News this Week

Science  10 Oct 2003:
Vol. 302, Issue 5643, pp. 206
  1. INFECTIOUS DISEASES

    New Biodefense Splurge Creates Hotbeds, Shatters Dreams

    1. Martin Enserink

    And the winners are … Boston and Galveston. That's the main conclusion from the final, $373 million installment of fiscal year 2003's biodefense bonanza, announced on 30 September. Eagerly awaited, the series of 11 grants from the National Institute of Allergy and Infectious Diseases (NIAID), which will fund new lab buildings across the nation, has the potential to shape the biodefense landscape for years to come. The awards cemented the reputations of Boston and Galveston —a small town on the Gulf Coast in Texas—as major magnets for infectious disease research; in New York and California, meanwhile, frustrated contenders were licking their wounds last week and wondering what went wrong.

    The latest funding round is part of a broader effort to boost research aimed at countering bioterrorism and to spread expertise and labs across the nation. Four weeks ago, NIAID announced that it would fund eight so-called regional centers of excellence, networks of many institutes that will carry out research and training (Science, 12 September, p. 1450).

    Last week's announcement was about the hardware. The big winners, Boston University (BU) Medical Center and the University of Texas Medical Branch in Galveston, will receive $128 million and $110 million, respectively, to build National Biocontainment Laboratories (NBLs), major new buildings that will include biosafety level 4 (BSL-4) facilities, the tightly controlled environments where researchers in pressure suits study agents such as Ebola. Only a handful of such labs currently exist in the country. Nine other institutions (see table) will receive one-time grants of between $7 million and $21 million to build Regional Biocontainment Laboratories, smaller-scale facilities with BSL-2 and -3 space only.

    Not in their backyard.

    Boston's proposed new lab faces resistance from local groups.

    CREDIT: BOSTON UNIVERSITY MEDICAL CENTER

    The past few months had seen feverish lobbying on behalf of the NBL candidates, says NIAID Director Anthony Fauci. But he insists those efforts had “0% influence.” Fauci says he made the final decision after getting input from two expert panels—one that judged the proposals and one that made site visits to the five most promising candidates. Galveston was widely considered a strong contender. But many had not expected BU to win because it doesn't have a strong tradition in biodefense. “I was surprised by that,” says Stanley Lemon, principal investigator for Galveston's application. But Fauci points out that BU is part of one of the new regional centers of excellence, led by Harvard, and that there are many infectious-disease researchers in the Boston area who can use the lab.

    In New York, Governor George Pataki said in a statement that he was “deeply disappointed” that a proposal sent in by the state's Department of Health laboratory had been rejected. “We are not at all convinced the sites selected by NIAID are scientifically superior,” Pataki continued, pointing out that the state had pledged $80 million in matching funds, twice the amount required by NIAID.

    Emotions also ran high at the University of California (UC), Davis. Many had considered UC a strong contender, if only because the western United States currently doesn't have a single BSL-4 lab. “We really felt that the West Coast is very, very vulnerable to a bioterrorist attack,” says UC Davis Associate Vice Chancellor Lynne Chronister. But a fair geographic distribution was only one of the goals of the program, says Fauci.

    View this table:

    UC Davis had clearly flunked one other criterion, however: winning support from the surrounding community. Fearing that the lab might unleash dangerous pathogens or attract terrorists, the city council, mayor, and private groups in the town had spoken out against the project. In a last-ditch effort to save the plan, UC Davis earlier this year said it could build the lab elsewhere; six nearby communities would welcome the building, Chronister says. But by that time, it was too late to change the proposal. “You can't just say, ‘Oops, excuse me, we're going to build it somewhere else,’” says Fauci.

    Not that the other labs face smooth sailing. In Boston, several groups are opposed to the lab, which is to be built at the edge of the densely populated South End neighborhood. One, the Alternatives for Community and Environment, says it will file suit on behalf of 10 local residents, alleging that the building plan violates the Massachusetts Environmental Policy Act. Boston City Council member Chuck Turner has proposed an ordinance that would ban BSL-4 labs from the city. But BU's principal investigator, Mark Klempner, says he's working hard to gain the community's trust and is confident he'll see the project through.

    Meanwhile, the game's not over for this year's losers. Although it's unlikely that there will be another round of similar grants next year, there may be one in the year 2005, Fauci says. Pataki said he “will not stop fighting” to get a lab built. In Davis, says Chronister, university officials have yet to decide on their next move.

  2. RESEARCH OVERSIGHT

    Panel Seeks to Balance Science and Security

    1. Martin Enserink

    Increase oversight but keep big government out of biotechnology labs. The National Research Council delivered that message in a report released this week that aims to help prevent bioterrorism while preserving science's open culture.

    Laws passed in 2001 and 2002 already regulate possession and exchange of infectious agents, as well as some experiments. The risks should be reduced further, the panel says, but it recommends that the government expand existing regulatory systems and rely on self-governance rather than adopt intrusive new policies. Some key recommendations from the group, chaired by Massachusetts Institute of Technology geneticist Gerald Fink:

    • Seven types of risky studies would require approval by the Institutional Biosafety Committees (IBCs) that already oversee recombinant DNA research at some 400 U.S. institutions. These “experiments of concern” include making an infectious agent more lethal or rendering vaccines powerless. IBCs would refer difficult cases to the Recombinant DNA Advisory Committee, an existing national panel whose powers and resources would need to be shored up.

    • A new National Science Advisory Board for Biodefense would provide guidance for the regulatory system. Made up of researchers and security experts, it would be part of the Department of Health and Human Services.

    • The government should not attempt to regulate scientific publishing but trust scientists and journals to screen their papers for security risks, a task some journals have already taken up.

    “Most researchers would not find [the proposed rules] a great departure from what they're already doing,” says Columbia University bioterrorism expert Stephen Morse, who reviewed a draft. “It seems a reasonable compromise to me.”

  3. RUSSIA'S NUCLEAR CITIES

    Swords-to-Plowshares Program Suffers Meltdown

    1. Paul Webster*
    1. Paul Webster is a freelance writer based in Toronto.

    The United States has pulled the plug on a controversial program to help steer Russian weapons scientists into civilian work. Last month the U.S. government quietly opted not to renew a 5-year agreement with Russia on the Nuclear Cities Initiative (NCI), a U.S. Department of Energy (DOE) effort that has channeled $87 million into business development at three once-secret cities devoted to nuclear weapons R&D.

    Negotiations broke down last month after Russia failed to grant U.S. contractors blanket immunity from legal claims if something were to go awry during an NCI project. Although comprehensive liability provisions are a standard feature of other U.S. nonproliferation programs aimed at helping Russia secure its nuclear stockpile, a recent agreement on similar projects between Russia and several European countries features a shared liability approach. The Russian and U.S. governments “have a disagreement,” says NCI director Paul Longsworth. “The U.S. had to draw a line in the sand.”

    Some analysts, however, contend that by letting the agreement lapse, the Bush Administration has signaled its intention to kill NCI. “The Administration's inflexibility on the liability issue demonstrates an unwillingness to try to preserve the NCI program,” says J. Raphael Della Ratta of the Russian American Nuclear Security Advisory Council, a think tank based in Philadelphia and Washington, D.C. Alexander Pikayev of the Carnegie Endowment for International Peace in Moscow agrees. A senior DOE delegation in Moscow late last month, he says, “seemed to be almost celebrating [NCI's] demise.”

    Back to their drawing boards.

    Weapons scientists here in Snezhinsk and in two other cities devoted to nuclear R&D may soon have fewer civilian jobs to choose from.

    CREDIT: ALL-RUSSIAN SCIENTIFIC RESEARCH INSTITUTE OF TECHNICAL PHYSICS

    NCI has been dogged by criticism for much of its 5-year life. In May 2001, the U.S. General Accounting Office rebuked NCI management after determining that 70% of the initiative's funds were being spent in the United States. It also accused NCI of creating too few jobs or sustainable commercial ventures in the nuclear R&D cities of Sarov, Snezhinsk, and Zheleznogorsk. Russia's Ministry of Atomic Energy echoed those concerns, and members of the U.S. Congress called for the program's termination.

    In response, NCI officials pushed harder at business and job creation—efforts that seemed to be paying off. A computing center and other new facilities in Sarov “have opened up new job possibilities,” says Vitaly Dubinin, deputy director of the All-Russian Scientific Research Institute of Experimental Physics in Sarov. And U.S. Representative Curt Weldon (R-PA), an erstwhile NCI critic, is now a convert. “We need to keep our focus on the nuclear cities,” he told Science. “The NCI should be renewed.”

    Longsworth says that all 69 NCI programs now under way will continue, including a $9 million cancer diagnostic center in Snezhinsk that Energy Secretary Spencer Abraham approved on 19 September—3 days before the agreement lapsed. But no new projects will be funded. Longsworth says it's still possible that a compromise over liability provisions could be reached. Other possibilities, he says, include fusing some NCI components with other DOE efforts, such as the Initiatives for Proliferation Prevention, or integrating it into the G8's $20 billion Global Partnership Against the Spread of Weapons and Materials of Mass Destruction, which would allow other nations to share the burden of finding more peaceful pastimes for Russia's nuclear elite.

