Study gets to root of rice's resilience to floods

"Our work is the most comprehensive look yet across species into what's really going on under the hood as plants respond to flooding," says Emory biologist Roger Deal. (Getty Images)

By Carol Clark

Climate change is increasing both the severity and frequency of extreme weather events, including floods. That’s a problem for many farmers, since rice is the only major food crop that’s resilient to flooding. A new study, published in Science, however, identified genetic clues to this resilience that may help scientists improve the prospects for other crops.

“Our work is the most comprehensive look yet across species into what’s really going on under the hood as plants respond to flooding,” says Roger Deal, associate professor of biology at Emory University and a lead author of the study. “Understanding the mechanism for flooding tolerance is the first step in understanding how you might increase it in plants that lack it.”

Rice was domesticated from wild species that grew in tropical regions, where it adapted to endure monsoons and waterlogging. The Science research looked at how other crops compare to rice when submerged in water. The plants included species with a range of flooding tolerance, from barrel clover (which is similar to alfalfa), to domesticated tomato plants, to a wild-growing tomato that is adapted for a desert environment.

The results showed that, although evolution separated the ancestors of rice and these other species as many as 180 million years ago, they all share at least 68 families of genes that are activated in response to flooding.

“That was surprising,” Deal says. “We thought we’d see different gene expression responses among these species related to their adaptation to wet or dry conditions. Instead, what was really different was that rice had far and away the most rapid and synchronous response. In comparison, the other plants’ responses were piecemeal and haphazard.”

The Deal lab experimented on barrel clover (Medicago truncatula) as part of the study. (Photo by Marko Bajic)

Deal’s research focuses on how plants build and adapt their bodies. By digging deep into the developmental biology and genetics of plant systems, he hopes to unearth secrets that could benefit both agriculture and human health.

Marko Bajic, an Emory graduate student in the Department of Biology and the Graduate Program in Genetics and Molecular Biology, is co-author of the Science paper.

The study was an international collaboration funded by the National Science Foundation’s Plant Genome Research Program. The authors include scientists from the University of California, Davis; the University of California, Riverside; Argentina’s National University of La Plata and the Netherland’s Ultrecht University.

UC Riverside researchers conducted flooding experiments and analysis of rice plant genomes, scientists at UC Davis did the same with the tomato species while the barrel clover work was done at Emory.

The results suggest that the timing and smoothness of the genetic response may account for the variations in the outcomes for the plants during the experiments.

The wild tomato species that grows in desert soil withered and died when flooded.

The team examined cells that reside at the tips of roots of plants, as roots are the first responders to a flood. Root tips and shoot buds are also where a plant’s prime growing potential resides. These regions contain cells with the ability to become other types of cells in the plant and serve as a repair system in plants and other living things.

Drilling down even further, the team looked at the genes in these root tip cells, to understand whether and how their genes were activated when covered with water and deprived of oxygen.

“We looked at the way that DNA instructs a cell to create particular stress responses in a level of unprecedented detail,” says Mauricio Reynoso, one of the lead authors from the University of California, Riverside.

The group is now planning additional studies to improve the survival rates of plants that currently die and rot from excess water.

This year is not the first in which excessive rains have kept farmers from being able to plant crops like corn, soybeans and alfalfa. Floods have also damaged the quality of the crops they were able to grow. This trend is expected to continue due to climate change.

“We as scientists have an urgency to help plants withstand floods, to ensure food security for the future,” says Julia Bailey-Serres, another lead author of the study and a professor of genetics at the University of California, Riverside.

Jules Bernstein, from the University of California, Riverside, contributed to this story. 

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DNA 'origami' takes flight in emerging field of nano machines

Making things out of DNA, nicknamed DNA origami after the traditional Japanese paper craft, is moving from a nanoscale novelty to a practical research tool. Emory chemists Khalid Salaita and Aaron Blanchard wrote about the emerging field of DNA mechanotechnology for the journal Science. (Getty Images)

By Carol Clark

Just as the steam engine set the stage for the Industrial Revolution, and micro transistors sparked the digital age, nanoscale devices made from DNA are opening up a new era in bio-medical research and materials science.

The journal Science describes the emerging uses of DNA mechanical devices in a “Perspective” article by Khalid Salaita, a professor of chemistry at Emory University, and Aaron Blanchard, a graduate student in the Wallace H. Coulter Department of Biomedical Engineering, a joint program of Georgia Institute of Technology and Emory.

The article heralds a new field, which Blanchard dubbed “DNA mechanotechnology,” to engineer DNA machines that generate, transmit and sense mechanical forces at the nanoscale.

“For a long time,” Salaita says, “scientists have been good at making micro devices, hundreds of times smaller than the width of a human hair. It’s been more challenging to make functional nano devices, thousands of times smaller than that. But using DNA as the component parts is making it possible to build extremely elaborate nano devices because the DNA parts self-assemble.”

Aaron Blanchard, left, an Emory graduate student of chemistry, and Khalid Salaita, professor of chemistry, are working at the forefront of DNA mechanotechnology.

