News this Week

Science  27 May 2011:
Vol. 332, Issue 6033, pp. 1016
1. Around the World

1 - Geneva, Switzerland
Smallpox Virus Wins 3-Year Reprieve
2 - Arecibo, Puerto Rico
Famous Observatory Changes Hands
3 - Kennedy Space Center, Florida
Cosmic Ray Detector Up and Running
4 - China
AIDS Deaths Plummet With Government's About-Face

Geneva, Switzerland

Smallpox Virus Wins 3-Year Reprieve

The smallpox virus, on death row for decades, will live to see another day. On 24 May, the World Health Assembly (WHA) decided not to set a deadline for the destruction of the last samples of the virus, called variola, and to revisit the issue in 2014.

Smallpox was eradicated in the 1970s, but the planned destruction of the two remaining repositories has been postponed because their holders, the United States and Russia, argue that they need more time to develop new vaccines, treatments, and diagnostics. In recent years, however, pressure has built to set a deadline for destruction (Science, 28 January, p. 389).

Yet in the run-up to the WHA, “a lot of arm-twisting” by the United States had brought many developing countries over to the U.S.-Russian camp, says Jonathan Tucker, a biosecurity specialist at the Federation of American Scientists in Washington, D.C. The European Union was in favor of retaining the virus as well, but a group of at least 20 countries, many in the Middle East, remained firmly opposed. The 3-year extension that emerged as a compromise is “regrettable,” says Donald Henderson of the University of Pittsburgh in Pennsylvania, who spearheaded the smallpox eradication campaign and is a leading advocate of destruction. http://scim.ag/smallpox-stays

Arecibo, Puerto Rico

Famous Observatory Changes Hands

After 4 decades under the direction of Cornell University, Arecibo Observatory in Puerto Rico, home to the largest radio telescope in the world, will have a new manager. The National Science Foundation (NSF) has decided to award a 5-year contract to a consortium comprising SRI International, the Universities Space Research Association, Universidad Metropolitana, and other institutions. Aided by money from NASA, NSF last year agreed to a level of funding that will keep Arecibo open at least through 2016. It also launched a competition to run the facility; a Cornell-led consortium and the SRI-led partnership were the only bidders. An Arecibo researcher who confirmed the decision notes that SRI had circulated a memo among staff members indicating that the new management would do its best to maintain current salaries and staffing. The status of observatory employees on Cornell's campus is uncertain, as is the fate of some Arecibo-related technology development projects at Cornell. http://scim.ag/_arecibo

Kennedy Space Center, Florida

Cosmic Ray Detector Up and Running

The largest and most expensive particle detector ever to be flown in space was safely bolted onto the International Space Station on 19 May during the space shuttle Endeavour's last mission and is already recording celestial hits.

The nearly 7-ton, $2 billion Alpha Magnetic Spectrometer (AMS), detects charged cosmic rays, particles that whizz through space at high speeds. Logging 10,000 cosmic rays per minute, AMS should be able to measure the flux of particles far more precisely than balloon-borne experiments. Its creators hope to solve one of astrophysics' most enduring mysteries: What cosmic event launches the particles off into space at nearly the speed of light? The researchers also hope to catch particles from theorized antimatter galaxies, and even elusive dark matter, in the bargain. After the 3-hour transfer operation, involving both the shuttle's and the station's robot arms, physics Nobelist Samuel Ting, who masterminded AMS, thanked the astronauts for “a great ride and a safe delivery,” adding, “You made a great contribution to our understanding of the universe.” China AIDS Deaths Plummet With Government's About-Face Encouraging new results from China's recent campaign against HIV reflect a dramatic change in the country's attitude toward the disease. In 2002, China introduced antiretroviral (ARV) drugs to treat HIV-infected people. Over the next 7 years, mortality from the disease dropped by 60%, according to a new report from the Chinese Center for Disease Control and Prevention (CDC). The results, published online 19 May in The Lancet Infectious Diseases, highlight China's evolution from a country in denial about its epidemic to one that has now mounted a serious response. The Chinese CDC estimates that the country has 740,000 HIV-infected people and that slightly under half of them know their status. As of the end of 2009, China—with the help of more than$500 million in grants from the Global Fund to Fight AIDS, Tuberculosis and Malaria—provided ARVs to 82,450 HIV-infected people, which the report authors note is a “remarkable” 63.4% of those identified as infected and in immediate need of the drugs.

China's response still falls far short of what's needed, the CDC report says. It calls for scaling up HIV testing to detect more infections, increasing efforts to start ARVs earlier, and more aggressively monitoring for drug resistance. Yet the government has not committed new money to these efforts and, in a sobering turn of events, the Global Fund last week halted payments to China because of concerns about how the country manages its grants.

