News this Week

Science  19 Oct 2012:
Vol. 338, Issue 6105, pp. 310
  1. Around the World

    1 - New Delhi
    Advisory Panel Defends GM Research
    2 - Tokyo
    Pioneering Stem Cell Research Called Into Question
    3 - Washington, D.C.
    Protections for Whole Genome Data
    4 - Amsterdam and Trieste, Italy
    A Guide to Responsible Research
    5 - London
    GSK Announces New Data Sharing Policy
    6 - Austin
    Texas Cancer Research Agency Loses Peer Reviewers

    New Delhi

    Advisory Panel Defends GM Research

    A brinjal field. CREDIT: © PALLAVA BAGLA/CORBIS

    A report released on 9 October by the Indian prime minister's Scientific Advisory Council (SAC) makes a strong pitch for wider acceptance of genetic engineering and biotechnology. The report from the 32-member SAC panel describes genetic modification as a transformational technology that has benefited agriculture and health. The endorsement differs sharply from the conclusion of a parliamentary panel on agriculture, which gave a thumbs-down to genetically modified (GM) technology this summer.

    Opinion is heavily divided on the use of agricultural GM technology in India. Ten years ago, India adopted Bt cotton, which uses modified bacterial genes to control pests. But in 2010, the government blocked similar technology in Bt brinjal, a type of eggplant.

    The SAC report also calls for establishing an independent watchdog called the Biotechnology Regulatory Authority of India, housed outside the ministry of science, to instill confidence in the GM crop regulatory process. A bill to establish such an authority is before the Parliament.

    http://scim.ag/GMres_India

    Tokyo

    Pioneering Stem Cell Research Called Into Question

    A Japanese researcher's claim to have performed a groundbreaking stem cell experiment was quickly called into question by Harvard Medical School in Boston and the University of Tokyo, the institutions that supposedly supported the work. The unusual case of Hisashi Moriguchi blew up last week when Moriguchi displayed a poster at a New York stem cell conference on 10 October that reportedly trumpeted the transplant of induced pluripotent stem (iPS) cells into heart patients.

    Harvard asserted that Moriguchi had been a visiting fellow there for a month in 1999 but had not had any affiliation with the institution since. A spokesperson for the University of Tokyo Hospital confirmed that Moriguchi is on staff as a project researcher, but emphasized that the work apparently reported in New York was not carried out in its labs.

    Meanwhile, Moriguchi has listed a secondary affiliation with Harvard on a number of published papers and correspondence over the years. The journals in question are investigating. The University of Tokyo and Tokyo Medical and Dental University have also launched inquiries into the iPS claims, as well as other work described by Moriguchi.

    Follow the coverage of this fast-moving story on ScienceInsider.

    http://scim.ag/Moriguchi

    Washington, D.C.

    Protections for Whole Genome Data

    CREDIT: MADS ABILDGAARD/ISTOCKPHOTO.COM

    A report released last week by the U.S. Presidential Commission for the Study of Bioethical Issues makes 12 recommendations for protecting the privacy of patients' whole genome data while allowing it to be used in research.

    The 150-page report finds that with prices heading toward $1000 per genome, whole genome sequencing will soon be widely available. To protect privacy, there should be “clear policies” defining who can access and use whole genome data. Federal and state governments should establish a “consistent floor” of protections that penalize those who sequence someone's DNA without his or her consent. Patients and volunteers in research studies need to be informed about how their data might be used and should know that unexpected results may be discovered.

    “This is a proactive and it's a forward-looking report. It's not a response to a crisis. But the commission understands that if this issue is left unaddressed, we could all feel the effects,” said the panel's chair, University of Pennsylvania President Amy Gutmann. http://scim.ag/genomeprotect

    Amsterdam and Trieste, Italy

    A Guide to Responsible Research

    The InterAcademy Council (IAC) and IAP—the global network of science academies—have put forward a common set of fundamental values and practices in an effort to promote responsible conduct among researchers around the world.

    In a policy report titled Responsible Conduct in the Global Research Enterprise released on 17 October, IAC and IAP identified seven qualities—honesty, fairness, objectivity, reliability, skepticism, accountability, and openness—as universal scientific values.

    The 62-page document offers researchers guidelines on topics as wide-ranging as social implications of dual-use research and initiating an international collaboration. “You have to agree ahead of time who is on the paper and who is the first author, because there are cultural differences,” says Ernst-Ludwig Winnacker, co-chair of the report's international authoring committee and secretary general of the Human Frontier Science Program in Strasbourg, France. The report also offers recommendations to research institutions, funding agencies, scientific journals, and national academies.

    Science today is very global, “and, therefore, the mechanisms of how to deal with misconduct should also be global,” Winnacker says.

    London

    GSK Announces New Data Sharing Policy

    Witty

    CREDIT: WIKIMEDIA COMMONS

    GlaxoSmithKline (GSK) last week announced what amounts to a glasnost policy, taking down high walls that until now have prevented outsiders from closely examining results of individual patients who have taken part in clinical trials run by the pharmaceutical giant. Company CEO Andrew Witty, who made the announcement at an 11 October meeting at the Wellcome Trust in London, also said GSK will make public details of more than 200 “hits” for possible tuberculosis drugs that their researchers discovered by screening its library of some 2 million compounds. For a long time, Witty said, there was “a mistaken judgment that actually by being more open and more transparent around data somehow that would destroy the fundamental business model.” Michael Merson, head of the Duke Global Health Institute in Durham, North Carolina, says GSK's new initiatives “provide an excellent example of how pharma can help find solutions to health problems that particularly affect the world's poorest populations.”

    Austin

    Texas Cancer Research Agency Loses Peer Reviewers

    The $3 billion Cancer Prevention and Research Institute of Texas (CPRIT) has been shaken by the resignation of its eight-member scientific review council over concerns about the integrity of the agency's peer review process.

    Approved by Texas voters in 2007, CPRIT has disbursed hundreds of millions of dollars in peer-reviewed research grants and recruited about 50 scientists to Texas. But CPRIT Chief Scientific Officer Alfred Gilman, a Nobel Prize–winning biologist, is stepping down over concerns that the CPRIT board delayed a slate of grants intended mostly for his former institution and approved an $18 million “incubator” grant without scientific peer review.