  4. COSMOLOGY

    Polyhedral Model Gives the Universe An Unexpected Twist

    1. Charles Seife

    A team of scientists from France and the United States has sifted through measurements from the Wilkinson Microwave Anisotropy Probe (WMAP) satellite to reach a surprising conclusion: The universe might be finite and 12-sided. Although the hypothesis is already being challenged, its proponents say it matches the known facts. “You really get a good fit” to WMAP data with a dodecahedron, says Jeffrey Weeks, a mathematician based in Canton, New York, who co-authored a paper in this week's issue of Nature laying out the evidence.

    A fit is precisely what physicists have been having for months over an anomaly in the WMAP data. In February, the satellite produced an incredibly detailed picture of the cosmic microwave background (CMB): the ubiquitous cold light that the universe gave off when it was about 400,000 years old. The sizes of hot and cold spots in the CMB revealed the age and composition of the cosmos (Science, 14 February, p. 991) but showed that on the very largest scales, there aren't as many temperature fluctuations as expected. If the shortage isn't a mere statistical fluke, it could imply that the universe has a finite size that doesn't leave room for the largest fluctuations.

    Earlier this year, some physicists speculated that a finite universe in the shape of a higher-dimensional doughnut called a 3-torus could account for the lack of large-scale structure. Now Weeks and his French colleagues have shown that a dodecahedral universe in a slightly curved space can also explain the anomaly. Imagine that you're sitting in the middle of a dodecahedron, a 12-sided object whose faces are made of pentagons. Opposite faces of the dodecahedron are associated; they are actually the same thing, so a spaceship zooming out one side of the universe winds up flying right back in the other. (This sort of thing is common in mathematics; for example, mathematicians often peel and flatten the two-dimensional surface of a torus into a rectangle whose opposite sides match up in an analogous way.)

    On a roll.

    In a 12-sided universe, objects framed in one pentagonal face appear, slightly skewed, in its opposite-side counterpart.

    CREDIT: (BOTTOM) J.-P. LUMINET ET AL., NATURE 425, 593 (2003)

    Different topologies for the universe suppress fluctuations of different sizes, so the CMB in a dodecahedral universe will look slightly different from the CMB in a less exotically configured one. Weeks and his colleagues tried a number of possibilities. “The plain old 3-torus fit isn't that precise,” says Weeks, but the dodecahedral space works rather well. “It's not exact, but it's pretty close.”

    If the dodecahedral picture is correct, then there are some odd consequences. Because opposite faces of a dodecahedron are rotated with respect to each other, a spaceship flying out one pentagon would acquire a roll as it flew in the other (see diagram). Light would behave the same way. As a result, Weeks says, “there would be a handedness to the universe.” More important for experimentalists, the large-scale shape of spacetime has to be slightly curved to get the sides of the dodecahedron to fit together, rather than flat as most cosmologists prefer. If the error bars on the WMAP data come down a bit more, the satellite might be able to spot the curvature if it exists.

    “The nice thing about their result is that it makes very testable predictions,” says Neil Cornish, a physicist at Montana State University in Bozeman. Nevertheless, says Cornish, other data already might belie the dodecahedral hypothesis. His team's analysis of the WMAP data, which will be submitted to Physical Review Letters shortly, shows no sign of duplicate features in the sky that would be the hallmark of a finite, periodic universe (Science, 22 June 2001, p. 2237).

    Even if the dodecahedral universe falls apart, as seems likely, physicists will still have to explain the puzzling lack of large-scale structure in the WMAP data. Cosmologists hope the anomaly will tell us whether we're bounded by a nutshell or whether we can count ourselves kings of infinite space.

  5. CLIMATE CHANGE

    Warming Indian Ocean Wringing Moisture From the Sahel

    1. Richard A. Kerr

    When drought hit the 5000-kilometer-long strip of marginally habitable land along the southern edge of the Sahara in the 1970s and '80s, the people of the Sahel suffered greatly. Soon some researchers were hypothesizing that intensive use of the land might have altered the surface of the Sahel enough to dry it out. The locals, although they have clearly used the land heavily, have since been absolved of fooling with the climate (Science, 31 July 1998, p. 633). Now researchers are pointing to another culprit—the warming Indian Ocean—but humans may still be to blame.

    The indictment of the Indian Ocean comes from two new climate-modeling studies that investigate the effects of the recent warming of tropical oceans. In a paper published online by Science this week (www.sciencemag.org/cgi/content/abstract/1089357), climate dynamicist Alessandra Giannini of the International Research Institute for Climate Prediction in Palisades, New York, and her colleagues report results from the first climate model to simulate accurately the history of Sahel rainfall. Earlier models simulating particular years of drought versus wet years had highlighted unusual warmth in tropical oceans—the Atlantic, the Indian, and even the Pacific. But Giannini and her colleagues took a more demanding approach. They simulated Sahel rainfall in their global model year by year from 1930 to 2000 while mimicking the way sea surface temperatures changed over that time.

    CREDIT: A. GIANNINI ET AL.

    In their model, the Indian Ocean's warming over the decades was the dominant driver of the drying of the Sahel, Giannini and her colleagues found. The model's greenhouse gas amounts were not changed over the 70 years, nor was the vegetation or any other surface property in or around the Sahel. Yet the model faithfully produced the long-term trend in Sahel rainfall: a slight dip around 1940, a rise to a peak in the early 1950s, a long decline into the 1980s, and a still-incomplete recovery in the 1990s. Run with no change in sea surface temperature, the model produced no trend at all. Tropical Pacific temperatures—the relatively rapid El Niño-La Niña cycle —accounted for much of the year-to-year variability of Sahel rain but not much of the long-term trend. The warming of the tropical Atlantic did play some role in long-term drying, but it was the Indian Ocean—which has warmed more than any other ocean basin—that drove most of the drying in the model. Because the model climate—even without any long-term land-surface changes—looks so much like the actual drought, Giannini says, the Indian Ocean appears to be the primary cause.

    Giannini's results “seem to show it's ocean sea surface temperatures that give a [Sahel rain] signal very close to nature,” says modeler Max Suarez of NASA's Goddard Space Flight Center in Greenbelt, Maryland. His group developed the model that Giannini used. Although “it's just one model,” he says, it seems to have been particularly successful because it realistically responds to an initial drying with additional drying.

    Now another model adds support to Giannini's conclusions. In a study recently submitted for publication, “we found that the Indian Ocean is probably the most important agent in driving decadal changes in Sahel rainfall,” says climate dynamicist Mojib Latif of the University of Kiel, Germany. Using a model developed at the Max Planck Institute for Meteorology in Hamburg, Jürgen Bader of the University of Cologne and Latif found that their model Sahel dried more when tropical seas were warmer during the past half-century than when they were cooler. When they changed sea surface temperatures one ocean basin at a time, it was the Indian Ocean that dominated. “The Bader and Latif experiments confirm the interpretation of Giannini that the Indian Ocean is indeed driving a Sahel drying,” says climate dynamicist Martin Hoerling of the U.S. National Oceanic and Atmospheric Administration's Climate Diagnostics Center in Boulder, Colorado.

    The link between the Indian Ocean and Sahel rainfall is only the latest ocean-drought connection. Earlier this year, a years-long drought across North America, southern Europe, and central-southwest Asia was linked to a temperature pattern in the tropical Pacific that was warm in the west and cold in the east (Science, 31 January, p. 636). In both cases, researchers have suggested that changes in sea surface temperature induced changes overhead in the energy released by tropical rain. That change in turn reached out across “atmospheric bridges” to shift distant atmospheric circulation, much the way El Niño does. The departure of the cold La Niña destroyed the warm-cold pattern in the Pacific, ending much of the globe-girdling drought, but the 50-year warming of the Indian Ocean may not be ending anytime soon. “People have put out the idea that it could be global warming” brought on by humankind, says Giannini, “but it's not at all tested. It's just an hypothesis.” But it's one that climate modelers no doubt will soon be testing.

  6. SCIENTIFIC PUBLISHING

    U.S. License Needed to Edit Iranian Papers

    1. Yudhijit Bhattacharjee

    The U.S. Department of Treasury has ruled that scientific journals based in the United States cannot edit papers submitted by authors from Iran unless they have the government's permission. The policy, described in a letter sent last week to the Institute of Electrical and Electronics Engineers (IEEE), stems from rules prohibiting U.S. organizations from engaging in trade with Iran. Although the trade embargo has been in place since 1997, the 1 October letter is the first time Treasury has spelled out how it would affect publishers.

    Editing is a “service” that requires a special license, notes the department's Office of Foreign Assets Control, which enforces trade sanctions. No license is needed for reviewing submissions, the letter states, or for publishing them if no revisions are made.

