Can A 10,000-Year-Old GMO Change How We Think About GMOs?

Researchers at Ghent University in Belgium have discovered ancient transgenic DNA from Agrobacterium in the sweet potato genome. The finding that DNA from the same microbe used to produce human-made transgenic crops—or genetically modified organisms, GMOs—resides in one of the world’s most important crops calls into question the classification of GMOs as unnatural. This new research could challenge the basis for regulating GMOs separately from non-transgenic crops and perhaps help rescue GMOs from their increasingly negative public image.

That is, if biotech advocates can harness this story to retell the GMO narrative from a new perspective.

The sweet potato was domesticated 8,000-10,000 years ago in South America, and today more than 100 million tons are grown every year around the world. It is grown for its fleshy storage root and leafy greens and, despite the name, is unrelated to the potato.  

While searching for regulatory bits of DNA in the sweet potato genome, the Belgian scientists discovered portions strikingly similar to well-known segments of DNA inserted by the bacteria Agrobacterium. Agrobacterium is a plant parasite. It inserts short sections of its DNA into plant cells that reprogram them to grow tumor-like structures called galls, which are often seen on tree trunks or crop plants. These galls are where the bacteria thrives when it gets the chance.

That Agrobacterium DNA might be in a crop plant is neither new nor altogether surprising. It has been found in tobacco before, although not in food crops. And a lot of DNA detritus floats around all of our genomes—viral DNA that does not function anymore, or truncated genes that are DOA.

But these microbial genes in sweet potato are actually active, albeit at a low level. What’s more, in studying hundreds of domesticated and wild sweet potato relatives, the researchers found that all of the crop plants, and none of their wild relatives, had one portion of this transgenic DNA. Although not proof, this strong association between the Agrobacterium DNA and the plants humans have domesticated is good evidence that the foreign DNA was selected for. That is, it might have helped produce a trait that humans kept around when taming sweet potatoes.

However, the scientists did not find a clear link between the DNA and the root we eat. It might be that the bacterial DNA produced stronger sweet potato plants, or conferred other useful traits, even if it does not account for the engorged root.

As a new lesson in the malleability of genomes during evolution, this study is fascinating enough. But the reason it was the cover of the latest issue of the Proceedings of the National Academy of Sciences has much more to do with the article’s final sentence:

“This finding could influence the public’s current perception that transgenic crops are ‘unnatural.’”

But will it?

In a recent survey by the Pew Research Center comparing the opinions of scientists and the general public, no topic—not vaccines, not evolution, not climate change—had as big of a gap between the two groups as whether GMOs are safe to eat. Google “GMOs” and the first hit is the non-GMO Project. Switch over to images and you’ll find that one syringe in a tomato just doesn't cut it these days, we've upped it to three!

Clearly companies like Monsanto, Syngenta and Bayer failed, and failed hard, in their consumer-oriented communication. They’re trying to make up for lost time. But the general public are not their customers, farmers are. And by the numbers, corn, cotton and soybean farmers sure like GMOs, so much so that 9 in 10 of each of these crops in the United States is genetically engineered. If biotech advocates want to pivot the conversation in the public sphere, this article could be that fulcrum. But there are no guarantees it will work.

Already the popular press has written it up and jump-started the conversation in a positive light. Biotech advocates should call into question the unnecessary exclusion of GMOs from the USDA organic label. Are organic sweet potatoes still a thing? If the organic label was changed to be exclusively about growing practices and not germplasm, we could have organic GMOs, as envisioned by rice geneticist Pamela Ronald and her organic farmer husband Raoul Adamchak.

Biotech advocates should call into question the label of GMO. Period.

This sweet potato study blurs the already unclear boundaries between crops created by artificial selection, induced mutation, hybridization, and genetic engineering. New genetic engineering methods that introduce no foreign DNA muddy the waters even more. By some definitions, organic sweet potatoes will be GMOs while genetically engineered potatoes won’t be. Before we start playing definitional Twister, let’s simplify the conversation so we can speak meaningfully about what matters—allergenicity, gene escape, industrial agriculture, and feeding billions of people healthfully in the era of climate change.