    Now CPRIT's scientific review council and many of its more than 100 peer reviewers are following Gilman out the door. “Nothing has changed since last spring” when questions regarding CPRIT's review process first arose, said Phillip Sharp, who resigned as council chair last week and is a Nobel laureate at the Massachusetts Institute of Technology in Cambridge. CPRIT said in a statement that it is “no surprise” that some reviewers are leaving along with Gilman. The agency says it has found several candidates to replace the chief scientific officer. http://scim.ag/Texaspeer

  2. Random Sample

    The View From Beneath

    CREDIT: (IMAGE AND INSET MAP) © AUV TEAM/AUSTRALIAN ANTARCTIC DIVISION

    Twenty meters beneath the surface of the Southern Ocean off the coast of East Antarctica, a free-swimming robot peers upward at sea ice floes and assesses their bulk. Most satellite data reveal changes to the area but not to the thickness of the ice, making it difficult to gauge the full impact of global climate change on this frozen environment. Now, this autonomous underwater vehicle (AUV) has produced the first 3D map of the underside of an East Antarctic sea ice floe, revealing an upside-down landscape reminiscent of mountains, lakes, and valleys. Researchers mounted the AUV's multibeam sonar, normally used to map the seafloor, on top of the vehicle rather than on the bottom, yielding a map of the base of the ice. The AUV's trek is part of the 7-week Sea Ice Physics and Ecosystem eXperiment II, an international project coordinated by the Australian Antarctic Division and the Antarctic Climate and Ecosystems Cooperative Research Centre.

    Dance Your Ph.D.: Burlesque Routine Takes Top Honors

    CREDITS: PETER LIDDICOAT (2)

    Peter Liddicoat, a materials scientist at the University of Sydney in Australia, admits to being shy, “more comfortable hiding behind the computer monitor.” So when his labmates urged him to take part in the “Dance Your Ph.D.” contest, he was reluctant. But he finally caved in to the pressure. “A turning point was my boss's enthusiastic laughter when encouraging me to do it,” Liddicoat says, “and the realization that this would tackle head-on the ominous question, ‘So what is your Ph.D. about?’ ”

    That is no easy task with a Ph.D. titled “Evolution of nanostructural architecture in 7000 series aluminium alloys during strengthening by age-hardening and severe plastic deformation.” But after 6 months of preparation, and the help of dozens of friends, he turned his Ph.D. into a burlesque. For using juggling, clowning, and a big dance number—representing the crystal lattices that he studies—Liddicoat is the winner of the 2012 Dance Your Ph.D. contest. Visit Science's Web site to see his video for yourself, as well as the other finalists in categories including physics, chemistry, biology, and social science. http://scim.ag/DancePhD2012

    ScienceLIVE

    Join us on Thursday, 25 October, at 3 p.m. EDT for a live chat on Neandertal intelligence. http://scim.ag/science-live

  3. Newsmakers

    Biomedical Research Loses Senate Champion

    Specter

    CREDIT: U.S. SENATE

    The biomedical research community is mourning the loss of former Pennsylvania Senator Arlen Specter, a loyal supporter of the National Institutes of Health (NIH) throughout his 30 years in Congress. Specter died on 14 October from complications of cancer at age 82.

    A moderate Republican who switched to the Democratic Party in 2009, Specter helped lead efforts to double the NIH budget from 1998 to 2003. He almost single-handedly added $10 billion in stimulus funding for NIH to the 2009 Recovery Act and sponsored legislation expanding federal funding for research on human embryonic stem cells. Specter also proposed the Cures Acceleration Network, an NIH program aimed at speeding drug development, created in 2010.

    Specter's personal battle with illness fueled his passion for NIH. He had a brain tumor removed, underwent bypass heart surgery, and was treated for Hodgkin's lymphoma in 2005 and 2008. This past summer, he was diagnosed with non-Hodgkin's lymphoma.

    NIH Director Francis Collins called Specter “a towering champion for biomedical research and the mission of the [NIH]” and said: “I truly miss Arlen's steady hand and vision for our agency.”

    http://scim.ag/_Specter

    Climate Change a Priority for World Bank

    Yong Kim

    CREDIT: WIKIMEDIA COMMONS

    Dealing with climate change will be one of the World Bank's priorities, said Jim Yong Kim, the first scientist to head the organization, in an 11 October press conference in Tokyo. “Since becoming president of the World Bank, I have looked deeply into the data on climate change, and I have to say I was surprised that even in the last 6 months to a year, the data has become ever more frightening,” he said. “As a scientist, I feel a moral responsibility to be very clear in communicating the dangers of climate change.”

    Kim, a public health specialist with a long track record of involvement in developing countries and the former president of Dartmouth College, took office on 1 July. He added that he wants to go beyond painting a “doomsday picture.” Encouraging companies and countries to understand that developing new technologies and approaches to combat climate change can lead to economic growth is vital, he says.

    http://scim.ag/bankclimate

  4. Contraception Research

    Reinventing the Pill: Male Birth Control

    1. Sam Kean

    Researchers tinkering with cancer drugs and related molecules have found reversible ways of altering sperm; now they need to secure money and regulatory support for drug testing.

    Zeroing in.

    James Bradner (left), Jun Qi, and others are working on contraceptives that, unlike old compounds, do not target male hormones.

    CREDIT: S. OGDEN/DANA-FARBER CANCER INSTITUTE

    In the late 1950s near Salem, Oregon, scientists started testing a birth control drug called WIN 18,446 in male prisoners. Men took responsibility for most birth control then, so a male contraceptive seemed a natural fit for American society. WIN 18,446 worked well, too: The prisoners felt fine and seemed quite healthy, except that their sperm was suddenly stunted and feeble. Unfortunately, when clinical trials shifted to the general population, men started getting sick—vomiting, sweating, headaches, blurry vision. They seemed poisoned. After some digging, scientists pinned down the culprit: alcohol. Because prisoners couldn't drink, no one had realized at first that WIN 18,446 did not mix well with liquor. The drug was abandoned, and 60 years later, no one has gotten any closer to the “male pill.”