DNA, or deoxyribonucleic acid, stores and transmits genetic information as a code made up of four chemical bases: adenine (A), guanine (G), cytosine (C) and thymine (T). The DNA bases have a natural affinity to pair up with each other — A with T and C with G. Synthetic strands of DNA can be combined with natural DNA strands from bacteriophages. By moving around the sequence of letters on the strands, researchers can get the DNA strands to bind together in ways that create different shapes. The stiffness of DNA strands can also easily be adjusted, so they remain straight as a piece of dry spaghetti or bend and coil like boiled spaghetti.

The idea of using DNA as a construction material goes back to the 1980s, when biochemist Nadrian Seeman pioneered DNA nanotechnology. This field uses strands of DNA to make functional devices at the nanoscale. The ability to make these precise, three-dimensional structures began as a novelty, nicknamed DNA origami, resulting in objects such as a microscopic map of the world and, more recently, the tiniest-ever game of tic-tac-toe, played on a DNA board.

Work on novelty objects continues to provide new insights into the mechanical properties of DNA. These insights are driving the ability to make DNA machines that generate, transmit and sense mechanical forces.

“If you put together these three main components of mechanical devices, you begin to get hammers and cogs and wheels and you can start building nano machines,” Salaita says. “DNA mechanotechnology expands the opportunities for research involving biomedicine and materials science. It’s like discovering a new continent and opening up fresh territory to explore.”

Watch a video about how DNA machines work


Potential uses for such devices include drug delivery devices in the form of nano capsules that open up when they reach a target site, nano computers and nano robots working on nanoscale assembly lines.

The use of DNA self-assembly by the genomics industry, for biomedical research and diagnostics, is further propelling DNA mechanotechnology, making DNA synthesis inexpensive and readily available. “Potentially anyone can dream up a nano-machine design and make it a reality,” Salaita says.

He gives the example of creating a pair of nano scissors. “You know that you need two rigid rods and that they need to be linked by a pivot mechanism,” he says. “By tinkering with some open-source software, you can create this design and then go onto a computer and place an order to custom synthesize your design. You’ll receive your order in a tube. You simply put the tube contents into a solution, let your device self-assemble, and then use a microscope to see if it works the way you thought that it would.”

The Salaita Lab is one of only about 100 around the world working at the forefront of DNA mechanotechnology. He and Blanchard developed the world’s strongest synthetic DNA-based motor, which was recently reported in Nano Letters.

A key focus of Salaita’s research is mapping and measuring how cells push and pull to learn more about the mechanical forces involved in the human immune system. Salaita developed the first DNA force gauges for cells, providing the first detailed view of the mechanical forces that one molecule applies to another molecule across the entire surface of a living cell. Mapping such forces may help to diagnose and treat diseases related to cellular mechanics. Cancer cells, for instance, move differently from normal cells, and it is unclear whether that difference is a cause or an effect of the disease.

In 2016, Salaita used these DNA force gauges to provide the first direct evidence for the mechanical forces of T cells, the security guards of the immune system. His lab showed how T cells use a kind of mechanical “handshake” or tug to test whether a cell they encounter is a friend or foe. These mechanical tugs are central to a T cell’s decision for whether to mount an immune response.

“Your blood contains millions of different types of T cells, and each T cell is evolved to detect a certain pathogen or foreign agent,” Salaita explains. “T cells are constantly sampling cells throughout your body using these mechanical tugs. They bind and pull on proteins on a cell’s surface and, if the bond is strong, that’s a signal that the T cell has found a foreign agent.”

Salaita’s lab built on this discovery in a paper recently published in the Proceedings of the National Academy of Sciences (PNAS). Work led by Emory chemistry graduate student Rong Ma refined the sensitivity of the DNA force gauges. Not only can they detect these mechanical tugs at a force so slight that it is nearly one-billionth the weight of a paperclip, they can also capture evidence of tugs as brief as the blink of an eye.

The research provides an unprecedented look at the mechanical forces involved in the immune system. “We showed that, in addition to being evolved to detect certain foreign agents, T cells will also apply very brief mechanical tugs to foreign agents that are a near match,” Salaita says. “The frequency and duration of the tug depends on how closely the foreign agent is matched to the T cell receptor.”

The result provides a tool to predict how strong of an immune response a T cell will mount. “We hope this tool may eventually be used to fine tune immunotherapies for individual cancer patients,” Salaita says. “It could potentially help engineer T cells to go after particular cancer cells.”

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Chameleons inspire 'smart skin' that changes color in the sun

A chameleon can alter the color of its skin so it either blends into the background to hide or stands out to defend its territory and attract a mate. The chameleon makes this trick look easy, using photonic crystals in its skin. Scientists, however, have struggled to make a photonic crystal “smart skin” that changes color in response to the environment, without also changing in size.

The journal ACS Nano published research led by chemists at Emory University that found a solution to the problem. They developed a flexible smart skin that reacts to heat and sunlight while maintaining a near constant volume.

“Watching a chameleon change colors gave me the idea for the breakthrough,” says first author Yixiao Dong, a PhD candidate in Emory’s Department of Chemistry. “We’ve developed a new concept for a color-changing smart skin, based on observations of how nature does it.”

Read the whole story and watch videos of the color-changing process here.

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