Listening in on Plant Defenses

It’s enchanting to consider that classical music might help plants grow better, like something out of a fairy tale. A simple Google search shows that a lot of people are interested in it, from the throngs at Yahoo Answers to marijuana growers looking for an edge. Mythbusters tested it, with mixed results. Academic researchers have explored the effects of tones on plant growth, finding frequency-specific gene regulation and growth responses. But it remains unclear what evolutionary benefit sensitivity to sound could provide, and a solid understanding of what is sometimes called ‘plant bioacoustics’ eludes researchers.

In a widely-reported study released last year, two researchers over at the University of Missouri, Columbia tested the effects on plant defenses of the vibrations caused by a caterpillar chewing on a leaf. Although much of the reporting fell prey to the temptation to claim the plants “heard” the chewing and responded, the real answer is both more complicated and more interesting. I had the opportunity to attend a talk Drs. Appel and Cocroft gave at Washington University a few months ago where I learned more than I could have extracted from their paper, published in Oecologia, alone.

Sound waves are longitudinal. Insect vibrations are transverse

Dr. Cocroft studies insect communication, especially the ability of insects to find mates and prey by sensing the vibrations of other insects on a plant. Like sound, the information is encoded in vibrational waves passing through a substance. Instead of a pressure wave like sound that varies in the same direction of travel—a longitudinal wave—insect vibrations on plants are transverse waves, moving up and down like a wave on the ocean (see figure).

We could never hear these kinds of waves ourselves, but their frequency can be directly translated to sounds we can hear. Cocroft played a number of humming soundscapes recorded with a laser on a wild prairie—the result of hundreds or thousands of insects communicating silently on stalks of grass. A plant, Cocroft noted, is a great conductor for these vibrations, flexible yet strong. His field studies how insects benefit from communicating this way, but he joined forces with Appel to ask: Do plants respond to the vibrations of insect herbivores in an adaptive way?

One major defense that plants have against pests is producing noxious compounds to deter feeding. Appel and Cocroft hypothesized that Arabidopsis plants would produce more defense compounds if they were exposed to the vibrations of herbivorous insects before actually being attacked. This effect is called priming, and could help defend against a second wave of insect damage.

To test this, the researchers first used lasers to record the vibrations of caterpillars allowed to eat the leaves of Arabidopsis plants. To play the vibrations back to undamaged plants, Cocroft attached leaves to tiny pistons driven, essentially, by speakers, ones that could replicate the vibrations of an insect chewing. Then caterpillars were allowed to feed on either the leaf that was vibrated or another, untouched leaf.

Both vibrated and distant leaves responded more vigorously to caterpillar attack than leaves on untouched plants. The plants that were primed by recorded caterpillar vibrations produced more glucosinolates, or mustard oils, than those of unvibrated plants. This is evidence of an adaptive response to insect vibrations, but leaves open the possibility that any vibration encouraged plant defenses.

To see if the effect really was specific to the herbivorous caterpillars, Appel and Cocroft played back vibrations of harmless insects, wind, or caterpillars on different plants and again measured defense compounds—this time anthocyanins, responsible for the deep reds and purples of many plants. Only caterpillar vibrations could prime plants to increase their defense response to herbivory; wind and the neutral insects had no effect.

One important caveat: although the researchers looked for an effect of vibrations alone, they found none. Only vibrations plus actual insect feeding induced higher defenses; the plants were primed for future attack, but vibrations alone made no difference. Of course, a real insect is more than just its vibrations. Herbivore attack is a physical, chemical, and auditory assault, and plants likely respond to each stimulus in different ways.

But how are plants able to sense the vibrations of caterpillars, and even differentiate them from similar sounds in nature? It’s entirely unknown. A very good candidate is a diverse group of proteins bound together by their responsiveness to physical forces—mechanoreceptors. These proteins can signal within a cell in response to vibration or touch and are potentially behind the priming effect that Appel and Cocroft observed.

