News this Week

Science  10 May 2002:
Vol. 296, Issue 5570, pp. 936
  1. ANTITERRORISM

    USDA Closes Lab Doors to Foreign Scientists

    1. Martin Enserink

    To guard against terrorism, the U.S. Department of Agriculture (USDA) will no longer apply for visas to permit foreign scientists and students to work in its labs. The policy, which went into effect last month with little fanfare, is prompting an outcry from critics, who say it is an overreaction to legitimate concerns about national security that could weaken U.S. agricultural science. It also runs counter to pronouncements by high-ranking Bush Administration officials about the importance of international cooperation in science.

    “It could be a disaster,” says Bruce Alberts, president of the National Academy of Sciences (NAS). The academy's 150-member section on agricultural and environmental science has asked Alberts to intervene to undo the policy, which came as a surprise to presidential science adviser John Marburger. Speaking last week at the academy's annual meeting in Washington, D.C., Marburger said there would be no “edict” from the Bush Administration to limit the influx of foreign scientists and that his office had “educated” several departments about the importance of scientific exchanges. When Alberts asked him after his speech about the policy, however, Marburger said that he did not know about it but that, in his view, it was “not a very good idea.”

    Some 200 foreign scientists and students currently work in labs of USDA's Agricultural Research Service (ARS). Most are employed under so-called H1-B visas, which allow the temporary entry of scientifically or technically skilled foreign nationals. The new policy, which was relayed to ARS personnel in a 12 April memo by ARS acting Administrator Edward Knipling, allows researchers already in place to stay until their visas expire. But they will not be able to apply for extensions. In addition, the department will not sponsor any new visa applications. There will be no exceptions for scientists whose country of origin or research interests would appear to pose little risk. “It's just easier for us to do this across the board,” says a spokesperson for Agriculture Secretary Ann Veneman.

    Foreign researchers can still work in ARS labs if they are hired by other organizations such as universities. ARS labs with close ties to a university may try to go this route, says wheat researcher James Cook of Washington State University, Pullman, who spent 33 years at ARS, although he says it would mean “transferring the burden of the paperwork and the responsibility.” Foreign nationals who are permanent residents of the United States also will not be affected by the new policy.

    Fear factor.

    New policy makes it more difficult for foreign scientists to work at ARS labs such as this one in Beltsville, Maryland.

    CREDIT: SCOTT BAUER/USDA

    As the custodian of the nation's food supply, USDA has made terrorism prevention a top priority since 11 September. Its labs, some of which handle dangerous agricultural pathogens such as the foot-and-mouth disease virus, are obvious potential targets. The new policy follows the results of an investigation by the Department of Justice into seven pending visa applications sponsored by USDA; three of the scientists were deemed security risks. The department is also investigating several cases in which foreigners apparently used USDA-sponsored visas to enter the country but did not show up at their labs. The department has neither the authority nor the funds to carry out background checks, according to the spokesperson.

    But USDA researchers say the department is shooting itself in the foot by adopting a blanket policy that limits all foreign nationals' access to its labs. “It's going to make it more difficult to get good researchers,” says James Tumlinson, a team leader at ARS's Center for Medical, Agricultural, and Veterinary Entomology in Gainesville, Florida, which currently employs five foreign scientists. Researchers also argue that scientific exchange is important for international development, which could ultimately help prevent terrorism. “This is a throwback to a very conservative approach, and it sends the wrong message,” says Cook.

    NAS members who are agricultural scientists were “deeply distressed” during a meeting of the group 2 weeks ago, says Ellis Cowling of North Carolina State University in Raleigh, and they adopted a resolution urging Alberts to use his influence to change the policy. Likewise, members of the National Research Council's Board on Agriculture and Natural Resources have spoken with high-level USDA officials, says that panel's chair, Harley Moon of Iowa State University in Ames. The board is considering a study of foreign scientists' contributions to U.S. agricultural science.

    USDA critics believe that they also have U.S. Secretary of State Colin Powell on their side. Powell spoke a few hours before Marburger at the NAS annual meeting and told his listeners that scientific collaboration could foster peace and stability. He urged them to “help us to share know-how and promote science education all around the world.”

    The new policy follows an earlier USDA policy shift that makes it more difficult for foreign physicians to remain in the United States. Immigration law requires exchange students to return to their home countries for at least 2 years before they're eligible to apply for a new visa. But under a special waiver program, medical graduates sponsored by USDA or one of three other government agencies are allowed to stay in the United States if they agree to spend the time as a doctor in an underserved rural area. The department, which supported the program to foster economic development in agricultural communities, withdrew from it in February.

  2. U.S. CLONING DEBATE

    Hatch Signs On to Pro-Research Bill

    1. Constance Holden

    More legislators took sides last week in one of the most emotional scientific debates ever to hit the U.S. Congress as the Senate prepares to vote this month on anticloning legislation.

    Proponents of therapeutic cloning welcomed the support of two right-to-life conservatives, senators Orrin Hatch (R-UT) and Strom Thurmond (R-SC), on a bill that would outlaw human reproductive cloning but allow what researchers prefer to call nuclear transplantation. The measure, introduced last week by Senator Arlen Specter (R-PA), is the scientist-backed response to a bill sponsored by Senator Sam Brownback (R-KS) that would ban all forms of human cloning; Brownback's measure is identical to a bill the House of Representatives passed last summer. Senate Majority Leader Thomas Daschle (D-SD) has promised to schedule a vote before the Senate takes a 1-week recess on 24 May.

    Science lobbyists who favor the Specter bill claim that the political climate has improved markedly from mid-April, when both President George W. Bush and influential physician-senator Bill Frist (R-TN) came out strongly for the Brownback bill. “I think Hatch deciding to join the [Specter] bill has decisively shifted the debate in the research community's favor,” says Pat White of the Federation of American Societies for Experimental Biology.

    The penultimate phase of the Senate battle opened on 1 May, when Specter and 11 co-sponsors introduced a new version of a bill originally crafted by senators Edward Kennedy (D-MA) and Dianne Feinstein (D-CA). Hatch, although a strong opponent of abortion, has made it clear over the past few months that he's sympathetic to the scientists' side. But he hadn't committed to a specific bill until a press conference the day before.

    Major catch.

    Senator Orrin Hatch tells colleagues that he supports their cloning bill.

    CREDIT: TERRY ASHE/AP

    The new bill, called the Human Cloning Prohibition Act of 2002 (S. 2439), contains no substantive changes from the Kennedy-Feinstein measure. However, it has been updated with references to a report published early this year by the National Academy of Sciences that said human cloning, but not research cloning, should be banned (Science, 25 January, p. 601). The bill also makes a determined attempt to establish nuclear transplantation as the accepted term for the latter. “Human cloning,” that is, cloning to make a baby, is pronounced “unsafe, immoral, and unacceptable.” Hatch said at the press briefing that he doesn't believe test-tube embryos are humans, because “human life requires and begins in a mother's nurturing womb.”

    S. 2439 anticipates the development of artificial uteri by banning implantation of a cloned human embryo not just in a uterus but in “the functional equivalent of a uterus.” Otherwise, it follows the earlier bill: It establishes criminal penalties—up to 10 years in jail and a $1 million fine—for implanting a cloned embryo, calls for nuclear transplantation research to be conducted according to federal rules on scientific and ethical review of research, and specifies penalties of up to $250,000 for violations.

    Lobbyists count roughly a dozen undecided—or at least opinion-withholding—senators, with the rest of the 100 members equally divided pretty much along party lines. Last month the National Right to Life organization launched radio ads in eight mostly southern and midwestern states that refer to the opposition as “clone and kill” advocates. Ads in Rhode Island accuse the state's biotech firms of wanting to get rich patenting human embryos. Last week a new group called CuresNow began airing TV commercials featuring Harry and Louise, a fictional couple created by the health insurance industry in 1993 to attack the Clinton Administration's proposed health care plan. Today the pair are talking about finding a cure for their diabetic niece.

    Adding to the suspense are the Senate's arcane rules, which leave plenty of room for surprises. Daschle has not explained the rules under which the bills will be debated or whether amendments will be permitted. Although it only takes 51 members to pass a bill, 60 are needed to overcome delaying tactics by opponents.

    Any bill that passes the Senate will then have to be reconciled with the House's version (H.R. 2505). Although Congress is likely to face intense pressure to do something, the deep philosophical divide on the issue leaves little room for it to maneuver. A temporary moratorium on nuclear transplantation “is not a compromise,” says Kevin Wilson of the American Society for Cell Biology. “It might as well be Brownback.” Douglas Johnson of National Right to Life also dismisses the idea of half a loaf. “A ban just on reproductive cloning would be worse than no bill at all,” he says, warning that it would open the door to “human embryo farms.”

  3. U.S. APPOINTMENT

    Zerhouni Confirmed as NIH Director

    1. Jocelyn Kaiser

    Elias Zerhouni's nomination to head the National Institutes of Health (NIH) sailed through the Senate last week. Two days after a gentle hearing that only briefly touched on tough topics such as stem cell research, legislators confirmed Zerhouni's appointment on a voice vote. Only his swearing-in remains before he takes the helm of the $23.6 billion biomedical research giant.

    This close.

    Elias Zerhouni clears Senate, awaits NIH swearing-in.

    CREDIT: KENNETH LAMBERT/AP

    Zerhouni, a radiologist and executive vice dean at Johns Hopkins University School of Medicine in Baltimore, Maryland, told members of the Senate Health, Education, Labor, and Pensions Committee that “disease knows no politics” and that NIH “must always remain factual,” not “factional.” Only Senator Paul Wellstone (D-MN) pressed Zerhouni on whether he agrees with President George W. Bush's decision to limit federally funded research to 78 approved lines of stem cells. “You can do a lot” with those lines, Zerhouni replied. However, he hinted that he might eventually make the case for more lines: “If it becomes evident through this research that there are pathways to develop cures and so on, I'm going to be the first one to assemble that information … and share that with everyone.”

    He said the director's “most important role … is to reestablish morale and momentum” as well as to recruit NIH institute directors. NIH has been run by acting director Ruth Kirschstein for more than 2 years, and five institutes do not have permanent directors. Zerhouni said he's interested in fostering “crosscutting initiatives” and promoting “access to new technologies,” such as a DNA chip he brought along as a prop.

  4. EVOLUTIONARY BIOLOGY

    Timing Is Everything for Wolbachia Hosts

    1. Carl Zimmer*
    1. Carl Zimmer is the author of Evolution: The Triumph of an Idea.

    Wolbachia may be the most common infectious bacteria on Earth, but they are by no means ordinary. Among their accomplishments: They manipulate their hosts' sex life to boost their own reproductive success. Researchers have long wondered what sort of molecular trickery Wolbachia use to pull off this feat. Now they know at least one of their secrets: Like an auto mechanic, they can alter the timing of a key step of their hosts' reproductive cycle so that it either misfires or runs smoothly. The finding is “a really major advance,” comments Wolbachia expert John Werren of the University of Rochester in New York state.

    Wolbachia infect millions of species of insects, crustaceans, and other invertebrates, but they can't live outside their hosts' cells. To jump to the next victim, they infect developing eggs that will grow into adult hosts. Because males cannot pass the bacteria on in sperm, Wolbachia have evolved many sophisticated strategies to skew populations in favor of infected females (Science, 11 May 2001, p. 1093).

    Out of sync.

    Parasitic bacteria delay a key chromosomal movement in Nasonia wasps.

    CREDIT: J. WERREN

    On page 1124 of this issue, researchers at the University of California, Santa Cruz, offer the first good glimpse of how Wolbachia do this in a species of wasp known as Nasonia vitripennis. In these wasps, as in many insects, the sex of the offspring is normally determined by a bizarre process: If an egg is fertilized by a sperm, the progeny will be female, but unfertilized eggs will divide and develop into male embryos. Wolbachia play havoc with Nasonia's reproduction. When an infected male mates with a healthy female, the offspring will all be male, but if two infected wasps mate, the result will be a normal ratio of male and female offspring, all infected with the bacterium.

    Skewing the sex ratio in this way works to Wolbachia's evolutionary advantage. By making uninfected female wasps produce only sons, the bacteria reduce the number of uninfected female wasps in the population. That makes it more likely that Wolbachia from other females will get carried down from one generation to the next.

    Researchers have been unable to expose how Wolbachia perform such manipulations largely because they haven't had the right tools, according to co-author William Sullivan. “You couldn't answer these questions 5 years ago,” he says. “The technology just wasn't there.” In recent years, however, Sullivan and others have figured out how to create movies of a developing embryo that reveal the activity of its proteins and genes. N. vitripennis's eggs develop slowly, making them ideal for a starring role.

    Once the wasp's egg is fertilized, its chromosomes go through a complex choreography. The compartments that contain each set of chromosomes (called the pronuclear envelopes) move to a special location in the egg known as the metaphase plate, then the envelopes break down, allowing the chromosomes to escape and find their correct place at the plate. Only then can they be duplicated as the egg divides into new cells.

    Sullivan and postdoc Uyen Tram observed this process using dyes that attach to proteins that help destroy the walls of the male and female pronuclei. They found that Wolbachia tinker with the timing mechanism. In healthy wasps, both pronuclear envelopes were destroyed at the same time. But when the sperm came from an infected male, its pronuclear envelope started decaying a minute or more after the uninfected female's, preventing the enclosed chromosomes from arranging appropriately before the cell divided. The egg then divided as if it had never been fertilized, using only the chromosomes from the mother to develop into a male.

    Because Wolbachia block an infected male's chromosomes with a simple change of timing, they can bring the process into sync with an equally simple trick. When Tram and Sullivan fertilized an infected egg with sperm from an infected male, the walls of the female's pronuclear envelope also took longer to disintegrate. As a result, both parents' chromosomes were released late, so that both became part of the embryo's genome. Such infected wasps, in turn, grow up to do their bacterial puppet masters' reproductive bidding.