    WIN 18,446 is a perfect example of why creating the male pill is so hard. It did exactly what it was supposed to do—stopped sperm production in everyone who took it—and it was reversible. Sperm levels returned to normal after men stopped taking it. Yet it failed anyway as a drug because of an arguably minor side effect.

    Male contraceptives are held to high standards partly because the calculus for male and female birth control is different. For example, taking the female pill increases a woman's chances of developing blood clots. But because pregnancy increases the chances of blood clots by 10 times more, the pill's side effects seem worth the risk. With men, there's no counterbalancing risk of pregnancy, so the tolerance for side effects drops to zero. That's especially true because “you're dealing with healthy people, not people with an illness, and you'd have to use [the pill] for long, long periods,” says Diana Blithe, a program director at the U.S. National Institute of Child Health and Human Development (NICHD) in Bethesda, Maryland, which funds research into male contraception.

    Drug companies have all but abandoned the male contraceptive field in the past decade. After acquiring smaller companies, for instance, both Bayer and Merck shut down those programs. (Bayer refused to say why, and a Merck spokesperson said only, “It is not a priority area.”) In addition to the medical challenges like the high safety standard, Blithe points out one other obstacle for companies: The U.S. Food and Drug Administration (FDA) has no guidelines about what levels of safety and efficacy the male pill would need to have to win approval. FDA declined to comment about whether it planned to develop guidelines or whether it has even discussed doing so.

    Over the past half-century, contraception has become largely a female issue—and drugs for women work relatively well, making a male pill seem less urgent. But intrauterine devices require a medical provider to insert, can have serious complications, and cost up to $1000. And not all women can tolerate the far more popular female pill, says Lawrence Finer, director of domestic research at the Guttmacher Institute in New York City, which specializes in reproductive issues. Because half of all U.S. pregnancies today are unplanned, he says, there's clearly a need “to increase our contraceptive repertoire.”

    With so little private support for a male pill, Blithe's program focuses as much on getting products to market as on basic biology. She will host a closed meeting in November in Houston, Texas, for about 30 top biologists to swap ideas about new genetic and biochemical leads for male contraceptives. The most promising leads involve disrupting the maturation of sperm in the testes, and although funds are tight, clinical trials for a few approaches could begin within the next few years. These researchers hope they can outsmart nature, but they know that producing an effective, safe, cheap, targeted, well-tolerated, bioavailable, easy-to-manufacture, side-effect-free, and (whew) completely reversible male pill won't be easy.

    Different targets

    Plugs. Hormones. Special underwear. Autoimmune attacks. The “dry orgasm.” There's no shortage of approaches to male contraception (see diagram, p. 319). But all share the same goal: slowing down the relentless proliferation of sperm in men and holding sperm counts to about 1 million per milliliter of ejaculate. Even the reduced concentration “may sound like a lot,” says John Amory, a doctor and reproductive biologist at the University of Washington, Seattle, “but that's a pretty good, effective contraceptive” that will reduce fertility by 99%.

    Until recently, scientists modeled most male pills on the female pill and attempted to disrupt male hormones—testosterone above all. The biochemistry is convoluted, but artificially raising testosterone levels suppresses other hormones necessary to make mature sperm. This works wonderfully—sperm levels plummet—but it's a sledgehammer approach that affects tissues throughout the body, causing widespread side effects. There's no good way to administer testosterone, either. Oral testosterone breaks down so quickly in the body that men must take several pills a day to keep levels high, and alternatives like testosterone gels or injections are a hassle. Hormonal contraception doesn't work anyway in 10% to 20% of men, Amory says.

    This strategy suffered its latest blow in April 2011, when a high-profile study led by the U.S. nonprofit group CONRAD and co-sponsored by the World Health Organization was called off early. The study had monitored more than 200 couples taking various hormones for more than a year, but side effects such as acne, weight gain, and mood changes convinced scientists that the therapy would fail in the marketplace.

    Most current research into a male pill has shifted away from widely circulating hormones toward molecules specific to the testes. One promising approach being explored by Amory and others involves disrupting retinoic acid, one of a group of molecules known collectively as vitamin A. Like hormones, vitamin A plays a role in many different tissues, so scientists can't just shut down the pathway. But sperm are so sensitive to retinoic acid that reducing its levels even a little could prove effective.

    CREDIT: Y. HAMMOND/SCIENCE

    Amory's research sprang from WIN 18,446, the failed prisoner drug. Because WIN 18,446 sickened people who drank, Amory suspected that it disrupted the breakdown of alcohols. Wine, beer, liquor, and other booze contain ethanol, which the body metabolizes into acetaldehyde. Because acetaldehyde is poisonous, an enzyme called ALDH converts it to acetic acid (vinegar, essentially). In a paper in the Journal of Andrology first published online in August 2010, Amory's team proved that WIN attaches to ALDH and gums up the process, allowing acetaldehyde to accumulate.

    Amory, though, saw the bright side. The testes also convert an alcohol (retinol, another form of vitamin A) into retinoic acid. During spermatogenesis, retinoic acid binds to the RAR protein, creating a complex that turns on genes necessary to convert precursor cells into mature sperm. The testes use a unique ALDH called ALDH1a2 in this conversion. So Amory's team tried to tweak WIN 18,446's molecular structure to make it lock onto ALDH1a2 only, and not onto the ALDH that prevents alcohol poisoning.

    It didn't work. “We tweaked the hell out of WIN 18,446,” he laughs. “Our poor organic chemist made 100 versions” in 2009 and 2010, but every one proved a dead end. Still, intrigued by the specificity of ALDH1a2, his team screened 60,000 other molecules and found seven more that gummed up ALDH1a2. They're now tweaking those seven to make them testes-specific. Amory expects four or five of them to fall short in future tests—some might prove toxic or might not cross the blood-testis barrier, a tissue firewall that separates the testes from general blood circulation. But within 5 years, he hopes to approach FDA about clinical trials.

    Debra Wolgemuth, a reproductive biologist at Columbia University Medical Center, is also targeting retinoic acid's role in sperm maturation. Through chemical screening, Wolgemuth's team identified a compound that prevents the binding of retinoic acid to RAR, so the downstream genes never get activated. Here, too, the effects are systemic: Retinoic acid binds to similar RAR proteins in other tissues, so Wolgemuth is working with chemists to tweak the drug and make it testes-specific.

    Like many in her field, Wolgemuth sees her work as important not just for domestic family planning but also for keeping Earth's overall population at sustainable levels. By some projections, Earth's population could top 10 billion by midcentury. She also says the research could help control animal populations around the world, an important application. She jokes that testing birth control in rodents gave her another idea as well. “We could use it for rats in the New York City subway,” she suggests.

    New approaches.

    Research teams led by John Amory (top) and Joseph Tash (bottom, front row) target testes-specific genes and molecules.

    CREDITS (TOP TO BOTTOM): CLARE MCLEAN/UNIVERSITY OF WASHINGTON MEDICINE; ELISSA MONROE/UNIVERSITY OF KANSAS MEDICAL CENTER

    Beyond retinoic acid pathways, there are hundreds of genes expressed only in the testes, and disturbing any one of them might disrupt the machinery of sperm production.

    One potential monkey wrench came from James Bradner, a chemical biologist at the Dana-Farber Cancer Institute in Boston. While screening potential cancer drugs a few years ago, Bradner came across JQ1, which inhibits cancer cell division. It does so by interfering with bromodomain (BRD) proteins, which turn on a master regulatory gene that promotes cancer cell proliferation. As part of the screening process, Bradner explores how drugs behave in various tissues, and he found that JQ1 also inhibited a testes-specific BRD called BRDT. Not long before, Wolgemuth's team had showed that knocking out BRDT made mice infertile, and research led by Douglas Carrell of the University of Utah in Salt Lake City showed that natural BRDT variations in men led to infertility. Bradner also knew from experience that many cancer drugs halt the proliferation of sperm, too. All signs suggested that JQ1 had potential as a contraceptive.

    Because Bradner lacked experience in the field, he called Martin Matzuk, a reproductive biologist at Baylor College of Medicine in Houston. Within 3 weeks of trying JQ1 in mice, Matzuk knew he had something special: With BRDT shut down, spermatogenesis all but stopped about halfway through the maturation process, and the sperm that did squeak through couldn't swim. Bradner and Matzuk reported these results in Cell in mid-August. Importantly, they also provided evidence that JQ1 didn't affect hormone levels and that it was reversible, because 4 weeks after mice went off it, they could father as many offspring as controls.

    Tissue targeting remains a challenge: To satisfy the demand for zero side effects, Bradner suspects the team will need to tweak JQ1 and make it perhaps 100-fold more specific for BRDT than other BRDs. As a hedge, they're also screening for other BRDT inhibitors. JQ1 may go into clinical trials next year as a cancer therapy, though, so Bradner and Matzuk may get early feedback on its contraceptive potential.

    Another compound inching toward human trials is H2-gamendazole, which is also a derivative of an old cancer drug. A team led by biologist Joseph Tash at the University of Kansas Medical Center in Kansas City determined that it disrupts Sertoli cells. In addition to providing support for sperm precursors, Sertoli cells bind the precursors in place with a sort of harness, keeping them in the testes until they mature. H2-gamendazole unravels the harness, and sperm drift off into the semen stream before they're capable of fertilizing eggs.

    Like other compounds, H2-gamendazole acts within weeks and is reversible. Its big advantage is that its target, the Sertoli cells, lie on the blood side of the blood-testis barrier. So unlike with other potential drugs, “one doesn't have to worry about that tight firewall for compounds getting across,” Tash says.

    Having completed many safety tests in rodents, Tash had hoped to start talking to FDA last year about clinical trials. But various bureaucratic delays hampered him. He had to focus on renewing his NICHD grant and also needed help from his university to hire consultants before approaching FDA. But for Tash, such delays are nothing new. He has pursued a male contraceptive since his student days in the late 1960s, when a stint in a Chicago hospital showed him how heavily the contraceptive burden fell on women. He laughs now, saying he never imagined back then that creating a male pill would take so long: “The naiveté of youth had not met the reality of funding and of collaborative research.”

    Valley of death

    Tash laments that his team has now entered the drug developer's “valley of death,” the gulf between cheap early testing and exponentially more costly human trials.

    The difficulty of bringing new drugs, especially contraceptives, to market influences how Blithe's program awards money, she says: “Applications are peer-reviewed with product development in mind. You might hear ‘It's too applied,’ or ‘That's something a pharmaceutical company should do’ in normal grant reviews, but not here.” Grants also include money to hire contractors for tasks like toxicology work.

    As for partnering with drug companies, most scientists say that companies urge them to keep them updated on any leads. But that's different from a company committing money. Blithe suspects that some companies view contraceptives as a zero-sum game—that every dollar spent on male contraceptives would mean one less dollar spent on female contraceptives. But she believes many couples will actually double up on pills. Amory does, too. “When I mention what I do at parties, people say men aren't interested in contraception,” he says. “But men were the ones responsible for most contraception before the 1960s” and still take responsibility for 30% of contraception today, he says, despite limited options. “Men are interested,” he insists.

    The NICHD meeting in November is closed to the public in part because discussing results openly could interfere with the ability to patent compounds. At the same time, both Blithe and Amory suspect that drug companies may hang back because of fears about litigation. Birth defects and infertility are common in the general population, and, statistically speaking, some couples who use the male pill will experience one or the other for reasons having nothing to do with the drug. But bad luck wouldn't necessarily stop people from suing, Amory points out.

    Still, the prize could be worth the risk. “Female oral contraception is one of the most important medicines ever developed,” Bradner says. The male counterpart could be in the same league worldwide, and the identification of testes-specific genes and enzymes makes scientists guardedly optimistic that the time for a safe, effective, targeted, and so on, male pill might be nigh. Blithe says: “To say it's a year off or 5 years off isn't accurate. [But] I suspect that if one gets out there, a lot more will follow.”

  5. Cell Biology

    Looking for a Sugar Rush

    1. Robert F. Service

    The sugar molecules that stud cell surfaces and coat many proteins play critical roles, but they are poorly understood and researchers want new tools to study them.

    Development aglow.

    Recently produced glycans (red) light up the jaw of this zebrafish embryo, while older glycans (green) have migrated inside cells.

    CREDIT: CAROLYN BERTOZZI, SCOTT LAUGHLIN, AND JEREMY BASKIN/UNIVERSITY OF CALIFORNIA, BERKELEY

    If a cell biologist wants to investigate the details of, say, breast cancer, she can follow a well-trodden path. After comparing the DNA of people with and without the disease to identify genetic sequences associated with the cancer, she may scan genome databases to pinpoint a gene of interest. With the DNA sequence in hand, she can determine the amino acid structure of the protein made by the gene, isolate the molecule to study its biochemical activity in test tubes, and even tag it with a fluorescent compound and watch where it goes inside cells to learn clues about its function. She can delete the gene from mice to learn further clues, and even synthesize drugs to enhance or block its activity. And on and on.

    If only life were that easy for researchers studying our cell's sugars.

    Chains of these sugar molecules, called glycans, polysaccharides, or sometimes carbohydrates, are a primary class of biomolecules, arguably as important as the nucleic acids DNA and RNA, proteins, and lipids. They decorate the outer surface of nearly all cells, directing communication and interactions not only between our cells but with bacteria and viruses as well. They also coat many proteins and help orchestrate the way those molecules fold into their three-dimensional shapes and bind to their targets. Scientists have never had the tools to synthesize and alter glycans in the same systematic way they've been able to with DNA and proteins. That makes glycans one of the least understood classes of molecules in biology.

    Now, glycoscience researchers say the field should make a big push to forge the suite of tools that they need to study their quarry. Even without these tools, “the pace of progress in glycoscience has been really good” in recent years, says Laura Kiessling, a chemist at the University of Wisconsin, Madison. With an appreciation for the role of sugars rising rapidly among researchers and an influx of scientific talent into the field, she adds, “the time is ripe.” That was also the conclusion of a report released in August by the National Research Council (NRC) of the U.S. National Academies, which argued that science funding agencies in the United States should focus their efforts to build tools to facilitate glycoscience research over the next decade, much as the U.S. Department of Energy and the National Institutes of Health have devoted considerable money to advancing DNA sequencing and analysis technologies.

    If scientists can master the molecular language of sugars, that could have a major impact on research areas including the development of novel vaccines and the creation of more energy-efficient biofuels. Glycoscience researchers are already pursuing such goals. But David Walt, the chemist at Tufts University in Medford, Massachusetts, who chaired the NRC study, says that without the same kinds of tools available to researchers who study DNA and proteins, such projects are typically heroic scientific pursuits that can only be pursued by specialty labs. “We want glycoscience to be democratized broadly within science and not [be] just a specialized discipline,” Walt says.

    Sweeter vaccines

    Glycans themselves certainly aren't relegated to a specialized domain. They are universal in living organisms and play a role in virtually all major human diseases. The molecules are the primary component of plant cell walls, where they are synthesized using the carbon dioxide that plants take in during respiration as raw material; as a result, plants serve as one of the biggest reservoirs for sopping up excess atmospheric carbon. Plant-based glycans can also provide a nonfossil source of fuel and novel materials. “People have recognized that glycoscience is important,” Walt says. “But by and large, people have viewed it as very complex.”

    That complexity comes from the fact that glycans are put together in a manner very different from that of more familiar families of biomolecules. In nucleic acids and proteins, the individual chemical units—nucleotide bases in the case of DNA and RNA, and amino acids in the case of proteins—are all linked by the same chemical bond. Once you master the making and breaking of that bond, you can synthesize virtually any nucleic acid or protein you want.

    Not so with glycans, which are constructed from more than a dozen individual sugar units connected with different bonds by a diverse family of enzymes. That diversity generates five main families of glycans and a wide variety of branched and chainlike structures. Moreover, unlike proteins that are synthesized according to their genetic blueprint, the structure of individual glycans is controlled only in part by the genes for those enzymes that link sugars together. Just as important, the architecture of a particular sugar chain also depends on the concentration of different enzymes in the cellular broth. This interplay between genetics and the local environment means that the glycans associated with a particular protein will vary according to the environment in which the protein was produced.

    Targeting HIV.

    Antibodies capable of inactivating the AIDS virus bind to bits of its glycan shield (blue) and the underlying coat protein.

    CREDIT: WILLIAM SCHIEF/IAVI AND THE SCRIPPS RESEARCH INSTITUTE

    That variability has been a barrier to studying the cell's sugars. For example, biologists have typically probed the structure of a protein—and gained clues to its function—by crystallizing it and using x-rays to map the location of amino acids in the protein. However, because most proteins are decorated with glycans, and the glycans on separate copies of the same protein often differ, it's a tough challenge to make coherent crystals. So structural biologists routinely strip away the glycans. But that means they have been getting an incomplete picture at best. Researchers are now getting better at keeping those components intact, in part by studying versions of proteins from insects, which typically have more uniform glycans.

    The importance of this has been illustrated by work on the glycoproteins of the AIDS virus. Last year, Ian Wilson, a structural biologist at the Scripps Research Institute in San Diego, California, and colleagues from 11 institutions reported that they engineered insect cells to express the crucial outer portion of the HIV envelope protein gp120, which they used to obtain x-ray crystal structures of two anti-HIV antibodies that neutralize up to 72% of all HIV strains (Science, 25 November 2011, p. 1097). These structures preserved the glycans that coated gp120 and revealed that the best antibody binds to two bits of highly conserved glycans, while also piercing the sugar shield to bind to the underlying protein. “Now that we're finding [binding] hotspots means we can use that to design some smaller molecules that can be used as an immune agent” and possibly a vaccine, Wilson says.

