John Wallingford admits he’s a bit of a Luddite. “I don’t like a lot of technology,” he says. “If I could put a record player in my car, I would.” And though he makes his living using cutting-edge microscopic techniques to watch developmental events unfold in real time, it’s the simple experiments that have brought Wallingford the most joy. “I love old-school, cut-and-paste embryology,” he says.
As a postdoctoral fellow in Richard Harland’s lab at the University of California, Berkeley, around the turn of the millennium, Wallingford was exploring the role that Dishevelled—a signaling protein that regulates a variety of developmental processes—plays in the elongation of the embryo. Starting with a frog embryo that lacked Dishevelled, Wallingford carefully excised a tiny piece of tissue from the neural plate—the structure that gives rise to the brain and spinal cord—then grafted that tissue into the same position on the back of...
“I don’t like a lot of technology. If I could put a record player in my car, I would.”
Much to Wallingford’s delight, the doctored embryo came down with a serious curvature of the spine: while the tissues along its belly lengthened normally, its back did not. That bent-back tadpole demonstrated that Dishevelled is needed for animal embryos to stretch full length. “It’s satisfying to be able to manipulate an embryo that way,” he says. “You’re doing the dissection with a watchmakers’ forceps and a knife made from an eyebrow hair. It’s really, really hard. These days you could do the same experiment better using conditional genetics. But where’s the fun in that?”
Today Wallingford and his team actually do enjoy using modern molecular tools to study morphogenesis—the process by which embryos change shape as they develop from a fertilized egg to a multicellular organism with distinct tissues and organs. Here he discusses how a pile of dead tadpoles can change the course of one’s career, why he’s not really a frog guy, and what’s so special about sitting on the porch.
Wallingford makes it work
Dishevelled dealings. In Harland’s lab, Wallingford was investigating convergent extension—a process by which cells in the embryo crawl across one another and squeeze themselves into a narrow, interdigitated column, thus elongating the body axis. “The cell behaviors that drive this movement had been really well worked out,” he says. “What we didn’t know were the molecules that control it. I had planned to do a functional screen to find genes involved. As a side project, I had picked a couple of molecules to start playing around with. One of them was Dishevelled.” Elimination of Dishevelled had previously been shown to disrupt convergent extension in frog embryos—although it wasn’t clear why it did so. The same protein had also been found to control the direction of? hairs on the fly wing—Drosophila lacking Dishevelled appear notably mussed.
A change of plans. Wallingford had been stockpiling the Drosophila papers. “But I had never taken the time to sit down and read them,” he says. Then one afternoon—when he was alone in the lab—he discovered that the tadpoles he’d planned on using that day had all croaked. “So I thought, ‘I’m just going to sit down and go through this big stack of papers’—about something called planar-cell polarity. As I read through them, I began to understand that this must be what Dishevelled was doing in the frog.” A few years before, Ray Keller—who, at the time, was also at UC Berkeley—had shown that during convergent extension in frogs, cells turn their long axes perpendicular to the direction of extension. In other words, the cells become polarized. “It was exactly the same thing that was described in these papers on planar-cell polarity in the fly. The realization compelled us to make time-lapse movies to see what these cells were doing in frog embryos that don’t have Dishevelled. And we were off to the races.” Wallingford saw that cells in the Dishevelled mutants do not orient themselves properly or establish the stable connections they need to form the slender column that will give rise to the embryo’s spine. “I’ll tell you one thing: the large-scale screen I was planning to do went right out the window,” says Wallingford. “This became my total focus.” The resulting Nature paper, published in 2000, was one of a trio of articles—all from different labs—that established that planar-cell polarity signaling is central to vertebrate development. It also launched Wallingford’s career.
Two labs are better than one. Wallingford’s postdoc experience was actually a twofer: he performed his molecular manipulations in Harland’s Berkeley lab and did his microscopy in the prodigiously equipped laboratory of Scott Fraser at the California Institute of Technology. “I spent about a week out of every month at Caltech,” says Wallingford. “I guess the price of the plane tickets and hotel room worked out to less than it would have cost to keep the core microscope facility at Berkeley burning as much as we would have.” Cost-effective or not, the arrangement had other benefits. “It gave me the opportunity to train in two labs with diametrically opposed worldviews: Richard’s lab is hard-core molecular biology and Scott’s is hard-core imaging. So I’d give a group meeting in one lab and they would yawn. But the same data would have the other group in paroxysms of excitement.” The experience made the resulting papers stronger, says Wallingford, “because we had to pitch to two audiences.”
A human connection. Planar-cell polarity is not only critical for giving embryos their elongated shape. “The genes are absolutely essential for neural tube closure,” says Wallingford. “Convergent extension is what elongates the embryo’s axis. And if you don’t elongate your axis, you can’t close your neural tube”—an observation Wallingford made in frogs and his collaborators made in mice. Mutant forms of the planar-cell polarity (PCP) genes, including Dishevelled, have also surfaced as culprits in patients with neural tube defects such as spina bifida. “So the connection is clear.”
“I think when people self-identify more strongly with their model organism than they do with the overall biology, it limits what they can discover.”