  5. MICROBIOLOGY

    New Method for Culturing Bacteria

    1. Katie Greene

    The well-trained Escherichia coli aside, the majority of bacteria don't take to the petri dish. Pull them out of their native environments, and microbe colonies seem to wither away with a terminal case of homesickness. Now, in work reported on page 1127, researchers at Northeastern University in Boston have managed to grow in the lab several strains of previously unculturable beach-growing bacteria—an advance that may provide a new means of exploring the vast diversity of microbial species.

    The key to their success: transplanting not just the organisms but their whole sandy neighborhood along with them. “If we recreate the natural conditions,” says microbial ecologist and team leader Slava Epstein, “the bacteria will never know they've been moved.”

    The inability to culture bacteria has dampened efforts to study microbial diversity. Whereas scientists have described roughly half of plants and animals and maybe a fifth of insects, “we know only a tiny fraction of a percent of the bacterial species,” says Abigail Salyers, a bacteriologist at the University of Illinois, Urbana-Champaign.

    Given the difficulty of culturing most microbes, researchers have mostly explored microbial diversity secondhand by hunting for RNA signatures in the environment that signal the presence of novel active genes. Although such information can point to the existence of microbial life, it doesn't help much when it comes to identifying and characterizing the organisms. “Nothing beats actually having the organism in culture,” says microbiologist Stephen Giovannoni of Oregon State University in Corvallis.

    Beach colonies.

    Beaches harbor a wealth of microbes now being cultured in the lab. The micrograph (bottom) shows a lab-grown colony.

    CREDITS: T. KAEBERLEIN

    Studying the organisms in culture can not only provide new information about microbial evolution and ecology but may also yield a host of useful compounds, such as antibiotics or enzymes with unexpected properties. For example, the Taq polymerase used in the polymerase chain reaction comes from a thermophilic bacterium.

    Because attempts to grow bacteria in standard lab cultures had so often failed, Epstein, microbial ecologist Tammi Kaeberlein, and molecular microbiologist Kim Lewis wanted to test their idea that a natural setting would supply the ingredients needed for the bugs to survive. To do this, the researchers collected samples of prime bacterial real estate on a sandy beach near the university's Marine Science Center on Nahant island north of Boston. The team cut blocks of sand that were 60 centimeters long, 30 cm wide, and about 15 cm deep. Although the bacteria reside on the surface, the depth was essential to maintain the same chemistry and oxygen conditions as at the beach, Kaeberlein says.

    Once each block of sand was in an aquarium, the team created chambers in which they hoped to mass-produce pure cultures of some bacterial strains. The chambers, which rested on the sand and were covered with seawater, had walls consisting of permeable membranes that allowed nutrients and other environmental chemicals to enter the chamber but prevented the bacteria from escaping.

    Bacteria in these chambers thrived, forming 300 times the number of colonies produced in conventional lab culture dishes. At least 20% of the organisms placed in the chambers formed colonies, compared to much less than 1% in the culture dishes, Epstein says. Using this technique, the researchers so far have isolated two previously unknown microbes, called MSC1 and MSC2 (MSC for Marine Science Center), and are investigating nine more.

    The work also provided an intriguing hint about why some microbes don't grow well. When Kaeberlein was cleaning out the refrigerator, she noticed that one supposedly pure bacterial strain that had surprisingly thrived in a culture dish wasn't pure after all. “There was more than one type of organism growing in there,” she says.

    When the researchers investigated, they found that MSC1 and MSC2 would grow in the petri dish only when both strains were present. Because the growth didn't seem to depend on the food supply, the team suggests that the bacteria may signal each other in the environment, transmitting some sort of “all's well” call that certain species need to hear before they'll proliferate. Such signals have been detected in the biofilms formed by many bacteria.

    Marine microbiologist Edward DeLong of Monterey Bay Aquarium Research Institute in Moss Landing, California, points out that the new method isn't going to solve all bacterial culture problems; many environmental niches aren't compatible with the diffusion-chamber format. Even so, he says, any advance in culturing microbes will help put more microbe species on the map.

  6. FISHERIES RESEARCH

    No More Surprises From Evanescent Squid

    1. Adam Bostanci

    CAMBRIDGE, U.K.—In a good year, fishing boats can haul almost 300,000 tons of squid out of the South Atlantic ocean. But this spring, many are returning virtually empty. In fact, 2002 is shaping up to be the poorest year for one of the world's largest squid fisheries—worth up to $1 billion in good years—since record keeping began in 1987. That's dismal news for squid fishers and calamari aficionados but no surprise to a team here at the British Antarctic Survey (BAS). Using a model based on ocean temperatures and currents, BAS researchers predicted the dearth of squid off the Falkland Islands.

    In contrast to many other fish stocks that are reeling, overfishing is not to blame for this year's pathetic catch of the Argentinean flying squid. The culprit is poor hatching and nursery conditions last year, says BAS biologist Paul Rodhouse, who developed the model with BAS's Claire Waluda. The model's success may help gird the industry for future off years, and it may serve as a template for predicting catches of other short-lived species, such as anchovies, in the South Atlantic and elsewhere.

    A key hurdle the researchers had to overcome in modeling the flying squid is its short life-span: only 1 year. The larvae hatch near the River Plate estuary off the coast of Argentina in July and then, after maturing, swim several hundred kilometers south to cooler, plankton-rich waters near the Falkland Islands. There they are caught by international fishing vessels using lines between February and June. Those that elude capture attempt to return to their breeding grounds, where they spawn and die. The fact that the population goes from larvae—“no squid at all”—to fully grown adults in only a few months makes sampling and predictions based on the previous year's catch difficult, says Robin Cook, a modeling expert at the Fisheries Research Services in Aberdeen, U.K. Indeed, last year's catch is mostly irrelevant, says Rodhouse, who compares the squid to the desert locust: “It doesn't make any difference how many you kill. When the environmental conditions are right, they return as a plague.”

    Here today …

    Researchers can now predict the ups and downs of the Argentinean flying squid.

    CREDITS: (TOP TO BOTTOM) SOURCE:BAS; C. GILBERT/BAS

    Rodhouse and Waluda zeroed in on sea temperature in the nursery area in July to predict the catch 8 months later. Last July, temperatures were 1.5° Celsius warmer than average, driving a shift in currents that swept larvae into the open ocean. “While they are small, they are at the mercy of the currents,” says Waluda.

    The duo predicted a catch of 73,000 tons this year, near the bottom of an annual catch that fluctuates wildly between 60,000 and 290,000 tons a year. With only a few weeks to go this season, the haul has barely reached 10,000 tons—a severe economic loss considering that the squid fetches $3000 per ton.

    The model's success may help fishery managers cope with future disastrous years by suggesting, for example, how many vessels should be licensed. In addition, this type of model could work for other fisheries—such as a squid fishery off the coast of South Africa—that are susceptible to the vagaries of currents, says Jean-Paul Robin, an expert on cephalopod fisheries at the University of Caen, France. In the meantime, managers at the South Atlantic squid fisheries are steeling themselves to this coming July's readings—and the omen they will offer.

  7. SCIENTIFIC COMMUNITY

    U.S. Science Academy Elects New Members

    The U.S. National Academy of Sciences last week elected 72 new members—11 women and 61 men. Among them was J. Craig Venter, the controversial leader of a private venture that last year completed a rough draft of the human genome. Some members were prepared for a challenge to Venter's election, but none materialized. The new members and their affiliations at the time of election* are:

    Harvey J. Alter, National Institutes of Health (NIH); Boris L. Altshuler, NEC Research Institute and Princeton University; Kathryn V. Anderson, Cornell University and Sloan-Kettering Institute; Barry C. Barish, California Institute of Technology (Caltech); Jacqueline K. Barton, Caltech; Adriaan Bax, NIH; Zdenek P. Bazant, Northwestern University; Philip A. Beachy, Howard Hughes Medical Institute (HHMI) and Johns Hopkins University School of Medicine; Manuel Blum, Carnegie Mellon University; John Bongaarts, The Population Council; Patrick O. Brown, HHMI and Stanford University School of Medicine; Carlos J. Bustamante, HHMI and University of California (UC), Berkeley; William C. Campbell, Drew University; Harvey Cantor, Harvard Medical School (HMS); Susan E. Carey, Harvard University; John E. Carlstrom, University of Chicago; Constance L. Cepko, HHMI and HMS; Vicki L. Chandler, University of Arizona; Francis V. Chisari, Scripps Research Institute; William C. Clark, Harvard University; George H. Denton, University of Maine, Orono; John Francis Doebley, University of Wisconsin, Madison; W. Ford Doolittle, Dalhousie University; Jennifer A. Doudna, HHMI and Yale University; Donald N. Duvick, Iowa State University; Richard A. Easterlin, University of Southern California;

    Charles T. Esmon, HHMI and University of Oklahoma Health Sciences Center; Richard Anthony Flavell, HHMI and Yale University School of Medicine; Joseph F. Fraumeni, NIH; Charles R. Gallistel, Rutgers University; Laurie H. Glimcher, HMS and Harvard School of Public Health; Michael F. Goodchild, UC Santa Barbara; Morris Goodman, Wayne State University School of Medicine; Richard H. Goodman, Oregon Health Sciences University; John P. Grotzinger, Massachusetts Institute of Technology (MIT); Willy R. G. Haeberli, University of Wisconsin, Madison; Charles B. Harris, UC Berkeley; Kristen Hawkes, University of Utah; John L. Hennessy, Stanford University; Vernon Martin Ingram, MIT; H. Jeffrey Kimble, Caltech; Eric I. Knudsen, Stanford University School of Medicine; Michael Levitt, Stanford University School of Medicine; Tom C. Lubensky, University of Pennsylvania; Alan G. MacDiarmid, University of Pennsylvania; Geoffrey W. Marcy, UC Berkeley; Gail Roberta Martin, UC San Francisco; Rowena G. Matthews, University of Michigan; David W. McLaughlin, New York University; James C. McWilliams, National Center for Atmospheric Research and UC Los Angeles; Richard E. Nisbett, University of Michigan; Saul Perlmutter, Lawrence Berkeley National Laboratory; Veerabhadran Ramanathan, UC San Diego;

    Mark A. Ratner, Northwestern University; Anatol Roshko, Caltech; Joshua R. Sanes, Washington University School of Medicine; Peter Sarnak, New York University; Stephen H. Schneider, Stanford University; Gerald Schubert, UC Los Angeles; Peter W. Shor, AT&T Laboratories Research; David O. Siegmund, Stanford University; Yum-Tong Siu, Harvard University; Patricia Gail Spear, Northwestern University Medical School; Bruce M. Spiegelman, HMS; Thomas Südhof, HHMI and University of Texas Southwestern Medical Center; Lawrence H. Summers, Harvard University; G. David Tilman, University of Minnesota, Twin Cities; Scott D. Tremaine, Princeton University; J. Craig Venter, The Institute for Genomic Research; Sheldon Weinbaum, City University of New York; Richard V. Wolfenden, University of North Carolina, Chapel Hill; Chi-Huey Wong, Scripps Research Institute.

    The following foreign associates were also elected last week:

    Juan Luis Arsuaga, Universidad Complutense de Madrid (Spain); Francisco De la Cruz, Instituto Balseiro (Argentina); Gerhard Ertl, Fritz Haber Institute, Max Planck Society for the Advancement of Science, Berlin (Germany); Lajos Ferenczy, University of Szeged (Hungary); Sergio Henrique Ferreira, University of São Paulo (Brazil); Jan-Åke Gustafsson, Karolinska Institute (Sweden); Brian John Hoskins, Reading University (U.K.); Thomas M. Jessell, HHMI and Columbia University College of Physicians and Surgeons (U.K.); Wolfgang Ketterle, University of Heidelberg and MIT (Germany); Ho Wang Lee, National Academy of Sciences of the Republic of Korea (Republic of Korea); Tak Wah Mak, University of Toronto (Canada); Gopinath Balakrish Nair, National Institute of Cholera and Enteric Diseases, Bangladesh (India); Tomoko Ohta, National Institute of Genetics, Mishima (Japan); David P. Ruelle, Institut des Hautes études Scientifiques, France (Belgium); David Schindler, University of Alberta (Canada).

  8. ANTHRAX SEQUENCE

    Useful Data But No Smoking Gun

    1. Martin Enserink

    Seven months after anthrax letters hit U.S. media and government offices, investigators still haven't nabbed a suspect—and the genome project launched in part to help them seems unlikely to provide a break either. An analysis of the genome of the strain used in the attacks, published online this week by Science (http://www.sciencexpress.org/), has yielded extra tools for fingerprinting the hundreds of different anthrax strains, but little in the paper suggests that it can help the FBI tie the attack strain to a specific lab.

    “I don't see how this could help us much,” says Barbara Hatch Rosenberg, director of the Federation of American Scientists' Chemical and Biological Arms Control Program, who has closely watched the federal investigation. But even without an immediate payoff, researchers at The Institute for Genomic Research (TIGR) in Rockville, Maryland, who conducted the research, say it provided experience in comparing microbial genomes that could be useful in future outbreaks.

    Last fall's letters contained spores of a Bacillus anthracis strain called Ames, which was collected from a dead cow in Texas in 1981, sent to the U.S. Army Medical Research Institute of Infectious Diseases in Fort Detrick, Maryland, and later forwarded for experiments to some 14 other labs.

    Because microbes mutate whenever they grow, it's possible that the current strain at each lab is a little different from the rest. And if one of them happens to match the attack strain, now dubbed Florida, it might lead to the bioterrorists. But until recently, genetic fingerprinting studies by Paul Keim's lab at Northern Arizona University in Flagstaff had looked at diversity at just several dozen markers, rather than the entire genome, and these had failed to discriminate among different Ames isolates.

