# News this Week

Science  18 Jul 2008:
Vol. 321, Issue 5887, pp. 324
1. CLIMATE CHANGE

# Bush Takes a Final Swipe, and Salute, at CO2 Emission Curbs

1. David Malakoff*
1. David Malakoff is a science writer in Alexandria, Virginia.

In the end, he just couldn't commit. Last week, the Bush Administration essentially ended its tumultuous relationship with climate change, unveiling two decisions that all but ensure that President George W. Bush will leave office without making a binding commitment to cut greenhouse gas emissions.

On 9 July, Bush and the other leaders of the Group of Eight (G8) industrial powers signed a largely symbolic pledge to help trim global emissions by 2050, rejecting stricter language. Then, on 11 July, the Administration announced that it would not use the nation's leading clean-air law to regulate heat-trapping gases, effectively sidestepping a U.S. Supreme Court decision.

Analysts say the two moves are probably the Administration's last gasp on climate. “These are the final major gestures; there's not much left for them to do. Now everybody's focused on what Congress and the next president will do,” says Jody Freeman, head of the Environmental Law Program at Harvard Law School.

Both announcements reflect the fierce internal disagreements that have become hallmarks of the Administration's climate policy. As a presidential candidate in 2000, Bush backed using the Clean Air Act to regulate greenhouse gases. But he quickly backpedaled after winning office. State and local officials continued to press for action, however, arguing that carbon dioxide was a “pollutant” covered by the law (Science, 8 September 2006, p. 1375). And last year their arguments prevailed, when the Supreme Court ordered the Environmental Protection Agency (EPA) to explain why it wasn't regulating the gas.

The Administration split over how to respond. One faction, led by senior EPA officials, drafted a detailed rationale for using the law to attack climate change. But that road map drew furious objections from Vice President Dick Cheney and other White House officials, including presidential science adviser John Marburger, according to documents released by EPA. A quartet of Cabinet members also chimed in, according to EPA; the secretaries of Agriculture, Transportation, Commerce, and Energy complained that it did not “fairly recognize the enormous and, we believe, insurmountable burdens, difficulties, and costs” of the strategy.

EPA chief Stephen Johnson told reporters that the infighting convinced him that “the Clean Air Act is the wrong tool for the job” and that it would be impossible to forge a consensus response “in a timely manner.” Instead, he issued a 588-page document that laid out dozens of complex questions raised by the law. The document also laid bare the squabbling and asked the public to join the debate. Johnson said he hopes the move will convince Congress that entirely new laws are needed to deal with climate change.

That's probably true, says Kevin Vranes, a former Senate staffer now working with Point 380—the name refers to the current level of carbon dioxide in the atmosphere, in parts per million—in Boulder, Colorado. Given the lack of White House leadership, he says that “Congress needs to stop stalling … and start addressing the problem itself.” Both major presidential candidates, senators Barack Obama (D-IL) and John McCain (R-AZ), have embraced some sort of controls on greenhouse gases, although in May the Senate handily rejected a plan to do so by means of a cap-and-trade system.

The G8 declaration to seek a 50% reduction in emissions includes no interim targets and no mechanism for achieving the goal. But it may polish Bush's legacy by pointing toward a new global climate deal in 2009. The Administration could still do “potentially very constructive work” on the global stage, says David Victor, director of an energy and development program at Stanford University in Palo Alto, California. But those efforts may not “have much lasting power, since nearly all the rest of the world is already looking beyond Bush.”

2. RESEARCH ETHICS

# Old Samples Trip Up Tokyo Team

1. Dennis Normile

TOKYO—A University of Tokyo team has retracted a published research paper because it apparently failed to obtain informed consent from tissue donors or approval from an institutional review board (IRB). Other papers by the same group are under investigation by the university. Observers believe problems stem in part from guidelines that don't sufficiently explain how to handle samples collected before Japan established informed consent procedures.

The alleged infractions were announced at a press conference on 11 July by Motoharu Seiki, dean of the university's Institute of Medical Science (IMS). Seiki did not identify the researchers, but Asahi Shimbun, a prominent daily, broke the story the morning of the press conference and reported that the authors are members of a group led by Arinobu Tojo, who works on molecular therapies for leukemia. No one answered Tojo's office phone, and he did not immediately respond to an e-mail from Science.

The withdrawn paper was published online on 21 May and in the 1 July issue of Haematologica. A statement on the journal's Web site says a paper on acute myeloid leukemia by Seiichiro Kobayashi et al. was retracted on 27 June by Tojo, the corresponding author, who had informed the editors that an investigation found that the “study had not been approved by the IRB.”

Seiki says tissue samples used for the retracted paper were collected before Japan's Ministry of Health issued guidelines for IRBs and informed consent in 2003. IMS's policies call for an IRB review of the use of old samples. “But [the researchers] did not follow that process,” says Seiki. Tohru Masui, a bioresources policy specialist at the National Institute of Biomedical Innovation in Osaka, says few researchers are aware of the ethical issues surrounding old samples because the ministry guidelines “do not have [anything] about legacy samples.”

Seiki says an external review panel has been established and will report its findings by the end of this month.

3. DEFENSE RESEARCH

# New Policy Tries to Ease Security Restrictions

1. Yudhijit Bhattacharjee

The grant that the U.S. Army Corps of Engineers awarded Zdenek Bazant of Northwestern University earlier this year to study how tough materials are able to withstand impact came with a catch: The corps had to vet any foreign nationals working on the project. Officials at the Evanston, Illinois, university balked, saying the requirement violates the school's antidiscrimination policies. Now the university has a new argument: The restriction also contradicts a new policy directive from the corps's parent agency, the Department of Defense (DOD), that's meant to resolve a 7-year dispute between the Pentagon and academic institutions over the rules governing unclassified research.

Since the terrorist strikes of 11 September 2001, research agencies have tried to prevent sensitive technical information from falling into enemy hands by creating a category known as “sensitive but unclassified” research. Academic officials have fought back, pointing to a 1985 directive from the Reagan Administration that exempts fundamental research on university campuses from such restrictions. Last month, the universities won a major victory when DOD Under Secretary John Young instructed agency officials that “classification is the only appropriate mechanism” for restricting publications or participation of foreign nationals in unclassified research projects. “The performance of fundamental research, with rare exceptions, should not be managed in a way that it becomes subject to restrictions on the involvement of foreign researchers or, publication restrictions,” the memo says, citing National Security Defense Directive 189, which President Ronald Reagan issued.

“We felt that there was a need to remind everyone” that fundamental research is to remain free of restrictions, says William Rees, the Pentagon's head of basic research, who led the internal review. “The strength of American science demands a research environment that is fully conducive to the free exchange of ideas.”

That hasn't been the case, says a report last year by the National Academies' National Research Council. A survey of more than 20 universities by the Association of American Universities (AAU) and the Council on Government Relations documents 180 instances of troublesome clauses in research contracts from federal agencies, a majority from DOD and the Department of Homeland Security (see graphic). So the new policy is a welcome change, says Jacques Gansler, a former Pentagon administrator who co-chaired the academies' report.

“We are very pleased with the directive,” says Gansler, now a professor at the University of Maryland, College Park, who hopes that other federal agencies will follow DOD's example. AAU's Toby Smith says he had hoped Young would also ban companies from passing along such restrictive language to university subcontractors, but he's glad the memo asks DOD authorities to retrain the agency's contracting officers.

Such training seems essential, say Northwestern officials, who are still negotiating with the Army over Bazant's award after a corps official said Young's memo did not invalidate the corps' own policies. “We may have to decline the award,” a university official told Science.

4. MEDICINE

# Stalled Trial for Autism Highlights Dilemma of Alternative Treatments

The tension between parents desperate to help their sick children and researchers who worry about quack medicine has long put public health agencies in a bind. Last week, a long-simmering controversy boiled over when newspapers across the country ran an Associated Press story claiming that “government researchers are pushing to test an unproven treatment on autistic children, a move some scientists see as an unethical experiment in voodoo medicine.” In fact, a trial of the controversial treatment was halted last year, and Thomas Insel, director of the National Institute of Mental Health (NIMH) in Bethesda, Maryland, says he's not pushing to restart it. The case, and the publicity surrounding it, illustrates the difficulty of deciding whether to test these questionable therapies, especially in children.

The “voodoo” here is chelation therapy. Believing that mercury in vaccines triggers autism, thousands of parents, often at the advice of their physicians, have given their autistic children drugs to bind, or chelate, and remove heavy metals from the body. Some say the over-the-counter or off-label treatment can improve poor language skills, social problems, and other symptoms of the disorder. And yet the drugs are not risk-free, and the underlying rationale—that mercury from vaccines causes or worsens autism—has been roundly rejected by many scientific studies.

NIMH has argued that the widespread use of the drugs creates a “public health imperative” to conduct a rigorous trial so that the institute can inform parents and physicians about any merits or dangers of the drugs. But some researchers and ethicists oppose studies that they say have no chance of working—and little chance of persuading the most zealous advocates—especially if the drug poses a substantial risk. “On balance, it's not an ethical study,” says vaccine researcher Paul Offit of the University of Pennsylvania.

This isn't the first time researchers at the National Institutes of Health (NIH) have felt compelled to react to the use of dubious autism treatments. In the late 1990s, a wave of media publicity touted the abilities of a gastrointestinal drug called secretin to “cure” symptoms of autism (Science, 5 October 2001, p. 37). So many parents were buying the drug that NIH decided to do a series of small, rapid clinical trials. Secretin flopped, and most parents eventually stopped clamoring for it. “It was a meteoric rise, and it fell just as quickly,” says one autism researcher, who asked not to be named to avoid offending advocates. “I haven't heard of anyone using secretin in years.”

Chelation therapy remains widely used. Some surveys have suggested that 2% to 8% of children with autism have had it, perhaps several thousand per year. Parents either buy unregulated supplements or have a doctor use a treatment for lead poisoning. Not only do the drugs bind to toxic metals, but they can also remove essential minerals such as calcium and iron.

NIMH wanted to conduct a study of the common chelator DMSA, which is approved by the Food and Drug Administration for treating lead poisoning. The idea was to give 120 children, aged 4 to 10, with a range of autism symptoms either DMSA or a placebo. After 12 weeks, NIMH researchers would evaluate the children to see if their social and language skills had improved. It would be the first controlled study of a chelator on autism.

But first the study had to pass ethical muster with a so-called institutional review board (IRB). Putting children at risk of side effects is considered unethical if they are unlikely to receive any direct benefit from the drug. And Insel acknowledges that “it is difficult to make the case” that a chelator would help children with autism. On the other hand, a well-conducted trial with negative results could help parents better choose whether to use a chelator, says pediatrician and bioethicist Douglas Diekema of the University of Washington, Seattle, who was not part of the IRB. The NIMH study, which included multivitamins to safeguard against most of the risks of the drug, passed review and was launched in September 2006.

A few months later, new research raised a red flag. An October 2006 online study in Environmental Health Perspectives examined the impact of DMSA on rodents. Although the drug helped rodents overcome lead poisoning, when it was given to rodents without lead it caused lasting cognitive and emotional problems. The finding “raises concerns about the use of chelating agents in treating autistic children without elevated levels of heavy metals,” says senior author Barbara Strupp of Cornell University, although she notes that it's not known what the threshold might be for such adverse effects. The children in the autism trial would not have had elevated levels of mercury in their blood (otherwise, they could not ethically be given a placebo).

NIMH officials halted the trial in February 2007 and sent it back to the IRB for further review. Given the new risks, the IRB concluded it did not have the authority to approve the trial, although NIMH's parent agency, the Department of Health and Human Services (HHS), could if it felt the societal benefit were large enough. Rather than appeal to HHS, Insel says, the principal investigator, NIMH's Susan Swedo, decided that NIMH's intramural resources were better focused elsewhere, on the possible benefit of reducing inflammation with an antibiotic called minocycline in children with so-called regressive autism. Some critics of the chelation therapy say it was a good call because there is some preliminary evidence to suggest why inflammation—as opposed to mercury—might be involved in autism.

5. PALEOCEANOGRAPHY

# Caribbean Megaeruptions Drove a Global Ocean Crisis

1. Richard A. Kerr

Things got pretty ugly in the world ocean 93.5 million years ago. Deeper waters turned foul as their oxygen disappeared and the sea floor around the globe became a lethal black ooze. Many bottom-dwelling shelled animals from the microscopic to the gigantic went extinct. Now new geochemical evidence recovered from that ancient muck strongly links this global crisis—called Oceanic Anoxic Event 2 (OAE2)—to one of the world's largest episodes of volcanism.

