research

Unmasking the unknown

Scientists explore genetic similarities between plants and mice

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University of Missouri PhD Candidate Daniel L. Leuchtman peers through an Arabidopsis plant. Leuchtman has been experimenting with replacing a gene in the plants immune system with a similar gene from mice. | Photograph by Justin L. Stewart/MU Bond Life Sciences Center

By Justin L. Stewart | MU Bond Life Sciences Center

Almost two-thirds of what makes a human a human and a fly a fly are the same, according to the NIH genome research institute.

If recent research at the University of Missouri’s Bond Life Sciences Center is verified, we’ll soon see that plants and mice aren’t all that different, either.

Dan Leuchtman studies a gene in Arabidopsis plants called SRFR1, or “Surfer One.” SRFR1 regulates plant immune systems and tell them when they are infected with diseases or illnesses. Leuchtman studies this model plant as a Ph.D. candidate at MU, splitting time between the labs of Walter Gassmann and Mannie Liscum.

His research involves breeding Arabidopsis plants missing the SRFR1 gene and then replacing it with the MmSRFR1 gene.

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A series of Arabidopsis plants show the differences between the plants, from left, without SRFR1, with MmSRFR1 and with SRFR1. | Photograph by Justin L. Stewart/MU Bond Life Sciences Center

So, what is MmSRFR1? Leuchtman and company believe it’s the animal equivalent of SRFR1, though they aren’t fully aware of all of its’ functions.

“We’re actually one of the first groups to characterize it,” Leuchtman said.

Arabidopsis plants missing the SRFR1 gene struggle to grow at all, appearing vastly different from normal plants. Leuchtman says that a plant missing the SRFR1 gene is a mangled little ball of leaves curled in on itself. “It’s really strange looking.”

While his experiments haven’t created statuesque plants equal to those with natural SRFR1 genes present, the Arabidopsis plants with MmSRFR1 show a notable difference from those completely lacking SRFR1. Leuchtman says the plants with MmSRFR1 lie somewhere in between a normal plant and one lacking SRFR1.

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University of Missouri PhD Candidate Daniel L. Leuchtman poses for a portrait in a Bond Life Sciences Center greenhouse. Leuchtman has been experimenting with replacing a gene in Arabidopsis plants immune system with a similar gene from mice. | Photograph by Justin L. Stewart/MU Bond Life Sciences Center

“At its’ core, it’s more understanding fundamental biology. How do we work? How do organisms tick? How do you go from DNA in a little bag of salts to a walking, talking organism?” Leuchtman said. “The more you know about how an organism functions, the more opportunities you have to find something that makes an impact.”

The view from the trenches: a conversation about Alzheimer’s disease

This is an immunofluorescence picture of a brain from an Alzheimer's disease mouse model, also known as the TgCRND8 mouse. In the picture the amyloid beta plaques have been stained green and the microglia, immune cells of the brain, are stained red. Image courtesy of Luke Woods.

This immunofluorescence picture shows the brain of an Alzheimer’s disease mouse model, also known as the TgCRND8 mouse. In the picture, the amyloid beta plaques are stained green and the microglia, or immune cells of the brain, are stained red. Image courtesy of Luke Woods.

By Caleb O’Brien | MU Bond Life Sciences Center

Jean Camden and Luke Woods have an ant’s-eye view of Alzheimer’s disease.

Both are bench scientists in the laboratory of Gary Weisman, a professor of biochemistry at the Bond Life Sciences Center. Jean has spent the past 12 of her 35 years at the University of Missouri in the Weisman lab, running experiments, managing the lab and working with students. Luke joined the Weisman lab six years ago, doing what he call’s the dirty work of science: “Gary does the writing and the NIH stuff, but down in the trenches — that’s me and Jean.”

Weisman’s lab studies Alzheimer’s and other diseases, so I sat down recently with Jean and Luke to talk about their research for Alzheimer’s & Brain Awareness Month.
 

Q: What does your lab do, and how does it involve Alzheimer’s?

Luke: We primarily have two projects. One, which has been a very longstanding project, is focused on salivary glands and salivary gland inflammation. The other is the Alzheimer’s project. The link between them is a particular type of cell surface receptor called a nucleotide receptor — more specifically, a P2 nucleotide receptor called P2Y2. These P2 receptors function in a lot of different ways, but the link is with inflammation: We look at P2 receptors in salivary gland inflammation and in Alzheimer’s disease, which has a very large inflammation component that often gets glossed over. In a lot of Alzheimer’s articles that the public reads, you hear about amyloid beta plaques and tau tangles and neurodegeneration, but a large component of that is inflammation, where some of the resident non-neurons in the brain start responding like there’s inflammation in the brain, and it actually kills neurons. That’s been the focus in Gary’s lab for the past 30-plus years.

JEAN: The P2 receptors — especially the P2X7 and P2Y2 which we focus on — Gary during his postdoctoral work started studying these receptors without really knowing that they existed. At the time, he just knew that there was a pore formed in cells caused by the addition of the nucleotide ATP which eventually leads to apoptosis (cell death). Eventually, we cloned the human P2Y2 receptor gene with another group in North Carolina, so we call it “our receptor.” It only appears in cells under inflammatory conditions, such as Alzheimer’s disease, salivary gland autoimmune disease and cardiovascular disease. Any time you have tissue damage, it looks like the P2Y2 receptor is up-regulated. And then once the damage is healed, the receptor goes away.

Inflammation is good — we want inflammation, that’s how we heal — it’s the chronic inflammation that’s bad. But we really don’t know how these receptors work and what their role is during chronic inflammation. Do we want to activate them, or do we want to inhibit them?

LUKE: Scientists have investigated P2X7 receptor antagonists in the treatment of Crohn’s disease and rheumatoid arthritis — there are several clinical trials that have been focused on these receptors, evaluating whether you want to block or activate them. If you block them, you prevent the acute inflammatory responses that are good for wound healing; if you activate them, you may extend those responses past the healing phase into a chronic inflammatory phase that can be quite damaging. So unraveling that fine line of what you want to be doing to these receptors in disease settings is sort of what we do here.

Jean Camden and Luke Woods look at images of a mouse brain with Alzheimer's disease. // Photo by CALEB O'BRIEN/Bond LSC

Jean Camden and Luke Woods look at images of a mouse brain with Alzheimer’s disease. // Photo by CALEB O’BRIEN/Bond LSC

Q: When I think of Alzheimer’s, I think of a shriveled, shrunken brain, but I associate inflammation with swelling. Why the difference?

LUKE: I think the distinction is acute versus chronic inflammation. With acute inflammation, you get swelling. The body has different types of immune responses: acute responders like neutrophils and macrophages are immune cells that act quickly. They come in, for example, if you have a scratch, and there can be swelling. Along with macrophages neutrophils can protect cells from bacteria. The macrophages can also clean up damaged tissue and then the repair cells go to work. Cells come in that lay down a new matrix, whereas undamaged cells then migrate onto the matrix and regenerate. Well, what happens after you’re done repairing is that there are signals that tell the inflammation to stop. In chronic inflammation, that’s where you have continued cell death, and the tissue would then shrivel up. The shriveled brain that you’re referring to is during chronic inflammation, and that’s an end-of-life case, after a very long bout with Alzheimer’s.

