Hot off the presses! Feb 18 Nature

The Feb 18 issue of the Nature is now up on Pubget (About Nature): if you're at a subscribing institution, just click the link in the latest link at the home page. (Note you'll only be able to get all the PDFs in the issue if your institution subscribes to Pubget.)

Latest Articles Include:

• Validation required
  - Nature 463(7283):849 (2010)
  Transparency and quality control are essential in the highly uncertain business of assessing the impact of climate change on a regional scale.
• Progressive thinking
  - Nature 463(7283):849 (2010)
  It is time to abandon GDP as the overriding measure of social development and economic health.
• Nature's choices
  - Nature 463(7283):850 (2010)
  Exploding the myths surrounding how and why we select our research papers.
• Ecology: why horses wear white
  - Nature 463(7283):852 (2010)
  
• Palaeontology: Do the locomotion
  - Nature 463(7283):852 (2010)
  
• Quantum chemistry: Never too cold
  - Nature 463(7283):852 (2010)
  
• Physical chemistry: Surface designers
  - Nature 463(7283):852 (2010)
  
• Genetics: Two strikes
  - Nature 463(7283):852 (2010)
  
• Condensed matter: Cutting it fine
  - Nature 463(7283):852 (2010)
  
• Neurobiology: The science of silence
  - Nature 463(7283):853 (2010)
  
• Geology: Mantle rising
  - Nature 463(7283):853 (2010)
  
• Astrophysics: Mystery medium
  - Nature 463(7283):853 (2010)
  
• Chemistry: Tie the knot
  - Nature 463(7283):853 (2010)
  
• Journal club
  - Nature 463(7283):853 (2010)
  
• News briefing: 18 February 2010
  - Nature 463(7283):854 (2010)
  The week in science This article is best viewed as a PDF. Research|Events|Business|Business watch|Policy|The week ahead|Number crunch|Sound bites On 11 February, the Missile Defense Agency in Washington DC used a powerful chemical laser mounted on an aircraft to destroy a short-range ballistic missile shortly after launch. A solid-fuel sounding rocket had been destroyed in similar manner on 3 February, the agency revealed. The experiment, at the Point Mugu Naval Air Warfare Center off the coast of California, was a proof-of-concept demonstration of the technology. The agency didn't disclose the range of the airborne laser system, which cost around US$4 billion to develop. The American Psychiatric Association has suggested a host of changes to its influential Diagnostic and Statistical Manual of Mental Disorders, which is used to diagnose patients and guide research, mainly in the United States. One of many proposed revisions is to unite several autism-related diagnoses into a single category of 'autism spectrum disorders'. The proposals (at www.dsm5.org) are open for public comment until 20 April. The fifth edition of the manual is due for release in May 2013. See go.nature.com/y2cAeo for more. NASA's Solar Dynamics Observatory launched successfully on 11 February. The orbiting satellite will take pictures every ten seconds for five years, giving astronomers their first near-continuous look at the Sun's activity. It will also investigate the flow of material inside the Sun, and measure its magnetic field. Solar sunspots and flares are on the rise after an unusually quiet period (see Nature 463, 414; 2010). A senior executive at the pharmaceutical firm Eli Lilly will become executive dean for research at Harvard Medical School in Boston, Massachusetts. William Chin, a Harvard-trained endocrinologist, has been at Lilly, based in Indianapolis, Indiana, since 1999, most recently as senior vice-president of discovery and clinical research. He will start in the newly created post on 1 May. Chin will oversee the school's biomedical research and its scientific interactions with industry, says dean Jeffrey Flier. Arnold Relman, a former editor of The New England Journal of Medicine, told The Boston Globe that the appointment raised concerns that "the separate roles for academic medicine and drug companies are becoming more confused". China released its first-ever national pollution census on 9 February. The 4-billion renminbi (US$585-million) project, conducted over 2 years, found that agriculture was more damaging to China's waterways than manufacturing. It also disclosed serious air pollution. The survey will provide the basis for setting environmental protection targets in the next 5-year plan of economic initiatives, which begins in 2011. Over-use of nitrogen fertilizer in agriculture is also rapidly acidifying China's soil, according to a separate study published last week (J. H. Guo et al. Science doi:10.1126/science.1182570; 2010). See go.nature.com/9dABUP and go.nature.com/L7mAay for more. Iranian president Mahmoud Ahmadinejad says that his country has enriched a quantity of uranium fuel to 20% pure uranium-235 — around four times higher than required in a commercial nuclear reactor. In a speech made on 11 February marking the 31st anniversary of the Iranian revolution, Ahmadinejad told supporters that Iran was now a "nuclear state". Iran claims to need the 20%-enriched fuel for a medical reactor in Tehran. Western officials questioned both Iran's intentions and its ability to reach the level of enrichment claimed. The statements are "based on politics, not on physics", said US White House press secretary Robert Gibbs. Amy Bishop, a neurobiologist at the University of Alabama at Huntsville, has been charged with the murder of three colleagues shot during a biology faculty meeting on 12 February. Three other people were wounded. See page 856 for more. NASA The space shuttle Endeavour silhouetted over Earth's horizon as it approached the International Space Station (ISS) for docking on 9 February. The picture was taken by an ISS crew member. Astronauts from the shuttle have now completed the ISS's last major extension, installing a new node with docking ports, life-support systems and workstations, and a giant window that will let those on board see out into space. Micron Technology, a semiconductor company based in Boise, Idaho, will acquire Numonyx of Rolle, Switzerland, in a stock transaction valuing the privately held firm at US$1.27 billion. Micron's chief executive Steven Appleton says that the deal would see his company become the world's second-largest producer of memory chips, behind South Korean manufacturer Samsung. In particular, Micron would gain Numonyx's technology in phase-change memory, a kind of flash memory chip that stores information by melting and freezing tiny crystals, and which may soon be used in mobile phones. See go.nature.com/iMHVrj for more. SOURCE: WIPO In 2009, the number of international patent applications dropped on the back of a double-digit fall in US applications (see chart). The dip was the first in the 31-year history of the Patent Cooperation Treaty, set up by the World Intellectual Property Organization (WIPO). But Francis Gurry, WIPO director-general, said that it was no surprise, given the economic conditions. China, with a 29.7% surge, claimed a bigger piece of a shrunken pie — continuing a shift to Asia seen over the past five years. China's rise is partly the result of greater government investment in research and development (R&D) over the past decade, and partly due to incentives at academic institutions that encourage patent filing. But observers say that the country still has a long way to go to become a dominant player in intellectual property, because the quality of applications has not kept pace with their volume. "There is still very little cutting-edge stuff," says Gerald Chan, co-founder of the Morningside Group, an investment firm in China. Kevin Rivette, a managing partner at intellectual-property specialists 3 LP Advisors in Palo Alto, California, says that Chinese companies should focus on buying patents to catch up with countries with similar industry-financed expenditure on R&D. See go.nature.com/6dvKon for more. A review into scientific practice at the University of East Anglia, UK, got under way last week. The review (cce-review.org) will investigate allegations arising from e-mails leaked from the university's Climatic Research Unit. Its chair, Muir Russell, former vice-chancellor of the University of Glasgow, UK, says that although funded by the university, the investigation will be independent. Nature editor-in-chief Philip Campbell stood down from the inquiry team after questions were raised about his impartiality. The university has also commissioned a separate review, assisted by the Royal Society, to assess the climate unit's scientific work. SAM PANTHAKY/AFP/GETTY IMAGES India's government has refused to allow commercial cultivation of the country's first genetically modified (GM) food crop, an insect-resistant aubergine. Following consultations and protests, environment minister Jairam Ramesh announced a moratorium until independent studies had established the crop's safety. It had been approved for cultivation last year by India's Genetic Engineering Approval Committee, and was developed by Mahyco–Monsanto Biotech, a joint venture between the Jalna-based Maharashtra Hybrid Seeds Company and the US seed giant Monsanto, based in St Louis, Missouri. See go.nature.com/K71k7s for more. Boulder, Colorado, hosts a conference dedicated to research opportunities in suborbital space. → go.nature.com/SJcEQn The American Association for the Advancement of Science holds its 176th meeting in San Diego, California. → go.nature.com/ZS5WSx The world's already-fragile supply chain of medical isotopes will be further disrupted when a major nuclear reactor in Petten, the Netherlands, is taken offline for repairs. → go.nature.com/QMT1ve India's parliament debates a controversial science-ministry bill modelled on the US 1980 Bayh–Dole act; it is intended to help publicly funded scientists and institutes to commercialize their research. Updates on the latest DNA sequencing technology should emerge from the advances in Genome Biology and Technology meeting in Marco Island, Florida. See page 858 for more. → http://agbt.org Estimated US deaths due to H1N1 pandemic flu, April 2009 to mid-January 2010. Source: US Centers for Disease Prevention and Control, 12 February hospital data Range for US deaths, predicted in August 2009. Source: President's Council of Advisors on Science and Technology, 7 August 2009 "You may be required to disclose genetic test results ... to life insurance ... providers." The fine print on an offer of discounted genetic tests sent by Australian private health insurer NIB to its customers. Source: The Age 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.