2. Newsmakers

1.7 million — Amount for which a California woman allegedly tried to sell what she claimed was a moon rock to NASA investigators during a sting operation last week. A Bright Mind Shines Again True to empirical tradition, while writing his new play on Marie Curie, actor Alan Alda once hurried through the streets of Paris from the Sorbonne to a certain apartment on Rue du Banquier. The goal: to see how breathless the physicist would have been upon arriving at trysts with her lover. On 1 June, a reading of Radiance: The Passion of Marie Curie, with Maggie Gyllenhaal reading the part of Curie, will kick off the World Science Festival in New York City. The play covers the interval between Curie's two Nobel prizes, during which she was reviled for “what people thought were transgressions in her personal life,” Alda says. The Nobel committee grudgingly included her with husband Pierre and Henri Becquerel for the physics prize in 1903 but demanded that she sit in the audience at the award ceremony “as if she was Pierre's assistant,” Alda says. “It was misogyny.” Because of an illicit romance after Pierre's death, in 1911 she was almost denied her second Nobel, in chemistry, for her work in radioactivity. “There's an arc to her character,” Alda says of those 8 years. “You see her gather her forces against tremendous obstacles.” Alda himself faced hindrances. Curie's letters are still radioactive, so he tracked down a rare French copy of her diaries. During a visit to her lab, his guide held a Geiger counter up to a notebook entry from the day she discovered radium. Says Alda, “The page clicked like a tap dancer.” 4. Scientific Community The Prion Heretic 1. Jennifer Couzin-Frankel For 30 years, Laura Manuelidis has rejected the dominant theory that misfolded proteins cause infection. Sticking to a minority view has become a career in itself. NEW HAVEN, CONNECTICUT—Laura Manuelidis has an acrobatic mind. Her train of thought evokes a circus performance. She soars up and drops down, she twirls, she swoops in one direction and swerves back to where she started. She titled her volume of poetry, published in 2007, Out of Order. “Isn't that fitting?” she says with a laugh. Manuelidis has spent her whole adult life here at the Yale School of Medicine, first as one of a half-dozen women in her 1967 graduating class and then as a parser of brain tissue. At 24, she ignored taboo and wed her professor, 48-year-old Elias Manuelidis. Despite naysayers who declared the marriage doomed, it turned out to be a lively and passionate one, lasting until her husband's death from a stroke in 1992. Since then Manuelidis has pursued the work they began together: challenging the now-entrenched view that prions, which are misshapen proteins, transmit disease. Skeptics linger but rarely speak out. Now 68 years old, Manuelidis has become the de facto representative for doubters worldwide. She knows that the history of science is littered with heretics who reject conventional wisdom, insisting that their experiments reveal the truth while others' do not. Often they turn out to be wrong and either abandon their view when the evidence against it grows overwhelming or go to their grave still believing. Sometimes they're right. Manuelidis, comfortable in the role of dissenter, likes to quote 20th century mathematician and philosopher Bertrand Russell: “Doubt is the essence of science,” she says. Her seeds of doubt—or rather, tall, flourishing plants—germinated years ago. In 1982, Stanley Prusiner, a neurologist at the University of California, San Francisco, gave prions their name. He described them as infectious particles made up mainly of a protein, PrP, that misfolds and goes awry in the brain, causing a cluster of rare, transmissible, and fatal brain diseases. Mad cow disease (officially known as bovine spongiform encephalopathy) is arguably the most famous. When first proposed, Prusiner's theory was widely dismissed as bizarre. Biology then held that infectious disease was caused by organisms built from DNA, RNA, or both, like viruses and bacteria—something containing a nucleic acid sequence that can replicate and spread through a cell. Proteins lack these sequences. But Prusiner promoted his thesis, snagging millions of dollars in grants and publishing his experiments widely. In 1997, he won the Nobel Prize. Today, Prusiner's view dominates. “It's the dogma,” says Adriano Aguzzi, a neuropathologist at the University Hospital of Zurich in Switzerland, who counts himself a believer. Manuelidis takes an opposing stance that we don't need to rewrite the book on infectious disease to accommodate prions. She regards the protein not as the cause of infection but as a pathological reaction to it and believes mad cow disease and others like it are triggered by viruses. What—and where—those viruses are, Manuelidis isn't sure. No one has found them. Whether that means they don't exist depends on whom you ask. She's not the only prion doubter, but her voice is by far the loudest. In part that's because she's safe. Long a tenured professor at Yale, Manuelidis still commands vast lab space she no longer uses. Her unpopularity among top prion scientists leaves her unfazed. “What can they do to me?” she says. “If I don't say it, nobody's going to say it.” Beginnings In her youth, Manuelidis aspired to be a poet. She enrolled at Sarah Lawrence College, a small liberal arts school outside New York City known for its strong focus on the arts and literature. Her older brother, with whom she'd always been close, was attending Harvard Medical School at the time. “He said, ‘I don't see any want ads in The New York Times for poets. … How long are you going to be a parasite on Mom and Dad?’” Manuelidis considered this problem and settled on medical school as an alternative. “My brother said, ‘Why don't you become a nurse?’ and I said, ‘Why don't you become a nurse?’” she remembers. “He wanted a normal sister.” In medical school she knew from the start that she would focus on the brain, hoping to cure schizophrenia. Manuelidis had been deeply affected by college summers spent volunteering at Waltham State Hospital outside Boston, where she says patients were rarely seen by physicians. (“I looked in the charts” to find out.) They were so heavily drugged that they reeked of Thorazine, an antipsychotic drug. “I saw people with frontal lobotomies,” she says. “I felt there was a certain arrogance in medicine. It was very good to see before I went to medical school.” Manuelidis embraced pathology, encouraged by a supportive department chair. Another draw was her neuropathologist husband-to-be, a confirmed bachelor when she met him. Their relationship was scandalous, she says. They lived together openly and threw large parties at his house attended by many of her friends. The two began exploring a class of deadly diseases called transmissible spongiform encephalopathies (TSEs), so named because once symptoms surface, the brain turns into spongy tissue with alarming speed. TSEs in people are rare; the most prevalent, sporadic Creutzfeldt-Jakob disease, strikes about one person in 1 million each year. A curious feature is that TSEs, like viral diseases, can be passed from one animal to another by injecting affected brain tissue. TSEs also have a long latency period in animals. The first guinea pigs Elias Manuelidis exposed to TSE thrived for 500 days before getting sick. But the virus, if there was one, was elusive. Some experiments indicated that there couldn't be a virus at all. A radiobiologist named Tikvah Alper showed in the 1960s that blasting infected tissue with radiation didn't destroy its ability to infect. And exposing tissue to high heat failed to prevent transmission of a TSE called scrapie, which kills sheep and goats. Strategies that annihilate the usual viruses didn't do much to halt disease. In the early 1980s, Prusiner began to advocate a different theory to explain where the “transmissible” in TSEs came from. The answer, he argued, was a particle he called a prion, in effect the first infectious protein. The evidence, “one has to admit, was very shaky” to start, Aguzzi says. But the work slowly advanced. Prusiner reported that purifying bits of scrapie-laden brain down to their infectious components always left behind a protein that resisted chemical breakdown, suggesting it might be misfolded. In 1985, the gene that generates the prion protein was cloned, and researchers were shocked to discover that the healthy prion protein, PrP, was naturally abundant in the brain tissue of normal people. Aguzzi became convinced of the prion hypothesis in the early 1990s, when he was working with prion biologist Charles Weissmann, then at the Institute of Molecular Biology in Zurich, and saw that mice genetically engineered to lack PrP didn't get sick when injected with infected material. This suggested to Aguzzi that the disease is transmitted by a misfolded PrP protein and that it targets healthy PrP in the brain and turns it toxic, killing neurons. “That was really the tipping point” for me, he says. Another tipping point came when Prusiner won the Nobel Prize in physiology or medicine in 1997 for “his discovery of prions—a new biological principle of infection,” the Nobel Committee announced. “Numerous attempts to disprove the prion hypothesis over the past 15 years have failed,” Prusiner declared in his Nobel lecture on 8 December of that year, shortly before accepting the prize in Stockholm, Sweden. For him, the case was settled. Days after the award was announced, Manuelidis shared her blunt assessment with The New York Times. “My fear is that debate is going to be stifled,” she told a reporter. “That's the problem with Nobel prizes. If people feel everything is decided, you can't possibly risk going against the grain.” Manuelidis keeps a yellowed clipping of that article pinned up outside her office door. Prusiner's Nobel came as fear of TSEs was running high. In 1995, the first person died of what would later be called variant Creutzfeldt-Jakob disease (vCJD): a version of the neurological ailment, transmitted by eating beef from affected cows. Panic ensued, especially in the United Kingdom, where 175 people were eventually diagnosed as having the lethal disease. But uncertainty about its cause hasn't been “an impediment to making sensible public health decisions,” says David Asher, chief of the laboratory of Bacterial and TSE Agents at the U.S. Food and Drug Administration (FDA). Governments simply took steps to keep meat from sick cows out of the food supply. Recently, cases of vCJD have dropped, and fear has subsided. Battle lines In the years since Prusiner won his Nobel, even some who have wavered on the prion hypothesis say that evidence has mounted steadily in its favor. About 10 years ago, neuroscientist Claudio Soto, who trained in Chile and is now at the University of Texas Medical School at Houston, developed a new technology called protein misfolding cyclic amplification (PMCA). As its name suggests, PMCA is designed to boost the concentration of prion protein in a sample and eliminate living cells (along with viruses they may contain). To test for infectivity, researchers run samples of brain homogenate through PMCA and inject the concentrated product into mice. Because the mice get sick, many believe this points to prions as the infectious culprit. The results have been difficult to argue with. Bruce Chesebro, who has long been on the fence about the prion hypothesis, is leaning in its favor. Chief of the Laboratory of Persistent Viral Diseases at the U.S. National Institute of Allergy and Infectious Diseases, based in Montana, Chesebro now says, “PMCA suggests it may not be a virus” that triggers these maladies. Biochemist Jiyan Ma of Ohio State University in Columbus and his colleagues reported online in Science on 28 January 2010 (http://scim.ag/prion_ma) that mixing PrP with various lipid molecules, which force it to misfold, and then injecting the mixture into the brains of healthy mice gave them prion disease. “The data show that prions exist,” says Surachai Supattapone of Dartmouth College, who published one of the landmark experiments in a 2007 issue of the Proceedings of the National Academy of Sciences (PNAS). “That's I think now clear.” And, he adds, prions are “not viruses.” This all sounds unambiguous, but even backers of the prion hypothesis admit to some gaps in the evidence. Misfolded PrP is sometimes found in noninfectious tissue, and sometimes it is not found in tissue that can infect other animals. Brain homogenates from people and animals afflicted by prion disease—even prion diseases from the same species—can have wildly different effects when injected into animals, including genetically identical ones. Some develop symptoms after a few months, others not until years later. Prion supporters attribute the variation to different “strains” of PrP, suggesting that the protein can misfold into different chemical conformations that have different levels of toxicity. Not everyone buys it. Another festering worry, Manuelidis and some others say, is that prion experiments are easily contaminated. Anyone examining the brains of animals with TSEs risks winding up with the infectious agent on their equipment, Chesebro says—on their test-tube racks, their benchtops, the hoods under which they work for protection. Although great care is taken to keep stray bits of brain tissue at