    Criminal code.

    The DNA of the anthrax strain sent to a Florida publishing company has been sequenced.

    CREDIT: LUIS M. ALVAREZ/AP

    Now, TIGR's Timothy Read, Keim, and others have sequenced the entire Florida strain and compared it with the so-called Porton strain, whose genome TIGR had already sequenced. (A paper describing that genome is due out later this year.) Like most strains, the Florida strain contains two extra rings of DNA, called plasmids, that the Porton strain lacks, so the researchers compared their sequences with the plasmids from two other strains. In all, the team found 53 places where the Florida genome differed from the Porton strain and the two previously sequenced plasmids.

    But could these apparent genetic hotspots also help tell apart other, previously indistinguishable anthrax strains? To find out, the researchers took four Ames isolates collected from various labs; another Ames strain from a dead goat in Texas; and two non-Ames strains found in cattle. For each strain, they determined the exact sequence at each of the 53 markers.

    Although the markers could clearly distinguish the samples from dead animals, they did a poor job of discriminating among the four lab strains. One had 36 copies of the nucleotide A where others had only 35—an almost meaningless difference. Another had 37 copies at that same spot; but that strain also lacked one of the plasmids, making it easy to tell apart anyway. At all the other markers, the four lab strains and the Florida strain were identical.

    Theoretically, more variation may emerge when the Ames strains from all 15 labs are put through the same 53-marker test. But the scant differences found so far “offer only slim hope that something useful will come out,” says Rosenberg. Still, says Keim, the study shows that full-genome sequencing could be a useful forensic tool. And in cases such as bioterror crimes, the price tag—some $125,000 for a bug's genome—is hardly an issue: “A lawyer's sneeze costs more than that.”

  9. ARCTIC RESEARCH

    A Man and His Dog, Adrift But Equipped

    1. Michael Balter

    PARIS—An aimless wanderer usually can't be expected to produce good science. But French physician Jean-Louis Etienne—who in 1986 was the first person to reach the North Pole alone on foot—is wandering with a purpose. He's drifting on the Arctic ice, collecting a wealth of hard-to-obtain data for a half-dozen research teams across France.

    On 11 April, a helicopter dropped off the adventurer and his dog Lynet at the North Pole, along with what they will call home until July: The 9-cubic-meter Polar Observer, which resembles the Mercury space capsules from the 1960s. The gas-heated, hydrogen- and solar-powered capsule, fitted with a range of scientific instruments, is perched on an ice floe that wind and marine currents are driving across the Arctic Ocean.

    For the researchers lucky enough to have equipment along for the $1 million ride—financed by the Midi Pyrénées regional council, Gaz de France, Unilever, and several other public and private sponsors—the mission is a unique opportunity to corroborate satellite data and fill holes in their knowledge. For example, Gérard Brogniez, an expert on atmospheric optics at the University of Lille, and his colleagues have outfitted the capsule with photometers for measuring visible, infrared, and ultraviolet (UV) light. Part of the data will allow them to determine the concentration of aerosols such as nitrous oxides and water vapor in the lower atmosphere that absorb infrared rays and contribute to the greenhouse effect. And data on how much energy the ice soaks up will help researchers predict global climate changes that are influenced by energy gains or losses at Earth's surface. The intensity of UV light that reaches the surface, meanwhile, serves as a proxy for the ozone layer's thickness. Normally these measurements are made by satellite and verified by ground stations—something that is not generally feasible in the Arctic Ocean. “The ice pack is always moving, and you can't put expensive equipment there,” says Brogniez.

    Catch his drift?

    Explorer Jean-Louis Etienne will collect valuable data from the comfort of this high-tech igloo.

    CREDIT: CHRISTOPHE ENA/AP

    Etienne's polar peregrinations are also a boon to paleoclimatologist Denis-Didier Rousseau's team at the University of Montpellier. The group has tracked pollen from Mediterranean plants such as grapes and olive trees several thousand kilometers to Greenland. But “there are no data on the transport of pollen over the Arctic Ocean,” says Rousseau, who has provided the Polar Observer with a device resembling a weathervane equipped with pollen-trapping filters. Filling this gap, he says, should help refine models of global wind patterns. It also should aid work on the distribution of fossil pollen in sediments and at archaeological sites. “We must have a good knowledge of the present if we want to study the past,” he says.

    As Science went to press, Etienne and his canine companion were drifting south-southeast of the North Pole, having covered nearly a quarter of the estimated 500-kilometer journey. In a recent Web dispatch (http://www.jeanlouisetienne.fr/, in French), Etienne describes a typical evening inside the cozy capsule: “The blizzard is blowing this evening at 30 kilometers per hour. It plays the evacuation vents and air intakes of the Polar Observer like an organ. Nice and warm, I am going to be able to sleep peacefully.” If their nights and days continue uneventfully, in July Etienne and Lynet should end up near the coast of Greenland, where a Russian icebreaker plans to pick them up.

  10. ENVIRONMENTAL POLICY

    EPA Gives Science a Bigger Voice

    1. Jocelyn Kaiser

    Although a new Bush Administration initiative to clean up U.S. power plants has its critics, even some environmentalists laud the plan for targeting several pollutants at once and using a market-based trading scheme that makes pollution control cheaper. The “clear skies” initiative also has something that past policies often lacked: a research program to collect data on how these pollutants move through the environment.

    Environmental Protection Agency (EPA) science officials say the program is proof that Administrator Christine Todd Whitman is injecting more science into the agency's activities. Last week, Whitman used EPA's first-ever agency-wide scientific forum, complete with plenary talks and poster sessions, to highlight several steps she's taking to better integrate science and policy. She noted that she's beefing up the science team that helps develop regulations. She also plans to name Paul Gilman, the new head of EPA's Office of Research and Development (ORD), as her science adviser. The latter step is in part a reaction to legislation passed last month by the House of Representatives to create a science czar to oversee EPA research, an idea Whitman views as an unnecessary layer of bureaucracy.

    Sound science duo.

    Whitman and Gilman say they hope to boost EPA science.

    CREDIT: EPA

    Creation of the new position was one of several recommendations made 2 years ago by a National Academy of Sciences panel that studied the agency's practices. Gilman says EPA has already responded to this and other critiques since 1990, organizing its priorities by risk, balancing basic and applied research, improving peer review, and creating new postdoc slots and an extramural grants program. To bolster these efforts, Whitman has requested authority to pay higher salaries to lure academic scientists.

    Outside scientists agree that EPA science is moving in the right direction. “It's a whole lot better,” says environmental engineer Raymond Loehr of the University of Texas, Austin. But Loehr and other observers are skeptical about whether Gilman's double duty as science adviser would be as effective as appointing a deputy administrator for science and technology. “It's not the same,” says vice president for research Robert Huggett of Michigan State University in East Lansing, a former head of ORD under Clinton, who says it didn't mean much when EPA chief Carol Browner gave him the added title. It's tough for one person to “have time for both [jobs],” adds Loehr, a member of EPA's Science Advisory Board.

    One chronic restraint is the budget, which Representative Sherwood Boehlert (R-NY), a keynote speaker at the forum, points out “has been stagnant at best” since 1990. And this year is no exception: Whitman reportedly fought hard against a planned shift of ORD's $110 million extramural grants program to another agency, eventually retaining all but $10 million for graduate fellowships (Science, 29 March, p. 2345). The proposal, say Loehr and others, suggests that Whitman still faces an uphill battle to convince the Administration that science is central to EPA's work.

  11. GENOME SEQUENCING

    Public Group Completes Draft of the Mouse

    1. Eliot Marshall

    There was no military band or White House reception this time, but researchers celebrated the release of an important mammalian genome last week—that of a laboratory mouse called the “black 6.” The Mouse Genome Sequencing Consortium announced 6 May that it has put together a draft of the C57BL/6J mouse genome that is 96% complete, and it is making the data available for free on the Internet. Last year, Celera Genomics of Rockville, Maryland, announced that it had completed a draft of the mouse genome, but its data are available only by subscription.

    Two groups assembled the data independently: the Whitehead Institute Center for Genome Research in Cambridge, Massachusetts, and the Sanger Centre in Hinxton, U.K. Both teams used the “whole-genome shotgun” method—the technique Celera used to sequence both the mouse and human genome—which involves chopping up the genome into overlapping fragments, sequencing them, and putting them in the right order with the aid of powerful computers. Each base was sequenced seven times on average. The results suggest that this much-criticized technique works on mammalian genomes. The consortium adopted the Whitehead assembly for further analysis, according to a member, because it was “slightly better.”

    The mouse genome project began in 1999 with a series of pilot studies, then went into high gear at three big centers last year: the Whitehead Institute, the Sanger Centre, and the Genome Sequencing Center of Washington University in St. Louis, Missouri. Of the estimated $150 million spent so far, two-thirds came from the U.S. National Human Genome Research Institute (NHGRI). The Wellcome Trust, a British charity, provided the rest.

    Mouse timeline.

    The consortium plans to finish the sequence by 2006.

    SOURCE: MGSC/NIH

    The draft genome turned out to be “of surprisingly better quality than anyone had expected,” says NHGRI director Francis Collins. He attributes the good outcome to the quality of the raw data, the sophistication of the assembly algorithms, and the “fact that we were dealing with an inbred strain where you don't have to deal with polymorphisms.” The results are “significantly better” than for the draft human genome a year ago, according to Collins.

    The mouse consortium says it has identified 22,500 genes with high confidence, fewer than the 34,000 in the human genome. But Collins says the disparity arises mainly from differences in the way the genes are defined. He thinks the final count for both human and mouse will be “between 30,000 and 40,000 genes.” Molecular geneticist Eric Lander of the Whitehead Institute predicts that it will take less than 3 years to fill the gaps and completely finish the mouse.

    Mouse researchers have not yet studied the new genome closely, but a few have checked it out. Maja Bucan of the University of Pennsylvania in Philadelphia says the new draft “looks excellent.” Last year, she was having so much trouble making use of preliminary government-funded mouse sequencing data that she turned to Celera's database. But now she praises as “even more user friendly” an annotated version of the consortium's data released by the European Molecular Biology Laboratory (www.ensembl.org/Mus_musculus). Geneticist Neal Copeland of the National Cancer Institute has also been using Celera's database, but he thinks now that the consortium has finally caught up, Celera has lost its advantage.

  12. PLANETARY SCIENCE

    Safety Versus Science on Next Trips to Mars

    1. Richard A. Kerr

    Rover-driving scientists eager to “follow the water” on Mars next year are struggling with the tightening constraints of safety-conscious engineers

    ARCADIA, CALIFORNIA—The sound of huge posters peeling off the walls and flopping to the floor might have been a warning. The planetary geologists filling a hotel meeting room here near the Jet Propulsion Laboratory (JPL) had come to recommend two sites on Mars where the engineers of JPL should set down instrument-laden rovers in January 2004 on the next leg of NASA's program to seek out the planet's potentially life-supporting water. The scientists had duct-taped posters around the room portraying their six favorite potential landing sites—from what may be the exposed roots of ancient hot springs to a chasm harboring bizarre “fried egg” structures that make any geologist salivate.

    But JPL engineers were warning the scientists that the proposed landing sites had more problems than mere duct-tape failure. There was a real danger, they announced, that of the four sites under final consideration and two backups, only one would prove safe enough to risk a $300 million landing attempt. Although the scientists had already narrowed down 185 possible sites to four, the engineers warned that they had better start looking around for more safe places. Finding ones that are safe but not geologically boring was up to them. After 3 full days of discussion, the geologists had no choice: They made no final recommendations and began looking for alternative sites.

    There has always been tension between maximizing the chances for a successful landing on another planet and pursuing the most enticing science. An engineer's ideal landing site would be smooth, flat, and featureless. Geologists, on the other hand, love rocks. They naturally gravitate to boulders, cliff faces, and mountainsides. In the past, safety has largely dictated planetary landing site selection, including the three successful U.S. landings on Mars and most of the Apollo landings on (and takeoffs from) the moon. The engineers told the scientists what it would take to get there in one piece, and the scientists chose among the meager possibilities.

    The two Mars Exploration Rovers (MERs) scheduled for launch in mid-2003 seemed different. Well into the landing site selection process, limitations imposed by spacecraft design and the martian environment still allowed a variety of intriguing geologic targets. That is, until the engineers took a closer look. “Fear is the great motivator,” MER landing site engineer Mark Adler of JPL told the workshop in late March. And the stakes are high: MER will be the first attempt at a Mars landing after two failures at Mars, and it's a central part of a 15-year Mars exploration program. “We knew there are no perfect landing sites, [but] there are new data on the [martian] environment that bring all the sites into question,” Adler said. “The more we learn, the more we get scared. I'm concerned if we don't consider new sites, we may not end up with two acceptable sites.” Mars scientists are concerned that they may have to go to a “big, flat, ugly, and boring” site, as JPL geologist Matthew Golombek, co-chair of the MER landing site steering committee, described possible alternative sites.

    Limits of bouncing to Mars

    Getting down to four plus two sites proved to be a fairly straightforward application of site-selection procedures developed for the landing of Mars Pathfinder in 1997 (Science, 19 April 1996, p. 347). The MERs will arrive on Mars bouncing across the landscape cocooned in airbags, the same way the spectacularly successful Pathfinder lander did. At the time, this approach—a bulletlike atmospheric entry, a parachute descent, a 20-meter drop to the surface, and 2 kilometers of beach-ball action—seemed like a Rube Goldberg engineering demonstration unlikely to be repeated. But after the Mars Polar Lander mysteriously failed in its classic sci-fi approach of landing on the flaming tail of big retrorockets and three legs (Science, 10 December 1999, p. 2051), NASA went back to its successful Pathfinder approach.