    IEEE officials, who plan to apply at once for a license, say they pursued the issue to clarify the matter for all publishers. “Once our license is granted, other scientific societies will have much less to do,” says Michael Adler, president of IEEE. But some societies are less than pleased with the outcome, which they see as based on a “nonsensical” view of editing. “The ruling shows a clear misunderstanding of scientific publishing,” says Irving Lerch, director of international affairs at the American Physical Society. “The central value of a technical paper lies in its content. The correction of syntax and grammar is of little consequence.”

    IEEE stripped its 1700 members in Iran of several benefits in January 2002 after deciding that providing these services could be illegal. Adler says the association plans to restore electronic access to its journals, which is exempt under the regulations, once it separates journal access from other Web-based membership services. The association's Iranian membership has dwindled to under 400.

  7. BIOTECHNOLOGY

    The Ultimate Gene Gizmo: Humanity on a Chip

    1. Elizabeth Pennisi

    Commercial genomics reached a landmark last week, and several companies are jostling to share the limelight. Affymetrix Inc. of Santa Clara, California, announced that it is now selling the first research device that contains a complete set of 50,000 candidate genes covering the entire human genome. The GeneChip, as this microarray is called, can be used to measure the activity of all known human genes in a biological sample. Meanwhile, another California company, Agilent Technologies Inc. of Palo Alto, has begun distributing its own human genome array as an experimental prototype, and since June NimbleGen Systems Inc. of Madison, Wisconsin, has been using yet another whole-genome setup to support a DNA-scanning service at a lab in Iceland.

    These arraymakers use a variety of techniques to attach minuscule dots of DNA onto glass slides, silicon wafers, or nylon membranes. When exposed to a mix of RNAs from a biological sample, each DNA latches onto the RNA that matches its sequence. The RNA carries a fluorescent tag, marking the place where it attaches. Based on the location and intensity of the signal, researchers can tell which gene is the source and how active it is.

    At a glance.

    Microarrays, such as Affymetrix's GeneChip (above), now include all known human genes.

    CREDIT: AFFYMETRIX

    Affymetrix has adapted a form of semiconductor photolithography to create arrays that are similar to electronic chips; NimbleGen incorporates photochemistry and digital mirror technology; and Agilent uses ink-jet machines. All have been shrinking the DNA-containing dots on their devices, thereby squeezing in more dots per array. For example, Affymetrix's first chips contained just a few thousand genes. More recently, the company developed a two-chip set covering most of the known human genes. The new version compresses the two chips into one and includes 6500 more genes. According to Stan Rose of NimbleGen, that company's array now covers 38,109 gene candidates. Agilent says its array will have more than 36,000.

    These achievements “will reduce the [amount of] time and effort required to do an experiment, reduce the expense, … and make the data more uniform,” says Joseph Ecker, a plant scientist at the Salk Institute for Biological Studies in La Jolla, California, who has helped pioneer whole-genome chips for Arabidopsis tumefaciens. Needing less RNA for an experiment can be critical, he adds, because sometimes researchers can isolate only tiny amounts of it.

    Whole-genome chips exist already for four other organisms: the yeast Saccharomyces cerevisiae, the nematode Caenorhabditis elegans, the fruit fly Drosophila melanogaster, and the gut bacterium Escherichia coli. They have made possible wholesale scans that turn up new gene modifications and variations, says Ecker. The same should prove true for the new human gene arrays. In short, says Ernest Kawasaki, a molecular biologist who runs the microarray unit of the National Cancer Institute in Gaithersburg, Maryland, “we've come a long way.”

  8. INFECTIOUS DISEASES

    SARS Researchers Report New Animal Models

    1. Martin Enserink

    WASHINGTON, D.C.—Scientists have reported three new animal models that could provide relatively cheap and practical ways to test drugs and vaccines against severe acute respiratory syndrome (SARS), the disease that erupted from southern China last spring but was stamped out by summer. Researchers at the U.S. National Institute of Allergy and Infectious Diseases (NIAID) said at a meeting here last week that they have managed to get the SARS virus to replicate in mice; separately, a team from the Netherlands says it has infected two bigger animals with the virus.

    During the peak of the SARS crisis last April, virologist Ab Osterhaus and colleagues at Erasmus University in Rotterdam reported that cynomolgus macaques infected with a newly discovered coronavirus developed a pulmonary infection resembling SARS in humans. That study provided proof that the new virus was indeed the culprit, as well as the first animal model. In Rotterdam and elsewhere, researchers are now studying SARS pathogenesis and testing candidate drugs in infected monkeys.

    But using monkeys poses ethical questions; besides, they're cumbersome and expensive animals to experiment with, especially under strict biocontainment standards. At a meeting last week, organized by the Institute of Medicine's Board on Global Health, NIAID's Kanta Subbarao said she had sprayed the SARS virus into the noses of mice and found that, although the animals didn't get sick, the virus started replicating inside their bodies—sufficient for an animal model. “Everybody is calling us to test their pet vaccine,” says Subbarao, who has submitted the results for publication.

    In a paper that has been accepted by Nature, meanwhile, Osterhaus reports that his group has infected two other species with SARS and found that the virus readily replicates in both. Osterhaus declined to reveal the two species pending publication, but he says they are more closely related to masked palm civets and ferret badgers—two species in which the SARS virus has been found in China (Science, 18 July, p. 297)—than they are to mice. The findings suggest that the virus may have a remarkably broad range of hosts, Osterhaus says.

    Subbarao's announcement was one of the few tangible steps forward reported during last week's meeting. With drug and vaccine studies in their infancy and the flu and cold season about to hit the Northern Hemisphere, many questioned whether overstretched public health systems will be able to cope if SARS reemerges. Summarizing his feelings after the meeting, National Center for Infectious Diseases director James Hughes said, “What I've heard doesn't make me sleep any better.”

  9. DEEP-SEA DRILLING

    Same Crew to Run New Program

    1. Richard A. Kerr

    Thanks to a budget squeeze on its U.S. sponsor, the future of scientific ocean drilling will look a lot like the past—at least for a few years.

    Last week the National Science Foundation (NSF) awarded the same team that has managed the 19-year-old Ocean Drilling Program a 10-year, $626 million contract to run its successor, the International Ocean Drilling Program (IODP). Initially, the new program—a joint U.S.-Japan project that also hopes to have European participation—will rely on the current drill ship, the JOIDES Resolution. The contract went to Joint Oceanographic Institutions Inc., which has teamed up with the Lamont-Doherty Earth Observatory of Columbia University and with Texas A&M University to run IODP.

    NSF's original plan was to either upgrade the Resolution or acquire another ship, says Bruce Malfait, head of the NSF marine geosciences section. Japan would finish outfitting and testing its behemoth drill ship Chikyu by late 2006 and join the United States in funding IODP, matching NSF's contribution over the decade.

    Plugging away.

    The JOIDES Resolution will resume scientific drilling next summer for a new international program.

    CREDIT: JOINT OCEANOGRAPHIC INSTITUTIONS

    But that plan went by the boards earlier this year, when NSF couldn't get approval from the White House to ask Congress for the $100 million or so needed for the acquisition and upgrade. Waiting another year to begin the project would have meant “a long drilling hiatus” until the middle of 2006, says Malfait, “which is probably unacceptable to the community.”

    Instead, an unmodified Resolution will return to scientific drilling next June in the northeast Pacific Ocean—its last ODP voyage ended last month—and continue 2-month drilling cruises possibly through fall 2005. If legislators grant it the money next year, NSF hopes to upgrade the Resolution or convert another ship by fall 2006, says Malfait.

    The only prospect for enhanced scientific drilling before then comes from Europe. The European Consortium for Ocean Research Drilling met earlier this month with Japanese representatives to discuss taking another drilling platform to the ice-covered Arctic Ocean as early as next summer as part of IODP.

  10. CELL BIOLOGY

    How Cells Step Out

    1. Jean Marx

    Some gaps and controversies remain, but cell biologists are beginning to develop a clearer picture of how cells move by remodeling their filaments composed of the protein actin

    From the amoeba crawling along a microscope slide to the neuron searching out a connection in the developing brain of a human embryo, cells have a remarkable facility for movement. Once a cell detects an appropriate signal—food, say, for the amoeba— it changes its shape, putting out a sort of thin, flat extension of the outer membrane that draws it toward the signal's source. Scientists peering through their microscopes have witnessed such shape-changing feats for decades.

    They've found that these movements require the cell skeleton, particularly filaments made of the protein actin, to constantly change—growing, shortening, and then growing again. Only recently, however, have cell biologists been able to develop a clear picture of the intricate signals and molecular changes that cells use to control this “remodeling” of their actin skeletons. “We've identified the key players needed for [cell] motility and the signal pathways leading to them,” says cell skeleton researcher Gary Borisy of Northwestern University School of Medicine in Chicago. “It's really galvanized the field.”