In fact, to test this, the Haswell lab is working with Appel and Cocroft to see if our favorite mechanosensitive ion channels are part of the vibrational-response pathway. I got to see Liz’s face pop up in the corner at the end of their presentation over on the medical campus as they told us that work was underway. We’ll just have to wait to find out.

[A version of this post first appeared on my lab's blog]

Beer in the Garden

As humans first started to settle down from nomadic hunter-gatherers into early agricultural societies, they took what must have been an exceedingly keen understanding of the diverse plants in their environment and applied that knowledge to the cultivation of crops. Instead of relying on the bounty provided by nature, these people began to select the most appealing and nutritious plants to work deliberately. In so doing, they actively produced brand new crops and developed an even deeper relationship with the plant world.

And here, at the very dawn of civilization, early agriculturalists took their growing understanding of plants, and perhaps a bit of serendipity, and developed something to rival agriculture itself—beer. Agriculture and brewing developed side-by-side because both required a deepening understanding of the plant world. Today, the increasingly popular hobbies of home gardening and homebrewing can bring us back to this early world thousands of years ago where an appreciation for and knowledge of the plant world translated into intoxicating, frothy, delicious brews.

This past Wednesday I was invited to give a presentation on the intersection between gardening and homebrewing at the wonderful, new(ish) Urban Chestnut bierhall in The Grove. I was invited by Gateway Greening, which runs a monthly seminar series called, appropriately, Pints ‘N’ Plants. Around fifty people came to learn and talk about the understanding of barley and hops that is required to make great beer, and the many plants we can grow right here in St. Louis to brew with.

Bread baking and brewing happened under the same 

roof in ancient Egypt. Photo by Keith Schengili-Roberts

Barley of course provides the essence of beer, the sugars that yeast ferment into alcohol and carbon dioxide. But barley kernels straight from the field are full of starch, a form of sugar inaccessible to yeast. To unlock this sugar, maltsters control the germination of barley seeds, the developmental program that converts starch into sugar for the young seedlings. Instead of letting the seed continue to produce a whole new barley plant, maltsters instead dry and roast the sweet malted barley to halt the process and caramelize the sugars.

Fermented malted barley is all that is needed to make an intoxicating beverage, but it will result in a cloyingly sweet, unpalatable beer. Hops, the aromatic female flowers from the hop plant, perform the job of balancing the saccharine barley with bitter hoppiness while flavoring the beer as well. Hops took over from a diverse array of local herbs, fruits, and other plants around a thousand years ago to become the exclusive flavoring of most beer.

These earlier brews—called gruits—also relied on a strong sense of the qualities of local flora to produce drinkable beer that would not poison the drinkers. Hops likely superseded these hundreds or thousands of other plants because of their ability to protect beer from bacterial infections so well, but they also make a damn fine beer. The dozens of different varieties of hops lend distinct flavors and aromas from dry and earthy to bright and citrusy, helping to recover the diversity in flavorings lost with the gruits.

As any would-be usurper of the Busch crown will tell you, beer only requires barley, hops, yeast, and water. However, the craft beer and homebrewing renaissance has helped rediscover the variety of beer flavorings that harken back to an earlier time when all manner of local plants found their way into the brew kettle. Here, gardeners and homebrewers can join together in search of homegrown, quality ale.

Any number of bizarre plants can find their way into homebrewed beer. I covered just a handful to consider and get started in my talk, some I have experience with and some I do not. By far the easiest to grow is cilantro, the herb flavoring a lot of Mexican dishes. Instead of the leaves, however, brewers seek the bright, citrusy seeds called coriander. They have a completely different taste and are used in a very popular style of beer called Belgian witbier. This is the style of Blue Moon and is a very refreshing beer brewed with wheat, bitter orange peel, and coriander. In fact, the witbier is light on hops and calls back to the gruits that were flavored with an array of herbs and spices. Cilantro is so easy to grow it will even reseed itself from year to year, reliably producing pods of brown, crunchy seeds in the summer. Only about five tablespoons are required with an equal weight of orange peel to flavor the beer, an amount easy to acquire from just a plant or two.

