causes decreased yield.

RKN is a silent killer of profits, Wan continued. Often, it thrives as a parasite throughout a growing season in annuals, or over many years in perennial crops, without any above-ground signs or symptoms. Only when harvest is over and yield has been quantified is the parasite’s damage commonly seen.

Jinrong Wan.

Jinrong Wan.

No method currently used effectively controls RKN. Crop rotation is a typical technique, but with incomplete results because RKN can live for a long time and can infect an enormous variety of plants. Nematicides are another intervention, but are dangerous to the respiratory systems of animals. Biological control is practiced in some cropping systems, with two organisms showing only limited success. Clearly the most efficient method of control is by using resistant cultivars, said Nguyen.

A Faster and Better Assay

Nguyen said next-generation sequencing technology is a new and important tool for plant scientists.

Henry Nguyen.

Henry Nguyen.

Currently, scientists use single nucleotide polymorphisms to map genetic markers to determine what genes are responsible for important traits, such as disease resistance. That process, said Nguyen, is too slow considering the tens of thousands of genes that have to be surveyed.

To speed up the process, Nguyen’s team used Next-Generation Sequencing Technology to sequence the whole genome of more than 200 soybean inbred lines. Another advantage of using this method is that the mapping resolution can be significantly improved – the genes can be narrowed down to a very small chromosome region quickly, Tri Vuong, MU research scientist, added.

This story was originally posted on CAFNR News  where you can find on MU agriculture research.

The secret of the legume: Bond Life Sciences Center researchers pinpoint how some plants fix nitrogen while others do not

Yan Liang, an MU post doc, and Gary Stacey, a Bond Life Sciences investigator, stand in front of soybean plants from their greenhouse. The researchers focus on understanding the symbiotic relationship between legumes like soybean and nitrogen-fixing bacteria.

Yan Liang and Gary Stacey research the symbiosis between legumes, like these soybeans, and nitrogen-fixing bacteria at the Bond Life Sciences Center.

A silent partnership exists deep in the roots of legumes.

In small, bump-like nodules on roots in crops like soybeans and alfalfa, rhizobia bacteria thrive, receiving food from these plants and, in turn, producing the nitrogen that most plants need to grow green and healthy.

Scientists have wondered for years exactly how this mutually beneficial relationship works. Understanding it could be the first step toward engineering other crops to use less nitrogen, benefitting both the bottom line and the environment.

University of Missouri Bond Life Sciences Center researchers recently identified what keeps crops like corn and tomatoes from the sort of symbiotic relationship enjoyed by legumes. Science published this discovery online Thursday, September 5, 2013.

“Our work uniquely shows that all flowering plants, not just legumes, actually do recognize the chemical signal given off by rhizobia bacteria,” said Gary Stacey, Bond LSC investigator and plant sciences professor.

His lab identified the most likely receptor for this chemical and showed that the signal suppresses the plant immune response, which normally protects plants from pathogens. This allows rhizobia a better chance to infect and live inside the plant.

Grounded

Chemical signals are extremely important to plants.

Since plants can’t walk around to explore or avoid danger, receptors in cells of each plant act as its eyes and ears. They gather information about insects, bacteria and other threats and stresses from chemicals. These signals allow the plant to respond and adapt to its environment, such as resisting stresses like drought and infection by pathogens.

With rhizobia, the bacteria produce lipo-chitin, a sugar polymer with a fatty acid attached. This molecule is similar to chitin normally found in the cell walls of fungi, the exoskeletons of crustacea or insects.

Legumes, such as soybean, sense this signal – called a NOD factor since it triggers nodulation – and create the nodules where the bacteria fix atmospheric nitrogen into the soil.

That doesn’t happen in other plants.

Two possibilities

Scientists once gravitated toward thinking that non-legumes, which are not infected by rhizobia, just weren’t capable of receiving the NOD factor signal. But, a less popular theory guessed that plants like corn do receive the NOD factor signal but interpret it differently or have a problem with the mechanistic pathway.