    Although the more robust airbag landers can go where no Viking-style lander has gone before, they have their limits. The elevation of the landing site can't be too high or the parachute won't grab enough atmosphere to slow the lander. That eliminates almost all of the ancient highlands that cover most of the martian southern hemisphere. The slope of the land can't be too steep or the airbag-encased lander could have a dangerously long drop from its parachute or fail to fire its small retrorockets before impact. That rules out landing anywhere near the geologist-magnet slopes of a large impact crater or chasm wall. And rocks can still be a problem: If they're more than half a meter high, they could rip the airbag, so the lander must avoid areas more than 20% covered by rocks. These include tempting places where water erosion has scattered debris.

    Landing aside, the MERs impose their own limitations. Energized by sunlight, they must operate in a sunny 20° band of latitude near the equator or risk an energy crisis. Rovers wouldn't like plowing through deep dust, nor would geologists want to scrape off obscuring dust to get a look at rocks, so dusty regions of the dust-laden planet are out.

    TOP FOUR PROSPECTIVE MARS LANDING SITES

    Site #1: Terra Meridiani (hematite site)

    Pros: Hematite mineral could mark site of early martian life Cons: Practically perfect but for some possible wind

    Site #2:Gusev Crater

    Pros: An ancient lakebed where signs of life may be found Cons: Access to sediments not assured

    Site #3: Isidis

    Pros: Strewn with ancient rocks possibly weathered in early warm and wet climate Cons: Possibly windy

    Site #4: Melas Chasma

    Pros: Geologic variety possibly formed beneath a lake Cons: Unacceptably windy; steep slopes; sand dunes abundant

    CREDITS: KEES VEENENBOS

    What remained after this whittling down of landing site prospects was small—perhaps 10% to 15% of the planet—but still interesting. Geologically enticing prospects included Terra Meridiani (where orbital surveys detected the possible hot spring mineral hematite), several former crater lakebeds, water-washed chasms or canyons, and canyon outflow debris deposits. But the engineers weren't finished. Mission navigators can't guarantee delivery to a specific spot. They can only promise, with a certain probability, that the lander will come down within a long, narrow target area, the landing ellipse. Positioning landing ellipses is a great deal like fitting a cookie cutter on the dough while excluding any imperfections.

    The cookie-cutter exercise eliminated an early favorite of the geologists, the former crater lake Gale and its well-exposed layered sediments, because the roughly 20 kilometer by 160 kilometer ellipse wouldn't fit in without including overly steep crater walls. The landing ellipse also presents a problem for the Athabasca site, currently one of the backups. One of the top four coming out of the previous workshop, it was bumped down when Earth-based radar showed extreme roughness in that area, making roving likely impossible. But that roughness is probably confined to the lava flows at either end of the landing ellipse, not in the intriguing central channel, which was swept in recent geologic time by waters gushing from the great crustal cracks of Cerberus Fossae (Science, 30 November 2001, p. 1820).

    Might the engineers ease off on the size of the landing ellipse? geologist Alfred McEwen of the University of Arizona in Tucson inquired without much hope. McEwen is the leading proponent of the cramped Athabasca site. Landing ellipses as drawn are “3 sigma” size, promising a 99% chance of landing within them, he noted. Might not a 2 sigma ellipse suffice? In a word, no, replied Adler. A 99% ellipse is “baseline” that offers a “safe” landing, he said.

    Push comes to shove

    The geologists might have been feeling a bit cramped, but the real bad news was yet to break. The weather expected at the sites under consideration was looking iffy, the engineers reported. In particular, the proposed Melas Chasma site, which geologist Timothy Parker of JPL called the “best landing site on Mars” because of its weird “fried eggs” terrain that may have formed beneath 3 kilometers of water, would in all likelihood be too windy for an airbag landing. Winds kicked up by the midday sun would blow down the canyon at up to 50 kilometers per hour, according to new computer simulations.

    “Winds are now more of a concern than rocks and slopes,” observed Adler. “Melas is definitely not safe by this [criterion],” said engineer Wayne Lee of JPL. Both Gusev and fellow contender Isidis, just inside a great impact crater on an apron of ancient rocks washed down from the highlands, are “probably on the borderline,” said Lee. Even the hematite site—as flat and featureless a place as anyone has found—is now suspect. There's no topography there to help stir higher winds, but its relative darkness could mean extra solar heating and strong afternoon churning of the atmosphere.

    On the move.

    A Mars Exploration Rover checks out the local geology in an artist's dramatic version of the ideal landing site.

    CREDIT: JPL/NASA

    Ironically enough, the weather problem has cropped up because the engineers were told to address another safety concern. When Mars Polar Lander disappeared without a trace, it could send no word back about what went wrong; radio communication was impossible once it entered the atmosphere. NASA was determined not to let that happen again. But to have communications from the spacecraft during entry, parachute descent, and landing, the landing site must be visible from Earth for direct radio contact. That dictates a midafternoon landing, the warmest, windiest, most dangerous time of day on Mars. The Pathfinder landed at 3 a.m. Mars time, about the quietest time of day, but no one was thinking much about the effect of wind on the airbag landing system back then. Now engineers are running some of the first fine-scale simulations of martian weather ever made.

    Given that such cutting-edge, and rather uncertain, weather modeling was threatening to wipe out all the interesting sites, one geologist asked whether the requirement for communications during entry, descent, and landing might be relaxed, at least for one site. In a word, no, replied MER project manager Peter Theisinger of JPL: “Your discussion is biased by [thinking] the spacecraft will work, mine by [thinking] it won't. … I would love to push the envelope, [but] we are in a completely different game from Mars Pathfinder.” Moreover, he warned, “the fear factor will only increase [as we move] forward.”

    Taking stock

    The mounting safety concerns gave workshop scientists pause. “I'm really worried there aren't any safe sites,” said Melas Chasma advocate Parker. “We may have no choice but to eliminate [all] sites and go to the moon.” No one laughed. The enticing geology of Melas Chasma, more than once referred to as “the scary site,” had been ruled out by high winds, but it also has 40-meter cliffs and offers a 50-50 chance of landing on boring sand dunes. Backup Eos Chasma suffers from similar problems. The other backup, Athabasca Vallis, looks less promising now given the uncertain prospect of finding interesting flood deposits even if the lander avoids the impassable lavas and finds the channel.

    The rock-strewn fields of Isidis may or may not be swept by winds falling off the highlands (the computation-intensive modeling has yet to be done), but workshop participants found a full range of other safety concerns, from big rocks to steep slopes. More of a worry, perhaps, might be the uncertain scientific payoff in looking there for rocks altered in Mars's early warm and wet climate; at an early landing site workshop, only one scientist recommended Isidis as a site, whereas 14 voted for the hematite site.

    At the end of this workshop, Gusev crater ended up a distant second to the hematite site. All agreed that Gusev held a deep lake early in Mars history, but many wondered out loud whether a rover on the crater floor—limited to its 600-meter roving range—would see anything more than a vast and vastly boring plain rather than the outcrops of exposed sediment layers that geologists yearn for. The accessible surface might even just be volcanic ash blown into the crater.

    With Eos, Melas, and possibly Athabasca knocked out, Gusev and Isidis uncertain, and only the hematite site an apparent winner, participants left with plenty of work to do. Fortunately, project engineers had already convinced themselves that each spacecraft would have enough fuel to delay final commitment to specific landing sites until early next year. They also will be working on a system of small, horizontally firing rockets that could help the descending lander compensate for strong winds.

    The geologists, reluctantly, are looking farther afield. “Hematite is still the favorite by far,” says Golombek, but he and others are considering four new possibilities, including ones that would exceed the latitude and elevation limits. The safest of the safe might be deep in Isidis basin where the European Beagle 2 lander is targeted, away from slope winds and rocks. “No one is very excited scientifically about” that area, says Golombek. More than once during the workshop, geologists called the Beagle site “boring” because it lacks an obvious scientific target. Planetary scientist Philip Christensen of Arizona State University in Tempe called it “crummy.” He noted that less wind seems to mean more dust on the surface, and judging by surface brightness, which varies with the amount of dust, the interior of Isidis is dusty indeed. “You don't want to go there,” he concluded.

    But scientists will have to consider going to boring but safe places, if only to show NASA headquarters that going to scientifically exciting sites would be worth the risk. They'll also have to get more duct tape.

  13. PHYSICS

    The Ultimate Bright Idea

    1. Adrian Cho*
    1. Adrian Cho is a freelance writer in Boone, North Carolina.

    Physicists think they can make an x-ray source 10 billion times brighter than today's best, opening new horizons in biology, chemistry, materials science, and physics. But to do it, they have to pull off a grand trick without mirrors

    Some researchers are never satisfied with what they've got. In the past 2 decades, physicists have perfected the art of extracting intense beams of x-rays from synchrotrons—huge ring-shaped accelerators with circumferences of about a kilometer. Such synchrotron x-ray sources have revealed the structures of thousands of proteins, probed the intricacies of materials such as high-temperature superconductors, imaged tiny creatures only a millionth of a meter long, and advanced frontiers in a wide range of research fields. Yet even before they'd completed the latest synchrotrons, physicists dreamt of far brighter sources. Now, after a decade of planning, they are preparing to build their dream machines, x-ray sources 10 billion times brighter than synchrotrons. And to it make it possible, they're reinventing the laser.

    The machines are known as x-ray free-electron lasers (X-FELs), and they promise to reveal the structures of the most recalcitrant molecules, make movies of individual atoms bonding, and produce a state of matter similar to that found in the centers of planets. And that's just for starters, says physicist Stephen Milton of Argonne National Laboratory in Illinois: “There will be revolutionary experiments that we haven't even dreamt up yet that will be done on such a machine.”

    An X-FEL is far from most people's image of a tabletop laser, however, so those dreams come with a hefty price tag. An X-FEL consists of a linear particle accelerator a kilometer or more long that produces an exquisitely groomed beam of electrons. The beam from the “linac” shoots through an elaborate 100-meter-long array of tightly spaced magnets called an undulator, the magnetic fields of which cause the electrons to move from side to side and emit x-ray photons (see third figure below). If the undulator and the electron beam are tuned just right, the photons and wriggling electrons will interact to generate an unprecedented blast of x-ray laser light. Building the entire rig from scratch could cost as much as a billion dollars, so two groups are looking for a way to put one together on the cheap.

    Physicists at DESY, Germany's particle physics lab in Hamburg, plan to build an X-FEL alongside the lab's proposed particle physics collider, dubbed TESLA. By sharing parts and technology with the bigger machine, the DESY X-FEL should cost a relatively thrifty $470 million and could start cranking out x-rays for as many as 10 experiments in 2010. DESY researchers have demonstrated the basic principle in a test facility producing longer wavelength ultraviolet light. Physicists at the Stanford Linear Accelerator Center (SLAC) in Menlo Park, California, hope to be first off the starting blocks using an idle 1-kilometer stretch of the lab's existing 3-kilometer linac to build an X-FEL to serve four experiments. They hope to have the $220 million machine running by 2008.

    X-ray portrait.

    Scattered X-FEL photons (simulated at top) might enable researchers to reconstruct individual molecules such as this lysozyme (bottom).

    CREDITS: (TOP TO BOTTOM) DAVID VAN DER SPOEL; EDGAR WECKERT/DESY

    However, neither project is a done deal. DESY x-ray researchers are waiting for the German Science Council to give TESLA its blessing, says DESY's Jochen Schneider. “The government will come up with a decision at the end of 2003 or the beginning of 2004,” he says, “and we don't know what they will tell us.” The U.S. Department of Energy (DOE) has already committed to building SLAC's machine, but the agency has yet to give researchers the green light to start building. “They would like us to get started in 2005,” says SLAC's John Galayda, “but the question is how big a start.”

    Look, ma, no mirrors!

    Today's brightest x-ray sources, such as the European Synchrotron Radiation Facility in Grenoble, France, and the Advanced Photon Source at Argonne, wring x-rays from the electron beams circulating in synchrotrons. As a beam goes around, it emits photons much as a wet dishcloth flicks off drops of water if it is twirled from one end. To maximize the photon output, the electron beam runs through a series of undulators, each several meters long. Researchers have used the intense x-rays from synchrotrons to study matter ranging from cold viruses to molten iron under tremendous pressure. But experimenters would like still more intense and shorter pulses of x-rays, and synchrotrons cannot provide them because the bunches of electrons whirling inside them cannot be made sufficiently dense and short.

    However, researchers believe they can obtain far brighter x-ray pulses with a clever rethink of a device called a free-electron laser, which was invented in the 1970s by John Madey and colleagues at Stanford University. Madey, now at the University of Hawaii, Manoa, showed that the photons produced in an undulator can induce the electrons to emit still more photons. Such “stimulated emission” is the key to making a laser. To do so, physicists place mirrors at each end of the undulator. These trap some of the light so that it bounces back and forth, stimulating the production of more photons from subsequent bunches of electrons as they circulate through. Researchers already use free-electron lasers to produce beams of longer wavelength light. But for decades, an x-ray free-electron laser remained out of reach because it would require a very dense electron beam and because there are no simple workable mirrors for x-rays.

    Then in the early 1980s physicists in Russia, Italy, and the United States figured out how to do away with the mirrors. Photons emitted in an undulator essentially travel along with the electrons, which are moving very close to the speed of light. As the photons accumulate, they jostle the electrons, slowing those with slightly more energy and accelerating those with slightly less. If the undulator is very long, these interactions corral the electrons into a series of evenly spaced “microbunches” that move in synchrony and produce far more photons all moving in quantum-mechanical lockstep. Thus a wave of x-rays accumulates as the electrons make a single pass through the undulator.