The power of shroom. As he was transitioning from his bipolar postdoc to running his own lab at the University of Texas at Austin, Wallingford showed that a protein called shroom is sufficient to cause epithelial cells to constrict at one end. “Apical constriction is this completely essential cell-shape change involved in bending epithelial sheets,” he says. Such tissue bending is critical for neural tube closure, for invagination of the lens of the eye, and for many of the events in gastrulation, whereby embryos develop the three germ layers that will give rise to all their organ systems. Mice lacking the protein fail to close their neural tubes, so Wallingford decided to take a look in frogs. As a first experiment, he had his student Saori Haigo try overexpressing the protein. “Overexpression is easy, and I typically start with the easy experiments and see if they’re interesting. If not, I give up and do something else. For shroom, the overexpression phenotype was really striking. It caused the cells on the embryo to turn black. At first I thought they were dead. Saori insisted they were not. Then we realized the other thing that causes cells to look black is when the apical surface constricts, which concentrates all the pigments there.” Finding a single protein that is sufficient to drive that sort of shape change was exciting, says Wallingford, because “it demonstrated that this constriction is an intrinsic property of the cells, not a passive thing that happens because of forces generated elsewhere.”
Suddenly cilia. Not all planar-cell polarity proteins are the same. “Our biggest surprise was that genes that control planar-cell polarity in flies seem to control cilia in vertebrates.” In flies, the core PCP genes, like Dishevelled, control planar-cell polarity all over the body. But other PCP genes are more limited in their influence, affecting polarity in, say, just the wings. “We thought that was kind of cool and we’d take a look at those guys in frog,” says Wallingford. When student Tae Joo Park depleted frog embryos of two of these proteins—called Inturned and Fuzzy—“we got these phenotypes that were totally unexpected.” Convergent extension was only mildly diminished. “But the embryos all had these craniofacial defects”—the same sorts of defects seen in patients with ciliopathies, diseases that stem from a failure to produce cilia.
Biological boy scout. Wallingford and his group continue to work toward understanding just how proteins like Inturned and Fuzzy affect ciliated cells. In collaboration with Edward Marcotte, whose lab is across the road, Wallingford and student Ryan Gray found that Fuz (the murine version of Fuzzy) promotes the trafficking of proteins to the base of the cilia—work published in Nature Cell Biology in 2009. And more recently Wallingford and student Eric Brooks found that eliminating this protein from frogs disables the intraflagellar transport system needed to build a functional cilium. That paper, which came out in July, was Wallingford’s first publication in the Journal of Cell Biology. “It’s like I got my cell biology merit badge. Now a lot of developmental biologists think I must be a cell biologist by training. The cell biologists know better.”
See the full slide show, "Of Frogs and Embryos"
Science rewriting. “Writing is a bit like science in that it’s iterative—and it always takes longer than you think. One of my friends from the old days is a poet, studied with Ginsberg. Going around to readings with him, I realized these people are not just reading their poetry in clubs, they’re workshopping it. And even though the poem may be only half a page long, they may tweak it for years before they call it finished.” Scientists don’t have the luxury of time—but revision is still key to success. “I can crank out a draft in a weekend. But then I’ll give it to someone else and it’ll go through how many revisions—maybe 20. I’ve never actually submitted a paper that I felt totally satisfied with. It’s just at some point you’ve got to pull the trigger.”
Don’t call him a frog guy. “I know a lot about genes that control morphogenesis in Xenopus. But I don’t think of myself as a Xenopus biologist. Ultimately I’m interested in what these genes do in all animals. I think when people self-identify more strongly with their model organism than they do with the overall biology, it limits what they can discover. Not all model systems are great for everything you might want to do.” In Wallingford’s lab, trainees manipulate mice and worms in addition to frogs. “I really think you should not be scared to go grab the animal that’s going to give you the best chance of answering the question you want to answer. I’m looking forward to a post-model system future.”
But if he had to choose . . . The model system Wallingford would most like to see studied is: “The star-nosed mole. I use it as a test case in all my developmental biology exams. What’s the ‘fate map’ of the star nose? It’s got some muscle in there because it moves. It’s got some neurons, some skin. I think the morphogenesis of the star nose has got to be one of the great unanswered questions in biology.” (See "A Nose for Touch," The Scientist, September 2012.)
“Not just genes.” “We understand so little about how animals develop in the real world. We’re still very focused on genes and proteins. But it’s clear that mechanical signals matter. Cells can sense who’s pushing on them and they change their gene expression accordingly. I think that the integration of developmental biology with other spheres of inquiry will be the next big step—and we’re just scratching the surface.”
Wallingford’s No Wallflower
Lab playlist. Wallingford’s website includes a list of tunes currently in rotation. In addition to Fitz and the Tantrums, the Ettes, and a local band called Sincola, he’s been grooving on Dolly Parton’s Little Sparrow. “Barring that bad period in the ’80s when all country music got really awful, I think Dolly Parton is highly reliable.” And though he doesn’t get out to clubs as often as he used to, Wallingford says, “the nice thing about Austin is that great bands play at my grocery store.”
Invincible Prince. “My friends and I used to play a game where we tried to come up with the coolest superpower. No one wanted to play anymore after I said that I wanted to remain the same size”—Wallingford is 6-foot-4 and weighs 210 pounds—“but be able to dance like Prince.”
Talk to the rock. Wallingford enjoys taking to the mountains and scaling rocks. “The beautiful thing is the enforced focus. It absolutely demands that you stop thinking about everything else. Meditation does the same thing, but with rock climbing I find it’s a little easier to get to that mental state. It’s one of the few things that quiets my mind.” It’s also a way for Wallingford—who has two young kids—to enjoy some “alone time” with his wife. “We’ve basically given up on date nights and dinners out and movies and stuff, and we try to take climbing days together.”
Porch potato. Wallingford and his family vacation in Colorado, where his parents have a house. When he’s not climbing, Wallingford says, “I spend a lot of time sitting on the porch, staring at the mountains. Like, a LOT of time. I’m pretty much a ‘do-nothing-on-vacation’ kind of guy. People who think you need to be doing something on vacation don’t understand: I AM doing something. I’m sitting on the porch.”