JEAN: What we think of as inflammation is often a cut or a wound. It’s only been in recent years that Alzheimer’s disease has been considered an inflammatory disease. We have a phenomenal immune system, but when it goes awry, you have problems. In the other disease we look at — an autoimmune disease — your immune system starts to attack your own body. It’s hard to treat and understand the underlying mechanism.

Q: So how are you trying to unravel the role of inflammation in Alzheimer’s?

JEAN: To study Alzheimer’s, we have an Alzheimer’s mouse model. It overexpresses a gene for the amyloid precursor protein that enables the brain to accumulate high amounts of beta-amyloid plaques that you always hear about. So we’re using this mouse model that we’ve crossed with a mouse that does not express any P2Y2 receptor, so it’s called a knockout mouse. The P2Y2 receptor knockout mouse by itself is fine, and the Alzheimer’s mouse does develop Ab plaques, but it lives to approximately 6 months old before it will develop behavioral defects. The interesting thing is that when we cross the P2Y2 receptor knockout mouse with the Alzheimer’s mouse, the offspring that are Alzheimer’s mice without P2Y2 receptors prematurely die. So at least in this Alzheimer’s mouse model, it looks like the presence of the P2Y2 receptor is protective, because without it, the Alzheimer’s mice die much earlier. But we don’t really know which cell type is most important: Is it the P2Y2 receptor up-regulated on neurons that acts to repair them —which we’ve already shown happens — or is it the P2Y2 receptor on microglia (an immune cell of the brain), or is it the P2Y2 receptor on blood vessels in the brain that help recruit immune cells from the cardiovascular system to help with repair?

So we’re using this mouse model to investigate the role of the P2Y2 receptor, plus we also use cell lines because we can easily control the environment for these cell lines in culture. We isolate primary neurons, we can prepare primary microglial cells or we can purchase cell lines that comprise blood vessels. We can then utilize these tools to investigate cell signaling mechanisms for the P2Y2 receptor in individual cell types.

LUKE: One of the findings that we have found interesting in these primary cells is when you take them fresh out of the mouse, put them in a dish and then treat them as you wish. We’ve shown that if you activate the P2Y2 receptor in primary microglia from the mouse, they will actually engulf and chew up beta-amyloid. And so one of the things we think might be happening in this Alzheimer’s mouse model is that P2Y2 receptor activation in these microglial immune cells in the brain is working to break down those beta-amyloid plaques. And when you lose the P2Y2 receptor in that mouse model, those plaques develop quicker because the immune cells are no longer offering protection by chewing up that beta-amyloid. That’s one of the hypotheses we’re exploring right now.

Q: So you’d bet that these receptors are actually protective against Alzheimer’s?

JEAN: Yes. Going back to the human — it’s hard to get human tissues, especially brain tissues, but there is one published study that has shown that in Alzheimer’s patients who have passed away the P2Y2 receptor is down-regulated, meaning there’s not much left. Which would make sense. If it’s down-regulated, the plaques aren’t able to be chewed up, per se, by these microglia. There’s a correlation between low levels of P2Y2 receptors and Alzheimer’s disease that is apparent at the end of life.

LUKE: It’s very difficult to do some of these studies in humans because most of the available Alzheimer’s tissues are from end of life cases where you can only look at the end result of the disease without looking at the progression of the disease. Obviously you can’t take brain tissue from a living person, so the ability to study live cells from Alzheimer’s patients is limited. We rely very heavily on mouse models.

Primary microglia

This immunofluorescence picture shows microglia cells that were isolated from the brain of an Alzheimer’s mouse model called TgCRND8 and cultured in a dish for further analysis. Image courtesy of Luke Woods.

Q: What have been the biggest shifts in our understanding of Alzheimer’s in recent years?

LUKE: Maybe one shift — I may not be the best expert to speak about it — is the idea that the beta-amyloid plaques are the cause of disease. It is now being mostly recognized that they’re really the tombstones of the disease. They’re not the initial cause, but rather the end result of the disease. For a long time investigators were focused on trying to prevent the buildup of beta-amyloid because that was one aspect of Alzheimer’s disease that you could see and measure. Now the thinking is that maybe the beta-amyloid does not contribute as much to disease progression as originally thought, and rather is the end result of a complicated mechanism that is actually causing the neurodegeneration.

JEAN: There’s still debate on what causes Alzheimer’s disease. There is a small percentage of patients where it’s actually related to a genetic alteration in the amyloid precursor protein gene.

LUKE: Another link has been with the ApoE (apolipoprotein E) gene, which makes a lipoprotein and cholesterol transporter. We inherit 1 copy of the ApoE gene from each of our parents and it has been shown that individuals who have at least 1 copy of a particular variant of the gene called ApoE4 are at increased risk of developing Alzheimer’s disease.

Q: From the perspective of a lab scientist, why do you care about Alzheimer’s?

JEAN: We care about any disease, really, and if we can show that our receptors have anything to do with any disease, we’d be proud to have a role in that.

LUKE: We don’t do much clinical science here, it’s mostly basic science. We contribute to the basic understanding of the disease so that drug companies and medicinal chemists who develop drugs for clinical use in Alzheimer’s patients can say, “Hey, this group’s research found a new mechanism related to Alzheimer’s disease, so let’s target this pathway to treat the disease.” It’s always nice to contribute to that sort of ground-level science.

JEAN: That would be the ideal, to show that whether you have to activate or inhibit the P2Y2 receptor, it does something to improve the clinical outcome in Alzheimer’s patients. A better understanding of Alzheimer’s and other diseases is what’s needed — we’re just working to provide a piece of the puzzle.

Q: How has being down in the trenches changed your perspective on research and Alzheimer’s in general?

 JEAN: We’re the ones who are hoping to clarify the direction for science to go. We do the experiments and we are the first ones to see the data. We collect the data that becomes the cornerstone for deciding the direction our research goes. I think Gary would agree with that — he depends on us a lot to collect the data and we depend on him to help determine which scientific findings to chase and which ones not to chase.

I’ve been doing this for 35 years, and I really do enjoy the science. I’ve seen the science of these nucleotide receptors come a long way. These receptors have in common their use of extracellular nucleotides, particularly ATP (or adenosine triphosphate, more commonly known as the intracellular high energy molecule of all cells). And this ATP, is at a high concentration inside cells, so when it is released by cell damage, it can easily activate nucleotide receptors on nearby cells. It was Dr. Geoffrey Burnstock, now considered to be the grandfather of nucleotide receptors, who claimed a long time ago that there are receptors on the outside of cells that respond to ATP. Everybody kind of laughed at him, “Yeah, sure, right. There’s no way: ATP belongs inside the cell.” So for me personally, to come in on the ground level for these receptors and find a role for them in a variety of diseases has been exciting for me.

LUKE: ATP is the energy currency inside of all cells, so it’s use outside cells would be like tossing money out the window. Why would they want ATP outside the cell? It didn’t make any sense at the time, but looking back I think it does. What happens if you damage or rupture a bunch of cells during an injury? You get the release of a high concentration of ATP that neighboring cells recognize as a danger signal telling them that an injury has occurred. In that sense, ATP makes the perfect signaling molecule to tell other cells that an injury has occurred and they need to start the repair work by recruiting immune cells to the damaged tissue.