Stacey said figuring out which is happening is like fixing a motion-detecting light.

“If you walk into a room and the light doesn’t turn on, either the motion detector is broken or there’s a breakdown of the electrical circuit between the detector and the light bulb,” Stacey said. “The analogy in a corn plant would be that it either doesn’t recognize the signal or recognizes the signal but lacks the ability to couple it with downstream developmental effects.”

Stacey’s lab set out to determine which was true.

Corn, soybean, tomato and Arabidopsis were treated with bacterial flagellin, a protein known to cause a strong immune response, and also received doses of the NOD factor. These represent a diverse spectrum of plants to ensure the results were wide ranging. Results showed the NOD factor suppressed the immune response by 60 percent.

“After these results, what allowed us to take the next step forward is that we were able to make mutant plants with changes in what we think is the receptor for the NOD factor,” Stacey said. “That step showed that when plants lack the ability to recognize the NOD factor, you don’t see the suppression of the immune system.”

Since all plants seem to respond to the NOD factor, scientists think this immunity suppression ability could be evolutionarily ancient and part of how rhizobia bacteria changed from foe to a symbiotic partner.

“There’s this back and forth battle between a plant and a pathogen,” said Yan Liang, an MU post doc in Stacey’s lab. “Rhizobia eventually developed this chemical to inhibit the defense response and make the plant recognize it as a friend.”

A future in the field

Nitrogen has both an environmental impact and high price tag.

Fossil fuels are combined with nitrogen from the atmosphere to create the fertilizer.

When applied to fields, the excess fertilizer also ends up in rivers and streams, contributing to nitrification and hypoxia in waterways.

“The dead zone in the Gulf of Mexico is generally attributed to agricultural runoff and producing nitrogen fertilizer increases dependence on fossil fuels,” Stacey said.  U.S. farms used almost 13 million tons in 2011, according to the USDA, with almost half of it being applied to corn. Nitrogen prices ranged from $400-$850 per ton in the U.S. in 2013.

Nitrogen fixed in the soil by rhizobia is the closest thing to a free lunch a plant can get. For farmers, that’s one less input needed and is part of why legumes remain a staple of crop rotations.

In 2012, the Bill & Melinda Gates Foundation donated $10 million to the John Innes Center in Norwich, United Kingdom, to study and develop symbiotic relationships between bacteria and cereal crops, most notably corn. It hopes to bolster subsistence farming in Africa through the five-year project.

While it’s a long way off, Stacey’s research is another step to improving crops.

“Since the discovery in 1888 of this nitrogen-fixing symbiosis between this bacteria and plants like soybean, the dream has always been to transfer this technology into other plants like corn, wheat or rice,” Stacey said. “Once we understand exactly what’s mechanistically unique in a legume, then we hope to be able to transfer that trait into corn many years down the road.”

A grant from the Office of Basic Energy Sciences of the U.S. Department of Energy funded this research. Gary Stacey is a Bond Life Sciences Center investigator, a professor of plant science in the University of Missouri College of Agriculture, Food and Natural Resources and has an adjunct appointment in MU’s biochemistry department.

Canary in the water: The impact of BPA and estrogen on aquatic life

MU Bond Life Sciences Center investigator Cheryl Rosenfeld is studying the impact of BPA on painted turtles in collaboration with scientists from MU, the St. Louis Zoo, the U.S. Geological Survey and Westminster College. These turtles and many amphibians are extremely sensitive to environmental contaminants and may indicate wider issues from certain types of environmental contaminants.

Bisphenol-A (BPA) and other estrogenic compounds are becoming increasingly prevalent in the environment. More than 8 billion tons of BPA are produced each year in manufacturing, and pharmaceutical compounds like ethinyl estradiol make their way into rivers and streams. They can affect the sexual and cognitive development of animals.

