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Choi honored for distinguished dissertation

Jeongmin Choi (left), Gary Stacey (center) and postdoc Kiwamu Tanaka recently discovered the first plant receptor for extracellular ATP.

Jeongmin Choi (left), Gary Stacey (center) and postdoc Kiwamu Tanaka recently discovered the first plant receptor for extracellular ATP. Choi received the 2014 Distinguished Dissertation Award for her part in this work.

A former Bond LSC graduate student is being recognized for a dissertation that stands out from the crowd.

Jeongmin Choi received the 2014 Distinguished Dissertation Award this month from MU’s Graduate Faculty Senate for her work identifying the first plant receptor for extracellular ATP. The journal Science published Choi’s “Identification of a plant receptor for extracellular ATP”  Jan. 17, 2014.

Choi completed her dissertation working as a member of Gary Stacey’s lab team. Stacey, a Bond LSC researcher, nominated her work for this award. This is the second year work completed in Bond LSC garnered this award after Lefteris Michailidis won in 2013 for work on the HIV drug EFdA.

Choi has since received her Ph.D. and now resides in Cambridge, England.

Read more about her work in Bond LSC team identifies first plant receptor for extracellular ATP published in January.


Mind map: Bond LSC research explains how proteins guide migrating neurons

Bond LSC scientist Anand Chandrasekhar uses zebrafish as a model to study how motor neurons develop. These adult zebrafish lay eggs that are used in experiments to gain insight into how motor neurons arrange themselves as embryos grow into adults.

Bond LSC scientist Anand Chandrasekhar studies the zebrafish model to learn how motor neurons develop. These adult zebrafish lay eggs used to gain insight into how motor neurons arrange themselves as embryos grow into adults. Roger Meissen/ Bond LSC

Three thousand zebrafish swim circles in tanks located on the ground floor of the Bond Life Sciences Center, content to mindlessly while away their existence by eating their fill and laying eggs.

Despite their very basic higher functions, Bond LSC researcher Anand Chandrasekhar wants to understand how their brains work. More importantly, he wants to know how individual neurons end up ordered, all in the right place to support the animal’s automatic functions like breathing, swallowing and jaw movement.

This could one day lead to better understanding of specific neuronal disorders in humans.

“We are studying how cells end up where they are, and in the nervous system that’s especially critical because these neurons are assembling circuits just like in computers,” Chandrasekhar said. “If those circuits don’t form properly, and if different types of neurons don’t end up where they are supposed to, the behavior of the animal is going to be compromised.”

Zebrafish are a perfect model to study for many scientists.

Given plentiful food, adult zebrafish lay thousands of eggs that fall through a screen in the bottom of fish tanks to be collected. These eggs turn into new embryos that are nearly transparent, allowing for easy observation of the 3-4 mm fish under a microscope.

Zebrafish embryos are nearly transparent when born, making internal processes easy to observe. Only as they mature into adults like these do their scales develop pigment.

Zebrafish embryos are nearly transparent when born, making internal processes easy to observe. Only as they mature into adults like these do their scales develop pigment. Roger Meissen/ Bond LSC

Scientists have not only sequenced the zebrafish genome, but they’ve also inserted fluorescent jellyfish protein genes into the genome. This allows easy tracking of neurons.

“It’s called a reporter, and it’s used all the time to visualize a favorite group of cells. In our case, all of these green clusters of lighted up cells are motor neurons,” Chandrasekhar said. “Some groupings are shaped like sausages, some are more round, but each cluster of 50-150 cells sends out signals to different groups of muscles.”

These motor neurons are concentrated in the hindbrain. Akin to the brain stem, it controls the gills, breathing and jaw movement in these tiny fish. Genes controlling these functions are similar in zebrafish, higher vertebrates and humans despite their evolutionary paths diverging millions of years ago.

“The brain stem is the so-called reptilian brain that has changed very little, looking very similar in a lamprey or an eel all the way up to humans. All the elaborate brain structures you see in the cerebellum and the cortex are built up on top of that,” Chandrasekhar said. “Motor neurons from the brain stem send connections to muscles of the head including the gills, jaw and, in humans, the tongue, neck, voice box and muscles for breathing. We study those motor neurons and they undergo migration in many of these vertebrates systems.”

Zebrafish embryos measure only 3-4 mm seven days after they hatch. Chandrasekhar observes their motor neurons in this stage to discern how they migrate as the embryo develops.

Zebrafish embryos measure only 3-4 mm seven days after they hatch. Chandrasekhar observes their motor neurons in this stage to discern how they migrate as the embryo develops. Courtesy of Anand Chandrasekhar.

This migration and signals that control it are what Chandrasekhar’s research is all about.

For example, his recent studies suggest that a protein called Vangl2 plays an important role in regulating movement of neurons through the zebrafish embryo’s matrix of tissue. Proteins like this are present in many organisms, from flies to fish to mammals.