• Three biologists slain on campus
  - Nature 463(7283):856 (2010)
  Professor's arrest sends shock waves around the University of Alabama in Huntsville. Students paid tribute to the professors who died.B. Dill/AP The close-knit biology community in Huntsville, Alabama, is reeling after a professor allegedly turned a 9-millimetre pistol on her colleagues in a 12 February faculty meeting at a University of Alabama campus. Three professors were killed and three other people wounded. Amy Bishop, a neuroscientist who earned her PhD at Harvard University in Cambridge, Massachusetts, was denied tenure by the University of Alabama in Huntsville (UAH) last spring. She allegedly opened fire in a meeting of a dozen people in a small conference room. The three people killed were Gopi Podila, the biology department's chairman; Maria Ragland Davis, an expert in plant pathology; and Adriel Johnson, a cell biologist. Luis Cruz-Vera, a molecular biologist, was wounded but discharged from hospital a day later. Microbiologist Joseph Leahy remained in critical condition from the shooting as Nature went to press, and Stephanie Monticciolo, a staff assistant and the departmental linchpin, was in a serious condition. Bishop is in police custody, charged with murder. The shootings stunned the Huntsville campus, where many of the 7,400 students read science or engineering. The tragedy effectively halved the biology department's full-time faculty. "When you look at the fact that there are 13 professors and half have passed away or are in the hospital or in jail, and the other half witnessed the shootings, I just don't know how we pick up the pieces," says a departmental graduate student, who asked not to be identified. University president David Williams called the shootings "a terrible tragedy". The shock waves extended beyond the campus in a city where biotechnology has thrived in the past decade, and where the links between university and off-campus research are unusually tight. "They are our colleagues, our friends. And this is devastating," says Richard Myers, president and director of the HudsonAlpha Institute for Biotechnology, a non-profit academic centre that opened its doors in 2007 some 5 kilometres from the UAH. Myers, a former chair of genetics at the Stanford University School of Medicine in Palo Alto, California, is also an adjunct professor at the UAH. The university's biology department was built in recent years by Podila, whom colleagues and students described as an affable man with an easy-going nature coupled with a deep devotion to his department and to the broader biology community in Huntsville. Podila was a pivotal member of the Partnership for Biomedical Research, a group that works to support and draw research to the area. Colleagues remembered Chris Gunter, director of research affairs at the HudsonAlpha Institute, an adjunct biology professor at the UAH and a former senior editor at Nature, recalls Podila presenting a seminar at the institute last June on his speciality: symbiosis between fungi and tree roots. "He gave a great analogy about the fungi and roots seeking each other out and how this was like dating," she says. "You could tell he was very gifted at teaching undergraduates." All three professors "cared about students, and they cared about producing good researchers and good scientists", another graduate student in the department says. Gunter attended a 5 February biology faculty meeting with Bishop, Podila, Davis, Johnson and others to talk about the interdisciplinary graduate programme that also involves the chemistry and chemical engineering departments. "They were trying to invest in the students and make this programme work," she says. Davis in particular was trying to figure out ways to answer complaints about the programme's qualifying exam. Davis "was always very passionate about her research and very enthusiastic for students to be involved", adds the second graduate student. Johnson was remembered as a teacher who was excellent because he was exacting. One student recalls him counselling people to be ready for bumps in the academic road: "'I'll give you a KimWipe to wipe your tears and then we're going to move forward,' he would say." Johnson also required students in a once-weekly lab to come in for extra nights each week, encouraging them to design their own experiments and "get their money's worth". Bishop had garnered local attention after she and her husband, computer engineer and biologist James Anderson, co-invented a device that is essentially a sealed Petri dish. Bishop had grown frustrated with repeated contamination of the plates on which she was growing nerve cells. The device drew US$1.25 million from local angel investors, and is expected to make it to the market this summer. A local company, Prodigy Biosystems, was founded to commercialize the invention. Prodigy Biosystems chairman Dick Reeves calls Bishop "extremely smart" and outspoken: "You never had any doubts about where Amy was on an issue." He says that Bishop often got involved in issues beyond her laboratory, such as helping the family of a Huntsville entrepreneur whose son has amyotrophic lateral sclerosis understand the disease. Reeves says that Bishop was "frustrated" by her failure to receive tenure and that she felt the university's decision was unfair. Anderson told media outlets over the weekend that he had no hint the shootings were going to occur. In 1986, Bishop shot and killed her teenage brother in Braintree, Massachusetts. The death was deemed accidental. The Boston Globe newspaper has also reported that Bishop and Anderson were questioned in the 1993 investigation of a mailed pipe-bomb received by Paul Rosenberg of Boston Children's Hospital, where Bishop worked in the human-biochemistry lab. No one was ever charged. 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.
• Africa yields two full human genomes
  - Nature 463(7283):857 (2010)
  To the growing list of people with fully sequenced genomes, two memorable names have now been added: Archbishop Desmond Tutu, the South African civil-rights activist, and !Gubi, a Namibian hunter-gatherer. !Gubi hails from the Khoisan community, one of the most ancient and diverse human populations. There are currently no comments.
• How accurate are cancer cell lines?
  - Nature 463(7283):858 (2010)
  For decades, cancer cell cultures grown in Petri dishes have been the foundation of cancer biology and the quest for drug treatments. But now that biologists are exploring cancer genomes, some are asking whether they should pursue a more expensive, less proven strategy that may give a truer picture of key mutations: sequencing cells from tumours plucked directly from patients. There are currently no comments.
• Genomics firms turn to other markets
  - Nature 463(7283):859 (2010)
  The democratization of genomics looks set to accelerate. Next week, at the annual Advances in Genome Biology and Technology meeting in Marco Island, Florida, genomics companies will still be concentrating on impressing the large sequencing centres, their most high-profile customers. There are currently no comments.