    Indeed, a grasp of cell motility is key to understanding everything in biology from embryonic development to immune system function and wound healing—all of which depend on cell migrations. It's also important for understanding the diseases that can result from the wrong kind of cell migrations. These include chronic inflammation, which results when an overactive immune response causes inflammation-promoting cells to keep pouring into and damaging a tissue, and cancer metastases, which occur when cancer cells move out of the original tumor and seed new tumors at other sites.

    Even infection by certain pathogenic bacteria and viruses depends on the pathogens taking over the cellular actin system to promote their own entry into cells. Understanding precisely how the process works might make it possible to disrupt the harmful forms of cell migration that cause disease.

    Bacteria show the way

    Cell biologists have known for more than 3 decades that cell movement depends on filaments consisting of molecules of a globular protein called actin that link together to form helical polymers. They knew from microscopic studies, for example, that actin filaments form inside the leading edge of a cell when it begins to slither over a surface. But those movements are triggered by a great variety of different external signals that act on receptors on the outer cell membrane. And that raised some big questions, says cell biologist Thomas Stossel of Harvard Medical School in Boston: “How do signals from the surface tell the cell to remodel actin into and out of filaments? And how are the filaments organized into three-dimensional structures?”

    In test tube studies, actin filament formation looked fairly simple. Early on, researchers had learned that actin filaments have two distinct ends, described as “barbed” or “pointed” because of the arrowhead pattern produced when they are “decorated” by staining with the protein myosin. (Myosin filaments partner with actin filaments to produce muscle contraction, but they're not required for cell motility.) Other studies revealed that actin monomers, each carrying a bound molecule of the high-energy compound ATP, add on the barbed end. At the same time, monomers with ATP that was converted to the less energetic ADP are removed from the pointed end.

    Cell support.

    The blue staining outlines the actin filaments on the leading edge of this cell. As indicated by the electron micrograph of a portion of a similar cell, those filaments are dense and highly branched.

    CREDIT: ADAPTED FROM T. M. SVITKINA ET AL., JOURNAL OF CELL BIOLOGY 139, 397 (1997)

    This process results in what biophysicists called “treadmilling” of the filaments. But cells can move rapidly when appropriately stimulated, and researchers “knew from the beginning that such treadmilling is very slow and probably irrelevant,” says Thomas Pollard of Yale University, who has been studying actin polymerization for many years. Thus, cells must have some kind of control machinery that responds to motility signals to produce fast filament growth.

    Over the years, cell biologists had identified numerous cellular proteins that appeared to be part of that machinery, but they didn't have a clear understanding of how they all fit together. That began to change about 5 years ago, aided by studies of bacterial pathogens, particularly Listeria monocytogenes.

    Listeria, which causes meningitis in pregnant women and people with poorly functioning immune systems, infects cells by tricking them into engulfing the bacteria. Once inside an infected cell's cytoplasm, the bacteria spread by traveling rapidly to its outer membrane and inducing the formation of projections that are then engulfed by another cell. Evidence that actin polymerization might drive their movement came in the late 1980s and early 1990s.

    Lewis Tilney and Daniel Portnoy of the University of Pennsylvania in Philadelphia made the first connection. They showed that when Listeria bacteria enter the cell cytoplasm, actin filaments polymerize around them, eventually forming long cometlike trails behind the bacteria as they move toward the cell membrane. Subsequent work by Tilney and Portnoy, in collaboration with Julie Theriot and Timothy Mitchison at Harvard Medical School, and also by Frederick Southwick, then at the University of Pennsylvania School of Medicine, and his colleagues showed that this actin tail formation was somehow moving the bacteria along. For example, the researchers found that inhibitors of actin polymerization stop the bacteria in their tracks.

    Listeria moves within the cell and from cell to cell by hijacking the host actin machinery,” Mitchison says. That's highly advantageous to the bacteria, because they can spread in the body without exposing themselves to destruction by the immune system. It also proved to be an advantage to cell biologists seeking to unravel the mysteries of cell movements. They thought that the actin polymerization triggered by Listeria might be similar to the actin filament formation that cells themselves use to move. In cells, for example, the barbed ends of actin filaments, where actin monomers are added, are located just under the membrane of the leading edge of a moving cell, whereas the pointed ends extend inward.

    Examination of the filaments growing from Listeria revealed a similar pattern; the growing barbed ends are adjacent to the bacterial cells being propelled through the cytoplasm. Consequently, researchers thought that Listeria and other bacteria that trigger actin polymerization in cells, such as Shigella, might provide simple systems for studying the process—and they were right. “Listeria is important because the folks working on that have been able to do some real biology,” says Pollard.

    Growing an actin filament.

    Once a WASP family member is turned on by a motility signal activating its receptor (red bar), it binds the Arp2/3 complex, thus activating the complex's ability to nucleate branched actin filament growth. A capping protein (orange) terminates that growth while another protein (cofilin) begins severing the filaments, releasing monomers that bind either the storage protein thymosin or profilin. Profilin replaces the monomers' ADP with ATP, thus readying them for another cycle of filament formation. This diagram shows filament growth from the barbed end, but some researchers think the Arp2/3 complex nucleates growth from the filament sides.

    CREDIT: ADAPTED FROM M.-F. CARLIER ET AL., BIOASSAYS 4, 336 (2003)

    Researchers tackled the problem from two directions. On the bacterium's side, Pasquale Cossart of the Pasteur Institute in Paris showed that a Listeria surface protein called ActA is needed to trigger actin polymerization in infected cells. Meanwhile, Matthew Welch, then a postdoc with Mitchison, and his colleagues were using a cell-free system devised by Theriot to search for cellular proteins required to initiate actin polymerization by the bacteria.

    In 1997, they came up with something called the Arp2/3 complex, which contains seven different proteins bound together. Pollard, with Laura Machesky, now at the University of Birmingham, U.K., and colleagues, had discovered the complex a few years before. At the time, its function wasn't known, but there were reasons to suspect that it might be involved in actin polymerization. For example, the Pollard team had shown that it is present at the leading edge of moving cells, and an analysis of Arp structure suggested that the protein might bind to actin filaments and nucleate filament growth.

    Further work showed that the Arp2/3 complex interacts with Listeria's ActA protein to foster actin polymerization. But although that explained how the bacteria trigger the process, a big question remained: What is the trigger for the cell itself? Machesky and her husband Robert Insall soon provided an answer. In 1998, they showed that a protein known as WASP—which when mutated causes the human genetic disease called Wiskott-Aldrich syndrome—interacts with one of the components of the Arp2/3 complex, as does a related protein called SCAR. In collaboration with Pollard's team, the Machesky group went on to show that this interaction fosters actin polymerization.

    At almost the same time, four other groups were coming to a similar conclusion from studies of other members of the WASP family, including the yeast version of the protein and N-WASP, so called because it was discovered in neurons. “Everybody got to the same place at the same time,” Pollard says. The result was intriguing because researchers knew that the WASP proteins were part of the pathways that transmit external motility signals to the actin system, but they didn't know how they worked. “The discovery connected the signaling pathways to the nucleation [of actin filaments],” Mitchison says. “It really broke open the field.”

    What apparently happens is that various incoming motility signals, acting through appropriate receptors on the cell surface, turn on enzymes known as Rho GTPases. Next, these enzymes activate a WASP family protein that binds to the Arp2/3 complex, thereby activating it. The complex then latches onto an existing filament, bringing in the first actin monomers and thus nucleating the growth of a new filament branch. This filament growth leads to a flat outward extension of the membrane, called a lamellipodium, that forms in the region where the cell picked up the motility signal and helps move the cell toward the chemical signal.

    About face.

    A pipette dispensing EGF (upper right in both panels) causes the mammary tumor cell, which had been moving to the left (top panel), to put out a lamellipodium and move toward the pipette (bottom panel).

    CREDIT: J. CONDEELIS/ALBERT EINSTEIN COLLEGE OF MEDICINE

    How actin filament growth provides the force for that cell movement is still unclear, although some researchers think that the elongating filaments simply push the membrane outward—something apparently made easier because of the way that Arp2/3 fosters actin filament growth. Single filaments are thin and weak, presenting what Borisy describes as a “major conceptual problem. How do you push [a cell] with a long, thin filament?” he asks. But work done a few years ago by Borisy, Tanya Svitkina, also at Northwestern, and their colleagues showed that the filaments at the leading edge of the cell are highly branched. This branching, now known to be produced by nucleation by the Arp2/3 complex, should create a much stronger filament network. “It's like pushing with a brush,” Borisy says.

    Stossel disputes this idea, however. His work shows, he says, that the branching produced by the Arp2/3 complex does not strengthen the actin network. He maintains that the strengthening comes instead from addition of another protein, called filamin A, that was discovered by his team 30 years ago. “Cells that don't have filamin can survive and change shape,” Stossel says, “but they don't crawl.”

    There is also disagreement on exactly how Arp2/3 produces a branched network of actin filaments. Many researchers, including Pollard and Borisy, think that the complex starts the growth of a new branch by attaching to the side of a filament. With Kurt Amann of the Salk Institute in La Jolla, California, Pollard had made movies of the growth of actin filaments. “We can directly watch [new filaments] form on the sides of old filaments,” he says.