bay, there isn't an airtight solution short of switching to a new lab each time. What does this mean, practically speaking? If an unidentified infectious agent exists, it could be a stealthy actor even in the best-controlled experiments. The Ma study, many argue, has come the closest to definitively proving the prion hypothesis. Researchers synthesized misfolded PrP in the lab, injected it into normal animals, and watched them develop symptoms of TSEs. But no one has replicated this result. Instead, researchers often use genetically engineered mice that overproduce healthy PrP because they develop symptoms faster once infected. This makes for cheaper and easier experiments. Normal mice can take an eternity to show symptoms. It “might take longer than the life span of the mouse,” Aguzzi says. “So it helps to have an overexpresser.” Casting a long shadow over the field is Prusiner, who is as tight-lipped in public as Manuelidis is loquacious. He almost never talks to the press and declined, through his correspondence manager, to be interviewed for this article. Minority views Asking Manuelidis to elaborate on her prion skepticism can be an exercise in frustration. Encouraging her to talk is not the problem—but grasping her case against prions isn't easy. Manuelidis is aware of this. “I can't think in a straight sentence,” she says, soon after parking her low-slung Mazda convertible and sitting down for dinner at a Portuguese restaurant. “My brain goes into literature.” Many prion biologists—even some with questions about the current dogma—are disappointed by the evidence she's turned up. In 2007, Manuelidis published a paper in PNAS, describing small viruslike particles in TSE-infected tissue but not in uninfected samples. That's a correlation, however, not proof that the particles are causing disease, Chesebro says. “I'm sympathetic of her battle,” he notes. “I wish she were more convincing.” Weissmann, Aguzzi's colleague, who's now at the Scripps Research Institute in Palm Beach, Florida, has been both friend and foil of Manuelidis over the years and was the only one to mention her unprompted in conversation. (More often there is a long pause after her name is brought up.) “The work itself is sound; she's done some interesting work with cell cultures,” Weissmann says. “But then she tries to force it into the viral hypothesis,” going through “contortions” to interpret the data. His language is nearly identical to Manuelidis's descriptions of the work of the “prion cabal.” Manuelidis and others say she has paid a price for holding so tightly and so publicly to her virus theory. She describes a prominent prion scientist walking out when she took the lectern at a meeting, and another screaming at her in a room full of people. Anonymous reviews of her papers have sometimes been caustic and personal, she says. “She's had a very tough time scientifically, but she also has many friends and allies,” says Robert Somerville, who studies TSEs at the Roslin Institute at the University of Edinburgh in the United Kingdom. He's known Manuelidis since 1980 and considers himself a good friend. “The divisions run perhaps deeper in our field than others and are longer lasting. Which is sad, really—it can be difficult to have a useful, constructive discussion.” Like Somerville, Asher of FDA worries about the path prion biology has taken. “I'm still left with this nagging concern that the abnormal protein, important though it may be, has not been demonstrated to be the infectious agent,” he says. “The field has been very forgiving of failures of the prion hypothesis to predict things that are found in the laboratory.” Asher also complains that prion studies are almost never repeated—scientists just move on to a new one. And, he says, papers that fit the dogma are more readily published than those that do not. Maurizio Pocchiari, a neurologist at the Istituto Superiore di Sanità in Rome, agrees that siding with the vocal majority can certainly help one's career. “If you are aligned with the prion hypothesis, it is very easy to publish, … [and] it's easier to get a good result” experimentally, he thinks, thanks partly to the genetically modified mice churning out PrP that are so popular. Pocchiari is another member of the Manuelidis fan club. He disagrees that a conventional virus is lurking behind TSEs, believing it would have been found by now—but he isn't satisfied with the protein-only dogma, either. “We now are pretty aware that when we try to purify infectivity, we purify the pathological prion protein, but we also purify something else,” he says. “There is a something else, … [but] we have no idea what we are looking for.” Some, like Somerville, wonder about a “virino,” a small viral particle that doesn't code for proteins on its own and acts in conjunction with PrP. Virinos fit the bill in part because of their size, which is useful because of long-ago studies suggesting that nothing as large as a virus was hiding in TSE-infected tissue. But virinos are a concept invented to fit the experimental data that haven't been found anywhere else. Then again, many argued before the prion theory took hold that prions shared this feature, too. Tenacity If there is a virus behind TSEs, how could it have stayed hidden for so long? Isolating these tiny snippets, Manuelidis argues, is just plain difficult because copies are so scarce, even in brain tissue where disease concentrates. Most people disagree with her, but not everyone. “The fact that we can't detect it is, I would argue, not a statement of what's present or not, but maybe more a statement about our abilities as scientists to discover it,” Somerville says. Asher hopes that Manuelidis will continue her work with the viruslike particles she identified in the 2007 PNAS paper. “Far too little has been done with it,” he says. Manuelidis perseveres, working near the morgue in the basement of the surgery building, where she's been since the mid-1970s. The labs are old; her husband's office remains largely untouched. Like everywhere else, precautions against infection were an after-thought when they first began this work. “My husband was determined you had to feel the stuff; nobody put on gloves and then [we] ate lunch,” Manuelidis says. A guinea pig injected with CJD that mysteriously didn't get sick was christened Harold and lived for 12 years in the lab's biohazard facility. Manuelidis accidentally squirted herself once in the eye with an infectious brain sample and took out a1 million life insurance policy for 10 years for her two sons. She never developed the disease, reinforcing her view that TSEs are not particularly virulent and may need to be injected or ingested in large quantities for someone to get sick.