• Pharaoh puzzle
  - Nature 463(7283):859 (2010)
  What really killed Tutankhamun? P. TURNER/STONE/GETTY A research team thinks it has solved the mystery surrounding the death of Egyptian 'boy king' Tutankhamun, who died in about 1324 BC aged just 19. Imaging results suggest that Tutankhamun had osteonecrosis of two bones in one foot, and DNA evidence suggests he was infected with the malaria parasite Plasmodium falciparum. These factors, combined with a leg fracture — perhaps resulting from his foot problems — may have led to his death, asserts the team led by Zahi Hawass, head of Egypt's Supreme Council of Antiquities in Cairo. Several outside experts, however, are sceptical, and say that the paper's conclusions overstep its data. Genetic fingerprinting done on Tutankhamun and ten other mummies has also yielded a putative five-generation family tree (Z. Hawass et al. J. Am. Med. Assoc. 303, 638–647; 2010). See go.nature.com/c7dFly for more. 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.
• 'Climategate' scientist speaks out
  - Nature 463(7283):860 (2010)
  Embattled climatologist Phil Jones faces his critics. Phil Jones was director of the Climatic Research Unit (CRU) at the University of East Anglia in Norwich, UK, when, last November, more than 1,000 e-mails were illegally obtained from the university and posted on the Internet. Their contents sparked allegations of poor scientific practice at CRU, now the subject of an investigation that was launched on 11 February. Phil Jones stands by his research.C. BOURCHIER/ Yet until recently, Jones had remained almost silent on the affair, despite being vilified by critics and even receiving death threats. It's no wonder that in an interview with Nature last week, he spent much of his time with his arms crossed tightly in front of his chest, as if shielding himself from further attack. One issue now under investigation is whether Jones or his CRU colleagues ever published data that they knew were potentially flawed, in order to bolster the evidence for man-made global warming. Under scrutiny is one of Jones's research papers (P. D. Jones et al. Nature _ 347, 169–172; 1990) on whether the apparent rise in temperature readings in the late twentieth century could be an artefact of measurement sites that shifted from the countryside to cities, which are warmer. The study concluded that this 'urban heat island' effect was negligible, and that the dominant effect was global climate change. Jones and his co-authors used data from weather stations around the world; those in China "were selected on the basis of station history: we chose those with few, if any, changes in instrumentation, location or observation times", they wrote. But when this claim was questioned in 2007, it became clear that the raw data were obtained from a Chinese contact of one of Jones's co-authors, Wei-Chyung Wang of the University at Albany in New York, and details of the stations' locations had subsequently been lost. "I thought it was the right way to get the data," Jones says, but he now acknowledges that "the stations probably did move", and that not having a detailed history of stations' locations was sloppy. "It's not acceptable," he says. "[It's] not best practice." Despite this, Jones says that follow-up studies (P. D. Jones, D. H. Lister and Q. Li J. Geophys. Res. 113, D16122; 2008) verified the original conclusions for the Chinese data for the period 1954–83, showing that the precise location of weather stations was unimportant. Jones says that he did not know that the stations' locations were questionable when they were included in the paper, but as its lead author he acknowledges his responsibility for ensuring the quality of the data. Asked if he will submit a correction to Nature, he replies: "I will give that some thought. It's worthy of consideration." Jones rejects other allegations that he has selectively used data from tree rings — the thickness of which reflect annual temperatures and rainfall — to play down the importance of the Medieval Warm Period (MWP), a phase of natural warming that may have occurred 1,000 years ago. If the MWP was restricted to mild local warming, it would mean that present-day global warming is unprecedented for the past 1,000 years. Scientists agree that the past 40 years of tree-ring data are unreliable temperature proxies, and some argue that using them in older temperature reconstructions, as Jones has done, could understate past warm periods, including the MWP (see Nature 463, 284–287; 2010). "It potentially does," admits Jones, but he adds that analyses using other methods — proxy temperature markers from ice-core samples, for example — still show much the same temperature change over the past millennium. ADVERTISEMENT Jones, an author on the most recent climate assessment report of the United Nations' Intergovernmental Panel on Climate Change (IPCC), also denies trying to censor dissenting voices but defends the right of IPCC authors to exclude papers if they are scientifically weak or irrelevant. "The IPCC [report] is an assessment, it's not a review," he says. But he fears that this message, and the broader evidence for man-made climate change, is being lost in the aftermath of the 'climategate' affair as blogs and media reports dominate the debate. Jones is emphatic that climate researchers should speak out to defend their research. "[I'd] like to see the climate science community supporting the climate science more," he says. "Lots of them are trying but they're being drowned out." 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.
• Asian pollution delays inevitable warming
  - Nature 463(7283):860 (2010)
  Dirty power plants exert temporary protective effect. The grey, sulphur-laden skies overlying parts of Asia have a bright side — they reflect sunlight back into space, moderating temperatures on the ground. Scientists are now exploring how and where pollution from power plants could offset, for a time, the greenhouse warming of the carbon dioxide they emit. A new modelling study doubles as a thought experiment in how pollution controls and global warming could interact in China and India, which are projected to account for 80% of new coal-fired power in the coming years. If new power plants were to operate without controlling pollution such as sulphur dioxide (SO2) and nitrogen oxides (NOX), the study finds, the resulting haze would reflect enough sunlight to overpower the warming effect of CO2 and exert local cooling. But this effect would not be felt uniformly across the globe and would last only a few decades. In the long run, CO2 would always prevail, and the world could experience a rapid warming effect if the skies were cleaned up decades down the road. "The paper highlights the fundamental inequity and iniquity of anthropogenic climate change: 'enjoy now and make others pay later'," says Meinrat Andreae, an aerosol expert at the Max Planck Institute for Chemistry in Mainz, Germany, who was not involved in the work. In fact, he says, dirty coal plants could be seen as "a very primitive form of geoengineering". The study, which is under review at Atmospheric Chemistry and Physics, builds on a well-established idea. Global temperatures were relatively stable in the decades leading up to the 1970s, even as fossil-fuel consumption shot up. Then industrialized countries began curbing SO2 and NOX to reduce acid rain and protect public health — and temperatures increased rapidly. The latest work, led by Drew Shindell at NASA's Goddard Institute for Space Studies in New York, looks at how the climate effects of air pollutants and greenhouse gases could play out over time and geography. The study analysed a suite of scenarios for the years 2000 to 2080, mixing annual rates of power-plant growth from 5% to 10% with various controls on SO2 and NOX pollution. SO2 is a precursor to sulphate aerosols and dominates the cooling effect, which varies depending on when plants adopt pollution controls. The sooner controls are put in place, the sooner the warming potential of CO2 kicks in. ADVERTISEMENT In one scenario assuming rapid growth in coal power with pollution controls phased in between 2040 and 2060, the effect of aerosols from the plants outweighs the effect of their CO2 until the year 2046, when the CO2 effect catches up and then overtakes aerosols. But the effect isn't uniform: the SO2 emissions produce a net cooling across much of the Northern Hemisphere. The Southern Hemisphere and the Arctic see fewer aerosols and, because CO2 has global effects, they exhibit net warming. How quickly China and India will move to clean up their coal emissions is unclear. In the past few years China has been aggressively installing SO2 scrubbers on many of its power plants in an attempt to improve air quality and protect public health. But some experts have questioned whether those scrubbers are being used properly — or even turned on. 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.