I also covered how to grow and brew with pumpkin, chili peppers(!), and potted citrus plants. Perhaps the best plant to get in the ground this spring, however, is hops! A perennial, fast-growing vine, hops do well in community spaces where they can spread out and grow stronger year-over-year, or in the backyard of an enthusiastic gardener-brewer who has enough space for a sturdy trellis. Each spring, homebrew supply stores sell chunks of hop rhizomes, a root-like structure that overwinters to produce vines the next season. This vegetative means of propagation ensures that gardeners get only the female plants and clones of their favorite variety. After growing up to thirty feet high and maturing at the end of summer, the hops are ready to be tossed in the brew kettle for truly homegrown brewing.

My former community garden, Block 1035. Hops growing

on the common space trellis in the background.

To combine gardening and brewing, with an eye for creativity and variety, is truly to travel back in time to eras when most beer was brewed at home alongside the baking of bread, and when a knowledge of local plants was required for making delicious brews. For a time it seemed we had lost both of these skillsets. But now with the ongoing popularity of home and community gardening and the rapid rise in homebrewing, we all have the opportunity to capture again that intrinsic link between the growing of plants and the brewing of beer. Prost!

[I relied heavily on The Drunken Botanist by Amy Stewart and The Complete Joy of Homebrewing 3rd ed. by Charlie Papazian]

Keeping Spuds Safe--And Humans Too

Fortunately, potatoes are never quite as toxic as the alien carrots
in the Looney Tunes "Invasion of the Bunny Snatchers" episode

A team of Japanese scientists has published research that may help both protect potatoes from serious diseases and safeguard humans from poisonous spuds. The researchers, led by Dr. Kazui Saito, were able to identify a gene critical for making the toxic alkaloid chemicals that potatoes produce to protect themselves from pests. Although commonly-eaten varieties contain safe, low levels of these alkaloids, they are also more susceptible to certain major diseases. To combat infections, breeders want to crossbreed these safe spuds with disease-resistant—but poisonous—wild potato species without increasing the levels of toxic alkaloids in the potatoes we eat. Dr. Saito’s group has discovered a way to largely disable the production of these chemicals, opening up safer avenues to breed strong, resistant potatoes that do not make people sick.

Although normally safe, potatoes are serious contenders for the most toxic vegetable in the American diet. Potatoes, tomatoes, and eggplants are all members of the nightshade family, which produces a group of chemicals called steroidal glycoalkaloids to defend against pests. In small amounts, these chemicals may cause an upset stomach, but extremely high doses can lead to dizziness, hallucinations, and even death.

Human domestication long ago selected for potatoes with low levels of these alkaloids. But domestication also produces crops that cannot defend themselves as well against diseases—in particular, our efforts to make potatoes safer, larger, and tastier have impaired the spud’s ability to protect itself against late blight disease, the most damaging potato infection. Late blight led to starvation in Ireland in the 1840s, and today accounts for billions of dollars in lost productivity worldwide.

Crop breeders routinely scout out hearty wild relatives of our foods, seeking to breed in traits like disease resistance. For potatoes, scientists must ensure that borrowing beneficial traits from wild varieties does not increase the levels of steroidal glycoalkaloids above a safe threshold. One way to limit this risk is to reduce the production of these alkaloids in potatoes before breeding programs even start.

So Dr. Saito’s group set out to understand how potatoes make these chemicals in order to control and limit their production. Steroidal glycoalkaloids primarily consist of a steroid backbone, which is made from cholesterol. As a result, the scientists searched for genes in the potato genome that resembled a human gene that helps synthesize cholesterol. Although humans, peas, and rice have only one copy of the gene, potatoes have two—SSR1 and SSR2.