In the late 1990s, Manuelidis began downsizing her lab, frustrated by how grueling her struggle for money had become—a shift that began after Prusiner's Nobel, she says. Now she has three recent Yale undergraduates working for her, as they bridge time between college and medical or graduate school. Her students learned the prion gospel in biology class and are fascinated by what, to them, is a new controversy. They're not sure where they stand. As they tell it, Manuelidis doesn't push them. “The data doesn't seem to contradict” the virus theory, says Terry Kipkorir, a thoughtful 2010 graduate who grew up in Kenya and slouches at a desk, a blue stocking cap on his head. Kipkorir and the others are looking for viral particles in infected tissue and trying to determine which components are infectious. But “I don't want to dismiss the prion theory” either, he says. If there's one thing he's realized as he ends an academic year in Manuelidis's lab, it is to prize autonomy. “I don't think I'm going to work under a lot of direction” going forward, he says.

Manuelidis attributes the slow pace of her never-ending virus hunt to technical challenges and a shortage of money. She has the same CJD grant from the National Institutes of Health that she's had for more than 30 years; it now brings in $539,000 a year, nearly$200,000 of which goes to Yale for overhead costs. Multimillion-dollar awards—the kind that allow you to work with hundreds of animals—are not in her future, she thinks.

Should they be? The same researchers who lament how incomplete her work is say no. “To be quite frank, I don't think it's worth funding,” Weissmann says. “In the 19th century, there were still people who thought that life could originate from boiled hay. These people just die out—there's always fewer and fewer of them.” He believes that Manuelidis will never relinquish a theory to which she's held tight for decades, no matter what story the data tell.

Asked if letting go would be hard for her, Manuelidis is unambiguous. “No, no,” she says. “All I know is that my experiments don't show” that prion protein is causing disease. She's hopeful now that she's on the cusp of something new. “I think I can crack this stuff,” she says.

5. Bio-Inspired Engineering

Manta Machines

1. Elizabeth Pennisi

By observing manta rays in the wild, modeling them, and building robots, researchers are learning how these agile animals ply the oceans.

Swimming like butterflies underwater, with mesmerizing ease and grace, manta rays are the envy of engineers seeking more efficient underwater vehicles. For the past 3 years, researchers at Princeton University and the University of Virginia (UVa) have been working to understand how these meters-wide fish are so light on their fins. Now, their students are putting the insights they have gained to the test—in a manta robot competition between the two collaborating universities.

On this April afternoon, Princeton mechanical engineering senior Mohammad Javed is scrambling to show how close his manta robot comes to emulating the animal's dexterity.

“Three minutes left,” a judge calls out.

“I'm going to try one more time,” Javed responds as he frantically lifts “A Bot Named Sue” out of the water to remove a weight from its back and to screw another weight onto its front. He needs to adjust the buoyancy enough that the robot can dive down a meter, swim under a bar, surface, and swim back over the bar.

Less than 3 weeks ago, his robot was still in pieces. The body of his first iteration leaked, ruining the electronics that moved the fins. By the time he got a replacement, he barely had time to test it.

Earlier in the day, UVa's contender, Manny, had dashed down the length of the pool at twice Sue's speed. But it was not as good at diving or turning as Javed's robot and never succeeded in the “under and over the bar” test. So this was Javed's chance to clinch victory. During his first try on this test, one of the servomotors driving the fins overheated and the robot shut down. This time around, the weights caused it to nose-dive to the bottom and flip onto its back so it couldn't come back up.

Javed puts the robot back into the water, and a diver positions it in front of the bar. It dives, but the weights still aren't quite right and the clock runs out.

There's no clear winner—the judges declared a tie—but the onlookers and the contestants are quite pleased. “For the first time out, [both teams] are doing pretty well,” says judge Gilbert Lee, a materials scientist at the Carderock Division of the U.S. Naval Surface Warfare Center in West Bethesda, Maryland, where the competition is being held. “They were successful in achieving raylike propulsion,” adds Robert Brizzolara, a program officer with the Office of Naval Research (ONR) in Arlington, Virginia.

That was the goal. Mantas are everything one could want in an autonomous underwater vehicle (AUV). “I've thought for a long time that the people who are interested in robotic mimicry were missing the boat in not looking at manta rays,” says Adam Summers, a comparative biomechanist at Friday Harbor Laboratories in Washington state. Most fish swing their body from side to side, and “that's not very handy if you are trying to stuff [instruments] inside.” The manta body is stiff. Mantas are also quiet, efficient swimmers—AUVs tend to be one or the other. The best AUVs have a turning radius of 0.7 body lengths; the manta needs just 0.27 its body length and maneuvers like a fighter plane. Based on the two robots' performance, “in terms of maneuverability, we're on the right track” in understanding how mantas achieve such grace, says Frank Fish, a functional morphologist at West Chester University in Pennsylvania who is working with UVa and Princeton on the manta project.

Understanding manta rays

The focus on manta rays traces back to a snorkeling trip Alexander Smits took in Australia about a decade ago. “They are such self-possessed, graceful animals,” he says. “It was almost mystical,” he recalls about his experience swimming among these 2-meter- to 5-meter-wide fish. “I decided I've got to know something about them.”