• Trees spit out gas from soil microbes
  - Nature 463(7283):861 (2010)
  Trunks act as giant methane chimneys. Waterlogged soils provide the perfect environment for methane-producing soil bacteria.J. E. Roche/naturepl.com The atmospheric concentration of methane, a greenhouse gas with 25 times the heating power of carbon dioxide, has more than doubled over the past 200 years. Researchers have long known that methane comes from anaerobic processes in waterlogged soils such as swamps, wetlands and rice fields, as well as in the guts of termites and ruminant animals such as cows and sheep. But in 2006, a team proposed the surprising idea1 that plants, too, produce methane — as much as 10–30% of the world's total methane emissions. If true, that would require a major overhaul of global carbon budgets. Now a study suggests that trees can act like chimneys, moving methane gas produced by soil microbes up through roots, stems and leaves before releasing it into the atmosphere. This effect could account for as much as 10% of methane emissions globally2. It could also help to explain why methane fluxes are higher than expected in wet tropical regions. Ellen Nisbet, an evolutionary biologist at the University of South Australia in Adelaide, previously reported that plants do not have the biochemical pathways needed to generate methane3. "I'm pretty sure from our studies that [plants] aren't making methane themselves," she says. "This paper is really showing that methane is moving around the plants, that it's being transported up and out." The team responsible for the latest work, led by atmospheric scientist Andrew Rice of Portland State University in Oregon, measured methane flow in three tree species, which were flooded to create conditions ripe for anaerobic microbes to start churning out methane. Rice says that the work does not rule out the possibility that plants themselves can produce methane aerobically; for instance, light at a certain intensity and wavelength could create a photolytic reaction that produces methane, as the 2006 work suggested. "The question is the magnitude of that source," says Rice. The latest study also found that the isotopic composition of the microbial methane transported through the trees was almost identical to that of the methane emissions observed in the 2006 study. This means that it could be tough to distinguish in the field between methane produced anaerobically and that produced aerobically. The idea of aerobic methane production "is still a hard pill for a lot of scientists to swallow", says Patrick Megonigal, a biogeochemist at the Smithsonian Environmental Research Center in Washington DC. "This paper shows that there are other mechanisms that we understand a little better, which could give you the same isotopic ratio and fit into the budget nicely." The team leader of the original paper says he remains confident that plants are making their own methane, although soils clearly also contribute. "It's getting clearer that living vegetation is maybe playing a more active role in emitting methane to the atmosphere than we previously thought," says Frank Keppler, a geochemist at the Max Planck Institute for Chemistry in Mainz, Germany. * References * Keppler, F., Hamilton, J. T. G., Braß, M. & Röckmann, T. Nature439, 187-191 (2006). | Article | PubMed | ISI | ChemPort | * Rice, A. L. et al. Geophys. Res. Lett.doi:10.1029/2009GL041565 (2010). * Nisbet, R. E. R. et al. Proc. R. Soc. B276, 1347-1354 (2009). | Article | PubMed 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.
• General relativity tested on a tabletop
  - Nature 463(7283):862 (2010)
  Atomic-clock experiment pins down accuracy of fundamental gravity measurement. By measuring a spectacularly small difference in the ticks of two quantum clocks, physicists have proven a pillar of Albert Einstein's theory of gravity to be on firmer footing than ever before. Holger Müller used laser-trap technology to test one of Einstein's predictions from general relativity.D. ENGLISH The experiment is the latest in a series of tests in which scientists have scrutinized one of Einstein's more profound predictions: that clocks in stronger gravitational fields run more slowly. For decades they have put clocks at higher elevations, where Earth's gravity is slightly weaker, and measured the ensuing changes. From a clock in a tower at Harvard University in Cambridge, Massachusetts, in the 1960s, to others flown on planes in the 1970s, to a clock that flew thousands of kilometres into space on a rocket in 1980, physicists have not been able to show that Einstein was wrong. Now, a team led by Holger Müller of the University of California, Berkeley, has measured the time-shifting effects of gravity 10,000 times more accurately than ever before. They show that gravity's effect on time is predictable to 7 parts per billion (H. Müller, A. Peters and S. Chu Nature 463, 926–929; 2010). And they did it using two laboratory clocks with a height difference of just 0.1 millimetres — a set-up that seems quaintly small in this day of big physics. "Precision experiments on a tabletop are not something of the past," says Müller, whose research team consisted of Achim Peters of the Humboldt University of Berlin and Steven Chu, the US Secretary of Energy. "Precision experiments on a tabletop are not something of the past." Many atomic clocks use the extremely regular pulsations of atoms shifting between excited energy states. But Müller's apparatus relied on the fundamental quantum frequency of a caesium atom associated with the atom's rest energy. This frequency was so high that physicists never thought to use it as a clock. But a special interferometer could measure the difference between two such clocks experiencing gravity's effect. "What's fascinating about their work is that they were using the entire atom as a clock," says atomic-clock expert Jun Ye of the Joint Institute for Laboratory Astrophysics in Boulder, Colorado. Müller and his team shot caesium atoms, cooled nearly to absolute zero, in an arc across a gap. Mid-stream, photons from a laser bumped the atoms into two, quantum-mechanical alternate realities. In one, an atom absorbed a photon and arced on a slightly higher path, experiencing a tiny weakening of gravity and speed-up of time. In the other, the atom stuck to the lower path, where gravity was stronger and time moved slightly more slowly. A difference in phase in the atom's fundamental frequency, measured by the interferometer, indicated a tiny difference in time. Laser traps The experiment takes advantage of the laser atom trap, for which Chu won a Nobel prize in 1997. The data for the current study were obtained shortly after that, when Chu was using the set-up to measure a different constant, the acceleration of gravity (A. Peters, K. Y. Chung and S. Chu Nature 400, 849–852; 1999). But Müller says that in October 2008, he had an epiphany that the same data could be used to show the constancy of gravity's effect on time. He e-mailed Chu, then the director of the Lawrence Berkeley National Laboratory in Berkeley, California, who responded three days later saying it was a good idea. Chu says in an e-mail that he found time to work on the current study during nights, weekends and on planes — after putting in 70–80-hour weeks as energy secretary. "I like juggling a lot of balls," he says. The result could one day have practical applications. If gravity's time-shifting effect were not constant, then researchers might have had to worry about the accuracy of new atomic clocks as they are flown into orbit on Global Positioning System (GPS) satellites. But Müller has demonstrated the effect to be extraordinarily consistent. "Now we know that the physics is fine," he says. ADVERTISEMENT The test also puts pressure on the Atomic Clock Ensemble in Space (ACES), an experiment being run by the European Space Agency that is due to be attached to the International Space Station in 2013. The current study already betters ACES's planned measurement of gravity's time-shifting effect by almost three orders of magnitude. ACES's principal investigator Christophe Salomon says that the mission will cost about €100 million (US$136 million), plus the cost of a launch rocket. By comparison, Müller says that his tabletop apparatus cost much less than $1 million. Salomon says that ACES is still justified because it will perform two other fundamental physics tests, as well as help researchers to improve the coordination of ground-based atomic clocks. Physicist Clifford Will of Washington University in St Louis, Missouri, says that Müller's result narrows the window for the alternative theories of gravity that some theorists are exploring. Will was also impressed that Chu found time to contribute to the study. "When was the last time that a sitting member of the president's cabinet had a paper in Nature on fundamental physics?" he asks. 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.
• Evolution: Revenge of the hopeful monster
  - Nature 463(7283):864 (2010)
  Since the origin of evolutionary science, biologists have insisted that adaptation is an achingly slow process. '_Natura non facit saltum_' (nature does not take leaps) was a favourite incantation of Charles Darwin. There are currently no comments.
• Astronomy: The decadal dinner club
  - Nature 463(7283):868 (2010)
  In a Lebanese restaurant in Washington DC, seven astronomers are sitting down to dinner. It is a crisp evening in January, and the researchers are here at Nature's request to discuss the challenges faced by their discipline and the future directions it might take. There are currently no comments.