    Researchers dubbed the phenomenon “self-amplification of spontaneous emission”—abbreviated SASE and pronounced sassy—and Claudio Pellegrini of the University of California, Los Angeles, likens the harmonizing interplay between x-rays and electrons to the effects of a musical conductor on human voices. “Instead of a big room with everyone talking, you have a choir,” he says. By coaxing the electrons to radiate in unison, SASE boosts the output of an undulator by a factor equal to the number of electrons in the beam—which can be as high as 10 billion.

    But to make SASE work, researchers still needed much better electron beams. Those became available in the late 1980s, thanks to the efforts of Richard Sheffield and colleagues at Los Alamos National Laboratory in New Mexico, who developed a better electron injector for linacs. The Los Alamos researchers placed a metal target inside an accelerator cavity and blasted it with a pulse of ordinary laser light. That kicked up a cloud of electrons, which was immediately sucked up into a dense beam by the accelerator before the like-charged electrons had a chance to push themselves apart. The result was dense, short pulses of electrons with less tendency to spread.

    All together now.

    In an X-FEL, accumulating photons herd electrons into microbunches that radiate in unison, hugely amplifying x-ray output.

    ILLUSTRATION: A. STONEBRAKER

    When researchers put these two technological advances together, they realized they could make a SASE x-ray laser out of a linac, says SLAC's Herman Winick. In 1992, he and colleagues at SLAC began planning to use the lab's existing linac as an X-FEL, which they dubbed the Linac Coherent Light Source. A year later, DESY physicists incorporated an X-FEL into their design for the TESLA collider. Since then, researchers at several laboratories have demonstrated SASE at longer ultraviolet wavelengths, and DESY researchers have even begun experiments with their SASE laser, which pumps out photons with wavelengths of 80 nanometers. Researchers in Japan, Italy, Germany, and the United Kingdom have also proposed SASE machines that would produce longer wavelength soft x-rays.

    A new scientific landscape

    To justify building such a machine, researchers have been trying to predict what they'll be able to do with it. And although this wasn't entirely obvious at first, physicists now believe that an X-FEL will open entirely new fields of research, especially if they can get down to wavelengths of about a tenth of a nanometer and pulse durations of 1/10,000 of a nanosecond. “I think we will reach a new scientific landscape where no one has done experiments before,” says DESY's Thomas Tschentscher.

    For example, pulses of 1/10,000 of a nanosecond would be shorter than the time it takes for individual chemical bonds to change. Moreover, the x-rays could have wavelengths comparable to the lengths of such bonds. This should make it possible to study the activity of individual bonds within molecules, Tschentscher says. By taking strobelike snapshots of a molecule as it reacts to some stimulus, researchers could make a movie of its behavior.

    The very short, intense bursts of x-rays might also enable researchers to determine the structures of important but uncooperative biological molecules, says Janos Hajdu, an x-ray crystallographer at Uppsala University in Sweden. To determine a molecule's structure, researchers usually shine x-rays on a crystal; the multiple copies of the molecule produce a scatter pattern that reveals its shape. Some molecules, however, refuse to form large crystals. But a single blast from an X-FEL could shower a tiny sample—perhaps just a single molecule—with enough x-rays to reveal the molecular structure, just before it blows the sample to bits, Hajdu says. “It could allow you to use tiny samples because it is so intense,” he says, “and because it is so short, the atoms don't have time to move.”

    X-rays from an X-FEL could also produce a state of matter similar to that found in centers of planets, called “warm condensed matter.” Such matter has the density of a solid but is heated to temperatures of about 10,000 kelvin, which are more typical of an ionized gas or plasma. The x-rays from an X-FEL could produce this type of matter by heating a sample so rapidly that it doesn't have time to expand. X-FEL studies of warm condensed matter should provide new data for astrophysicists studying planet formation and for engineers and physicists developing laser-induced nuclear fusion, says physicist Dick Lee of Lawrence Livermore National Laboratory in California.

    For the moment, though, all these studies remain thought experiments, as researchers await the political and financial decisions that will determine when the first X-FELs shine. DESY's X-FEL, for example, is currently tied to the fate of TESLA, Europe's bid for the next international particle physics experiment after the Large Hadron Collider now under construction at CERN in Switzerland. Japanese and U.S. researchers are working on rival linac designs, and particle physicists worldwide will have to pick one before any money arrives (Science, 27 July 2001, p. 582).

    But SLAC's Linac Coherent Light Source already has DOE's backing, says Patricia Dehmer, DOE's director of basic energy science. SLAC researchers should receive $6 million in 2003 to plan the construction of the machine, she says, but “it's premature to say when it's going to be commissioned.”

    Some researchers worry that in some regards the scientific potential of X-FELs is being oversold. For example, Richard Henderson, a structural biologist at Cambridge University, U.K., says that the first X-FELs won't be able to determine the structures of single molecules any better than an electron microscope can when a sample is frozen to slow radiation damage. Henderson says that, overall, X-FELs have great potential and that one should be built. “But,” he says, “what you mustn't do when you're asking for a lot of money is overstate your case.”

    And even x-ray physicists say there are still challenges to be met in building the machines. For example, to make an X-FEL work at wavelengths of a tenth of a nanometer, researchers must be able to control the position of the electron beam to within 20 micrometers over the entire length of the undulator, says DESY's Joerg Rossbach. They will also have to double the current in their beams while reducing the beams' size and tendency to spread by a factor of 2. “We know how to do this,” Rossbach says, “because we understand the underlying mechanism and we understand the technology.”

    Despite the scientific and political challenges, physicists are confident that their turbo-charged x-ray sources will be well worth the money and years of effort. “I personally believe it will be a revolution,” Rossbach says. And just maybe that will be enough to satisfy the physicists—at least until they come up with an even brighter idea.

  14. EVOLUTION OF DEVELOPMENTAL DIVERSITY

    Evo-Devo Devotees Eye Ocular Origins and More

    1. Elizabeth Pennisi

    COLD SPRING HARBOR LABORATORY, NEW YORK—From 17 to 21 April, evo-devo researchers met here for the Evolution of Developmental Diversity meeting to discuss how environment and quirks in development prompted the branching of the tree of life.

    Did Eyes Come From Microbes?

    In the mid-1990s, developmental biologist Walter Gehring came up with a heretical proposition: Eyes evolved only once. The idea was a hard sell. Because eyes are ubiquitous and come in vastly different varieties, most evolutionary biologists assumed that they arose independently many times. Now, Gehring has come up with an even more eye-popping suggestion: The original eye belonged to a microbe that later became a chloroplast, a subcellular center of photosynthesis best known for fueling growth in plants.

    “It's a wild idea,” says Richard Behringer, a developmental biologist at the University of Texas M. D. Anderson Cancer Center in Houston. If true, “it would be fantastic,” adds Nipam Patel, an evo-devo researcher at the University of Chicago. But he and others have their doubts.

    At the meeting, Gehring of the University of Basel, Switzerland, described the thinking behind his new view of eye evolution. His proposal that eyes evolved only once rests on his 1995 discovery of a gene called Pax-6 that is involved in eye formation in fruit flies, mice, and humans. Since then, he and others have been shaking the tree of life in search of more versions of this gene.

    It has turned up in some 20 species; even primitive ones, such as sponges, have precursor versions of the gene. Each new find has convinced him that his proposition is correct. However, the notion remains controversial—indeed, it met with some opposition at the meeting—in part because it's hard to imagine how a primitive eye from a common ancestor could lead to the great diversity seen today. So Gehring has been looking at the simpler animals for clues to support his theory.

    He has found Pax-6 in Planaria, primitive flatworms that can regenerate their bodies. And he has used a technique called RNA interference (RNAi) to demonstrate that the gene is involved in the animal's eye formation. He reported at the meeting that if he interferes with Pax-6 function when a planarian is growing back a severed head, “it can regenerate the brain, but it can't regenerate the eyes.” Once the RNAi effect wore off, eyes appeared. The same proved true in eye regeneration in ribbonworms.

    Eye to eye.

    This schematic of the eye of an obscure species of dinoflagellate reveals a complexity akin to that of our own eyes.

    CREDIT: MARIE-ODILE SOYER

    Gehring hadn't really considered an even more primitive origin for eyes until a French colleague sent him a 40-year-old Ph.D. thesis that described an obscure dinoflagellate—a single-cell plankton—that has an eye “basically like a human eye and could focus light,” Gehring said. This eyespot, which is presumably derived from the dinoflagellate's chloroplast, has a lens, protective pigments, and a stacked layer of membranes akin to a retina.

    Over the past decade, many evolutionary biologists have become convinced that, like mitochondria, chloroplasts were once independent microbes. According to one scenario, early in life's history, these productive bugs were engulfed by a larger microbe and subsequently became part of that microbe's cellular machinery. Gehring suggests that the independent microbes may have developed a light-sensing mechanism: “There's a great selective advantage,” he explained, “as sensing light could have enabled these early organisms to avoid damaging UV light and track down light for photosynthesis.” These proto-chloroplasts, he suggests, were engulfed by dinoflagellates, which in turn became symbionts of more complex organisms. “It could be that eyes are coming from a symbiont within a symbiont,” he says.

    Some colleagues are skeptical, however. “It's hard to understand how you would take [a subcellular component] and have it become a multicellular structure” such as a modern eye, Patel notes. But others find the theory intriguing. “It's a neat idea, and [he] can really check into it,” says Ronald Ellis, a developmental biologist at the University of Michigan, Ann Arbor.

    To do that, Gehring wants to isolate DNA from the species of dinoflagellate with the eyespot to check for Pax-6 and other genes related to vision. “The dinoflagellate is very difficult to find,” he notes. At the same time, he's planning to scour the genomes of other animals for chloroplast genes. “If my prediction is right, we should be able to find some chloroplast genes in multicellular animals and dinoflagellates.” If so, that would be a real eye-opener.

    Good Diet Hides Genetic Mutations

    After Claudia Kappen moved from the University of Arizona in Tucson to the University of Nebraska Medical Center in Omaha 2 years ago, she couldn't figure out why the mice she was studying were suddenly much healthier. A developmental biologist, she was interested in skeletal diseases and had bred a strain of transgenic mice whose bones were so fragile that the rib cage couldn't withstand breathing and the animals died soon after birth. But in Nebraska, their skeletons were much stronger.

    In her quest to understand the animals' newfound vigor, Kappen and her colleagues have demonstrated again that diet can protect against some genetic diseases: She reported at the meeting that folate, part of the vitamin B complex, compensates for an overactive gene involved in cartilage formation.

    The study suggests a way that mutations could build up in a population, says Nipam Patel, an evo-devo researcher at the University of Chicago. If good nutrition can mask harmful genetic changes, mutations might accumulate unnoticed. Should diet then change, the mutations would exert their influence, possibly changing the animals' physical or behavioral traits. Then evolution could take its course, selecting against some of these traits while favoring others.

    Mutation masker.

    Folate can help mutant mice with defective ribs (top) develop more normal ones (bottom). Immature cartilage in the defective ribs makes them too weak to support breathing.

    CREDIT: Y. G. YUEH, D. P. GARDNER, C. KAPPEN, PNAS 95, 9956 (1998)

    “I don't know of anyone in the field who had thought about folate in this regard,” says Richard Behringer, a developmental biologist at the University of Texas M. D. Anderson Cancer Center in Houston. He and others have shown that folate can prevent neural tube defects such as those that cause spina bifida in humans, but he had not suspected that the same nutrient could affect skeletal growth.

    Kappen and her colleagues realized that the mice were chewing on their bedding—corncobs—a nutrient source they didn't have in the Arizona lab. On a hunch, Kappen decided to see if folate was the secret ingredient that compensated for an aberrant Hox gene she had introduced into the mice. The gene helps control the maturation of cartilage precursor cells. The overactive form prevents the formation of intact cartilage in the animals, although the researchers aren't sure why. They found that cartilage cells from the defective mice matured as well as those from healthy embryos if grown in a folate-rich environment. Without folate, “the cells shriveled up and died,” she reported. Transgenic mice given extra folate also fared well: Their skeletons stayed intact rather than shattering. “The faulty Hox gene can be modified by an environmental substance,” she concluded.

    It's still unclear how folate makes up for the bad gene. Kappen suspects that folate might speed up cell growth and differentiation, thereby compensating for the defective Hox, she explained. At this time, no one knows how important folate in the mother's diet is to cartilage development in human fetuses, she says.

  15. VIROLOGY

    Monkey Virus Link to Cancer Grows Stronger

    1. Dan Ferber

    A virus that contaminated early batches of polio vaccine was deemed safe decades ago, but it keeps turning up in tumors. Now researchers are figuring out how the virus might imperil cells and are searching for ways to stop it

    The old man had been trying to tell Michele Carbone something for months. He'd buttonholed the molecular virologist on the last day of a busy conference, but they kept getting interrupted. He'd sent a pile of journal articles from the 1950s to Carbone's office at Loyola University Medical Center in Chicago, but they sat unread on Carbone's desk. He'd called and called again. Carbone finally relented when he realized that the 89-year-old physician, named Herbert Ratner, lived in the Chicago suburb of Oak Park, less than a kilometer from Carbone's house. “At a certain point I thought, ‘I have to go’” see what he wants, Carbone recalls.

    At the conference where he first met Ratner, held in 1997 at the National Institutes of Health (NIH) in Bethesda, Maryland, Carbone and colleagues reported finding traces of a monkey virus called SV40 in a rare form of cancer of tissue surrounding the lung. SV40 had been spotted in 1960 in monkey tissue used to make the polio vaccine and was soon found to cause four types of tumors in hamsters, sparking widespread alarm. By 1963, when the polio vaccine supply had been screened to ensure that it was free of the virus, more than 98 million people in the United States and hundreds of millions worldwide had been exposed to potentially contaminated vaccine. Researchers have been arguing ever since about whether that SV40 exposure increased their risk of cancer.

    Carbone wanted to know whether the SV40 he'd found in tumors could have come from the polio vaccine. But a 3-year search among manufacturers, government officials, and researchers for possibly contaminated samples of vaccine had come up empty. Over tea at Ratner's home on a spring afternoon, Ratner explained that he had been director of public health for the town of Oak Park in 1955, when the polio vaccine was first released. Fearing that the new vaccine was unsafe, he refused to inject local children. Newspapers vilified him, but he stuck to his guns. Carbone thanked Ratner and headed for the door. “He said, ‘No, no, wait, I have something for you,’” Carbone recalls. Ratner returned from his basement with vials of polio vaccine produced in 1954. He told Carbone that he had kept it in his refrigerator for 42 years, hoping all along that someone would test it and prove him right.

    The 1997 NIH conference, dubbed a consensus conference, produced nothing of the kind. Believers and skeptics continued arguing about whether SV40 is present in human tumors and, if so, whether it's contributing to cancer in people. Skeptics pointed to a lack of epidemiological evidence linking pre-1963 polio vaccination to cancer and to other evidence suggesting that laboratory artifacts were responsible for some SV40 sightings in human tumors. Believers, meanwhile, cited decades of tissue-culture and animal research showing the virus's carcinogenic powers.

    Infiltrator.

    Hexagonal SV40 particles (magnified at bottom) dot the inside of a mesothelial cell's nucleus.

    CREDITS: M. CARBONE

    The battle continues today, but on new ground. Although most experts agree that SV40 infection is not a widespread public health problem, it clearly can cause cancer when given to newborn animals. Researchers still don't know whether the virus disproportionately infects cancer patients. Studies in the past 5 years have led many—but by no means all—to accept that SV40 genetic sequences are present in the same four types of human cancers that the virus causes in hamsters. In humans, however, it's not clear whether the virus helps cause cancer or just happens to infect cancer cells.

    Part of the problem is that none of the tests to detect the virus are universally trusted. Some teams are working on better tests, which could help confirm or refute virus sightings in tumors and reveal if and how far SV40 is spreading in people. Many cancer patients with SV40-laden tumors were not vaccinated with the early polio vaccine, and researchers aren't sure how they picked up the virus.

    Despite all the uncertainties, circumstantial evidence implicating the virus has piled up, particularly in the past year. Some groups are testing ways to block SV40 infection in an attempt to prevent or treat cancer. Skeptics of the SV40-cancer link remain, but more than a few are starting to come around. “I used to think it was all artifact,” says cancer biologist Denise Galloway of the Fred Hutchinson Cancer Research Center in Seattle. “I wouldn't say I'm convinced, but I don't think it deserves to be pooh-poohed anymore.”

    Four furies

    Alarmed by the early reports of SV40's carcinogenic effects in hamsters, researchers at the National Cancer Institute (NCI) and elsewhere did a series of epidemiological studies, beginning in the 1960s and 1970s, that seemed to dispel the worry about human risk. None found any increase in cancer risk in people who had received potentially tainted vaccines as infants or children. Studies in the United States and Europe tracked thousands of people for up to 20 years. However, the studies were not powerful enough to rule out a rise in rare cancers, says pediatric oncologist Bob Garcea, now at the University of Colorado School of Medicine in Denver.

    The case was reopened in 1992, when Garcea, then at Harvard Medical School, and colleagues stumbled onto SV40 DNA in childhood brain tumors while searching for traces of two related human viruses. Soon after, Garcea, Carbone, and colleagues spotted SV40 DNA sequences in a bone cancer called osteosarcoma. Then Carbone and Harvey Pass, now at Karmanos Cancer Institute of Wayne State University in Detroit, spotted it in mesothelioma, a rare and uniformly fatal cancer of the tissue lining the lungs. That meant the virus had shown up in three of the four types of cancer that it caused in hamsters.

    But other researchers looked for the virus and didn't find it. For instance, cancer epidemiologist Howard Strickler, then at NCI, and Keerti Shah of the Johns Hopkins Bloomberg School of Public Health in Baltimore found no sign of SV40 in osteosarcoma and mesothelioma. At the 1997 consensus conference, Strickler and other skeptics said the virus sightings could have come from contamination by lab strains of SV40, which are used widely by cancer researchers.

    To resolve the dispute, two researchers arranged multilab studies on mesothelioma—and came to opposite conclusions. One, led by Strickler, involved nine different labs. It found traces of SV40 in a small fraction of mesothelioma samples—but the virus was just as likely to appear in control samples of lung tissue. Strickler, who's now at Albert Einstein College of Medicine in New York City, says the study casts doubt on a role for SV40 in mesothelioma. He points out that when SV40 DNA is found in tumors, it's scarce—too scarce to be causing cancer. Furthermore, the proportion of tumors with SV40 varies greatly from one study to another, which he says casts doubt on the reliability of the screening methods used.

    Meanwhile, molecular geneticist Joseph Testa of the Fox Chase Cancer Center in Philadelphia and colleagues reported in 1998 that nine of 12 mesothelioma samples turned up positive when tested in all four participating labs. Testa says the results mean that lab contamination was not to blame, but Strickler disagrees, pointing out that the researchers did not test normal tissue to make sure the assay was working properly.

    Since then, several studies have replicated Testa's positive findings using other methods. Marc Ramael's team at St. Elisabeth General Hospital in Herentals, Belgium, used fluorescent tags to spot SV40 DNA and protein inside mesothelioma cells in preserved tumor tissue. And molecular biologist Adi Gazdar of the University of Texas Southwestern Medical Center in Dallas and colleagues found SV40 in 50% of the mesotheliomas they dissected from preserved human tissue. In both cases, no SV40 showed up in nearby normal lung tissue, ruling out contamination, Gazdar says. At first, “I was skeptical of the whole thing,” Gazdar says, but “there's no question that the sequences are present.”

    Carrier.

    SV40 from rhesus monkeys contaminated early batches of polio vaccine.

    CREDIT: WOLFGANG KOEHLER/CORBIS

    Recently, SV40 went four for four. Researchers found the virus in humans with non-Hodgkin's lymphoma, a cancer found in SV40-infected hamsters. Teams led by Gazdar and Janet Butel of Baylor College of Medicine in Houston tested hundreds of human tumors. As both groups reported in the 9 March issue of The Lancet, they found SV40 DNA in about four in 10 samples, but not in normal lymph tissue or blood cells. The results still need to be confirmed in other studies, Butel says, but the virus “might account for a large fraction of non-Hodgkin's lymphoma.”

    Virus hunting

    When Carbone's team analyzed Ratner's old polio vaccine, they found that it was contaminated with a variant of SV40, the genome of which differed from that of common lab strains of the virus. The distinctive strain has now been found again, in three non-Hodgkin's lymphoma patients, Butel's team reported in its recent Lancet paper. The patients' SV40 and that extracted from Ratner's vaccine have an identical molecular fingerprint, a matching DNA sequence in a stretch of an SV40 gene that varies from strain to strain. “This is the ultimate proof you'd want that at least some of this virus [infecting cancer patients] came from the polio vaccine,” Carbone says.

    Butel and colleagues didn't emphasize the match when they reported their findings. “I don't want to be responsible for scaring people so that they are afraid to use the polio vaccine,” Butel says. She points to all the good the vaccine has done: It has practically eradicated the dread disease in much of the world, saving tens of thousands from paralysis and saving thousands of lives. And the polio vaccine now used in the United States is grown in cultured monkey kidney cells uninfected by SV40.

    Still, the largest human exposure to SV40 probably came from contaminated vaccines between 1955 and 1963, many researchers say. But SV40 DNA has turned up in people who never received possibly contaminated vaccine. Some skeptics see this as evidence of an alternative source, such as an endemic strain of SV40 in the population, possibly introduced through monkey bites. Those who point to the vaccine link say that SV40 from contaminated vaccines has spread from person to person. SV40 can replicate in people, Butel and others say, and it can also be excreted in feces and urine. “It seems to me that there's no way around arguing [that there has been] transmission of the virus,” says Galloway of Fred Hutchinson Cancer Research Center.

    It's been difficult to track the virus's progress, however, because there's no widely trusted test to quickly detect antibodies against SV40 in human blood. Existing tests are either too slow to screen a large number of samples, or they have trouble telling SV40 from two of its cousins, JC virus and BK virus, both of which are common in people. Galloway is “very optimistic” that an as-yet-unpublished assay her group has developed, which distinguishes BK from JC, can be modified to distinguish both from SV40. A reliable test could confirm or refute disputed SV40 sightings and reveal whether cancer patients have more SV40 infections than healthy people, Galloway says.

    Even if SV40 infection is found in cancer patients, that doesn't mean it causes cancer. Epidemiological studies continue to show no increased risk of cancer in people exposed to the polio vaccine, Strickler says. A 1998 study he co-authored, for example, examined data on millions of patients from NCI's national cancer registry and found no rise in the incidence of cancer—rare or common—in people who have been exposed to contaminated vaccine.

    Even where the virus seems to be present in tumors, says Strickler, it does not infect every cancer cell, raising the question of how the virus could cause cancer in cells it doesn't infect. And unlike known cancer-causing viruses, which usually infect a single tissue, SV40 seems to turn up in a wide variety of tumor types. “It's hard to see how a virus can go to all these tissues and produce all these cancers,” Shah of Johns Hopkins says.

    Proponents counter that some of the putative SV40-induced cancers are so rare that a link to polio vaccination wouldn't reach statistical significance even in huge epidemiological studies. They also say that if SV40 is indeed spreading through the population, studies based on polio vaccine exposure wouldn't have a reliable measure of who's been exposed. Those who suspect a causal role say the scarcity of DNA can be explained if SV40 causes cancer via a temporary infection that is later undetectable. Alternatively, the virus might release cancer-promoting molecules that act at a distance.

    Cellular havoc

    Evidence that SV40 acts directly on cells to cause at least one cancer, mesothelioma, has been growing. As early as 1997, teams led by Carbone and Antonio Giordano, now at Temple University in Philadelphia, showed that in animals and lab-grown human mesothelioma cells, an SV40 protein called the large T antigen turns off two tumor-suppressor proteins, Rb and p53, removing two separate brakes that keep genetically damaged cells from multiplying.

    But according to 1999 work by NCI's David Schrump and colleagues, removing most of SV40's large T antigen can thwart tumor cells. The strategy restored the p53 pathway in mesothelioma cells isolated from a human tumor; in response, the tumor cells stopped growing and self-destructed. George Klein of the Karolinska Institute in Stockholm, who did pioneering work linking the Epstein-Barr virus to cancer, says that such experiments are “the strongest piece of evidence you can obtain to say that the virus is essential for the growth of the tumor,” but he adds that more experiments are needed to prove a causal role.

    Like a bomb.

    Compared to normal chromosomes (left), those from a SV40-infected cell are multiplied and often abnormal (right, red arrows).

    CREDIT: J. TESTA

    Other studies in mesothelia show that SV40 infection induces several hallmarks of cancer. Testa's team showed in 1999 that SV40 causes dramatic chromosome rearrangements and damage. “It looks like you set a bomb off in these cells,” he says. In work published in the 21 February issue of Oncogene, Carbone, Testa, and colleagues report that SV40 spurs activity of an enzyme called telomerase that extends the tips of chromosomes, thus allowing cells to become immortal. And in work that was presented in April at a meeting of the American Association for Cancer Research, Gazdar, Carbone, and colleagues show that SV40 infection causes cells to disable a tumor suppressor gene called RassF1 several weeks after infection, just when cells are becoming malignant.

    Another new study, in the October 2001 issue of the Proceedings of the National Academy of Sciences, suggests that SV40 doesn't have to be in every cell to cause cancer. Giovanni Gaudino of the University of Piemonte Orientale in Novara, Italy, Luciano Mutti of the Maugeri Foundation in Pavia, and their colleagues showed that SV40 infection caused mesothelium cells to secrete a growth factor. When it diffuses to neighboring cells, it activates a gene that starts the cells down the road to cell division.

    A clean vaccine

    As evidence for SV40's ability to induce mesothelioma builds, some researchers are trying to disable the virus as a way to treat or prevent this fatal cancer. Martin Sanda and Michael Imperiale of the University of Michigan Medical School in Ann Arbor came up with an SV40 vaccine in 1999. They found that a virus called vaccinia containing a neutered SV40 T antigen held off SV40-induced mesothelioma in mice and shrunk preexisting tumors. Others have shown that injecting naked DNA encoding the SV40 T antigen accomplishes the same thing.

    Pass of Wayne State University is planning a phase I clinical trial. The vaccine could eventually help treat patients whose tumors show signs of SV40 infection, and it might be given to people already at high risk of mesothelioma, such as asbestos workers, he says. NCI is looking for a company to manufacture the vaccine.

    But longtime SV40 researchers claim that few other funds have been available from the government, which oversaw distribution of early batches of contaminated polio vaccine and vouched for its safety. The lack of funds means that key questions have remained unanswered for years, many SV40 researchers say. “The federal government's attitude has been, ‘We don't believe this story; it's not proven; so we're not going to fund it,’” Gazdar says.

    May Wong, program director for DNA viruses at NCI, acknowledges that funding has fallen far short of what SV40 researchers have sought, mostly because the work was considered “very speculative and controversial.” “I don't think the government was trying to cover up anything. It was just that the data wasn't there,” she says. But the stream of new reports has begun to change that, she adds: NCI recently funded Carbone and Butel. And a new NCI program to look at possible cancer-causing microbes, including SV40, is in the works.