The new work “nails the coffin shut” on this long-suspected volcanic connection, says paleoceanographer Timothy Bralower of Pennsylvania State University in State College. The finding also adds support to nearly a half-dozen other proposed volcanic crises during the past 250 million years, including the greatest mass extinction of them all.

OAE2 “was the big one,” says Bralower, who was not involved in the new work. “It was the most global, the most dramatic” of a half-dozen OAEs during the exceptional warmth of the mid-Cretaceous period 120 million to 80 million years ago. The young Atlantic Ocean was as narrow as a few hundred kilometers, the sea ran free between Europe and Africa and into the western Pacific, and high sea levels drove the ocean up onto the continents.

Something in this mid-Cretaceous world had made the ocean liable to shift dramatically the way it operated. During OAE2 about 93.5 million years ago, for example, life-giving oxygen abruptly disappeared from deeper waters, and so much organic matter accumulated in muddy bottom sediments that for a half-million years the sediment turned black until the seas recovered. Paleoceanographers looking for triggers of OAEs, especially OAE2, have long turned their attention to humongous volcanic eruptions, such as the lava outpourings of a large igneous province (LIP) now lying beneath the Caribbean Sea. A shift in lead isotopes recorded at the very onset of OAE2 in Italy supported that idea (Science, 27 April 2007, p. 527), but the evidence remained regional in scale.

This week in Nature, paleoceanographers Steven Turgeon and Robert Creaser of the University of Alberta (UA) in Edmonton, Canada, report geographically broad-based isotopic evidence for a volcano-OAE2 link. They measured the element osmium in sediments across OAE2 from Italy—which was in the Tethys seaway between Europe and Africa at the time—and just off northeast South America, which was then in the opening Atlantic.

At both sites, the osmium abundance shot up by a factor of 30 to 50 above background just before the onset of OAE2. In the Atlantic, the lag between osmium increase and anoxia was between 10,000 and 20,000 years, the UA researchers estimate. And just as vastly more osmium was entering the ocean, the ratio of osmium-187 to osmium-188 plummeted. All that is just what would happen, say Turgeon and Creaser, when thousands upon thousands of cubic kilometers of lava delivered osmium from Earth's mantle to the sea floor of the Caribbean, a LIP eruption previously dated to within a few million years of OAE2.

The new osmium data “do make the argument more compelling” that the largest eruptions can trigger anoxic crises in the ocean, says Millard Coffin of the University of Southampton, U.K., who specializes in LIPs. The trigger “is most likely volcanic,” he agrees. The work has broader implications too. The largest LIP of the past half-billion years—the Siberian Traps—seems to have coincided with the largest mass extinction, the Permian- Triassic, but dating uncertainties still allow the extinctions to precede the eruptions by hundreds of thousands of years (Science, 25 April, p. 434). In the case of OAE2, at least, the coincidence was tighter still.

6. NUCLEAR PHYSICS

# Two U.S. Labs Vie for Long-Delayed Exotic Nuclei Source

Can a small group of university researchers triumph over a big national laboratory in a competition to build and operate a $550 million piece of scientific machinery? C. Konrad Gelbke, a nuclear physicist at Michigan State University in East Lansing, and his colleagues are about to find out. Next week, the U.S. Department of Energy (DOE) will accept proposals for a Facility for Rare Isotope Beams (FRIB), an accelerator to make fleeting nuclei never before produced outside stellar explosions. Gelbke and colleagues want to build FRIB at Michigan State's National Superconducting Cyclotron Laboratory (NSCL), a facility already pursuing such work with 300 employees and an annual budget of$20 million from the U.S. National Science Foundation (NSF). But researchers from Argonne National Laboratory in Illinois also want to host the machine. Argonne is a DOE lab with a staff of 2800 and a $530 million budget. DOE says it will decide by year's end. Gelbke insists that Michigan State is not an underdog. “We've got the best people and the most experienced group,” he says. “That's just established fact.” But others who have observed similar competitions say Argonne's greater resources and existing infrastructure could give it a significant edge. “It is fundamentally an asymmetric situation, and it gets down to how important is that existing infrastructure?” says Michael Witherell, a particle physicist at the University of California, Santa Barbara, and former director of Fermi National Accelerator Laboratory in Batavia, Illinois. FRIB is the second design of a machine that could reveal the birthplace of many heavy elements and hammer out a unified theory of nuclei large and small. Scientists know that more than half the elements heavier than iron originate somewhere in exploding stars through the so-called r-process, in which a light nucleus quickly absorbs many neutrons. FRIB would make some of the intermediary nuclei and help pin down exactly when and where within a stellar explosion the r-process takes place. More generally, it would help scientists weave a hodgepodge of theoretical models into a comprehensive understanding of the nucleus. Researchers started planning for such a machine, originally dubbed the Rare Isotope Accelerator (RIA), in 1999. The heart of the machine is a superconducting linear accelerator that can accelerate any nucleus from hydrogen to uranium. With a price tag of$1 billion, RIA aimed to set new standards for every method of producing isotopes (see figure).

In 2003, RIA tied for third place in a list of 28 facilities DOE hoped to build in the following 20 years. The next year, it passed the first of five “critical decision” reviews. But in February 2006, Secretary of Energy Samuel Bodman unexpectedly announced that the project would be delayed at least 5 years (Science, 24 February 2006, p. 1082). A month later, DOE asked for a cheaper, more focused design.

The community responded with FRIB, whose linear accelerator will reach energies half as high as those planned for RIA. The new design also accentuates one means of making isotope beams, called reacceleration. Still, the machine would produce exotic nuclei at rates up to 100 times greater than those achieved by competing machines in Japan and Germany. The Michigan State and Argonne teams won't discuss their designs until they've been submitted, but in the past the teams have emphasized different secondary techniques in addition to reacceleration.

The current contest is the latest in which size may matter. In 1993, DOE chose its own Stanford Linear Accelerator Center (SLAC) in Menlo Park, California, over Cornell University for the site of a particle smasher that would crank out particles called B mesons and study the asymmetry between matter and antimatter. Like Michigan State, Cornell had a smaller NSF-funded facility, and some accused DOE of nepotism. But even Karl Berkelman of Cornell says SLAC's resources contributed to the project's success. “I'm not sure we could have done as good a job,” he says.

Michigan State's Bradley Sherrill says NSCL's track record proves it's up to the task. “We have already demonstrated that we can design, build, and operate a rareisotope user facility,” he says. For his part, Walter Henning, a nuclear physicist who leads Argonne's effort, says that “all factors should be considered.”

In 2006, the NSF renewed Michigan State's grant for 5 more years, so the lab's immediate future is secure. But if it does not land FRIB, the lab may close once the new machine is turned on.

DOE hopes to begin construction in 2013 and finish within 5 years. But that depends on its budget. DOE has requested $7 million for design work in 2009, but it will be up to Congress and the next Administration to follow through on the project. 7. SOCIOLOGY # Survey Finds Citations Growing Narrower as Journals Move Online 1. Jennifer Couzin Millions of scholarly articles have migrated online in recent years, making trips to library stacks mostly obsolete. How has this affected research, which depends on published work to guide and bolster academic inquiry? A sociologist at the University of Chicago in Illinois argues on page 395 that the shift has narrowed citations to more recent and less diverse articles than before—the opposite of what most people expected. Working solo, James Evans of the University of Chicago was curious about how citation behavior has changed in the sciences and social sciences. In theory, online access should make it quicker and easier for researchers to find what they're looking for, particularly now that more than 1 million articles are available for free. Relying on Thomson Scientific's citation indexes and Fulltext Sources Online, Evans surveyed 34 million articles with citations from 1945 to 2005. For every additional year of back issues that a particular journal posted online, Evans found on average 14% fewer distinct citations to that journal, suggesting a convergence on a smaller pool of articles. In other words, as more issues of a journal were posted online, fewer distinct articles from that journal were cited, although there were not necessarily fewer total references to that journal. It suggests herd behavior among authors: A smaller number of articles than in the past are winning the popularity contest, pulling ahead of the pack in citations, even though more articles than ever before are available. The average age of citations also dropped. Valuable papers might “end up getting lost in the archives,” says Evans. Oddly, “our studies show the opposite,” says Carol Tenopir, an information scientist at the University of Tennessee, Knoxville. She and her statistician colleague Donald King of the University of North Carolina, Chapel Hill, have surveyed thousands of scientists over the years for their scholarly reading habits. They found that scientists are reading older articles and reading more broadly—at least one article a year from 23 different journals, compared with 13 journals in the late 1970s. In legal research, too, “people are going further back,” says Dana Neac u, head of public services at Columbia University's Law School Library in New York City, who has studied the question. One possible explanation for the disparate results in older citations is that Evans's findings reflect shorter publishing times. “Say I wrote a paper in 2007” that didn't come out for a year, says Luis Amaral, a physicist working on complex systems at Northwestern University in Evanston, Illinois, whose findings clash with Evans's. “This paper with a date of 2008 is citing papers from 2005, 2006.” But if the journal publishes the paper the same year it was submitted, 2007, its citations will appear more recent. Evans disputes that this affected his results, noting that in many fields, such as economics, the time to publication remains sluggish. In other ways, Evans's findings reflect the efficiency that comes with online searching. “There's always been a desire to be focused in your citations, but it was impossible to manifest that in the old world,” says Michael Eisen, a computational biologist at the University of California, Berkeley, who helped found the Public Library of Science. In the end, Evans notes that “I don't have snapshots of people in their offices searching.” But, he says, his findings show that “everyone's shifting to this central set of publications”—an effect that may lead to easier consensus and less active debate in academia. 8. AGRICULTURAL RESEARCH # Reinventing Rice to Feed the World 1. Dennis Normile With prices of rice and other cereals soaring and granaries emptying, it might take a second green revolution to avert widespread famine. With prices of rice and other cereals soaring and granaries emptying, it might take a second green revolution to avert widespread famine South Asia's monsoon is a mixed blessing for rice farmers. The rains fill paddies. Light flooding brings sediment that replenishes soil nutrients. But almost every year, somewhere, flooding is so severe it wipes out the crop. In 2007, disaster struck the floodplains of the Tista and Jamuna rivers in north-central Bangladesh. Over a million hectares of farm fields were flooded, some inundated for as long as 3 weeks. Agricultural losses topped$600 million. A few pioneering farmers, however, were testing an experimental rice variety that tolerates submergence, and their plants recovered even after 12 days underwater—three times longer than normal varieties can endure. Yields suffered: They got about 4 tons per hectare, about 1 ton less than they would have without flooding, according to M. A. Salam, research director at the Bangladesh Rice Research Institute (BRRI) in Gazipur. “The farmers were very happy to get this yield under these circumstances,” he says, because many of their neighbors were left with nothing.

Submergence-tolerant rice and other new yield-boosting varieties are arriving at a critical time. In recent weeks, the collision of rising demand and tightening supplies has driven a phenomenal spike in rice prices that sparked riots in Haiti, Bangladesh, and Egypt. A dozen countries, including India and China, have restricted rice exports, deepening the crisis. Exacerbating a bad situation, rice production in Myanmar this year will likely drop 6%, to 9.4 million tons, according to a U.S. Department of Agriculture (USDA) forecast, after extensive damage from Cyclone Nargis in early May. A storm surge flooded about 1.75 million hectares of the Irrawaddy River delta with saltwater and destroyed embankments and irrigation systems.

The global food crisis grabbed the attention of G8 leaders meeting in Japan last week. They pledged to reverse the decline of aid and investment in agriculture and accelerate research and development (R&D) to boost food production. Nevertheless, the looming food shortage “is a story that's going to be here for a while,” says Philip Pardey, an agricultural economist at the University of Minnesota, St. Paul. Demand will continue to rise, he says, as the world's population grows and more grain is diverted to produce biofuels and to feed livestock as meat consumption rises. At the same time, Pardey says, funding constraints have slowed R&D on improving grain yields and have crippled developing country extension systems, which get the latest seeds and techniques into farmers' hands.

All grains are affected by the trend. But a rice shortfall could be disastrous. In 2005, rice supplied 20% of total calories consumed worldwide, including 30% in Asia, according to the International Rice Research Institute (IRRI) in Los Baños, Philippines. IRRI claims that two-thirds of the world's poor—those living on less than $1 per day—subsist primarily on rice. And production is stagnant. Over the past several years, more rice has been consumed than grown—the difference made up by dipping into world rice stockpiles, which peaked at 146.7 million tons in 2001 but declined to 73.2 million tons in 2006, according to USDA. Prices were already rising, then lackluster harvests, export restrictions, and speculative buying sent prices soaring. For example, a popular export variety of Thai rice jumped from$362 per ton last December to $1000 per ton in April. Prices have retreated to$720 per ton.