• Carbon sequestration: Buried trouble
  - Nature 463(7283):871 (2010)
  The idea of injecting 400,000 tonnes of carbon dioxide under a shopping mall was always going to be a tough sell. And so it proved when the Dutch minister of economic affairs, Maria van der Hoeven, came to the small town of Barendrecht in December to explain why the government supported the proposal, made by the petroleum company Shell. There are currently no comments.
• World view: Calling science to account
  - Nature 463(7283):875 (2010)
  As you read this I will be in San Diego for the annual meeting of the American Association for the Advancement of Science (AAAS). For policy wonks like me, it's an unmissable event. There are currently no comments.
• Transdisciplinary EU science institute needs funds urgently
  - Nature 463(7283):876 (2010)
  Europe's future hinges on funding transdisciplinary scientific collaboration. But career paths, peer recognition, publication channels and the public funding of science are still mostly geared to maintain and reinforce disciplinarity.
• The Rubisco enzyme and agricultural productivity
  - Nature 463(7283):876 (2010)
  Improving Rubisco's carbon-dioxide-fixing capability by genetic engineering is unlikely to enhance crop productivity significantly on its own (R. J. Ellis Nature 463, 164–165; 2010
• Parliament needs members who are scientifically literate
  - Nature 463(7283):876 (2010)
  One important factor is missing from your Editorial on batting for science in the current UK economic climate (Nature 463, 402; 2010): the need for scientists to engage more fully in the political arena, and, in particular, to stand for public office. Many new members of the UK Parliament after the 1997 general election had a scientific or medical background.
• Outcry stopped approved pig study of avalanche survival
  - Nature 463(7283):877 (2010)
  Animal testing is unavoidable for scientific progress, but mainland Europe has no equivalent to the UK group Pro-Test to speak out for it. Our negative experience demands that scientists and politicians rectify this deficit in public information.
• University overhaul vital to end Bulgarian science's long decline
  - Nature 463(7283):877 (2010)
  The reforms under way in Bulgaria's research and higher education (Nature463, 283; 2010) are not enough. A full-scale external evaluation of the entire university system is also needed.
• China fights fraud with tough tactics and integrity training
  - Nature 463(7283):877 (2010)
  Scientific fraud is indeed rampant in China (Nature463, 142–143; 2010). Sanctions against guilty individuals can help in countries everywhere, but these aren't enough in the longer term to correct a dangerous misperception of misconduct among China's scientific community.
• Lessons from the Haiti earthquake
  - Nature 463(7283):878 (2010)
  Roger Bilham, one of the first seismologists to visit Haiti after last month's earthquake, calls for UN enforcement of resistant construction in cities with a history of violent tremors.
• Two views of collapse
  - Nature 463(7283):880 (2010)
  We need realism, not positivity, to learn lessons from past societal demises, urges Jared Diamond.
• The unfolding of time
  - Nature 463(7283):881 (2010)
  Why does time run forwards, not backwards? In his much-anticipated book, theoretical physicist Sean Carroll offers an explanation that unifies thermodynamics and cosmology.
• Oceania's musical technology
  - Nature 463(7283):882 (2010)
  The unique musical technology of Oceania — the region that encompasses Melanesia, Polynesia, Micronesia, Australia and Island Southeast Asia — is highlighted in an eclectic exhibition at New York's Metropolitan Museum of Art. Running until September, Sounding the Pacific charts the techniques by which local instrument builders created and resonated sound for diverse uses, from the sacred to the prosaic.
• Books in brief
  - Nature 463(7283):882 (2010)
  Engineering needs an image boost — one that is delivered by Henry Petroski in The Essential Engineer (Knopf, 2010). Explaining how the discipline can solve the planet's problems, he discusses how engineers turn the abstract ideas of scientists into reality, from implementing biofuels and electric cars to producing nuclear power and mitigating climate change.
• Q&A: David Brin on writing fiction
  - Nature 463(7283):883 (2010)
  After obtaining a PhD in planetary physics, David Brin found that he could make a better living as a science-fiction novelist than a researcher. In the third in our series of five interviews with authors who each write science books for a different audience, Brin reveals that criticism — and a thick skin — are the keys to good creative writing.
• Early life: Ancient acritarchs
  - Nature 463(7283):885 (2010)
  Big and beautiful microfossils have been extracted from rocks that are more than 3 billion years old. They offer tantalizing hints about the antiquity of the eukaryote lineage of organisms that includes ourselves.
• Astrophysics: Cosmic jet engines
  - Nature 463(7283):886 (2010)
  In some galaxies, matter falling onto a supermassive black hole is ejected in narrow jets moving at close to the speed of light. New observations provide insight into the workings of these cosmic accelerators.
• Gene regulation: A chromatin thermostat
  - Nature 463(7283):887 (2010)
  When environmental temperatures rise, plants seek help from their core molecular mechanisms to adapt. The chromatin protein H2A.Z, which regulates gene expression, is one such rescue molecule.
• Animal behaviour: An ill wind for finches
  - Nature 463(7283):888 (2010)
  The house finch Carpodacus mexicanus, a native of North America, may have been snared by an evolutionary trap. Karen Bouwman and Dana Hawley draw this conclusion from their video evidence of feeding behaviour in experiments with caged finches (K. M. Bouwman and D. M. Hawley Biol. Lett. doi:10.1098/rsbl.2010.0020; 2010
• Structural biology: Transformative encounters
  - Nature 463(7283):889 (2010)
  Researchers have met the challenge of capturing transient states of the SUMO E1 activating enzyme. Their pictures show radically different crystal structures for two of the steps in this enzyme's activity.
• Quantum measurement: A light touch
  - Nature 463(7283):890 (2010)
  A technique used primarily to study fundamental issues in quantum mechanics has now been shown to have promise as a powerful practical tool for making ultra-precise measurements.
• Genetics: Random expression goes binary
  - Nature 463(7283):891 (2010)
  The production of intestinal cells in a worm embryo is regulated by a network of transcription factors. Studies of these networks in mutant worms provide evidence for stochastic effects in gene expression.
• 50 & 100 years ago
  - Nature 463(7283):892 (2010)
  A further Committee of the Commonwealth Education Conference considered the extent to which the countries of the Commonwealth could help each other to meet their needs for training teachers ... Already more than 2,500 teachers a year leave the United Kingdom for service in other Commonwealth countries and the Government is to make every effort to increase this number. Canada, Australia and New Zealand made definite offers of assistance at the Conference, and both India and Pakistan hope to encourage their teachers to serve in other Commonwealth countries ... Steps should also be taken to promote a climate of opinion which will recognise service abroad as a professional asset.
• Multilevel and kin selection in a connected world
  - Nature 463(7283):E8 (2010)
  Arising from: G. Wild, A. Gardner & S. A. West Nature 459, 983–986 (2009); Wild, Gardner & West reply Wild et al.1 argue that the evolution of reduced virulence can be understood from the perspective of inclusive fitness, obviating the need to evoke group selection as a contributing causal factor. Although they acknowledge the mathematical equivalence of the inclusive fitness and multilevel selection approaches, they conclude that reduced virulence can be viewed entirely as an individual-level adaptation by the parasite1. Here we show that their model is a well-known special case of the more general theory of multilevel selection, and that the cause of reduced virulence resides in the opposition of two processes: within-group and among-group selection. This distinction is important in light of the current controversy among evolutionary biologists in which some continue to affirm that natural selection centres only and always at the level of the individual organism or gene, despite mathematical demonstrations that evolutionary dynamics must be described by selection at variou! s levels in the hierarchy of biological organization.