    Researchers are itching to get started on a backlog of work, including studies that track the cancer risk of SV40-infected people. They want to test whether SV40 assists other carcinogens such as asbestos and see if blocking an SV40 infection could help treat mesothelioma or other cancers. Those studies will take money and time, and the answers won't just turn up in someone's refrigerator.

    View this table:
  16. Deep Life in the Slow, Slow Lane

    1. Richard A. Kerr

    Microbial life may seem infinitely adaptable and durable, but microbiologists and geologists probing the most voluminous part of the biosphere—the deep subsurface—are finding it slow going

    Life is a hardy sort. In recent years, microbes have been reported in the most unlikely nooks and crannies of the planet living under incredible conditions: in mine drainage with a pH of 1; 1500 meters down in ancient lavas, living off the rock itself; in ice-encased brines; 3.2 kilometers deep in sweltering South African gold mines; in cloud droplets; and, albeit in suspended animation, preserved for more than 250 million years in ancient brine pockets in subterranean salt.

    Microbes seem to be thriving wherever there is liquid water at temperatures below the reigning lethal limit of 113°C. Indeed, an estimate by microbiologist William Whitman and colleagues at the University of Georgia in Athens has almost all the planet's microbes out of sight beneath their familiar haunts of soil and sea floor. Geologist William Fyfe of the University of Western Ontario in London has said that “probably the top few kilometers of the entire basaltic ocean crust is alive with … microbes.” Going farther, Thomas Gold of Cornell University has proposed a “deep hot biosphere” that extends down everywhere into the crust as much as 6 kilometers. That's an extreme view, but the recognition of pervasive, all-enduring life has sparked visions of alien life just waiting to be found beneath the inhospitable surface of Mars.

    Researchers exploring the deep subsurface here on Earth—continental crust, marine sediments, and ocean crust—are not so optimistic, however. They are finding deep life, but it mostly seems to be living indirectly off the energy of sunlight rather than using local, less tempting sources of energy, such as the rock itself. Even when feeding off organic matter that trickles down from plant life at the surface, deep microbes are usually starved into apparent dormancy; when cut off from photosynthetic fuel supplies, they can simply disappear.

    “We're not finding a prolific amount of life” even when temperatures would allow it, says hydrogeologist Tullis Onstott of Princeton University, who leads a group studying microbial life in the rock of deep South African gold mines. What deep life they are finding is living “very, very slowly.” Microbiologist Stephen Giovannoni of Oregon State University (OSU) in Corvallis finds the same leisurely lifestyle in the ocean crust. “One often gets the impression that the deep subsurface is just a Garden of Eden for microorganisms,” he says. “I don't see from our research that is true.” To pin down where and how life can exist, much less thrive, researchers of the deep Earth will have to manipulate microbial communities in situ and take up new molecular genetics tools, not to mention bolster waning funding.

    Living off the rock?

    The latest cautionary note for deep-life enthusiasts comes, ironically enough, from the recent discovery of a microbial community apparently living quite independently of the surface beneath hot springs in Idaho, the way any life on Mars would presumably be living. In their research, hydrogeologist Francis Chapelle of the U.S. Geological Survey in Columbia, South Carolina, and his colleagues took advantage of a landowner's personal geothermal energy setup. To heat everything from his house to his dog's house, the owner had dug wells tapping Lidy Hot Springs. The hydrogeologists used the wells to sample uncontaminated waters as they rose from more than 200 meters down in a 6-million-year-old volcanic ash bed. In these 60°C waters, they found relatively high levels of hydrogen gas and a community of microorganisms well suited to living off the hydrogen.

    According to several different types of DNA analyses, more than 95% of the hot-spring microbes are Archaea, the domain of microbial life distinct from bacteria that inhabits some of the most extreme environments on Earth. Further gene analysis turned up gene patterns in 95% of these Archaea that were closely related to those of known methanogens, which derive their energy from the reaction of hydrogen with carbon dioxide to produce methane. Not that they were “thriving” on the nanomolar concentrations of hydrogen. About 100,000 cells per milliliter came up in the springs, compared with 10 to 1000 times that abundance of microorganisms in surface waters.

    Down and dirty.

    Detecting sparse life in rock kilometers down in muggy, less-than-sterile South African gold mines takes some doing.

    CREDIT: DUANE MOSER/PNNL

    The catch for astrobiologists is the apparent source of the hydrogen. The normally scarce gas is presumably produced through some sort of interaction between water and rock. That's how microbiologist Todd Stevens and geochemist James McKinley of Pacific Northwest National Laboratory in Richland, Washington, explained the hydrogen in water 1500 meters down in the Columbia River basalt lavas of eastern Washington (Science, 20 October 1995, p. 377). Iron in the basalt seemed to be chemically reducing the hydrogen of water to hydrogen gas. Thus, according to this scheme for deep hydrogen production, the life-sustaining gas would be available anywhere that water and basalt come together. This hypothesis has implications for life on Mars: The Red Planet is mostly basalt.

    But this pervasive hydrogen source has since been called into question. Microbiologist Robert Anderson of the University of Massachusetts, Amherst, Chapelle, and Derek Lovley of UMass, a co-author on the Lidy Hot Springs paper, found that an unnaturally low pH is required to produce any hydrogen from water and basalt, and even then production quickly peters out. And microbiologist Norman Fry of the Central Public Health Laboratory in London and colleagues found that only 3% of Columbia River basalt microorganisms were hydrogen-consuming methanogens, according to their gene sequences; the rest make a living in diverse ways. That “looked very much like a microbial community you might see in a sediment,” says Lovley, “in which organic matter is fueling metabolism.” In that case, the bugs would be living off dissolved organic matter carried down from the surface or from fossil soils layered among the lava flows.

    The Lidy Hot Springs organisms are probably not running their hydrogen economy on fuel generated by ubiquitous water-rock reactions, says Chapelle. Instead, they're most likely subsisting on hydrogen produced when the active faults that crisscross the area crack and crush rock. Fracturing creates active sites on mineral surfaces that can extract hydrogen from water to form hydrogen gas. Without the daily shifting of faults to produce fresh rock surfaces, he says, hydrogen would likely be truly scarce. He has screened more than a dozen other hot-spring sites around the Snake River Plain of Idaho and found that they appear to support carbon-based, not hydrogen-based, microbial communities. “I don't think hydrogen-based communities are going to be all that common,” he says. “Carbon-based will be much, much more common.” That should be discouraging for Mars explorationists. The Red Planet hasn't seen photosynthesizing life for billions of years, if it ever did.

    Hope for a sizable continental biosphere independent of the surface may rest with another source of hydrogen: the natural radioactivity of certain crustal rocks. The radioactive elements such as uranium that decay and heat Earth's interior tend to be concentrated in the crust's most silica-rich rocks, such as granite. Mars doesn't have any detectable granite, but that's just what underlies Sweden, where microbiologist Karsten Pedersen of Göteborg University works in a subterranean laboratory tunneled as deep as 400 meters under 2-billion-year-old granite.

    Rock lovers.

    Some microbes from hundreds of meters deep in Swedish granite may be living off hydrogen split off water by rock radioactivity.

    CREDITS: KARSTEN PEDERSEN/GÖTEBORG UNIVERSITY

    Pedersen finds “lots of microorganisms” in water samples taken from fractures in the deep granite: 10,000 to 100,000 cells per milliliter, about “what you can pick up in clean surface water.” He also finds lots of hydrogen, micromolar concentrations rather than nanomolar. And some of those microorganisms are hydrogen-consuming methanogens. What he doesn't know is how fast they are living. Life in deep granite is “probably quite slow,” Pedersen assumes. Researchers are typically able to culture only 0.1% of the microorganisms they see in samples from any part of the deep subsurface. And even under optimal conditions, that small fraction takes weeks or months to grow into the density of cells generated overnight in vigorous lab cultures.

    Taking it slow deep down

    Just how slow and sparse deep life may get can be seen in the South African gold mines that Onstott and 30-some collaborators have been studying. In yet-to-be-published work, they find a density of microorganisms comparable to Pedersen's at similar depths. And at their greatest depth, 3.2 kilometers, they have found cells whose DNA marks them as one of the “hyperthermophile” archaeans known from sea-floor hot springs. But on descending from the shallowest depths, biomass decreases rapidly, in places to undetectable levels. The dearth of detectable life at greater depth puzzles Onstott. Life's currently known upper temperature limit of 113°C isn't approached until far below the mines. And there's plenty of fuel for living. Hydrogen concentrations soar to a million times what's typical of shallow aquifers. Most likely, radioactivity is generating hydrogen that accumulates in the water during the millions of years since the water trickled down from the surface to “puddle” in the deep rock.

    “It appears there's far more energy there than is being utilized by microorganisms,” says Onstott. He guesses that although there's plenty of fuel available, there's nothing left to burn it with. The deep mine water is devoid of oxygen, and other oxidizing agents, such as ferric iron, may not be exposed on mineral surfaces accessible to microorganisms, says Onstott. “Are they really doing anything down there?,” he wonders. “They could be dormant cells with sequenceable DNA that we're not able to resuscitate.”

    Researchers have been examining another major compartment of the deep biosphere—ocean sediments—to gauge just how slow life can go this side of outright death. All ocean sediments are buried with varying amounts of organic matter that microorganisms might feed on, but oxygen that can be used to burn that fuel runs out a few centimeters beneath the sea floor. Then the dissolved sulfate of seawater takes over from oxygen as the sulfate diffuses downward through the sediment. The balance between the downward diffusion of sulfate and its consumption by microorganisms, as evidenced in its changing concentration with depth in the sediment, is a measure of how fast life is living beneath the sea floor—at least, life that uses sulfate as an oxidizing agent.

    Oceanographers Steven D'Hondt, Scott Rutherford, and Arthur Spivack of the University of Rhode Island (URI), Narragansett Bay, drew on sulfate profiles measured in Ocean Drilling Program (ODP) sediment cores from around the world in order to estimate deep life's pace (Science, 30 November 2001, p. 1820, and 15 March, p. 2067). Assuming that all the cells counted in deep-sea cores are alive, each on average is metabolizing sulfate at a rate 1/100,000 that of the least active microbes in near-shore sediments, the URI group reported. “Either these things are taking very few breaths very rarely, or they're generally inactive,” says D'Hondt.

    Oceanographer John Parkes of the University of Bristol, U.K., who has counted cells found as deep as 850 meters in 14-million-year-old sediment, thinks most of the cells he sees are alive if not “well.” For one, the URI group did not account for any oxidizing agents except sulfate, he notes; other agents, such as iron in sediment minerals, could be contributing as well. And life may have a way of shutting itself down for millions of years, he says, holding itself together molecularly but not growing. Then it might bounce back briefly and divide relatively frequently, say, once every decade, before putting itself to “sleep” once again.

    D'Hondt is now seeing some support for Parkes's view. D'Hondt and 26 colleagues returned at the end of March from 2 months of coring sediments off Peru from ODP's JOIDES Resolution. They found clear evidence that manganese and iron were being used as oxidizing agents in energy production, not just sulfate. Shipboard geochemists also found signs that oxygen and nitrate, powerful oxidants, were diffusing up from the underlying crust to drive microbial activity in the bottom few tens of meters of sediment. Even so, a glance at the initial geochemical results suggests that deep-sediment metabolic activity beyond the near shore is still low in the extreme, says D'Hondt.

    Coming in from the cold

    The third realm of the deep biosphere, the ocean crust that covers two-thirds of the planet, is if anything more mysterious than the continental crust or the overlying sediments. Microorganisms are down there, but “we don't know what they're doing or what they're using for an energy source,” says geochemist Jeffrey Alt of the University of Michigan, Ann Arbor.

    When deep-diving oceanographers stumbled on a riot of life at sea-floor hot springs dotting the ridge crests in 1979, microbes were obviously a crucial part of it. More apparent evidence of vibrant deep microbial activity came in 1991, when oceanographers observed clouds of “fluffy white stuff” billowing from the East Pacific Rise following a volcanic eruption. After researchers found more flocs laden with thermophilic microorganisms pouring from recently disturbed hot springs, they concluded that “there's a biosphere below the sea floor,” says oceanographer John Delaney of the University of Washington, Seattle.

    Smelly work.

    Processing ocean sediment cores onboard JOIDES Resolution can require respirators for the mud's hydrogen sulfide, but it can yield slow-living microbes (bottom, green dots) from 30 meters deep.

    CREDITS: (TOP TO BOTTOM) HERIBERT CYPIONKA/UNIVERSITY OF OLDENBURG; DAVID C. SMITH/URI

    Just how massive this ocean crustal biosphere might be remains unclear. Microbes are obviously active along the crest of the midocean ridge system, which stretches for 60,000 kilometers through the global ocean. For example, something seems to be nibbling on the glass that makes up about 5% of ocean crustal rock; samples of the glass brought up by deep drilling are scarred with pits filled with DNA-containing material (Science, 2 May 1997, p. 703). But the “snowblower events” of white floc billowing from ridge crests may not reflect a deep aquifer system “humming with life,” as one oceanographer put it. On closer inspection, microbiologist Craig Taylor of Woods Hole Oceanographic Institution in Massachusetts found that the white stuff is not so much bacteria as sulfur filaments produced by bacteria consuming the hydrogen sulfide in hot spring waters. And the mats are probably the product of a brief “bloom” of bacteria feeding on a surge of hydrogen sulfide released by a quake or eruption rather than the release of a huge bacterial mass that's always feeding beneath the surface.

