How, exactly, does a soup of stem cells turn into an exquisitely specialized organ, such as a plant root?

Over the past three decades, Duke University biologist Philip N. Benfey has probed this question in the sleek and structured root of the mustard plant Arabidopsis thaliana. The Arabidopsis root develops continuously from four sets of stem cells in its tip. Beginning with simple genetic screens, Benfey’s group has identified key genes that guide the development of particular cells in the root. He has since created several technologies for tracking gene expression and growth patterns of the root—tools that have helped his lab and dozens of others make additional discoveries.

Plant engineering technologies, such as those developed by Benfey, could help reduce carbon emissions. Plants naturally absorb carbon dioxide in their leaves and store it in their roots. "For taking carbon dioxide out of the air, there’s nothing better than photosynthesis. And it all comes down to the roots," he says.

	Philip Benfey, Ph.D. Photos: Jim Bounds/AP, © HHMI High-resolution photographs are available on request. benfey1_lg.jpg 4x6 inches @300ppi, vertical crop Request this photo benfey2_lg.jpg 4x6 inches @300ppi, horizontal crop Request this photo Benfey Lab Image View image

The man so wrapped up in roots began his adult life searching for his own. At age 19, Benfey dropped out of college and spent six years wandering the globe: riding the Trans-Siberian Railway across Russia, working in the iron mines in Australia and as a gardener in Japan. He later settled in a small apartment in Paris and tried, unsuccessfully, to publish short stories. His girlfriend (who would later become his wife) gently suggested getting a day job as a lab technician, so he enrolled in the University of Paris to study biochemistry.

He was lucky, he says, because it was 1979—early days in the recombinant DNA era, when researchers learned to clone genes and insert them into other cells. "These tools were opening up the possibility of attacking fundamental biological questions in ways that could only be dreamed about 10 or 20 years earlier," Benfey says. He was excited enough to put his writing career on hold and move to Cambridge, eager to begin graduate school at Harvard University.

A decade later, after he had launched his own laboratory at New York University, Benfey and his colleagues discovered two genes that play crucial roles in root development. They showed that mutations in genes dubbed short-root and scarecrow (after the Wizard of Oz character who's missing a brain) result in roots that lack entire layers of certain cell types.

Pinpointing the genes involved in developmental processes is important, but scientists are generally more interested in the next steps: how are these genes transcribed into RNA and then translated into protein? Which cells express these genes, and when?

At the time, the primary way to measure gene expression was to grind up an entire root and scan it for RNA fragments. This method isn't ideal because many cell types in roots make up less than 10 percent of the total tissue. So if a particular gene is expressed only in those cells, its RNA is difficult to detect when looking at the whole root. "There was a large amount of information that was missing that we just had no idea about," Benfey says.

To solve this problem, Benfey aimed to create a comprehensive map showing the expression of each gene in every one of the 15 cell types in the root. He did this by inserting fluorescent proteins into specific types of cells, separating the glowing cells from the rest, and analyzing for gene expression by looking at the RNA.

Developing this cell sorting technology was a risky move; the approach required new and expensive microarrays, and many researchers were skeptical that it would work on enough cells to provide an accurate readout. But Benfey and his team persevered—and succeeded. Thanks to this method, plant researchers now know, for example, that cell types in the root are incredibly diverse, differing from each other as much as they differ from shoot cells. Using the information gained from this approach, his lab has identified genes that control the transition from rapid cell division to elongation to differentiation and discovered that periodic waves of gene expression affect root development.

Benfey has developed several other innovative technologies. One, called the RootArray, uses fluorescent tags to track gene expression in the roots of 64 seedlings at once while they're exposed to different kinds of stresses, such as high salt or low iron. Another tool, called a root imaging platform, reconstructs the three-dimensional picture of root growth by taking photos of plants’ roots as they grow in a clear, gel-filled matrix in the lab.

"I believe that much of science, and particularly much of biology, is driven by improvements in technologies that allow us to ask new biological questions," Benfey says. "So I've always seen it as important to be on the cutting edge."

Philip Benfey is the Paul Kramer Professor of Biology at Duke University and Director of the Duke Center for Systems Biology. He earned his DEUG degree from the University of Paris VI, and received his Ph.D. from Harvard University. He is a Member of the National Academy of Sciences and a Fellow of the American Association for the Advancement of Science.