• Wild, Gardner & West reply
  - Nature 463(7283):E9 (2010)
  Replying to: M. J. Wade et al.Nature 463, 10.1038/nature08809 (2010) We previously showed how inclusive-fitness theory separates various components of selection on parasite virulence1. Wade et al.2 do not seem to dispute our results or make new predictions. Instead, they state that insufficient attention was given to multilevel-selection theory2. However, we pointed out the links to multi-level selection1, and we believe that a misunderstanding has arisen because they have fundamentally conflated selection and adaptation.
• Signatures of mutation and selection in the cancer genome
  - Nature 463(7283):893 (2010)
  The cancer genome is moulded by the dual processes of somatic mutation and selection. Homozygous deletions in cancer genomes occur over recessive cancer genes, where they can confer selective growth advantage, and over fragile sites, where they are thought to reflect an increased local rate of DNA breakage. However, most homozygous deletions in cancer genomes are unexplained. Here we identified 2,428 somatic homozygous deletions in 746 cancer cell lines. These overlie 11% of protein-coding genes that, therefore, are not mandatory for survival of human cells. We derived structural signatures that distinguish between homozygous deletions over recessive cancer genes and fragile sites. Application to clusters of unexplained homozygous deletions suggests that many are in regions of inherent fragility, whereas a small subset overlies recessive cancer genes. The results illustrate how structural signatures can be used to distinguish between the influences of mutation and sele! ction in cancer genomes. The extensive copy number, genotyping, sequence and expression data available for this large series of publicly available cancer cell lines renders them informative reagents for future studies of cancer biology and drug discovery.
• The landscape of somatic copy-number alteration across human cancers
  - Nature 463(7283):899 (2010)
  A powerful way to discover key genes with causal roles in oncogenesis is to identify genomic regions that undergo frequent alteration in human cancers. Here we present high-resolution analyses of somatic copy-number alterations (SCNAs) from 3,131 cancer specimens, belonging largely to 26 histological types. We identify 158 regions of focal SCNA that are altered at significant frequency across several cancer types, of which 122 cannot be explained by the presence of a known cancer target gene located within these regions. Several gene families are enriched among these regions of focal SCNA, including the BCL2 family of apoptosis regulators and the NF-κΒ pathway. We show that cancer cells containing amplifications surrounding the MCL1 and BCL2L1 anti-apoptotic genes depend on the expression of these genes for survival. Finally, we demonstrate that a large majority of SCNAs identified in individual cancer types are present in several cancer types.
• Active site remodelling accompanies thioester bond formation in the SUMO E1
  - Nature 463(7283):906 (2010)
  E1 enzymes activate ubiquitin (Ub) and ubiquitin-like (Ubl) proteins in two steps by carboxy-terminal adenylation and thioester bond formation to a conserved catalytic cysteine in the E1 Cys domain. The structural basis for these intermediates remains unknown. Here we report crystal structures for human SUMO E1 in complex with SUMO adenylate and tetrahedral intermediate analogues at 2.45 and 2.6 Å, respectively. These structures show that side chain contacts to ATP·Mg are released after adenylation to facilitate a 130 degree rotation of the Cys domain during thioester bond formation that is accompanied by remodelling of key structural elements including the helix that contains the E1 catalytic cysteine, the crossover and re-entry loops, and refolding of two helices that are required for adenylation. These changes displace side chains required for adenylation with side chains required for thioester bond formation. Mutational and biochemical analyses indicate these m! echanisms are conserved in other E1s.
• Variability in gene expression underlies incomplete penetrance
  - Nature 463(7283):913 (2010)
  The phenotypic differences between individual organisms can often be ascribed to underlying genetic and environmental variation. However, even genetically identical organisms in homogeneous environments vary, indicating that randomness in developmental processes such as gene expression may also generate diversity. To examine the consequences of gene expression variability in multicellular organisms, we studied intestinal specification in the nematode Caenorhabditis elegans in which wild-type cell fate is invariant and controlled by a small transcriptional network. Mutations in elements of this network can have indeterminate effects: some mutant embryos fail to develop intestinal cells, whereas others produce intestinal precursors. By counting transcripts of the genes in this network in individual embryos, we show that the expression of an otherwise redundant gene becomes highly variable in the mutants and that this variation is subjected to a threshold, producing an ON! /OFF expression pattern of the master regulatory gene of intestinal differentiation. Our results demonstrate that mutations in developmental networks can expose otherwise buffered stochastic variability in gene expression, leading to pronounced phenotypic variation.
• A change in the optical polarization associated with a γ-ray flare in the blazar 3C 279
  - Nature 463(7283):919 (2010)
  It is widely accepted that strong and variable radiation detected over all accessible energy bands in a number of active galaxies arises from a relativistic, Doppler-boosted jet pointing close to our line of sight1. The size of the emitting zone and the location of this region relative to the central supermassive black hole are, however, poorly known, with estimates ranging from light-hours to a light-year or more. Here we report the coincidence of a gamma (γ)-ray flare with a dramatic change of optical polarization angle. This provides evidence for co-spatiality of optical and γ-ray emission regions and indicates a highly ordered jet magnetic field. The results also require a non-axisymmetric structure of the emission zone, implying a curved trajectory for the emitting material within the jet, with the dissipation region located at a considerable distance from the black hole, at about 105 gravitational radii.
• An upper limit on the contribution of accreting white dwarfs to the type Ia supernova rate
  - Nature 463(7283):924 (2010)
  There is wide agreement that type Ia supernovae (used as standard candles for cosmology) are associated with the thermonuclear explosions of white dwarf stars1, 2. The nuclear runaway that leads to the explosion could start in a white dwarf gradually accumulating matter from a companion star until it reaches the Chandrasekhar limit3, or could be triggered by the merger of two white dwarfs in a compact binary system4, 5. The X-ray signatures of these two possible paths are very different. Whereas no strong electromagnetic emission is expected in the merger scenario until shortly before the supernova, the white dwarf accreting material from the normal star becomes a source of copious X-rays for about 107 years before the explosion. This offers a means of determining which path dominates. Here we report that the observed X-ray flux from six nearby elliptical galaxies and galaxy bulges is a factor of ~30–50 less than predicted in the accretion scenario, based upon an e! stimate of the supernova rate from their K-band luminosities. We conclude that no more than about five per cent of type Ia supernovae in early-type galaxies can be produced by white dwarfs in accreting binary systems, unless their progenitors are much younger than the bulk of the stellar population in these galaxies, or explosions of sub-Chandrasekhar white dwarfs make a significant contribution to the supernova rate.
• A precision measurement of the gravitational redshift by the interference of matter waves
  - Nature 463(7283):926 (2010)
  One of the central predictions of metric theories of gravity, such as general relativity, is that a clock in a gravitational potential U will run more slowly by a factor of 1 + U/c2, where c is the velocity of light, as compared to a similar clock outside the potential1. This effect, known as gravitational redshift, is important to the operation of the global positioning system2, timekeeping3, 4 and future experiments with ultra-precise, space-based clocks5 (such as searches for variations in fundamental constants). The gravitational redshift has been measured using clocks on a tower6, an aircraft7 and a rocket8, currently reaching an accuracy of 7 × 10-5. Here we show that laboratory experiments based on quantum interference of atoms9, 10 enable a much more precise measurement, yielding an accuracy of 7 × 10-9. Our result supports the view that gravity is a manifestation of space-time curvature, an underlying principle of general relativity that has come! under scrutiny in connection with the search for a theory of quantum gravity11. Improving the redshift measurement is particularly important because this test has been the least accurate among the experiments that are required to support curved space-time theories1.
• Upside-down differentiation and generation of a 'primordial' lower mantle
  - Nature 463(7283):930 (2010)
  Except for the first 50–100 million years or so of the Earth's history, when most of the mantle may have been subjected to melting, the differentiation of Earth's silicate mantle has been controlled by solid-state convection1. As the mantle upwells and decompresses across its solidus, it partially melts. These low-density melts rise to the surface and form the continental and oceanic crusts, driving the differentiation of the silicate part of the Earth. Because many trace elements, such as heat-producing U, Th and K, as well as the noble gases, preferentially partition into melts (here referred to as incompatible elements), melt extraction concentrates these elements into the crust (or atmosphere in the case of noble gases), where nearly half of the Earth's budget of these elements now resides2. In contrast, the upper mantle, as sampled by mid-ocean ridge basalts, is highly depleted in incompatible elements, suggesting a complementary relationship with the crus! t. Mass balance arguments require that the other half of these incompatible elements be hidden in the Earth's interior. Hypotheses abound for the origin of this hidden reservoir3, 4, 5, 6. The most widely held view has been that this hidden reservoir represents primordial material never processed by melting or degassing. Here, we suggest that a necessary by-product of whole-mantle convection during the Earth's first billion years is deep and hot melting, resulting in the generation of dense liquids that crystallized and sank into the lower mantle. These sunken lithologies would have 'primordial' chemical signatures despite a non-primordial origin.
• Organic-walled microfossils in 3.2-billion-year-old shallow-marine siliciclastic deposits
  Javaux EJ Marshall CP Bekker A - Nature 463(7283):934 (2010)
  Although the notion of an early origin and diversification of life on Earth during the Archaean eon has received increasing support in geochemical, sedimentological and palaeontological evidence, ambiguities and controversies persist regarding the biogenicity and syngeneity of the record older than Late Archaean1, 2, 3. Non-biological processes are known to produce morphologies similar to some microfossils4, 5, and hydrothermal fluids have the potential to produce abiotic organic compounds with depleted carbon isotope values6, making it difficult to establish unambiguous traces of life. Here we report the discovery of a population of large (up to about 300 μm in diameter) carbonaceous spheroidal microstructures in Mesoarchaean shales and siltstones of the Moodies Group, South Africa, the Earth's oldest siliciclastic alluvial to tidal-estuarine deposits7. These microstructures are interpreted as organic-walled microfossils on the basis of petrographic and geochemic! al evidence for their endogenicity and syngeneity, their carbonaceous composition, cellular morphology and ultrastructure, occurrence in populations, taphonomic features of soft wall deformation, and the geological context plausible for life, as well as a lack of abiotic explanation falsifying a biological origin. These are the oldest and largest Archaean organic-walled spheroidal microfossils reported so far. Our observations suggest that relatively large microorganisms cohabited with earlier reported benthic microbial mats8 in the photic zone of marginal marine siliciclastic environments 3.2 billion years ago.
• A bony connection signals laryngeal echolocation in bats
  - Nature 463(7283):939 (2010)
  Echolocation is an active form of orientation in which animals emit sounds and then listen to reflected echoes of those sounds to form images of their surroundings in their brains1. Although echolocation is usually associated with bats, it is not characteristic of all bats2, 3. Most echolocating bats produce signals in the larynx, but within one family of mainly non-echolocating species (Pteropodidae), a few species use echolocation sounds produced by tongue clicks4, 5. Here we demonstrate, using data obtained from micro-computed tomography scans of 26 species (n = 35 fluid-preserved bats), that proximal articulation of the stylohyal bone (part of the mammalian hyoid apparatus) with the tympanic bone always distinguishes laryngeally echolocating bats from all other bats (that is, non-echolocating pteropodids and those that echolocate with tongue clicks). In laryngeally echolocating bats, the proximal end of the stylohyal bone directly articulates with the tympanic bone! and is often fused with it. Previous research on the morphology of the stylohyal bone in the oldest known fossil bat (Onychonycteris finneyi) suggested that it did not echolocate6, but our findings suggest that O. finneyi may have used laryngeal echolocation because its stylohyal bones may have articulated with its tympanic bones. The present findings reopen basic questions about the timing and the origin of flight and echolocation in the early evolution of bats. Our data also provide an independent anatomical character by which to distinguish laryngeally echolocating bats from other bats.
• Complete Khoisan and Bantu genomes from southern Africa
  - Nature 463(7283):943 (2010)
  The genetic structure of the indigenous hunter-gatherer peoples of southern Africa, the oldest known lineage of modern human, is important for understanding human diversity. Studies based on mitochondrial1 and small sets of nuclear markers2 have shown that these hunter-gatherers, known as Khoisan, San, or Bushmen, are genetically divergent from other humans1, 3. However, until now, fully sequenced human genomes have been limited to recently diverged populations4, 5, 6, 7, 8. Here we present the complete genome sequences of an indigenous hunter-gatherer from the Kalahari Desert and a Bantu from southern Africa, as well as protein-coding regions from an additional three hunter-gatherers from disparate regions of the Kalahari. We characterize the extent of whole-genome and exome diversity among the five men, reporting 1.3 million novel DNA differences genome-wide, including 13,146 novel amino acid variants. In terms of nucleotide substitutions, the Bushmen seem to be, on ! average, more different from each other than, for example, a European and an Asian. Observed genomic differences between the hunter-gatherers and others may help to pinpoint genetic adaptations to an agricultural lifestyle. Adding the described variants to current databases will facilitate inclusion of southern Africans in medical research efforts, particularly when family and medical histories can be correlated with genome-wide data.
• Rapid spine stabilization and synaptic enhancement at the onset of behavioural learning
  - Nature 463(7283):948 (2010)
  Behavioural learning depends on the brain's capacity to respond to instructive experience and is often enhanced during a juvenile sensitive period. How instructive experience acts on the juvenile brain to trigger behavioural learning remains unknown. In vitro studies show that forms of synaptic strengthening thought to underlie learning are accompanied by an increase in the stability, number and size of dendritic spines, which are the major sites of excitatory synaptic transmission in the vertebrate brain1, 2, 3, 4, 5, 6, 7. In vivo imaging studies in sensory cortical regions reveal that these structural features can be affected by disrupting sensory experience and that spine turnover increases during sensitive periods for sensory map formation8, 9, 10, 11, 12. These observations support two hypotheses: first, the increased capacity for behavioural learning during a sensitive period is associated with enhanced spine dynamics on sensorimotor neurons important for the ! learned behaviour; second, instructive experience rapidly stabilizes and strengthens these dynamic spines. Here we report a test of these hypotheses using two-photon in vivo imaging to measure spine dynamics in zebra finches, which learn to sing by imitating a tutor song during a juvenile sensitive period13, 14. Spine dynamics were measured in the forebrain nucleus HVC, the proximal site where auditory information merges with an explicit song motor representation15, 16, 17, 18, 19, immediately before and after juvenile finches first experienced tutor song20. Higher levels of spine turnover before tutoring correlated with a greater capacity for subsequent song imitation. In juveniles with high levels of spine turnover, hearing a tutor song led to the rapid (~24-h) stabilization, accumulation and enlargement of dendritic spines in HVC. Moreover, in vivo intracellular recordings made immediately before and after the first day of tutoring revealed robust enhancement of synaptic! activity in HVC. These findings suggest that behavioural lear! ning results when instructive experience is able to rapidly stabilize and strengthen synapses on sensorimotor neurons important for the control of the learned behaviour.
• Rere controls retinoic acid signalling and somite bilateral symmetry
  - Nature 463(7283):953 (2010)
  One of the most notable features of the vertebrate body plan organization is its bilateral symmetry, evident at the level of vertebrae and skeletal muscles. Here we show that a mutation in Rere (also known as atrophin2) leads to the formation of asymmetrical somites in mouse embryos, similar to embryos deprived of retinoic acid1, 2, 3, 4. Furthermore, we also demonstrate that Rere controls retinoic acid signalling, which is required to maintain somite symmetry by interacting with Fgf8 in the left–right signalling pathway. Rere forms a complex with Nr2f2, p300 (also known as Ep300) and a retinoic acid receptor, which is recruited to the retinoic acid regulatory element of retinoic acid targets, such as the Rarb promoter. Furthermore, the knockdown of Nr2f2 and/or Rere decreases retinoic acid signalling, suggesting that this complex is required to promote transcriptional activation of retinoic acid targets. The asymmetrical expression of Nr2f2 in the presomitic mesoder! m overlaps with the asymmetry of the retinoic acid signalling response, supporting its implication in the control of somitic symmetry. Misregulation of this mechanism could be involved in symmetry defects of the human spine, such as those observed in patients with scoliosis.
• CHD7 cooperates with PBAF to control multipotent neural crest formation
  - Nature 463(7283):958 (2010)
  Heterozygous mutations in the gene encoding the CHD (chromodomain helicase DNA-binding domain) member CHD7, an ATP-dependent chromatin remodeller homologous to the Drosophila trithorax-group protein Kismet1, 2, result in a complex constellation of congenital anomalies called CHARGE syndrome, which is a sporadic, autosomal dominant disorder characterized by malformations of the craniofacial structures, peripheral nervous system, ears, eyes and heart3, 4. Although it was postulated 25 years ago that CHARGE syndrome results from the abnormal development of the neural crest, this hypothesis remained untested5. Here we show that, in both humans and Xenopus, CHD7 is essential for the formation of multipotent migratory neural crest (NC), a transient cell population that is ectodermal in origin but undergoes a major transcriptional reprogramming event to acquire a remarkably broad differentiation potential and ability to migrate throughout the body, giving rise to craniofacial! bones and cartilages, the peripheral nervous system, pigmentation and cardiac structures6, 7. We demonstrate that CHD7 is essential for activation of the NC transcriptional circuitry, including Sox9, Twist and Slug. In Xenopus embryos, knockdown of Chd7 or overexpression of its catalytically inactive form recapitulates all major features of CHARGE syndrome. In human NC cells CHD7 associates with PBAF (polybromo- and BRG1-associated factor-containing complex)8 and both remodellers occupy a NC-specific distal SOX9 enhancer9 and a conserved genomic element located upstream of the TWIST1 gene. Consistently, during embryogenesis CHD7 and PBAF cooperate to promote NC gene expression and cell migration. Our work identifies an evolutionarily conserved role for CHD7 in orchestrating NC gene expression programs, provides insights into the synergistic control of distal elements by chromatin remodellers, illuminates the patho-embryology of CHARGE syndrome, and suggests a broader funct! ion for CHD7 in the regulation of cell motility.
• TCR–peptide–MHC interactions in situ show accelerated kinetics and increased affinity
  - Nature 463(7283):963 (2010)
  The recognition of foreign antigens by T lymphocytes is essential to most adaptive immune responses. It is driven by specific T-cell antigen receptors (TCRs) binding to antigenic peptide–major histocompatibility complex (pMHC) molecules on other cells1. If productive, these interactions promote the formation of an immunological synapse2, 3. Here we show that synaptic TCR–pMHC binding dynamics differ significantly from TCR–pMHC binding in solution. We used single-molecule microscopy and fluorescence resonance energy transfer (FRET) between fluorescently tagged TCRs and their cognate pMHC ligands to measure the kinetics of TCR–pMHC binding in situ. When compared with solution measurements, the dissociation of this complex was increased significantly (4–12-fold). Disruption of actin polymers reversed this effect, indicating that cytoskeletal dynamics destabilize this interaction directly or indirectly. Nevertheless, TCR affinity for pMHC was significantly elevat! ed as the result of a large (about 100-fold) increase in the association rate, a likely consequence of complementary molecular orientation and clustering. In helper T cells, the CD4 molecule has been proposed to bind cooperatively with the TCR to the same pMHC complex. However, CD4 blockade had no effect on the synaptic TCR affinity, nor did it destabilize TCR–pMHC complexes, indicating that the TCR binds pMHC independently of CD4.
• Enzyme-inhibitor-like tuning of Ca2+ channel connectivity with calmodulin
  Liu X Yang PS Yang W Yue DT - Nature 463(7283):968 (2010)
  Ca2+ channels and calmodulin (CaM) are two prominent signalling hubs1 that synergistically affect functions as diverse as cardiac excitability2, synaptic plasticity3 and gene transcription4. It is therefore fitting that these hubs are in some sense coordinated, as the opening of CaV1–2 Ca2+ channels are regulated by a single CaM constitutively complexed with channels5. The Ca2+-free form of CaM (apoCaM) is already pre-associated with the isoleucine–glutamine (IQ) domain on the channel carboxy terminus, and subsequent Ca2+ binding to this 'resident' CaM drives conformational changes that then trigger regulation of channel opening6. Another potential avenue for channel–CaM coordination could arise from the absence of Ca2+ regulation in channels lacking a pre-associated CaM6, 7. Natural fluctuations in CaM concentrations might then influence the fraction of regulable channels and, thereby, the overall strength of Ca2+ feedback. However, the prevailing view has b! een that the ultrastrong affinity of channels for apoCaM ensures their saturation with CaM8, yielding a significant form of concentration independence between Ca2+ channels and CaM. Here we show that significant exceptions to this autonomy exist, by combining electrophysiology (to characterize channel regulation) with optical fluorescence resonance energy transfer (FRET) sensor determination of free-apoCaM concentration in live cells9. This approach translates quantitative CaM biochemistry from the traditional test-tube context into the realm of functioning holochannels within intact cells. From this perspective, we find that long splice forms of CaV1.3 and CaV1.4 channels include a distal carboxy tail10, 11, 12 that resembles an enzyme competitive inhibitor that retunes channel affinity for apoCaM such that natural CaM variations affect the strength of Ca2+ feedback modulation. Given the ubiquity of these channels13, 14, the connection between ambient CaM levels and Ca2+ e! ntry through channels is broadly significant for Ca2+ homeosta! sis. Strategies such as ours promise key advances for the in situ analysis of signalling molecules resistant to in vitro reconstitution, such as Ca2+ channels.
• Whole-animal imaging: The whole picture
  - Nature 463(7283):977 (2010)
  As the techniques for imaging whole animals become more sophisticated, researchers are able to get a clearer picture of what is going on inside. Monya Baker looks at the options available.
• Whole-animal imaging: Probe progress
  - Nature 463(7283):979 (2010)
  A big limitation of molecular imaging in whole animals is how hard it is to measure multiple signals, says Sanjiv Sam Gambhir, who directs the Molecular Imaging Program at Stanford in California. "Unlike our colleagues who remove tissues or blood samples from animals and can analyse many, many things, we're very limited in how many signals we can get simultaneously," he says.
• Whole-animal imaging: Table of suppliers
  - Nature 463(7283):981 (2010)
  Table 1
• Unfinished business
  - Nature 463(7283):990 (2010)
  In cold storage.