Jean Camden has spent 35 years working at the University of Missouri and more than a decade in Gary Weisman's lab.  // Photo by CALEB O'BRIEN/Bond LSC

Jean Camden has spent 35 years working at the University of Missouri and more than a decade in Gary Weisman’s lab. // Photo by CALEB O’BRIEN/Bond LSC

Q: Where would you like to be in five years with this research?

JEAN: I talked about determining how the P2Y2 receptor in this mouse model was protective. It would be nice to find out which cell type on which the P2Y2 receptor is expressed in contributes most to neuroprotection. Our hypothesis would be that the microglial cells are very important, since they gobble up beta-amyloid, but other cell types including neurons and endothelial cells are likely involved. We’re also anxious to look at other inflammatory diseases to see if the P2Y2 receptor plays a similar role there.

LUKE: From somebody who does a lot of bench work, something I would like to see is a really good tool, a specific agonist or antagonist of the P2Y2 receptor that could be used in the clinic. There are a few suitable compounds available that we use to investigate the P2X7 receptor— I’ve told you that some have been tested in clinical trials — but the P2Y2 receptor has been sort of an enigma, due to the lack of selective inhibitors and agonists that are specific enough for clinical use. I’d like to see the development of a specific agonist or antagonist that could eventually be used to treat inflammatory diseases. There’s no reliable drug that is currently suitable to investigate the P2Y2 receptor in animals or humans, so clearly more work is needed there.

This interview has been edited for length and clarity.

Translating soybean cyst nematode research

Roger Meissen/Bond Life Sciences Center -  These soybean roots show some nematode cysts. The small, white circles are the hardened body of the nematodes and form when the nematode attaches itself to the root to create a feeding cell.

Roger Meissen/Bond Life Sciences Center – These soybean roots show some nematode cysts. The small, white circles are the hardened body of the nematodes and form when the nematode attaches itself to the root to create a feeding cell.

Beneath a North Carolina field in 1954, a tiny worm inched its way through the soil and butted against a soybean root. The worm pierced the plant, slipped inside and inserted a needle-like appendage into a cell. It pumped a mixture of proteins into the root cell and waited for the potent blend to take effect on the unsuspecting soybean.

Since the first detection of soybean cyst nematode (SCN) in the US, the worm Heterodera glycines has spread to about 80 percent of American soybean fields. In Missouri, SCN attacks soybeans in almost every county and causes decreased yields even in robust, healthy-looking fields. Nationwide, SCN wreaks havoc to the tune of $1.2 billion per year, making it by far the most costly soybean pest.

Despite the hefty toll, farmers still depend on the same small handful of resistant soybean varieties to combat SCN that they have used for years. But those natural defenses are becoming less effective as nematodes evolve.

“More than 90 percent of the soybean cultivars that farmers plant derive their resistance from a single source,” said Melissa Mitchum, a plant nematologist at the University of Missouri Bond Life Sciences Center and Division of Plant Sciences faculty member in the College of Agriculture, Food and Natural Resources. “Consequently, this has led to widespread virulence in the pathogen population, thereby reducing the effectiveness of those resistant cultivars.”

But in the past 10 years, researchers studying SCN have made numerous breakthroughs, unlocking the secrets of the nematode and exploring how the worm interacts with host plants. Now, scientists are poised to bring that knowledge from the laboratory to the field.

Found in translation

Relatively little was known about SCN a decade ago.

Scientists could determine the type of nematode in a soil sample and had just figured out the cocktail of proteins a nematode pumps into the soy root cell that transform it into a syncytium, or feeding cell.

Working in part with funding from commodity boards and farmer checkoff dollars, researchers around the country made breakthrough after breakthrough, deepening our understanding of SCN and equipping scientists with new tools to fight the pest.

That money helped scientists sequence the soybean genome, draft a SCN genome and pinpoint important soy and SCN genes.

Checkoff investments continued to pay dividends in 2012 when Mitchum and colleagues cloned the first gene linked to natural soybean cyst nematode resistance. This breakthrough is one key step in moving science from the laboratory into the field. With a SCN resistance gene in hand, new avenues for creating soybean varieties that fight off the nematode are opening up.

But other areas of research also hold promise in the struggle against soybean cyst nematode’s parasitic ways.

Mitchum’s group also identified the plant receptors that recognize and respond to the blend of proteins an attacking nematode inserts into a plant. In a recent project published in Plant Biotechnology Journal, Xiaoli Guo, a postdoctoral fellow in Mitchum’s lab demonstrated that silencing those receptors in soybean roots helped the plant resist SCN.

This work has implications for more crops than just soybeans: Working with collaborator Xiaohong Wang at Cornell, Mitchum’s group used their understanding of plant receptors to develop a potato resistant to potato cyst nematode.

A roadmap for discovery

To build on the momentum of recent research, experts drafted a roadmap for the next decade of nematode research. Their goal, Mitchum said, is to address the challenge of translating these research breakthroughs into something tangible for the farmer.

With support from state farmer run organizations such as the Missouri Soybean Merchandising Council, the North Central Soybean Research Program and the United Soybean Board, researchers are formulating teams that “bring together commodity, industry and university funding to develop collaborative, interdisciplinary, multistate projects,” said Mitchum.

And there’s plenty of scientific firepower to advance research: MU’s College of Agriculture, Food and Natural Resources alone has more than 90 faculty studying plant science, plant genetics and other areas of agriculture-related science.

The scientists’ plan for the next 10 years involves a blend of molecular research, plant breeding, population biology and outreach. Researchers will focus on refining the existing draft SCN genome, which will help to develop a quick, inexpensive test for HG type and eventually contribute to understanding of how SCN overcomes a plant’s resistance. They’ll create an “atlas” of SCN genes researchers can use to block the pest. Updating yield loss estimates and mapping SCN distribution will also give scientists a better idea of the nematode’s national impact. Other efforts will allow breeders to incorporate new sources of resistance into commercially-available varieties, refine the use of non-host species to control SCN and develop a pipeline for creating and testing transgenic SCN-resistant soybeans. Finally, videos, webinars and training modules will help scientists, students and producers take advantage of new discoveries and techniques.

Roger Meissen/Bond Life Sciences Center -  Michael Gardner, Ph.D. student, Melissa Mitchum, associate professor of Plant Sciences, Xiaoli Guo, post doctoral fellow, conduct research at the University of Missouri. They investigate how soybean cyst nematode overcomes soybean resistance to identify novel approaches for management.

Roger Meissen/Bond Life Sciences Center – Michael Gardner, Ph.D. student, Melissa Mitchum, associate professor of Plant Sciences, Xiaoli Guo, post doctoral fellow, conduct research at the University of Missouri. They investigate how soybean cyst nematode overcomes soybean resistance to identify novel approaches for management.

Onward with research

A thorough understanding of SCN resistance and virulence starts with basic research and then moves into the field. “We all need to come together to transfer this knowledge to the breeder,” Mitchum said, “and from there it gets out to the farmer.”

 Her lab recently received a National Science Foundation grant to continue their work on soybean protein receptors. Specific targeting of the receptors is just one potential strategy for producing new kinds of SCN-resistant plants. A second grant, from the National Institute of Food and Agriculture, will allow the lab to continue refining their understanding of how SCN proteins overcome a host plant’s defenses. To that end, Mitchum’s graduate student Michael Gardner is identifying the genetic blueprint of the different SCN types present in Missouri fields.