To balance production and consumption, IRRI forecasts that by 2015 the world must grow 50 million tons more rice per year than the 631.5 million tons grown in 2005. This will require boosting global average yields by more than 1.2% per year, or about 12% over the decade, says IRRI's research director, Achim Dobermann. In the near term, he says, farmers could wring an extra 1 to 2 tons of grain per hectare by growing the latest varieties and improving farm management—everything from optimizing fertilizer use to building rat-proof granaries that stem postharvest losses. A long-term trial plot at IRRI produces 18 to 20 tons of grain per year per hectare, but the average field in Asia yields half of that. Existing technologies “haven't been moved out sufficiently to farmers,” Dobermann says, because many extension systems are poorly funded and staffed. IRRI runs a training program that helps address this issue (see sidebar, p. 332).

In the long term, superior rice varieties are key to averting widespread food scarcity, says Pardey: “The yield levels we're seeing are historically high, and to even maintain them let alone increase them, you have to run pretty hard to keep ahead of evolving pests and diseases and other stresses.” Given how long it takes to develop new varieties, he adds, “you've just got to keep priming the pump of the research.”

Submergence-tolerant rice shows the years of effort it often takes to produce a new variety. Flooding costs South Asia about $1 billion a year in rice losses. Although paddy rice is grown in standing water, most varieties die if submerged for 3 or 4 days. Researchers had long known of varieties that apparently evolved to withstand monsoon flooding. An Indian variety known as FR (flood resistant) 13A can recover and produce rice even after 3 weeks underwater. Despite that advantage, farmers have largely abandoned such varieties in favor of modern cultivars that produce double or more grain under normal conditions. In the 1970s, IRRI tried crossing FR13A with high-yield varieties. But farmers rejected the resulting cultivars because they didn't like the taste and had difficulty adapting the plants to local conditions, says David Mackill, head of plant breeding at IRRI. In the early 1990s, Mackill, then at USDA's Agricultural Research Service in Davis, California, and colleagues at the University of California (UC), Davis, set out to identify the gene or genes in FR13A responsible for submergence tolerance. His team hybridized a variety derived from FR13A and an intolerant rice cultivar and tested hundreds of plants to see which recovered from submergence. Using molecular markers, or segments of easily identifiable DNA, they compared the genomes of the tolerant and nontolerant offspring, linking a region of chromosome 9 to submergence tolerance. They enlisted colleagues at UC Riverside and IRRI to isolate the gene responsible, Submergence 1A (Sub1A). The group determined that Sub1A is expressed in FR13A only when the plant is submerged and that many nontolerant rice varieties don't have Sub1A. To confirm its role, they introduced Sub1A into an intolerant variety lacking the gene and got submergence tolerance. The group reported its findings in Nature in 2006. IRRI plant physiologists, meanwhile, concluded that Sub1A inhibits stem and leaf elongation and the loss of chlorophyll that typically occurs in submerged plants. Limiting elongation conserves energy, and preserving chlorophyll, essential for photosynthesis, enhances chances of recovery. Mackill joined IRRI in 2001 and 2 years later started working to get Sub1A into commercial varieties. Using marker-assisted selection, which links a DNA segment to a trait of interest, his team screened crosses for plants with Sub1A but otherwise identical to the target variety. The Swarna variety popular in India and Bangladesh was one of the first to get Sub1A, and germ plasm was given to BRRI and its counterpart in India in 2005. This year, BRRI has four varieties with the Sub1A gene in field trials, Salam says. They will ramp up seed production of the best candidate, which will take another 2 years. Varieties are being tested in eight other Asian countries. Production of submergence-tolerant rice will become appreciable sometime after 2010, Dobermann says. It's fortunate that a single gene confers a high degree of submergence tolerance. Researchers aren't always so lucky. In 2002, a team at IRRI, the Philippine Rice Research Institute in Muñoz, BRRI, and UC Davis identified Saltol, short for salt tolerance, on rice chromosome 1. A rice variety carrying Saltol is now in field trials in Bangladesh. But Saltol confers tolerance only during the seedling stage. This works for wet-season rice, because adult plants are saved by monsoon rains that reduce soil salinity as the season progresses. But dry-season varieties face increasing salinity during the critical flowering period in spring, when coastal groundwater turns brackish. Researchers are probing for other genes that might protect these types. Scientists are using molecular techniques to boost resistance to diseases and pests as well. “But with biotic stresses, it is more complicated because you're defending the plant against pathogens or insects that are evolving,” says Dobermann. Getting durable resistance to insects often requires several genes with different properties, continual improvement, and wise farming practices, as illustrated by the fight against the brown planthopper. The tiny insect sucks the sap from rice stalks and often infects the plant with viruses. Infestation can be deadly. In the 1970s, the planthopper was brought to heel through integrated pest management—which encourages the use of natural predators—and the development of resistant varieties. But in just 10 years, planthoppers developed an ability to attack resistant plants as well as resistance to a widely used pesticide. Annual losses in China are estimated to run 2.77 million tons and in Vietnam about 700,000 tons, says Kong Luen Heong, an IRRI entomologist. The root problem is overuse of pesticides, which kill off the planthopper's natural predators. “This is a problem of unsustainable practices,” Heong says. Breeding resistant varieties might help, he says, but to be effective, new varieties must be integrated with changes in farming practices. IRRI is planning a pest-management demonstration project in China in 2009 that minimizes pesticide use. Researchers have cultivars that are resistant to other stresses—including drought, cold, and iron toxicity—in the R&D pipeline. Teams are also working on genetically modified (GM) varieties. Public antipathy, particularly in Asia, has kept GM rice confined to labs. A variety modified to produce pro- vitamin A could force governments to come to terms with transgenic crops (Science, 25 April, p. 468). IRRI now has the so-called golden rice in a field trial, and trials in farm fields in Bangladesh could start in about 2 years, Dobermann says. But he thinks it will take at least a decade for GM rice to have a significant impact on production. Another factor slowing work on new varieties is the structure of the rice market. Private companies conduct a lot of research on crops such as maize and soybeans because there is a thriving seed business. Rice farmers, on the other hand, retain part of each season's crop as seed for the next crop, so there is a smaller seed business and advances depend heavily on public-sector efforts. Pardey says little public spending in advanced countries goes to increasing grain productivity; instead, it is spent mostly on fruits and vegetables and environmental concerns. Contributions to organizations like IRRI have waned: IRRI's budget has eroded from a peak of$44.4 million in 1993 to $27.9 million in 2006. And few developing countries, aside from China and India, have been ramping up spending as quickly as they need to, Pardey says. As a result, over the past 10 years maize yields have risen by nearly 1.8% per year while growth in rice yields has slipped below 1% annually and is virtually nil across Asia, Dobermann says. ## Closing the gap Reducing losses to stresses can only partly ameliorate a crisis. Varieties tolerant to submergence, drought, and salinity are useful in environments that account for about 25% of global rice production. “If we want to do something in terms of food security,” says Dobermann, “we need to invest much more in improving varieties” for the 75% of rice grown in favorable environments. Recent improvements in potential rice yields have been incremental in part because breeders have already picked the low-hanging fruit. In a sign of the challenges ahead, Qifa Zhang, a rice geneticist at Huazhong Agricultural University in Wuhan, China, identified a gene on chromosome 7 that plays a key role in boosting yield potential. He found, however, that most modern cultivars already carry the gene. Understanding how it works might lead to yield gains, says Zhang, whose findings appeared in Nature Genetics last May. “But we'll have to be creative in deciding how to make use of it.” Higher yields could come from greater reliance on hybrid rice. Hybrids of genetically diverse plants benefit from heterosis, or hybrid vigor, which produces yields up to 20% greater than inbred varieties. China pioneered the use of hybrid rice in the 1970s and now plants it on 16 million hectares, or 57% of its total rice area. Last year, hybrid rice accounted for about 65% of China's 186 million ton rice production, according to Longping Yuan, director-general of the China National Hybrid Rice R&D Center and a professor at Hunan Agricultural University in Changsha. The average yield of hybrids is 7.1 to 7.2 tons per hectare versus 5.8 to 5.9 tons per hectare for inbred varieties. But several factors have limited the spread of hybrid rice. Yuan's hybrids are indica varieties suited for the tropics. His team has not yet produced an effective japonica hybrid for temperate regions. In addition, Yuan admits, the hybrid rice he introduced in 1976 “was just so-so” in taste and quality. It was promoted by a central government anxious to feed its people, he says. His center is striving to improve the rice's taste. Because of quality concerns, breeders in other countries have been slow to adapt hybrids to local conditions. Hybrid rice also requires a change in farming culture and infrastructure. The practice of retaining part of a crop as seed works for inbred varieties that are self-pollinating. But the yield benefit of heterosis is seen only in first-generation crosses. This means new hybrid seed must be purchased for each crop. The drawbacks have limited hybrid rice to about 4 million hectares outside China. But Dobermann foresees that total rising to as much as 20 million hectares in a decade as varieties improve. One alternative—looking to wild and exotic strains—promises to boost yields of inbred varieties. For decades, breeders have worked with a limited number of rice varieties chosen for observable traits, says Susan McCouch, a rice geneticist at Cornell University. Wild and exotic varieties were ignored, she says, because they yield less rice than modern cultivars and thus were not obvious sources of beneficial genes. In the 1990s, McCouch and Cornell colleague Steven Tanksley crossed wild and exotic rice varieties with modern cultivars and then used molecular linkage maps to identify genes in offspring that increased yield. They almost always found some yield-boosting genes from the wild parent, McCouch says. They then added targeted genes from the wild parent to modern cultivars. This strategy appears to have an effect similar to heterosis, but the desired trait is fixed and boosts yields in later generations. Now about a dozen groups around the world are using wild rice genes in this way to improve local varieties. Sang-Nag Ahn, a rice breeder at Chungnam National University in Daejeon, South Korea, and his colleagues crossed four elite Korean rice cultivars with wild species. Some offspring yielded 10% to 20% more grain than the parents, says Ahn. The most promising lines are in field trials; he expects to release the first of these crosses to farmers in 3 to 5 years. A more ambitious plan is to convert rice from a C3 to a C4 plant that's better at bulking up on carbon. C3 plants—the majority of species, including wheat, barley, and potatoes—use the enzyme RuBisCO to turn carbon dioxide into a three-carbon compound that is fixed into the plant's biomass. Less common C4 plants, such as maize and sugar cane, have an additional enzyme, PEP carboxylase, which produces a four-carbon compound that RuBisCO fixes more efficiently. C4 plants, which probably evolved from C3 plants millions of years ago, are 50% more efficient at turning sunlight into biomass. John Sheehy, an IRRI plant physiologist, says that a C4 rice plant could boast 50% greater yield while requiring less water and fertilizer (Science, 28 July 2006, p. 423). Sheehy and colleagues have screened wild relatives of rice and found some evidence of the close vein spacing in leaves, the large numbers of photosynthesizing chloroplasts, and the CO2-absorption high-pay characteristics that are typical of C4 plants. “They are not C4 plants but are closer to C4 than normal C3 plants,” Sheehy says. He predicts it could take several years to prove that rice can be transformed into a C4 plant and a decade or more to produce a prototype. That's just the kind of long-term, high-payoff research that governments should be funding, says Pardey. A meta-analysis of hundreds of studies that Pardey's group is preparing for publication shows “a pretty well-established relationship” between R&D and increasing yields. They also found that the peak effect of a discovery comes 20 to 25 years after the research was initiated. Conversely, sagging growth in agricultural productivity is the direct result of limited increases in R&D funding since the late 1970s, Pardey says. Reversing the trend requires “a decadal response,” he says, “not a political cycle response.” The rice crisis that caught the world off-guard may take many years to resolve. 