    Another area of progress involves synthesizing glycans—a skill that may also have biomedical implications. Scientists can easily make almost any small protein and assemble increasingly long strands of RNA or DNA, but they are only slowly gaining the ability to make complex glycans. At the biannual American Chemical Society (ACS) meeting in August in Philadelphia, Pennsylvania, for example, Samuel Danishefsky, a synthetic organic chemist at the Memorial Sloan-Kettering Cancer Center in New York City and Columbia University, described how his team has developed a strategy to synthesize sugars associated with tumor cells in order to spark the immune system to fight cancer.

    Researchers have known for years that many cancer cells undergo significant changes to their cell surface glycans. Some have tried to use those changes to identify molecular markers for various cancers to serve as diagnostics and as molecules that stimulate an immune response.

    Getting the body's immune system to pay attention to a sugar is a challenge, however. Cell surface glycans, even when altered in cancer cells, are usually not seen as “foreign” by the immune system. So an early cancer vaccine approach was to synthesize a fragment of a common cancer cell surface glycan and link it to an immune-stimulating compound, such as a peptide or nanoparticle, as well as adding additives called adjuvants that can also spark an immune response to the sugars. One candidate anticancer vaccine following this strategy targets a sugar known as globoH, and the vaccine is now in phase II and III clinical trials against breast cancer and phase I clinical trial against prostate cancer.

    Early results have been promising, but different cells in a single tumor often express different cell surface glycans that serve as the “antigen” targets of antibodies. “It's not likely cancer vaccines will get all the cells, since each vaccine goes against one antigen,” Danishefsky says. That's why he and his group came up with the idea of synthesizing five known tumor-specific sugars, linking them together, and then attaching them to an immune-stimulating protein. At the ACS meeting, Danishefsky reported that early animal results look promising and that the vaccine has entered initial clinical trials against ovarian cancer.

    But that's only the beginning, Danishefsky says. His group has also begun to tackle complex sugars on prostate-specific membrane antigen (PSMA), a glycoprotein expressed on prostate cancer cells (and different from the well-known prostate-specific antigen, PSA). At the ACS meeting, Danishefsky reported that one of his postdoctoral assistants, Maciej Walczak, recently synthesized two different complex PSMA glycans, one made up of 14 sugars linked together, the other with 17 sugars. A major challenge for the project was that each pair of adjacent sugars in the molecule can bind in one of two different orientations. So Walczak had to control the binding direction at each point. He also broke the problem apart, initially synthesizing multiple pieces of the molecule and then linking them together into the final structures. Those compounds are now being readied as cancer vaccines for testing in animals.

    Geert-Jan Boons of the University of Georgia in Athens is taking a more streamlined approach. Although he acknowledges that linking tumor-bound sugars to proteins can induce an immune response, Boons argues that in many cases the strongest response is against the carrier proteins and not the sugars. So he and his colleagues have focused their efforts on linking their sugar targets to a small peptide, known as MUC1, that triggers a strong immune reaction, but is also small enough that antibodies bind both to it as well as to its associated sugars, much as Wilson's broadly neutralizing antibodies bind both to the HIV coat protein and the sugars on top. At the ACS meeting, Boons reported that his team's slimmed-down vaccine using sugars from breast cancer cells reduced tumor sizes by 80% in mouse models of breast cancer. Peng George Wang, a glycochemist at Georgia State University in Atlanta, says that both the slimmed-down and hefty vaccine approaches look promising for now, increasing optimism that at least one will pan out in the clinic.

    Fueling up on sugar

    Even though scientists have identified many of the enzymes that assemble sugars in vivo, they are still sorting out exactly how they work and learning how to manipulate the synthesis of glycans in living animals or plants. Eventually, they hope to be able to control the way organisms produce glycans, in much the same way biologists have long used genetic engineering to alter the production of proteins. For example, at the ACS meeting, Markus Pauly, a chemist at the University of California (UC), Berkeley, reported that his group has been making strides in reengineering the way plants make their sugars, which may enable the creation of next-generation biofuels.

    Seeing stem cells.

    Fluorescent blue compounds attach to glycans on pluripotent stem cells, as they differentiate to form nerve cells (green).

    CREDIT: SAMIRA MUSAH AND LAURA L. KIESSLING/UNIVERSITY OF WISCONSIN, MADISON

    Today's primary biofuel, ethanol, is made by microbes that ferment the sugars in corn kernels and sugar cane. Both of those crops compete with food crops for agricultural land, however. Researchers have worked for decades to get those sugars instead from agricultural wastes, such as wood chips and corn stovers. But plant cell walls typically contain lignin and a form of sugars called hemicellulose that microbes that make ethanol can't handle.

    Hoping to reengineer plants to produce less hemicelluloses and lignin, Pauly and his colleagues have started with the well-studied mustard Arabidopsis thaliana. Like most plants, this one makes several different sugar polymers, each of which contains a sugar backbone with extra side chain sugars dangling off. Pauly's group blocked the genes for the enzymes in the mustard plant that tack on those side chains and, not surprisingly, found that those plants grew poorly, if at all. They then introduced a gene from a tomato plant for an enzyme that tacks on a sugar called arabinose, which Arabidopsis doesn't normally use, to growing sugar backbones. The mustard plants grew normally. “It doesn't matter what sugar is [in the side chain] as long as there is a sugar,” Pauly says. It's too early to tell if this will make it possible to design plants with more sugars that microbes can ferment, Pauly says, but he adds that they're beginning such tests now.

    Even as some research teams grow more adept at altering the glycans of living organisms, others are finding new ways to image sugars in and around cells—a key technology to showing the impact of any manipulation. In 2006, for example, Carolyn Bertozzi, a chemist at UC Berkeley, and her colleagues developed a two-step technique to image glycans in living organisms. They created sugar building blocks containing a chemical group called an azide that's not found in organisms. They then created fluorescent probes containing other compounds that seek out and bind solely to azides. That way, when the modified sugars are incorporated in glycans, Bertozzi's group could image where those glycans ended up.

    The group went on to use that technique to track how glycans change in zebrafish during embryonic development (Science, 2 May 2008, p. 664). And more recently, they've begun using the technique to track how bacteria use a combination of sugars and peptides, called peptidoglycans, to build their cell walls. Because peptidoglycans are a primary target of antibiotics, the new approach could lead to novel antibiotics against a host of infectious diseases. “We think that this will be a really nice method to monitor what happens when you block peptidoglycan synthesis,” Bertozzi says.

    The road ahead

    With strides being made across all these areas of glycoscience, Walt and others say the field now needs to focus on making it easier for other groups to reach the cutting edge. “There is recognition that it is important that we apply the same kind of tools and innovation to glycoscience as areas of molecular biology that have already been revolutionized,” Walt says. “I think it's more difficult but completely tractable.”

    NRC outlined some specific recommendations to bring about this glycorevolution. It called on federal agencies to fund technology development programs to create techniques to better image, sequence, and synthesize glycans. As work like that from Danishefsky and Bertozzi shows, the cupboard isn't bare. But, Walt notes, individual advances are typically only applicable to a subset of glycans. He and the other authors of the report also suggest creating a centralized database of mammalian, plant, and microbial glycans, similar to the Protein Data Bank for proteins and GenBank for genes.

    In this era of tight budgets, Walt says he doesn't know where the money will come from to build the needed foundation for glycoscience. But perhaps new money isn't needed: He hopes that the NRC report will help science funding agencies focus their efforts on particular projects and coordinate their work. If so, Walt suggests, in a decade or so, scientists may be ready to launch a human glycome project and pull back the curtain on the role of sugars in biology just as they have done with genes.

  6. Nuclear Physics

    Primordial Matter Comes Into Focus in Many Tiny Big Bangs

    1. Adrian Cho

    A standard model is emerging of the quark-gluon plasma produced in collisions of heavy nuclei. But will a key atom smasher run long enough to flesh it out?

    Kapow!

    Thousands of subatomic particles streak through the ALICE detector at Europe's Large Hadron Collider as two lead nuclei collide head-on.

    CREDIT: CERN

    WASHINGTON, D.C.—It's a scientific sea change that rolled in without a decisive measurement or cry of “Eureka!” Twelve years ago, physicists first used an atom smasher to reproduce an exotic form of nuclear matter known as the quark-gluon plasma, which filled the universe microseconds after the big bang. But only now, after myriad subtle measurements, is a clear understanding of the stuff emerging, as physicists reported here at a recent meeting.* A standard model of the quark-gluon plasma is finally coming into focus, they say, and another decade or so of experiments should nail that model down.

    Each puff of quark-gluon plasma is like a tiny big bang. Studying the stuff won't reveal a lot about how the universe grew up; eddies in the plasma could not leave their traces in the distribution of galaxies. But probing the plasma enables physicists to glimpse the infant cosmos and to explore nuclear matter at its most extreme.

    Physicists say the study of the plasma is evolving much like earlier work on the big bang's afterglow, the cosmic microwave background (CMB). Scientists stumbled on the CMB in 1965 and in 1992 detected tiny variations in its temperature across the sky. But only in 2003 did they measure those variations well enough to deduce the exact composition and age of the universe. “Our field is on the same journey from ‘Wow!’ effects to numbers and, finally, to textbook physics,” says Urs Wiedemann, a theorist at the European particle physics laboratory, CERN, near Geneva, Switzerland.

    But will physicists get to complete that journey? Only two atom smashers can make the quark-gluon plasma: the Large Hadron Collider (LHC) at CERN and the Relativistic Heavy Ion Collider (RHIC) at Brookhaven National Laboratory in Upton, New York. And RHIC is the only machine dedicated to such work and can do things that the LHC cannot. However, the U.S. Department of Energy (DOE), which owns Brookhaven, faces a budget crunch that may force it to choose between running RHIC and supporting other nuclear physics facilities (Science, 27 January, p. 392). Physicists studying the quark-gluon plasma say they could lose their main machine just as years of effort are about to pay off.

    Nuclear fondue

    To create a quark-gluon plasma, physicists must literally melt atomic nuclei. A nucleus consists of protons and neutrons, each composed of three particles called quarks bound by a haze of others called gluons that convey the strong nuclear force. Quarks attract one another so strongly that one cannot be isolated. Knock a quark out of a proton, and on its way out it will rip quarks and antiquarks out of the vacuum to produce a “jet” of quark-filled particles.

    But slam two heavy nuclei together with enough energy, and the protons and neutrons can melt to form a soup of unbound quarks and gluons that is the plasma. More quarks, antiquarks, and gluons spring from the superheated vacuum. For a few trillionths of a trillionth of a second, the trillion-degree plasma is the hottest stuff in the universe. Then it cools to form thousands of ordinary particles, which physicists can detect.

    Probing the plasma is a subtle art. Physicists can study how it flows by scrutinizing the almond-shaped puffs of plasma formed when nuclei collide off-center, as most do. In 2001, physicists working with STAR—one of two detectors currently fed by RHIC—found that the ensuing sprays of particles carried more momentum out of the sides of the cloud than through its ends. Such “elliptic flow” shows that, unlike ordinary matter, the plasma flows like a liquid with almost no viscosity.

    Researchers can also study how the sticky plasma snuffs out jets within it. Measurements from STAR and RHIC's other detector, PHENIX, found that plasma-producing collisions of gold nuclei created fewer jets than collisions of protons did (Science, 20 June 2003, p. 1861).

    The plasma should also weaken the bond between quarks and antiquarks, and physicists can measure how that effect reduces the production of certain particles in a collision. For example, a particle called the J/ψ contains a charm quark—a massive and unstable cousin of the up quarks and down quarks in protons and neutrons—and an anticharm quark. In 2007, the PHENIX team found a suppression of J/ψs in collisions of gold nuclei relative to collisions of protons.

    The emerging model

    Thanks to such measurements, a clearer picture is emerging of how the quark-gluon plasma flashes into and out of existence, physicists say. As the nuclei speed toward each other at near-light speed, the weird effects of relativity take over, explains Raju Venugopalan, a theorist at Brookhaven. The so-called Lorentz contraction flattens the nuclei like pancakes. Time dilation also slows their inner workings, so that the haze of gluons in each nucleus resembles a disk of glass called a color glass condensate.