MU researchers tackle tough grapevine pest

MU researchers tackle tough grapevine pest

Division of Plant Sciences and Bond LSC investigators Jack Schultz and Heidi Appel have been awarded a grant by the National Science Foundation to unravel the mystery of how an insect pest gets the better of the world’s – and Missouri’s – most valuable fruit crop. Grape phylloxera is an insect that infests grapevine leaves and roots, reducing the plant’s production and cutting off its water supply. The insect somehow convinces the plant to construct a complex home and feeding site around itself, called a gall. Many kinds of insects can cause plants to create galls, but no one knows how they do it. Clues suggest that the insect uses chemical signals to alter the activity of genes needed to develop these unique organs. The Schultz/Appel team, helped by collaborators at the University of Florida, will identify grapevine genes the insect manipulates to form a gall. Not only will this solve a long-standing mystery about the galling process, but it will also offer the grape/wine industry a means of identifying resistant vines. Missouri saved the world’s wine industry once before, by exporting phylloxera-resistant vines. This research project offers a second opportunity to defeat this scourge of the vineyard.

Bond LSC post doc recognized for his research on novel HIV drug

Lefteris Michailidis received the 2013 Distinguished Dissertation Award for his work to understand EFdA, a new drug that shows promise to treat resistant HIV viruses with fewer side effects.

Lefteris Michailidis received the 2013 Distinguished Dissertation Award for his work to understand EFdA, a new drug that shows promise to treat resistant HIV viruses with fewer side effects.

A four-letter drug could be the next generation of AIDS treatment.

EFdA, a new anti-viral drug in development, promises HIV treatment that is more effective with fewer side effects and less resistance.

Lefteris Michailidis received the 2013 Distinguished Dissertation Award earlier this year from the MU’s Graduate Faculty Senate for his work to understand how EFdA works on a molecular level. Michailidis currently works as a post-doc in Stefan Sarafianos’ lab. Sarafianos is an MU associate professor of Molecular Microbiology and Immunology and a Bond Life Sciences Center investigator.

“My work shows EFdA works with a different mechanism and that could change the way we design drugs to combat HIV in the future,” Michailidis said. “It’s also a very potent drug and it’s not just proof of concept of this idea, but hopefully it can be used in the clinic.”

A month after Michailidis defended his dissertation in 2012, the drug company Merck licensed EFdA and it is currently in preclinical trials.

Collaboration made this progress possible.

EFdA was discovered in 2001 by Japanese researchers at Yamasa Corporation, a soy sauce producing Japanese company. Sarafianos’ lab at the Bond Life Sciences Center cooperated with them and Michael Parniak at the University of Pittsburgh to explore the drug.

Michailidis looked at the structure of EFdA, comparing the way it works to widely used anti-HIV drugs. These current drugs, called Nucleoside Reverse Transcriptase Inhibitors (NRTIs), are used as one of the first therapies in AIDS treatment. They target reverse transcriptase (RT), an enzyme that starts viral replication. By competing with natural nucleotides, NRTIs can terminate DNA synthesis, stopping the spread of the virus.

Michailidis found that EFdA ‘s structure includes a hydroxyl group that is missing from current NRTIs like tenofovir, the most prescribed HIV drug. This difference makes EFdA effective against resistant, mutated HIV strains where traditional classes of HIV drugs fail.

AIDS was first reported in 1981, and its diagnosis was equivalent to a death sentence. Since the first NRTI drug was approved in 1987, HIV has progressed to more of a manageable, chronic disease in the developed world. The World Health Organization estimated in 2011 that 34 million people live with HIV, with 1.4 million of those living in North America.

Michailidis hopes his research will help lead to future drugs on the market that will counter HIV resistance and improve the lives of patients.

“These new insights into the mechanism of action and resistance of NRTIs may lead to development of novel antiviral regimens in the near future,” Micharilidis said. “It’s not just a theoretical base to prove something unique, but eventually we hope it will have an application.”

Claiming Kin, MU’s 9th annual Life Sciences and Society Symposium kicks off today

20121003-DSC_0876resize

Stephanie Coontz, award-winning writer on the history of marriage, chatted with Jack Schultz, director of the Bond Life Sciences Center. Coontz presented the keynote address Friday night at Claiming Kin, MU’s 9th annual Life Sciences and Society Symposium.

Check out Saturday and Sunday’s speakers on the subject of kinship athttp://lssp.missouri.edu/claimingkin/schedule.

Renowned anthropologist speaks about Noble Savages

Chagon1resizeweb

Napolean Chagnon spoke to a full house Tuesday in Monsanto Auditorium about his new book, Noble Savages. Chagnon joined MU’s Department of Anthropology as Distinguished Research Professor and Chancellor’s Chair of Excellence in 2013. He was elected to the National Academy of Sciences in 2012, but is most known for contributions to his genealogical research, his contributions to evolutionary theory in cultural anthropology and his work in the study of warfare.

His new book is a retrospective look at his work as an anthropologist, where he most famously document the Amazonian Yanomamö tribe of Venezuela in the 1960s. His work caused controversy because it detailed a tribe violence within the tribe, an attribute at the time thought to be caused by the intrusion of modern societies on native people.

Read more about Chagnon and Noble Savages: My Life Among Two Dangerous Tribes—the Yanomamö and the Anthropologists from Mizzou Weekly.

It’s a matter of territory

Territory matters to California mice when it comes to mating.

Males in this monogamous mouse species use their scent glands to mark the boundaries of their home range, making their dominance known one scent at a time to other males. Too much bisphenol A (BPA) in their environment can change that, short-circuiting their ability to complete this crucial task. Male mice fed BPA couldn’t mark territory when a normal male entered their environment, putting them at a disadvantage. That means the chemical could seriously impact whether these mice pass their genes on to the next generation.

Cheryl Rosenfeld, a researcher here at MU’s Bond Life Sciences Center, recently published these results in PLOS ONE. Rosenfeld previously studied deer mice, finding BPA disrupted the ability of males to find their mates. She decided to repeat the experiment with California mice because their monogamous relationships, where both parents care for their offspring together, might mirror human relationships more closely.

If you’re interested in the nuts and bolts, read Rosenfeld’s the whole study at PLOS ONE, an international open-source science journal.

A National Institute of Health Challenge Grant, a Mizzou Advantage grant and support from Food for the 21th Century Program made this research possible. Rosenfeld collaborated across disciplines with teams from the Bond Life Sciences Center, Biological Sciences, Interdisciplinary Neuroscience, Department of Psychological Sciences, Thompson Center for Autism and Neurodevelopmental Disorders, Animal Science, Biochemistry, Biomedical Science, Genetics and CAFNR.

Read MU’s News Bureau release on Rosenfeld’s work.

Welcome

Jack Schultz, Professor of Plant Sciences and Director of the Bond Life Sciences Center

Jack Schultz, Professor of Plant Sciences and Director of the Bond Life Sciences Center

Welcome to Decoding Science, a new science blog from the Christopher S. Bond Life Sciences Center at the University of Missouri! The Bond Center is a highly interdisciplinary research organization that promotes collaboration to address questions where different disciplines and study systems meet. Our approaches range far and wide through the life sciences and beyond. So we have lots of stories of our own and we follow interesting science tales everywhere we find them.

So, why “Decoding Science”? Well, we realize that scientists speak their own language, loaded with strange jargon and complicated logic. That can make them hard to understand. We really want to change that, so that anyone can enjoy the exciting science stories we find. We’ll be decoding the strange words and concepts so we can share them with all.

Stay with us and you’ll wind up as excited as we are about what’s happening in science and our world, and you’ll pick up stories and factoids you may even want to retell. So – let’s get started!