9. AGRICULTURAL RESEARCH # Sowing the Seeds of Expertise 1. Dennis Normile An innovative training program at the International Rice Research Institute aims to hone the skills of established rice researchers and entice young scientists into the field. Money alone won't reinvigorate agricultural R&D; fresh talent is needed, too. An innovative training program at the International Rice Research Institute (IRRI) in Los Baños, Philippines, aims to hone the skills of established rice researchers and entice young scientists into the field. The 3-week course, supported by the U.S. National Science Foundation and the U.K.'s Gatsby Charitable Foundation, was held for the second time in late May and early June. Participants got hands-on experience in how rice is sown, cultivated, and harvested. They also heard about the latest progress in research and plant breeding and discussed practical problems such as fertilizer management with scientists and farmers. The course, developed by IRRI and Susan McCouch, a rice geneticist at Cornell University, attempts to put rice in a social, economic, and cultural context. “There are students of molecular biology for whom rice is a series of A's and G's and T's and C's,” McCouch says, referring to DNA's four nucleotides. Meanwhile, researchers and extension workers from rice-growing countries in Asia and Africa often have little exposure to advanced lab techniques and few contacts. Roughly half of the 29 participants came from Europe or the United States, and half from Asia or Africa. The “very multicultural and interdisciplinary” mix gave participants a taste of international collaboration, says Margaret Mangan, who starts work on a Ph.D. in agroecology at the University of Minnesota, St. Paul, this fall. Scientists from rice-growing countries took away methods for improving practices at home. Abubakary Kijoji, a technical assistant with the Eastern and Central Africa Rice Research Network in Dar es Salaam, Tanzania, learned a new irrigation technique in which paddies are watered rather than flooded. “That is something we can apply [to] the challenge of water shortages,” he says. Mangan, who admits that she never saw a rice plant before coming to the Philippines, says the course “helped me remember why I got into agriculture.” While concentrating on basic research for her Ph.D., she intends to keep the big picture in mind in hopes of making connections between “the very technical side and the very practical side of agriculture.” A few bumper harvests of such scientists might turn today's rice crisis into tomorrow's surplus. 10. GENETICS # Simple Sleepers 1. Elsa Youngsteadt* 1. Former Science intern Elsa Youngsteadt is a freelance writer in Raleigh, North Carolina. Classic genetic model organisms--fruit flies, zebrafish, and roundworms--are popular newcomers in sleep research laboratories, although debate continues about how much their dozing relates to human slumber. Classic genetic model organisms—fruit flies, zebrafish, and roundworms—are popular newcomers in sleep research laboratories, although debate continues about how much their dozing relates to human slumber Joan Hendricks thought she had killed her charges. She had been sitting under a dim red light in a basement for hours, tapping on vials of fruit flies to keep the insects active. Eventually, the flies rolled around seemingly lifeless; her tapping didn't rouse them. But a couple of hours later, Hendricks, a sleep researcher who is now the dean of the University of Pennsylvania veterinary school, realized her flies were simply sacked out. “They were just so sleepy,” Hendricks says. “They were basically dead on their little fruit fly feet.” That was in the late 1990s. The experiments by Hendricks and her colleagues led to the first published description of fruit fly sleep, in 2000. A second group reported similar findings a few months later, and the drowsy insects began to usher sleep research into a new molecular age. Scientists hope the new approach will help answer a question that has baffled people for centuries: Why sleep? Sleep-deprived humans feel awful and perform poorly; rats deteriorate and die if they're kept awake for barely more than 2 weeks. But no one knows the reason. Now, arguing that most organisms slumber much as humans do, a growing number of sleep researchers are welcoming fruit flies, zebrafish, and roundworms—classic simple animal models—into their labs. Already, these creatures, with their easy-to-study genomes and simple nervous systems, have yielded new evidence for how sleep maintains the brain and metabolism. They've also revealed genes that regulate sleep—including a fly gene called sleepless, described on page 372. Not everyone is convinced that fish, fly, and worm sleep will shed light on human slumber, or that sleep even has a common function across the animal kingdom, but some promising parallels have convinced many researchers that they're on the right track. “I'm a true believer,” says Chiara Cirelli, a neuroscientist at the University of Wisconsin (UW), Madison, who, like Hendricks, was among the first to study sleep in the fruit fly Drosophila melanogaster. “The more we look at them, the more they look very similar to mammals.” Even some human sleep researchers share her optimism. Psychiatrist Eric Nofzinger of the University of Pittsburgh School of Medicine in Pennsylvania, who studies sleep disorders using brain imaging, is eager for the genetic insights that only the simpler organisms can provide. “There is a lot of promise and possibility,” he says. ## Fatigued flies There's a reason simple animals such as flies and worms escaped the attention of sleep researchers for so long. When birds and mammals sleep, their brains generate characteristic electrical patterns that denote deep sleep and dreaming. Since discovering this phenomenon in 1953 using electroencephalogram recordings of human brains, scientists have incorporated EEG patterns into the definition of sleep. But the simpler brains of flies, worms, and even reptiles don't produce those patterns, and no one was certain these animals even sleep. So by the mid-1990s, when new molecular and genetic techniques pioneered in fruit flies and worms were illuminating everything from memory formation to embryonic development, sleep researchers were still stuck with model organisms such as cats, rats, and dogs. But some researchers, such as Allan Pack of the University of Pennsylvania School of Medicine, suspected that fruit flies did snooze, and they hoped that studying flies would similarly illuminate the genetics of sleep and its disorders. To confirm that flies doze, Pack and his colleagues, including Hendricks, resurrected and refined older behavioral criteria that had been superseded by the EEG: A sleeping animal should be still and difficult to rouse. It should assume a habitual posture or protected location. And most important, Hendricks says, sleep-deprived animals should try to make up for lost slumber, just like people do. This would indicate that sleep isn't just a time-killer but a basic need. “It's regulated like hunger,” Hendricks says. “If you don't eat for a long time, you eat more. If you can't sleep for a while, the need builds up and you sleep more.” That's where her sleep-deprived flies came in: They desperately needed to make up for lost sleep after a night of vial-tapping. The insects met the other sleep criteria too. They snoozed mainly at night, always a few millimeters away from their food, and it took more-vigorous tapping to rouse sleeping insects than alert ones, Hendricks and her colleagues reported in Neuron in 2000. Coincidentally, Paul Shaw, as a postdoc with neurobiologist Giulio Tononi of the Neurosciences Institute in San Diego, California, was getting similar results, and that group published their work a few months later (Science, 10 March 2000, p. 1834). To see if the molecular underpinnings of sleep were conserved, both teams gave their flies food laced with caffeine at one-quarter to five times the concentration of a cup of coffee. The ones that consumed the highest dose dozed only half as much as caffeine-free controls, and some even died. Other compounds that affect human sleep similarly influenced flies: Amphetamines kept them awake, and antihistamines made them fall asleep. Even the pattern of rest over the flies' roughly 2-month life span was reminiscent of that of mammals: The youngest flies slept the most and elderly flies the least. The two fly-sleep papers started a trend. Researchers published behavioral and pharmacological evidence of slumbering zebrafish (Danio rerio) in 2002 and dozing roundworms (Caenorhabditis elegans) in 2008. As for flies, there are excellent genetic tools for both fish and worms, and the two animals are well-suited to studies relating sleep to nervous system structure and maintenance. The worm, however, has an odd sleep schedule. From the time it hatches, C. elegans takes just a few days to mature. Rather than sleep daily like flies and other animals, the growing worm takes a 2-hour nap (a state called lethargus) every 7 to 12 hours at each of four developmental transitions. During these periods, the worm builds a new cuticle, restructures body parts, and, finally, reaches sexual maturity. From then on, at least in the lab, the worm never sleeps again. David Raizen, a neurologist who studies C. elegans sleep at the University of Pennsylvania Medical School, says the contrast to mammalian sleep is actually a good thing: Lethargus is so different that anything the two have in common is probably important to sleep's universal function. “The trick,” Raizen says, “is to look at similarities.” ## Promising parallels Indeed, deep homologies have begun to emerge among the cell-signaling systems that promote sleep and wakefulness in different species. Earlier this decade, Hendricks and a team led by neurobiologist Amita Sehgal at the University of Pennsylvania Medical School found that mutant flies with excessive signaling from a transcription factor called CREB slept up to 50% more than normal flies. Some flies with a crippled CREB system slept less than half the usual amount and had an abnormally long sleep rebound after deprivation. Two years later, a research group that included Pack found that mutant mice lacking CREB also slept less than controls. Similar congruence has emerged for epidermal growth factor (EGF) signaling, which promotes sleep in worms, flies, rabbits, and hamsters. Still, Pack points out, molecules such as CREB and EGF “are involved in lots of [biological] processes,” from storing memories to governing cell fate during development. They couldn't represent a dedicated sleep mechanism, he contends. Rather, Pack says, sleep must emerge from the combined action of these signals on neural circuits in the brain. Pack predicts that flies, worms, and fish could help sort out how brain regions communicate to produce sleep. He cites the neurotransmitter dopamine, which acts only on a subset of neurons in flies and mammals—and in both, it promotes wakefulness. Similarly, in both groups of animals, GABA promotes sleep. What's more, the genetic tools available for these simple animals allow researchers to map which brain regions respond to specific sleep-regulating molecules. In flies, CREB promotes wakefulness by acting on the mushroom bodies, a part of the insect brain in charge of learning and memory. And the EGF pathway affects sleep through two regions of the fly brain and exactly one C. elegans neuron. Yet it's not obvious how such findings will translate to humans. “The brain neurochemistry and architecture are fundamentally different,” warns Emmanuel Mignot, a sleep researcher at Stanford University in Palo Alto, California, who pioneered the study of narcolepsy in dogs. He points out that, unlike dopamine and GABA, some critical neurotransmitters involved in mammalian sleep are entirely absent in flies and worms. Hypocretin, for example, has been linked to narcolepsy in mice, dogs, and people, but flies and worms don't even make it. Given such differences, Mignot doesn't expect flies and worms to reveal much about mammalian sleep at the level of the whole brain. Rather, he says, the utility of these animals is to uncover functions and mechanisms of sleep in individual cells. ## Finding a function One way to get at the basic cellular purpose of sleep is to compare which genes and proteins are active only during sleeping or waking. In mice, rats, sparrows, and flies, numerous genes involved in protein synthesis and cholesterol metabolism work mainly during sleep. An accumulation of such research, including their own mouse studies, led Pack and colleagues to propose in 2007 that a key function for sleep is to give the body time and energy to rebuild molecules that are used up during waking. The C. elegans nap cycle squares with this idea, Raizen says. During lethargus, the worms synthesize a new skin-like cuticle and double the cell nuclei in their intestines, even though the cells themselves don't divide. “Those are two intensely biosynthetic events,” he says. Tired insects have helped suggest that the nervous system may need sleep for a related reason. When comparing genes in rats and flies that are active during waking and turned off during sleep, Cirelli and Tononi, both now at UW Madison, noticed that several were involved in building and strengthening synapses, connections among neurons in the brain that are a result of learning. If all the new synapses accumulated day after day, the brain would soon run out of space and energy, says Cirelli. (Already, the brain accounts for one-fifth of human metabolism.) She suggests that during sleep, the synapses are trimmed so that only the most robust connections remain. “You don't lose the memories, but … you wake up with a leaner brain,” Cirelli says. That hypothesis remains to be tested, but there is a general sense that sleep has something to do with taking the nervous system offline for maintenance. Sleep-deprived humans and rats perform poorly in mental tasks from college exams to mazes—and flies are looking quite similar. Shaw, now at Washington University in St. Louis, Missouri, and his colleagues have done experiments, not yet published, demonstrating that sleep-deprived flies make about 50% more mistakes than well-rested flies in a learning test. ## Looking forward Like many in the sleep research community, Sehgal suspects there's some big idea about the function of sleep that has been missed. “We're looking for fundamental advances,” she says. The best way to find such a new idea, she says, is to screen for abnormal sleep among flies, worms, and fish whose DNA has been mutated at random positions. Such screens avoid any preconceived notions about what sleep does. “You just … identify the genes that correspond to those mutations,” Sehgal says, and ultimately, “maybe the function will fall out of those things.” In 2005, Cirelli and her team reported in Nature the first dividend of such a random genetic screen. Her team observed 9000 different mutant fly lines for altered sleep need. One of the most extreme lines slept only 4 to 5 hours per day, compared with the normal 9 to 15 hours—and remained alert even after sleep deprivation. These restless flies, which tended to die earlier than normal, turned out to have a mutation in a gene called Shaker, which encodes a protein channel that controls the flow of potassium across cell membranes. Functional Shaker channels help neurons return to baseline after firing; defects in them increase neuronal excitability and had been previously linked to epilepsy but not to sleep. Unlike flies, which have one version of the Shaker gene, mice have more than a dozen Shaker-like genes. Cirelli's team rolled the dice, picked one, and introduced a mutation into it. The resulting mutant rodents spent 21% more time awake than normal mice, the team reported in BMC Biology in 2007. In the new Science paper, Sehgal's team reports another extravagantly short-sleeping fly strain that underlines the importance of the Shaker channel and neuronal excitability for sleep. Created for a genetic screening effort, these flies had a mutation in a previously undescribed gene and as a