    Others, including Marie-France Carlier of the CNRS Laboratoire d'Enzymologie et Biochimie Structurales in Gif-sur-Yvette, France, think that branching starts instead at a barbed end, with both the old filament and the newly initiated one growing simultaneously at the same rate. If so, both branches will be of equal length, whereas side branching will result in the two arms of a branch having different lengths. The Carlier team did in fact find that the mother and daughter branches have the same lengths.

    In addition, the cell terminates growth of actin filaments by covering the barbed ends with a “capping protein.” Such caps would presumably not be an impediment to side branching, but the CNRS researchers found that only uncapped filaments can grow. This indicates that the free barbed ends are needed for attachment of the Arp2/3 complex and actin monomers.

    While both camps are maintaining their positions, John Condeelis of Albert Einstein College of Medicine in New York City thinks that his experiments provide a middle ground between the two points of view. “We've watched the filaments grow,” he says, “and while Arp2/3 binds to the side of the mother filament, the binding is very close to the barbed end.” He suggests that this happens because the complex only binds to freshly added actin monomers, before they change shape following the conversion of ATP to ADP.

    However filament growth occurs, it's only temporary. The capping proteins are added to the barbed ends very quickly. That apparently prevents the filaments from getting so long that they lose their pushing power. After a slight lag, a protein called cofilin severs the actin filaments from the rear, releasing actin monomers bound to ADP. Then another protein, profilin, exchanges that ADP for an ATP, readying the monomers for a new round of polymerization—and the cell for another step forward.

    Although all this sounds pretty complicated, the core machinery for actin polymerization consists of just a few proteins: the Arp2/3 complex, a WASP family member for activating the complex, the capping protein, and cofilin. Indeed, a few years ago, Carlier and her colleagues showed that the proteins drive Listeria movements by adding just those purified proteins to a solution containing the bacteria and monomers of actin-ATP. “Among all the proteins in the cell, only four or five were needed to reconstitute movement,” Carlier says.

    More actin partners

    Although the core machinery for actin polymerization is relatively simple, it has a lot of helpers, including, for example, filamin A. In addition, recent evidence shows that Arp2/3 is not the only protein that nucleates actin-filament formation. Other proteins also have that ability, although they apparently act in different circumstances.

    Central character.

    The protein complex Arp2/3, shown here with its various components denoted by different colors, plays a major role in nucleating actin filament formation.

    CREDIT: R. C. ROBINSON ET AL., SCIENCE 294,1679 (2001)

    Some of this work comes from Condeelis and his colleagues, who have been focusing on actin polymerization in metastatic breast cancer cells. The Condeelis team had previously shown that when breast cancer cells become metastatic, they acquire the ability to migrate in response to epidermal growth factor (EGF), a change that helps them spread in the body. Recently, the Albert Einstein team has found that cofilin plays a key—and somewhat unexpected—role in the cell's chemotactic response to EGF.

    Most work has centered on the protein's role in disassembling actin filaments so that the resulting actin monomers can be recycled for new filament formation. But Condeelis and his co-workers, including former postdoc Maryse Bailly, who's now at University College London, have found that cofilin's filament-severing activity also comes into play during initiation of actin polymerization in response to EGF. For example, they found that inhibiting the protein with an antibody blocks the lamellipodium extension that would normally occur when metastatic cancer cells are tweaked with the growth factor. “By severing filaments,” Condeelis says, “cofilin creates free barbed ends and a large number of nucleating sites” for subsequent Arp2/3 action.

    Condeelis proposes that the results of cofilin activity depend on the condition of the cell where the protein is working. In cells that have been moving, most of the actin monomers have been used to make filaments, and in that case cofilin promotes filament disassembly. But a quiescent cell has a lot of actin monomer, and so cofilin promotes its polymerization by Arp2/3. “I think [Condeelis] is on the right track,” says Pollard. “Cofilin is important in helping cells that aren't moving get started.”

    In addition to the branched actin filaments produced by Arp2/3, cells also contain unbranched actin filaments. These include the so-called contractile ring that separates the two daughters produced when a cell divides. Exactly what nucleates formation of these unbranched filaments has been something of a mystery. But within the past year, several groups have shown that in yeast and in the mouse, members of a widespread group of cytoskeleton-organizing proteins called formins can do the job.

    Given the importance of actin filaments to the life of the cell and of the whole organism, it's perhaps not surprising that there is more than one way to promote their formation. But one thing is sure, cell biologists aren't going to run out of questions to ask about the process anytime soon.

  11. YOSHIHIDE HAYASHIZAKI PROFILE

    He's Writing the Book on the Mouse Genome

    1. Dennis Normile

    A Japanese researcher has come up with a better way to collect, analyze, and distribute mouse cDNA clones

    YOKOHAMA—It will never be a bestseller, and you won't find it on Amazon.com. But a book produced by Japanese genome scientist Yoshihide Hayashizaki seems destined to become a classic. It's like no other volume ever published—a textbook-sized tome containing 60,770 clones of mouse complementary DNA (cDNA), a comprehensive collection of the animal's protein-coding sequences. Researchers can simply punch the clones out of the page, dissolve them in water, amplify them with the polymerase chain reaction, and put them to use.

    The work is drawing rave reviews, even before it is “published” and distributed this fall by Hayashizaki's employer, the Institute of Physical and Chemical Research (RIKEN). “The concept is truly revolutionary,” says Claes Wahlestedt, a genomicist at the Karolinska Institute in Stockholm, Sweden. “It's an enormously powerful resource,” adds John Reed, a molecular biologist and president of the Burnham Institute in La Jolla, California. John Mattick, director of the University of Queensland's Institute for Molecular Bioscience in Brisbane, Australia, predicts that the encyclopedia “is a model that others may take up” to provide cheap, easy access to physical clones. And Carol Bult, a bioinformaticist at the Jackson Laboratory in Bar Harbor, Maine, says that Hayashizaki's early recognition of the importance of cDNA and his novel approach to sharing resources makes him “a visionary scientist and leader.”

    Make us famous

    Those leadership traits aren't obvious when you first meet the 46-year-old Hayashizaki. Frequent smiles have left laugh lines radiating from the corners of his eyes, and his sly sense of humor—Wahlestedt describes him as “an extrovert, especially for a Japanese” —can be disarming. For example, one conference he organized included a visit to a Zen temple. “I just thought we would all benefit from some meditation on the next step [for genomics],” he quips.

    But his easygoing manner is deceptive. “I think he's pretty driven,” says Paul Lyons, an immunogeneticist at the University of Cambridge's Institute for Medical Research. Hayashizaki denies being a workaholic, but he admits that science is his hobby as well as his vocation. He puts in long hours, and so does his staff: A recent meeting with a reporter began at 5 p.m. and ended at 9, at which point key members of his 100-person staff were still hard at work. “When he has an objective, he goes unrelentingly straight at it,” says Jun Kawai, a genomicist in Hayashizaki's group.

    Man about mice.

    Yoshihide Hayashizaki has delivered on his employer's hope that he would “make RIKEN famous.”

    CREDIT: D. NORMILE

    What Hayashizaki has been tracking for the past decade is mouse cDNA. His gene-cloning technique as a graduate student had impressed senior scientists at Osaka University, and he developed a new genome-scanning method at the National Cardiovascular Center Research Institute in Osaka. In 1992, RIKEN recruited the 35-year-old Hayashizaki as part of its efforts to rebuild its genomics program, which had been disbanded after a failed attempt to develop an automated sequencer.

    Hayashizaki decided Japan couldn't match efforts then getting under way elsewhere to sequence the entire human genome. So he proposed starting at the other end of the transcription process and focusing on cDNA, which is synthesized from the messenger RNA (mRNA) that codes for proteins. Obtaining cDNA would, in effect, allow researchers to work backward from actual gene products to try to identify the underlying genes in the genomic sequence. And the ubiquitous laboratory mouse seemed like the ideal organism.

    As he fleshed out his cDNA plans, he gained the confidence of RIKEN's managers, who were looking for a distinctive direction for their genome efforts. Then in mid-1994, they vaulted him over several more senior scientists and put him in charge of the institute's Genome Science Laboratory. “We thought he was a young man who would accomplish something,” says Masami Muramatsu, director of the Saitama Medical School Research Center for Genomic Medicine and a scientific adviser on genomics to RIKEN.

    “They told me to please do something that would be a contribution to global genomic efforts and make RIKEN famous,” Hayashizaki recalls. One year later, he unveiled the five components of his Mouse Genome Encyclopedia: a library of full-length cDNA clones, a database with their sequences, links of the clones to the mouse genomic sequence, expression profiles, and a protein-protein interaction database.