“When I say a neuron is migrating in its environment, it’s actually pushing its way in between all these other cells,” Chandrasekhar said. “Cells in the environment of this migrating neuron secrete proteins that may diffuse away from the cell and bind to a receptor on a migrating neuron and then kind of beckon this neuron to keep moving.”

Chandrasekhar’s work contributes to a better understanding of how basic neuronal networks are created in development. That sort of knowledge could one day help with understanding the mechanistic bases of diseases like spina bifida, a nervous system disorder that results in muscle control problems due to the spinal cord not completely closing. Versions of this defect affect 1 in every 2,000 births, according to the National Institutes of Health.

“The significance of the work that we are doing is quite high for development,” Chandrasekhar said. “It is clear that even for the process of closing of the neural tube in the spinal cord and the brain, those cells closing the neural tube actually know left side from right side. The same kinds of mechanisms are going to be important and required whether you are talking about zipping together the neural tube or about allowing cells to squeeze between other cells to migrate and end up in a target position.”

Chandrasekhar’s work on Vangl2 recently published in the Feb. 2014 edition of Mechanisms of Development and the Oct. 2013 edition of Developmental Biology. Chandrasekhar is a professor of biological sciences in the Division of Biological Sciences and Bond LSC researcher.

Read more about his work at www.chandrasekharlab.net.

Bond LSC team identifies first plant receptor for extracellular ATP

Jeongmin Choi (left), Gary Stacey (center) and postdoc Kiwamu Tanaka recently discovered the first plant receptor for extracellular ATP.

Jeongmin Choi (left), Gary Stacey (center) and Kiwamu Tanaka recently discovered the first plant receptor for extracellular ATP using Arabidopsis plants.  Roger Meissen/Bond LSC

It’s the genetic equivalent to discovering a new sensory organ in plants.

A team at the University of Missouri Bond Life Sciences Center found a key gene that sniffs out extracellular ATP.

Scientists believe this is a vital way plants respond to dangers, such as insects chewing on its leaves. The journal Science published their research Jan. 17.

“Plants don’t have ears to hear, fingers to feel or eyes to see. They recognize these chemical signals as a way to tell themselves they are being preyed upon or there’s an environmental change that could be possibly detrimental, and they have ways to defend themselves,” said Gary Stacey, a Bond LSC biologist. “We have evidence that extracellular ATP is probably a central signal that controls the ability of plants to respond to a whole variety of stresses.”

ATP (adenosine triphosphate) is the main energy source inside any cell. All food converts to it before being used in a cell, and ATP is necessary to power many of the cell processes that create more energy. Its value as an energy reserve is squandered outside the cell.

Scientists spent years trying to figure out what this compound did while floating outside cell walls. Animal researchers found that answer in the 1990s. They identified the first ATP receptors, now seen to play roles in muscle control, neurotransmission, inflammation and development.

Plant scientists observe similar extracellular ATP responses in plant biochemistry, but until now could not identify the exact receptor for it or what it did.

“We call this new receptor P2K, and it’s unique to plants,” Stacey said. “Even though animals and plants hold some responses in common, they have evolved totally different mechanisms to recognize extracellular ATP.”

Led by Stacey, MU graduate student Jeongmin Choi and postdoc Kiwamu Tanaka screened 50,000 mutant Arabidopsis plants to find ones that didn’t respond to extracellular ATP. Using a protein called aequorin – which causes jellyfish to glow – the two-year process boiled down to whether a plant would produce light when ATP was added. Since aequorin only luminesces when it binds to calcium, those plants without extracellular ATP receptors stayed dark.

“If you add ATP to wild-type plants, calcium concentrations go up and the plants produce more blue light,” Choi said. “We found nine mutant plants with no increase in calcium and, therefore, no increase in light emission.”

These Arabidopsis plants contain aequorin. Aequorin produces blue light as a result of oxidation of the substrate, in a calcium-dependent manner. When wild-type seedlings were treated with 500 uM of ATP, intracellular calcium concentration is rapidly elevated. Increased calcium were bound to aequorin, which leads to blue light emission. Courtesy Jeongmin Choi

These Arabidopsis plants contain aequorin. Aequorin produces blue light as a result of oxidation of the substrate, in a calcium-dependent manner. When wild-type seedlings were treated with 500 uM of ATP, intracellular calcium concentration is rapidly elevated. Increased calcium were bound to aequorin, which leads to blue light emission. Courtesy Jeongmin Choi

By comparing the genetic sequences of these nine mutants, Stacey’s lab pinpointed the gene to chromosome 5 and labeled it DORN 1, since it doesn’t respond to the nucleotide ATP.

This discovery casts a different light on previous research.

“What we think is happening is that when you wound a plant, ATP comes out in the wound and that ATP triggers gene expression, not the wounding in and of itself,” Stacey said. “We think ATP is central to this kind of wound response and probably plays a role in development, in a lot of other kinds of things.”

Future research will focus on exactly how this receptor works with ATP. Tanaka plans to study its protein structure, how it reacts to pests in lab situations and possible co-receptors that could also play a role in recognizing ATP.

Grants from the U.S. Department of Energy Office of Basic Energy Sciences and the Republic of Korea supported this research.

Bond LSC researchers search for causes of complex pregnancy disorder

Toshihiko Ezashi, Danny Schust, Laura Schulz and Michael Roberts collaborate on new research to discover the causes of preeclampsia.

Toshihiko Ezashi (left), Danny Schust (middle), Laura Schulz (middle) and Michael Roberts (right) collaborate on new research to discover the causes of preeclampsia. Roger Meissen/ Bond LSC

You can’t see the resemblance, but cells in Michael Roberts’ lab share a family tree with some newborns.

Their common genetics may help explain severe, early-onset preeclampsia, an inherited disorder that leads to a placenta that is often small and inefficient and possibly due to the mother’s body not fully welcoming her pregnancy.

University of Missouri Health Center scientists such as Danny Schust and Laura Schulz, work with Roberts and Toshihiko Ezashi, both Bond Life Sciences Center reproductive biologists, to search for its complex cause.

That starts in the delivery room. OBGYN’s Danny Schust and his residents save small pieces of umbilical cord from preeclampsia pregnancies, allowing Roberts and Ezashi to grow cells with the disease.

“We’re essentially recreating the previous pregnancy, going back in time as far as that baby is concerned,” Roberts said. “That allows us to look at the disease in a Petri dish, look at the properties of these cells to try and figure out what’s wrong with them.”

Preeclampsia affects 3-7 percent of births worldwide, and leads to around 50,000 deaths annually. Symptoms like high blood pressure and protein in the urine tip off doctors to the disorder, but it can go unnoticed until late in the pregnancy unless the symptoms are severe. Left unchecked the disease can lead to seizures and death. The only cure for the serious early-onset form of the disease is to deliver the baby prematurely, usually between 28-33 weeks. This leaves the newborn underweight and with complications like underdeveloped lungs.

Creating useful cells from the collected umbilical cords takes a little bit of work. Cells grown from the umbilical cords are converted into induced pluripotent stem cells, with potential to become any type of cell in the body. Researchers then use a series of hormones, growth factors and other conditions to create placental cells mirroring the previous pregnancy.

Normally the placenta – containing genes from both mother and father – grows into the wall of the uterus to establish a supply of blood, nutrients and oxygen to support the embryo. But in preeclampsia, those cells encounter problems.

Roberts and Schulz focus on extravillous trophoblasts, placental cells that invade the wall of the womb, while collaborators Toshihiko Ezashi and Danny Schust  study synctiotrophoblasts, placental cells responsible for uptake of oxygen and nutrients from the mother’s blood.

“The question becomes do these placental cells grow too much or too little, and it appears that in preeclampsia they don’t grow enough,” Roberts said. “We’re just beginning to look at their ability to move and grow through a jelly-like substance that impedes a cell’s mobility and ability to pass through small pores on a membrane. We’re also comparing the gene expression of the cells from preeclamptic patients with those from normal births..”

The Roberts/Ezashi/Schulz/Schust team still has several years left on two five-year National Institutes of Health grants and hopes to narrow the search for genes linked to preeclampsia. If they pinpoint the culprit genes, scientists could one day potentially correct the problem by developing drugs that restore normality to the placental cells or even by using an induced pluripotent stem cell approach.

“It might mean you could go back to correct the defect in those cells or take that patient’s cells, make some normal cells and perhaps substitute them back in to effect a cure,” Roberts said. “My own feelings are that we’re a very long way from doing that, but that is the thought.”

Michael Roberts is a Curators’ Professor of Animal Science, Biochemistry and Veterinary Pathobiology in the College of Agriculture, Food and Natural Resources (CAFNR) and the College of Veterinary Medicine, respectively. Toshihiko Ezashi is a research associate professor in CAFNR. Danny Schust is an associate professor and Laura Schulz an assistant professorof Obstetrics, Gynecology, & Women’s Health,  at MU’s School of Medicine.

The sweet path: how scientists try to understand sugar movement in plants

Roots play a key role in regulating where sugar ends up, such as in this tomato plant.

Roots play a key role in regulating where sugar ends up in plants like tomato.

Plant scientists are borrowing a tool from medicine to unravel how plants fight off an attack.

The Schultz-Appel Chemical Ecology lab used PET scans to decipher how and when a plant uses resources to fight off a disease or insect.

Positron emission tomography (PET) scans detect radioactive tracers and how they travel over time. In humans the scan tracks blood flow to find cancers, understand brain activity and show uptake of drugs in preclinical trials.

