Hot off the presses! Mar 01 Nature

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Latest Articles Include:

• Simplification is essential
  - Nature 463(7284):999 (2010)
  The new European research commissioner deserves political support from member states of the European Union to drastically reduce the dead weight of Brussels bureaucracy.
• Bridges, not barriers
  - Nature 463(7284):999 (2010)
  Industry talent should be welcomed into academia, not seen as a corrupting influence.
• An absurd law
  - Nature 463(7284):1000 (2010)
  Turkey's government is about to pass legislation that could cripple the country's biological research.
• Energy: Carbon from the mountains
  - Nature 463(7284):1002 (2010)
  
• Neuroscience: Baby blues
  - Nature 463(7284):1002 (2010)
  
• Particle physics: Dazzling dysprosium
  - Nature 463(7284):1002 (2010)
  
• Molecular imaging: Tumour glows out
  - Nature 463(7284):1002 (2010)
  
• Evolutionary biology: On the invasion front
  - Nature 463(7284):1002 (2010)
  
• Cell biology: Lost in the mail
  - Nature 463(7284):1002 (2010)
  
• Organic chemistry: Catalysts cooperate
  - Nature 463(7284):1003 (2010)
  
• Biology: Colour-blind
  - Nature 463(7284):1003 (2010)
  
• Genetics: Male regulator switched
  - Nature 463(7284):1003 (2010)
  
• Developmental biology: Heads or tails
  - Nature 463(7284):1003 (2010)
  
• Journal club
  - Nature 463(7284):1003 (2010)
  
• News briefing: 25 February 2010
  - Nature 463(7284):1004 (2010)
  The week in science. This article is best viewed as a PDF Policy|Business|Research|Events|People|Business watch|The week ahead|Number crunch|Sound bites The US National Institutes of Health (NIH) is considering extending the definition of human embryonic stem-cell lines eligible for federal funding, to include those from earlier-stage embryos than currently allowed. Pre-blastocyst embryos might become eligible under a revised rule proposed on 19 February. It is a "trivial, small change of the wording that could have enormous scientific benefit", says Susan Fisher, a stem-cell biologist at the University of California, San Francisco, who recently submitted ten lines derived from pre-blastocyst embryos to the NIH. See go.nature.com/vmucio for more. Drug-maker GlaxoSmithKline (GSK) was aware of cardiac risks associated with its diabetes drug Avandia (rosiglitazone) years before they became public but sought to minimize the findings, said the US Senate finance committee in a report released last week. Two senators also challenged Margaret Hamburg, the commissioner of the US Food and Drug Administration (FDA), to justify an ongoing trial that compares Avandia with a competing drug. The finance committee released documents from the FDA — where an advisory committee voted in 2007 to keep Avandia on the market — in which two FDA safety experts called the trial "unethical and exploitative". GSK says that the Senate report cherry-picked information and mischaracterized its efforts to research and communicate the risks of Avandia. The Wellcome Trust, Britain's biggest charitable funder of biomedical research, has for the first time explicitly set out five priority areas it wants to fund, in a ten-year strategic plan announced on 22 February. The "research challenges" where funding will be focused include studies into chronic diseases and the effects of ageing on cell function, and the interplay between the environment, nutrition and health. In 2008–09 the trust spent a total of £720 million (US$1.1 billion) on research. The large Brazilian ethanol producer ETH Bioenergia announced on 18 February that it would take over the debt-ridden Brazilian Renewable Energy Company (Brenco) to create a world-leading company to make ethanol from biomass. The combined firm aims to produce 3 billion litres of ethanol annually by 2012, ETH stated, by which time the companies will have invested 3.5 billion reals (US$2 billion) on top of existing investments of 3.8 billion reals. The move follows Shell's 2 February announcement of its joint venture with another big Brazilian ethanol firm, Cosan (see Nature 463, 592; 2010). The US Department of Energy on 16 February issued an US$8.3-billion loan guarantee for a pair of nuclear power plants in Georgia, potentially clearing the way for the first new commercial reactors to be granted permits in more than three decades. The federal support would cover debt in case of loan default, allowing a consortium led by Southern Company, based in Atlanta, Georgia, to secure lower-interest commercial loans from skittish Wall Street banks. The Obama administration hopes to issue loan guarantees for seven to ten plants country-wide, to build confidence in the industry. SOURCE: NOVOZYMES Enzymes that convert woodchips, maize leaves and stalks, and municipal waste to sugars are getting cheaper. At a national US ethanol conference in Orlando, Florida, last week, biotech companies Novozymes and Genencor launched new generations of enzymes that they claim will cut the enzyme-related production costs of cellulosic ethanol to less than US$0.13 a litre. Poul Ruben Andersen, global marketing director at Novozymes, based in Bagsværd, Denmark, says that a few years ago enzymes accounted for more than half the cost of cellulosic ethanol production, but now only contribute a quarter (see chart). "Enzyme costs are not the number-one concern any more," agrees Aaron Kelley, a senior engineer at Genencor, based in California, which is a subsidiary of Danisco, headquartered in Copenhagen, Denmark. Despite the economic downturn, cellulosic ethanol companies such as Poet, in Sioux Falls, South Dakota, are expecting to start commercial production in late 2011 or early 2012 at a total cost of under $0.53 per litre — roughly on a par with that of 'corn' ethanol produced from sugar-rich maize cobs. Lower enzyme costs are already factored in to these projections, notes Kelley, but their progress — though expected — may bring confidence to wary investors. Out of 52 initial proposals and a shortlist of 6, on 18 February the European Space Agency selected three medium-sized missions to continue development within its 'Cosmic Vision 2015–2025' programme, with an eye towards launching two of them in 2017–18. Cost-capped at €450 million (US$610 million) each, the missions are: Euclid, to measure dark energy and dark matter; Planetary Transits and Oscillations of stars (PLATO), to detect extrasolar planets when they pass in front of their stars; and Solar Orbiter, which would sidle up to within 62 solar radii of the Sun. A decision on the two winners is expected in mid-2011. The company developing South Africa's pebble-bed nuclear reactor said on 18 February that it is contemplating shedding three-quarters of its 800-strong staff after losing government funding. See page 1008 for more. The European Space Agency has postponed the planned 25 February launch of its satellite for monitoring variations in the extent and thickness of polar ice. The agency says that the Russian launch rocket that will carry CryoSat-2 into its required orbit did not have enough spare fuel in its second-stage engine. The delay could be around a month. NASA/JPL-CALTECH/UCLA NASA's Wide-field Infrared Survey Explorer (WISE) has offered up the first pictures since its 14 December launch, including these colour-altered images of the comet Siding Spring (right) and the Andromeda galaxy. WISE will mainly seek the cool glow of asteroids and brown dwarfs, almost-stars that aren't quite massive enough to ignite. Whereas the infrared Spitzer Space Telescope honed in on specific objects, WISE, with its huge field of view, will take an infrared census. It should complete 1.5 sweeps of the sky before its cryogens run out around October. Raynard Kington, deputy director of the US National Institutes of Health (NIH), will leave the biomedical agency in late July to become president of Grinnell College in Iowa, NIH director Francis Collins announced on 17 February. Kington, a physician with a doctorate in health policy and economics, became a key administrator at the NIH over the past decade. As acting director before Collins took the helm last August, he oversaw the allocation of US$10.4 billion in economic stimulus funds and the development of new guidelines for funding of human embryonic stem-cell research. Austrian social scientist Helga Nowotny has been elected president of the European Research Council (ERC), which funds cutting-edge research in Europe. Currently vice-president, Nowotny is based in Vienna and is an emeritus professor at the Swiss Federal Institute of Technology in Zurich. She will take up the position on 1 March, replacing the ERC's founding president, Fotis Kafatos, who resigned last month (see Nature 463, 407; 2010). K. NAVNTOFT/EPA/CORBIS Yvo de Boer (pictured), executive secretary of the United Nations Framework Convention on Climate Change, unexpectedly announced his resignation on 18 February after almost four years leading climate negotiations. "I believe the time is ripe for me to take on a new challenge," he said, telling Associated Press that the failure of the climate talks in Copenhagen last year was not a factor in his decision to quit. De Boer leaves his post on 1 July, and will join consultancy group KPMG, where he will advise on climate and sustainability. Federal authorities in the United States announced on 19 February the conclusion of their investigation into the 2001 anthrax attacks, which killed five people. They determined that biodefence researcher Bruce Ivins was the sole perpetrator; he committed suicide in July 2008, before indictment. A National Academy of Sciences panel commissioned last year is still reviewing the scientific evidence used in the case, such as analysis tracing mailed Bacillus anthracis spores back to a single-spore batch in Ivins's lab at the US Army Medical Research Institute of Infectious Diseases in Fort Detrick, Maryland. The World Health Organization reviews its Framework Convention on Tobacco Control, on the fifth anniversary of the treaty's entry into force. → go.nature.com/RMwxIo The 41st Lunar and Planetary Science Conference takes place at the Woodlands, Texas. Special sessions focus on recent findings from lunar orbiters LCROSS, Chandrayaan-1 and Chang'e-1. → go.nature.com/QIbppz The International Emissions Trading Association joins with various United Nations agencies to host the second Africa Carbon Forum in Nairobi, Kenya. The meeting aims to boost lowcarbon projects in Africa under the Kyoto Protocol's Clean Development Mechanism. → go.nature.com/Nz7bZt Number of authors on two 2001 papers announcing the draft sequence of the human genome. Number of authors on 2010 paper of initial results from the Compact Muon Solenoid detector at the Large Hadron Collider. Jeff Greason, president of XCOR Aerospace, based in Mojave, California, gets excited by the promise of cheap spaceflight, at a space-research conference in Boulder, Colorado, last week. See go.nature.com/AjykOj for more on the conference. There are currently no comments. This is a public forum. Please keep to our Community Guidelines. You can be controversial, but please don't get personal or offensive and do keep it brief. Remember our threads are for feedback and discussion - not for publishing papers, press releases or advertisements.