    Microbes are making some sort of living at the ridge crest, where seawater heated to hundreds of degrees by underlying magma extracts the most chemicals from the fractured rock. But the crust cools as it spreads away from the ridge crest, and as the temperature drops, deep microbial life diminishes too. Ninety kilometers east of the Juan de Fuca Ridge, water rises through an ODP drill hole that penetrates 3.5-million-year-old crust. The water is 60°C, and microbiologists James Cowen of the University of Hawaii, Manoa, and Giovannoni of OSU find a concentration of cells less than that in seawater. A common misconception holds that “the deep-sea subsurface is packed with cells,” says Giovannoni. “It's not; it's a fairly low biomass.”

    In even older, colder crust, life seems to have quit, or nearly so. The diffusion of oxygen and nitrate up from 40-million-year-old crust into the lowermost sediment, as found during the most recent ODP cruise, means that “whatever [biological] activity is going on in the crust isn't enough to strip out the nitrate and oxygen,” says D'Hondt. “There's not much activity in old, cold crust.”

    To pin down how much life the bulk of the deep biosphere harbors and how much living it is doing, researchers will have to sharpen their tools of exploration. Oceanographers will have to figure out how to retrieve uncontaminated samples of ocean crustal life, as colleagues have done for marine sediments and continental crust. Then a means of gauging the pace of deep life must be developed. Culturing microorganisms in place will soon be attempted in deep mines, but molecular techniques for measuring gene expression may prove useful as well.

    Deep-life researchers will also have to look for new sources of funding. Radioactive waste disposal in Sweden will keep work on deep granites going, and ocean drillers have made sedimentary and crustal life a focus of their next 10-year international drilling program (Science, 13 November 1998, p. 1251). But elsewhere attention is shifting toward shallow ground where microbes might help clean up pollutants. Life beneath the surface of Mars may get more attention than Earth's vast if thinly spread store of deep life.

  17. Geobiologists: As Diverse as the Bugs They Study

    1. Elizabeth Pennisi

    Derek Lovley and Kenneth Nealson have alternately sparred with each other and spurred each other on as leaders of the field they helped create

    In the mid-1980s, Derek Lovley and Kenneth Nealson achieved something most scientists can only dream about: They put their stamp indelibly on a nascent scientific discipline. The two researchers independently announced the discovery of microbes that live off metals. The claims were surprising, even heretical, but the near-simultaneous findings “opened up a new field of study,” particularly in the United States, says Yuri Gorby, a microbiologist at Pacific Northwest National Laboratory (PNNL) in Richland, Washington. It turns out that these tiny metal-processing organisms have played a pivotal role in the vast sweep of geological history.

    Since those early discoveries, Lovley's and Nealson's careers have followed similar trajectories. Today, the two men are considered intellectual leaders. Lovley chairs the microbiology department at the University of Massachusetts (UMass), Amherst; Nealson is now a distinguished geobiology professor at the University of Southern California (USC) in Los Angeles, and he works part-time in the astrobiology program at the Jet Propulsion Laboratory (JPL) in neighboring Pasadena. “There are a lot of parallels in what they have contributed and similarities in what they have worked on,” says PNNL microbiologist Jim Fredrickson. Yet the two are opposites in personality and outlook, and according to numerous colleagues, their scientific and professional relationship is often characterized as one of intense rivalry.

    Each has championed his own findings and the importance of the particular bacteria he first worked on 20 years ago. As a result, Lovley and Nealson have sometimes clashed at meetings and in print. “For a long time, the two weren't talking to each other,” says William Ghiorse, a geomicrobiologist at Cornell University in Ithaca, New York. Even now, adds John Coates, a microbiologist at Southern Illinois University, Edwardsville, “there's no love lost between the two of them.” Nealson and Lovley, however, don't like to talk about their conflicts, insisting that they are “really just differences in interpretation,” as Lovley puts it.

    Yet, as is often the case in science, they seem to have spurred each other on. Both have continued to make new discoveries, with Lovley in particular producing a blizzard of papers that have resulted in “phenomenal steps forward [scientifically] for the field,” says Coates. Nealson has taken a more broad-based view, Coates adds, and “has been a tremendous spokesperson for geomicrobiology.” Their individual successes—as well as progress in geobiology—speak to the fact that there's room for many temperaments in science. Nealson agrees: “Competition and healthy debate are the heart and soul of a field.”

    Lovley: Seeking the perfect microbe

    When Lovley joined the U.S. Geological Survey (USGS) in 1984 as a budding microbial physiologist, few had considered the possibility that microbes might “eat” or “breathe” metals. Lovley, however, was convinced such organisms exist. Earth's most abundant element, iron, provides a vast quantity of raw material that some microbes might thrive on. Lovley reasoned that in environments where no oxygen is present, microbes might convert insoluble ferric oxide to the more soluble ferrous form as they generated the energy they needed to survive. This would also mobilize iron, allowing the soluble form to move through the environment until it was eventually oxidized and made insoluble again.

    Lovley set out sifting through river sediments, hoping to be the first to find bacteria that perform this feat. In just a few years he found what he was looking for: a class of bacteria he eventually called Geobacter. Since then, some 30 Geobacter species have been found in many types of sediments and soils, including deep in Earth's subsurface and in marine sediments. “We've been incredibly lucky,” says Lovley.

    Lucky—and hardworking, say his colleagues. Lovley churns out scientific discoveries like “a big rolling stone that you can't stop,” says Cornell's Ghiorse. And he expects the same from his collaborators. Former Lovley postdoc Tim Magnuson, now a microbial physiologist at Idaho State University in Pocatello, remembers that when he worked with Lovley, the motto was “Finish an experiment a day and at least one publishable figure a week.” “I thought it was a joke, but it was what he expected from his people,” he recalls. That workaholic drive has paid off. Lovley has had a long string of publications in Nature and Science, and he continues to discover new organisms and metabolic pathways.

    Lovley's studies of the biochemistry of Geobacter has borne out his early theories about their role in moving iron through the environment. In 1987, Lovley and his colleagues also found that some types of Geobacter help form a magnetic mineral called magnetite, which makes up a large percentage of rocks from 500 million years ago. These processes, says John Baross, a microbiologist at the University of Washington, Seattle, have “tremendous implications for virtually all of our mineral cycles on Earth.”

    Moreover, Lovley and his colleagues have shown that some Geobacter types use iron to metabolize complex organic compounds, explaining in part how the carbon in these compounds is recycled. Geobacter themselves “gain energy to grow from that process,” says PNNL's Gorby, adding that this finding is Lovley's “seminal contribution.” And in the early 1990s, Lovley and his colleagues helped prove that Geobacter is capable of processing gold or uranium.

    To work their magic on iron or other metals, Lovley has found, Geobacter must first make direct contact with the metal. When iron is present in the environment, his team reported in the 18 April issue of Nature, Geobacter can grow flagella and home in on iron particles. Once they make contact, the microbes use a series of enzymes called cytochromes to move electrons from the interior to cell membranes for transfer to the iron, changing the metal's chemical state. The electron transfer helps generate adenosine triphosphate, which fuels all cellular activity.

    The more Lovley learned about Geobacter, the more he began to think about harnessing it to clean up toxic wastes. He has found, for example, that Geobacter can degrade benzene and toluene, which might prove useful in bioremediation of oil-contaminated aquifers. He has also looked at contaminated soils and, in particular, at Geobacter's potential to alter the chemistry of uranium so that—in contrast to iron—it precipitates out of the water column. When Lovley moved from USGS to UMass in 1995, his research focus shifted somewhat. “When I started, I was more of a field person; I was not even sure I would buy an autoclave for sterilizing instruments or media for culturing organisms,” he recalls. Now he runs an established but active lab focused in part on understanding Geobacter's lifestyle and biochemical makeup. He pushed to have the bug's genome sequenced, which he expects The Institute for Genomic Research (TIGR) in Rockville, Maryland, to complete very soon. As researchers merge field studies, lab results, and genome data, he says: “Things are coming together.”

    A man and his microbe.

    Derek Lovley made Geobacter (top) a poster bacterium in geobiology.

    CREDITS: (TOP TO BOTTOM) D. LOVLEY; NANCY PALMIERI

    Nealson: Taking a broad view

    While Lovley was making a name for himself with his studies of Geobacter, Nealson was concentrating on another versatile bug, a bacterium called Shewanella that also influences geological processes. He didn't start out with a geobiological bent, though.

    As a young environmental microbiologist at Scripps Institution of Oceanography in La Jolla, California, in the 1970s, Nealson worked on luminescent bacteria that live in the light organs of fish. He discovered a protein called lux that was key to microbe-to-microbe communication, and he spent the next dozen years looking at how bacteria use lux to assess their density, a process called quorum sensing. He says his physical oceanography colleagues used to tease him, saying he should “work on something important”—such as Earth's geochemistry. In the early 1980s, he started to dabble in geobiology, specifically the geochemistry of manganese. He turned that into a virtually full-time endeavor in 1985 when he joined the Center for Great Lakes Studies at the University of Wisconsin, Milwaukee. He also imagined that lakes might be “more tractable” to study than oceans.

    He was right. While tracking geochemical cycles involving manganese in Lake Oneida in upstate New York, Nealson says, “we lucked into an organism that lived by ‘breathing’ rocks,” in particular iron and manganese oxides. The organism, part of a genus now named Shewanella, “breathes” manganese in the same way that Geobacter “breathes” iron. He and his colleague Charles Myers, now at the University of Wisconsin, Milwaukee, described this manganese-processing bug in 1988 in Science, just months after Lovley and his colleagues described microbial iron-reduction in Nature.

    Nealson worked on Shewanella extensively for a decade, getting hooked on them in the same way that Lovley was hooked on Geobacter. As a result, Nealson's team “was instrumental in demonstrating the importance of these types of organisms in manganese biogeochemistry,” says PNNL's Fredrickson: “He has great vision. He thinks outside the box very well.”

    To get an idea of Shewanella's impact, Nealson measured manganese entering and leaving Lake Oneida over time. Based on the rate at which Shewanella processes manganese, he concluded that it played a big role in cycling this element through the environment. He also looked for Shewanella in different environments—and found new strains and species in many places, including the Black Sea. Nealson and his colleagues have since worked out how the 15 known species of Shewanella are related to each other and to other organisms.

    Shewanella bacteria aren't hugely finicky, as it turns out. Nealson learned that they can interact with other minerals, for example, shifting electrons to iron even when that metal is locked in a clay called smectite. And when iron isn't available, the microbe can reduce sulfur and about a dozen other compounds, thereby helping recycle many different metals through the environment and changing the properties of soils. With Nealson's help, Shewanella became popular microbes for geobiologists to study in the lab.

    Like Geobacter, Shewanella has become a leading model for bioremediation efforts. Nealson and others have shown that Shewanella can interact with chromium, uranium, cobalt, and nitrates, making it a possible candidate for cleaning up sites contaminated with several toxic wastes. To better understand these interactions, Nealson and his colleagues have been identifying specific proteins involved in transferring electrons from the cell to the different metals. In many ways, says Lovley, “we've studied the same issues in parallel.”

    After shifting from oceans to lakes, Nealson made another career change in 1998, turning to outer space. He moved to JPL to head up an interdisciplinary group of astrobiology researchers. Together, they developed the use of biosignatures—alterations made by organisms in rock texture, chemistry, and even appearance—as a means of detecting extraterrestrial life. “There's a lot of interest in methods we've been developing,” he notes.

    From mud to Mars.

    In addition to showing that Shewanella was important in geobiology, Ken Nealson helped pioneer astrobiology.

    CREDITS: (TOP TO BOTTOM) K. NEALSON; IRENE FERTIK/USC NEWS SERVICE

    Nealson yearned to get back to his earthly, mineral-eating bugs in the lab, however. Although he still works part-time at JPL, he returned to USC as a researcher in 2001. He is now taking a more extensive look at some of the diverse Shewanella species both in the lab and in the field.

    Champion microbes

    Ever since Nealson and Lovley first published papers on their favorite organisms, people have asked the inevitable question: Which is more important—Geobacter or Shewanella? Lovley and Nealson have been staunch defenders of their particular bugs. On the one hand, Geobacter seems more common. “In every environment we look at, we see Geobacter; sometimes it's so abundant that it represents 50% of the microbes detected,” says Lovley. In contrast, he says he rarely finds Shewanella. And his colleagues are impressed with all that Geobacter can do. The microbes will interact with “just about anything metal you give them,” says Caroline Harwood, a microbiologist at the University of Iowa in Iowa City.

    On the other hand, Shewanella “is a truly cosmopolitan organism,” Nealson points out. It exists at very high pressures, for example. Furthermore, it can live in environments both with and without oxygen, and thus it can thrive right at the boundary between aerobic and anaerobic conditions. “That's where iron cycling is most active,” says PNNL's Gorby. As a result, in some researchers' eyes, “Shewanella takes the prize for being flexible,” says Cornell's Ghiorse.

    However, “we don't know enough about the distribution of these organisms to say with confidence one is really more relevant than others,” says PNNL's Fredrickson. Indeed, there may be other challengers waiting in the wings. For example, Joel Kostka, a microgeologist at Florida State University, Tallahassee, and his colleagues have recently isolated a class of Gram-positive bacteria from the same environments that are home to Nealson's and Lovley's favorites. “We really have very little information” about this class of organisms, says Kostka. “We've just scratched the surface of the diversity of organisms that are out there.”

    Lovley and Nealson, meanwhile, have moved far beyond the original studies that led them onto parallel paths in geomicrobiology. But in a few respects, the two are still competing. Each has embraced genomics to help elucidate how his favorite bug works, and each is racing to get his organism sequenced. TIGR started sequencing a Shewanella genome before it tackled Geobacter. But “[Nealson] was slow in the interpretation of the genome data,” a prerequisite for publishing the completed sequence, says TIGR president Claire Fraser. When she hinted that Lovley's Geobacter genome might be published first, “that kicked Nealson into high gear,” she says. Geobacter and Shewanella are in the final stretch, and everyone is expecting a close finish.

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