In plants, PET scans shine light on how plants divvy up sugars to protect against attackers.

“Doctors inject radioactive tracers into a patient, and it lights up a tumor on a PET scan because the tumor accumulates a lot of sugar and energy to grow,” said Jack Schultz, director of MU’s Bond Life Sciences Center. “The question in plants is how and where do sugars travel when young leaves are attacked by a pest.”

The sugar trip

Young leaves are of particular interest.

They attract pests because they are full of the nutrients while also being more vulnerable to attack. These youngsters can’t photosynthesize enough sugar to build chemical defenses for themselves, so they get sugars elsewhere through the phloem, part of the plant’s transportation system.

“Think of phloem as a tube with ports for the leaves,” Schultz said. “Older leaves are almost always making sugars, loading them into the phloem where they are transported to various places.”

Abbie Ferrieri, a former doctoral student in Schultz’ lab, wondered if these old leaves were supplying young leaves directly or otherwise. Using Arabidopsis thaliana, she worked with Brookhaven National Laboratory to investigate using PET scans. This mustard plant is commonly used as a model in research because of its relative simplicity and the breadth of knowledge about its inner workings.

This image shows radioactive sugar concentrations 2.5 hours after these tracer molecules were fed to older leaves in the plant. The reds indicate high concentrations in young leaves that draw sugar from the older leaves since they are the growing the most. This PET scan technique is similar to how doctors  detect some fast-growing cancer tumors.

This image shows radioactive sugar concentrations 2.5 hours after tracer molecules were fed to older leaves in the plant. The red color indicates high levels of beta particles as those sugars emit radioactivity. Concentrated in young leaves, the image indicates that these fast-growing young leaves draw the radioactive sugar from the older leaves. This PET scan technique is similar to how doctors detect some fast-growing cancer tumors.

First, she fed radioactive sugar – 2-[18F]fluoro-2-deoxy-d-glucose – to old leaves on the plant. Then she injured young leaves with a mechanical wheel and introduced methyl jasmonate to the wounds. Methyl jasmonate works as a chemical signal, telling other parts of the plant that an attack is happening.

The researchers took PET scans to determine where these sugars traveled. Ferrieri found that most sugars travel to roots and also to leaves in a line above and below them, a connection called orthostichy, in the injured plant.

But, three hours later, PET scans showed that radioactive sugars migrated to the attacked leaves regardless of whether they were in the same row on the stem. Damaged leaves then used those sugars to make phenolic glycosides, compounds that help defend the leaf.

Using the more short-lived radioactive tracers, Ferrieri saw leaves send sugar to the roots within minutes of an attack on nearby leaves. But 24 hours later, damaged leaves started receiving more sugar.

Root of the issue

This change in sugar flow and its control is a continuing curiosity that scientists like Schultz want to decipher.

Schultz’ lab knew from previous research that an insect chewing on a young leaf triggered an enzyme called invertase to break down sugars faster and call for more. But, Ferrieri thought roots might play a bigger role in controlling sugar.

To test her theory, she decided to shut the roots of her plants down using ice water.

“Plants are cold-blooded, essentially, so by submerging their roots in a lake of ice water, she found that the roots altered the rates all these things happened,” Schultz said. “You could say the roots are acting somewhat like a brain, controlling how fast carbon is moving from one place to another at any point in time.”

From human to plant

Plant scientists have been playing with radioactive particles for decades. Researchers like Melvin Calvin used radioactive carbon in the 1940s to figure out how plants capture carbon dioxide for photosynthesis.

But, this field focused more on medical applications until the past decade when plant research received renewed interest.

“The focus has changed a bit to move more into general biological and not just nuclear medicine,” said Silvia Jurrison, an MU professor of chemistry who works to find better uses of the technology.

Bond LSC labs – including those of Gary Stacey, Paula McSteen and Jack Schultz – collaborate with Jurrison to use radiotracers to explore plant processes. Jurrison hopes new compounds will make that easier.

“We’re working to develop other fluorinated compounds, such as sucrose, which could be more relevant and useful in studying plants since they use sucrose more readily.”

While research in Schultz’ lab works to explain basic plant processes, it one day could lead to new advancements.

It could help sequester carbon to slow global warming or be used to better protect future crops from pests.

“Plant defense’ effectiveness depends not only on what they are made of, but also how fast and how strongly they can respond. Anything you can understand about how a plant defends itself against pests is potentially useful,” Schultz said.

The Department of Energy’s Biological and Environmental Research division funded this research. Ferrieri now works at the Max Planck Institute for Chemical Ecology in Germany.

Read more about some of this research in the journal Plant Physiology. 

Schultz atrium web 082013-2514

Jack Schultz is director of the Bond Life Sciences Center.

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.


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.

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.”