    Each step required a number of technological advances. For starters, current techniques degraded mRNA before the entire coding region was captured. So the RIKEN team had to develop new transferase processes that enabled full-length cDNAs to be cloned. In addition, most sequencing projects discarded their clones as soon as they were sequenced, using computer programs to assemble the data. But Hayashizaki wanted both the clones and their sequences, which meant keeping track of the connection. The result was what Hayashizaki calls “a pipeline for pumping out full-length cDNA data from mouse house to database.” Soon, both data and clones were flowing. By spring 2002, RIKEN had 60,770 clones and their sequences.

    The next step was to invite scientists from around the world to come to Yokohama and add functional data for each cDNA to the database. The Burnham Institute's Reed says that the clone library and the functional data are “extraordinarily complementary with the [mouse] genome sequencing effort. You really need one to interpret the other.”

    Scientists have already learned something that could change the way biomedical researchers go about their business. Reed says differences in the proteins involved in autoimmunity in human and mouse, for example, have revealed that “there might be caveats for how accurately a mouse model works for certain inflammatory diseases in humans.” Colin Semple, head of bioinformatics at the Medical Research Council's Human Genetics Unit in Edinburgh, U.K., says the data “have increased our knowledge of the repertoire of proteins involved in fundamental processes in the cell.”

    Hayashizaki expected such results from the outset. But the focus on cDNA is proving more fortuitous than he foresaw. It is now clear that genes are spliced in different ways to produce a variety of proteins with, perhaps, non-protein-coding RNA influencing or controlling the process. The entire transcription process is now poorly understood. “The RIKEN data is our first good, comprehensive look into it in mammals,” says the University of Queensland's Mattick. Mattick is now collaborating with RIKEN in a series of experiments that he hopes will show that these noncoding RNAs “are regulators and not transcriptional noise.”

    More results are on the way. In the past year or so, RIKEN has sent upward of 400 batches of clones, ranging from a few to the full set, to some 100 collaborating groups. Another several hundred clone orders have been sent out by Dnaform, a company that distributes clones to noncollaborating groups. (The company is involved in a broader patent dispute that prevents it from shipping clones to noncollaborating groups in the United States.)

    DNA publishing

    Distributing clones has long been a logistical nightmare. Currently, each batch of clones is packed in dry ice—100 kilograms for the full set—and the clones must be stored in freezers. So Hayashizaki and his group began looking for better methods soon after the mouse genome project was launched.

    The idea of “printing” DNA samples isn't new, says Kawai, but existing techniques used cardboard, which “didn't suit our book concept.” Instead, the RIKEN group developed its own stabilizers and tested different papers. The real challenge was to find a means of mass production. For the first sample book, displayed at conferences earlier this year, technicians used pipettes to transfer each clone to a page. RIKEN has since developed an automated printer with a robotic arm that dips an array of tiny cones into sample solutions in a standard 384-well plate and then stamps the samples onto the paper at a rate of three sheets per minute. Faster printers are under development.

    The new encyclopedia makes distribution and storage much easier. The Mouse Genome Encyclopedia can be set on a shelf and its clones made ready for experiments in just hours. And there are cost savings. Although RIKEN collaborators get clones for free, noncollaborating academic groups must pay $40,000 for the collection. Hayashizaki hopes to get the price for the encyclopedia “below $10,000, possibly to $1600.”

    In addition to printing 200 copies of the Mouse Genome Encyclopedia by next spring, Hayashizaki is weighing whether to print collections targeting cDNAs associated with particular tissues or certain phenomena, such as apoptosis. He would like to see this technology spread, through licensing or a spinoff company focused on printing DNA books. Other labs have asked for help in printing their own material collections, he says.

    Meanwhile, Hayashizaki's group is busy adding more cDNA clones to the library and using screening programs to determine expression profiles and protein-protein interactions. And next year, Hayashizaki expects to get initial funding from Japan's Ministry of Education for an ambitious genome network that would tie together large centers working on large databases and genomewide issues and small groups focused on specific diseases or developmental issues. Adroit sharing of resources and results should allow researchers to go beyond simply linking a gene to its phenotype to elucidating the details of the molecular mechanisms involved.

    Integrating genomic, biochemical, and cellular data is the next grand challenge in biology, says Mattick. Hayashizaki's team, he predicts, “will be one of the influential groups in the world wrestling with this issue.” And it's a good bet that Hayashizaki's progress will be an open book to the rest of the world.

  12. MOLECULAR MEDICINE

    NIH Dives Into Drug Discovery

    1. Jennifer Couzin

    NIH unveils an ambitious plan to create molecular libraries as a first step to finding potential new drugs. But is it feasible?

    Why would Elias Zerhouni want to quiz me about drug discovery? wondered Merck neurogeneticist Chris Austin after getting a phone call last year from the new director of the National Institutes of Health (NIH). After all, Austin reasoned, the painstaking process of dissecting which proteins make good drug targets and which synthetic chemicals affect them isn't something that normally excites an agency focused on basic biomedical science.

    But Austin soon learned that change is in the air. Last week Zerhouni unveiled a road map that contains several initiatives aimed at enlisting basic researchers in the war against disease (Science, 3 October, p. 28). And Austin, who joined NIH in January from Merck's lab in West Point, Pennsylvania, is one of those responsible for making it happen.

    It's a tall order. One question is whether NIH can balance free access to the data with sticky intellectual property issues. Another is whether academic scientists are well suited to tackling this research. Then again, if NIH can convince drug companies to pick up where academic science leaves off, the eventual windfall—new ways of understanding disease and powerful therapies to treat it—could be tremendous.

    “Outside people scratch their heads and wonder whether you can really pull this off,” says Glen Hanson, a former acting director of the National Institute on Drug Abuse (NIDA) and now a pharmacologist at the University of Utah in Salt Lake City (although he retains an affiliation with the institute). But “if we don't do this, then how do we fix what I perceive as a broken system?”

    An expensive gamble

    Hanson has seen many drug-development opportunities fall by the wayside. One reason is their poor—or poorly perceived—economic prospects. Companies “seem not to be terribly interested in devising therapeutics for cocaine addicts,” Hanson says wryly. The same applies to rare diseases and illnesses, such as tuberculosis and malaria, that disproportionately afflict developing countries.

    Targeted recruit.

    Chris Austin was hired from Merck to help launch NIH's effort to identify possible new drug compounds.

    CREDIT: NHGRI/NIH

    Another problem comes from the needle-in-the-haystack approach that kicks off drug development. This early stage, called drug discovery, involves matching a biological target—normally a protein that appears to spur a particular disease—with a chemical compound that disables it. With potentially millions of synthetic chemical matchups to test, pharmaceutical corporations often rely on so-called compound libraries of possible inhibitors for this phase. And they are generally averse to sharing them.

    These searches are expensive—taking up an estimated 5% of the $800 million it costs to develop a single therapy (a figure that includes failures along the way). And it's not research that NIH typically funds, says Philip J. Rosenthal, an infectious-disease specialist at the University of California, San Francisco, who is developing a malaria drug with GlaxoSmithKline, the global pharmaceutical company based in London.

    Shortly after Zerhouni was sworn in as NIH director in May 2002, Hanson discovered their shared passion for translating basic research into tangible clinical benefits. NIDA had recently launched a program for neurological drug discovery, along with the mental health and neurological disorders institutes. (A handful of other institutes have individualized drug-development or-discovery programs.) Over the next year, Zerhouni and others discussed how to extend this effort across NIH. The road map supplied that opportunity. And Austin, from his new perch at the National Human Genome Research Institute (NHGRI), supplied the know-how.

    Forty-two NIH staffers from 21 institutes helped draft NIH's drug-discovery initiative. Called the “molecular library,” it will make available to academic and government scientists the kind of compound libraries that, with some exceptions, have until now been available only to industry researchers. In planning the library, Austin was joined by Linda Brady, the chief of molecular, cellular, and genomic neuroscience at the National Institute of Mental Health (NIMH). The library's initial 500,000 chemical compounds—the total may eventually reach 3 million—are fewer than those at a drug company but far more than in academic labs. (An exception is Stuart Schreiber's 6-year-old Institute of Chemistry and Cell Biology at Harvard University, with 250,000 compounds.)

    Most of these compounds have some of the right stuff; for example, they might disrupt a key cellular process such as cell division or force a diseased cell to look more like a healthy one. But even compounds that perform well would need to be altered so they can treat disease without harming the patient.

    The most dramatic growth for NIH's molecular library will occur over the next 6 years. In that time, NIH plans to establish six centers—the first intramurally, and the rest outside NIH—to screen potential drug targets, such as proteins, against a library's raft of synthetic compounds. Although these centers will replicate parts of some existing libraries, such as Schreiber's, they will far outstrip academic screening centers—and, maybe eventually, some drug companies—in the volume of incoming targets they can handle. Anyone interested in testing a target or a compound must first pass peer review. Each screening center might have its own specialty, such as a specific disease area, says Austin, although the details are still being worked out.

    Costly search.

    Stuart Schreiber's Harvard lab features the sophisticated technology needed for modern drug discovery.