• 'Seek, test and treat' slows HIV
  - Nature 463(7284):1006 (2010)
  Studies in several nations show that treating people before they fall ill can curb the spread of disease. Testing whole populations for HIV and treating those infected may slow the spread of the disease.P.-A. Pettersson/Getty Treating HIV infection aggressively before symptoms appear could help to control the spread of the disease, according to data presented at a retroviral conference last week. Independent studies in Canada, the United States and Africa support the strategy in both the developed and developing world. However, the studies are not definitive and some scientists argue that improperly expanding treatment could cause problems. Evidence in favour of 'treatment as prevention' has been building for more than a decade. Treating pregnant women who are HIV-positive, for instance, decreases disease transmission to their babies by lowering virus levels in the mother1. Modellers with the World Health Organization last year predicted that HIV could be almost eliminated within 50 years by finding and treating every HIV-infected person immediately — rather than waiting for the disease to advance to the point at which treatment is recommended by current guidelines2. At the annual Conference on Retroviruses and Opportunistic Infections in San Francisco, California, on 16–19 February, Deborah Donnell of the Fred Hutchinson Cancer Research Center in Seattle, Washington, bolstered the 'seek, test and treat' strategy with data from a study of 3,408 couples from seven African nations in which only one partner had HIV. During the study, HIV-positive individuals who were receiving treatment almost never passed the virus on to their partner, whereas many untreated individuals did. "Rather than an all-or-nothing phenomenon, let test and treat be part of a more aggressive prevention armamentarium." In another study, Moupali Das of the San Francisco Department of Public Health reported that as 'community viral load' — the amount of virus in the blood of all HIV-infected individuals tested in San Francisco — declined from 2005 to 2008 because of drug treatment and increased awareness, the number of new infections in the city also dropped. Julio Montaner, director of the British Columbia Centre for Excellence in HIV/AIDS, described similar results last year for a study of intravenous drug users in Vancouver3. At the conference, he reported that when treatment was expanded to intravenous drug users with HIV throughout British Columbia, new HIV diagnoses in that group dropped by around 50%. "The fact that more treatment would curb the epidemic is clear at a population level, and we would like to see the seek, test and treat strategy endorsed throughout the developed and developing world," Montaner says. However, these studies do not prove that treatment itself caused the declines in new infections because there were many confounding factors beyond the investigators control. And other data presented at the meeting introduced a cautionary note about the strategy. Sally Blower of the University of California, Los Angeles, argued that scarce resources in developing countries would be better spent reaching the more than 9 million people who already need treatment and are not getting it. And she reported on model results suggesting that if therapies were offered to almost everyone in South Africa who needed them, drug-resistant strains could surge until they comprised up to 20% of circulating HIV strains. Yet in Montaner's study, drug resistance actually dropped across the province when treatment was extended to all intravenous drug users. Clinical trials of the seek, test and treat strategy will begin this year in New York and Washington DC, and others are planned by French and British agencies. A randomized trial already under way in nine countries is testing whether early treatment leads to durable prevention of transmission within couples. That study will not report results for several years. ADVERTISEMENT Even if the most optimistic models are not correct, more aggressive efforts to expand treatment to everyone will probably dent the spread of the epidemic, says Anthony Fauci, director of the US National Institute of Allergy and Infectious Diseases in Bethesda, Maryland. "Rather than saying it's an all-or-nothing phenomenon — that we're going to eliminate the epidemic without anything else but test and treat — what I argue for is, why don't we let test and treat be part of a more aggressive prevention armamentarium," Fauci says. "I would be satisfied with the epidemic if not disappearing, then at least declining, and I see seek, test and treat as one of several tools in the tool kit that will get us there." * References * De Cock, K. M.et al. J. Am. Med. Assoc.283, 1175-1182 (2000). * Granich, R. M.et al. Lancet373, 48-57 (2009). * Wood, E.et al. Br. Med. J.338, b1649 (2009). There are currently no comments. This is a public forum. Please keep to our Community Guidelines. You can be controversial, but please don't get personal or offensive and do keep it brief. Remember our threads are for feedback and discussion - not for publishing papers, press releases or advertisements.
• Reserves 'win–win' for fish and fishermen
  - Nature 463(7284):1007 (2010)
  Marine protection areas could offer fisheries a boost. The diverse ecosystem of California's Monterey Bay is the focus of a National Marine Sanctuary.R. Schwemmer, CINMS, NOAA Although fisherman routinely fight bans on fishing, studies indicate that the creation of protected marine reserves in key areas can both raise the profits of fishermen and boost fish populations. Researchers presented evidence of these dual benefits in several sessions over the past week at the annual meeting of the American Association for the Advancement of Science (AAAS) in San Diego, and in a suite of papers published in the Proceedings of the National Academy of Sciences. Marine reserves could help to make nearby fisheries profitable by acting as nurseries for fish larvae that are later spread by ocean currents, for example. "Reserves allow a win–win situation — better conservation and higher profitability for fishing," says Christopher Costello, a resource economist at the University of California, Santa Barbara (UCSB). His group's modelling study of southern Californian waters suggests that fishing profits are maximized when significant areas are closed to fishing1. Steven Gaines, a UCSB marine ecologist who organized an AAAS symposium on marine reserves, adds that his own team's research with ocean circulation models shows that protected areas do not need to be extensive. Strategic positioning of smaller reserves in a network can create pathways for fish outside protected zones, which can boost the yields of fishermen. Research on one of the world's largest marine conservation efforts, along Australia's Great Barrier Reef, shows how quickly such efforts can make a difference. Nearly one-third of the 2,000-kilometre-long reef off Queensland is set aside as 'no-take' zones, after stringent controls were put in place in 2004. Terry Hughes, director of the Australian Research Council's Centre of Excellence for Coral Reef Studies in Townsville, Queensland, said at the symposium that his team's reef research2 found that, in the no-take zones he studied, overall fish densities have doubled since they were created. On some reefs, the population of certain species, such as grouper, doubled within just two years of fishing closures. "The reef generates far more economic benefit to Australia than the cost of protecting it," he adds, estimating that the costs are less than 1% of annual revenue generated from other reef activities, such as tourism. The experience of the Great Barrier Reef could inform an ongoing debate in California. The state is involved in a contentious process to create networks of reserves that could eventually encompass 10–20% of the state's coastline and stretch up to 5 kilometres from shore. The Marine Life Protection Act was approved by Californian voters in 1999, but attempts to establish the reserves it mandated have been delayed by strong resistance. The battle between marine conservationists and fishermen has become so bitter that armed game wardens now attend public hearings about the plan. Fist fights have broken out at some meetings and, at one, Paul Dayton, a marine biologist at the Scripps Institution of Oceanography in La Jolla, was spat at by a fisherman. A reserve system has so far been adopted for two regions along the central coast; a plan for a southern coastal region is under review; and plans are to be developed for the final two areas by the end of 2011. Many complain that the scheme is too costly, and argue that there is little evidence that reserves successfully protect marine wildlife. But marine biologist Jennifer Caselle at the UCSB and her colleagues have put paid to this claim3. ADVERTISEMENT Her team studied ten no-take and two fishing-restricted zones created in 2003 within the 100-kilometre-long Channel Islands National Marine Sanctuary off Santa Barbara. The scientists found that the number and size of the fish targeted for protection was greater in the reserve than outside. They also found that the ecosystem was healthier overall, with more predators such as spiny lobster and California sheephead helping to keep sea urchins under control. Because the urchins graze on kelp — an important habitat for many fish species — Caselle says that "the increased abundance of predators may help to prevent the transition of productive kelp forests into unproductive urchin barrens". The research was greeted cautiously by Norman de Vall, president of Redwood Coast Watersheds Alliance in Elk, California, where reserve planning is now under way. Even if reserves produce larvae that move into unprotected areas, that may not be enough to help fishermen, says de Vall, a former commercial fisherman. What is needed, he said, is smarter management of fishing stocks overall and "less fishing everywhere". * References * Costello, C. et al. Proc. Natl Acad. Sci. USAdoi.10.1073/pnas.0908057107 (2010). * McCook, L. J. et al. Proc. Natl Acad. Sci. USA doi:10.1073/pnas.0909335107 (2010). * Hamilton, S. L., Caselle, J. E., Malone, D. P. & Carr, M. H. Proc. Natl Acad. Sci. USAdoi:10.1073/pnas.0908091107 (2010). There are currently no comments. This is a public forum. Please keep to our Community Guidelines. You can be controversial, but please don't get personal or offensive and do keep it brief. Remember our threads are for feedback and discussion - not for publishing papers, press releases or advertisements.
• Did design flaws doom the LHC?
  - Nature 463(7284):1008 (2010)
  Catastrophic failure that caused accelerator shutdown was not a freak accident, says project physicist. It took months to repair magnets that were damaged in a major accident to the LHC in September 2008.M. Brice/CERN Running more than a year behind schedule and at half its intended energy, the world's most powerful particle accelerator is slated to begin its first full scientific run this week. Along with relief, the occasion is bringing some soul-searching. One senior scientist who helped to build the Large Hadron Collider (LHC) at CERN, Europe's particle-physics laboratory near Geneva, Switzerland, is claiming that the cause of the delay — a major accident in 2008 — could have been avoided. "Any technical fault is a human fault," says Lucio Rossi, a physicist who oversaw the production of the accelerator's superconducting magnets. In a paper published on 22 February (L. Rossi Supercond. Sci. Technol. 23, 034001; 2010), he concludes that the catastrophic failure of a splice between two magnets was not a freak accident but the result of poor design and lack of quality assurance and diagnostics. The project, he says, will be coping with the consequences for many months to come. "What we have to do is learn from our mistakes and make it better." On 19 September 2008, just weeks before the LHC was first scheduled to start colliding protons, an electrical short caused massive damage. A connection between two superconducting cables developed a small amount of resistance, which warmed the connection until the cables — cooled by liquid helium to superconducting temperatures — lost their ability to carry current. Thousands of amps arced through the machine, blowing a hole in its side and releasing several tonnes of liquid helium. The expanding helium gas created havoc, spewing soot into the machine's ultraclean beamline and ripping magnets from their stands. Repairs took more than a year, and the LHC successfully restarted last November. An investigation revealed that technicians had not properly soldered the cables together. With tens of thousands of such connections, it is perhaps inevitable that some were faulty, Rossi says, but design flaws worsened the problem. The silver–tin solder that was used melted at high temperatures and did not flow easily into the cable joints. Moreover, workers did not adequately check to see if each connection was electrically secure. Sensors to detect an overheating circuit, which might have helped prevent the accident, were not installed until after it happened. Worse, says Rossi, when the wires were originally joined, the same silver–tin solder was used to connect them to an adjacent copper stabilizer, meant to provide an escape route for current in the event of a failure. That step risked reheating and destroying the original connection, he says. Making the second connection to the stabilizer with a different type of solder that had a lower melting point could have avoided the problem. Lyn Evans, who oversaw the LHC from 1994 to 2009, says that the idea was considered and rejected because the alternative solder contained lead, a hazard to workers. A detailed analysis last summer revealed several more bad connections, and CERN now says that it will take a year to correct the problem throughout the machine. As a result, the LHC will not run at its full collision energy of 14 tera-electronvolts (1012 eV) until around 2013. Many LHC scientists involved say that the accident was a natural consequence of constructing such a large and unique machine. "I personally think he [Rossi] is a bit too harsh on himself and the management of the time," says Steve Myers, the current project head of the LHC. "In such a technically complicated project with tight schedules it is almost inevitable that things go wrong." ADVERTISEMENT But Jim Strait, a physicist at Fermilab in Batavia, Illinois, says that Rossi's analysis is fundamentally right. The connections between the LHC's magnets aren't robust enough, Strait says. "The design looks like one that is optimized to make installation easy," he says. "These stupid little corners [of the design] get short shrift because they are boring." Only constant project reviews and more-integrated management can catch such problems, he says. Rossi says that he doesn't blame any one person for what happened at the LHC. "In Italian we say, Chi non fa, non sbaglia: 'He who doesn't work makes no mistakes'. What we have to do is learn from our mistakes and make it better." There are currently no comments. This is a public forum. Please keep to our Community Guidelines. You can be controversial, but please don't get personal or offensive and do keep it brief. Remember our threads are for feedback and discussion - not for publishing papers, press releases or advertisements.
• Pebble-bed nuclear reactor gets pulled
  - Nature 463(7284):1008 (2010)
  South Africa cuts funding for energy technology project. Bedtime for pebbles?Pebble Bed Modular Reactor (Pty) Hopes for the development of pebble-bed nuclear reactor technology, long held up as a safer alternative to conventional nuclear power, have suffered a blow. Last week, the South African government confirmed that it will effectively stop funding a long-term project to develop the technology. The development company, Pebble Bed Modular Reactor (PBMR), based near Pretoria, says that it is now considering axing three-quarters of its 800 staff, about half of whom are scientists or engineers. "The resources available to the company will not sustain the current cost structure," the company says. The cuts could trigger an exodus of nuclear expertise from South Africa, although some argue that government funding has kept the project going for too long in the face of growing problems. South Africa started to develop its pebble-bed reactor design in the mid-1990s, hoping that it would deliver cheap electricity and open up a lucrative export industry. It licensed the technology from Germany's Jülich Research Centre, which abandoned a working prototype reactor in 1991 after citing poor business opportunities. Eskom, South Africa's main electricity generator, based in Johannesburg, set up the PBMR in 1999 to develop the technology into a economically viable reactor. "It caught the mood in South Africa, and the feeling among South Africans was that their technology was as good as anybody's," says Steve Thomas, an energy-policy researcher at the University of Greenwich, London. "This was their chance to show the world what they could do." The proposed reactor would have used enriched uranium fuel embedded within tennis-ball-sized graphite spheres ('pebbles'). These should enable it to run at temperatures of between 750 °C and 1,600 °C yet resist a core meltdown even if the helium-gas coolant is lost, an attractive safety feature. "This was South Africa's chance to show the world what it could do." But several of the firm's biggest investors, including the utility firm Exelon in Chicago, Illinois, withdrew during the feasibility phase, which ended in 2004. In the four years up to March 2007, the South African government contributed 7.2 billion rands (US$935 million) in funding, on the condition that the PBMR "attract additional investment through investors other than government, and that it secure a customer for its product", according to a government statement. However, despite a revised business model and product offering, the firm has been unable to do either of these, the government says. Funding was last week slashed to 11 million rands over the next three years, which is "not enough to keep a nuclear design and engineering company going", according to the PBMR. Runaway costs and technical problems helped to doom the project, says Thomas. "In 1998, they were saying that they would have the demo plant online in 2003" at a cost of 2 billion rands, he says. "The final estimate was that the demo plant would be online in 2018 and it would cost 30 billion rands." Furthermore, he adds, the PBMR has never been held to account for why costs rose every year, why the completion date was continually pushed back or the nature of its design problems. In a final twist, the PBMR announced last year that it was indefinitely shelving plans to build a demonstration plant. The programme's demise will not help South Africa's goal of doubling its 35,000-megawatt power-generating capacity by 2025. One problem was that the design became too ambitious, says John Walmsley, past president of the South African branch of the Nuclear Institute, a professional society for nuclear engineers. The PBMR hoped to push the reactor's operating temperature as high as possible to enable not just electricity generation, but also 'process heat' applications such as turning coal into liquid fuels, he says. It also aimed to boost the power output to the very limits of the design to make the reactor more economical. "They tried to build a BMW when they maybe should have started with a Morris Minor," he says. ADVERTISEMENT Although many scientists had hoped that the safety system of the pebble-bed design would win over opponents of nuclear power, a 2008 report from the Jülich Research Centre cast doubt on those claims, suggesting that core temperatures could rise even higher than the safe threshold. Tsinghua University in Beijing now hosts the only operational prototype pebble-bed reactor, although similar reactors are being developed in the United States and the Netherlands. But the PBMR's problems are not unique, says Thomas. "Every nuclear nation in the world has had a programme to commercialize this type of reactor, and they all got nowhere." This is a public forum. Please keep to our Community Guidelines. You can be controversial, but please don't get personal or offensive and do keep it brief. Remember our threads are for feedback and discussion - not for publishing papers, press releases or advertisements.
• German paper chase to end
  - Nature 463(7284):1009 (2010)
  Funding agency cuts number of publications needed for grant applications. Sometimes less is more — at least in grant proposals. That's the hope of the DFG, Germany's main research-funding agency, which plans to drastically restrict the number of papers that researchers can list in their grant applications. From July, someone applying for a year's funding will be able to include only two publications closely related to the proposed project and a maximum of five other papers illustrating their scientific career. The agency hopes that the new rules will help ease the burden on reviewers faced with vast publication lists, and counter the pressure on scientists to publish as many papers as possible in order to win funding or academic appointments. "It is quality, not quantity, which matters," says Matthias Kleiner, president of the DFG. But some fear that the new rules might deprive reviewers of crucial information, particularly in fields with high publication rates, such as molecular biology. "As a reviewer I am reliant on getting all the information," says Benedikt Grothe, dean of biology at Ludwig Maximilian University in Munich. "And as an applicant I find it dissatisfying not to be able to cite all the papers that I think reviewers should be aware of." ADVERTISEMENT The DFG — which controls an annual budget of more than €2 billion (US$2.7 billion) and funded about half of its 23,000 grant applications last year — is the first funding agency in Europe to cap citations in this way. In the United States, similar rules apply to grants from the National Science Foundation (NSF). But the DFG's plan goes a step further: it will not consider supporting papers that have been submitted to academic journals but not yet accepted for publication. The move aims to counter problems with seemingly impressive publication lists that were brought to light last year when members of a DFG-funded Collaborative Research Centre (SFB) at the University of Göttingen were reprimanded for including unfinished manuscripts in grant applications (see Nature 460, 791; 2009). There are currently no comments. This is a public forum. Please keep to our Community Guidelines. You can be controversial, but please don't get personal or offensive and do keep it brief. Remember our threads are for feedback and discussion - not for publishing papers, press releases or advertisements.
• Cosmic-ray theory unravels
  - Nature 463(7284):1011 (2010)
  Astrophysicists ponder whether ultrahigh-energy particles really do come from the centre of galaxies. The black hole at the centre of the galaxy Centaurus A is just one potential source of cosmic rays.NASA/CXC/CfA/R. Kraft et al.; MPIfR/ESO/APEX/A.Weiss et al.; ESO/WFI High-energy cosmic rays pack a punch: their particles hold some 10 million times more energy than can be produced by accelerators on Earth. Astronomers had thought that they were getting close to understanding the origins and composition of these intense particles. Now it seems they must think again. Data collected three years ago by a team at the Pierre Auger Observatory in Mendoza, Argentina, suggested a tentative alignment between these incoming particles and active galactic nuclei (AGN). This hinted that the supermassive black holes in the AGN might be the long-sought cosmic particle accelerators that give the rays their huge energies (The Pierre Auger Collaboration Science 318, 938–943; 2007). The apparent connection with black holes electrified the astrophysics community. "We thought a new astronomy had been born: charged particle astronomy," says Charles Dermer, a cosmic-ray astrophysicist at the US Naval Research Laboratory in Washington DC. But at a meeting of the American Physical Society in Washington DC on 16 February, the Auger team began to backpedal on its original conclusions. The group revealed new data that weaken the link between the high-energy particles and the AGN. Compounding the mystery, the team has found evidence that these highest-energy cosmic rays might be iron nuclei, rather than the protons that make up most cosmic rays. "There are some puzzles," says Paul Sommers, co-spokesperson for the Auger collaboration at Pennsylvania State University in University Park. "We're not close to writing the final chapter." Low-energy cosmic rays, made mostly of protons, strike Earth continually. They originate within the Milky Way but are seen coming from all directions in the sky because magnetic fields in the Galaxy bend their paths and obscure their original sources. Higher-energy cosmic rays from outside the Galaxy are much less frequent, but are potentially more valuable as astronomical tracers because they barrel into the Galaxy on straighter paths. "It looks like nature is throwing us a few curve balls." The most extreme of them hit the planet with enormous energies of 1 × 1020 electronvolts (eV; by comparison, protons produced by the Large Hadron Collider will top out at 7 × 1012 eV). These high-energy particles could provide a way to detect new physics beyond the standard model of subatomic particles and the forces that control them. When high-energy particles strike the upper atmosphere, they create 'air showers' of billions of particles and a faint flash of light that, on moonless nights, can be seen at places such as the Auger Observatory, a 3,000-square-kilometre array of detectors on the dry plains of Patagonia. But gleaning clues about these cosmic rays is difficult because of their rarity; on average, fewer than one particle per century strikes a square kilometre of ground. Over the years, astronomers have considered a handful of possible origins besides the AGN for these rarest of rays. Some suspect the exploding stars that create γ-ray bursts, and Dermer says that it is possible that even small black holes and neutron stars could ramp the particles up to the necessary energies. The latest results from the Auger scientists put all of these potential origins back in the game. Although the 2007 paper was based on just 13 of the highest energy cosmic rays, Sommers says that the team is preparing a new analysis for publication that is based on 44 more events. Fewer than 40% of these cosmic rays seemed to be coming from the AGN, a much weaker correlation than previously reported. The rays are not randomly distributed but follow the distribution of matter visible in the Universe. The strangest aspect of the latest results relates to the particles' composition. As the team reports in a paper accepted for publication in Physical Review Letters (The Pierre Auger Collaboration, preprint at http://arxiv.org/abs/1002.0699; 2010), they are seeing small air showers that are indicative of iron nuclei, rather than the larger showers that point to protons. Ultrahigh-energy cosmic rays made of iron nuclei would be harder to explain because such nuclei are less common than protons and are more likely to be broken down by the violent mechanisms thought to accelerate cosmic rays. ADVERTISEMENT Complicating the picture further is the fact that a rival experiment in the Northern Hemisphere — the older and smaller High Resolution Fly's Eye (HiRes) experiment in Utah — has produced contradictory data. Spokesman Pierre Sokolsky of the University of Utah in Salt Lake City says that his team's results, based on just ten cosmic rays, suggest that they are protons and come from a random distribution in the sky. The analysis is under review at Astrophysical Journal Letters. Sokolsky points out that the cosmic-ray flux at HiRes could just be different from that seen in Argentina. Earth's Northern Hemisphere (and therefore HiRes) generally faces away from the centre of the Milky Way, so the magnetic fields in that direction could differ. By contrast, several prominent and nearby potential sources of cosmic rays, such as the AGN of the galaxy Centaurus A, are visible from the Southern Hemisphere. "Nature is throwing us a few curve balls, it looks like," says Sokolsky. This is a public forum. Please keep to our Community Guidelines. You can be controversial, but please don't get personal or offensive and do keep it brief. Remember our threads are for feedback and discussion - not for publishing papers, press releases or advertisements.
• A land without Google?
  - Nature 463(7284):1012 (2010)
  "Research without Google would be like life without electricity," says Xiong Zhenqin, an ecologist at Nanjing Agricultural University in Jiangsu province. Xiong is not alone in thinking that Google is indispensable. There are currently no comments.
• Earth science: The climate machine
  - Nature 463(7284):1014 (2010)
  The government building in the south of England looks open and airy with its three-storey glass facade. But security measures such as guards stationed at the front serve as a reminder that this Ministry of Defence property is carrying out sensitive work important to the nation's future. There are currently no comments.
• Research thrives on integration of natural and social sciences
  - Nature 463(7284):1018 (2010)
  Emerging collaborations between social and natural scientists face challenges, as you acknowledge (Nature 462, 825–826, 2009).
• Rigid animal-rights views not useful to ethics debate
  - Nature 463(7284):1018 (2010)
  Fern Wickson calls for animal-rights activists to be formally consulted on university animal-research programmes (Nature 463, 293; 2010).
• New NMR machines are set to boost biomedical potential
  - Nature 463(7284):1018 (2010)
  You made some excessively pessimistic assessments in your News Feature about the arrival of the first 1-gigahertz high-resolution nuclear magnetic resonance (NMR) spectrometer at the European Centre for High Field NMR, and its reception by the biological NMR community (Nature463, 605–606; 2010).To predict potential benefits from this advance, we should remember NMR's earlier contributions to biology and medicine, and not just focus on it as a structural tool.
• Skewed assessment values have stifled textbook-writing
  - Nature 463(7284):1018 (2010)
  I welcome your Editorial encouraging career recognition for writers of science books (Nature 463, 588; 2010). But nothing will change for British scientists unless books are properly valued within the new Research Excellence Framework, which assesses the quality of research in UK higher-education institutions.
• Futures perfect — food for thought and welcome light relief
  - Nature 463(7284):1018 (2010)
  Please do not listen to the likes of Denis Alexander (Nature 463, 425; 2010).
• Globe still in grip of addiction
  - Nature 463(7284):1020 (2010)
  After five years, the World Health Organization's tobacco-control treaty is starting to have an effect, but we need to tackle the smoking epidemic in the developing world, say Jonathan M. Samet and Heather L. Wipfli.
• Theft or innovation?
  - Nature 463(7284):1022 (2010)
  A history of intellectual-property rights reveals how the pirating of ideas and goods has transformed science publishing, drug development and software, explains Michael Gollin.
• Stamps celebrate Royal Society scientists
  - Nature 463(7284):1023 (2010)
  
• Symmetry and hubris
  - Nature 463(7284):1023 (2010)
  Francis Crick was not your run-of-the-mill scientist, as Robert Olby makes clear in his superb biography. A tall man given to verbal diarrhoea and infectious laughter, Crick did his Nobel-prizewinning work before he finished his PhD.
• How lateral thinking saved lives
  - Nature 463(7284):1024 (2010)
  Martin Kemp is struck by the surreal quality of a home-made iron lung.
• Q&A: Georgina Ferry on writing biography
  - Nature 463(7284):1025 (2010)
  Acclaimed biographer Georgina Ferry has chronicled the lives of two Nobel prizewinning chemists, Dorothy Hodgkin and Max Perutz. In the fourth in our series of five interviews with authors who each write science books for a different audience, Ferry reveals how detachment is needed to turn an attic's worth of personal letters into a compelling story.
• Applied mathematics: The statistics of style
  - Nature 463(7284):1027 (2010)
  A mathematical method has been developed that distinguishes between the paintings of Pieter Bruegel the Elder and those of his imitators. But can the approach be used to spot imitations of works by any artist?
• Cell biology: A brake on lipid synthesis
  - Nature 463(7284):1028 (2010)
  Although sphingolipids are vital cellular components, the path to their production is paved with toxic intermediates. Orm proteins allow cells to form these lipids without killing themselves in the process.
• Low-temperature physics: Surprise in the strong regime
  - Nature 463(7284):1029 (2010)
  The finding that the normal phase of an ultracold gas of fermionic atoms in the strongly interacting regime is close to a Fermi liquid isn't quite what theorists expected for these systems.
• 50 & 100 years ago
  - Nature 463(7284):1030 (2010)
  In my opinion the trouble with African agriculture is not that information is not properly co-ordinated, but that the basic facts are simply not known. So little fundamental agricultural research has been done ... Even attempts at developments like the Groundnut Scheme ... seem less wasteful when it is realized that for every pound lost in this and in all agricultural schemes attempted in Africa since the War, much more than a hundred pounds has been spent in subsidizing British agriculture at home.
• Regenerative medicine: Cell reprogramming gets direct
  - Nature 463(7284):1031 (2010)
  In a feat of biological wizardry, one type of differentiated cell has been directly converted into another, completely distinct type. Notably, the approach does not require a stem-cell intermediate stage.
• Climate change: Tropical cyclones in the mix
  - Nature 463(7284):1032 (2010)
  What was responsible for the unusual climatic conditions that prevailed during the early Pliocene, 5 million to 3 million years ago? Modelling studies point to intense tropical-cyclone activity as a possible answer.
• Geomicrobiology: Sediment reactions defy dogma
  - Nature 463(7284):1033 (2010)
  Redox reactions in widely spatially separated layers of marine sediments are coupled to each other. This suggests that bacteria mediate the flow of electrons between the layers — an idea that would previously have been dismissed.
• Location of corneal epithelial stem cells
  - Nature 463(7284):E10 (2010)
  Arising from: Majo, F., Rochat, A., Nicolas, M., Jaoude, G. A. & Barrandon, Y. Nature 456, 250–254 (2008).; Majo et al.reply The longstanding concept that corneal epithelial stem cells reside mainly in the limbus is supported by the absence of major corneal epithelial differentiation markers, that is, K3 and K12 keratins, in limbal basal cells (these markers are expressed, however, in corneal basal cells, thus distinguishing the mode of keratin expression in corneal epithelium from that of all other stratified epithelia), the centripetal migration of corneal epithelial cells, the exclusive location of slow-cycling cells in the limbal basal layer, the superior in vitro proliferative potential of limbal epithelial cells, and the transplanted limbal cells' ability to reconstitute corneal epithelium in vivo (reviewed in refs 1–4). Moreover, previous data indicate that corneal and conjunctival epithelia represent two separate cell lineages (reviewed in refs 1–4). Majo et al.5 suggested, however, that corneal and conjunctival epithelia are equipotent, and that identical oligopotent stem cells are ! present throughout the corneal, limbal and conjunctival epithelia. We point out here that these suggestions are inconsistent with many known growth, differentiation and cell migration properties of the anterior ocular epithelia.
• Majo et al. reply
  - Nature 463(7284):E11 (2010)
  Replying to: T.-T. Sun, S. C. Tseng & R. M. Lavker Nature 463, 10.1038/nature08805 (2010) Our claim is not that there are no stem cells in the limbus, but that there is more to corneal renewal than the limbus and that the double-dome-shaped structure of the cornea and physical constraints have a crucial impact on cell dynamics 1.
• Direct conversion of fibroblasts to functional neurons by defined factors
  Vierbuchen T Ostermeier A Pang ZP Kokubu Y Südhof TC Wernig M - Nature 463(7284):1035 (2010)
  Cellular differentiation and lineage commitment are considered to be robust and irreversible processes during development. Recent work has shown that mouse and human fibroblasts can be reprogrammed to a pluripotent state with a combination of four transcription factors. This raised the question of whether transcription factors could directly induce other defined somatic cell fates, and not only an undifferentiated state. We hypothesized that combinatorial expression of neural-lineage-specific transcription factors could directly convert fibroblasts into neurons. Starting from a pool of nineteen candidate genes, we identified a combination of only three factors, Ascl1, Brn2 (also called Pou3f2) and Myt1l, that suffice to rapidly and efficiently convert mouse embryonic and postnatal fibroblasts into functional neurons in vitro. These induced neuronal (iN) cells express multiple neuron-specific proteins, generate action potentials and form functional synapses. Generation ! of iN cells from non-neural lineages could have important implications for studies of neural development, neurological disease modelling and regenerative medicine.
• Reprogramming towards pluripotency requires AID-dependent DNA demethylation
  Bhutani N Brady JJ Damian M Sacco A Corbel SY Blau HM - Nature 463(7284):1042 (2010)
  Reprogramming of somatic cell nuclei to yield induced pluripotent stem (iPS) cells makes possible derivation of patient-specific stem cells for regenerative medicine. However, iPS cell generation is asynchronous and slow (2–3 weeks), the frequency is low (<0.1%), and DNA demethylation constitutes a bottleneck. To determine regulatory mechanisms involved in reprogramming, we generated interspecies heterokaryons (fused mouse embryonic stem (ES) cells and human fibroblasts) that induce reprogramming synchronously, frequently and fast. Here we show that reprogramming towards pluripotency in single heterokaryons is initiated without cell division or DNA replication, rapidly (1 day) and efficiently (70%). Short interfering RNA (siRNA)-mediated knockdown showed that activation-induced cytidine deaminase (AID, also known as AICDA) is required for promoter demethylation and induction of OCT4 (also known as POU5F1) and NANOG gene expression. AID protein bound silent methyl! ated OCT4 and NANOG promoters in fibroblasts, but not active demethylated promoters in ES cells. These data provide new evidence that mammalian AID is required for active DNA demethylation and initiation of nuclear reprogramming towards pluripotency in human somatic cells.
• Orm family proteins mediate sphingolipid homeostasis
  - Nature 463(7284):1048 (2010)
  Despite the essential roles of sphingolipids both as structural components of membranes and critical signalling molecules, we have a limited understanding of how cells sense and regulate their levels. Here we reveal the function in sphingolipid metabolism of the ORM genes (known as ORMDL genes in humans)—a conserved gene family that includes ORMDL3, which has recently been identified as a potential risk factor for childhood asthma. Starting from an unbiased functional genomic approach in Saccharomyces cerevisiae, we identify Orm proteins as negative regulators of sphingolipid synthesis that form a conserved complex with serine palmitoyltransferase, the first and rate-limiting enzyme in sphingolipid production. We also define a regulatory pathway in which phosphorylation of Orm proteins relieves their inhibitory activity when sphingolipid production is disrupted. Changes in ORM gene expression or mutations to their phosphorylation sites cause dysregulation of sphingol! ipid metabolism. Our work identifies the Orm proteins as critical mediators of sphingolipid homeostasis and raises the possibility that sphingolipid misregulation contributes to the development of childhood asthma.
• WASP-12b as a prolate, inflated and disrupting planet from tidal dissipation
  - Nature 463(7284):1054 (2010)
  The class of exotic Jupiter-mass planets that orbit very close to their parent stars were not explicitly expected before their discovery1. The recently discovered2 transiting planet WASP-12b has a mass M = 1.4 ± 0.1 Jupiter masses (MJ), a mean orbital distance of only 3.1 stellar radii (meaning it is subject to intense tidal forces), and a period of 1.1 days. Its radius 1.79 ± 0.09RJ is unexpectedly large and its orbital eccentricity 0.049 ± 0.015 is even more surprising because such close orbits are usually quickly circularized. Here we report an analysis of its properties, which reveals that the planet is losing mass to its host star at a rate of about 10-7MJ per year. The planet's surface is distorted by the star's gravity and the light curve produced by its prolate shape will differ by about ten per cent from that of a spherical planet. We conclude that dissipation of the star's tidal perturbation in the planet's convective envelope provide! s the energy source for its large volume. We predict up to 10 mJy CO band-head (2.292 μm) emission from a tenuous disk around the host star, made up of tidally stripped planetary gas. It may also contain a detectable resonant super-Earth, as a hypothetical perturber that continually stirs up WASP-12b's eccentricity.
• Exploring the thermodynamics of a universal Fermi gas
  - Nature 463(7284):1057 (2010)
  One of the greatest challenges in modern physics is to understand the behaviour of an ensemble of strongly interacting particles. A class of quantum many-body systems (such as neutron star matter and cold Fermi gases) share the same universal thermodynamic properties when interactions reach the maximum effective value allowed by quantum mechanics, the so-called unitary limit1, 2. This makes it possible in principle to simulate some astrophysical phenomena inside the highly controlled environment of an atomic physics laboratory. Previous work on the thermodynamics of a two-component Fermi gas led to thermodynamic quantities averaged over the trap3, 4, 5, making comparisons with many-body theories developed for uniform gases difficult. Here we develop a general experimental method that yields the equation of state of a uniform gas, as well as enabling a detailed comparison with existing theories6, 7, 8, 9, 10, 11, 12, 13, 14, 15. The precision of our equation of state le! ads to new physical insights into the unitary gas. For the unpolarized gas, we show that the low-temperature thermodynamics of the strongly interacting normal phase is well described by Fermi liquid theory, and we localize the superfluid transition. For a spin-polarized system16, 17, 18, our equation of state at zero temperature has a 2 per cent accuracy and extends work19, 20 on the phase diagram to a new regime of precision. We show in particular that, despite strong interactions, the normal phase behaves as a mixture of two ideal gases: a Fermi gas of bare majority atoms and a non-interacting gas of dressed quasi-particles, the fermionic polarons10, 18, 20, 21, 22.
• Simultaneous phase and size control of upconversion nanocrystals through lanthanide doping
  - Nature 463(7284):1061 (2010)
  Doping is a widely applied technological process in materials science that involves incorporating atoms or ions of appropriate elements into host lattices to yield hybrid materials with desirable properties and functions. For nanocrystalline materials, doping is of fundamental importance in stabilizing a specific crystallographic phase1, modifying electronic properties2, 3, 4, modulating magnetism5 as well as tuning emission properties6, 7, 8, 9. Here we describe a material system in which doping influences the growth process to give simultaneous control over the crystallographic phase, size and optical emission properties of the resulting nanocrystals. We show that NaYF4 nanocrystals can be rationally tuned in size (down to ten nanometres), phase (cubic or hexagonal) and upconversion10, 11, 12 emission colour (green to blue) through use of trivalent lanthanide dopant ions introduced at precisely defined concentrations. We use first-principles calculations to confirm t! hat the influence of lanthanide doping on crystal phase and size arises from a strong dependence on the size and dipole polarizability of the substitutional dopant ion. Our results suggest that the doping-induced structural and size transition, demonstrated here in NaYF4 upconversion nanocrystals, could be extended to other lanthanide-doped nanocrystal systems for applications ranging from luminescent biological labels12 to volumetric three-dimensional displays13.
• Tropical cyclones and permanent El Niño in the early Pliocene epoch
  - Nature 463(7284):1066 (2010)
  Tropical cyclones (also known as hurricanes and typhoons) are now believed to be an important component of the Earth's climate system1, 2, 3. In particular, by vigorously mixing the upper ocean, they can affect the ocean's heat uptake, poleward heat transport, and hence global temperatures. Changes in the distribution and frequency of tropical cyclones could therefore become an important element of the climate response to global warming. A potential analogue to modern greenhouse conditions, the climate of the early Pliocene epoch (approximately 5 to 3 million years ago) can provide important clues to this response. Here we describe a positive feedback between hurricanes and the upper-ocean circulation in the tropical Pacific Ocean that may have been essential for maintaining warm, El Niño-like conditions4, 5, 6 during the early Pliocene. This feedback is based on the ability of hurricanes to warm water parcels that travel towards the Equator at shallow depths and ! then resurface in the eastern equatorial Pacific as part of the ocean's wind-driven circulation7, 8. In the present climate, very few hurricane tracks intersect the parcel trajectories; consequently, there is little heat exchange between waters at such depths and the surface. More frequent and/or stronger hurricanes in the central Pacific imply greater heating of the parcels, warmer temperatures in the eastern equatorial Pacific, warmer tropics and, in turn, even more hurricanes. Using a downscaling hurricane model9, 10, we show dramatic shifts in the tropical cyclone distribution for the early Pliocene that favour this feedback. Further calculations with a coupled climate model support our conclusions. The proposed feedback should be relevant to past equable climates and potentially to contemporary climate change.
• Electric currents couple spatially separated biogeochemical processes in marine sediment
  - Nature 463(7284):1071 (2010)
  Some bacteria are capable of extracellular electron transfer, thereby enabling them to use electron acceptors and donors without direct cell contact1, 2, 3, 4. Beyond the micrometre scale, however, no firm evidence has previously existed that spatially segregated biogeochemical processes can be coupled by electric currents in nature. Here we provide evidence that electric currents running through defaunated sediment couple oxygen consumption at the sediment surface to oxidation of hydrogen sulphide and organic carbon deep within the sediment. Altering the oxygen concentration in the sea water overlying the sediment resulted in a rapid (<1-h) change in the hydrogen sulphide concentration within the sediment more than 12 mm below the oxic zone, a change explicable by transmission of electrons but not by diffusion of molecules. Mass balances indicated that more than 40% of total oxygen consumption in the sediment was driven by electrons conducted from the anoxic zone. A! distinct pH peak in the oxic zone could be explained by electrochemical oxygen reduction, but not by any conventional sets of aerobic sediment processes. We suggest that the electric current was conducted by bacterial nanowires combined with pyrite, soluble electron shuttles and outer-membrane cytochromes. Electrical communication between distant chemical and biological processes in nature adds a new dimension to our understanding of biogeochemistry and microbial ecology.
• Fossilized melanosomes and the colour of Cretaceous dinosaurs and birds
  Zhang F Kearns SL Orr PJ Benton MJ Zhou Z Johnson D Xu X Wang X - Nature 463(7284):1075 (2010)
  Spectacular fossils from the Early Cretaceous Jehol Group1, 2 of northeastern China have greatly expanded our knowledge of the diversity and palaeobiology of dinosaurs and early birds, and contributed to our understanding of the origin of birds, of flight, and of feathers. Pennaceous (vaned) feathers and integumentary filaments are preserved in birds3, 4, 5 and non-avian theropod dinosaurs6, 7, 8, 9, 10, 11, 12, but little is known of their microstructure. Here we report that melanosomes (colour-bearing organelles) are not only preserved in the pennaceous feathers of early birds, but also in an identical manner in integumentary filaments of non-avian dinosaurs, thus refuting recent claims13, 14, 15, 16 that the filaments are partially decayed dermal collagen fibres. Examples of both eumelanosomes and phaeomelanosomes have been identified, and they are often preserved in life position within the structure of partially degraded feathers and filaments. Furthermore, the da! ta here provide empirical evidence for reconstructing the colours and colour patterning of these extinct birds and theropod dinosaurs: for example, the dark-coloured stripes on the tail of the theropod dinosaur Sinosauropteryx can reasonably be inferred to have exhibited chestnut to reddish-brown tones.
• Arthropod relationships revealed by phylogenomic analysis of nuclear protein-coding sequences
  Regier JC Shultz JW Zwick A Hussey A Ball B Wetzer R Martin JW Cunningham CW - Nature 463(7284):1079 (2010)
  The remarkable antiquity, diversity and ecological significance of arthropods have inspired numerous attempts to resolve their deep phylogenetic history, but the results of two decades of intensive molecular phylogenetics have been mixed1, 2, 3, 4, 5, 6, 7. The discovery that terrestrial insects (Hexapoda) are more closely related to aquatic Crustacea than to the terrestrial centipedes and millipedes2, 8 (Myriapoda) was an early, if exceptional, success. More typically, analyses based on limited samples of taxa and genes have generated results that are inconsistent, weakly supported and highly sensitive to analytical conditions7, 9, 10. Here we present strongly supported results from likelihood, Bayesian and parsimony analyses of over 41 kilobases of aligned DNA sequence from 62 single-copy nuclear protein-coding genes from 75 arthropod species. These species represent every major arthropod lineage, plus five species of tardigrades and onychophorans as outgroups. Our! results strongly support Pancrustacea (Hexapoda plus Crustacea) but also strongly favour the traditional morphology-based Mandibulata11 (Myriapoda plus Pancrustacea) over the molecule-based Paradoxopoda (Myriapoda plus Chelicerata)2, 5, 12. In addition to Hexapoda, Pancrustacea includes three major extant lineages of 'crustaceans', each spanning a significant range of morphological disparity. These are Oligostraca (ostracods, mystacocarids, branchiurans and pentastomids), Vericrustacea (malacostracans, thecostracans, copepods and branchiopods) and Xenocarida (cephalocarids and remipedes). Finally, within Pancrustacea we identify Xenocarida as the long-sought sister group to the Hexapoda, a result confirming that 'crustaceans' are not monophyletic. These results provide a statistically well-supported phylogenetic framework for the largest animal phylum and represent a step towards ending the often-heated, century-long debate on arthropod relationships.
• Ancient animal microRNAs and the evolution of tissue identity
  - Nature 463(7284):1084 (2010)
  The spectacular escalation in complexity in early bilaterian evolution correlates with a strong increase in the number of microRNAs1, 2. To explore the link between the birth of ancient microRNAs and body plan evolution, we set out to determine the ancient sites of activity of conserved bilaterian microRNA families in a comparative approach. We reason that any specific localization shared between protostomes and deuterostomes (the two major superphyla of bilaterian animals) should probably reflect an ancient specificity of that microRNA in their last common ancestor. Here, we investigate the expression of conserved bilaterian microRNAs in Platynereis dumerilii, a protostome retaining ancestral bilaterian features3, 4, in Capitella, another marine annelid, in the sea urchin Strongylocentrotus, a deuterostome, and in sea anemone Nematostella, representing an outgroup to the bilaterians. Our comparative data indicate that the oldest known animal microRNA, miR-100, and the! related miR-125 and let-7 were initially active in neurosecretory cells located around the mouth. Other sets of ancient microRNAs were first present in locomotor ciliated cells, specific brain centres, or, more broadly, one of four major organ systems: central nervous system, sensory tissue, musculature and gut. These findings reveal that microRNA evolution and the establishment of tissue identities were closely coupled in bilaterian evolution. Also, they outline a minimum set of cell types and tissues that existed in the protostome–deuterostome ancestor.
• Neural evidence for inequality-averse social preferences
  - Nature 463(7284):1089 (2010)
  A popular hypothesis in the social sciences is that humans have social preferences to reduce inequality in outcome distributions because it has a negative impact on their experienced reward1, 2, 3. Although there is a large body of behavioural and anthropological evidence consistent with the predictions of these theories1, 4, 5, 6, there is no direct neural evidence for the existence of inequality-averse preferences. Such evidence would be especially useful because some behaviours that are consistent with a dislike for unequal outcomes could also be explained by concerns for social image7 or reciprocity8, 9, which do not require a direct aversion towards inequality. Here we use functional MRI to test directly for the existence of inequality-averse social preferences in the human brain. Inequality was created by recruiting pairs of subjects and giving one of them a large monetary endowment. While both subjects evaluated further monetary transfers from the experimenter t! o themselves and to the other participant, we measured neural responses in the ventral striatum and ventromedial prefrontal cortex, two areas that have been shown to be involved in the valuation of monetary and primary rewards in both social and non-social contexts10, 11, 12, 13, 14. Consistent with inequality-averse models of social preferences, we find that activity in these areas was more responsive to transfers to others than to self in the 'high-pay' subject, whereas the activity of the 'low-pay' subject showed the opposite pattern. These results provide direct evidence for the validity of this class of models, and also show that the brain's reward circuitry is sensitive to both advantageous and disadvantageous inequality.
• An essential role for XBP-1 in host protection against immune activation in C. elegans
  - Nature 463(7284):1092 (2010)
  The detection and compensatory response to the accumulation of unfolded proteins in the endoplasmic reticulum (ER), termed the unfolded protein response (UPR), represents a conserved cellular homeostatic mechanism with important roles in normal development and in the pathogenesis of disease1. The IRE1–XBP1/Hac1 pathway is a major branch of the UPR that has been conserved from yeast to human2, 3, 4, 5, 6. X-box binding protein 1 (XBP1) is required for the differentiation of the highly secretory plasma cells of the mammalian adaptive immune system7, 8, but recent work also points to reciprocal interactions between the UPR and other aspects of immunity and inflammation9, 10, 11. We have been studying innate immunity in the nematode Caenorhabditis elegans, having established a principal role for a conserved PMK-1 p38 mitogen-activated protein kinase (MAPK) pathway in mediating resistance to microbial pathogens12. Here we show that during C. elegans development, XBP-1 has! an essential role in protecting the host during activation of innate immunity. Activation of the PMK-1-mediated response to infection with Pseudomonas aeruginosa induces the XBP-1-dependent UPR. Whereas a loss-of-function xbp-1 mutant develops normally in the presence of relatively non-pathogenic bacteria, infection of the xbp-1 mutant with P. aeruginosa leads to disruption of ER morphology and larval lethality. Unexpectedly, the larval lethality phenotype on pathogenic P. aeruginosa is suppressed by loss of PMK-1-mediated immunity. Furthermore, hyperactivation of PMK-1 causes larval lethality in the xbp-1 mutant even in the absence of pathogenic bacteria. Our data establish innate immunity as a physiologically relevant inducer of ER stress during C. elegans development and indicate that an ancient, conserved role for XBP-1 may be to protect the host organism from the detrimental effects of mounting an innate immune response to microbes.
• Tbx3 improves the germ-line competency of induced pluripotent stem cells
  Han J Yuan P Yang H Zhang J Soh BS Li P Lim SL Cao S Tay J Orlov YL Lufkin T Ng HH Tam WL Lim B - Nature 463(7284):1096 (2010)
  Induced pluripotent stem (iPS) cells can be obtained by the introduction of defined factors into somatic cells1. The combination of Oct4 (also known as Pou5f1), Sox2 and Klf4 (which we term OSK) constitutes the minimal requirement for generating iPS cells from mouse embryonic fibroblasts. These cells are thought to resemble embryonic stem cells (ESCs) on the basis of global gene expression analyses; however, few studies have tested the ability and efficiency of iPS cells to contribute to chimaerism, colonization of germ tissues, and most importantly, germ-line transmission and live birth from iPS cells produced by tetraploid complementation. Using genomic analyses of ESC genes that have roles in pluripotency and fusion-mediated somatic cell reprogramming, here we show that the transcription factor Tbx3 significantly improves the quality of iPS cells. iPS cells generated with OSK and Tbx3 (OSKT) are superior in both germ-cell contribution to the gonads and germ-line tra! nsmission frequency. However, global gene expression profiling could not distinguish between OSK and OSKT iPS cells. Genome-wide chromatin immunoprecipitation sequencing analysis of Tbx3-binding sites in ESCs suggests that Tbx3 regulates pluripotency-associated and reprogramming factors, in addition to sharing many common downstream regulatory targets with Oct4, Sox2, Nanog and Smad1. This study underscores the intrinsic qualitative differences between iPS cells generated by different methods, and highlights the need to rigorously characterize iPS cells beyond in vitro studies.
• Genome-wide erasure of DNA methylation in mouse primordial germ cells is affected by AID deficiency
  Popp C Dean W Feng S Cokus SJ Andrews S Pellegrini M Jacobsen SE Reik W - Nature 463(7284):1101 (2010)
  Epigenetic reprogramming including demethylation of DNA occurs in mammalian primordial germ cells (PGCs) and in early embryos, and is important for the erasure of imprints and epimutations, and the return to pluripotency1, 2, 3, 4, 5, 6, 7, 8, 9. The extent of this reprogramming and its molecular mechanisms are poorly understood. We previously showed that the cytidine deaminases AID and APOBEC1 can deaminate 5-methylcytosine in vitro and in Escherichia coli, and in the mouse are expressed in tissues in which demethylation occurs10. Here we profiled DNA methylation throughout the genome by unbiased bisulphite next generation sequencing11, 12, 13 in wild-type and AID-deficient mouse PGCs at embryonic day (E)13.5. Wild-type PGCs revealed marked genome-wide erasure of methylation to a level below that of methylation deficient (Np95-/-, also called Uhrf1-/-) embryonic stem cells, with female PGCs being less methylated than male ones. By contrast, AID-deficient PGCs were up ! to three times more methylated than wild-type ones; this substantial difference occurred throughout the genome, with introns, intergenic regions and transposons being relatively more methylated than exons. Relative hypermethylation in AID-deficient PGCs was confirmed by analysis of individual loci in the genome. Our results reveal that erasure of DNA methylation in the germ line is a global process, hence limiting the potential for transgenerational epigenetic inheritance. AID deficiency interferes with genome-wide erasure of DNA methylation patterns, indicating that AID has a critical function in epigenetic reprogramming and potentially in restricting the inheritance of epimutations in mammals.
• The sequence and de novo assembly of the giant panda genome
  - Nature 463(7284):1106 (2010)
  Nature 463, 311–317 (2010) In this Article, the Latin species name of the giant panda was written incorrectly as Ailuropoda melanoleura. The correct name is Ailuropoda melanoleuca.
• Dense packings of the Platonic and Archimedean solids
  - Nature 463(7284):1106 (2010)
  Nature 460, 876–879 (2009) In the Introduction and in the Figure 4 legend of this letter, it was stated that the truncated tetrahedron is the only Archimedean solid that is not centrally symmetric. The correct statement is that the truncated tetrahedron is the only non-chiral Archimedean solid that is not centrally symmetric. This subtle distinction does not affect any of the results, conclusions or conjectures in our paper.
• Distraction
  - Nature 463(7284):1112 (2010)
  A fine romance.