consequence slept less than an hour per day. The team then found a second line of flies with a different mutation in the same gene. Although these flies had a normal amount of spontaneous daily sleep, they had almost no rebound following deprivation. Sehgal's team dubbed the new gene sleepless and ultimately showed that it codes for a small protein in the brain, a protein that may regulate expression of the Shaker channel: sleepless mutants had barely detectable levels of the Shaker channel protein. Mignot says the Shaker and sleepless mutants together point to a previously unsuspected importance of neuronal excitability in sleep. “It's an idea that has emerged from [these mutant flies],” he says. Still, it's not clear that neuronal excitability varies across the natural sleep-wake cycle. “I'm worried,” he says, “that … it could be a pathological way to induce waking.” To get the vertebrate side of the sleep story, both Mignot and Harvard University neurobiologist Alexander Schier have begun their own randomized genetic screens using zebrafish—and Schier's team has also tested thousands of drugs for their effects on zebra-fish sleep in a study yet to be published. Mignot predicts rapid progress as flies, worms, and fish reveal new sleep genes and begin to cross-pollinate with human research. “In the next 5 years, there will be an avalanche of knowledge,” he says. Others are less certain. Jerome Siegel, who studies regulation of REM sleep in mammals at the University of California, Los Angeles, worries that his colleagues, in their rush to embrace the new animal models, are overinterpreting similarities among species. “We have to appreciate that there is a tremendous diversity of sleep, even within mammals,” he says. Indeed, giraffes may snooze only a few hours per day, while some bats sack out 20 hours at a stretch. And dolphins rest only half their brains at any one time. “Looking for a brain function for sleep doesn't make a lot of sense,” Siegel says. Rather, he argues, sleep could just be a way to save energy and to stay out of trouble once other needs are met. Mignot disagrees, insisting that there is a 90% consensus that sleep has some restorative function—even if that function is yet to be revealed. And at the very least, researchers studying flies, worms, and fish can now dream of solving that grand mystery. 11. ACOUSTICS '08 # Sound Science Maps Venetian Canals and Peruvian Ruins 1. John Bohannon A new generation of archaeologists is harnessing sound waves to reveal the invisible and studying sound as an artifact itself, according to research presented at the Acoustics '08 meeting. ACOUSTICS '08, 29 JUNE-4 JULY, PARIS, FRANCE Think of archaeologists out in the field and you probably picture them carrying shovels and sample bags—perhaps also a bullwhip if you're an Indiana Jones fan. But the newest generation of researchers may be as likely to wield sensitive microphones and recorders, according to several sessions in Paris devoted to archaeological acoustics. Some are harnessing sound waves to reveal the invisible. Fantina Madricardo, a geologist at the Institute of Marine Science in Venice, Italy, presented a dramatically different map of her famous city's lagoon. Using a newly developed shallow-water sonar system, she and colleagues charted subtle differences in sediment density, tracing the contours of canals and structures buried for millennia beneath the shifting water. The sonar map led archaeologists to dig in places “where they did not think to look,” Madricardo says. A previously undiscovered Roman brick embankment is now being unearthed. Because river deltas have been a favorite site for human occupation going back to Neolithic times, the method could reveal many more submerged artifacts elsewhere. Other archaeological studies are turning to sound not as a tool but as an artifact itself. “Ancient soundscapes have been largely ignored by archaeology,” says David Lubman, a veteran acoustical scientist who is now an industry consultant based in Westminster, California. One reason is that “sound is ephemeral,” so reconstructing what an environment sounded like hundreds or even thousands of years ago is a daunting task. Then, he says, “comes the question of intentionality—how do you prove that people were aware of particular acoustic phenomena?” For example, for about a decade, Lubman has argued that the Maya Temple of Kukulkan step pyramid in Chichen Itza, Mexico, was designed with sound in mind. In Paris, he convinced scientists in the audience that the temple's peculiar shape makes it reflect the sound of clapping back as a chirp that closely matches the call of the quetzal, a bird revered by the Maya. But few of his listeners agreed that the effect was deliberately built into the temple. “I do not believe it,” says Jorge Cruz, an acoustics Ph.D. student at the Mexican National Polytechnic Institute in Mexico City. The question of intentionality may also arise from an ongoing study described by Miriam Kolar and Patty Huang, acoustics Ph.D. students at Stanford University in Palo Alto, California. As part of a team led by Stanford archaeologist John Rick, they are mapping the acoustic environment within the 3000-year-old labyrinthine galleries of Chavín de Huántar in the Peruvian highlands. Conch-shell trumpets previously discovered within the galleries indicate that the underground chambers were used for music and ritual ceremonies. The new work shows that the layout of the galleries creates reverberations that make it impossible to pinpoint sound sources. Rick hypothesizes that a ruling priest class exploited the disorienting acoustic effect to instill awe and fear. The study “is persuasive because it builds on evidence of performance in the space,” says Christopher Scarre, an archaeologist at Durham University in the U.K. In collaboration with Stanford composer John Chowning, the team plans to use its three-dimensional acoustic map of the galleries to create a virtual simulation of the rituals that took place at Chavín de Huántar. “In a couple of years, the galleries are going to be reinforced to prevent collapse, which will change their acoustics,” says Kolar. “So this is really the last chance to preserve this ancient soundscape.” Listen to roaring tigers, snorting polar bears, a cracking mountain of ice, and more from Acoustics 2008. 12. ACOUSTICS '08 # Ultrasound Uses in Medicine Heat Up 1. John Bohannon New ultrasound-based technologies, described at the Acoustics '08 meeting, are poised to probe the inner structure of bones and treat otherwise incurable cancers. ACOUSTICS '08, 29 JUNE-4 JULY, PARIS, FRANCE Hospitals have used ultrasound for decades to see fetuses and kidney stones without breaking a patient's skin. Now doctors' sonic toolkits are about to expand, as new ultrasound-based technologies are poised to probe the inner structure of bones and treat otherwise incurable cancers. X-ray photography “only gives you the average density of the bone,” says Pascal Laugier, a medical researcher at Université Pierre et Marie Curie in Paris. “To determine the quality of bone, you need to see its inner structure, and only ultrasound can reveal this.” That information is particularly crucial in aging populations of the industrialized countries, where the burden of treating bone fractures from osteoporosis and falls has ballooned. As a bonus, ultrasonic devices require none of the radioisotopes or heavy shielding of x-ray machines. The bone biophysicists gathered in Paris compared notes on the many problems with interpreting the ultrasonic sounds that propagate through the body's hardest material. A team led by Victor Humphrey, a physicist at the University of Southampton, U.K., presented an acoustic study of how bones heal after a break. Bones typically form a thick “callus” of tissue around fractures, cement the gap, and then reabsorb the callus. A bone's stage of healing can be quickly assessed, Humphrey reports, by transmitting ultrasound through the fracture—at least for long bones such as those in the arm. But one of the most medically important bones still defies ultrasound analysis. “We have not figured out the hip,” says Laugier. “It has such complex geometry and diverse structure.” Cancer researchers discussed high-intensity focused ultrasound (HIFU) therapy, which focuses ultrasound beams on a single spot inside the body, such as the center of a tumor. The mechanical energy of the acoustic waves converts into heat, and the tissue dies in a sizzle. HIFU is already used to treat cancer in easily accessible tissue such as in the prostate and uterus, but the brain has so far been off-limits because the skull makes focusing the beams nearly impossible. The solution, says Mathias Fink, a physicist and medical researcher at the University of Paris, is “time-reversal acoustics,” a strategy that uses echo patterns as a guide for focusing waves through a barrier. Fink has used the technique to successfully target brain tumors in animals. As the hype for HIFU grows—it's widely used to treat cancer in China and is being evaluated in the United States and Europe—some scientists at the meeting urged caution. HIFU often generates transient microscopic bubbles that can boost the temperature of the surrounding tissue to potentially dangerous levels. “No simple way exists … to calculate temperature rise and therapeutic dose in tissue,” says Peter Kaczkowski of the University of Washington, Seattle. The ultrasound engineer calls for more basic research on HIFU and better “regulatory oversight.” Listen to roaring tigers, snorting polar bears, a cracking mountain of ice, and more from Acoustics 2008. 13. ACOUSTICS '08 # Snapshots From the Meeting 1. John Bohannon Snapshots from the Acoustics '08 meeting include studies of how speech betrays fatigue and how polar bears and tigers hear. ACOUSTICS '08, 29 JUNE-4 JULY, PARIS, FRANCE Sleepy talking. Slumped posture and bloodshot eyes are giveaways of extreme lack of sleep, but speech betrays fatigue, too. A team led by Suzanne Boyce, a linguist at the University of Cincinnati in Ohio, recorded people giving directions after a good night's rest and after 34 to 58 hours of sleep deprivation. By analyzing phonetic features of each person's speech—pauses and the loss of syllables—a computer spotted a pattern associated with drowsiness. “This work is very exciting,” says Sarah Hawkins, a linguist at the University of Cambridge, U.K. “It promises to … not only help with practical applications such as detecting when machine operators like airline pilots are tired but will also give us greater insight into … how speech is produced.” How polar bears and tigers hear. The results of the first hearing tests of large carnivores were welcomed by conservationists eager to know the frequency ranges at which these animals can perceive human noise. A team led by Anne Bowles, a biologist at the Hubbs-Sea World Research Institute in San Diego, California, trained polar bears to respond to tones in order to receive a snack. The bears had a hearing range similar to that of humans, between 125 and 20,000 hertz. Meanwhile, tiger hearing was tested at Henry Doorly Zoo in Omaha, Nebraska. A team led by Edward Walsh, a physiologist at nearby Boys Town National Research Hospital in Omaha, analyzed the spectrum of tiger roars and also used electrodes to monitor brain activity in anesthetized tigers while playing a range of sounds. The results, says Walsh, support theories that tigers communicate with each other by infrasound, sound of lower frequency than most mammals perceive. “Confrontational roars” contain infrasonic energy, and other tigers can hear it, Walsh says. But such sounds are absent from the “territorial roars” that tigers use to maintain their vast domains. 14. ACOUSTICS '08 # Listening to Distant Ice Crack 1. John Bohannon At the Acoustics '08 meeting, scientists described using acoustic instruments designed to detect nuclear explosions to listen to the crumbling of the Antarctic ice shelf. ACOUSTICS '08, 29 JUNE-4 JULY, PARIS, FRANCE Using satellites, scientists have kept a wary eye on the crumbling Antarctic ice shelf, tracking the movement of titanic chunks that break free. Now, using acoustic instruments designed to detect nuclear explosions, they are putting an ear to the ice as well. Big breaks in the ice shelf over the past 2 decades have been dramatic, but it remains unclear whether they are due to global warming. That's partly because most cracks and breaks are too small to be seen from space. Getting a statistical handle on those smaller events, said polar scientists at the meeting, will help determine whether the rate of ice-shelf degradation stays within natural bounds or steadily increases. The sound of an ice mountain cracking quickly dissipates through air and land, but it can propagate through water for thousands of kilometers. So Alexander Gavrilov and Binghui Li, marine acousticians at Curtin University of Technology in Perth, Australia, took advantage of a Cold War legacy: three hydrophone arrays in the Indian Ocean that listen for nuclear explosions as part of the Comprehensive Nuclear Test Ban Treaty. Each 2-kilometer-wide array reveals the direction of sounds; by triangulating data from the three stations, researchers can trace the location of the sound sources. The first result is that the system works. “Antarctica is the major source of low-frequency noise in the Southern Ocean and southern parts of the Indian Ocean,” Gavrilov reports. To confirm that these sounds originated from distant ice cracking, he and Li compared a year of the sounds with recordings from a hydrophone they installed on the Antarctic sea floor. Next, the scientists focused on the dozen or so daily “cracking and breaking events” from the ice shelf that could be detected in the Indian Ocean data. Over the past 7 years, they found seasonal variation in the sounds but no significant increase—or decrease—over time. This is “good news,” says Gavrilov, because the data set can be used as a baseline for monitoring the ice in coming years. “Seismologists a decade ago would have never dreamed that these kinds of signals would be broadcast from the ice masses into the far fields of the world's oceans,” says Douglas MacAyeal, a geophysicist at the University of Chicago in Illinois. But there may be limits to the interpretation of these acoustic signals. So far, says Ursula Schauer, a geophysicist at the Alfred Wegener Institute for Polar and Marine Research in Bremerhaven, Germany, scientists cannot use the sounds to calculate the volume of ice breaking off the shelves. “But this might be possible in the future with more sophisticated signal processing,” she says. The study is a “major innovation,” adds Terence Hughes, a glaciologist at the University of Maine, Orono, but more ears in the water are needed. “It should be employed all around Antarctica, not just in the Indian Ocean sector.” 