    CREDIT: SATOSHI AMAGAI/HHMI

    The plan also calls for basic research on chemical structures. A third, crucial aspect is improving robotic technologies. Austin recalls that Merck spent 13 years screening 3000 compounds for a single target for bipolar depression (none worked); he's convinced that speed will help define success for molecular therapy development. NIH officials decline to say how much the molecular library will cost, although they have requested $26 million for the 2004 fiscal year that began last week.

    Although the NIH effort will replicate some drug company work, Austin says there's a fundamental difference between the two. Pharmaceutical firms start with a protein target, notes Schreiber, whereas academics frequently embrace a cellular model of disease and perturb it, “allowing the system to reveal itself,” he says. “That alone will not yield a drug,” Schreiber adds. But “it pushes you in the right direction” toward a class of promising drug targets.

    Finding a niche

    Outsiders agree that the time is ripe for NIH to plunge into drug discovery. The good timing, says Steven Hyman, former director of NIMH and now Harvard's provost, comes partly from the blurring of disease boundaries. The sequenced human genome, meanwhile, has added an abundance of potential drug targets. We need to “make sure that our treatment-development efforts don't lag by a decade,” Hyman says.

    The fact that drug companies are barely dipping their toes into the “data dump” that is the human genome sequence gives NHGRI, which will house the intramural screening center, a chance to play a leading role in the new initiative. The molecular library also may help shield NHGRI from a recommendation in a June report from the Institute of Medicine that NHGRI be merged with another institute now that the genome has been sequenced (Science, 27 June, p. 2015).

    Austin initially doubted NIH's commitment to the molecular library. But having won approval for most of what he requested in a 6-year budget plan, he says he's now a convert.

    Not everyone's certain, however. “I think it's going to be a little more difficult than people might imagine” to do large-scale drug discovery, says Tadataka Yamada, chair of research and development for GlaxoSmithKline, citing its slow speed and high costs. Many NIH library compounds will likely be created from scratch, because it's unlikely that drug companies will turn over large portions of their libraries.

    Another tough challenge facing NIH will be to coax drug companies to pick up library compounds and transform them into drugs. NIH “is trying to walk a fine line” between providing free and open access and granting exclusive licenses, says Austin, particularly for smaller companies that may need the licenses most acutely. Francis Collins, NHGRI's director, says it's possible to do both, although the agency wouldn't make money off any license.

    Industry will also be watching closely to see how far NIH moves beyond basic research. The more the agency helps transform small molecules into usable drugs—say, by altering their chemistry to make them more targeted or enhance their metabolic activity—the stickier the intellectual property issues become, says P. Jeffrey Conn, who recently left Merck to head a program in translational neuropharmacology at Vanderbilt University in Nashville, Tennessee.

    For his part, Yamada questions whether GlaxoSmithKline would even bother pursuing specific compounds in the library. A pharmaceutical company might prefer to start over with a target that the library has studied and deemed promising, he says, and identify its own swath of compounds, because the likelihood that a single compound will stumble remains high.

    Another concern for companies and NIH alike is whether academic scientists are capable of pursuing drug discovery. The work requires close collaboration between biologists and chemists, a rarity in most universities. “That's a considerable problem,” agrees Austin.

    NIH hopes that education—possibly by bringing researchers to the Bethesda screening center for a week and teaching them how the library works—will boost participation. And although officials know that drug discovery and the academic community might at first make for awkward bedfellows, they don't see an alternative if they hope to fulfill their mission to conquer disease.

  13. ECOLOGY

    Freshwater Eels Are Slip-Sliding Away

    1. Richard Stone

    Eel populations worldwide are crashing; scientists don't know why precisely, and they can only guess at what it will take to save this beguiling fish

    CAMBRIDGE, U.K.—Eels are renowned for their endurance. Atlantic fry drift thousands of kilometers across open ocean, a months-long journey, to estuaries and rivers, where they can live to the ripe old age of 50 or more. But one of nature's premier survivors is facing its sternest test yet: Hammered by an array of threats that include overfishing, pollution, and climate change, populations of freshwater eels, also known as river eels, have fallen to catastrophic lows.

    The latest data suggest that European fry have plummeted as much as 99% since 1980, and their Asian cousins have declined around 90%. North American eels are suffering steep drop-offs as well. The alarming trend shocked researchers at a meeting last month in Tallinn, Estonia, of the International Council for the Exploration of the Sea (ICES), a Copenhagen-based body that advises the European Union on fish stocks in the North Atlantic. Many experts were unaware that freshwater eels are in such dire straits. “I was astonished that they didn't know it was that bad,” says Håkan Wickström of the Institute of Freshwater Research in Drottningholm, Sweden, who presented the disturbing numbers.

    Although experts suspected that eel populations have been eroding steadily since at least 1980, the animal's elusiveness has made it easy to rationalize that it's simply hard to count with confidence. Moreover, fishing hauls began to nose-dive only recently, as the slow-growing animal has been gradually fished out. Now “we realize we're seeing real declines,” says Willem Dekker of the Netherlands Institute for Fisheries Research in Ijmuiden, who heads ICES's eel assessment. But whether the eel can be saved in the long term, along with the livelihoods of roughly 25,000 eel fishers in Europe alone, is an open question. That's because the precise cause of the eel's misfortunes is the biggest mystery of all. “Nobody knows for sure why it's happening,” says Wickström.

    Part of the reason for the uncertainty over eel numbers is the fact that it leads one of the most opaque lives of any vertebrate. It was only a decade ago, for instance, that Katsumi Tsukamoto of the University of Tokyo discovered that Japanese eels (Anguilla japonica) appear to spawn in the vicinity of the Mariana Trench. The European (A. anguilla) and slightly smaller North American (A. rostrata) varieties are believed to converge on the warm waters of the Sargasso Sea south of Bermuda to spawn, because the smallest larvae of these species are found there. No adult eel, however, has ever been observed anywhere near the presumed spawning grounds.

    The eel's complex life cycle makes it all the more difficult to unmask the archvillain behind its declining numbers. The transparent, leaf-shaped larvae, or leptocephali, look so different from adults that it wasn't until the turn of the 20th century that they were identified as baby eels. These minuscule critters have countless predators, but they may also be falling prey to alterations in the Gulf Stream, which normally sweeps the leptocephali to Europe and North America. Even subtle shifts in the Gulf Stream linked to cyclical phenomena such as the North Atlantic Oscillation—seesawing changes in atmospheric pressure systems that redirect winds around the North Atlantic—may doom many to a watery grave in the Arctic, for example. Fluctuations in currents “seem to have made it more difficult for larvae to get to Europe,” says Wickström.

    On the road to nowhere?

    Alterations in the Gulf Stream may be preventing untold numbers of eel larvae from reaching coastal waters.

    CREDIT: UWE KILS

    Japanese eel larvae, too, may be vulnerable to oceanic vagaries. The number of survivors reaching eastern Asia appears to be acutely sensitive to shifts in the trade winds—“when they are blowing too strong or too weak,” says Tsukamoto. Local salt concentrations may also be a factor. Tsukamoto discovered that Japanese eels follow a north-south salinity gradient in the Western Pacific as a navigational cue to their spawning area. El Niño conditions, he says, nudge this gradient southward, possibly throwing the eels off course.

    Those lucky leptocephali that reach estuaries and rivers transform into elvers, or glass eels. These transparent juveniles are netted by the millions primarily because they can be raised in farms to satisfy massive consumer demand in Japan, where grilled unagi is a favorite dish. Glass eels are also likely to be falling victim to organic pollutants and dams that pinch off upstream habitat, researchers surmise.

    One critical knowledge gap is that scientists don't have a ballpark estimate for how many adult eels are spawning. In 1998, a team led by Tsukamoto and Hans Fricke of the Max Planck Institute for Behavioral Physiology in Seewiesen, Germany, used a submersible to try to pinpoint the Japanese eel's spawning area along the Western Mariana Ridge. But the researchers drew a blank at the seamount Tsukamoto believes the eels use as a cue to end their migration.

    Tsukamoto hopes to mount a return trip to the Marianas. In the meantime, his team has devised a radiotag for tracking eels that pops off and floats to the surface to transmit data by satellite. The researchers plan to test the tags next month when the eels begin their spawning migration. Efforts to tag Atlantic eels, meanwhile, are lagging: “The technique isn't there yet,” says Wickström.

    Although eel spawning remains cloaked in mystery, some have argued that farming fry may eventually reduce fishing pressure on elvers and aid a reintroduction program in the wild. A team led by Hideki Tanaka of the National Research Institute of Aquaculture in Japan announced last July that it had finally succeeded in raising leptocephali in captivity by discovering at last something the fry will eat: shark eggs, especially the yolks. The costs of captive breeding remain prohibitive, however, and many are skeptical. “I don't think breeding will ever solve the problem,” says Wickström. Dekker argues that habitat loss or other human-induced pressures may finish the eels off anyway.