An expert in experimental fluid mechanics at Princeton, Smits persuaded Hilary Bart-Smith, a postdoc at the time designing flexible aircraft wings, to consider instead developing shape-morphing fins for underwater locomotion, based on manta ray swimming. They couldn't get funding at first, so the research didn't get very far. But Bart-Smith took the project with her to UVa and got fellowships to work toward building an artificial structure that could recapitulate the highly maneuverable, seemingly effortless movements of manta rays.

Then 4 years ago, ONR issued Bart-Smith's dream request for proposals: a solicitation for “bio-inspired” sea vehicles. She called Smits and recruited him, Fish, and three other researchers to look at not just mantas but also other rays from biological, engineering, fluid dynamics, and modeling perspectives. In 2008, their proposal was awarded \$6.5 million over 5 years. “They've got a challenging problem to solve: to produce a flexible mantalike wing that could have its motion controlled accurately,” says George Lauder, a biomechanist at Harvard University.

It fell on Fish, the biologist on the grant, to get the nitty-gritty details of the manta ray's swimming behavior. His first job was to catch the animals in action. For that he headed to Yap, an island in Micronesia where manta rays regularly visit the protected waters inside the island's reefs to be cleaned by tiny fish living there. Fish and his colleagues set up two video cameras in water 24 meters deep to capture manta movements in three dimensions. They came home with 36 hours of video.

Back in Pennsylvania, he and his team have been analyzing the videos through a painstaking process of digitizing key landmarks of the manta's body—the fin tip, eye, and so forth—frame by frame. “We want to define the motion for animals going at a variety of speeds as well as up and down maneuvers,” he explains.

Already they have been able to figure out the details of how the winglike fins deform. Two waves are set in motion in the fins as they flap. One travels from front to back of the fin. A second ripple extends out from the base of the fin to the tip. “The motion is far more complicated than what we find from a dolphin or tuna,” Fish explains.

To complement the video footage, Fish has used computed tomography (CT) scans to probe the internal structure of the fins of several ray species. UVa biomechanics expert Silvia Blemker used the scans to construct 3D renditions of the underlying cartilage, revealing large differences between the fin skeletons. “It's a very complicated structure, with many elements and many links,” Bart-Smith says.

UVa computational hydrodynamicist Hossein Haj-Hariri has created mathematical models based on the underlying cartilage structures to learn how different skeletal configurations contribute to swimming performance. “To mimic [the fin] exactly is incredibly challenging,” Bart-Smith says, so she wants to know how much they can simplify the robot's “skeleton” and still have it work well.

What Haj-Hariri does in a computer, Smits tries to do in a tank at Princeton. He and his colleagues have built manta ray fins of flexible plastic and examined water as it flows over them. They are testing how different fin shapes and movements affect thrust and efficiency in steady swimming.

From the videos, the researchers had observed that manta fins both flap up and down and undulate, sending a traveling wave from the front to the rear of the fin. “This undulatory part of the swimming is really the most important part of it,” Smits says, based on his measurements. It is four times more important than flapping for propelling the fish forward.

Making mantabots

Over beers one night, Haj-Hariri, Bart-Smith, and Smits decided to recruit undergraduates to the project for a competition in which the students build manta ray robots. “It's a good way to test out a variety of prototypes,” Lauder says. “You learn a tremendous amount by trying to build something even before you think you know enough to try.”

At UVa, Bart-Smith and Haj-Hariri organized a yearlong senior engineering class whose goal was to build a robot for the competition. The students used a cable-rod matrix—called a tensegrity structure—encased in a soft silicon material as a fin. Tensegrity structures are rigid rods held together by tensioning cables, which creates a stiff, lightweight structure. Pulling on the cables in different combinations bends the tensegrity rods into a curved shape that allows the fin to move up or down.

The CT scans gave the students a sense of the range of shapes and physical characteristics possible for ray swimming: They decided to follow nature's design fairly closely. Then they had to scale those parameters down from several meters to a robot that was 60 centimeters long from wingtip to wingtip. Whereas the real fish has muscles in the fin itself, the UVa team put their “muscles”—devices called actuators—inside the “body” to reduce the weight of what had to move up and down. The body itself was made with a 3D printer, but because the plastic used was porous, they had to coat it with epoxy.

They studied the videos to decide on their turning strategies. For fast turns, they held one fin steady and flapped the other vigorously; for slow ones, they flapped the inner fin more slowly than the one on the outer edge of the turn.

At Princeton, Smits and his team persuaded Javed to represent them in the competition as the university's sole contender. His robot looks less manta-ish than UVa's. Seen from above, the UVa manta ray fin is triangular, but Princeton's is much more lobular. Javed put a horizontal rudder in the back that moves up and down and helps pitch the manta for diving and surfacing.

His manta's body is a single piece of machined plastic sealed with a lid screwed down like a manhole cover. Instead of containing a tensegrity structure, each fin has four parallel steel cables the diameter of toothpicks that extend from the body core toward the tip. They are arranged with two on top and two on the bottom and connected in the body to a cylinder driven by a servo-motor. Pulling on the top cables curves the fin upward; pulling on the bottom causes the fin to flap downward.

Each team had 1 hour to complete five tasks: the over-and-under bar move, diving to the bottom of the tank and resurfacing, making the tightest 360° turn possible, going the fastest for a specified distance, and demonstrating the robot's swimming prowess with a freestyle maneuver. Both teams excelled at flapping the fins, but both had issues with buoyancy and water leaking into the bodies. But that didn't faze Brizzolara. “In any number of technologies that I have been associated with, the first time they put something in the water there are always hiccups and bumps,” he says. Just getting to this point of having robots to test was “a step forward in the science.”