15. # The Bacteria Fight Back 1. Gary Taubes In their ongoing war against antibiotics, the bacteria seem to be winning, and the drug pipeline is verging on empty Maybe it was just a bad month—an unfortunate statistical fluctuation. Maybe not. As Vance Fowler, an infectious-disease specialist at Duke University Medical Center in Durham, North Carolina, tells it, the first case appeared in early spring 2008: a 13-yearold girl whose bout with the flu evolved into a life-and-death struggle, still ongoing, with necrotizing pneumonia and a particularly pernicious strain of bacteria known as methicillin-resistant Staphylococcus aureus (MRSA). Should the girl survive, her life will be “forever changed,” says Fowler, from pulmonary disease caused by the death of the lung tissue. The next case, a week or so later, was a research technician from Fowler's laboratory, admitted to the hospital with a facial abscess that showed no signs of healing. Again, MRSA was the cause. A week or so after that, the victims were a husband and wife. “Both were admitted with life-threatening acute MRSA infections out of nowhere,” he says. “Multiple surgeries. Life- and limb-threatening infections.” Neither one worked in a hospital or a long-term care facility, the kind of environments in which such bacteria might commonly be found. Nor had they visited one recently. So how did they get it? “Bad luck, bad genes, a bad bug, or all three,” says Fowler. The last decade has seen the inexorable proliferation of a host of antibiotic-resistant bacteria, or bad bugs, not just MRSA but other insidious players as well, including Acinetobacter baumannii, Enterococcus faecium, Klebsiella pneumoniae, Pseudomonas aeruginosa, and Enterobacter species. The problem was predictable—“resistance happens,” as Karen Bush, an anti-infectives researcher at Johnson and Johnson (J&J) in Raritan, New Jersey, puts it—but that doesn't make it any easier to deal with. In 2002, the U.S. Centers for Disease Control and Prevention (CDC) estimated that at least 90,000 deaths a year in the United States could be attributed to bacterial infections, more than half caused by bugs resistant to at least one commonly used antibiotic. Last October, CDC reported in the Journal of the American Medical Association that the number of serious infections caused by MRSA alone was close to 100,000 a year, with almost 19,000 related fatalities—a number, an accompanying editorial observed, that is larger than the U.S. death toll attributed to HIV/AIDS in the same year. So far these outbreaks have been concentrated in hospitals, where the environment is particularly conducive to the acquisition and spread of drug-resistant bugs. But the big worry, for Fowler and others, is that they will spread to the wider community—a nightmare scenario, he says. MRSA is particularly worrisome, but so is another class of bacteria, called Gram-negative bacteria, that are even tougher to defeat. These include A. baumannii, which has plagued injured soldiers returning from Iraq. For these bacteria, the pipeline of new antibiotics is verging on empty. “What do you do when you're faced with an infection, with a very sick patient, and you get a lab report back and every single drug is listed as resistant?” asks Fred Tenover of CDC. “This is a major blooming public health crisis.” ## Right bug, wrong place One of the many misconceptions about bacterial infections is that the bugs involved are not native to the human body or are particularly pernicious to begin with. Virtually all bacteria are capable of causing serious infections, at least in immunocompromised patients, although most do not. In hospitalized patients, many infections arise from the patient's own bacterial flora, flourishing where they're not supposed to be. Pneumonia, for instance, can be caused when bacteria from the mouth are aspirated to the lungs. Just as Escherichia coli is a normal inhabitant of the gut, S. aureus colonizes the skin and mucosal surfaces in the nose in 30% of the population. When it sets up shop somewhere else, S. aureus can cause a host of infections, including skin abscesses, necrotizing pneumonia, joint infections, and heart valve infections known as endocarditis. Similarly, S. epidermidis normally colonizes the human skin, but when it gets into the bloodstream, it can cause sepsis and endocarditis, as well as infections involving prosthetic devices such as pacemakers and artificial joints. The risk of acquiring one of these serious infections is highest in hospitals and health-care facilities simply because these environments offer the greatest opportunities for bacteria to enter the bloodstream or infect open wounds. Treating a bacterial infection with antibiotics is the obvious first step. But in the 65 years since the first widespread use of penicillin during World War II, infectious-disease specialists have been treated to an ongoing tutorial in the many ways bacteria can acquire and spread resistance to these drugs. Unlike tuberculosis and other bacteria, in which antibiotic therapy simply selects for rare resistance-bestowing mutants, the bacterial strains that are so insidious in hospitals employ far more diverse techniques, says Louis Rice of Case Western Reserve University and the Louis Stokes Cleveland VA Medical Center in Ohio. S. aureus and Enterococcus, for instance, can acquire resistance by exchanging entire genes or multiple genes with other bacteria, either through plasmids—loops of DNA that are independent of the bacterial chromosomal DNA—or so-called gene cassettes or transposable elements that can be inserted directly into the chromosomal DNA. Penicillin and all penicillin-like antibiotics are ringlike molecular structures, known technically as β-lactams. They work by attacking a particular cell wall enzyme in the bacteria. The first strains of penicillin-resistant S. aureus, which arose within a few years of penicillin's introduction, were strains that have a survival advantage because they naturally produce an enzyme—penicillinase, one of a class of enzymes known as β-lactamases—that destroys the ring structure of penicillin. Within a decade, the effectiveness of penicillin against hospital-acquired staph infections was “virtually annulled,” says microbiologist Alexander Tomasz of Rockefeller University in New York City, by “plasmid epidemics” that then spread the penicillinase gene through the entire species of S. aureus. The pharmaceutical industry responded in the 1950s with a host of semisynthetic penicillins designed to be resistant to penicillinases. Methicillin, introduced in 1959, was believed to be the most effective. As Graham Ayliffe, a veteran hospital infection expert at the University of Birmingham in the U.K., recalled, “this was [supposed to be] the end of the resistant staphylococcus.” Within 2 years, however, hospitals in Europe were identifying strains of S. aureus that were resistant to methicillin: the first MRSA strains. Researchers later realized that these strains had taken a different route to acquiring resistance. Rather than generating new or different β-lactamases, which could attack the antibiotic directly, they had acquired a new gene entirely, called mecA, that coded for a variant of the antibiotic's target: the penicillin-binding protein. When the antibiotics attack the original penicillin-binding protein, explains Tomasz, this “surrogate” binding protein “takes over the task of cell wall synthesis” and works to keep the antibiotic at bay. The mecA gene itself, says Tomasz, appears to derive from a common bacterium on the skin of domestic and wild animals known as S. sciuri. How S. aureus came to acquire the gene is a mystery, but since it did, it passes it on by exchanging entire gene cassettes with the mecA gene on them. ## Breaking out Through the 1970s and 1980s, MRSA remained little more than a nuisance bug, although occasional hospital outbreaks would have to be reined in with strict isolation and control programs. In the mid-1980s, typically only 1% to 5% of all S. aureus isolates were methicillin-resistant, says Henry Chambers, an infectious-disease specialist at the University of California, San Francisco. Around that time, S. aureus began to acquire genes that confer resistance to other common antibiotics, apparently from methicillin-resistant S. epidermidis and carried on the same mobile cassettes as mecA. The result was a bug that was both far more difficult to treat and, as Chambers says, “pretty adaptive to surviving in hospitals.” Today, 60% to 70% of all S. aureus strains found in hospitals are multidrug-resistant MRSA. Worries intensified when MRSA appeared a decade ago as a community-acquired infection rather than one exclusive to health-care settings. In 1999, CDC reported on four deaths in Minnesota and North Dakota, all children, all caused by MRSA infections that could not be traced back to hospitalizations by either the patients or family members. Somehow the mecA gene had emerged in S. aureus strains outside hospitals or health-care facilities. “This was a real biological success story,” says CDC's Tenover. “And it all happened off our radar screens.” MRSA isolates then began to appear in a range of unexpected community settings: children in day-care centers, army recruits, athletes in contact sports, native Americans living on reservations, prison populations, intravenous drug users, and among men who have sex with men. The possibility that these MRSA strains were simply hospital strains that had migrated out into the community was refuted by analysis of the gene cassettes carrying the resistance. In hospital strains, these cassettes are relatively large and carry multiple resistance-bestowing genes, explains Tomasz. The “oddball” cassettes carrying the mecA gene in the early community-acquired isolates were small and contained only the one gene. In the last few years, however, MRSA strains in the community have begun to acquire multidrug resistance, suggesting that they've been intermingling with the hospital strains. A half-dozen community-acquired MRSA clones have now spread around the world as their prevalence in the community has continued to increase; in San Francisco, for instance, up to 50% of all S. aureus isolates outside health-care settings are now methicillin-resistant. “These methicillin-resistant strains seem to be replacing the susceptible strains of S. aureus in the general population,” says Mark Enright, an infectious-disease specialist at Imperial College London (ICL), “which means people are carrying strains of MRSA in their nose in the community. Now when they get infections, ones that were formerly treatable are going to be replaced with difficult-to-treat infections.” The public health anxiety increased still further in 2002 with the detection of isolates of MRSA that were fully resistant to the antibiotic vancomycin, traditionally considered the last resort for treating resistant staphylococcal infections. These S. aureus isolates seem to have acquired a gene for vancomycin resistance—vanA—from enterococci, and specifically E. faecalis, which are part of the natural flora of the intestinal tract and can cause serious infections in hospitalized patients. When the enterococci developed resistance to common antibiotics in the 1980s, physicians had responded by using vancomycin to treat them. Vancomycin-resistant Enterococcus (VRE) was first reported in 1986, and the vanA gene soon spread throughout the species. Because enterococci readily exchange genetic information with other bacterial species, says Tenover, he and other experts assumed that it would soon pass vanA and vancomycin resistance to MRSA. “Everybody was waiting for the shoe to drop,” says Tenover. In 2002 it did, when the Michigan Department of Community Health reported the first isolate of MRSA that had vanA-mediated resistance to vancomycin. The patient was a 40-year-old diabetic who had recently been given an extended course of vancomycin for a foot ulcer. Fortunately, vancomycin-resistant MRSA—now known as VRSA—has not developed into the nightmare researchers feared. Only nine isolates have been detected worldwide in 6 years, seven from the same region in Michigan, which suggests that S. aureus, unlike Enterococcus, loses the ability to compete in the broader environment when it takes on the vanA gene. That only one of these infections was life-threatening suggests that the vancomycin-resistant bug also loses its virulence. ## A paltry pipeline Although MRSA and other Gram-positive bacteria remain a major threat, a half-dozen new antibiotics have either just been approved or are in the pipeline that should work well against them—at least until the bugs evolve more resistance. This is not the case, however, for Gram-negative bacteria, such as P. aeruginosa, A. baumannii, and K. pneumoniae. These bacteria have both an inner and outer cell membrane, as opposed to the single cell membrane of Gram-positive bugs like MRSA. (The name comes from how these bacteria stain on a Gram stain test.) The pipeline for antibiotics against Gram-negative bacteria, says Bush of J&J, is limited to development programs in a few small companies; only one drug has made it through phase I clinical trials. Prompted by the emergence of MRSA and VRE in the late 1980s, pharmaceutical companies focused their attention on Gram-positive bugs. Meanwhile, many Gram-negative bugs became resistant to virtually every known antibiotic, or at least every antibiotic that isn't toxic. “These organisms may well start to spread into the community,” says Tenover, “and then we really will be in trouble. We have drugs to fall back on for Staphylococcus. But when you say, ‘Where's the next anti-Pseudomonas drug?' I have to scratch my head.” One reason for the dearth of drug candidates is that Gram-negative bacteria are simply harder to kill. First, they have the extra cell membrane the drug has to penetrate. Then they have other defense mechanisms that Gram-positives lack, such as the ability to activate pumps or close down protein channels in the membranes that let these antibiotics in. “They can have three or four mechanisms working at once,” says Case Western's Rice. “Even if you develop a new drug entirely, these bacteria may be just as likely to be resistant to new drugs as old ones. It's just really hard.” View this table: The problem has been exacerbated by the gradual exodus of pharmaceutical companies from antibiotic development—a trend that began in the 1980s and has accelerated since 2000, in large part because the market is iffy and the chances of success are slim. Of the 15 major pharmaceutical companies that once had flourishing antibiotic discovery programs, eight have left the field entirely, and two others have reduced their efforts significantly. That leaves only five—GlaxoSmithKline, Novartis, AstraZeneca, Merck, and Pfizer—that still have antibiotic discovery efforts commensurate with the size of the problem. Even though the market for antibiotics is in the neighborhood of$25 billion a year, says Steve Projan, vice president of biological technologies at Wyeth Research in Cambridge, Massachusetts, other drugs, such as antidepressants or antihypertensives, offer a greater bang for the buck because they are often taken for years or decades rather than just a 7-to 14-day course. Resistance only compounds the problem: A drug that takes a decade to develop might be useful clinically for only a handful of years.