    In the meantime, scientists are hoping to persuade governments to regulate eel fishing. “It's an absolutely uncontrolled industry” in Europe, says Dekker. The European Commission last week announced that it will draw up an emergency conservation plan early next year and called on member states to develop policies to sharply limit eel catches at all stages of the life cycle. Scientists are lobbying for similar measures in Japan, where illegal eel netting has exacerbated the decline. And later this month the East Asian Eel Research Committee will meet in South Korea to discuss ways to rehabilitate and safeguard eel habitat. Unless strong measures of this sort are taken soon, warns Dekker, “the future for the eels will be bleak.”

  14. INFECTIOUS DISEASES

    An Obscure Weapon of the Cold War Edges Into the Limelight

    1. Gretchen Vogel

    The tularemia bacterium sickened thousands during World War II and was stockpiled by the superpowers. Now researchers are racing to comprehend this potential bioterror threat

    BATH, U.K.—In the winter of 1999 in war-torn Kosovo, scores of people started coming down with headaches and sore throats that hung on much longer than a normal flu. In many cases, the patients' lymph nodes swelled to gigantic proportions and sometimes broke through the skin to form hideous open sores. It took half a year for scientists from the World Health Organization to make a surprising diagnosis: tularemia, a rare bacterial infection most often seen in North American rabbit hunters, villagers in central Sweden, and farmers in southern Russia. Tularemia succumbs readily to antibiotics, and by May the outbreak had subsided after 327 cases, none of which were fatal.

    But although the bug was vanquished, a disconcerting question remained. Tularemia had never been spotted before in Kosovo. Had someone deliberately spread the bacterium?

    This was not an idle fear. Japan tested the bacterium Francisella tularensis as a potential weapon during World War II, and the United States and the Soviet Union stockpiled it during the Cold War. Although those munitions are supposedly long gone, experts argue that tularemia remains a bioterror threat. It is one of the most infectious organisms known: Inhaling as few as 10 of the microbes can cause debilitating illness. A few grams of a virulent strain of F. tularensis dispersed in a city could quickly sicken thousands, says Anders Sjöstedt of the University of Umeå in Sweden.

    For rogue governments and terrorists, tularemia's allure is that of a weapon of mass disruption, not mass murder. This possibility, combined with the bug's checkered past, has made it one of the latest targets of the U.S. government's massive R&D effort to defend against bioweapon attacks. Civilian tularemia research, once a backwater, is now flush with cash, and new researchers are rushing in. The fourth International Conference on Tularemia, held here from 15 to 18 September, drew nearly 200 participants, more than twice as many as previous gatherings.

    There are plenty of puzzles for the recent converts to tackle. It's still unknown where the bacterium lives in the wild, how exactly it is transmitted, or even how it makes people sick. At the meeting, however, scientists reported tantalizing clues to the bug's virulence from its nearly finished genome sequence as well as new leads to track it in the environment and after it infects people.

    Rabbits and reservoirs

    Tularemia was first identified in California in 1911 and was soon recognized as the cause of epidemics in Russia and Scandinavia. In North America, the disease was associated primarily with hunters who skinned and ate infected animals; as hunting has declined, so has the disease. There are still several dozen cases of tularemia in the United States each year, however. One of the highest risk factors—blamed for recurrent outbreaks on Martha's Vineyard island in Massachusetts and for a cluster of cases this summer in Nebraska—is lawn mowing. Unsuspecting yard workers who run over a sick or dead rabbit can unleash tularemia-laden droplets into the air. Two of Germany's three reported cases in 2001 were a father and daughter who had eaten a rabbit the father had hit with his car.

    No ordinary gardeners.

    Scientists with the U.S. Centers for Disease Control and Prevention attempt to track the source of a tularemia outbreak on Martha's Vineyard, Massachusetts.

    CREDIT: RUSSELL ENSCORE/CDC

    Fortunately, the bacterium does not spread from person to person, but it has a wide repertoire of ways into the body. In some cases, doctors have attributed infections to tick or mosquito bites, although it is unclear whether the bacterium thrives in such insects. Tainted milk was blamed for an outbreak in Moscow in 1995; other outbreaks have been traced to contaminated wells. Epidemiologists have yet to pinpoint the source of the Martha's Vineyard cases. As for Kosovo, epidemiologists say a terror attack is an unlikely explanation. They now believe that a runaway population of rats and mice gorging on unharvested crops and contaminating human food and water supplies triggered the outbreak.

    One of the largest known epidemics sickened tens of thousands of soldiers and civilians during the battle of Stalingrad in the winter of 1942 to 1943. In his 1999 book Biohazard, Ken Alibek, a former top official in the Soviet bioweapons program, alleges that the Soviet army unleashed airborne tularemia bacteria on German troops during the battle, which was a turning point of World War II. But many medical historians doubt that claim, arguing that miserable conditions for the besieged German soldiers, rampant rodents, and contaminated water and food combined for an unprecedented but natural outbreak. “To my knowledge, there is no hard proof for the deliberate spread of these organisms,” says Sjöstedt. The Stalingrad outbreak followed the epidemiological pattern of previous outbreaks in the region, he says: “People were relying on water sources from rivers or lakes, and there were huge numbers of dead rodents.”

    Sjöstedt and his colleague Mats Forsman of the Swedish Defense Research Agency in Umeå are hoping to track down the source of the perennial outbreaks in central Sweden; nearly 500 people have fallen ill this year alone. Few Swedish patients report recent contact with rabbits or other small mammals, leading doctors to speculate that mosquitoes may be transmitting the bacterium. In Bath, Forsman noted progress in flushing out Francisella's Swedish retreat. It has been cultured from streams and lakes, but researchers suspect that its reservoir is a water-dwelling host, perhaps a protozoan. Forsman says that F. tularensis indeed grows in lab cultures of amoebae as well as several freshwater species of flagellates and ciliates common in central Sweden. But the team has yet to detect the bacterium in wild microorganisms.

    Genetic insights

    Researchers have made a bit more progress unraveling Francisella's genetic secrets. A consortium from Sweden, the United States, and the United Kingdom is nearly finished sequencing the genome of two strains: a weakened strain used in an experimental vaccine from the 1960s and a virulent one. Complementing that effort are new techniques for making mutant versions of the finicky organism to assess the importance of various genes. “Having tools to generate mutants makes a huge difference,” says Karen Elkins of the U.S. Food and Drug Administration (FDA) in Rockville, Maryland. “You can knock something out and test whether it still makes an animal sick.”

    Researchers are especially intrigued by a possible “pathogenicity island,” a DNA region that looks like it might have found its way into the genome relatively recently. The island includes several genes that appear to have something to do with the bacterium's ability to enter and grow inside other cells, Francis Nano of the University of Victoria in British Columbia, Canada, told those attending the meeting. And Igor Golovliov of Umeå University reported that he and his colleagues at the State Research Center for Applied Microbiology in Obolensk, a former bioweapons lab near Moscow, have modified a version of the live vaccine strain, stripping it of a protein in the region called iglC. The knockout bacteria are not as good at multiplying in cell lines, and they make mice only mildly ill. (For some reason, mice readily succumb to the vaccine strain, which doesn't sicken humans.)

    Sordid history.

    Francisella tularensis can cause open sores. It was weaponized by Japan, the United States, and the Soviet Union.

    CREDITS: (TOP TO BOTTOM) KARI LOUNATMAA/PHOTO RESEARCHERS INC.; PUBLIC HEALTH IMAGE LIBRARY/CDC

    One aim of such work is a smarter tularemia vaccine. Several strains that prompt immunity but don't cause disease were isolated in Russia in the 1930s. A mixture of those strains was brought out of the Soviet Union by a researcher with the U.S. Army Medical Research Institute of Infectious Diseases (USAMRIID) in the 1950s. Scientists at USAMRIID cultured the mixture in the lab and in mice, eventually recovering a single effective vaccine strain that was used to inoculate lab workers and military personnel for decades. But in 2001 the FDA halted use of the vaccine because of concerns about the stability and potency of the vaccine strain; there is currently no vaccine available outside Russia. Knowing how the bacterium causes severe disease would allow researchers to design a more reliable vaccine, says Elkins. “You need to know if the crippled bacteria are going to revert to wild type.” If manufacturers could test a strain for the absence of specific virulence genes, they could reasonably assure a vaccine's safety.

    Mining the bacterium's genome should also help speed the development of diagnostic tests. Because tularemia is so rare, it often goes undiagnosed for weeks. “No one thinks Francisella unless you're in central Sweden,” says Elkins. Standard tests involve culturing the bacterium or checking whether a patient has antibodies. But antibody tests work reliably only several weeks into an infection, and because the bacterium is so infectious, few labs are willing or able to handle it. Such tests “are 20 years out of date and are only applied very late in the disease—after doctors have tested for everything else they can think of,” Elkins says. “We now have genomics information that can be used within a day or two” in polymerase chain reaction tests for the bacterium.

    Some tularemia experts confess that a disease causing fewer than 50 deaths a year worldwide may not merit all the money and attention it's getting. Nonetheless, the effort to understand tularemia won't go unrewarded, argues Elkins: “There's new biology lurking everywhere”—not to mention a once and possibly future bioweapon threat.

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