“If we better understand nematode populations and what makes those populations distinct, we can better advise farmers confronted with virulent nematodes,” Gardner said. “We’ll be able to go one step beyond the HG type test and understand how nematodes are able to adapt in the long term, not just the next growing season.”

But these breakthroughs do little good unless they then become useful tools for breeders and ultimately farmers. To that end, Mitchum and other researchers will help breeders use research results to produce soybeans with durable resistance. They‘ll also develop guides so farmers can easily incorporate new technologies and management strategies into their farms.

It’s important for farmers, breeders and researchers to take a unified approach to fighting SCN, Mitchum said, because a tactic that seems successful at first could backfire.

For instance, combining resistance genes in a single soybean variety could actually be harmful. “When we deploy it in the field, we select for nematodes that can overcome multiple types of resistance,” Mitchum said.

A better approach might be to perfect varieties with distinctive resistance mechanisms and insure durable resistance by rotating among the resistant varieties and non-host crops.

“It’s similar to taking antibiotics,” Mitchum said. “Improper use and overuse selects for resistance.” The strategic planning document should help everyone working with soybeans and SCN leverage and build upon new knowledge.

Despite all the research and recent breakthroughs, there remains only one certainty in the ongoing arms race between soybeans and SCN: “It is highly unlikely that we will eradicate it.” Mitchum said, “We’re going to have to find new strategies to protect and bolster soybean yields.”

Thanks to the efforts of researchers such as Mitchum, in the future SCN might be a little easier to get along with.

 

 

Roger Meissen/Bond Life Sciences Center - Research specialist and coordinator for the Plant Nematology Lab Amanda Howland processes soil samples for nematodes. Howland replaced Bob Heinz earlier this year.

Roger Meissen/Bond Life Sciences Center – Research specialist and coordinator for the Plant Nematology Lab Amanda Howland processes soil samples for nematodes. Howland replaced Bob Heinz earlier this year.

University of Missouri Plant Nematology Laboratory: An extensive legacy

Bob Heinz spent his last day at work in December surrounded by nematodes. Heinz served as Mitchum’s research specialist and coordinator of the Plant Nematology Laboratory, where he processed soil samples, responded to growers and assisted researchers. After 35 years on the job, he’s retired, and Amanda Howland is now filling his shoes. The scientists and farmers who’ve worked with Bob over the decades thank him for his dedication and wish him luck in his retirement. And Amanda: Welcome aboard.

The Plant Nematology Lab, housed within Mitchum’s lab at MU, represents a successful model for how research, teaching and extension program integration can promote interdisciplinary collaboration. Such an approach helps maintain an effective pipeline that brings research-based information and resources from MU to Missourians. The lab offers an array of tests that help farmers understand and manage nematode populations. The available tests include:

Vermiform Nematode Identification: Soybean Cyst? Root Knot? Lesion? Find out what kinds of nematodes are in your fields with this test.

Soybean Cyst Nematode Egg Count: This procedure provides an estimate of the number of SCN eggs in your field.

Soybean Cyst Nematode HG Type Test: Different types of SCN have overcome various sources of soybean resistance. A HG type test will help you determine the best source of resistance for the particular type of SCN in your field.

For more information, go to http://soilplantlab.missouri.edu/nematode/ or contact the Lab.
Phone: 573-884-9118
Email: nematodelab@missouri.edu

 

Five things you wanted to know about epigenetics (But were afraid to ask)

10960203_781430608590258_4910408420147962125_oWhat the heck is it, anyway?

Epigenetics involves changes in how your genes work.

In classical genetics, traits pass from generation to generation in DNA, the strands of genetic material that encode your genes. Scientists thought alterations to the DNA itself was the only way changes could pass on to subsequent generations.

So say you lost a thumb to a angry snapping turtle: Because your DNA hasn’t changed, your children won’t be born with smaller thumbs. Classic.

Things get way more complicated with epigenetics. It turns out that some inherited changes pass on even though they are not caused by direct changes to your DNA. When cells divide, epigenetic changes can show up in the new cells.

Getting nibbled on by an irate turtle isn’t likely to epigenetic changes, but other factors such as exposure to chemicals and an unhealthy diet, could cause generation-spanning epigenetic changes.

 

How does it work?

The main players in epigenetics are histones and methyl groups.

Imagine your genes are like pages in a really long book. Prior to the mid-1800s, books came with uncut edges, so in order to read the book, you’d have to slice apart the uncut pages. That’s sort of what a histone does to DNA: They are proteins that wrap DNA around themselves like thread on a spool. They keep the DNA organized and help regulate genes.

Methyl groups (variations on CH3) attach to the histones and tell them what to do. These molecules are like notes in a book’s margin that say, “These next few pages are boring, so don’t bother cutting them open.” As you read the book, you’ll save time and effort by skipping some sections even though those sections still exist. Or maybe the note will say, “This next section is awesome; you’ll want to read it twice.”

That’s epigenetics. Higher level cues that tell you whether or not to read a gene.

And when a scribe makes a copy of the book, they’ll not only copy all the words in the novel, but all the other stuff, too: the stuck-together pages and the margin notes.

 

What about my health?

Many areas of health — including cancer, autoimmune disease, mental illness and diabetes — connect with epigenetic change.

For example, scientists link epigenetic changes to neurons to depression, drug addiction and schizophrenia. And environmental toxins — such as some metals and pesticides — can cause multigenerational epigenetic effects, according to research. Once scientists and doctors decipher those processes work, they will be better equipped to treat the sick and be able to take preventative measures to help insure our health and the health of our kids.

 

Is it epigenetics or epigenomics?

Confusing, I know.

As we learned from the first question, epigenetics is “the study of heritable changes in gene function that do not involve changes in the DNA sequence,” according to my trusty Merriam-Webster.

Epigenomics is the study and analysis of such changes to many genes in a whole cell or organism. It’s comparable to the difference between genetics (dealing with particular pieces of DNA, usually a gene) and genomics (involving the whole genetic shebang).

 

Where can I learn more?

Start at this year’s Life Sciences and Society Program Symposium, “The Epigenetics Revolution: Nature, Nurture and What Lies Ahead,” on March 13-15, 2015. Speakers from all over the country will delve into the puzzles and possibilities of epigenetics.

For more background, Nature magazine also created this supplement on epigenetics.

The search for oxidative stress treatment continues

A yellow light indicates oxidant production in the tissue of a migrating fly larva. Source: Tobias Dick, German Cancer Research Center | Illustration by Paige Blankenbuehler Read more at: http://phys.org/news/2011-12-oxidative-stress.html#jCp

A yellow light indicates oxidant production in the tissue of a migrating fly larva. Source: Tobias Dick, German Cancer Research Center | Illustration by Paige Blankenbuehler

University of Missouri research characterizes a novel compound

By Paige Blankenbuehler

Your body has an invisible enemy.

One that it creates all on it’s own called oxidative stress, long thought of as an underlying cause of some of humanity’s most insidious diseases – cancer, Alzheimer’s, Parkinson’s Disease, cardiovascular disease and diabetes.

Every day, our bodies are exposed to harmful free radicals known as reactive oxygen species as a result of our environment.

But, when something goes wrong with this energy extraction process, cells become inundated with reactive oxygen compounds that cause oxidative stress. The search for drugs to treat the problem have been ongoing, and with a complicated problem like oxidative stress, it’s all about finding the right combination.

Recent research by Bond Life Sciences Center investigator and Biochemistry Department Professor, Mark Hannink, provides a new approach for addressing the problem of oxidative stress and a starting point on developing a drug in pill form.

Mark Hannink and Kimberly Jasmer, a Ph.D. student in his lab, recently helped characterize a new molecule (called HPP-4382) that provides a novel way to treat oxidative stress. Their research was done in a partnership with High Point Pharmaceuticals, LLC, of North Carolina, where this new molecule was developed.

Oxidative stress can cause damage to the building blocks of a cell, resulting in excessive cell proliferation in the case of cancer or cell death in the case of neurodegenerative diseases like Parkinson’s.

Often, the majority of stressors are actually created inside our own cells as a byproduct of how our cells extract energy from the food that we eat and the air that we breathe.

Specimen of protein are prepared for an experiment in a lab at the Bond Life Sciences Center at the University of Missouri.

Specimen of protein are prepared for an experiment in a lab at the Bond Life Sciences Center at the University of Missouri.

Understanding oxidative stress

Most simply, oxidative stress is an imbalance that happens when the body uses oxygen to produce energy.

Superoxide, a “promiscuous and nonspecific” compound produced as a byproduct of this process, is a highly reactive molecule that can damage DNA and other cellular components, Hannink said.

The superoxide molecule is a “free radical.” That means it’s especially promiscuous and reacts with many different types of cellular molecules, leaving destruction in its wake, he said.

That damage can lead to a long list of problems, including cancer or neurodegenerative diseases like Parkinson’s disease.

In response to oxidative stress, the cell produces protective “anti-oxidant” proteins, which help remove the harmful reactive oxygen species and minimize damage.

But a heavy anti-oxidant response could be dangerous, too. The bottom line: it’s about maintaining a fine balance between “oxidants” and “anti-oxidants”.

 

Search for right combination continues

A drug that corrects the imbalance of oxidative stress could one day have wide applicability.

Jasmer developed a test to measure how specific compounds altered gene expression. The genetic response to oxidative stress has both an “ON” switch and an “OFF” switch.

Using this test, Jasmer determined how each compound affected specific genetic switches and, in turn, how the response to oxidative stress is regulated.

This test helped identify which molecules might be promising candidates for treating oxidative stress, leading them to one in particular that seemed to have the desired properties: HPP-4382.

But creating effective drugs is a long process of trial and error. Once molecules have been identified that show efficacy in lab-based assays, scientists try different combinations to increase their potency and drug-like properties, and High Point is currently testing other molecules that behave like HPP-4382.

The compound serves as a good starting point for researchers who are interested in understanding how oxidative stress affects cellular processes, such as cell proliferation or cell death.“Now we have a better understanding of what this compound is doing,” Hannink said. “This compound can be used to test different ideas of how the balance between oxidants and anti-oxidants is achieved in healthy cells and how perturbation of this balance can lead to different diseases.”

This research was published in PLoS One in July and was funded by High Point Pharmaceuticals, LLC.

Viruses as Vehicles: Finding what drives

Graduate students Yuleam Song and Dan Salamango inoculate a bacteria culture in Johnson's lab. The inoculation takes a small portion of a virus and multiplies the sample, allowing researchers to custom-make viruses.

Graduate students Yuleam Song and Dan Salamango inoculate a bacteria culture in Johnson’s lab. The inoculation takes a small portion of a virus and multiplies the sample, allowing researchers to custom-make viruses.

By Madison Knapp | Bond Life Sciences Center summer intern

Modern science has found a way to turn viruses —tiny, dangerous weapons responsible for runny noses, crippling stomach pains and worldwide epidemics such as AIDS— into a tool.

Gene therapy centers on the idea that scientists can hijack viruses and use them as vehicles to deliver DNA to organs in the body that are missing important genes, but the understanding of virus behavior is far from exhaustive.

Marc Johnson, researcher at the Christopher S. Bond Life Sciences Center and associate professor of molecular microbiology and immunology in the MU School of Medicine, has been building an understanding of viral navigation mechanisms which allow a virus to recognize the kind of cell it can infect.

Johnson’s research specifically explores the intricacies of the viral navigation system and could improve future direction of gene therapy, he said.

 

Marc Johnson (left) with a post doctoral student that works in his lab. The lab does important research on the basic function and mechanisms of viral navigation and transport.

Marc Johnson (left) with Dan Salamango, a graduate student that works in his lab. The lab does important research on the basic function and mechanisms of viral navigation and transport.

Turning a virus into a tool

Conceptualized in the 1970s, gene therapy was developed to treat patients for a variety of diseases, including Parkinson’s, leukemia and hemophilia (a genetic condition that stops blood from clotting).

To treat disease using gene therapy, a customized virus is prepared. A virus can be thought of as a missile with a navigation system and two other basic subunits: A capsule that holds the ammunition and the ammunition itself.

The viral genetic material can be thought of as the missile’s ammunition. When a cell is infected, this genetic material is deployed and incorporated into the cell’s DNA. The host cell then becomes a factory producing parts of the virus. Those parts assemble inside the cell to make a new virus, which then leaves the cell to infect another.

The capsule is made of structural protein that contains the genetic material, and the navigation system is a protein that allows the virus to recognize the kind of cell it can infect.

 

Viral navigation

Gene therapy uses viruses to solve many problems by utilizing a virus’ ability to integrate itself into a host cell’s DNA; to do this successfully, researchers need to provide a compatible navigation component.

In the body, viruses speed around as if on a busy highway. Each virus has a navigation system telling it which cells to infect. But sometimes if a virus picks up the wrong type of navigation system, it doesn’t know where to go at all.

“What you can do is find a virus that infects the liver already, steal its navigation protein and use that to assemble the virus you want to deliver the gene the liver needs,” Johnson said. “You can basically take the guidance system off of one and stick it onto another to custom design your virus.”

But this doesn’t always work because of incompatibility among certain viruses, he said.

Johnson and his lab are working to understand what makes switching out navigation proteins possible and why some viruses’ navigation systems are incompatible with other viruses.

“I’m trying to understand what makes it compatible so that hopefully down the road we can intelligently make others compatible,” Johnson said.

 

The right map, the right destination

Johnson creates custom viruses by introducing the three viral components—structural protein, genetic material, and navigation protein—to a cell culture. The structural protein and genetic material match, but the navigation component is the wild card. It could either take to the other parts to produce an infectious virus, or it could be incompatible.

Johnson uses a special fluorescent microscope to identify which viruses assembled correctly and which didn’t.

A successful pairing is like making a match. If a navigation protein is programmed to target liver cells, it’s considered a successful pairing when the virus arrives at the liver cell target location.

The scope of gene therapy continues to widen. Improved mechanisms for gene therapy, and greater knowledge of how a navigation protein drives a virus could help more people benefit from the vehicles viruses can become.

Johnson uses several high-profile model retroviruses, including human immunodeficiency virus (HIV), which affects an estimated 35 million people worldwide each year, according to the World Health Organization.

Understanding nuances of HIV in comparison to other viruses allows Johnson to pick out which behaviors might be common to all retroviruses and others behaviors that might be specific to each virus.

Johnson said his more general approach makes it easier to understand more complex viral features.

“If there are multiple mechanisms at work, it gets a little trickier,” Johnson said. “My angle is more generic, which makes it easier to tease them apart.”

Supervising editor is Paige Blankenbuehler

Researchers flex new muscle in SMA drug development

By Paige Blankenbuehler

Lauren and Claire Gibbs share contagious laughter, ambition and a charismatic sarcasm.

Both are honor students at Shawnee Mission East High School in a Kansas City suburb.

They also share a neuromuscular disease called spinal muscular atrophy (SMA), designated as an “orphan disease” because it affects fewer than 200,000 people in the U.S.

However, the landscape for individuals with SMA is quickly changing with the development of new drugs.

More than 7 million people in the United States are carriers (approximately 1 in 40) of the so-called “rare” neurodegenerative disease, SMA.

 

Lauren,17 (left) and Claire, 16 (right), say their shared SMA diagnosis has strengthened their relationship and presented them with opportunities to travel and share their experiences. | Photo provided by the Gibbs family.

Lauren,17 (left) and Claire, 16 (right), say their shared SMA diagnosis has strengthened their relationship and presented them with opportunities to travel and share their experiences. | Photo provided by the Gibbs family.

SMA-sidebar

Faces of SMA

The success of therapeutics in lab experiments provides a new layer of hope for individuals and families living with the disease.

Lauren, now 17, fit the criteria for SMA Type III, while Claire, now 16, showed symptoms of a more severe manifestation of the disease, SMA Type II.

Lauren and Claire Gibbs were diagnosed on the same day.

Despite their numerous similarities, the biggest disparity between them is mobility.

Claire uses a power wheel chair while Lauren is able to use a manual chair. It’s not unusual to see Lauren being pulled along in her chair, playfully hanging onto the back of Claire’s motorized chair.

Lauren is participating in a clinical trial with ISIS-SMNRx a compound developed by Isis Pharmaceuticals, a leading company in the antisense drug discovery and development based in Carlsbad, Calif. Lauren feels that she has gained stamina and a greater ability to walk  — a feat that wasn’t routine just five years ago.

Prior to the trial, Lauren was able to walk only for short distances.

Time and Natalie Gibbs with their daughters Lauren, 17 (left) and Claire, 16 (right) in Washington D.C. The family have been visible advocates in the fight for a cure for spinal muscular atrophy. | Photo provided by the Gibbs family.

Tim and Natalie Gibbs with their daughters Lauren, 17 (left) and Claire, 16 (right) in Washington D.C. The Gibbs have been visible advocates in the fight for a cure for spinal muscular atrophy. | Photo provided by the Gibbs family.

 

Bringing New Hope

A new experimental drug developed by researchers at the Christopher S. Bond Life Sciences Center, is bringing hope to individuals with the orphan disease affecting one in 6,000 people.

Christian Lorson PhD, investigator in the Bond Life Sciences Center and Professor of Veterinary Pathobiology at the University of Missouri, has been researching SMA for seventeen years and has made a recent breakthrough with the development of a novel compound found to be highly efficacious in animal models of disease. In April, a patent was filed for Lorson’s compound for use in SMA.

Lorson’s therapeutic, an antisense oligonucleotide (a fancy name for a small molecule therapeutic that falls under the umbrella of gene therapy), repairs expression from the gene affected by the disease. The research was published May in in the Oxford University Press, Human Molecular Genetics.

The drug developed by Lorson’s lab is conceptually similar to ISIS-SMNRx already in clinical trial developed by Isis Pharmaceuticals and a team of investigators at Cold Spring Harbor Laboratory headed by Dr. Adrian Krainer.

Antisense drugs are not a new practice, but their wide-spread adoption seems to be on the cusp with recent success stories like the commercialization of an FDA-approved antisense compound produced by Isis in 2013 called Kynamro for the treatment of homozygous familial hypercholesterolemia, a high cholesterol disorder that is passed down through families.

 

Science behind success

The National Institutes of Health has listed SMA as the neurological disease closest to finding a cure. Discoveries made by the Lorson Lab have contributed significantly to current scientific understanding of the disease mechanisms and to the advances being made in finding an effective treatment for SMA.

These antisense therapies work because of the genetic makeup of SMA —the genetics are incredibly clear: a single, specific gene called Survival Motor Neuron 1  (SMN1) has been pinpointed as the cause of SMA.

SMA is a neurodegenerative disorder, meaning muscles become weaker over time due to sick or dying neurons.

These neurons become less functional because of low levels of the SMN.

Remarkably, the disease can be reversed in animal models of disease if the nearly identical duplicate gene, SMN2, can be “turned on” to compensate for low SMN levels.

Lorson’s antisense oligonucleotide therapeutic provides incredible specificity because it hones in on a specific genetic target sequence within SMN2 RNA and allows proper “editing” of the RNA encoding the SMN protein. The strategy is to “repress the repressor,” Lorson said.

The SMA-specific defect lies at the RNA step – the “cutting and splicing” of important RNA sequences does not happen efficiently in SMN2 RNAs because of a several “repressor” signals.

“The final chapter of the book — or the final exon — is omitted,” Lorson said. “But the exciting part is that the important chapter is still there – and can be tricked into being read correctly: if you know how.”

The new, antisense oligonucleotide seems to know how to get the job done.

The existence of such similar genes as SMN1 and SMN2 in humans creates a rare genetic landscape lending itself especially to a therapeutic development for SMA.

Humans are unique in this duplication — something Lorson calls a “genetic happenstance” that, on an evolutionary scale, may as well have happened yesterday.

Why humans have developed this redundant gene is unknown.

Thalia Sass, a University of Missouri biology major, genotypes samples in Christians Lorson's lab that conducts research on spinal spinal atrophy.

Thalia Sass, an MU biological sciences major, genotypes samples in the Lorson Lab where spinal muscular atrophy is researched.

 

Timing is everything

In addition to the developments of new SMA therapeutics, Lorson and his lab sought to answer an important biological question concerning the disease: When can a therapeutic be administered and still show some degree of efficacy?

Lorson’s research found that the earliest administration of a treatment provided the best outlook— extending the survival of laboratory mice by 500 to 700 percent, “a profound rescue,” according to his research published in April in the Oxford University Press, Human Molecular Genetics.

A near complete, 90 percent rescue was demonstrated in severe SMA mouse models. But even when the therapeutic was administered after the onset of SMA symptoms, there was still a significant impact on the severity of the disease.

“If you replace SMN early and get (a therapeutic) to cells that are important to the disease, you correct it,” Lorson said. “This provides hope that patients who have been diagnosed will still see some therapeutic benefit even if it is clear that the best results will likely come from early therapeutic administration.”

In Lorson’s study it’s definitive that the earlier a therapeutic can be administered, the better the outcome for individuals with SMA.

“This really points towards a strong push for neonatal screening,” Lorson said. “Infant screening would likely be incredibly beneficial for SMA and that’s something that the SMA community is really excited about.”

 

A breakthrough for families

On June 2, Lauren and Claire Gibbs attended a routine, annual rehab appointment with Dr. Robert Rinaldi, MD, division of pediatric rehabilitation medicine and attending physician at Children’s Mercy Hospital in Kansas City, Mo Dr. Rinaldi is not associated with the Isis clinical trial.

The appointment was like a reunion among close friends — Rinaldi began seeing Claire and Lauren Gibbs 16 years ago, the first year that he began working at the hospital and when the girls were one- and two-years-old, respectively.

The girls did all of the routine tests —measuring strength of grip and breathing, and assessing range of movement with the occupational and physical therapists.

A little later, Rinaldi sat with Natalie Gibbs, Lauren and Claire’s mother and a relentless advocate for advancement in SMA awareness.

Typically the muscles of individuals with SMA deteriorate over time, but together they inspected the definition of a new calf muscle on Lauren’s left leg.

For a young woman with Type III SMA — this means she can walk for short distances with little discomfort but still uses her wheel chair a majority of the time — Lauren’s new calf muscle is a remarkable achievement.

clinicaltrialinfoboxAs Lauren continues to participate in the ISIS antisense therapy clinical trial, her conditions continue to improve dramatically, even with the late administration of the therapy — in her case, 16 years after her diagnosis and onset of effects.

Lauren believes her ability and stamina for walking have increased significantly.

“Quite frankly my jaw almost hit the ground when she stood up — the change was that impressive to me,” Rinaldi said.

Rinaldi, also the co-director of the Nerve and Muscle Clinics at the hospital, had last seen Lauren two years ago. He said the Lauren he saw during a routine rehab appointment in June was like seeing a new person altogether.

“The way she stood up from the wheel chair — how quickly she did that with no support — her posture when she was standing up was more upright, her pelvis was in a much better position, her core was straighter,” Rinaldi said. “It struck me immediately how much better she looked.”

Lauren Gibbs is the first of Rinaldi’s patients to have participated in the ISIS clinical trial.

“It’s moving very fast in this field,” Rinaldi said. “I think the technology that’s evolving in research is opening up more avenues for investigation for us and there’s a big desire to find a cure for these types of diseases.”

The progress has rewarded the Gibbs family’s advocacy in SMA awareness and they’ve been able to set new goals they didn’t imagine were possible when the diagnoses for Lauren and Claire were made. Natalie Gibbs is a long-time member of Families of SMA and is currently on their Board of Directors.

The organization Families of SMA is currently providing funding to Lorson to advance this research area.

“We’re able to see first hand — and our physician who has been watching them for sixteen years has seen — that everything we’re doing in the clinical trials is really making a difference,” Natalie Gibbs said.

Over the course of their daughters’ lives, Natalie and her husband Tim Gibbs say a shift in momentum has accelerated the technology and research toward finding a cure for SMA.

“I am really impressed with the progress Lauren has made with the trial and how well Claire is doing overall,” Natalie Gibbs said. “Even though it’s a progressive and very devastating type of disease, I feel like we’re really conquering it.”

 

Link to publications:

Therapeutic window study:  http://www.ncbi.nlm.nih.gov/pubmed/24722206

University of Missouri ASO:  http://hmg.oxfordjournals.org/content/early/2014/04/29/hmg.ddu198.full.pdf+html

For more information on spinal muscular atrophy, visit FightSMA.org and fsma.org

 

Nerve cell communication mechanisms uncovered, may lead to new therapeutic approaches for neurodegenerative diseases

 

Story by Madison Knapp/ Bond Life Sciences summer intern

Simple actions like walking, swallowing and breathing are the result of a complex communication system between cells. When we touch something hot, our nerve cells tell us to take our hand off the object.

This happens in a matter of milliseconds.

This hyperspeed of communication is instrumental in maintaining proper muscle function. Many degenerative diseases affecting millions of people worldwide result from reduced signaling speed or other cellular miscommunications within this intricate network.

Michael Garcia, investigator at the Christopher S. Bond Life Sciences Center and associate professor of biology at the University of Missouri, conducts basic research to answer fundamental questions of nerve cell mechanics.

“In order to fix something, you need to first understand how it works,” Garcia said.

Garcia’s research illuminates relationships between nerve cells to find factors affecting function.  His goal is to provide insight on fundamental cellular mechanisms that aren’t fully understood.

Garcia’s research has been funded partly by the National Science Foundation and National Institutes of Health.

Technological advancements have made it possible to better understand disease development in the human body to create more effective treatments. Alas, a scientist’s work is never finished— when the answer to one question is found, ten more crop up in its wake.

Garcia’s research, which appeared in several journals including Human Molecular Genetics andthe Journal of Neuroscience Research initially sought to shed light on the neuronal response to myelination, the development of an insulating border around a nerve cell, called a myelin sheath, which is critical in rapid communication between cells.

Eric Villalon, a graduate student in Michael Garcia's lab at the Bond Life Sciences Center, examines results. The Garcia Lab is answering news questions in cell mechanics. | PAIGE BLANKENBUEHLER

Eric Villalon, a graduate student in Michael Garcia’s lab at the Bond Life Sciences Center, examines results. The Garcia Lab is answering news questions in cell mechanics. | PAIGE BLANKENBUEHLER

How it works: Rebuilding cell theory

Garcia’s early research disproved a long-standing hypothesis concerning this cellular feature.

Mammals’ nervous systems are uniquely equipped with myelination, which has been shown to increase conduction velocity, or the speed at which nerve cells pass signals. Low velocity is often associated with neurodegenerative diseases, so research exploring why could later have application in therapeutic technology.

In addition to myelination, cell size makes a big difference in conduction velocity — the bigger the nerve cells, the faster they can pass and receive signals. Garcia’s findings disproved a hypothesis that related myelination to this phenomenon.

The hypothesis, published in a 1992 edition of Cell, claimed that myelination causes a cellular process called phosphorylation which then causes an increase in the axonal diameter (width of the communicating part of a nerve cell), leading to faster nerve cell communication. Garcia found that myelination did cause an increase in axonal diameter, and myelination was required for phosphorylation, but that the two results were independent of one another.

To narrow in on the processes affecting axonal diameter, Garcia identified the protein responsible for growth.

Garcia followed earlier work, showing that one subunit controls whether there is growth at all with myelination, by identifying the domain of this protein that determines how much growth.

After clarifying this part of the process, a question still remains: If not to control myelination, why does phosphorylation happen?

 

Looking forward

Jeffrey Dale, a recent PhD graduate from Garcia’s lab, said current research is in part geared toward finding a connection between phosphorylation and a process called remyelination.

Remyelination could be key to new therapeutic approaches. When a cell is damaged (as in neurodegenerative disease) the myelin sheath can be stripped away. Remyelination is the process a cell goes through to replace the myelin.

Imagine you have a new wooden toy boat, painted and smooth. If you take a knife and whittle away all the paint and then repaint it—even exactly how it was painted before—the boat is not going to be as shiny and smooth as it was before. This is how remyelination works (or rather, doesn’t).  When nerve cells are damaged, the myelin sheath is stripped away and even after the cell rebuilds it, the cell can’t conduct signals at the same speed it was able to before.

“If you can learn what controls myelination, maybe you can improve effectiveness of remyelination,” Dale said.

Garcia said it is possible that revealing the mechanics involved in phosphorylation could lead to better treatments. In context of neurodegenerative diseases, the question why don’t axons function properly might be wrapped up in Garcia’s question: In healthy cells, why do they?

Supervising editor: Paige Blankenbuehler

SoyKB: Leading the convergence of wet and dry science in the era of Big Data

Yaya Cui, an investigator in plant sciences at the Bond Life Sciences Center examines data on fast neuron soybean mutants that are represented on the SoyKB database.

Yaya Cui, an investigator in plant sciences at the Bond Life Sciences Center examines data on fast neuron soybean mutants that are represented on the SoyKB database.

The most puzzling scientific mysteries may be solved at the same machine you’re likely reading this sentence.

In the era of “Big Data” many significant scientific discoveries — the development of new drugs to fight diseases, strategies of agricultural breeding to solve world-hunger problems and figuring out why the world exists — are being made without ever stepping foot in a lab.

Developed by researchers at the Bond Life Sciences Center, SoyKB.org allows international researchers, scientists and farmers to chart the unknown territory of soybean genomics together — sometimes continents away from one another — through that data.

 

Digital solutions to real-world questions

As part of the Obama Administration’s $200 million “Big Data” Initiative, SoyKB (Soy Knowledge Base) was born.

The digital infrastructure changes the way researchers conduct their experiments dramatically, according to plant scientists like Gary Stacey, Bond LSC researcher, endowed professor of soybean biotechnology and professor of plant sciences and biochemistry.

“It’s very powerful,” Stacey said. “Humans can only look at so many lines in an excel spreadsheet — then it just kind of blurs. So we need these kinds of tools to be able to deal with this high-throughput data.”

The website, managed by Trupti Joshi, an assistant research professor in computer science at MU’s College of Engineering, enables researchers to develop important scientific questions and theories.

“There are people that during their entire career, don’t do any bench work or wet science, they just look at the data,” Stacey said.

The Gene Pathway Viewer available on SoyKB, shows different signaling pathways and points to the function of specific genes so that researchers can develop improvements for badly performing soybean lines.

“It’s much easier to grasp this whole data and narrow it down to basically what you want to focus on,” Joshi said.

A 3D-protein modeling tool lends itself especially to drug design. A pharmaceutical company could test the hypothesis and in some situations, the proposed drug turns out to yield the expected results — formulated solely by data analysis.

The Big Data initiative drives a blending of “wet science” — conducting experiments in the lab and gathering original data — and “dry science” — using computational methods.

Testament of the times?

“Oh, absolutely,” Joshi said.

 

Collaboration between the “wet” and “dry” sciences

Before SoyKB, data from numerous experiments would be gathered and disregarded, with only the desired results analyzed. The website makes it easy to dump all of the data gathered to then be repurposed by other researchers.

“With these kinds of databases now, all the data is put there so something that’s not valuable to me may be valuable to somebody else,” Stacey said,

Joshi said infrastructure like SoyKB is becoming more necessary in all realms of scientific discovery.

“(SoyKB) has turned out to be a very good public resource for the soybean community to cross reference that and check the details of their findings,” she said.

Computer science prevents researchers having to reinvent the wheel with their own digital platforms. SoyKB has a translational infrastructure with computational methods and tools that can be used for many disciplines like health sciences, animal sciences, physics and genetic research.

“I think there’s more and more need for these types of collaborations,” Joshi said. “It can be really difficult for biologists to handle the large scope of data by themselves and you really don’t want to spend time just dealing with files — You want to focus more on the biology, so these types of collaborations work really well.

It’s a win-win situation for everyone,” she said.

The success of SoyKB was perhaps catalyzed by Joshi. She adopted the website and the compilation of data in its infant stages as her PhD dissertation.

Joshi is unique because she has both a biology degree and a computer science background. Stacey said Joshi, who has “had a foot in each camp,” serves as an irreplaceable translator.

Most recently, the progress of SoyKB as part of the Big Data Initiative was presented at the International Conference on Bioinformatics and Biomedicine Dec. 2013 in Shanghai. The ongoing project is funded by NSF grants.

New screening tool gives scientists more control over genetic research

A tangled spool of yarn represents DNA, while the fingers holding the section represent the insulators just added by MU researchers to improve a scientific, screening tool. | Paige Blankenbuehler

A tangled spool of yarn represents DNA, while the fingers holding the section represent the insulators just added by MU researchers to improve a scientific, screening tool. | Paige Blankenbuehler

Here’s a scenario: You are trying to find a lost section of string in the world’s most massively tangled spool of yarn. Then try cutting that section of yarn that’s deeply embedded in the mess without inadvertently cutting another or losing track of the piece you’re after.

For researchers, this problem is not unlike something they encounter in the study of genetic information in the tangled spool that is DNA.

A new tool will help scientists straighten things out.

The tool, developed by University of Missouri Bond Life Sciences Center investigators helps researchers effectively screen cell behavior by limiting epigenetic silencing, which occurs when a cell packages and stows away important genetic information, much like an accountant puts a client’s information away in a filing cabinet.

The cell can go digging to find that information when it absolutely needs it, but otherwise that information is tucked away and inactive.

Professors of biochemistry Mark Hannink, Tom Mawhinney and research assistant professor Valeri V. Mossine used insulators to develop the piggyBac transposon plus insulators, a better reporter of signaling between cells that makes improved screening possible.

This simple addition to an existing screening tool used in laboratories will help streamline research and contribute to screening products like vitamins and supplements and medicines for authenticity, Hannink said.

This is why the insulator addition to the piggyBac reporter assay by MU researchers is a game changer in the scientific world.

 

How it works

DNA stretches out to nearly 10 feet when it’s uncoiled. That’s 10 feet of your body’s deepest secrets coiled into a microscopic package and tucked away into each and every one of your cells. The human body, by the way, holds an estimated 10 trillion cells. An inconceivable number, right?

Let’s go back to our yarn analogy. You’re trying to find one specific piece to cut but it’s deeply tangled in the mass of yarn. You need to find the piece that you really care about and clamp your fingers onto the yarn to reduce the slack — straighten it out — so you can cut it easily.

Think of your fingers as the insulators.

The insulators of the new piggyBac transposon tool perform the same task of stretching out the DNA so certain expressions through signaling pathways are held open, enabling the investigation of specific genetic material.

Hannink hypothesizes this new reporter could provide answers to questions like: Does an anti-migraine medicine have the component that will relieve that ailment? Does a multi-vitamin deliver all of the nutrients on its label?

“A lot of botanicals are said to have anti-inflammatory benefits,” Hannink said. “By using an assay like this, we can easily determine if they actually do and if so, what molecules in these complex mixtures are in fact the cause of the punitive inflammatory activity.”

 

 

Reproducing results

Replication is a critical part of verifying scientific discovery and epigenetic silencing is a big headache for investigators trying to reproduce results.

Scientists studying genetic material can open certain expressions with other reporter tools but often, the cell will turn expressions off and block signaling pathways, causing an expected result to fail because of epigenetic silencing.

The new assay preserves conditions of an experiment so the same results can be reached. Cell behavior under the same conditions and expressions that were switched on during the experiment will be expressed.

The new version of the reporter assay is being used at the MU Center for Botanical Interaction Studies to understand how botanical compounds affect the immune system and in other research on the central nervous system and on the development of prostate cancer.

This research appeared in the Dec. 20, 2013 edition of PLoS ONE. It was funded by the University of Missouri Agriculture Experiment Station Laboratories and grants from the National Center for Complementary and Alternative Medicines, Office of Dietary Supplements and the National Cancer Institute.