Bart-Smith hopes to hold another robot competition next year. One of her UVa colleagues has built his own manta ray robot, one that is supposedly waterproof. And a company in Germany has a version whose fins are based on fish tail mechanics. Manta “bots,” Summers says, are “getting far enough along that people are learning something about how the animals work by looking at how the robots work.”

6. THE BIOLOGY OF GENOMES

DNA Circles Cause Cow Coat Color Changes

1. Elizabeth Pennisi

At the Biology of Genomes meeting, a geneticist reported what seems to be a new way that a cell shuffles its genes around: by forming a loop of DNA that then breaks apart in a different place before inserting into a different chromosome.

Keith Durkin wasn't trying to figure out why some Belgian Blues, a cattle breed known for its big muscles, have a wide white stripe down their backs. And the young geneticist certainly didn't expect to uncover what seems to be a new way that a cell shuffles its genes around. A postdoc at the University of Liège in Belgium in 2009, Durkin was scanning a database containing the genotypes of 4400 animals to flag duplicated chromosomal regions. One such region, which showed up in nine of the cattle, caught his eye because it included a gene called KIT that is involved in coloring animal coats. When he checked on those nine, each animal had the telltale white stripe.

Durkin was a little puzzled at first because the database information suggested the repeated DNA was on chromosome 6. His University of Liège colleague Carole Charlier had been homing in on the mutation for this “color-sided” trait and had seemingly localized it to chromosome 29, not chromosome 6. By using fluorescing tags that home in on specific pieces of DNA, Durkin and his colleagues showed that a copy of a piece of chromosome 6 had at some point jumped to chromosome 29. It seems that when the 480,000-base-long stretch of DNA broke away, KIT became separated from some regulatory DNA, and the subsequent misregulation led to the unusual coat color pattern.

But the sequence of the duplicated region on chromosome 29 was also somewhat confusing. The researchers could tell from the chromosome 6 sequence what the beginning and end of the duplicated DNA should be, but these sequences were instead in the middle of the chromosome 29 copy. When the segment jumped out of chromosome 6, Durkin concluded, it must have formed a loop of DNA that then broke apart in a different place before inserting into chromosome 29. Imagine forming a circle out of a sequence of letters, such as A, B, C, D, E, and F, then snipping that loop someplace different from where the ends originally joined. If the break came between C and D, for example, the new linear sequence would be D, E, F, A, B, C.

Durkin's story doesn't end there. In color-sided Brown Swiss cattle, he and his colleagues found that the KIT-containing chromosome 29 segment had copied itself into another loop and then hopped back into chromosome 6 next to the original sequence. Durkin also found scrambled duplications of this DNA sequence in other color-sided breeds, including distantly related cattle from Ireland and Ethiopia. That observation suggests that this circularized DNA shuffling must have occurred early in the development of cattle breeds.

Geneticists say they haven't seen genes move between chromosomes in quite this way before. “The circular mechanism is really novel,” says Douglas Antczak, a veterinary geneticist at Cornell University. “The mechanism by which fragments of genes go to another place is not well-known,” adds Xavier Estivill, a geneticist at the Center for Genomics Regulation in Barcelona, Spain. There is a group of so-called transposable elements called Heliotrons that also seem to jump around the genome as circles of DNA, but the sequences of the circles in these cattle look nothing like these transposable elements, Durkin says. Estivill wonders whether this circle-driven, gene-shuffling mechanism will prove common. “We are now trying to find some examples in humans,” he says.

7. THE BIOLOGY OF GENOMES

On the Trail of Brain Domestication Genes

1. Elizabeth Pennisi

Researchers have found that the activity of a group of genes in the prefrontal cortex of bonobos was clearly "domesticated" compared with that of chimps, they reported at the Biology of Genomes meeting.

Domesticated animals have far more in common than service to humankind. As Charles Darwin observed, compared with their wild counterparts, dogs, pigs, and cattle tend to be smaller, have finer bones, and sport spotted coats. Domesticated animals generally are also less aggressive, less fearful, and more playful.

Fascinated by these behavioral similarities, Svante Pääbo, Frank Albert, and their colleagues at the Max Planck Institute for Evolutionary Anthropology in Leipzig, Germany, wondered whether these tamed species—and perhaps even some primates, including humans—also share similar patterns of gene expression in their brains. Researchers as far back as Darwin have speculated that humans underwent “self-domestication,” and, more recently, Brian Hare of Duke University in Durham, North Carolina, proposed that bonobos evolved domesticated behavior to encourage group living.

To explore this issue, Albert, now at Princeton University, turned to the genes active in the prefrontal cortex, which is responsible for long-term planning and associative thinking. Albert isolated genetic material representing active genes from the prefrontal cortex of a half-dozen dogs and wolves, as well as from the brains of a half-dozen domestic pigs and rabbits and their wild counterparts. He sequenced these genetic fragments to determine the genes from which they derived and then estimated each gene's level of activity by quantifying how often his sequencing highlighted it.

He looked for genes whose activity was increased or decreased in the three domesticated species compared with in the wild ones. He found 60 such genes and then sought confirmation by doing a similar comparison of the domestic guinea pig and its close wild relative, a cavy. About 40 of the 60 genes displayed the same boost or drop, he reported at the meeting.

With these 40 putative brain domestication genes in hand, Albert compared their expression in humans versus chimps. No clear pattern of human domestication emerged. But the activity of that gene group in bonobos was clearly “domesticated” compared with chimps, Albert reported. “What causes this very dramatic behavior in bonobos is somehow mechanistically similar to what was selected for when the dog and pig were domesticated,” Pääbo says.

Hare is delighted with the new study. “These results not only provide exciting support for the self-domestication hypothesis of bonobos but also point to domestication as an exciting model for potentially revealing the evolutionary process by which psychology more generally evolves, including in our own species,” he says.

“That the same genes would be involved in domestication in this wide range of species is really cool,” adds geneticist Magnus Nordborg of the Gregor Mendel Institute of Molecular Plant Biology in Vienna. Still, he calls for more comprehensive statistical analyses of the gene expression data, which Pääbo says are being done. His team also hopes to pin down the changes in the regulatory DNA that create the domesticated gene profile in the brain.

8. THE BIOLOGY OF GENOMES

Disease Risk Links to Gene Regulation

1. Elizabeth Pennisi

Two teams at the Biology of Genomes meeting reported that gene regulatory sites surprisingly often are the spots where single-nucleotide polymorphisms identified by genome-wide association studies fall.

Two of the hotter areas in genomics research came together last week, sending sparks flying that could boost the search for causes and treatments of common diseases. Over the past 6 years, biomedical researchers have looked for genetic variants associated with particular disorders by scanning the genomes of tens of thousands of people with and without the diseases (Science, 11 May 2007, p. 820). Some have called these so-called genome-wide association studies (GWAS) a bust because the variants identified so far typically account for just a small portion of a disease's risk. Moreover, GWAS usually pinpointed just subtle variations in the human genome, known as single-nucleotide polymorphisms, without revealing if the SNPs themselves boosted disease risk or were simply markers for something nearby that did. “You could find associations but not the causal variant,” says computational biologist Chris Ponting of the University of Oxford in the United Kingdom.

In another corner of the genomics community, researchers, including those who are part of an international project called ENCODE, have been surveying regions of the human genome to identify functions of DNA outside the protein-coding portions of genes. They have, for example, generated genomewide maps showing places where gene regulation occurs. Now, two teams at the meeting here report that gene regulatory sites surprisingly often are the spots where GWAS-identified SNPs fall. “We're seeing how pervasive a role gene regulation is playing in disease,” says genomicist John Stamatoyannopoulos of the University of Washington, Seattle, who led one of the groups.

A variety of techniques allow researchers to find where along DNA gene regulation occurs, often by pinpointing places where a cell's protein-DNA complex, called chromatin, has been modified to allow a gene to become active. For example, Stamatoyannopoulos uses a method called DNaseseq that depends on an enzyme, DNaseI, to cut DNA wherever chromatin has unwound enough to let regulatory proteins bind to it. Stamatoyannopoulos then sequences the resulting fragments and matches them back up to a finished human genome to pinpoint the locations of these so-called DNaseI hypersensitive sites. He has cataloged such gene regulatory sites in 130 human cell types and developmental stages, including fetal tissues, adult organ tissues, and cancer cell lines. Different cell types have different subsets of hypersensitive sites, depending on their gene expression profiles.

Stamatoyannopoulos reported finding 2.1 million of these sites, taking up well more than 11% of the genome. Some 7500 were identified in all cell types, while about 450,000 were found in just one cell type, suggesting that those latter sites are involved in regulating genes for specific kinds of cells.

GWAS have so far linked 3800 SNPs to 427 diseases and traits, and Stamatoyannopoulos looked at where these markers were located relative to the hypersensitive sites. About 53% “were dead hits,” Stamatoyannopoulos reported. In contrast, only about 7% of the SNPs fall in the DNA sequences that actually encode proteins. Stamatoyannopoulos's team has “provided the resolution required to identify the functional variants in a vast number of diseases,” Ponting says. By pointing out gene regulatory regions that may influence disease risk, this analysis “gives us particular functional elements that are likely to be biologically important,” adds Joel Hirschhorn, a geneticist at the Broad Institute in Cambridge, Massachusetts.

Often the bull's-eyes Stamatoyannopoulos found were in a relevant cell type: SNPs associated with heart disease coincided with DNase hypersensitive sites in developing heart tissue, while those tied to autoimmune disease matched up with gene regulation sites in immune cells, for example. Also, in many cases, the cell types where disease SNPs matched gene regulatory regions tended to be fetal tissue, suggesting that perhaps some of these disorders have roots in development, Stamatoyannopoulos said.

At the meeting, Jason Ernst of the Massachusetts Institute of Technology in Cambridge also reported on combining GWAS data with gene regulatory sites. He and his colleagues took into account nine surveys that revealed in nine cell types, including embryonic stem cells and muscle and lung cells, where along the human genome chromatin had been modified. At these sites, they assessed the type of gene regulation that occurred—such as activation or repression—and what transcription factors were involved. They also discovered that disease-linked SNPs from 10 different studies coincided, in cells appropriate for the given disease, with sites regulating genes already implicated in the particular condition. (Ernst and his colleagues' study also appeared in the 5 May issue of Nature.) “We're starting to get to the scale of data where we are starting to see patterns,” says Hirschhorn, who thinks many more connections between gene regulation and diseases will be forthcoming.