    When the two nuclei collide, the quarks in the protons and neutrons pass through each other. But the disks of gluons clap together to create a hot nonequilibrium state known as a “glasma.” That stuff quickly equilibrates to make the plasma, which expands and flows before cooling into particles. Basic questions remain: Can plain old “quantum field theory” describe the plasma, or do the quarks and gluons interact so strongly that theorists must use exotic methods borrowed from string theory? However, “for the picture as a whole, there are no big conceptual alternatives,” CERN's Wiedemann says.

    Drilling down.

    U.S. researchers have lowered their atom smasher's energy in search of a transition from nuclear matter to quark-gluon plasma.

    CREDIT: G.GRULLÓN/SCIENCE

    Physicists are now trying to test that model. Some of the most telling data for that work comes from CERN's LHC, which normally blasts protons together to try to create new particles, such as the recently discovered Higgs boson (Science, 13 July, p. 141). But the LHC also smashed lead nuclei for a month in 2010 and again in 2011 at an energy 14 times as high as RHIC's maximum. The LHC feeds a huge detector called ALICE that is dedicated to quark-gluon plasma work, as well as others known as ATLAS and CMS that study the plasma when not hunting new particles.

    Those state-of-the-art detectors can probe the plasma as never before. For example, physicists had assumed that nuclei colliding exactly head-on would produce dull round whiffs of plasma. Instead, researchers at the LHC found that in an “ultracentral” collision, they could detect flow patterns caused by quantum-mechanical fluctuations in the shapes of the nuclei. They could describe each collision's unique shape as a sum of an oval, a triangle, a square, and other shapes.

    Now, Björn Schenke, a theorist at Brookhaven, has fit the average distributions of those shapes measured by ATLAS. To do that, he has to include the distribution of gluons within a proton or neutron as measured in electron-proton collisions. The analysis supports the general scheme and shows that the plasma's viscosity is within a factor of 2 of a conjectured fundamental lower limit, Schenke reported. “That guy really made a splash,” says Ulrich Heinz, a theorist at Ohio State University, Columbus. “For me, this is like a lot of pieces of the puzzle starting to come together.”

    CMS researchers have achieved a similar feat of precision. Within the plasma, they can spot a particle known as the ϒ(1s), or “upsilon-one-s,” that contains a superheavy bottom quark and an antibottom quark. They can also identify two slightly heavier “excited” versions of the particle known as the ϒ(2s) and ϒ(3s). The quark-gluon plasma suppresses the formation of ϒ(3s) more than the formation of the ϒ(2s), which it suppresses more than that of the ϒ(1s), reported Camelia Mironov of the École Polytechnique in Palaiseau, France. That's just what should happen if the quark-gluon plasma gets between the massive quark and antiquark and “screens” them from each other, as the ϒ(3s) is more loosely bound than the ϒ(2s), and the ϒ(1s) more loosely bound still. Screening probes other properties of the plasma, theorists say.

    Surprises still

    Given such results, some researchers say the LHC has eclipsed RHIC. “It's undeniably a higher precision tool,” says Georg Wolschin, a theorist at Heidelberg University in Germany. Still, RHIC is more flexible than the LHC. It can collide various nuclei, including unlike ones such as copper and gold, and it can step down in energy.

    RHIC'S ability to dial down the energy gives it a shot at mapping out the conceptual border between ordinary nuclei and quark-gluon plasma. At the LHC's energy and RHIC's highest energy, the transition from nuclei to plasma and back appears to be a smooth “crossover.” But under the right conditions the transition may become abrupt, like the boiling of water. That change would mark a “critical point” on a graph of the properties of nuclear matter with temperature on one axis and the initial density of protons and neutrons on the other (see diagram).

    In 2010 and 2011, RHIC researchers set out to find that critical point. They reduced RHIC's energy to as little as 8% of its maximum of 200 giga-electron volts (GeV) per proton or neutron, to lower the temperature and, counterintuitively, increase the proton and neutron density. Between 27 and 19 GeV, subtle changes in the number of protons relative to antiprotons hint that the critical point may be near, reported Lokesh Kumar of Kent State University in Ohio.

    Others view the energy-scan data differently. If RHIC turns down its energy until it stops producing quark-gluon plasma, the elliptic flow ought to change dramatically, notes Miklos Gyulassy, a theorist at Columbia University. But STAR researchers see no such sudden change. That finding could overturn the theoretical apple cart, Gyulassy says. “They haven't found the critical point, but they've found a systematic sameness that's shocking,” he says. The result suggests that even at the lowest energy, RHIC still produces the plasma, says Jürgen Schukraft, an ALICE team member from CERN. “For 20 years, our biggest problem was to find the quark-gluon plasma,” he says. “Now our biggest problem is not to find it but to make it go away.”

    DOE officials may soon have to decide if such problems are worth pursuing. In addition to RHIC, DOE also runs an electron accelerator at Thomas Jefferson National Accelerator Facility in Newport News, Virginia, to probe the structures of the proton, the neutron, and nuclei. And researchers at Michigan State University in East Lansing plan to build a $615 million accelerator to generate exotic nuclei. But the three projects won't all fit into DOE's $550 million annual budget for nuclear physics, which is unlikely to increase soon.

    RHIC researchers argue that it would make no sense for them to stop now. “You don't build a Ferrari to drive it 10,000 miles and then give it away,” Ohio State's Heinz says. “To make this emerging picture really stick together, another 10-year program is still needed.” LHC researchers agree that RHIC should keep going. “The physics that we do at the LHC, we do very well,” Schukraft says. “But we can't do the same physics as at RHIC.” Besides, the LHC will smash nuclei for only 6 months total in the next 10 years. RHIC can smash them for 6 months each year.

    Whether such arguments hold sway should soon become clearer. DOE has asked a panel of experts to evaluate its options and report back in January, says Timothy Hallman, DOE's associate director for nuclear physics. Physicists may then have a better idea of just how long RHIC will keep banging away.

    • * Quark Matter 2012 International Conference, 13–18 August.

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