Having two similar genes is often a sign that the two copies have evolved to specialize. While most plants use a single gene to make cholesterol and other important chemicals like hormones, Dr. Saito and his colleagues reasoned that potatoes might have divided those two tasks between the two SSR genes.

To test this, they put the genes into yeast that made the chemical precursors of either cholesterol or plant hormones and measured what chemicals each SSR gene produced. They found that while SSR1 efficiently produced plant hormones, SSR2 excelled at making cholesterol. This specialization means that disabling SSR2 would shut down cholesterol and steroidal glycoalkaloid production without affecting SSR1’s synthesis of important hormones.

Scientists can add snippets of a plant’s own gene to activate a natural viral defense mechanism—a kind of plant immune system—and impair the native gene’s function. When the Japanese researchers did this with SSR2, alkaloid levels plummeted to a tenth their normal level, while the plants themselves grew just fine, a sign that hormones still functioned properly.

Another technology, called genome editing, can produce permanent errors in a specific gene, turning it off completely. The researchers added an editing protein that disrupted SSR2 and found that the alkaloid levels again dropped to a fraction of their normal amount. The editing protein can be removed in the next generation. This leaves only the precise changes dialed in by the scientists and 100 percent potato DNA, unlike most crop genetic modifications that add DNA from other species.  

The ability to produce specific new changes with the potato’s own DNA may reduce widespread concerns about genetically modified crops, which, although shown to be safe, are rejected by a large number of consumers.  This would be good news for scientists looking for new tools to improve potatoes and other foods.  Late blight and other diseases are ongoing scourges and the expanded toolbox for safely combating them provided by Dr. Saito’s group may help keep the world’s fourth-largest crop on a level playing field with these infections while keeping spuds safe.

[This news story served as part of my application to the AAAS Mass Media Fellowship]

Pollen in the Windy City

The view from outside the lab

I went to Chicago to figure out how pollen senses the world around it.

My colleagues and I want to understand how plants sense and respond to mechanical force. One might think that we have this figured out for all kinds of creatures, but really we don’t. We kind of have no idea how animal nerves sense touch. We think we have a good idea of how hearing works, but we could end up being quite wrong.

In plants, we know even less. Plants are really sensitive to gravity, touch, and all kinds of forces, we just don’t have a good idea of how they really perceive them and change their behavior appropriately. One way to do this is to use an ion channel that opens and closes based on pressure: a mechanosensitive ion channel.

That’s how hearing works, converting air pressure into electricity through an ion channel. A pressure wave—sound—in air enters the ear and bends a molecular lever so that an ion channel opens. Instantly, charged particles can flow through the channel, millions of them every second, and zzzp this makes a little electrical pulse that our brains can decode into sound. That is a mechanosensitive ion channel at work, and there is one in pollen and we do not know why.

My plants packed into my car for the trip

(We always think of electrical impulses as the workings of nerves. The cool thing is, even without nerves, these signals can be interpreted by cells and used to change behavior. Ions also play a big role in controlling how water flows, and we think that is what might be happening in my pollen.)

My pollen has a protein that looks like a mechanosensitive ion channel, but we don’t really know if it functions like that. So, I went to Chicago to find out.

Dr. Paul Malchow has equipment we don’t, namely an electrode that is extremely sensitive and can distinguish between different ions. By using a putty that only lets individual ions through—hydrogen, calcium, chloride, or the like—the voltage that the electrode measures near a cell can be linked directly to the concentration of ions there. The tool I brought along was a mutant plant, one that’s missing our potential ion channel. So, if I can see a difference in the flow of ions near pollen grains with and without this channel, we’d have good evidence that this channel is functional and can control how ions flow around pollen.

An electrode measuring ions near pollen

Does that tell us how pollen senses the world around it? No, not exactly. It’s just a small piece of the puzzle that we rearrange and try to piece together every week. If the channel does work like we expect, then we can try to figure out what forces it responds to in pollen, why ion flow is so important. If it is a dud, then we have to think harder about why pollen has this imposter ion channel at all, and what exactly it’s doing, and whether that has anything to do with mechanical force. We just don’t know. I don’t even have the answer from the electrode data yet, that alone can be hard to interpret.  