What's more, the better the antibiotic, the less health experts want to see it used to avoid the development of resistance. “It's probably the only area of medicine where a drug company can invest all this money to develop a drug, come up with a good one, and then the so-called thought leaders in the field, like myself, will tell people not to use it,” says Rice. “We say it's such a good drug that we should save it.”

As a result, virtually all the new antibiotics and all those in the pipeline for Grampositive bacteria are second-generation drugs, that is, incremental improvements on existing classes. The one conspicuous exception—daptomycin, developed for S. aureus by the late Frank Tally at Cubist in Lexington, Massachusetts—was first identified 20 years ago by Eli Lilly and Co. and then shelved because it had toxicity problems at high doses.

To the surprise of many, the recent sequencing of more than 650 bacterial genomes has been a “dismal failure” when it comes to drug development, says ICL's Enright. Although genome sequences were expected to yield a “treasure trove of new targets for entirely new classes of antibiotics,” as David Pompliano and colleagues at GlaxoSmithKline in Collegeville, Pennsylvania, recently wrote, this simply hasn't panned out. At GlaxoSmithKline, Pompliano and his colleagues spent 7 years and more than $70 million evaluating more than 300 “canonical” bacterial genes that they thought were essential to the viability of the bacteria. The result was just five leads, a success rate, they estimated, that was four-to fivefold lower than for other areas of therapeutics. Genomics is simply not a good paradigm for discovering new antibiotics, suggests Projan. The genetic approach assumes that a candidate drug can knock out a single gene in the bacterium to render it unfit for survival. But the drugs don't knock out a gene's activity entirely, he says; instead they modulate activity. “As we found out in oncology,” says Projan, “sometimes leaving even 5% activity is enough for the tumor to grow. The same thing is true for bacteria.” Projan and others suggest that the only route to a new antibiotic—short of pure luck—will be through more fundamental research on the basic biology of the bacteria. ## Cutting back Barring the discovery of miracle antibiotics to which bacteria cannot evolve resistance—a “laughable” notion, says one expert—the only foreseeable route to curbing antibiotic resistance will be to rein in the use of antibiotics. One obvious way is to lower the risk of acquiring resistant bugs in the hospital. Countries that have mandated rigorous infection control in hospitals, such as Denmark, the Netherlands, and Finland, have been able to keep MRSA infection rates low. These infection-control procedures, however, go far beyond physicians and nurses wearing gloves and protective masks and washing their hands before and after patient contacts, essential as those are. These nations employ a technique known as “active detection and isolation,” or “search and destroy,” as it's called in the Netherlands. Patients considered at high risk of carrying MRSA and other antibiotic-resistant bugs are cultured when they're admitted to the hospital, and periodic cultures are taken of all patients, particularly those in high-risk wards. The greater the prevalence of pathogens and risk factors, the more frequent this surveillance. Patients who are infected or are carriers are isolated. Health-care workers who are colonized with resistant bacteria can be “decolonized,” using skin washes and nasal ointments. Whether U.S. hospitals should be required to implement active detection and isolation is a long-running controversy. Some specialists—led by University of Virginia epidemiologist Barry Farr, an expert on controlling VRE and MRSA—have argued that it's the only proven method to control hospital MRSA infections. Others have questioned the technique's cost-effectiveness and viability, particularly when rates of MRSA in the community are beginning to rival those in many hospitals. Vaccines against antibiotic-resistant bacteria would also go a long way to reining in resistance, but only one such vaccine candidate, against S. aureus, has ever made it through phase III clinical trials: StaphVAX, licensed by Nabi Biopharmaceuticals. Although patients who received the vaccine had significantly lower rates of S. aureus infections at 40 weeks compared to controls, this apparent protection was lost at 54 weeks. A follow-up trial also failed to demonstrate efficacy. Several more vaccines are in development, including a new-generation StaphVAX. Even temporary protection could be useful, argue some experts, either for health-care workers, who could be vaccinated regularly, or for patients who are about to be hospitalized to undergo a procedure. Ultimately, physicians will have to be persuaded to reduce their use of antibiotics, although that will be a hard sell. One step, for instance, would be to persuade physicians outside hospitals to treat only those patients who are truly infected. A 2001 study from the University of Colorado Health Sciences Center estimated that 55% of all antibiotics prescribed in the United States for upper respiratory infections were unnecessary. This is what Rice describes as the “get-a-little-sniffle-get-a-little-Levaquin” problem. “The patients want it,” he says, and “the doctor wants to get the patient out of the office, and the quickest way to do it is to write a prescription.” But the societal problem of antibiotic resistance should outweigh whatever personal peace of mind comes from the indiscriminate use of antibiotics, says Tenover (see sidebar on p. 360). Similarly, many times physicians prescribe combination “broad-spectrum” antibiotics when a single “narrow-spectrum” antibiotic would do the trick. Understandably, says Rice, physicians are unwilling to wait to treat serious infections until the bug is cultured and they learn to which antibiotics it's still susceptible. But once the crisis is over, usually 1 to 3 days after starting therapy, physicians could switch their patients to the appropriate narrow-spectrum antibiotic. What the field desperately needs, these experts say, are randomized, controlled trials to establish how long antibiotic therapy should be prescribed for different infections. The data are scarce, and misconceptions abound. The ubiquitous advice in the field—from physicians, patients, and even CDC—is that patients should continue the full course of antibiotics even after they feel better. Because antibiotics tend to have few side effects, physicians consider a longer course to be a no-lose proposition. But from the perspective of preventing antibiotic resistance, says Rice, “this is totally wrong-headed.” In patients with healthy immune systems, he explains, most antibiotics merely stun the bacteria sufficiently to make it easier for the host immune system to do its job. “You can take tetracycline until the cows come home,” Rice says, and “all it does is stop most bacteria from growing. It doesn't kill them.” Extending the course of the antibiotics unnecessarily increases the likelihood that the patient's normal flora will be inhibited to the point that bacteria resistant to the antibiotic will fill the void. The few existing studies on the necessary length of therapy have suggested that it is often surprisingly short. Urinary tract infections in young women can be treated with 1-to 3-day courses of antibiotics. The Infectious Diseases Society of America recommends a 3-day treatment for traveler's diarrhea, while acknowledging that 1 day appears to be equally effective. Studies from the 1940s suggested that the “vast majority” of patients with pneumonia get better after 2 or 3 days, says Rice: “Somewhere along the line, that morphed into 7 days, 10 days, 21 days, with no real reason other than making the doctor more comfortable.” In May, the U.S. National Institute of Allergy and Infectious Diseases responded to the expert demand and put out a request for proposals for clinical studies that would determine the optimal use of antibiotics, including the optimal duration of therapy. “I think most physicians would respond to compelling data from a well-done trial,” says Rice. One beneficial side effect to curbing antibiotic use is that it may serve to rehabilitate those antibiotics that have lost their effectiveness. “Many of these were wonderful new drugs just 20 years ago, able to treat a wide variety of bugs, both inside and outside the hospital,” says Rice. “Now we're at a point where some of them are next to useless, because they've been used for everything.” 16. # Collateral Damage: The Rise of Resistant C. difficile 1. Gary Taubes Resistance to antibiotics can bestow on a bacterial strain the advantage it needs to spread through the hospital environment. Clostridium difficile is an unfortunate case in point. In April 2002, Mark Miller, an infectious-disease specialist and microbiologist working at Jewish General Hospital in Montreal, Canada, began to suspect that he had an outbreak on his hands. He was used to dealing with the bacteria Clostridium difficile, which can cause severe diarrhea in debilitated patients and had been a common problem in hospitals for more than 30 years. But now the number of cases had started to climb, as did their severity. “One of the first indications that we knew we had a problem,” says Miller, “was when one of the colorectal surgeons called me and said, ‘I just took out my second colon in a month on a C. difficile patient.' When we started looking at the numbers, they were absolutely horrendous.” At the peak of the outbreak, says Miller, there were 50 new cases of C. difficile diarrhea every month in their 600-bed hospital. “Of those, about one in six was dying or going for a colectomy. That's kind of staggering.” Resistance to antibiotics makes for bacteria that are harder to kill, but it can also bestow on a bacterial strain the advantage it needs to spread through the hospital environment and perhaps around the world—a kind of collateral damage in the escalating war between man and microbes. C. difficile is an unfortunate case in point. The bacterium has currently been linked to at least 5000 deaths a year in the United States; at the height of the Quebec epidemic it caused more than 7000 serious infections and 1200 deaths in a single year. In many hospitals, C. difficile constitutes a greater risk to patients than methicillin-resistant Staphylococcus aureus or any other bacteria. The symptoms of a C. difficile infection range from mild diarrhea to severe colitis, and the elderly bear the brunt of the disease. One in four patients will have a recurrence or multiple recurrences. “It's a horrible problem,” says Dale Gerding, an infectious-disease specialist at Hines Veterans Administration Hospital and Loyola University in Chicago, Illinois. Patients have to be treated almost constantly with oral vancomycin to prevent recurrences, he says. C. difficile diarrhea first appeared in the medical literature in the 1970s, mistaken for a side effect of the antibiotic clindamycin. In 1978, physicians realized that the diarrhea was induced by toxins from clindamycin-resistant C. difficile, which had colonized the victim's colon after their normal gut flora had been decimated by the clindamycin treatment. C. difficile has remained a common hospital infection ever since because the bacteria produce heat-resistant spores that are exceedingly difficult to kill. “They're very resistant to detergents and cleaning agents,” says Gerding. “Really, the only thing that destroys them is bleach or hydrogen peroxide.” Through the 1990s, however, C. difficile wasn't considered a major threat because the bacteria were susceptible to two antibiotics, vancomycin and metronidazole, the latter of which is inexpensive. As many as 40% of all hospitalized patients are colonized with C. difficile, but most tolerate it without symptoms. A series of hospital outbreaks in six U.S. states, beginning around 2000 and capped by the severe Quebec outbreak in a dozen hospitals, suggested that a new, hypervirulent strain of C. difficile was circulating. Since then, the same offending strain has been identified in hospitals in 38 states and has also been linked to outbreaks in Western Europe. What sets it apart from its predecessors, say Gerding and Miller, is its high resistance to the newer fluoroquinolone antibiotics, such as levofloxacin and moxifloxacin. These antibiotics began to be used widely in the late 1980s, and usage has increased steadily ever since. Why this strain induces more severe disease—with a death rate among those infected of 10% compared with 1% percent in the 1980s—is still a mystery, but one possibility, says Gerding, is a mutation that enables the strain to produce more toxin. Although Quebec hospitals have reduced the incidence of C. difficile infections by two-thirds since the height of the outbreak, through very tight isolation and control and rigorous “housekeeping,” says Miller, they have yet to get back to the levels preoutbreak. “C. difficile in health-care facilities and hospitals is a very unforgiving organism,” he says. It exploits “any lapse in isolation, in housekeeping, in hygiene—whatever it is—and it comes back with a vengeance.” 17. # Trench Warfare in a Battle With TB 1. Eliot Marshall As tuberculosis took off in Russia in the 1990s, one antibiotic after another failed; the state of Tomsk responded with an epidemic-fighting strategy pioneered by the Boston nonprofit Partners in Health. Deaths have declined, but resistance to drugs remains high. As tuberculosis took off in Russia in the 1990s, one antibiotic after another failed; the state of Tomsk responded with an epidemic-fighting strategy pioneered by the Boston nonprofit Partners in Health. Deaths have declined, but resistance to drugs remains high TOMSK, RUSSIA—Six mornings a week, nurse Galina Kruchinina circles this Siberian city with a black medicine bag. She's hunting for people infected with tuberculosis—some of them rough customers—who don't show up at the clinic. She and a driver track them down and give them antibiotics. The search this morning leads down a rutted lane near the banks of the Tom River. They're looking for Oleg, 35, who will get three kinds of pills plus an injection, if they find him. The car pulls up under some tall birch trees. Kruchinina disappears into a wooden building and brings down a sleepy-looking man. It's Oleg, who recently got out of prison, bringing Mycobacterium tuberculosis with him. Like many convicts, he has tattoos, including two stark blue ovals inked onto his eyelids that watch you when he blinks. Oleg takes his medicine in the car, accepting juice and food as part of the treatment from “Mother,” as he calls Kruchinina. If his infection isn't treated continuously for 6 months with a four-drug blitz, it could flourish and kill Oleg. A bigger worry for public health is that intermittent or weak therapy could spawn drug-resistant bacteria. Multidrug-resistant TB (MDR TB), as it's called, is on the rise here and across most of the globe, but luckily Oleg doesn't have it. If he keeps taking his antibiotics twice a day for several more months, he should be okay—which is why Kruchinina and her colleagues seek him out. Kruchinina and her driver go next into a warren of rickety houses after Ivan, an alcoholic 21-year-old, and his older brother Ruslan, both infected. They've gone away for potatoes, someone says. The medical team doubts this; they track the men to a nearby house. Next they look for Liliana, who's been known to hide under the furniture; then Alexei, a brawny man in his 30s who lives with his mother. All the patients are difficult at first, says Kruchinina, “but they adapt.” At 2 p.m., she gives her seat to another nurse, who completes the day's cycle. This seek-and-treat program is called “Sputnik” (“companion” in Russian) by its creator, Partners In Health (PIH), a nonprofit linked to Harvard University's Brigham and Women's Hospital in Boston, Massachusetts. Sputnik workers are like family for the 28 people they follow. They reflect the PIH credo that no matter how poor or difficult the patient, the medic's duty is to deliver treatment. PIH has joined with leaders of the Tomsk oblast, or state, and the Tomsk prison to deploy this aggressive strategy in a place where TB was raging out of control a decade ago. Sputnik is one component of Tomsk's effort, which in recent years has won millions of dollars in international aid. The result, says Harvard-based PIH physician Salmaan Keshavjee, is a program that would be “avant-garde, even in the United States.” PIH doesn't aim to hospitalize patients, as the Russian national TB system often does. Putting people in institutions tends to increase transmission of bacteria, PIH doctors argue. PIH focuses on home treatment or day clinics, with care by nurses or community workers rather than doctors, a method PIH pioneered in Haiti and Peru. In 1999, PIH founders Paul Farmer and Jim Yong Kim began pushing for changes in international guidelines that once set aside MDR TB patients as untreatable. Farmer and Kim argued that the World Health Organization (WHO) should alter its policy to treat such patients, on both moral and economic grounds (Science, 10 August 2001, p. 1049). “If you don't treat MDR TB, it doesn't go away,” says PIH doctor Michael Rich: “It only gets bigger and bigger.” And the cost of treating each case of TB escalates. PIH has put its ideas on the line here, making Tomsk a training center for dealing with TB in “resource-limited” jurisdictions. With 5 years of significant outside aid, the results are encouraging, but the statistics are still worrisome. The TB death rate is down; the cure rate is up; but the percentage of new infections that are drug-resistant is higher than in 2002, officially having risen to about 16%. And a new specter looms: extensively drug resistant, or XDR, TB. ## Where TB lives M. tuberculosis is a tough organism, protected by a waxy lipid coat and an ability to hunker down and fend off immune and chemical attacks. It can travel in droplets expelled from the lungs—studies indicate it may live for several hours this way—and readily infects a new host. Lung infections are the most common, although other tissues can get infected. Poor nutrition increases risk, and some people can't handle the anti-TB drugs or may have an inherited vulnerability to TB. Coinfection with HIV makes TB more deadly, but Tomsk officials say they see relatively little of that. TB is concentrated in a vast reservoir of the poor, particularly in prisons and hospitals. But everyone is in danger, says Edward Nardell, a PIH doctor, Tomsk consultant, and chief TB control officer for the state of Massachusetts. “The big risk factor is breathing.” Maria Rubina, a young patient at the main TB hospital in Tomsk, illustrates the point. She was diagnosed with TB when she was a student 3 years ago, at age 20. Since then, she has been living full-time in the Tomsk TB hospital, a big pink sanatorium built in 1937 across the river from town. No one knows for sure where she got the infection, but in retrospect, it seems she may have contracted it from a neighbor who died in her apartment complex (not in Tomsk). A postmortem showed that he had MDR TB. Aivar Strelis, the top surgeon and a renowned TB expert at the hospital, has concluded that Rubina has XDR TB. This means that even the “second-line” products commonly used against MDR TB—the bulky injectables and less potent drugs with nastier side effects—cannot be given to her. A large part of her left lung has been removed. The infection is dormant, meaning that it has lapsed into the latent state of most TB infections, when bacteria are not ejected in sputum. WHO estimates there are a staggering 2 billion people in the world infected with this dormant type of TB. WHO also estimates there are 450,000 new cases of MDR TB each year. Cases like Rubina's are the legacy of what Sergey Mishustin, the chief TB officer of Tomsk oblast, describes as a “collapse” of the health system after the end of the Soviet Union in the 1990s. He was formerly head TB physician in the Tomsk prison, part of the federal justice system. He recalls that there just wasn't enough money to buy medicines. Ventilation wasn't adequate in prisons or hospitals, and there was little effort to segregate MDR TB prisoners from so-called drug-susceptible cases. A short stay in prison could become a death sentence. “I was in horror,” Mishustin says, to find that medics in one clinic were feeding TB patients whatever antibiotics they had at hand. Because there was no systematic testing for resistance, they were amplifying resistant organisms in patients already infected with them by wiping out only the competing bacteria. It's called an “epidemiological pump,” an effective way to incubate lethal bacteria. In his own clinic, Mishustin says, he wouldn't allow antibiotics to be given this way. When people learned that he left thousands of dollars' worth of drugs on the shelf and threw them out on their expiration date, Mishustin says, investigators accused him of misconduct. But he says he was excused when TB experts came to his defense. By 2000, the incidence of TB had increased among Russians to more than 107 cases per 100,000 people, according to WHO. For comparison, the U.S. rate is below 5 per 100,000 (see table). Since 2000, Tomsk has brought TB incidence to a “stable” state (102.7 per 100,000), Mishustin says. View this table: View this table: A British medical group, MERLIN (Medical Emergency Relief International), was the first, in 1994, to bring outside help to Tomsk. The group distributed microscopes around this Poland-sized oblast, parts of it unreachable by car, so that medics could examine sputum samples and quickly determine who was shedding infectious bacteria. Billionaire George Soros provided more support in the mid-1990s, then turned the operation over to PIH. Tomsk got a World Bank loan and, with PIH advice, won the first anti-TB grant (for about$11 million) from the Global Fund to Fight AIDS, Tuberculosis, and Malaria. Through the Global Fund, Eli Lilly and Co. in Indianapolis, Indiana, agreed to provide capreomycin and cycloserine at cost.