That may sound unsatisfying. It can certainly be frustrating. But it’s never boring, because every week my mentor and I reconsider everything we think we know about our pollen, about the evolution of these channels, about what pollen needs to respond to in order to be successful. It’s a little arcane, but it’s just a tiny piece of the puzzle for figuring out how plants respond so elegantly to the world they inhabit, twisting and turning to find nutrients and light, avoiding herbivores and pests. Playing a part in painting this picture of how plants are themselves really is satisfying.

So I went to Chicago, largely ignoring this beautiful city to huddle in a cold laboratory watching videos of pollen being prodded with electrodes. Happily.

Climate Change and Midwest Agriculture

This year, farmers will collect a record harvest of corn and soybeans in the United States, according to the USDA. This is good news for a world increasingly concerned about both a growing population and the agricultural challenges produced by advancing climate change. Predictions by the United Nations put global population at around nine billion by 2050, with the possibility of this being the eventual stable resting point of human population due to decreasing fertility rates around the world. Global food production needs to increase substantially—around 70% according to the FAO— by 2050 in order to feed more mouths and increasingly affluent populations seeking more animal products. As a major breadbasket of the world, the Midwestern U.S. will play a significant role in meeting these demands.

As the capstone to the Workshop on Climate Change and Agriculture in the Midwest hosted by the International Center for Advanced Renewable Energy and Sustainability at Washington University, Professor David Lobell of Stanford University presented on his research into the impacts of climate change on agricultural production in the Midwest. 

Dr. Lobell had two themes: First, respect the problem. Although rising CO₂ levels may improve photosynthetic efficiency to a degree, the global increase in temperature is a net drawback to productivity. Second, we can address the problem rationally. Knowing how crops will likely respond to these stresses can help scientists identify the traits that can help meet production requirements.

The most dramatic impact of temperature increases will be reduced relative humidity. As the air warms, it can hold more water. Yet without an increase in water vapor, the relative humidity will decrease significantly. For us humans, that will hopefully offset the effects of hotter summers; we curse humidity in the Midwestern August. However, plants are exceptionally susceptible to humidity, especially when flowering.

In a tie-in to my own research, pollen, which comes to a sort of equilibrium with its environment, is easily damaged if the air is too dry when the flower opens. As it happens now, corn typically flowers during the hottest weeks of the summer, leaving its pollen susceptible to decreasing humidity. Less water vapor in the air also means the plant will transpire much more, increasing the amount of water needed in the soil to keep the crop happy and productive.

How do we combat this inherent weakness? Perhaps plant biologists can identify traits, or contribute new genes, that make crops use water more efficiently and protect pollen from excessive desiccation. Intensive research is being done in these areas already.

One idea that Dr. Lobell put forward was new to me, but apparently not to some farmers in the Southern United States: double cropping. With the right climate, fields can be planted with wheat in the fall to harvest in the spring, with just enough time left over to harvest soybeans in the fall. Under these conditions, flowering occurs outside the hottest months, and yield can be protected from the extreme heat to an extent. In fact, as the climate warms, Midwestern states will acquire longer growing seasons that make this option available to more farmers. Although this strategy does not necessarily out-produce the incredibly abundant maize crop, it is an example of alternatives immediately available to farmers even without significant improvements in crop germplasm.

Other strategies for helping crops cope with increasing temperatures will likely involve infrastructure, such as how to provide plants with enough water without losing as much to the soil and evaporation. Smarter irrigation systems may help in this goal.

The bottom line from Dr. Lobell’s talk is that adapting already-productive areas like the United States Midwest to climate change will require multiple strategies, because the effects of a warming world are multiple. This will require the sustained efforts of plant scientists, engineers, and innovative farmers. I, for one, am hopeful about the future of agriculture. Us humans seem to do a decent job of getting ourselves out of a mess, even if it is at the last moment. Let’s hope that’s the case here.