Prison and city clinicians say that the joint TB control system they've created here is unique. TB prison doctor Alexander Pushkarev took some Western visitors around to show off the improvements in June. Prisoners are now segregated into 14 wards and separated by medical status. MDR TB cases have a dorm and exercise area. All patients are registered in a 7000-record database, and by law, when they leave prison, medical details are shared with the Tomsk city operation overseen by chief doctor Vera Golubchikova. Her staff keeps tabs on each case and tries to get all of them cured—by Sputnik's team if need be. Both the prison hospital (1000 inmates) and the oblast TB hospital (370 beds, 1000 patients per year) have new ventilation systems and—a recent addition—airtight cabinets to hold sputum samples while they're waiting to be tested. Basic improvements have made a difference. The prison hospital, which reported 60 TB deaths in one recent year, according to Pushkarev, has had none so far in 2008.

## Making existing tools work

Even in well-funded Tomsk, resource limits are visible. The TB hospital's forbidding “department four” is not much more than a shelter for tough MDR TB cases, a way station on the final descent. In the larger “department three” building next door, MDR TB patients, including contagious ones, live four to a room.

The grim dorms and complex 2-year treatment regimens for MDR patients wouldn't be needed if doctors had a single pill they could give, say, once a day for a couple of weeks and knock out the mycobacterium. No such dream medicine is on the horizon. But several new prospects are in clinical development—for the first time in 4 decades—thanks to work by nonprofits such as the Global Alliance for TB Drug Development and a few companies (see sidebar). Perhaps one will be available in Tomsk in 5 to 10 years.

This is encouraging, but what excites Tomsk TB doctors is the near-term plan for rapid diagnostics. Tomsk oblast has bought a building for a dedicated diagnostic lab, says health department chief Albert Adamyan; by the end of the year, he hopes it will be using liquid media in drug-susceptibility testing.

Drug-susceptibility testing with solid culture media can take several months, and even that isn't done routinely across Russia. The liquid media should enable Tomsk clinics to get results in 3 weeks, officials say. Shorter diagnosis times make it possible to use medicine more efficiently, reduce MDR TB transmission, and attack the worst infections earlier—a critical factor in this battle, says PIH expert Rich.

“What we really need,” Rich adds, “is a good, cheap, point-of-service test.” Wealthier countries have access to polymerase chain reaction tests that monitor variable TB organism genes, signaling within 24 hours whether the strain is resistant to the first-line drugs isoniazid and rifampin. It's still expensive for Tomsk. But a new, gene-based test that costs \$8 is being promised by WHO and the Foundation for Innovative New Diagnostics in Geneva, Switzerland.

For now, PIH leaders put most of their time and energy into teaching medical workers in places with a heavy TB burden how to use the cheapest susceptibility testing methods and how to deploy antibiotics already in the cabinet. Medics from 10 nations, for example, were in Tomsk in June for training by PIH and local physicians. Keshavjee chairs an international group called the Green Light Committee that works with drug companies to distribute high-quality TB medicines at cost to programs that meet its standards.

What Tomsk has done, says Neel Gandhi, the AIDS researcher at Albert Einstein College of Medicine in New York City who reported a famous outbreak of XDR TB in KwaZulu-Natal, South Africa, in 2006, “will create a center of excellence and a model” for others. “What works in Tomsk may not work” everywhere, partly because HIV is a bigger factor in Africa, he says; climate, government, and cultures differ. But Gandhi adds, “It would be wonderful to create a center of excellence in South Africa” like the one in Tomsk.

With creative drug cocktails and carefully staged protocols, it's been possible to extend the use of decades-old drugs that are losing much of their punch. But it requires vigilance and huge persistence—the kind provided by Sputnik's workers. That could prove a tall order elsewhere.

18. # Anti-TB Drugs: And Then There Were None

1. Eliot Marshall

Two crucial antituberculosis drugs, capreomycin and cycloserine, are valued today precisely because they didn't seem valuable a short time ago.

Two crucial antituberculosis drugs are valued today precisely because they didn't seem valuable a short time ago. Capreomycin and cycloserine were nobody's first choice when Eli Lilly and Co. in Indianapolis, Indiana, developed them as antibiotics in the 1950s, says Lilly Vice President Gail Cassell. Capreomycin must be injected; cycloserine causes psychosis in 1% or more of those who take it. Patients must be watched closely for central nervous system effects. But because the drugs were little used, bacteria were not widely exposed to them and didn't develop much resistance. Now they are among the best “second-line” treatments for people with multidrug-resistant TB (MDR TB).

In 2001, however, Lilly decided to get out of antibiotics after a “very painful” review of its “limited resources,” says Cassell. (Antibiotics are not big moneymakers.) In recent years, nonprofit groups have been working with Lilly and other companies to extend the life of the few effective drugs on a dwindling list. Lilly, for example, makes capreomycin and cycloserine available at cost to programs vetted by the so-called Green Light Committee of the Global Fund to Fight AIDS, Tuberculosis, and Malaria. The company is transferring manufacturing expertise to nonprofits as well. Other companies—such as Bayer, GlaxoSmithKline, Johnson & Johnson, and Novartis—are looking for ways to subsidize antibiotics for developing nations, which need them desperately.

Melvin Spigelman, clinical chief of the Global Alliance for TB Drug Development in New York City, recently drew up a list of the most promising TB drugs on the horizon; it's alarmingly short (see table). Some prospects, such as moxifloxacin, are simply refurbished versions of existing medicines. Even so, when pressed to say when one might be ready for wide use, experts speak of 3 to 4 years at best, not months.

View this table: